TY - JOUR A1 - Neitzel, Ira A1 - Prüfert, Uwe A1 - Slawig, Thomas T1 - Strategies for time-dependent PDE control using an integrated modeling and simulation environment. Part one Y1 - 2007 IS - 408 PB - Matheon CY - Berlin ER - TY - JOUR A1 - Neitzel, Ira A1 - Prüfert, Uwe A1 - Slawig, Thomas T1 - Strategies for time-dependent PDE control using an integrated modeling and simulation environment. Part two Y1 - 2007 IS - 24-02 PB - SPP 1253 ER - TY - JOUR A1 - Schenk, O. A1 - Wächter, Andreas A1 - Weiser, Martin T1 - Inertia Revealing Preconditioning For Large-Scale Nonconvex Constrained Optimization JF - SIAM J. Sci. Comp. Y1 - 2008 VL - 31 IS - 2 SP - 939 EP - 960 ER - TY - JOUR A1 - Bodermann, Bernd A1 - Buhr, Egbert A1 - Danzebrink, Hans-Ulrich A1 - Bär, Markus A1 - Scholze, Frank A1 - Krumrey, Michael A1 - Wurm, Matthias A1 - Klapetek, Petr A1 - Hansen, Poul-Erik A1 - Korpelainen, Virpi A1 - van Veghel, Marijn A1 - Yacoot, Andrew A1 - Siitonen, Samuli A1 - El Gawhary, Omar A1 - Burger, Sven A1 - Saastamoinen, Toni T1 - Joint Research on Scatterometry and AFM Wafer Metrology JF - AIP Conference Proceedings Y1 - 2011 U6 - https://doi.org/10.1063/1.3657910 VL - 1395 IS - 1 SP - 319 EP - 323 PB - AIP ER - TY - JOUR A1 - Boer, H. Marike T. A1 - Stötzel, Claudia A1 - Röblitz, Susanna A1 - Deuflhard, Peter A1 - Veerkamp, Roel F. A1 - Woelders, Henri T1 - A simple mathematical model of the bovine estrous cycle JF - Journal of Theoretical Biology Y1 - 2011 U6 - https://doi.org/10.1016/j.jtbi.2011.02.021 VL - 278 IS - 1 SP - 20 EP - 31 ER - TY - JOUR A1 - Boer, H. Marike T. A1 - Röblitz, Susanna A1 - Stötzel, Claudia A1 - Veerkamp, Roel F. A1 - Kemp, Bas A1 - Woelders, Henri T1 - Mechanisms regulating follicle wave patterns in the bovine estrous cycle investigated with a mathematical model JF - Journal of Dairy Science Y1 - 2011 U6 - https://doi.org/10.3168/jds.2011-4400 VL - 94 IS - 12 SP - 5987 EP - 6000 ER - TY - JOUR A1 - Boer, H. Marike T. A1 - Apri, Mochamad A1 - Molenaar, Jaap A1 - Stötzel, Claudia A1 - Veerkamp, Roel F. A1 - Woelders, Henri T1 - Candidate mechanisms underlying atypical progesterone profiles as deduced from parameter perturbations in a mathematical model of the bovine estrous cycle JF - Journal of Dairy Science Y1 - 2012 UR - http://www.sciencedirect.com/science/article/pii/S0022030212003621 U6 - https://doi.org/10.3168/jds.2011-5241 VL - 95 IS - 7 SP - 3837 EP - 3851 ER - TY - JOUR A1 - Braess, Dietrich A1 - Deuflhard, Peter A1 - Lipnikov, Konstantin T1 - A Subspace Cascadic Multigrid Method for Mortar Elements JF - Computing Y1 - 2002 VL - 69 SP - 205 EP - 225 ER - TY - JOUR A1 - Bredies, Kristian A1 - Lorenz, Dirk A. A1 - Maass, Peter A1 - Teschke, G. T1 - A partial differential equation for continuous non-linear shrinkage filtering and its application for analyzing MMG data JF - Proc. SPIE Vol. 5266, p. 84-93, Wavelet Applications in Industrial Processing; Frederic Truchetet; Ed. Y1 - 2004 ER - TY - JOUR A1 - Burger, Sven T1 - Simulation method improves accuracy for optical metrology and nanooptics design JF - SPIE Newsroom Y1 - 2009 U6 - https://doi.org/10.1117/2.1200905.1629 ER - TY - JOUR A1 - Bergmann, G. A1 - Graichen, F. A1 - Rohlmann, A. A1 - Bender, Alwina A1 - Ehrig, Rainald A1 - Westerhoff, P. A1 - Heinlein, B. T1 - Design and calibration of load sensing orthopaedic implants JF - Journal Biomech. Eng. Y1 - 2008 SP - 02109 EP - 1–02109–9 ER - TY - JOUR A1 - Babicheva, Viktoriia E. A1 - Vergeles, Sergey S. A1 - Vorobev, Petr E. A1 - Burger, Sven T1 - Localized surface plasmon modes in a system of two interacting metallic cylinders JF - J. Opt. Soc. Am. B Y1 - 2012 U6 - https://doi.org/10.1364/JOSAB.29.001263 VL - 29 IS - 6 SP - 1263 EP - 1269 ER - TY - JOUR A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Hiptmair, Ralf A1 - Hoppe, Ronald H. W. A1 - Wohlmuth, Barbara T1 - Adaptive multilevel methods for edge element discretizations of Maxwell’s equations JF - Surv. Math. Ind. Y1 - 1999 VL - 8 IS - 3-4 SP - 271 EP - 312 ER - TY - JOUR A1 - Bethge, Jens A1 - Steinmeyer, Günter A1 - Burger, Sven A1 - Lederer, Falk A1 - Iliew, Rumen T1 - Guiding properties of chirped photonic crystal fibers JF - Journal of Lightwave Technology Y1 - 2009 U6 - https://doi.org/10.1109/JLT.2009.2021583 VL - 27 SP - 1698 ER - TY - JOUR A1 - Blome, Mark A1 - McPeak, Kevin A1 - Burger, Sven A1 - Schmidt, Frank A1 - Norris, David T1 - Back-reflector design in thin-film silicon solar cells by rigorous 3D light propagation modeling JF - COMPEL: Int. J. Comput. Mathem. Electr. Electron. Eng. Y1 - 2014 U6 - https://doi.org/10.1108/COMPEL-12-2012-0367 VL - 33 IS - 4 SP - 1282 EP - 1295 ER - TY - JOUR A1 - Weiser, Martin A1 - Deuflhard, Peter T1 - Inexact central path following algorithms for optimal control problems JF - SIAM J. Control Opt. Y1 - 2007 VL - 46 IS - 3 SP - 792 EP - 815 ER - TY - JOUR A1 - Casas, E. A1 - de Los Reyes, J. A1 - Tröltzsch, Fredi T1 - Sufficient second-order optimality conditions for semilinear control problems with pointwise state constraints JF - SIAM Journal on Optimization Y1 - 2007 U6 - https://doi.org/10.1137/07068240X VL - 19 IS - 2 SP - 616 EP - 643 ER - TY - JOUR A1 - Ackermann, Jörg A1 - Erdmann, Bodo A1 - Roitzsch, Rainer T1 - A self-adaptive multilevel finite element method for the stationary Schrödinger equation in three space dimensions JF - J. Chem. Phys. Y1 - 1994 VL - 101 SP - 7643 EP - 7650 ER - TY - JOUR A1 - Abendroth, Frank A1 - Bujotzek, Alexander A1 - Shan, Min A1 - Haag, Rainer A1 - Weber, Marcus A1 - Seitz, Oliver T1 - DNA-controlled bivalent presentation of ligands for the estrogen receptor JF - Angew. Chem. Int. Ed. Y1 - 2011 ER - TY - JOUR A1 - Antoine, Xavier A1 - Arnold, Anton A1 - Besse, Christophe A1 - Ehrhardt, Matthias A1 - Schädle, Achim T1 - A Review of Transparent and Artificial Boundary Conditions Techniques for Linear and Nonlinear Schrödinger Equations JF - Commun. Comput. Phys. Y1 - 2008 UR - http://www.global-sci.com/openaccess/v4_729.pdf VL - 4 SP - 729 EP - 796 ER - TY - JOUR A1 - Andrae, Karsten A1 - Dinh, P. A1 - Reinhard, P.-G. A1 - Suraud, E. T1 - Pump and probe analysis of metal cluster dynamics JF - Computational Materials Science Y1 - 2006 UR - http://www.sciencedirect.com/science/article/pii/S0927025605001163 U6 - https://doi.org/DOI: 10.1016/j.commatsci.2004.09.062 VL - 35 IS - 3 SP - 169 EP - 173 ER - TY - JOUR A1 - Andrae, Karsten A1 - Reinhard, P.-G. A1 - Suraud, E. T1 - Crossed Beam Pump and Probe Dynamics in Metal Clusters JF - Phys. Rev. Lett. Y1 - 2004 U6 - https://doi.org/10.1103/PhysRevLett.92.173402 VL - 92 IS - 17 SP - 173402 PB - American Physical Society ER - TY - JOUR A1 - Andrae, Karsten A1 - Reinhard, P.-G. A1 - Suraud, E. T1 - Systematics of spin-polarized small Na clusters JF - Annals of the European Academy of Science Y1 - 2007 ER - TY - JOUR A1 - Asam, P. A1 - Deuflhard, Peter A1 - Kaiser, Wolfgang T1 - Intensity Limiting and Stimulated Brillouin Scattering in Germanium JF - Physics Letters Y1 - 1968 VL - 27 A SP - 78 EP - 79 ER - TY - JOUR A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - FEM Simulation of Plasmon Laser Resonances JF - AIP Conference Proceedings Y1 - 2010 U6 - https://doi.org/10.1063/1.3498131 VL - 1281 SP - 1613 EP - 1616 PB - AIP ER - TY - JOUR A1 - Burger, Sven A1 - Bongs, Kai A1 - Dettmer, Stefanie A1 - Ertmer, Wolfgang A1 - Sengstock, Klaus A1 - Sanpera, Anna A1 - Shlyapnikov, Gora A1 - Lewenstein, Maciej T1 - Dark Solitons in Bose-Einstein Condensates JF - Phys. Rev. Lett. Y1 - 1999 U6 - https://doi.org/10.1103/PhysRevLett.83.5198 VL - 83 IS - 25 SP - 5198 EP - 5201 ER - TY - JOUR A1 - Burger, Sven A1 - Cataliotti, F. A1 - Fort, C. A1 - Minardi, F. A1 - Inguscio, Massimo A1 - Chiofalo, M. A1 - Tosi, M. T1 - Superfluid and Dissipative Dynamics of a Bose-Einstein Condensate in a Periodic Optical Potential JF - Phys. Rev. Lett. Y1 - 2001 VL - 86 IS - 20 SP - 4447 EP - 4450 ER - TY - JOUR A1 - Burger, Sven A1 - Carr, L. A1 - Öhberg, P. A1 - Sengstock, Klaus A1 - Sanpera, Anna T1 - Generation and interaction of solitons in Bose-Einstein condensates JF - Phys. Rev. A Y1 - 2002 VL - 65 SP - 043611 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Birkl, G. A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang A1 - Rzazewski, K. A1 - Sanpera, Anna A1 - Lewenstein, Maciej T1 - Coherent Evolution of Bouncing Bose-Einstein Condensates JF - Phys. Rev. Lett. Y1 - 1999 VL - 83 IS - 18 SP - 3577 EP - 3580 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Dettmer, S. A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang T1 - Manipulation of Bose-Einstein condensates by dipole potentials JF - J. Mod. Opt. Y1 - 2000 U6 - https://doi.org/10.1080/09500340008232190 VL - 47 SP - 2697 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Dettmer, S. A1 - Hellweg, D. A1 - Arlt, J. A1 - Ertmer, Wolfgang A1 - Sengstock, Klaus T1 - Waveguide for Bose-Einstein condensates JF - Phys. Rev. A Y1 - 2001 VL - 63 SP - 31602 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Deuflhard, Peter T1 - The cascadic multigrid method for elliptic problems JF - Numer. Math. Y1 - 1996 VL - 75 SP - 135 EP - 152 ER - TY - JOUR A1 - Böck, J. A1 - Deuflhard, Peter A1 - Hoeft, A. A1 - Korb, H. A1 - Wolpers, H. A1 - Steinmann, J. A1 - Hellige, G. T1 - Thermal recovery after passage of the pulmonary circulation assessed by deconvolution JF - J. Appl. Physiol. Y1 - 1988 VL - 64 IS - 3 SP - 1210 EP - 1216 ER - TY - JOUR A1 - Böck, J. A1 - Deuflhard, Peter A1 - Hoeft, A. A1 - Korb, H. A1 - Steinmann, J. A1 - Wolpers, H. A1 - Hellige, G. T1 - Evaluation of monoexponential extrapolation of transpulmonary thermal-dye kinetics by use of a new model-free deconvolution algorithm JF - Med Instrum Y1 - 1988 VL - 22 IS - 1 SP - 20 EP - 28 ER - TY - JOUR A1 - Schmidt, Frank A1 - Friese, T. A1 - Yevick, David T1 - Transparent Boundary Conditions for Split-Step Padé Approximations of the One-Way Helmholtz equation JF - J. Comp. Phys Y1 - 2001 VL - 170 SP - 696 EP - 719 ER - TY - JOUR A1 - Schiela, Anton A1 - Günther, Andreas T1 - An Interior Point Algorithm with Inexact Step Computation in Function Space for State Constrained Optimal Control JF - Numer. Math. Y1 - 2011 U6 - https://doi.org/10.1007/s00211-011-0381-4 VL - 119 IS - 2 SP - 373 EP - 407 PB - Springer Berlin / Heidelberg ER - TY - JOUR A1 - Schmidt, Frank A1 - Gottschling, K. T1 - Improved Method of Mode Determination in Planar Optical Waveguides Using Line Transmission Approach JF - J. Opt. Commun. Y1 - 1992 VL - 12 IS - 3 SP - 112 EP - 114 ER - TY - JOUR A1 - Schmidt, Frank A1 - Hohage, Thorsten A1 - Klose, Roland A1 - Schädle, Achim A1 - Zschiedrich, Lin T1 - Pole condition: A numerical method for Helmholtz-type scattering problems with inhomogeneous exterior domain JF - J. Comput. Appl. Math. Y1 - 2008 U6 - https://doi.org/10.1016/j.cam.2007.04.046 VL - 218 IS - 1 SP - 61 EP - 69 ER - TY - JOUR A1 - Schaber, Karlheinz A1 - Koerber, Jens A1 - Ofenloch, O. A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Aerosol Formation in Gas-Liquid Contact Devices- Nucleation, Growth and Particle Dynamics JF - Chem.Eng.Sci. Y1 - 2002 VL - 57 SP - 4345 EP - 4356 ER - TY - JOUR A1 - Schädle, Achim A1 - López-Fernández, María A1 - Lubich, Christian T1 - Fast and oblivious convolution quadrature JF - SIAM J. Sci. Comput. Y1 - 2006 U6 - https://doi.org/http://dx.doi.org/10.1137/050623139 VL - 28 IS - 2 SP - 421 EP - 438 ER - TY - JOUR A1 - Schmidt, Frank A1 - März, Reinhard T1 - On the Reference Wave Vector of Paraxial Helmholtz Equations JF - IEEE Journal of Lightwave Technology Y1 - 1996 VL - 14 SP - 2395 EP - 2400 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Erdmann, Bodo A1 - Roitzsch, Rainer A1 - Lines, Glenn Terje T1 - Adaptive Finite Element Simulation of Ventricular Dynamics JF - J. Computing and Visualization in Science Y1 - 2009 VL - 12 SP - 201 EP - 205 ER - TY - JOUR A1 - Pomplun, Jan A1 - Schmidt, Frank T1 - Accelerated a posteriori error estimation for the reduced basis method with application to 3D electromagnetic scattering problems JF - SIAM J. Sci. Comput. Y1 - 2010 U6 - https://doi.org/10.1137/090760271 VL - 32 SP - 498 EP - 520 ER - TY - JOUR A1 - Pedri, P. A1 - Pitaevskii, L. A1 - Stringari, S. A1 - Fort, C. A1 - Burger, Sven A1 - Cataliotti, F. A1 - Maddaloni, P. A1 - Minardi, F. A1 - Inguscio, Massimo T1 - Expansion of a Coherent Array of Bose-Einstein Condensates JF - Physical Review Letters Y1 - 2001 VL - 87 SP - 220401 ER - TY - JOUR A1 - Pearce, G. J. A1 - Wiederhecker, G. S. A1 - Poulton, Christopher G. A1 - Burger, Sven A1 - Russell, P. St. J. T1 - Models for guidance in kagome-structured hollow-core photonic crystal fibres JF - Optics Express Y1 - 2007 U6 - https://doi.org/10.1364/OE.15.012680 VL - 15 SP - 12680 ER - TY - JOUR A1 - Muschinski, A. A1 - Lehmann, V. A1 - Justen, L. A1 - Teschke, G. T1 - Advanced Radar Wind Profiling JF - Meteorologische Zeitschrift Y1 - 2005 VL - 5 IS - 14 SP - 609 EP - 626 ER - TY - JOUR A1 - Nadobny, Johanna A1 - Fähling, Horst A1 - Hagmann, M. A1 - Turner, P. A1 - Wlodarczyk, Waldemar A1 - Gellermann, Johanna A1 - Deuflhard, Peter A1 - Wust, Peter T1 - Experimental and numerical investigation of feed-point parameters in a 3-D hyperthermia applicator using different FDTD models of feed networks JF - IEEE Trans Biomed Eng Y1 - 2002 VL - 49 IS - 11 SP - 1348 EP - 1359 ER - TY - JOUR A1 - Nadobny, Johanna A1 - Pontalti, R. A1 - Sullivan, Dennis A1 - Wlodarczyk, Waldemar A1 - Vaccari, A. A1 - Deuflhard, Peter A1 - Wust, Peter T1 - A Thin-Rod Approximation for the Improved Modeling of Bare and Insulated Cylindrical Antennas Using the FDTD Method JF - IEEE Transactions on Antennas and Propagation Y1 - 2003 VL - 51 IS - 8 SP - 1780 EP - 1796 ER - TY - JOUR A1 - Nadobny, Johanna A1 - Sullivan, Dennis A1 - Wlodarczyk, Waldemar A1 - Deuflhard, Peter A1 - Wust, Peter T1 - A 3-D Tensor FDTD-Formulation for Treatment of Sloped Interfaces in Electrically Inhomogeneous Media JF - IEEE Transactions on Antennas and Propagation Y1 - 2003 VL - 51 IS - 8 SP - 1760 EP - 1770 ER - TY - JOUR A1 - Schlegel, Martin A1 - Marquardt, Wolfgang A1 - Ehrig, Rainald A1 - Nowak, Ulrich T1 - Sensitivity analysis of linearly-implicit differential-algebraic systems by one-step extrapolation JF - Applied Numerical Mathematics Y1 - 2004 IS - 48 SP - 83 EP - 102 ER - TY - JOUR A1 - Schiela, Anton A1 - Weiser, Martin T1 - Superlinear convergence of the Control Reduced Interior Point Method for PDE Constrained Optimization JF - Computational Optimization and Applications Y1 - 2008 VL - 39 IS - 3 SP - 369 EP - 393 ER - TY - JOUR A1 - Schmidt, Frank A1 - Deuflhard, Peter T1 - Discrete Transparent Boundary Conditions for the Numerical Solution of Fresnel’s Equation. JF - Comput. Math. Appl. Y1 - 1995 VL - 29 SP - 53 EP - 76 ER - TY - JOUR A1 - Nadobny, Johanna A1 - Wust, Peter A1 - Seebass, Martin A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A Volume-Surface Integral Method for Solving Maxwell’s Equations in Electrically Inhomogeneous Media Using Tetrahedral Grids JF - IEEE Transactions on Microwave Theory and Techniques Y1 - 1996 VL - 44 IS - 4 SP - 543 EP - 554 ER - TY - JOUR A1 - Neve-Oz, Y. A1 - Pollok, T. A1 - Burger, Sven A1 - Golosovsky, M. A1 - Davidov, D. T1 - Fast Light and Focusing in 2D Photonic Quasicrystals JF - PIERS Online Y1 - 2009 U6 - https://doi.org/10.2529/PIERS081223080021 VL - 5 SP - 451 ER - TY - JOUR A1 - Neve-Oz, Y. A1 - Pollok, T. A1 - Burger, Sven A1 - Golosovsky, M. A1 - Davidov, D. T1 - Resonant Transmission of Electromagnetic Waves through 2D Photonic Quasicrystals JF - J. Appl. Phys. Y1 - 2010 U6 - https://doi.org/10.1063/1.3329542 VL - 107 SP - 063105 ER - TY - JOUR A1 - Neve-Oz, Y. A1 - Pollok, T. A1 - Burger, Sven A1 - Golosovsky, M. A1 - Lifshitz, R. A1 - Davidov, D. T1 - Negative Refraction and Omni Directionality in 2D Photonic Quasicrystal Superstructure JF - AIP Conference Proceedings Y1 - 2010 U6 - https://doi.org/10.1063/1.3498134 VL - 1281 SP - 1622 PB - AIP ER - TY - JOUR A1 - Nowak, Ulrich A1 - Deuflhard, Peter T1 - Numerical Identification of Selected Rate Constants in Large Chemical Reaction Systems JF - Appl. Numer. Math. Y1 - 1985 VL - 1 SP - 59 EP - 75 ER - TY - JOUR A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank A1 - Schliwa, Andrei A1 - Bimberg, Dieter A1 - Pietrzak, Agnieszka A1 - Wenzel, Hans A1 - Erbert, Götz T1 - Finite element simulation of the optical modes of semiconductor lasers JF - Phys. Status Solidi B Y1 - 2010 U6 - https://doi.org/10.1002/pssb.200945451 VL - 247 SP - 846 EP - 853 ER - TY - JOUR A1 - Pomplun, Jan A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Schmidt, Frank T1 - Adaptive finite element method for simulation of optical nano structures JF - Phys. Status Solidi B Y1 - 2007 U6 - https://doi.org/10.1002/pssb.200743192 VL - 244 SP - 3419 EP - 3434 ER - TY - JOUR A1 - Pomplun, Jan A1 - Zschiedrich, Lin A1 - Klose, Roland A1 - Schmidt, Frank A1 - Burger, Sven T1 - Finite element simulation of radiation losses in photonic crystal fibers JF - phys. stat. sol. (a) Y1 - 2007 U6 - https://doi.org/10.1002/pssa.200776414 VL - 204 IS - 11 SP - 3822 EP - 3837 ER - TY - JOUR A1 - Teschke, G. A1 - Zhariy, M. A1 - Maass, Peter A1 - Sassen, K. T1 - Extraction and Analysis of Structural Features in Cloud Radar and Lidar Data Using Wavelet Based Methods JF - Proceedings of ERAD Y1 - 2002 ER - TY - JOUR A1 - Rätsch, M. A1 - Romdhani, S. A1 - Teschke, G. A1 - Vetter, T. T1 - Wavelet Frame Accelerated Reduced Support Vector Machine JF - to appaer in: Y1 - 2006 ER - TY - JOUR A1 - Ramlau, R. A1 - Teschke, G. T1 - Regularization of Sobolev Embedding Operators and Applications Part I JF - Sampling Theory in Signal and Image Processing Y1 - 2004 VL - 3 IS - 2 SP - 175 EP - 196 ER - TY - JOUR A1 - Ramlau, R. A1 - Teschke, G. T1 - Regularization of Sobolev Embedding Operators and Applications Part II JF - Sampling Theory in Signal and Image Processing Y1 - 2004 VL - 3 IS - 3 SP - 225 EP - 246 ER - TY - JOUR A1 - Schmidt, Frank T1 - Pole Condition: A new Approach to Solve Scattering Problems JF - Oberwolfach Report Y1 - 2004 VL - 1 IS - 1 SP - 615 EP - 617 PB - Mathematisches Forschungsinstitut Oberwolfach ER - TY - JOUR A1 - Schmidt, Frank T1 - Simulation und Herstellung von Faserschleifkopplern JF - Wissenschaftliche Zeitschrift der Humboldt-Universität zu Berlin, R. Math./Naturwiss. Y1 - 1990 VL - 39 IS - 2 SP - 115 EP - 118 ER - TY - JOUR A1 - Schmidt, Frank T1 - An Adaptive Approach to the Numerical Solution of Fresnel’s Wave Equation. JF - IEEE Journal of Lightwave Technology Y1 - 1993 VL - 11 IS - 9 SP - 1425 EP - 1435 ER - TY - JOUR A1 - Schmidt, Frank T1 - Computation of Discrete Transparent Boundary Conditions for the 2D Helmholtz equation JF - Optical and Quantum Electronics Y1 - 1998 VL - 30 IS - 5,6 SP - 427 EP - 441 ER - TY - JOUR A1 - Schmidt, Frank T1 - Construction of Discrete Transparent Boundary Conditions for Schrödinger-Type equations JF - Surv. Math. Ind. Y1 - 1999 VL - 9 SP - 87 EP - 100 ER - TY - JOUR A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo JF - J. Comput. Phys. Y1 - 1999 UR - http://www.zib.de/PaperWeb/abstracts/SC-98-45 VL - 151 SP - 146 EP - 168 ER - TY - JOUR A1 - Ramlau, R. A1 - Teschke, G. T1 - Tikhonov Replacement Functionals for Iteratively Solving Nonlinear Operator Equations JF - InverseProblems Y1 - 2005 VL - 21 SP - 1571 EP - 1592 ER - TY - JOUR A1 - Ramlau, R. A1 - Teschke, G. T1 - A Projection Iteration for Nonlinear Operator Equations with Sparsity Constraints JF - Numerische Mathematik Y1 - 2006 VL - 104 SP - 177 EP - 203 ER - TY - JOUR A1 - Reinecke, Isabel A1 - Deuflhard, Peter T1 - A Complex Mathematical Model of the Human Menstrual Cycle JF - Journal of Theoretical Biology Y1 - 2007 VL - 247 IS - 2 SP - 303 EP - 330 ER - TY - JOUR A1 - Richter, Marten A1 - Schlosser, Felix A1 - Schoth, Mario A1 - Burger, Sven A1 - Schmidt, Frank A1 - Knorr, Andreas A1 - Mukamel, Shaul T1 - Reconstruction of the wave functions of coupled nanoscopic emitters using a coherent optical technique JF - Phys. Rev. B Y1 - 2012 U6 - https://doi.org/10.1103/PhysRevB.86.085308 VL - 86 SP - 085308 ER - TY - JOUR A1 - Ruprecht, Daniel A1 - Schädle, Achim A1 - Schmidt, Frank A1 - Zschiedrich, Lin T1 - Transparent boundary conditions for time-dependent problems JF - SIAM J. Sci. Comput. Y1 - 2008 U6 - https://doi.org/10.1137/070692637 VL - 30 IS - 5 SP - 2358 EP - 2385 ER - TY - JOUR A1 - Sarich, Marco A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Optimal Fuzzy Aggregation of Networks JF - Multiscale Modeling and Simulation Y1 - 2010 U6 - https://doi.org/10.1137/090758519 VL - 8 IS - 4 SP - 1535 EP - 1561 ER - TY - JOUR A1 - Bosse, Hartwig A1 - Grötschel, Martin A1 - Henk, Martin T1 - Polynomial inequalities representing polyhedra JF - Mathematical Programming Y1 - 2005 U6 - https://doi.org/10.1007/s10107-004-0563-2 VL - 103 IS - 1 SP - 35 EP - 44 ER - TY - JOUR A1 - Grötschel, Martin T1 - Telota baut das elektronische Hirn der Akademie zusammen JF - Circular der BBAW Y1 - 2005 IS - 31 SP - 34 EP - 35 ER - TY - JOUR A1 - Grötschel, Martin T1 - Matheon JF - Jahresbericht der DMV Y1 - 2005 VL - 107 IS - 4 SP - 173 EP - 196 PB - B. G. Teubner ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Lukac, Sascha A1 - Mitusch, Kay A1 - Schlechte, Thomas A1 - Schultz, Sören A1 - Tanner, Andreas T1 - An Auctioning Approach to Railway Slot Allocation JF - Competition and Regulation in Network Industries Y1 - 2006 VL - 1 IS - 2 SP - 163 EP - 196 ER - TY - JOUR A1 - Grötschel, Martin A1 - Hinrichs, Hinrich A1 - Schröer, Klaus A1 - Tuchscherer, Andreas T1 - Ein gemischt-ganzzahliges lineares Optimierungsmodell für ein Laserschweißproblem im Karosseriebau JF - Zeitschrift für wirtschaftlichen Fabrikbetrieb (ZWF) Karosseriebau Y1 - 2006 UR - http://opus.kobv.de/zib/volltexte/2006/915/ VL - 101 IS - 5 SP - 260 EP - 264 ER - TY - JOUR A1 - Achterberg, Tobias A1 - Grötschel, Martin A1 - Koch, Thorsten T1 - Teaching MIP Modeling and Solving JF - OR/MS Today Y1 - 2006 UR - http://www.lionhrtpub.com/orms/orms-12-06/freducation.html VL - 33 IS - 6 SP - 14 EP - 15 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Pfetsch, Marc T1 - A Column-Generation Approach to Line Planning in Public Transport JF - Transportation Science (INFORMS) Y1 - 2007 U6 - https://doi.org/10.1287/trsc.1060.0161 VL - 41 IS - 1 SP - 123 EP - 132 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Neue Perspektiven eines Informationssystems für die Mathematik JF - Rundbrief der Gesellschaft für Angewandte Mathematik und Mechanik Y1 - 1994 VL - 3 SP - 4 EP - 7 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Neue Wege für die Fachinformation JF - DFN-Mitteilungen Y1 - 1994 VL - 34 SP - 4 EP - 7 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - New Perspectives of a Distributed Electronic Information System for Mathematics, Part I JF - European Mathematical Society Newsletter Y1 - 1994 VL - 13 SP - 6 EP - 17 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - New Perspectives of a Distributed Electronic Information System for Mathematics, Part II JF - European Mathematical Society Newsletter Y1 - 1994 VL - 14 SP - 6 EP - 14 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - Verteiltes Informationssystem für die Mathematik JF - Mitteilungen der Deutschen Mathematiker-Vereinigung Y1 - 1995 VL - 1 SP - 52 EP - 54 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Berliner Telebussystem bietet Mobilität für Behinderte JF - Der Nahverkehr Y1 - 1997 VL - 1/2 SP - 20 EP - 22 ER - TY - JOUR A1 - Grötschel, Martin T1 - Der Weg der Mathematik in die Informationsgesellschaft – Teil II JF - DMV-Mitteilungen Y1 - 1997 VL - 4 SP - 43 EP - 48 ER - TY - JOUR A1 - Grötschel, Martin T1 - Der Weg der Mathematik in die Informationsgesellschaft – Teil I JF - DMV-Mitteilungen Y1 - 1997 VL - 3 SP - 48 EP - 57 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - The Steiner tree packing problem in VLSI design JF - Mathematical Programming Y1 - 1997 VL - 78 IS - 2 SP - 265 EP - 281 ER - TY - JOUR A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Jonas, Peter A1 - Paul, Uwe A1 - Wessäly, Roland T1 - Survivable Mobile Phone Network Architectures JF - IEEE Communications Magazine Y1 - 1998 SP - 88 EP - 93 ER - TY - JOUR A1 - Alevras, Dimitris A1 - Grötschel, Martin A1 - Wessäly, Roland T1 - Cost-efficient network synthesis from leased lines JF - Annals of Operations Research Y1 - 1998 VL - 76 SP - 1 EP - 20 ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Kamin, Nicola A1 - Rambau, Jörg T1 - Combinatorial online optimization in practice JF - OPTIMA Y1 - 1998 VL - 57 SP - 1 EP - 6 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Martin, Alexander T1 - Frequency assignment in cellular phone networks JF - Annals of Operations Research Y1 - 1998 U6 - https://doi.org/10.1023/A:1018908907763 VL - 76 SP - 73 EP - 93 PB - J. C. Baltzer AG, Science Publishers ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Die Zukunft wissenschaftlicher Kommunikation aus Sicht der Mathematik JF - Spektrum der Wissenschaft Y1 - 1995 SP - 39 EP - 43 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Aufbau elektronischer Informations- und Kommunikationsstrukturen JF - Newsletter der Gesellschaft für Mathematik, Ökonomie und Operations Research Y1 - 1995 VL - 3/4 SP - 24 EP - 66 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Wissenschaftliche Kommunikation am Wendepunkt - Bibliotheken im Zeitalter globaler elektronischer Netze JF - Zeitschrift für Bibliothekswesen und Bibliographie Y1 - 1995 VL - 42 IS - 3 SP - 287 EP - 312 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Routing in Grid Graphs by Cutting Planes JF - ZOR - Mathematical Methods of Operations Research Y1 - 1995 VL - 41 IS - 3 SP - 255 EP - 275 ER - TY - JOUR A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - Polyhedral and Computational Investigations for Designing Communication Networks with High Survivability Requirements JF - Operations Research Y1 - 1995 VL - 43 IS - 6 SP - 1012 EP - 1024 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Die optimierte Odyssee JF - Spektrum der Wissenschaft Y1 - 1999 VL - 4 SP - 76 EP - 85 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Die optimierte Odyssee JF - Spektrum der Wissenschaft, Digest Y1 - 1999 VL - 2 SP - 32 EP - 41 ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Fischetti, Matteo A1 - Grötschel, Martin T1 - A Polyhedral Study of the Asymmetric Traveling Salesman Problem with Time Windows JF - Networks Y1 - 2000 VL - 36 IS - 2 SP - 69 EP - 79 ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Fischetti, Matteo A1 - Grötschel, Martin T1 - Solving the Asymmetric Travelling Salesman Problem with time windows by branch-and-cut JF - Mathematical Programming, Series A Y1 - 2001 VL - 90 IS - 3 SP - 475 EP - 506 PB - Springer ER - TY - JOUR A1 - Grötschel, Martin T1 - Copyright und elektronisches Publizieren JF - DMV-Mitteilungen Y1 - 2001 VL - 3 SP - 8 EP - 10 ER - TY - JOUR A1 - Grötschel, Martin T1 - Den Kohl heile rüberbringen … – Mathematische Methoden der Transportoptimierung JF - Unsere-Duisburger-Hochschule-Zeitschrift Y1 - 1996 VL - 48 IS - 1 SP - 15 EP - 17 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Wissenschaftliche Information und Kommunikation im Umbruch JF - Forschung & Lehre, Mitteilungen des Deutschen Hochschulverbandes Y1 - 1996 VL - 4 SP - 194 EP - 198 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner Trees: Further Facets JF - European Journal of Combinatorics Y1 - 1996 U6 - https://doi.org/10.1006/eujc.1996.0004 VL - 17 IS - 1 SP - 39 EP - 52 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner Trees: Separation Algorithms JF - SIAM Journal on Discrete Mathematics Y1 - 1996 U6 - https://doi.org/10.1137/S0895480193258716 VL - 9 IS - 2 SP - 233 EP - 257 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Optimum Path Packing on Wheels JF - Computers and Mathematics with Applications Y1 - 1996 VL - 31 IS - 11 SP - 23 EP - 35 PB - Elsevier ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner trees: Polyhedral Investigations JF - Mathematical Programming, Series A Y1 - 1996 U6 - https://doi.org/10.1007/BF02592085 VL - 72 IS - 2 SP - 101 EP - 123 ER - TY - JOUR A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert T1 - Packing Steiner trees: a cutting plane algorithm and computational results JF - Mathematical Programming, Series A Y1 - 1996 U6 - https://doi.org/10.1007/BF02592086 VL - 72 IS - 2 SP - 125 EP - 145 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Klostermeier, Fridolin A1 - Küttner, Christian T1 - Optimierung des Berliner Behindertenfahrdienstes JF - DMV-Mitteilungen Y1 - 1997 VL - 2 SP - 38 EP - 43 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Grötschel, Martin A1 - Winczewski, Vincent T1 - Mathe im Netz - Math-Net JF - DFN-Mitteilungen Y1 - 1998 VL - Heft 48 SP - 4 EP - 6 ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Grötschel, Martin A1 - Abdel-Hamid, Atef Abdel-Aziz T1 - Order picking in an automatic warehouse JF - Mathematical Methods of Operations Research Y1 - 1999 VL - 49 IS - 3 SP - 501 EP - 515 ER - TY - JOUR A1 - Grötschel, Martin T1 - My Favorite Theorem JF - OPTIMA Y1 - 1999 VL - 62 SP - 2 EP - 5 ER - TY - JOUR A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Wo bleibt der Aufzug? JF - OR News Y1 - 1999 VL - 5 SP - 11 EP - 13 ER - TY - JOUR A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg T1 - Wo bleibt der Aufzug? JF - OR News Y1 - 2006 VL - Sonderausgabe SP - 70 EP - 72 ER - TY - JOUR A1 - Grötschel, Martin A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Lügger, Joachim A1 - Rusch, Beate T1 - Der Kooperative Bibliotheksverbund Berlin-Brandenburg JF - ABI Technik – Zeitschrift für Automation, Bau und Technik im Archiv-, Bibliotheks- und Informationswesen Y1 - 1999 VL - 19 IS - 4 SP - 350 EP - 367 ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Koster, Arie M.C.A. T1 - Frequency Planning and Ramifications of Coloring JF - Discussiones Mathematicae, Graph Theory Y1 - 2002 IS - 22 SP - 51 EP - 88 ER - TY - JOUR A1 - Grötschel, Martin A1 - Krumke, Sven A1 - Rambau, Jörg A1 - Torres, Luis Miguel T1 - Making the Yellow Angels Fly JF - SIAM News Y1 - 2002 VL - 35 IS - 4 SP - 1,10,11 ER - TY - JOUR A1 - Grötschel, Martin T1 - P=NP? JF - Elemente der Mathematik, Eine Zeitschrift der Schweizerischen Mathematischen Gesellschaft Y1 - 2002 VL - 57 IS - 3 SP - 96 EP - 102 ER - TY - JOUR A1 - Grötschel, Martin A1 - Henk, Martin T1 - The Representation of Polyhedra by Polynomial Inequalities JF - Discrete & Computational Geometry Y1 - 2003 U6 - https://doi.org/10.1007/s00454-003-0782-y VL - 29 IS - 4 SP - 485 EP - 504 ER - TY - JOUR A1 - Grötschel, Martin T1 - Das elektronische Leben der Akademie JF - Circular der BBAW Y1 - 2003 IS - 28 SP - 14 EP - 15 ER - TY - JOUR A1 - Grötschel, Martin A1 - Kuberek, Monika A1 - Lill, Monika A1 - Lohrum, Stefan A1 - Lügger, Joachim A1 - Rusch, Beate T1 - Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) JF - Bibliothek, Forschung und Praxis Y1 - 2001 VL - 25 IS - 1 SP - 55 EP - 65 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - The Optimized Odyssey JF - AIROnews Y1 - 2001 VL - VI IS - 2 SP - 1 EP - 7 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Le stanze del TSP JF - AIROnews Y1 - 2001 VL - VI IS - 3 SP - 6 EP - 9 ER - TY - JOUR A1 - Grötschel, Martin T1 - Empfehlungen des Wissenschaftsrates zur digitalen Informationsversorgung durch Hochschulbibliotheken JF - DMV-Mitteilungen Y1 - 2001 VL - 4 SP - 40 EP - 43 ER - TY - JOUR A1 - Grötschel, Martin T1 - Telota - Was soll das? JF - Circular der BBAW Y1 - 2001 IS - 23 SP - 3 EP - 7 ER - TY - JOUR A1 - Grötschel, Martin T1 - Mein digitaler Traum JF - Gegenworte der BBAW Y1 - 2001 IS - 8 SP - 10 EP - 16 ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Grötschel, Martin A1 - Koster, Arie M.C.A. T1 - Frequenzplanung im Mobilfunk JF - DMV-Mitteilungen Y1 - 2002 IS - 1 SP - 18 EP - 25 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard A1 - Boche, Holger T1 - An Optimal Stopping Approach to ARQ Protocols with Variable Success Probabilities per Retransmission JF - 45th Ann. Allerton Conf. Y1 - 2007 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard A1 - Boche, Holger A1 - Stefanov, Stoycho T1 - Optimal Control of Transmission Errors with Power Allocation and Stability in ARQ Downlink JF - CISS’08, Princeton, USA Y1 - 2008 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard A1 - Buehler, Jörg T1 - Optimal Control of a Single Queue with Retransmissions JF - IEEE Trans. on Wireless Communications Y1 - 2009 VL - 8, no. 7 SP - 3736 EP - 3746 ER - TY - JOUR A1 - Wiese, M. A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard T1 - Optimal Power Allocation Policies for the Reliable Transmission of a Single Packet via ARQ Protocols JF - Asilomar Conf. on Sign. Sys. and Comp. Y1 - 2008 ER - TY - JOUR A1 - Boland, Natashia A1 - Dumitrescu, Irina A1 - Froyland, Gary A1 - Gleixner, Ambros T1 - LP-based disaggregation approaches to solving the open pit mining production scheduling problem with block processing selectivity JF - Computers & Operations Research Y1 - 2009 VL - 36 SP - 1064 EP - 1089 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Partial linear characterizations of the asymmetric travelling salesman polytope JF - Mathematical Programming Y1 - 1975 VL - 8 SP - 378 EP - 381 ER - TY - JOUR A1 - Deza, Michel A1 - Grötschel, Martin A1 - Laurent, Monique T1 - Clique-Web Facets for Multicut Polytopes JF - Mathematics of Operations Research Y1 - 1992 VL - 17 IS - 4 SP - 981 EP - 1000 ER - TY - JOUR A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - Computational Results with a Cutting Plane Algorithm for Designing Communication Networks with Low-Connectivity Constraints JF - Operations Research Y1 - 1992 VL - 40 IS - 2 SP - 309 EP - 330 ER - TY - JOUR A1 - Grötschel, Martin A1 - Monma, Clyde A1 - Stoer, Mechthild T1 - Facets for polyhedra arising in the design of communication networks with low-connectivity constraints JF - SIAM Journal on Optimization Y1 - 1992 VL - 2 IS - 3 SP - 474 EP - 504 ER - TY - JOUR A1 - Grötschel, Martin A1 - Win, Zaw T1 - A cutting plane algorithm for the windy postman problem JF - Mathematical Programming, Series A Y1 - 1992 VL - 55 IS - 3 SP - 339 EP - 358 ER - TY - JOUR A1 - Ascheuer, Norbert A1 - Escudero, Laureano A1 - Grötschel, Martin A1 - Stoer, Mechthild T1 - A Cutting Plane Approach to the Sequential Ordering Problem (with Applications to Job Scheduling in Manufacturing) JF - SIAM Journal on Optimization Y1 - 1993 VL - 3 IS - 1 SP - 25 EP - 42 ER - TY - JOUR A1 - Ferreira, Carlos A1 - Grötschel, Martin A1 - Martin, Alexander A1 - Weismantel, Robert A1 - Kiefl, Stefan A1 - Krispenz, Ludwig T1 - Some Integer Programs Arising in the Design of Main Frame Computers JF - ZOR - Methods and Models of Operations Research Y1 - 1993 VL - 38 IS - 1 SP - 77 EP - 100 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim A1 - Sperber, Wolfram T1 - DMV-Projekt “Fachinformation” JF - DMV-Mitteilungen Y1 - 1993 VL - 2 SP - 21 EP - 28 ER - TY - JOUR A1 - Grötschel, Martin A1 - Truemper, Klaus T1 - Master Polytopes for Cycles of Binary Matroids JF - Linear Algebra and its Applications Y1 - 1989 VL - 114/115 SP - 523 EP - 540 ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - A cutting plane algorithm for a clustering problem JF - Mathematical Programming, Series B Y1 - 1989 VL - 45 SP - 59 EP - 96 PB - Mathematical Programming, Series B ER - TY - JOUR A1 - Grötschel, Martin A1 - Monma, Clyde T1 - Integer Polyhedra Arising from Certain Network Design Problems with Connectivity Constraints JF - SIAM Journal on Discrete Mathematics Y1 - 1990 VL - 3 IS - 4 SP - 502 EP - 523 ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - Facets of the clique partitioning polytope JF - Mathematical Programming, Series A Y1 - 1990 VL - 47 IS - 3 SP - 367 EP - 387 ER - TY - JOUR A1 - Grötschel, Martin A1 - Holland, Olaf T1 - Solution of large-scale symmetric travelling salesman problems JF - Mathematical Programming, Series A Y1 - 1991 VL - 51 IS - 2 SP - 141 EP - 202 ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - Optimal Control of Plotting and Drilling Machines JF - Zeitschrift für Operations Research Y1 - 1991 VL - 35 IS - 1 SP - 61 EP - 84 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - Relaxations of Vertex Packing JF - Journal of Combinatorial Theory, Series B Y1 - 1986 VL - 40 SP - 330 EP - 343 ER - TY - JOUR A1 - Grötschel, Martin A1 - Pulleyblank, William T1 - Clique tree inequalities and the symmetric travelling salesman problem JF - Mathematics of Operations Research Y1 - 1986 VL - 11 IS - 4 SP - 537 EP - 569 ER - TY - JOUR A1 - Grötschel, Martin A1 - Holland, Olaf T1 - A Cutting Plane Algorithm for Minimum Perfect 2-Matchings JF - Computing Y1 - 1987 VL - 39 SP - 327 EP - 344 ER - TY - JOUR A1 - Barahona, Francisco A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - An application of combinatorial optimization to statistical physics and circuit layout design JF - Operations Research Y1 - 1988 VL - 36 IS - 3 SP - 493 EP - 513 ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - Via Minimization with Pin Preassignments and Layer Preference JF - ZAMM – Zeitschrift für Angewandte Mathematik und Mechanik Y1 - 1989 VL - 69 IS - 11 SP - 393 EP - 399 ER - TY - JOUR A1 - Grötschel, Martin A1 - Truemper, Klaus T1 - Decomposition and Optimization over Cycles in Binary Matroids JF - Journal of Combinatorial Theory, Series B Y1 - 1989 VL - 46 IS - 3 SP - 306 EP - 337 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - Lineare Charakterisierungen von Travelling Salesman Problemen JF - Zeitschrift für Operations Research, Series A Y1 - 1977 VL - 21 IS - 1 SP - 33 EP - 64 PB - Physica-Verlag ER - TY - JOUR A1 - Grötschel, Martin T1 - Hypo-Hamiltonian Facets of the Symmetric Travelling Salesman Polytope JF - Zeitschrift für Angewandte Mathematik und Mechanik Y1 - 1978 VL - 58 SP - T469 EP - T471 ER - TY - JOUR A1 - Grötschel, Martin A1 - von Randow, Rabe T1 - A property of continuous unbounded algorithms JF - Mathematical Programming Y1 - 1978 VL - 14 SP - 373 EP - 377 ER - TY - JOUR A1 - Grötschel, Martin T1 - On minimal strong blocks JF - Journal of Graph Theory Y1 - 1979 VL - 3 SP - 213 EP - 219 ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - A Cutting Plane Algorithm for the Linear Ordering Problem JF - Operations Research Y1 - 1984 VL - 32 IS - 6 SP - 1195 EP - 1220 ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - Optimal triangulation of large real world input-output matrices JF - Statistische Hefte Y1 - 1984 VL - 25 SP - 261 EP - 295 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - Corrigendum to our paper “The ellipsoid method and its consequences in combinatorial optimization” JF - Combinatorica Y1 - 1984 VL - 4 IS - 4 SP - 291 EP - 295 ER - TY - JOUR A1 - Grötschel, Martin A1 - Nemhauser, George T1 - A polynomial algorithm for the max-cut problem on graphs without long odd cycles JF - Mathematical Programming Y1 - 1984 VL - 29 IS - 1 SP - 28 EP - 40 PB - North-Holland ER - TY - JOUR A1 - Barahona, Francisco A1 - Grötschel, Martin A1 - Mahjoub, Ali T1 - Facets of the Bipartite Subgraph Polytope JF - Mathematics of Operations Research Y1 - 1985 VL - 10 SP - 340 EP - 358 ER - TY - JOUR A1 - Grötschel, Martin A1 - Holland, Olaf T1 - Solving matching problems with linear programming JF - Mathematical Programming Y1 - 1985 VL - 33 IS - 3 SP - 243 EP - 259 ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - On the acyclic subgraph polytope JF - Mathematical Programming Y1 - 1985 VL - 33 IS - 1 SP - 28 EP - 42 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin A1 - Jünger, Michael A1 - Reinelt, Gerhard T1 - Facets of the linear ordering polytope JF - Mathematical Programming Y1 - 1985 VL - 33 IS - 1 SP - 43 EP - 60 PB - North-Holland ER - TY - JOUR A1 - Barahona, Francisco A1 - Grötschel, Martin T1 - On the Cycle Polytope of a Binary Matroid JF - Journal of Combinatorial Theory, Series B Y1 - 1986 VL - 40 SP - 40 EP - 62 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - The ellipsoid method and its consequences in combinatorial optimization JF - Combinatorica Y1 - 1981 VL - 1 IS - 2 SP - 169 EP - 197 ER - TY - JOUR A1 - Grötschel, Martin A1 - Lovász, Lászlo A1 - Schrijver, Alexander T1 - The ellipsoid method and its consequences in combinatorial optimization JF - IIASA Collab. Proceedings Ser. CP-81-S1 Y1 - 1981 SP - 511 EP - 546 ER - TY - JOUR A1 - Grötschel, Martin A1 - Pulleyblank, William T1 - Weakly bipartite graphs and the max-cut problem JF - Operations Research Letters Y1 - 1981 VL - 1 IS - 1 SP - 23 EP - 27 ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - On the structure of the monotone asymmetric travelling salesman polytope I JF - Discrete Mathematics Y1 - 1981 VL - 34 SP - 43 EP - 59 ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - On the structure of the monotone asymmetric travelling salesman polytope II JF - Mathematical Programming Study Y1 - 1981 VL - 14 SP - 77 EP - 97 ER - TY - JOUR A1 - Grötschel, Martin A1 - Harary, Frank T1 - The Graphs for which All Strong Orientations Are Hamiltonian JF - Journal of Graph Theory Y1 - 1979 VL - 3 SP - 221 EP - 223 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - On the symmetric travelling salesman problem I JF - Mathematical Programming Y1 - 1979 VL - 16 SP - 265 EP - 280 ER - TY - JOUR A1 - Grötschel, Martin A1 - Padberg, Manfred T1 - On the symmetric travelling salesman problem II JF - Mathematical Programming Y1 - 1979 VL - 16 SP - 281 EP - 302 ER - TY - JOUR A1 - Grötschel, Martin T1 - On the symmetric travelling salesman problem JF - Mathematical Programming Study Y1 - 1980 VL - 12 SP - 61 EP - 77 PB - North-Holland ER - TY - JOUR A1 - Grötschel, Martin T1 - On the monotone symmetric travelling salesman problem JF - Mathematics of Operations Research Y1 - 1980 VL - 5 IS - 2 SP - 285 EP - 292 ER - TY - JOUR A1 - Grötschel, Martin A1 - Thomassen, Carsten A1 - Wakabayashi, Yoshiko T1 - Hypotraceable digraphs JF - Journal of Graph Theory Y1 - 1980 VL - 4 SP - 377 EP - 381 ER - TY - JOUR A1 - Grötschel, Martin A1 - Wakabayashi, Yoshiko T1 - Hypohamiltonian digraphs JF - Methods of Operations Research Y1 - 1980 VL - 36 SP - 99 EP - 119 ER - TY - JOUR A1 - Bachem, Achim A1 - Grötschel, Martin T1 - Homogenization of polyhedra JF - Methods of Operations Research Y1 - 1981 VL - 40 SP - 215 EP - 219 ER - TY - JOUR A1 - Golas, Ulrike A1 - Biermann, E. 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A1 - Erdmann, Bodo A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - Belastungssimulation beim menschlichen Biss im Vergleich mit der Dichtestruktur im Unterkieferknochen JF - Biomedizinische Technik Y1 - 2003 VL - 48 IS - Ergänzungsband 1 SP - 268 EP - 269 ER - TY - JOUR A1 - Durmaz, Vedat A1 - Weber, Marcus A1 - Becker, Roland T1 - How to Simulate Affinities for Host-Guest Systems Lacking Binding Mode Information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers JF - Journal of Molecular Modeling Y1 - 2012 U6 - https://doi.org/10.1007/s00894-011-1239-5 VL - 18 SP - 2399 EP - 2408 ER - TY - JOUR A1 - Weber, Marcus A1 - Bujotzek, Alexander A1 - Haag, Rainer T1 - Quantifying the rebinding effect in multivalent chemical ligand-receptor systems JF - J. Chem. Phys. Y1 - 2012 VL - 137 IS - 5 SP - 054111 ER - TY - JOUR A1 - Fasting, Carlo A1 - Schalley, Christoph A. 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T1 - Large-Area High-Quality Plasmonic Oligomers Fabricated by Angle-Controlled Colloidal Nanolithography JF - ACS Nano Y1 - 2011 U6 - https://doi.org/10.1021/nn203177s VL - 5 IS - 11 SP - 9009 ER - TY - JOUR A1 - Zschiedrich, Lin A1 - Greiner, Horst A1 - Burger, Sven A1 - Schmidt, Frank T1 - Numerical analysis of nanostructures for enhanced light extraction from OLEDs JF - Proc. SPIE Y1 - 2013 U6 - https://doi.org/10.1117/12.2001132 VL - 8641 SP - 86410B ER - TY - JOUR A1 - Arellano, Cristina A1 - Mingaleev, Sergei F. A1 - Koltchanov, Igor A1 - Richter, Andre A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Efficient design of photonic integrated circuits (PICs) by combining device- and circuit- level simulation tools JF - Proc. 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A1 - Schütte, Christof A1 - Noé, Frank T1 - EMMA - A software package for Markov model building and analysis JF - Journal of Chemical Theory and Computation Y1 - 2012 U6 - https://doi.org/10.1021/ct300274u VL - 8 SP - 2223 EP - 2238 ER - TY - JOUR A1 - Zschiedrich, Lin A1 - Klose, Roland A1 - Schädle, Achim A1 - Schmidt, Frank T1 - A new finite element realization of the Perfectly Matched Layer Method for Helmholtz scattering problems on polygonal domains in 2D JF - J. Comput. Appl. Math. Y1 - 2006 U6 - https://doi.org/10.1016/j.cam.2005.03.047 VL - 188 SP - 12 EP - 32 ER - TY - JOUR A1 - Hinze, Michael A1 - Schiela, Anton T1 - Discretization of Interior Point Methods for State Constrained Elliptic Optimal Control Problems: optimal error estimates and parameter adjustment JF - Comp. Opt. and Appl. Y1 - 2011 U6 - https://doi.org/10.1007/s10589-009-9278-x VL - 48 IS - 3 SP - 581 EP - 600 PB - Springer ER - TY - JOUR A1 - Meyer, Christian A1 - Prüfert, Uwe A1 - Tröltzsch, Fredi T1 - On two numerical methods for state-constrained elliptic control problems JF - Optimization Methods and Software Y1 - 2007 UR - http://www.math.tu-berlin.de/~pruefert/Publicat/index_en.html UR - /homes/numerik/pruefert/WWW/Publicat/on2numerical.pdf VL - 22 IS - 6 SP - 871 EP - 899 ER - TY - JOUR A1 - Prüfert, Uwe A1 - Schiela, Anton T1 - The Minimization of a maximum-norm functional subject to an elliptic PDE and state constraints JF - Z. angew. Math. Mech. Y1 - 2009 VL - 89 IS - 7 SP - 536 EP - 551 ER - TY - JOUR A1 - Prüfert, Uwe A1 - Tröltzsch, Fredi T1 - An interior point method for a parabolic optimal control problem with regularized pointwise state constraints JF - ZAMM Y1 - 2007 UR - http://www.math.tu-berlin.de/~pruefert/Publicat/index_en.html U6 - https://doi.org/10.1002/zamm.200610337 VL - 87 IS - 8–9 SP - 564 EP - 589 CY - Berlin ER - TY - JOUR A1 - Schiela, Anton T1 - A Simplified Approach to Semismooth Newton Methods in Function Space JF - SIAM J. on Optimization Y1 - 2008 VL - 19 IS - 3 SP - 369 EP - 393 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control with Rare State Observation JF - International Journal of Biomathematics and Biostatistics Y1 - 2012 UR - http://publications.mi.fu-berlin.de/1177/ ER - TY - JOUR A1 - Schiela, Anton T1 - Barrier Methods for Optimal Control Problems with State Constraints JF - SIAM J. on Optimization Y1 - 2009 VL - 20 IS - 2 SP - 1002 EP - 1031 ER - TY - JOUR A1 - Schiela, Anton T1 - State constrained optimal control problems with states of low regularity JF - SIAM J. on Control and Optimization Y1 - 2009 VL - 48 IS - 4 SP - 2407 EP - 2432 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Jahnke, Tobias A1 - Wulkow, Michael T1 - Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation JF - SIAM J. Sci. Comput Y1 - 2008 VL - 30 IS - 6 SP - 2990 EP - 3011 ER - TY - JOUR A1 - Kube, Susanna A1 - Lasser, Caroline A1 - Weber, Marcus T1 - Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics JF - Journal of Computational Physics Y1 - 2008 U6 - https://doi.org/10.1016/j.jcp.2008.11.016 VL - 228 IS - 6 SP - 1947 EP - 1962 ER - TY - JOUR A1 - Prüfert, Uwe A1 - Tröltzsch, Fredi A1 - Weiser, Martin T1 - The convergence of an interior point method for an elliptic control problem with mixed control-state constraints JF - Comput. Optim. Appl. Y1 - 2008 VL - 39 IS - 2 SP - 183 EP - 218 ER - TY - JOUR A1 - Dahlke, S. A1 - Lehmann, V. A1 - Teschke, G. T1 - Applications of Wavelet Methods to the Analysis of Meteorological Radar Data - An Overview JF - (invited paper) Arabian Journal of Science and Engineering Y1 - 2003 VL - 28 IS - 1C SP - 3 EP - 44 ER - TY - JOUR A1 - Dahlke, S. A1 - Maass, Peter A1 - Teschke, G. T1 - Reconstruction of Reflectivity Densities by Wavelet Transforms JF - Technical Report 01-10, ISSN 1435-7968 Y1 - 2007 ER - TY - JOUR A1 - Dahlke, S. A1 - Maass, Peter A1 - Teschke, G. T1 - Reconstruction of Wideband Reflectivity Densities by Wavelet Transforms JF - Advances in Computational Mathematics Y1 - 2003 VL - 2-4 IS - 18 SP - 189 EP - 209 ER - TY - JOUR A1 - Dahlke, S. A1 - Maass, Peter A1 - Teschke, G. T1 - Interpolating Scaling Functions with Duals JF - Journal of Computational Analysis and Applications Y1 - 2004 VL - 1 IS - 6 SP - 19 EP - 29 ER - TY - JOUR A1 - Dahlke, S. A1 - Maass, Peter A1 - Teschke, G. T1 - Reconstruction of Reflectivity Densities in a Narrowband Regime JF - IEEE Transactions on Antennas and Propagation Y1 - 2004 VL - 52 IS - 6 SP - 1603 EP - 1606 ER - TY - JOUR A1 - Dahlke, S. A1 - Fornasier, M. A1 - Rauhut, H. A1 - Steidl, G. A1 - Teschke, G. T1 - Generalized Coorbit Theory, Banach Frames, and the Relations to α–Modulation Spaces JF - under review Y1 - 2005 ER - TY - JOUR A1 - Köppen, Robert A1 - Becker, Roland A1 - Weber, Marcus A1 - Durmaz, Vedat A1 - Nehls, Irene T1 - HBCD stereoisimers: Thermal interconversion and enantiospecific trace analysis in biota JF - Organohalogen Compounds Y1 - 2009 VL - 70 SP - 910 EP - 913 ER - TY - JOUR A1 - Bujotzek, Alexander A1 - Weber, Marcus T1 - Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach JF - Journal of Bioinformatics and Computational Biology Y1 - 2009 VL - 7(5) SP - 811 EP - 831 ER - TY - JOUR A1 - Weber, Marcus A1 - Durmaz, Vedat A1 - Becker, Roland A1 - Esslinger, Susanne T1 - Predictive Identification of Pentabromocyclododecane (PBCD) Isomers with high Binding Affinity to hTTR JF - Organohalogen Compounds Y1 - 2009 VL - 71 SP - 247 EP - 252 ER - TY - JOUR A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Birkenheuer, Georg A1 - Brinkmann, André A1 - Grunzke, Richard A1 - Kacsuk, Peter A1 - Kohlbacher, Oliver A1 - Kozlovszky, Miklos A1 - Krüger, Jens A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas T1 - A Science Gateway Getting Ready for Serving the International Molecular Simulation Community JF - Proceedings of Science Y1 - 2012 UR - http://pos.sissa.it/archive/conferences/162/050/EGICF12-EMITC2_050.pdf VL - PoS(EGICF12-EMITC2)050 ER - TY - JOUR A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - dos Santos Vieira, Ines A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment JF - Journal of Cheminformatics Y1 - 2012 UR - http://www.jcheminf.com/content/4/S1/P21 U6 - https://doi.org/10.1186/1758-2946-4-S1-P21 VL - 4 IS - Suppl 1 SP - 21 ER - TY - JOUR A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Krüger, Jens A1 - Birkenheuer, Georg A1 - Wewior, Martin A1 - Schäfer, Patrick A1 - Schuller, Bernd A1 - Schuster, Johannes A1 - Herres-Pawlis, Sonja A1 - Breuers, Sebastian A1 - Balasko, Akos A1 - Kozlovszky, Miklos A1 - Szikszay Fabri, Anna A1 - Packschies, Lars A1 - Kacsuk, Peter A1 - Blunk, Dirk A1 - Steinke, Thomas A1 - Brinkmann, André A1 - Fels, Gregor A1 - Müller-Pfefferkorn, Ralph A1 - Jäkel, René A1 - Kohlbacher, Oliver T1 - A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics JF - Journal of Grid Computing Y1 - 2012 ER - TY - JOUR A1 - Enke, Harry A1 - Partl, Adrian A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Handling Big Data in Astronomy and Astrophysics JF - Datenbank-Spektrum Y1 - 2012 UR - http://dx.doi.org/10.1007/s13222-012-0099-1 U6 - https://doi.org/10.1007/s13222-012-0099-1 VL - 12 IS - 3 SP - 173 EP - 181 PB - Springer-Verlag ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Erol, Berkan A1 - Graffagnino, Thomas A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Optimizing the Simplon railway corridor JF - Annals of Operations Research Y1 - 2012 UR - http://dx.doi.org/10.1007/s10479-012-1260-9 U6 - https://doi.org/10.1007/s10479-012-1260-9 VL - 218 IS - 1 SP - 93 EP - 106 PB - Springer US ET - Annals of Operations Research ER - TY - JOUR A1 - Raack, Christian A1 - Koster, Arie M.C.A. A1 - Orlowski, Sebastian A1 - Wessäly, Roland T1 - On cut-based inequalities for capacitated network design polyhedra JF - Networks Y1 - 2011 UR - http://onlinelibrary.wiley.com/doi/10.1002/net.20395/abstract VL - 57 IS - 2 SP - 141 EP - 156 ER - TY - JOUR A1 - Achterberg, Tobias A1 - Raack, Christian T1 - The MCF-Separator – Detecting and Exploiting Multi-Commodity Flows in MIPs JF - Mathematical Programming C Y1 - 2010 UR - http://www.springerlink.com/content/383250gmx3184126/ IS - 2 SP - 125 EP - 165 ER - TY - JOUR A1 - Idzikowski, Filip A1 - Orlowski, Sebastian A1 - Raack, Christian A1 - Woesner, Hagen A1 - Wolisz, Adam T1 - Dynamic routing at different layers in IP-over-WDM networks – Maximizing energy savings JF - Optical Switching and Networking, Special Issue on Green Communications Y1 - 2011 UR - http://opus.kobv.de/zib/volltexte/2010/1230/ ER - TY - JOUR A1 - Schintke, Florian T1 - XtreemFS & Scalaris JF - Science & Technology Y1 - 2013 IS - 6 SP - 54 EP - 55 PB - Pan European Networks ER - TY - JOUR A1 - Berlin, Michael T1 - Consistent and Partition-Tolerant File Replication in the Cloud File System Xtreem FS JF - Praxis der Informationsverarbeitung und Kommunikation Y1 - 2013 UR - http://dx.doi.org/10.1515/pik-2012-0144 U6 - https://doi.org/10.1515/pik-2012-0144 VL - 36 IS - 1 SP - 39 ER - TY - JOUR A1 - Werner, Axel A1 - Wotzlaw, Ronald T1 - On linkages in polytope graphs JF - Adv. Geom. Y1 - 2011 U6 - https://doi.org/10.1515/ADVGEOM.2011.015 VL - 11 IS - 3 SP - 411 EP - 427 ER - TY - JOUR A1 - Werner, Axel T1 - Kombinatorische Optimierung und die 40-Punkte-Regel JF - Mitteilungen der DMV Y1 - 2011 VL - 19 SP - 153 EP - 157 ER - TY - JOUR A1 - Schütt, Thorsten A1 - Reinefeld, Alexander A1 - Döbbelin, Robert T1 - MR-search: massively parallel heuristic search JF - Concurrency and Computation: Practice and Experience Y1 - 2011 U6 - https://doi.org/10.1002/cpe.1833 VL - 25 IS - 1 SP - 40 EP - 54 ER - TY - JOUR A1 - Paffenholz, Andreas A1 - Werner, Axel T1 - Constructions for 4-polytopes and the cone of flag vectors. JF - Contemporary Mathematics Y1 - 2006 VL - 423 SP - 283 EP - 303 PB - Algebraic and geometric combinatorics. Euroconference in mathematics, algebraic and geometric combinatorics, Anogia, Crete, Greece, August 20–26, 2005. Providence, RI: American Mathematical Society (AMS) ER - TY - JOUR A1 - Sanyal, Raman A1 - Werner, Axel A1 - Ziegler, Günter T1 - On Kalai’s conjectures concerning centrally symmetric polytopes. JF - Discrete Comput. Geom. Y1 - 2009 U6 - https://doi.org/10.1007/s00454-008-9104-8 VL - 41 IS - 2 SP - 183 EP - 198 ER - TY - JOUR A1 - Janata, M. A1 - Loebl, M. A1 - Szabó, Jácint T1 - A Gallai-Edmonds type theorem for the k-piece packing problem JF - Electron. J. Combin Y1 - 2005 VL - 12 SP - 1 ER - TY - JOUR A1 - Janata, M. A1 - Szabó, Jácint T1 - The superstar packing problem JF - Combinatorica Y1 - 2009 VL - 29 IS - 1 SP - 27 EP - 48 PB - Springer ER - TY - JOUR A1 - Szabó, Jácint T1 - Upgrading edge-disjoint paths in a ring JF - Discrete Optimization Y1 - 2010 PB - Elsevier BV ER - TY - JOUR A1 - Hartvigsen, D. A1 - Hell, P. A1 - Szabó, Jácint T1 - The k-piece packing problem JF - Journal of Graph Theory Y1 - 2006 VL - 52 IS - 4 SP - 267 EP - 293 PB - John Wiley & Sons ER - TY - JOUR A1 - Heinz, Stefan A1 - Kaibel, Volker A1 - Peinhardt, Matthias A1 - Rambau, Jörg A1 - Tuchscherer, Andreas T1 - LP-Based Local Approximation for Markov Decision Problems Y1 - 2006 IS - 343 PB - Matheon ER - TY - JOUR A1 - Balas, Egon A1 - Stephan, Rüdiger T1 - On the cycle polytope of a directed graph and its relaxations JF - Networks Y1 - 2009 U6 - https://doi.org/10.1002/net.20303 VL - 54 IS - 1 SP - 47 EP - 55 ER - TY - JOUR A1 - Kaibel, Volker A1 - Stephan, Rüdiger T1 - On cardinality constrained cycle and path polytopes JF - Math. Program. Y1 - 2010 U6 - https://doi.org/10.1007/s10107-008-0257-2 VL - 123 IS - 2 (A) SP - 371 EP - 394 ER - TY - JOUR A1 - Stephan, Rüdiger T1 - Facets of the (s,t)-p-path polytope JF - Discrete Appl. Math. Y1 - 2009 U6 - https://doi.org/10.1016/j.dam.2009.06.003 VL - 157 IS - 14 SP - 3119 EP - 3132 ER - TY - JOUR A1 - Stephan, Rüdiger T1 - Cardinality constrained combinatorial optimization JF - Discrete Optim. Y1 - 2010 VL - 7 IS - 3 SP - 99 EP - 113 ER - TY - JOUR A1 - Stephan, Rüdiger A1 - Spiegelberg, Ingo T1 - On cardinality constrained polymatroids JF - Electronic Notes in Discrete Mathematics Y1 - 2010 UR - http://www.sciencedirect.com/science/article/B75GV-50JJF7F-4K/2/2761e6edfcb262af0ba4856767d82a42 U6 - https://doi.org/DOI: 10.1016/j.endm.2010.05.129 VL - 36 SP - 1017 EP - 1024 ER - TY - JOUR A1 - Bíró, István A1 - Szabó, Jácint T1 - Latent Dirichlet Allocation for Automatic Document Categorization JF - Machine Learning and Knowledge Discovery in Databases Y1 - 2009 SP - 430 EP - 441 PB - Springer ER - TY - JOUR A1 - Frank, A. A1 - Chi Lau, L. A1 - Szabó, Jácint T1 - A note on degree-constrained subgraphs JF - Discrete Mathematics Y1 - 2008 VL - 308 IS - 12 SP - 2647 EP - 2648 PB - Elsevier ER - TY - JOUR A1 - Recski, A. A1 - Szabó, Jácint T1 - On the generalization of the matroid parity problem JF - Graph Theory in Paris Y1 - 2007 SP - 347 EP - 354 PB - Springer ER - TY - JOUR A1 - Szabó, Jácint T1 - Matroid parity and jump systems JF - SIAM Journal on Discrete Mathematics Y1 - 2008 VL - 22 SP - 854 ER - TY - JOUR A1 - Király, T. A1 - Szabó, Jácint T1 - A note on parity constrained orientations JF - Combinatorica Y1 - 2009 VL - 29 IS - 5 SP - 619 EP - 628 PB - Springer ER - TY - JOUR A1 - Makai, M. A1 - Pap, G. A1 - Szabó, Jácint T1 - Matching problems in polymatroids without double circuits JF - Integer Programming and Combinatorial Optimization Y1 - 2007 SP - 167 EP - 181 PB - Springer ER - TY - JOUR A1 - Makai, M. A1 - Szabó, Jácint T1 - The parity problem of polymatroids without double circuits JF - Combinatorica Y1 - 2008 VL - 28 IS - 6 SP - 679 EP - 692 PB - Springer ER - TY - JOUR A1 - Szabó, Jácint T1 - Packing Trees with Constraints on the Leaf Degree JF - Graphs and Combinatorics Y1 - 2008 VL - 24 IS - 5 SP - 485 EP - 494 PB - Springer ER - TY - JOUR A1 - Király, Z. A1 - Szabó, Jácint T1 - Induced graph packing problems JF - Graphs and Combinatorics Y1 - 2010 VL - 26 IS - 2 SP - 243 EP - 257 PB - Springer ER - TY - JOUR A1 - Szabó, Jácint T1 - Good characterizations for some degree constrained subgraphs JF - Journal of Combinatorial Theory, Series B Y1 - 2009 VL - 99 IS - 2 SP - 436 EP - 446 PB - Elsevier ER - TY - JOUR A1 - Cook, William A1 - Koch, Thorsten A1 - Steffy, Daniel A1 - Wolter, Kati T1 - A hybrid branch-and-bound approach for exact rational mixed-integer programming JF - Mathematical Programming Computation N2 - We present an exact rational solver for mixed-integer linear programming that avoids the numerical inaccuracies inherent in the floating-point computations used by existing software. This allows the solver to be used for establishing theoretical results and in applications where correct solutions are critical due to legal and financial consequences. Our solver is a hybrid symbolic/numeric implementation of LP-based branch-and-bound, using numerically-safe methods for all binding computations in the search tree. Computing provably accurate solutions by dynamically choosing the fastest of several safe dual bounding methods depending on the structure of the instance, our exact solver is only moderately slower than an inexact floating-point branch-and-bound solver. The software is incorporated into the SCIP optimization framework, using the exact LP solver QSopt_ex and the GMP arithmetic library. Computational results are presented for a suite of test instances taken from the MIPLIB and Mittelmann libraries and for a new collection of numerically difficult instances. Y1 - 2013 U6 - https://doi.org/10.1007/s12532-013-0055-6 VL - 5 IS - 3 SP - 305 EP - 344 ER - TY - JOUR A1 - Stötzel, Claudia A1 - Ehrig, Rainald A1 - Boer, H. Marike T. A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - Exploration of different wave patterns in a model of the bovine estrous cycle by Fourier analysis JF - BIOMAT - Proceedings of the 14th International Symposium on Mathematical and Computational Biology, Bedlewo, Poland N2 - Cows typically have different numbers of follicular waves during their hormonal cycle. Understanding the underlying regulations leads to insights into the reasons for declined fertility, a phenomenon that has been observed during the last decades. We present a systematic approach based on Fourier analysis to examine how parameter changes in a model of the bovine estrous cycle lead to different wave patterns. Even without any biological considerations, this allows to detect the responsible model parameters that control the type of periodicity of the solution, thus supporting experimental planning of animal scientists. Y1 - 2014 ER - TY - JOUR A1 - Reinefeld, Alexander A1 - Schütt, Thorsten A1 - Döbbelin, Robert T1 - Analyzing the performance of SMP memory allocators with iterative MapReduce applications JF - Parallel Computing Y1 - 2013 U6 - https://doi.org/10.1016/j.parco.2013.09.007 VL - 39 IS - 12 SP - 879 EP - 889 PB - Elsevier ER - TY - JOUR A1 - Högqvist, Mikael A1 - Reinefeld, Alexander T1 - RECODE: Reconfigurable, Consistent and Decentralized Data Services JF - IEEE International Conference on Peer-to-Peer Computing (P2P’13) Y1 - 2013 U6 - https://doi.org/10.1109/P2P.2013.6688705 SP - 1 EP - 10 PB - IEEE ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Ligand Excluded Surface: A New Type of Molecular Surface JF - IEEE Transactions on Visualization and Computer Graphics N2 - The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes – including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules. Y1 - 2014 U6 - https://doi.org/10.1109/TVCG.2014.2346404 VL - 20 IS - 12 SP - 2486 EP - 2495 ER - TY - JOUR A1 - Becker, Christiane A1 - Wyss, Philippe A1 - Eisenhauer, David A1 - Probst, Jürgen A1 - Preidel, Veit A1 - Hammerschmidt, Martin A1 - Burger, Sven T1 - 5 x 5 cm2 silicon photonic crystal slabs on glass and plastic foil exhibiting broadband absorption and high-intensity near-fields JF - Sci. Rep. Y1 - 2014 U6 - https://doi.org/10.1038/srep05886 VL - 4 SP - 5886 ER - TY - JOUR A1 - Kaschke, Johannes A1 - Blome, Mark A1 - Burger, Sven A1 - Wegener, Martin T1 - Tapered N-helical metamaterials with three-fold rotational symmetry as improved circular polarizers JF - Opt. Expr. Y1 - 2014 U6 - https://doi.org/10.1364/OE.22.019936 VL - 22 IS - 17 SP - 19936 EP - 19946 ER - TY - JOUR A1 - Todt, Ingo A1 - Lamecker, Hans A1 - Ramm, Heiko A1 - Frenzel, Henning A1 - Wollenberg, Barbara A1 - Beleites, Thomas A1 - Zahnert, Thomas A1 - Thomas, Jan Peter A1 - Dazert, Stefan A1 - Ernst, Arneborg T1 - Entwicklung eines CT-Daten-basierten Vibrant-Bonebridge-Viewers JF - HNO N2 - Die Positionierung des B-FMT der Vibrant Bonebridge kann aufgrund der anatomischen Verhältnisse des Mastoids und der Größe des Aktuators ohne eine vorherige Beurteilung der individuellen Computertomographie (CT) des Felsenbeins problematisch sein. Die Entwicklung eines einfach zu bedienenden Viewers, welcher eine Positionierung des B-FMT im Felsenbeinmodell ermöglicht und hier auf individuelle potenzielle anatomische Konflikte hinweist sowie Lösungsmöglichkeiten anbietet, kann ein hilfreiches Werkzeug zur präoperativen Positionierung sein. Ziel der Arbeit war die Definition von Anforderungen und die Anfertigung eines Prototyps eines Vibrant-Bonebridge-Viewers. Auf der Basis einer ZIBAmira-Software-Version und der Inklusion eines B-FMT-Modells unter Erstellung eines Felsenbeinmodells, welches die intuitive Beurteilung von Konflikten ermöglicht, erfolgte die Erstellung des Prototyps eines Vibrant-Bonebridge-Viewers.Ergebnisse. Die Segmentierungszeit der individuellen DICOM-Daten („digital imaging and communications in medicine“) beträgt etwa 5 min. Eine Positionierung im individuellen 3-D-Felsenbeinmodell ermöglicht die quantitative und qualitative Beurteilung von Konflikten (Sinus sigmoideus, mittlere Schädelgrube) und das Aufsuchen einer bevorzugten Position. Das Anheben des B-FMT mittels virtueller Unterlegscheiben kann simuliert werden. Der erstellte Vibrant-Bonebridge-Viewer ermöglicht verlässlich eine Simulation der B-FMT-Positionierung. Die klinische Anwendbarkeit muss evaluiert werden. Y1 - 2014 U6 - https://doi.org/10.1007/s00106-014-2851-3 VL - 62 SP - 439 EP - 442 PB - Springer ER - TY - JOUR A1 - Wiesendanger, Samuel A1 - Bischoff, Thomas A1 - Jovanov, Vladislav A1 - Knipp, Dietmar A1 - Burger, Sven A1 - Lederer, Falk A1 - Rockstuhl, Carsten T1 - Effects of film growth modes on light trapping in silicon thin film solar cells JF - Appl. Phys. Lett. Y1 - 2014 U6 - https://doi.org/10.1063/1.4882997 VL - 104 IS - 23 SP - 231103 ER - TY - JOUR A1 - Potamitis, Ilyas A1 - Schäfer, Patrick T1 - On Classifying Insects from their Wing-Beat: New Results JF - Ecology and acoustics: emergent properties from community to landscape, Paris, France Y1 - 2014 ER - TY - JOUR A1 - Krüger, Jens A1 - Grunzke, Richard A1 - Gesing, Sandra A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - de la Garza, Luis A1 - Kohlbacher, Oliver A1 - Kruse, Martin A1 - Nagel, Wolfgang A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schärfe, Charlotta A1 - Steinke, Thomas A1 - Schlemmer, Tobias A1 - Warzecha, Klaus Dieter A1 - Zink, Andreas A1 - Herres-Pawlis, Sonja T1 - The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations JF - Journal of Chemical Theory and Computation Y1 - 2014 U6 - https://doi.org/10.1021/ct500159h VL - 10 IS - 6 SP - 2232 EP - 2245 ER - TY - JOUR A1 - Campoli, Gianni A1 - Baka, Nora A1 - Kaptein, Bart A1 - Valstar, Edward A1 - Zachow, Stefan A1 - Weinans, Harrie A1 - Zadpoor, Amir Abbas T1 - Relationship between the shape and density distribution of the femur and its natural frequencies of vibration JF - Journal of Biomechanics N2 - It has been recently suggested that mechanical loads applied at frequencies close to the natural frequencies of bone could enhance bone apposition due to the resonance phenomenon. Other applications of bone modal analysis are also suggested. For the above-mentioned applications, it is important to understand how patient-specific bone shape and density distribution influence the natural frequencies of bones. We used finite element models to study the effects of bone shape and density distribution on the natural frequencies of the femur in free boundary conditions. A statistical shape and appearance model that describes shape and density distribution independently was created, based on a training set of 27 femora. The natural frequencies were then calculated for different shape modes varied around the mean shape while keeping the mean density distribution, for different appearance modes around the mean density distribution while keeping the mean bone shape, and for the 27 training femora. Single shape or appearance modes could cause up to 15% variations in the natural frequencies with certain modes having the greatest impact. For the actual femora, shape and density distribution changed the natural frequencies by up to 38%. First appearance mode that describes the general cortical bone thickness and trabecular bone density had one of the strongest impacts. The first appearance mode could therefore provide a sensitive measure of general bone health and disease progression. Since shape and density could cause large variations in the calculated natural frequencies, patient-specific FE models are needed for accurate estimation of bone natural frequencies. Y1 - 2014 U6 - https://doi.org/10.1016/j.jbiomech.2014.08.008 VL - 47 SP - 3334 EP - 3343 PB - Elsevier ER - TY - JOUR A1 - Todt, Ingo A1 - Lamecker, Hans A1 - Ramm, Heiko A1 - Ernst, Arneborg T1 - A computed tomographic data-based vibrant bonebridge visualization tool JF - Cochlear Implants International N2 - Information about the temporal bone size and variations of anatomical structures are crucial for a safe positioning of the Vibrant Bonebridge B-FMT. A radiological based preoperative planning of the surgical procedure decreases the surgical time and minimizes the risk of complications. We developed a software tool, which allows a catch up of foreign DICOM data based CT temporal bone scans. The individual CT scan is transmitted into a 3D reconstructed pattern of the temporal bone. In this 3D reconstruction the individually favored position of the B- FMT should be found. The software allows a determination of a safe B-FMT position by identifying the individual relation of middle fossa, jugular bulb and external auditory canal. Skull thickness and screw length are contained parameters for the surgical planning. An easy to handle software tool allows a radiologically data based safe and fast surgical positioning of the B-FMT. Y1 - 2014 U6 - https://doi.org/10.1179/1467010014Z.000000000155 VL - 15 IS - S1 SP - 72 EP - 74 ER - TY - JOUR A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang T1 - Vorschrift oder Thunfisch? – Zur Langzeitverfügbarkeit von Forschungsdaten JF - LIBREAS - Library Ideas Y1 - 2013 IS - 23 ER - TY - JOUR A1 - Tuma, Christian A1 - Laino, Teodoro A1 - Martin, Elyette A1 - Stolz, Steffen A1 - Curioni, Alessandro T1 - Modeling the Impact of Solid Surfaces in Thermal Degradation Processes JF - ChemPhysChem Y1 - 2013 U6 - https://doi.org/10.1002/cphc.201200921 VL - 14 SP - 88 EP - 91 ER - TY - JOUR A1 - Schütte, Christof A1 - Nielsen, Adam A1 - Weber, Marcus T1 - Markov State Models and Molecular Alchemy JF - Molecular Physics N2 - In recent years Markov State Models (MSMs) have attracted a consid- erable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g., for peptides including time-resolved spectroscopic experiments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multivalent scenarios. In this article a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular properties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con- sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective energy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed. KW - MSM KW - Reweighting KW - Girsanov Y1 - 2015 U6 - https://doi.org/10.1080/00268976.2014.944597 VL - 113 IS - 1 SP - 69 EP - 78 ER - TY - JOUR A1 - Agarwal, Animesh A1 - Wang, Han A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Chemical potential of liquids and mixtures via Adaptive Resolution Simulation JF - The Journal of Chemical Physics Y1 - 2014 U6 - https://doi.org/10.1063/1.4886807 VL - 141 SP - 034102 ER - TY - JOUR A1 - Schäfer, Patrick T1 - The BOSS is concerned with time series classification in the presence of noise JF - Data Mining and Knowledge Discovery Y1 - 2014 U6 - https://doi.org/10.1007/s10618-014-0377-7 VL - 29 IS - 6 SP - 1505 EP - 1530 PB - Springer ER - TY - JOUR A1 - Moualeu-Ngangue, Dany Pascal A1 - Weiser, Martin A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Optimal control for a tuberculosis model with undetected cases in Cameroon JF - Communications in Nonlinear Science and Numerical Simulation N2 - This paper considers the optimal control of tuberculosis through education, diagnosis campaign and chemoprophylaxis of latently infected. A mathematical model which includes important components such as undiagnosed infectious, diagnosed infectious, latently infected and lost-sight infectious is formulated. The model combines a frequency dependent and a density dependent force of infection for TB transmission. Through optimal control theory and numerical simulations, a cost-effective balance of two different intervention methods is obtained. Seeking to minimize the amount of money the government spends when tuberculosis remain endemic in the Cameroonian population, Pontryagin's maximum principle is used to characterize the optimal control. The optimality system is derived and solved numerically using the forward-backward sweep method (FBSM). Results provide a framework for designing cost-effective strategies for diseases with multiple intervention methods. It comes out that combining chemoprophylaxis and education, the burden of TB can be reduced by 80 % in 10 years. Y1 - 2015 U6 - https://doi.org/10.1016/j.cnsns.2014.06.037 VL - 20 IS - 3 SP - 986 EP - 1003 ER - TY - JOUR A1 - Golas, Ulrike A1 - Habel, A. A1 - Ehrig, Hartmut T1 - Multi-Amalgamation of Rules with Application Conditions in M-Adhesive Categories JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000345 VL - 24 IS - 4 SP - 1 EP - 68 ER - TY - JOUR A1 - Hermann, Frank A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Orejas, Fernando T1 - Formal Analysis of Model Transformations Based on Triple Graph Grammars JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000370 VL - 24 IS - 4 SP - 1 EP - 57 ER - TY - JOUR A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Habel, A. A1 - Lambers, L. A1 - Orejas, Fernando T1 - M-Adhesive Transformation Systems with Nested Application Conditions. Part 1: Parallelism, Concurreny and Amalgamation JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000357 VL - 24 IS - 4 SP - 1 EP - 48 ER - TY - JOUR A1 - Gabriel, Karsten A1 - Braatz, Benjamin A1 - Ehrig, Hartmut A1 - Golas, Ulrike T1 - Finitary M-Adhesive Categories JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000321 VL - 24 IS - 4 SP - 1 EP - 40 ER - TY - JOUR A1 - Egger, Robert A1 - Dercksen, Vincent J. A1 - Udvary, Daniel A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - Generation of dense statistical connectomes from sparse morphological data JF - Frontiers in Neuroanatomy Y1 - 2014 U6 - https://doi.org/10.3389/fnana.2014.00129 VL - 8 IS - 129 ER - TY - JOUR A1 - Hochfeld, Mascha A1 - Lamecker, Hans A1 - Thomale, Ulrich W. A1 - Schulz, Matthias A1 - Zachow, Stefan A1 - Haberl, Hannes T1 - Frame-based cranial reconstruction JF - Journal of Neurosurgery: Pediatrics N2 - The authors report on the first experiences with the prototype of a surgical tool for cranial remodeling. The device enables the surgeon to transfer statistical information, represented in a model, into the disfigured bone. The model is derived from a currently evolving databank of normal head shapes. Ultimately, the databank will provide a set of standard models covering the statistical range of normal head shapes, thus providing the required template for any standard remodeling procedure as well as customized models for intended overcorrection. To date, this technique has been used in the surgical treatment of 14 infants (age range 6-12 months) with craniosynostosis. In all 14 cases, the designated esthetic result, embodied by the selected model, has been achieved, without morbidity or mortality. Frame-based reconstruction provides the required tools to precisely realize the surgical reproduction of the model shape. It enables the establishment of a self-referring system, feeding back postoperative growth patterns, recorded by 3D follow-up, into the model design. Y1 - 2014 U6 - https://doi.org/10.3171/2013.11.PEDS1369 VL - 13 IS - 3 SP - 319 EP - 323 ER - TY - JOUR A1 - Berthold, Timo A1 - Hendel, Gregor A1 - Koch, Thorsten T1 - From feasibility to improvement to proof: three phases of solving mixed-integer programs JF - Optimization Methods and Software N2 - Modern mixed-integer programming (MIP) solvers employ dozens of auxiliary algorithmic components to support the branch-and-bound search in finding and improving primal solutions and in strengthening the dual bound. Typically, all components are tuned to minimize the average running time to prove optimality. In this article, we take a different look at the run of a MIP solver. We argue that the solution process consists of three distinct phases, namely achieving feasibility, improving the incumbent solution, and proving optimality. We first show that the entire solving process can be improved by adapting the search strategy with respect to the phase-specific aims using different control tunings. Afterwards, we provide criteria to predict the transition between the individual phases and evaluate the performance impact of altering the algorithmic behaviour of the non-commercial MIP solver Scip at the predicted phase transition points. Y1 - 2017 U6 - https://doi.org/10.1080/10556788.2017.1392519 VL - 33 IS - 3 SP - 499 EP - 517 PB - Taylor & Francis ER - TY - JOUR A1 - Koch, Thorsten T1 - The ZIMPL modeling language JF - Optima Y1 - 2017 UR - http://www.mathopt.org/Optima-Issues/optima103.pdf VL - 103 SP - 8 EP - 9 ER - TY - JOUR A1 - Berg, Mascha A1 - Plöntzke, Julia A1 - Leonhard-Marek, Sabine A1 - Müller, Kerstin-Elisabeth A1 - Röblitz, Susanna T1 - A dynamic model to simulate potassium balance in dairy cows JF - Journal of Dairy Science N2 - High-performing dairy cows require a particular composition of nutritional ingredients, adapted to their individual requirements and depending on their production status. The optimal dimensioning of minerals in the diet, one being potassium, is indispensable for the prevention of imbalances. Potassium balance in cows is the result of potassium intake, distribution in the organism, and excretion, and it is closely related to glucose and electrolyte metabolism. In this paper, we present a dynamical model for potassium balance in lactating and nonlactating dairy cows based on ordinary differential equations. Parameter values were obtained from clinical trial data and from the literature. To verify the consistency of the model, we present simulation outcomes for 3 different scenarios: potassium balance in (1) nonlactating cows with varying feed intake, (2) nonlactating cows with varying potassium fraction in the diet, and (3) lactating cows with varying milk production levels. The results give insights into the short- and long-term potassium metabolism, providing an important step toward the understanding of the potassium network, the design of prophylactic feed additives, and possible treatment strategies. Y1 - 2017 U6 - https://doi.org/10.3168/jds.2016-12443 VL - 100 IS - 12 SP - 9799 EP - 9814 ER - TY - JOUR A1 - Hoffmann, René A1 - Lemanis, Robert A1 - Falkenberg, Janina A1 - Schneider, Steffen A1 - Wesendonk, Hendrik A1 - Zachow, Stefan T1 - Integrating 2D and 3D shell morphology to disentangle the palaeobiology of ammonoids: A virtual approach JF - Palaeontology N2 - We demonstrate, based on data derived from computed tomography, that integrating 2D and 3D morphological data of ammonoid shells represent an important new approach to disentangle the palaeobiology of ammonoids. Characterization of ammonite morphology has long been constrained to 2D data and only a few studies collect ontogenetic data in 180° steps. We combine this traditional approach with 3D data collected from high-resolution nano-computed tomography. For this approach, ontogenetic morphological data of the hollow shell of a juvenile ammonite Kosmoceras (Jurassic, Callovian) is collected. 2D data is collected in 10° steps and show significant changes in shell morphology. Preserved hollow spines show multiple mineralized membranes never reported before, representing temporal changes of the ammonoid mantle tissue. 3D data show that chamber volumes do not always increase exponentially, as was generally assumed, but may represent a proxy for life events, e.g. stress phases. Furthermore, chamber volume cannot be simply derived from septal spacing in forms comparable to Kosmoceras. Vogel numbers, a 3D parameter for chamber shape, of Kosmoceras are similar to other ammonoids (Arnsbergites, Amauroceras) and modern cephalopods (Nautilus, Spirula). Two methods to virtually document the suture line ontogeny, used to document phylogenetic relationships of larger taxonomic entities, were applied for the first time and seem a promising alternative to hand drawings. The curvature of the chamber surfaces increases during ontogeny due to increasing strength of ornamentation and septal complexity. As increasing curvature may allow for faster handling of cameral liquid, it could compensate for decreasing SA/V ratios through ontogeny. Y1 - 2017 UR - http://dx.doi.org/10.1111/pala.12328 U6 - https://doi.org/10.1111/pala.12328 VL - 61 IS - 1 SP - 89 EP - 104 ER - TY - JOUR A1 - Moldenhauer, Marian A1 - Weiser, Martin A1 - Zachow, Stefan T1 - Adaptive Algorithms for Optimal Hip Implant Positioning JF - PAMM N2 - In an aging society where the number of joint replacements rises, it is important to also increase the longevity of implants. In particular hip implants have a lifetime of at most 15 years. This derives primarily from pain due to implant migration, wear, inflammation, and dislocation, which is affected by the positioning of the implant during the surgery. Current joint replacement practice uses 2D software tools and relies on the experience of surgeons. Especially the 2D tools fail to take the patients’ natural range of motion as well as stress distribution in the 3D joint induced by different daily motions into account. Optimizing the hip joint implant position for all possible parametrized motions under the constraint of a contact problem is prohibitively expensive as there are too many motions and every position change demands a recalculation of the contact problem. For the reduction of the computational effort, we use adaptive refinement on the parameter domain coupled with the interpolation method of Kriging. A coarse initial grid is to be locally refined using goal-oriented error estimation, reducing locally high variances. This approach will be combined with multi-grid optimization such that numerical errors are reduced. Y1 - 2017 U6 - https://doi.org/10.1002/pamm.201710071 VL - 17 IS - 1 SP - 203 EP - 204 ER - TY - JOUR A1 - de Lasson, Jakob Rosenkrantz A1 - Frandsen, Lars Hagedorn A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Ivanskaya, Aliaksandra A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Häyrynen, Teppo A1 - Lavrinenko, Andrei A1 - Mork, Jesper A1 - Gregersen, Niels T1 - Benchmarking five numerical simulation techniques for computing resonance wavelengths and quality factors in photonic crystal membrane line defect cavities JF - Opt. Express Y1 - 2018 U6 - https://doi.org/10.1364/OE.26.011366 VL - 26 SP - 11366 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - Reliable approximation of long relaxation timescales in molecular dynamics JF - Entropy Y1 - 2017 U6 - https://doi.org/10.3390/e19070367 VL - 19 IS - 7 ER - TY - JOUR A1 - Akbari Shandiz, Mohsen A1 - Boulos, Paul A1 - Sævarsson, Stefan A1 - Ramm, Heiko A1 - Fu, Chun Kit A1 - Miller, Stephen A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Changes in Knee Shape and Geometry Resulting from Total Knee Arthroplasty JF - Journal of Engineering in Medicine N2 - Changes in knee shape and geometry resulting from total knee arthroplasty can affect patients in numerous important ways: pain, function, stability, range of motion, and kinematics. Quantitative data concerning these changes have not been previously available, to our knowledge, yet are essential to understand individual experiences of total knee arthroplasty and thereby improve outcomes for all patients. The limiting factor has been the challenge of accurately measuring these changes. Our study objective was to develop a conceptual framework and analysis method to investigate changes in knee shape and geometry, and prospectively apply it to a sample total knee arthroplasty population. Using clinically available computed tomography and radiography imaging systems, the three-dimensional knee shape and geometry of nine patients (eight varus and one valgus) were compared before and after total knee arthroplasty. All patients had largely good outcomes after their total knee arthroplasty. Knee shape changed both visually and numerically. On average, the distal condyles were slightly higher medially and lower laterally (range: +4.5 mm to −4.4 mm), the posterior condyles extended farther out medially but not laterally (range: +1.8 to −6.4 mm), patellofemoral distance increased throughout flexion by 1.8–3.5 mm, and patellar thickness alone increased by 2.9 mm (range: 0.7–5.2 mm). External femoral rotation differed preop and postop. Joint line distance, taking cartilage into account, changed by +0.7 to −1.5 mm on average throughout flexion. Important differences in shape and geometry were seen between pre-total knee arthroplasty and post-total knee arthroplasty knees. While this is qualitatively known, this is the first study to report it quantitatively, an important precursor to identifying the reasons for the poor outcome of some patients. Using the developed protocol and visualization techniques to compare patients with good versus poor clinical outcomes could lead to changes in implant design, implant selection, component positioning, and surgical technique. Recommendations based on this sample population are provided. Intraoperative and postoperative feedback could ultimately improve patient satisfaction. Y1 - 2018 UR - http://journals.sagepub.com/eprint/ZVgNrNESA9EjIcaFWSjb/full U6 - https://doi.org/10.1177/0954411917743274 VL - 232 IS - 1 SP - 67 EP - 79 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Objective priors in the empirical Bayes framework JF - Scandinavian Journal of Statistics N2 - When dealing with Bayesian inference the choice of the prior often remains a debatable question. Empirical Bayes methods offer a data-driven solution to this problem by estimating the prior itself from an ensemble of data. In the nonparametric case, the maximum likelihood estimate is known to overfit the data, an issue that is commonly tackled by regularization. However, the majority of regularizations are ad hoc choices which lack invariance under reparametrization of the model and result in inconsistent estimates for equivalent models. We introduce a nonparametric, transformation-invariant estimator for the prior distribution. Being defined in terms of the missing information similar to the reference prior, it can be seen as an extension of the latter to the data-driven setting. This implies a natural interpretation as a trade-off between choosing the least informative prior and incorporating the information provided by the data, a symbiosis between the objective and empirical Bayes methodologies. Y1 - 2021 U6 - https://doi.org/10.1111/sjos.12485 VL - 48 IS - 4 SP - 1212 EP - 1233 PB - Wiley Online Library ER - TY - JOUR A1 - Gul, Raheem A1 - Schütte, Christof A1 - Bernhard, Stefan T1 - Mathematical modeling and sensitivity analysis of arterial anastomosis in arm arteries JF - Applied Mathematical Modelling Y1 - 2016 U6 - https://doi.org/10.1016/j.apm.2016.03.041 ER - TY - JOUR A1 - Leeners, Brigitte A1 - Krüger, Tillmann H. C. A1 - Geraedts, Kirsten A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Ille, Fabian A1 - Egli, Marcel A1 - Röblitz, Susanna A1 - Saleh, Lanja A1 - Spanhaus, K. A1 - Schippert, Cordula A1 - Zhang, Y. A1 - Hengartner, M. P. T1 - Lack of association between female hormone levels and visuospatial working memory, divided attention and cognitive bias across two consecutive menstrual cycles JF - Front. Behav. Neurosci. Y1 - 2017 U6 - https://doi.org/10.3389/fnbeh.2017.00120 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems JF - The Journal of Chemical Physics N2 - Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations. Y1 - 2017 U6 - https://doi.org/10.1063/1.4986560 VL - 147 IS - 11 SP - 114115-1 EP - 114115-18 ER - TY - JOUR A1 - Fischer, Lisa A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Lossy data compression reduces communication time in hybrid time-parallel integrators JF - Comput. Vis. Sci. N2 - Parallel in time methods for solving initial value problems are a means to increase the parallelism of numerical simulations. Hybrid parareal schemes interleaving the parallel in time iteration with an iterative solution of the individual time steps are among the most efficient methods for general nonlinear problems. Despite the hiding of communication time behind computation, communication has in certain situations a significant impact on the total runtime. Here we present strict, yet no sharp, error bounds for hybrid parareal methods with inexact communication due to lossy data compression, and derive theoretical estimates of the impact of compression on parallel efficiency of the algorithms. These and some computational experiments suggest that compression is a viable method to make hybrid parareal schemes robust with respect to low bandwidth setups. Y1 - 2018 U6 - https://doi.org/10.1007/s00791-018-0293-2 VL - 19 IS - 1 SP - 19 EP - 30 ER - TY - JOUR A1 - Barth, Carlo A1 - Roder, Sebastian A1 - Brodoceanu, Daniel A1 - Kraus, Tobias A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - Increased fluorescence of PbS quantum dots in photonic crystals by excitation enhancement JF - Appl. Phys. Lett. Y1 - 2017 U6 - https://doi.org/10.1063/1.4995229 VL - 111 SP - 031111 ER - TY - JOUR A1 - Benn, Andreas A1 - Hiepen, Christian A1 - Osterland, Marc A1 - Schütte, Christof A1 - Zwijsen, An A1 - Knaus, Petra T1 - Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence JF - FASEB Journal N2 - Before the onset of sprouting angiogenesis, the endothelium is prepatterned for the positioning of tip and stalk cells. Both cell identities are not static, as endothelial cells (ECs) constantly compete for the tip cell position in a dynamic fashion. Here, we show that both bone morphogenetic protein (BMP) 2 and BMP6 are proangiogenic in vitro and ex vivo and that the BMP type I receptors, activin receptor-like kinase (ALK)3 and ALK2, play crucial and distinct roles in this process. BMP2 activates the expression of tip cell–associated genes, such as DLL4 (delta-like ligand 4) and KDR (kinase insert domain receptor), and p38-heat shock protein 27 (HSP27)–dependent cell migration, thereby generating tip cell competence. Whereas BMP6 also triggers collective cell migration via the p38-HSP27 signaling axis, BMP6 induces in addition SMAD1/5 signaling, thereby promoting the expression of stalk cell–associated genes, such as HES1 (hairy and enhancer of split 1) and FLT1 (fms-like tyrosine kinase 1). Specifically, ALK3 is required for sprouting from HUVEC spheroids, whereas ALK2 represses sprout formation. We demonstrate that expression levels and respective complex formation of BMP type I receptors in ECs determine stalk vs. tip cell identity, thus contributing to endothelial plasticity during sprouting angiogenesis. As antiangiogenic monotherapies that target the VEGF or ALK1 pathways have not fulfilled efficacy objectives in clinical trials, the selective targeting of the ALK2/3 pathways may be an attractive new approach. Y1 - 2017 U6 - https://doi.org/10.1096/fj.201700193RR VL - 31 IS - 11 SP - 4720 EP - 4733 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Weiser, Martin A1 - Santiago, Xavier Garcia A1 - Zschiedrich, Lin A1 - Bodermann, Bernd A1 - Burger, Sven T1 - Quantifying parameter uncertainties in optical scatterometry using Bayesian inversion JF - Proc. SPIE Y1 - 2017 U6 - https://doi.org/10.1117/12.2270596 VL - 10330 SP - 1033004 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Santiago, Xavier Garcia A1 - Rockstuhl, Carsten A1 - Burger, Sven T1 - Global optimization of complex optical structures using Bayesian optimization based on Gaussian processes JF - Proc. SPIE Y1 - 2017 U6 - https://doi.org/10.1117/12.2270609 VL - 10335 SP - 103350O ER - TY - JOUR A1 - Beckenbach, Isabel A1 - Scheidweiler, Robert T1 - Perfect f-Matchings and f-Factors in Hypergraphs - A Combinatorial Approach JF - Discrete Mathematics N2 - We prove characterizations of the existence of perfect f-matchings in uniform mengerian and perfect hypergraphs. Moreover, we investigate the f-factor problem in balanced hypergraphs. For uniform balanced hypergraphs we prove two existence theorems with purely combinatorial arguments, whereas for non-uniform balanced hypergraphs we show that the f-factor problem is NP-hard. Y1 - 2017 U6 - https://doi.org/10.1016/j.disc.2017.05.005 VL - 340 IS - 10 SP - 2499 EP - 2506 ER - TY - JOUR A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Eisenhauer, David A1 - Chen, Duote A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - Optical simulations of advanced light management for liquid-phase crystallized silicon thin-film solar cells JF - Proc. SPIE Y1 - 2017 U6 - https://doi.org/10.1117/12.2273994 VL - 10356 SP - 103560F ER - TY - JOUR A1 - von Tycowicz, Christoph A1 - Ambellan, Felix A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - An Efficient Riemannian Statistical Shape Model using Differential Coordinates JF - Medical Image Analysis N2 - We propose a novel Riemannian framework for statistical analysis of shapes that is able to account for the nonlinearity in shape variation. By adopting a physical perspective, we introduce a differential representation that puts the local geometric variability into focus. We model these differential coordinates as elements of a Lie group thereby endowing our shape space with a non-Euclidean structure. A key advantage of our framework is that statistics in a manifold shape space becomes numerically tractable improving performance by several orders of magnitude over state-of-the-art. We show that our Riemannian model is well suited for the identification of intra-population variability as well as inter-population differences. In particular, we demonstrate the superiority of the proposed model in experiments on specificity and generalization ability. We further derive a statistical shape descriptor that outperforms the standard Euclidean approach in terms of shape-based classification of morphological disorders. Y1 - 2018 U6 - https://doi.org/10.1016/j.media.2017.09.004 VL - 43 IS - 1 SP - 1 EP - 9 ER - TY - JOUR A1 - Santiago, Xavier Garcia A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Fernandez-Corbaton, Ivan T1 - Measuring the electromagnetic chirality of 2D arrays under normal illumination JF - Opt. Lett. Y1 - 2017 U6 - https://doi.org/10.1364/OL.42.004075 VL - 42 SP - 4075 ER - TY - JOUR A1 - Zinser, Max A1 - Zachow, Stefan A1 - Sailer, Hermann T1 - Bimaxillary "rotation advancement" procedures in patients with obstructive sleep apnea: A 3-dimensional airway analysis of morphological changes JF - International Journal of Oral & Maxillofacial Surgery Y1 - 2013 U6 - https://doi.org/10.1016/j.ijom.2012.08.002 VL - 42 IS - 5 SP - 569 EP - 578 ER - TY - JOUR A1 - Saevarsson, Stefan A1 - Sharma, Gulshan A1 - Amiri, Shahram A1 - Montgomery, Sigrun A1 - Ramm, Heiko A1 - Lichti, Derek A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Radiological method for measuring patellofemoral tracking and tibiofemoral kinematics before and after total knee replacement JF - Bone and Joint Research Y1 - 2012 UR - http://www.bjr.boneandjoint.org.uk/content/1/10/263.short U6 - https://doi.org/10.1302/2046-3758.110.2000117 VL - 1 IS - 10 SP - 263 EP - 271 ER - TY - JOUR A1 - Nguyen, The Duy A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Automatic bone and tooth detection for CT-based dental implant planning JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2012 VL - 7, Supplement 1 IS - 1 SP - 293 EP - 294 PB - Springer ER - TY - JOUR A1 - Westermark, Anders A1 - Zachow, Stefan A1 - Eppley, Barry T1 - 3D osteotomy planning in maxillofacial surgery, including 3D soft tissue prediction JF - Journal of Craniofacial Surgery Y1 - 2005 VL - 16(1) SP - 100 EP - 104 ER - TY - JOUR A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Topological methods for 2D time-dependent vector fields based on stream lines and path lines JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2005 U6 - https://doi.org/10.1109/TVCG.2005.68 VL - 11 IS - 4 ER - TY - JOUR A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Maxillofacial surgery planning with 3D soft tissue prediction - modeling, planning, simulation JF - 2. Int. Conf. on Advanced Digital Technology in Head and Neck Reconstruction, Abstract 33 Y1 - 2005 SP - 64 CY - Banff, Alberta, CA ER - TY - JOUR A1 - Saparin, Peter A1 - Thomsen, Jesper A1 - Prohaska, Steffen A1 - Zaikin, Alexei A1 - Kurths, Jürgen A1 - Hege, Hans-Christian A1 - Gowin, Wolfgang T1 - Quantification of spatial structure of human proximal tibial bone biopsies using 3D measures of complexity JF - Acta Astronautica Y1 - 2005 U6 - https://doi.org/10.1016/j.actaastro.2005.01.007 VL - 56 IS - 9-12 SP - 820 EP - 830 ER - TY - JOUR A1 - Alonso, Sergio A1 - Kähler, Ralf A1 - S. Mikhailov, Alexander A1 - Sagués, Francisco T1 - Expanding scroll rings and negative tension turbulence in a model of excitable media JF - Phys. Rev. E Y1 - 2004 U6 - https://doi.org/10.1103/PhysRevE.70.056201 VL - 70 IS - 5 SP - 056201 PB - American Physical Society ER - TY - JOUR A1 - Prohaska, Steffen A1 - Dreher, Matthew A1 - Dewhirst, Mark A1 - Chilkoti, Ashutosh A1 - Pries, Axel T1 - 3-D reconstruction of tumor vascular networks JF - J. Vas. Res. Y1 - 2004 VL - 41 SP - 463 ER - TY - JOUR A1 - Hierl, Thomas A1 - Zachow, Stefan A1 - Wollny, Gert A1 - Berti, Guntram A1 - Schmidt, Jens-Georg A1 - Fingberg, Jochen T1 - Computer-based simulation in distraction osteogenesis JF - Proc. of 3rd Int. Oxford Distraction Symposium of the Craniofacial Skeleton Y1 - 2004 SP - 33 EP - 34 ER - TY - JOUR A1 - Hierl, Thomas A1 - Zachow, Stefan A1 - Wollny, Gert A1 - Berti, Guntram A1 - Schmidt, Jens-Georg A1 - Fingberg, Jochen T1 - Concepts of computer-based simulation in orthognathic surgery JF - Journal of Cranio-Maxillofacial Surgery 32 Suppl. 1 Y1 - 2004 SP - 81 EP - 82 ER - TY - JOUR A1 - Haberl, Hannes A1 - Hell, Bertold A1 - Zöckler, Maja A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Sarrafzadeh, Asita A1 - Riecke, B. A1 - Langsch, Wolfgang A1 - Deuflhard, Peter A1 - Bier, Jürgen A1 - Brock, Mario T1 - Technical aspects and results of surgery for craniosynostosis JF - Zentralblatt für Neurochirurgie Y1 - 2004 VL - 65 IS - 2 SP - 65 EP - 74 ER - TY - JOUR A1 - Nkenke, Emeka A1 - Zachow, Stefan A1 - Benz, Michaela A1 - Maier, Tobias A1 - Veit, Klaus A1 - Kramer, Manuel A1 - Benz, St. A1 - Häusler, Gerd A1 - Neukam, Friedrich A1 - Lell, Michael T1 - Fusion of computed tomography data and optical 3D images of the dentition for streak artefact correction in the simulation of orthognathic surgery JF - Journal of Dento-Maxillofacial Radiology Y1 - 2004 U6 - https://doi.org/10.1259/dmfr/27071199 VL - 33 SP - 226 EP - 232 ER - TY - JOUR A1 - Hege, Hans-Christian T1 - Aktuelle Anwendungen der Wissenschaftlichen Visualisierung (Current Applications of Scientific Visualization) JF - it - Information Technology Y1 - 2004 U6 - https://doi.org/10.1524/itit.46.3.142.34213 VL - 46(3) SP - 142 EP - 147 ER - TY - JOUR A1 - Allen, Gabrielle A1 - Merzky, André A1 - Nabrzysk, Jarek A1 - Seidel, Edward T1 - GridLab - A Grid Application Toolkit and Testbed JF - Future Generation Computer Systems Y1 - 2002 VL - 18(8) SP - 1143 EP - 1153 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Merzky, André T1 - GriKSL - Immersive Überwachung und Steuerung von Simulationen auf entfernten Supercomputern JF - DFN-Mitteilungen, Heft 59 Y1 - 2002 SP - 5 EP - 7 ER - TY - JOUR A1 - Busch, Hubert A1 - Merzky, André T1 - Supercomputer: Auf zwei Standorte verteiltes Rechnersystem wird im Wissenschaftsnetz zum virtuellen Supercomputer JF - DFN-Mitteilungen, Heft 59 Y1 - 2002 SP - 8 EP - 10 ER - TY - JOUR A1 - V. 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Mader, Michael A1 - Grübel, Cornelia A1 - Heisenberg, Martin T1 - The Drosophila Standard Brain JF - Current Biology Y1 - 2002 U6 - https://doi.org/10.1016/S0960-9822(02)00656-5 VL - 12 IS - 3 SP - 227 EP - 231 ER - TY - JOUR A1 - Zöckler, Malte A1 - Stalling, Detlev T1 - Using confocal microscopy and advanced 3-d visualization to investigate the Drosophila brain JF - Scientific Computing & Instrumentation Y1 - 2002 ER - TY - JOUR A1 - Zeilhofer, Hans-Florian A1 - Hege, Hans-Christian T1 - Operieren im Medizin-Grid JF - DFN-Mitteilungen, Heft 60 Y1 - 2002 SP - 19 EP - 20 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Kähler, Ralf A1 - Seidel, Edward A1 - Radke, Thomas T1 - GriKSL zeigt Live-Demos auf der iGrid2002 JF - DFN-Mitteilungen, Heft 60 Y1 - 2002 SP - 21 EP - 22 ER - TY - JOUR A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - Visual Analysis of Trabecular Bone Structure JF - Journal of Gravitational Physiology Y1 - 2002 VL - 9 (1) SP - 171 EP - 172 ER - TY - JOUR A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Kurths, Jürgen A1 - Gowin, Wolfgang T1 - Bone Modeling and Structural Measures of Complexity JF - Journal of Gravitational Physiology Y1 - 2002 U6 - https://doi.org/10.1016/j.actaastro.2005.01.007 VL - 9 SP - 175 EP - 176 ER - TY - JOUR A1 - Gowin, Wolfgang A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Felsenberg, Dieter T1 - Femoral Neck Fractures: Reasons for the Most Common Location of Fractures JF - Acta Orthop. Scand. (Suppl. 304) Y1 - 2002 VL - 73 SP - 26 ER - TY - JOUR A1 - Kähler, Ralf A1 - Hege, Hans-Christian T1 - Texture-based volume rendering of adaptive mesh refinement data JF - The Visual Computer Y1 - 2002 VL - 18 IS - 8 SP - 491 EP - 492 ER - TY - JOUR A1 - Kähler, Ralf A1 - Simon, Mark A1 - Hege, Hans-Christian T1 - Interactive Volume Rendering of Large Data Sets Using Adaptive Mesh Refinement Hierarchies JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2003 U6 - https://doi.org/10.1109/TVCG.2003.1207442 VL - 9 IS - 3 SP - 341 EP - 351 ER - TY - JOUR A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - Anatomy- and physics-based facial animation for craniofacial surgery simulations JF - Med Biol Eng Comput. Y1 - 2004 U6 - https://doi.org/10.1007/BF02344627 VL - 42(2) SP - 167 EP - 170 ER - TY - JOUR A1 - Hildebrandt, Klaus A1 - Polthier, Konrad T1 - Anisotropic filtering of non-linear surface features JF - Computer Graphics Forum Y1 - 2004 VL - 23(3) SP - 391 EP - 400 CY - Grenoble, France ER - TY - JOUR A1 - Rigort, Alexander A1 - Günther, David A1 - Hegerl, Reiner A1 - Baum, Daniel A1 - Weber, Britta A1 - Prohaska, Steffen A1 - Medalia, Ohad A1 - Baumeister, Wolfgang A1 - Hege, Hans-Christian T1 - Automated segmentation of electron tomograms for a quantitative description of actin filament networks JF - Journal of Structural Biology Y1 - 2012 U6 - https://doi.org/10.1016/j.jsb.2011.08.012 VL - 177 SP - 135 EP - 144 ER - TY - JOUR A1 - Petz, Christoph A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Oliver A1 - Wygnanski, Israel A1 - Noack, Bernd A1 - Hege, Hans-Christian T1 - Global Modes in a Swirling Jet Undergoing Vortex Breakdown JF - Physics of Fluids Y1 - 2011 U6 - https://doi.org/10.1063/1.3640007 VL - 23 SP - 091102 PB - Awarded Visualization; First Prize at 28th Annual Gallery of Fluid Motion exhibit, held at the 63th Annual Meeting of the American Physical Society, Division of Fluid Dynamics (Long Beach, CA, USA, November 21-23, 2010). ER - TY - JOUR A1 - Lang, Stefan A1 - Dercksen, Vincent J. A1 - Sakmann, Bert A1 - Oberlaender, Marcel T1 - Simulation of signal flow in 3D reconstructions of an anatomically realistic neural network in rat vibrissal cortex JF - Neural Networks Y1 - 2011 U6 - https://doi.org/doi:10.1016/j.neunet.2011.06.013 VL - 24 IS - 9 SP - 998 EP - 1011 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Koppitz, Michael A1 - Marquardt, Falko A1 - McDonald, Chris A1 - Mielack, Christopher T1 - Visual Analysis of Quantum Physics Data JF - Quantum Dynamic Imaging Y1 - 2011 U6 - https://doi.org/10.1007/978-1-4419-9491-2_6 SP - 71 EP - 87 PB - Springer ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Kasten, Jens A1 - Hotz, Ingrid T1 - Distillation and Visualization of Spatiotemporal Structures in Turbulent Flow Fields JF - J. Phys. 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Y1 - 2000 U6 - https://doi.org/10.1016/S0360-3016(00)00425-9 VL - 47(4) SP - 1145 EP - 1156 ER - TY - JOUR A1 - Seebaß, Martin A1 - Beck, Rudolf A1 - Gellermann, Johanna A1 - Nadobny, Jacek A1 - Wust, Peter T1 - Electromagnetic Phased Arrays for Regional Hyperthermia - Optimal Frequency and Antenna Arrangement JF - Int. J. Hyperthermia Y1 - 2000 VL - 17(4) SP - 321 EP - 326 ER - TY - JOUR A1 - Wust, Peter A1 - Beck, Rudolf A1 - Berger, Jörn A1 - Fähling, Horst A1 - Seebaß, Martin A1 - Wlodarczyk, Waldemar A1 - Hoffmann, Werner A1 - Nadobny, Jacek T1 - Electric Field Distributions in a Phased-Array Applicator with 12 Channels - Measurements and Numerical Simulations JF - Medical Physics Y1 - 2000 VL - 27 SP - 2565 EP - 2579 ER - TY - JOUR A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Trepczynski, Adam A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian T1 - 3D Osteotomy Planning in Cranio-Maxillofacial Surgery: Experiences and Results of Surgery Planning and Volumetric Finite-Element Soft Tissue Prediction in Three Clinical Cases JF - Computer Assisted Radiology and Surgery (CARS) Y1 - 2002 SP - 983 EP - 987 PB - Springer Verlag ER - TY - JOUR A1 - Best, Christoph A1 - Hege, Hans-Christian T1 - Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories JF - IEEE Computing in Science & Engineering Y1 - 2002 U6 - https://doi.org/10.1109/5992.998642 VL - 4(3) SP - 68 EP - 75 ER - TY - JOUR A1 - Schmidt-Ehrenberg, Johannes A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Visually stunning - Molecular conformations JF - The Biochemist Y1 - 2001 VL - 23 IS - 5 SP - 22 EP - 26 ER - TY - JOUR A1 - Allen, Gabrielle A1 - Benger, Werner A1 - Dramlitsch, Thomas A1 - Goodale, Tom A1 - Hege, Hans-Christian A1 - Lanfermann, Gerd A1 - Merzky, André A1 - Radtke, Thomas A1 - Seidel, Edward A1 - Shalf, John T1 - Cactus Tools for Grid Applications JF - Cluster Computing Y1 - 2001 U6 - https://doi.org/10.1023/A:1011491422534 VL - 4 IS - 3 SP - 179 EP - 188 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Höllerer, Tobias A1 - Stalling, Detlev T1 - Volume Rendering: Mathematical Models and Algorithmic Aspects JF - Partielle Differentialgleichungen, Numerik und Anwendungen, Konferenzen des Forschungszentrum Jülich GmbH Y1 - 1996 SP - 227 EP - 255 PB - W. Nagel ER - TY - JOUR A1 - Nadobny, Jacek A1 - Wust, Peter A1 - Seebaß, Martin A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A Volume Surface Integral Equation Method for Solving Maxwell’s Equations in Electrically Inhomogeneous Media Using Tetrahedral Grids JF - IEEE Transactions Microwave Theory Techn. 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Journal Hyperthermia Y1 - 1999 VL - 15 IS - 6 SP - 519 EP - 540 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Cordes, Frank A1 - Roitzsch, Rainer A1 - Schütte, Christof T1 - Identification of Molecular Conformations via Statistical Analysis of Simulation Data JF - Comp. Chem. 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Y1 - 1999 U6 - https://doi.org/10.1109/10.784145 VL - 46 SP - 1129 EP - 1138 ER - TY - JOUR A1 - Rein, Karlheinz A1 - Zöckler, Malte A1 - Heisenberg, Martin T1 - A Quantitative Three-Dimensional Model of the Drosophila Optic Lobes JF - Current Biology Y1 - 1999 VL - 9 IS - 2 SP - 93 EP - 96 ER - TY - JOUR A1 - Reinefeld, Alexander A1 - Stüben, Hinnerk A1 - Schintke, Florian A1 - Din, George T1 - GuiGen: a toolset for creating customized interfaces for Grid user communities JF - Future Generation Comp. Syst. 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Journal of Hyperthermia Y1 - 1996 VL - 12 SP - 477 EP - 494 ER - TY - JOUR A1 - Hege, Hans-Christian T1 - Problems and Solutions: Product of Chebyshev Polynomials JF - Orthogonal Polynomials and Special Functions Y1 - 1996 VL - 6 (2) SP - 12 ER - TY - JOUR A1 - Höllerer, Tobias A1 - Tönnies, Klaus A1 - Hege, Hans-Christian A1 - Stalling, Detlev T1 - Der Einfluß der Datenapproximation bei Volume Rendering durch ein Emissions/Absorptions-Modell JF - Visualisierung - Dynamik und Komplexität Y1 - 1995 PB - CEVIS Universität Bremen und Fachgruppe 4.2.1 der Gesellschaft für Informatik CY - Bremen, Germany ER - TY - JOUR A1 - Hege, Hans-Christian T1 - Scaling study of pure SU(3) theory - the QCD-TARO collaboration JF - Nucl. Phys. B Proc. Suppl. Y1 - 1994 U6 - https://doi.org/10.1016/0920-5632(94)90358-1 VL - 34 SP - 246 EP - 252 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - QCD on the Massively Parallel Computer AP 1000 JF - Int. J. Mod. Phys. Y1 - 1993 U6 - https://doi.org/10.1142/S0129183193000975 VL - 4 IS - 6 SP - 1233 EP - 1253 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - Autocorrelation in Updating Pure SU(3) Lattice Gauge Theory by the Use of Overrelaxed Algorithms JF - Nucl. Phys. B Proc. Suppl. Y1 - 1993 U6 - https://doi.org/10.1016/0920-5632(93)90202-H VL - 30 SP - 253 EP - 256 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - Study of Spatial Size Effects in Quenched Wilson Hadron Spectroscopy at beta = 6.3 JF - Nucl. Phys. B Proc. Suppl. Y1 - 1993 U6 - https://doi.org/10.1016/0920-5632(93)90230-4 VL - 30 SP - 373 EP - 376 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - Monte Carlo Renormalization Study at Large beta in the Confinement Region JF - Nuclear Phys. B. Proc. Suppl. Y1 - 1993 U6 - https://doi.org/10.1016/0920-5632(93)90263-6 VL - 30 SP - 517 EP - 520 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Knecht, Renate T1 - Conference Report: Parallel Computing 91 JF - Parallel Computing Y1 - 1992 VL - 18 IS - 4 SP - 473 EP - 476 ER - TY - JOUR A1 - Hashimoto, T. A1 - Hege, Hans-Christian T1 - Hadron Spectroscopy on a 32^3 * 48 Lattice JF - Nucl. Phys. B Proc. Suppl. 26 Y1 - 1992 U6 - https://doi.org/10.1016/0920-5632(92)90257-S SP - 293 EP - 295 ER - TY - JOUR A1 - Ho, Karen A1 - Saevarsson, Stefan A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Sharma, Gulshan A1 - Rex, Erica A1 - Amiri, Shahram A1 - Wu, Barnabas A1 - Leumann, Andre A1 - Anglin, Carolyn T1 - Computed tomography analysis of knee pose and geometry before and after total knee arthroplasty JF - Journal of biomechanics Y1 - 2012 UR - http://www.ncbi.nlm.nih.gov/pubmed/22796002 U6 - https://doi.org/10.1016/j.jbiomech.2012.06.004 VL - 45 IS - 13 SP - 2215 EP - 21 ER - TY - JOUR A1 - Oberlaender, Marcel A1 - de Kock, Christiaan P. J. A1 - Bruno, Randy M. A1 - Ramirez, Alejandro A1 - Meyer, Hanno A1 - Dercksen, Vincent J. A1 - Helmstaedter, Moritz A1 - Sakmann, Bert T1 - Cell Type-Specific Three-Dimensional Structure of Thalamocortical Circuits in a Column of Rat Vibrissal Cortex JF - Cerebral Cortex Y1 - 2012 U6 - https://doi.org/doi:10.1093/cercor/bhr317 VL - 22 IS - 10 SP - 2375 EP - 2391 ER - TY - JOUR A1 - Weber, Britta A1 - Greenan, Garrett A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Müller-Reichert, Thomas A1 - Hyman, Anthony A1 - Verbavatz, Jean-Marc T1 - Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos JF - Journal of Structural Biology Y1 - 2012 UR - http://www.sciencedirect.com/science/article/pii/S1047847711003509 U6 - https://doi.org/10.1016/j.jsb.2011.12.004 VL - 178 IS - 2 SP - 129 EP - 138 ER - TY - JOUR A1 - Kasten, Jens A1 - Reininghaus, Jan A1 - Hotz, Ingrid A1 - Hege, Hans-Christian T1 - Two-Dimensional Time-Dependent Vortex Regions Based on the Acceleration Magnitude JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2011 VL - 17 IS - 12 SP - 2080 EP - 2087target ER - TY - JOUR A1 - Reininghaus, Jan A1 - Kotava, N. A1 - Günther, David A1 - Kasten, Jens A1 - Hagen, Hans A1 - Hotz, Ingrid T1 - A Scale Space Based Persistence Measure for Critical Points in 2D Scalar Fields JF - Visualization and Computer Graphics, IEEE Transactions on Y1 - 2011 U6 - https://doi.org/10.1109/TVCG.2011.159 VL - 17 IS - 12 SP - 2045 EP - 2052 ER - TY - JOUR A1 - Günther, David A1 - Reininghaus, Jan A1 - Wagner, Hubert A1 - Hotz, Ingrid T1 - Memory-Efficient Computation of Persistent Homology for 3D Images using Discrete Morse Theory JF - Proc. Sibgrapi – Conference on Graphics, Patterns and Images Y1 - 2011 PB - Kluwer Academic Publishers ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Voronoi-Based Extraction and Visualization of Molecular Paths JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2011 U6 - https://doi.org/10.1109/TVCG.2011.259 VL - 17 IS - 12 SP - 2025 EP - 2034 ER - TY - JOUR A1 - Kleinfeld, David A1 - Bharioke, Arjun A1 - Blinder, Pablo A1 - Bock, David A1 - Briggman, Kevin A1 - Chklovskii, Dmitri A1 - Denk, Winfried A1 - Helmstaedter, Moritz A1 - Kaufhold, John A1 - Lee, Wei-Chung A1 - Meyer, Hanno A1 - Micheva, Kristina A1 - Oberlaender, Marcel A1 - Prohaska, Steffen A1 - Reid, R. A1 - Smith, Stephen A1 - Takemura, Shinya A1 - Tsai, Philbert A1 - Sakmann, Bert T1 - Large-scale automated histology in the pursuit of connectomes JF - Journal of Neuroscience Y1 - 2011 UR - http://www.zib.de/prohaska/docs/Kleinfeld_JNS_Connectomes_2011.pdf U6 - https://doi.org/10.1523/JNEUROSCI.4077-11.2011 VL - 31 IS - 45 SP - 16125 EP - 16138 ER - TY - JOUR A1 - Lacarelle, Arnaud A1 - P. Moeck, Jonas A1 - Paschereit, Christian A1 - Gelbert, Gregor A1 - King, Rudibert A1 - M. Luchtenburg, Dirk A1 - Noack, Bernd R. A1 - Kasten, Jens A1 - Hege, Hans-Christian T1 - Modeling a Fuel/Air Mixing to Control the Pressure Pulsations and NOx Emissions in a Lean Premixed Combustor JF - Active Flow Control II Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-11735-0_20 VL - 108 SP - 307 EP - 321 PB - Springer, Berlin ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Accelerated Visualization of Dynamic Molecular Surfaces JF - Comput. Graph. Forum Y1 - 2010 U6 - https://doi.org/10.1111/j.1467-8659.2009.01693.x VL - 29 SP - 943 EP - 952 ER - TY - JOUR A1 - Rybak, Jürgen A1 - Kuß, Anja A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Lienhard, Matthias A1 - Singer, Jochen A1 - Neubert, Kerstin A1 - Menzel, Randolf T1 - The Digital Bee Brain: Integrating and Managing Neurons in a Common 3D Reference System JF - Front. Syst. Neurosci. Y1 - 2010 U6 - https://doi.org/10.3389/fnsys.2010.00030 VL - 4 IS - 30 ER - TY - JOUR A1 - Kuß, Anja A1 - Gensel, Maria A1 - Meyer, Björn A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen T1 - Effective Techniques to Visualize Filament-Surface Relationships JF - Comput. Graph. Forum Y1 - 2010 VL - 29 SP - 1003 EP - 1012 ER - TY - JOUR A1 - Otto, Mathias A1 - Germer, Tobias A1 - Hege, Hans-Christian A1 - Theisel, Holger T1 - Uncertain 2D Vector Field Topology JF - Comput. Graph. Forum Y1 - 2010 U6 - https://doi.org/10.1111/j.1467-8659.2009.01604.x VL - 29 SP - 347 EP - 356 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Thamsen, Bente A1 - Berthe, André A1 - Poethke, Jens A1 - Kertzscher, Ulrich A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Hoch, Heinrich A1 - Spuler, Andreas T1 - In Vitro Study of Near-Wall Flow in a Cerebral Aneurysm Model with and without Coils JF - American Journal of Neuroradiology Y1 - 2010 U6 - https://doi.org/10.3174/ajnr.A2121 VL - 31:8 SP - 1521 EP - 1528 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Laidlaw, David A1 - Machiraju, Raghu T1 - Guest Editor's Introduction: Special Section on Volume Graphics and Point-Based Graphics JF - IEEE Trans. Vis. Comput. Graph. Y1 - 2010 U6 - https://doi.org/10.1109/TVCG.2010.72 VL - 16 IS - 4 SP - 531 EP - 532 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Bondar, Ana-Nicoleta A1 - Hege, Hans-Christian T1 - Exploring cavity dynamics in biomolecular systems JF - BMC Bioinformatics Y1 - 2013 U6 - https://doi.org/10.1186/1471-2105-14-S19-S5 VL - 14 ET - (Suppl 19):S5 ER - TY - JOUR A1 - Galloway, Francis A1 - Kahnt, Max A1 - Ramm, Heiko A1 - Worsley, Peter A1 - Zachow, Stefan A1 - Nair, Prasanth A1 - Taylor, Mark T1 - A large scale finite element study of a cementless osseointegrated tibial tray JF - Journal of Biomechanics Y1 - 2013 U6 - https://doi.org//10.1016/j.jbiomech.2013.04.021 VL - 46 IS - 11 SP - 1900 EP - 1906 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Goubergrits, Leonid A1 - Heppt, Werner A1 - Bessler, Stefan A1 - Zachow, Stefan T1 - Evaluation of the Intranasal Flow Field through Computational Fluid Dynamics (CFD) JF - Journal of Facial and Plastic Surgery Y1 - 2013 UR - https://www.thieme-connect.de/DOI/DOI?10.1055/s-0033-1341591 U6 - https://doi.org/10.1055/s-0033-1341591 VL - 29 IS - 2 SP - 93 EP - 98 PB - Thieme ER - TY - JOUR A1 - Saevarsson, Stefan A1 - Sharma, Gulshan A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Hutchison, Carol A1 - Werle, Jason A1 - Montgomery, Sigrun A1 - Romeo, Carolina A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Kinematic Differences Between Gender Specific And Traditional Knee Implants JF - The Journal of Arthroplasty Y1 - 2013 U6 - https://doi.org/10.1016/j.arth.2013.01.021 VL - 28 IS - 9 SP - 1543 EP - 1550 ER - TY - JOUR A1 - Pöthkow, Kai A1 - Petz, Christoph A1 - Hege, Hans-Christian T1 - Approximate Level-Crossing Probabilities for Interactive Visualization of Uncertain Isocontours JF - International Journal for Uncertainty Quantification Y1 - 2013 U6 - https://doi.org/10.1615/Int.J.UncertaintyQuantification.2012003958 VL - 3 IS - 2 SP - 101 EP - 117 ER - TY - JOUR A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Zöckler, Maja A1 - Haberl, Ernst T1 - Computergestützte Planung zur chirurgischen Korrektur von frühkindlichen Schädelfehlbildungen (Craniosynostosen) JF - Face 02/09, Int. Mag. of Orofacial Esthetics, Oemus Journale Leipzig Y1 - 2009 SP - 48 EP - 53 ER - TY - JOUR A1 - Oberlaender, Marcel A1 - Dercksen, Vincent J. A1 - Egger, Robert A1 - Gensel, Maria A1 - Sakmann, Bert A1 - Hege, Hans-Christian T1 - Automated three-dimensional detection and counting of neuron somata JF - Journal of Neuroscience Methods Y1 - 2009 U6 - https://doi.org/10.1016/j.jneumeth.2009.03.008 VL - 180 IS - 1 SP - 147 EP - 160 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Weber, Sarah A1 - Petz, Christoph A1 - Spuler, Andreas A1 - Pöthke, Jens A1 - Berthe, André A1 - Hege, Hans-Christian T1 - Wall-PIV as a Near Wall Flow Validation Tool for CFD JF - Journal of Visualization Y1 - 2009 VL - 12 IS - 3 SP - 241 EP - 250 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Wellnhofer, Ernst A1 - Kertzscher, Ulrich A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Hege, Hans-Christian T1 - Coronary Artery WSS Profiling Using a Geometry Reconstruction Based on Biplane Angiography JF - Annals of Biomedical Engineering Y1 - 2009 U6 - https://doi.org/s10439-009-9656-7 VL - 37 IS - 4 SP - 682 EP - 691 PB - Springer ER - TY - JOUR A1 - Langenhan, Andreas A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Schulz, Christof A1 - Weider, Steffen ED - Muñoz, J. C. ED - Voß, S. T1 - Duty Scheduling Templates JF - Proceedings of Conference on Advanced Systems for Public Transport 2012 (CASPT12) N2 - We propose duty templates as a novel concept to produce similar duty schedules for similar days of operation in public transit. Duty templates can conveniently handle various types of similarity requirements, and they can be implemented with ease using standard algorithmic techniques. They have produced good results in practice. Y1 - 2012 ER - TY - JOUR A1 - Pfetsch, Marc A1 - Fügenschuh, Armin A1 - Geißler, Björn A1 - Geißler, Nina A1 - Gollmer, Ralf A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Martin, Alexander A1 - Morsi, Antonio A1 - Rövekamp, Jessica A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schultz, Rüdiger A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Stangl, Claudia A1 - Steinbach, Marc A1 - Vigerske, Stefan A1 - Willert, Bernhard T1 - Validation of Nominations in Gas Network Optimization: Models, Methods, and Solutions JF - Optimization Methods and Software N2 - In this article we investigate methods to solve a fundamental task in gas transportation, namely the validation of nomination problem: Given a gas transmission network consisting of passive pipelines and active, controllable elements and given an amount of gas at every entry and exit point of the network, find operational settings for all active elements such that there exists a network state meeting all physical, technical, and legal constraints. We describe a two-stage approach to solve the resulting complex and numerically difficult feasibility problem. The first phase consists of four distinct algorithms applying linear, and methods for complementarity constraints to compute possible settings for the discrete decisions. The second phase employs a precise continuous programming model of the gas network. Using this setup, we are able to compute high quality solutions to real-world industrial instances that are significantly larger than networks that have appeared in the mathematical programming literature before. Y1 - 2014 U6 - https://doi.org/10.1080/10556788.2014.888426 PB - Taylor & Francis ER - TY - JOUR A1 - Sagnol, Guillaume T1 - On the semidefinite representation of real functions applied to symmetric matrices JF - Linear Algebra and its Applications N2 - We present a new semidefinite representation for the trace of a real function f applied to symmetric matrices, when a semidefinite representation of the convex function f is known. Our construction is intuitive, and yields a representation that is more compact than the previously known one. We also show with the help of matrix geometric means and the Riemannian metric of the set of positive definite matrices that for a rational number p in the interval (0,1], the matrix X raised to the exponent p is the largest element of a set represented by linear matrix inequalities. We give numerical results for a problem inspired from the theory of experimental designs, which show that the new semidefinite programming formulation yields a speed-up factor in the order of 10. Y1 - 2013 U6 - https://doi.org/10.1016/j.laa.2013.08.021 VL - 439 IS - 10 SP - 2829 EP - 2843 ER - TY - JOUR A1 - Sagnol, Guillaume T1 - Approximation of a maximum-submodular-coverage problem involving spectral functions, with application to experimental designs JF - Discrete Applied Mathematics N2 - We study a family of combinatorial optimization problems defined by a parameter $p\in[0,1]$, which involves spectral functions applied to positive semidefinite matrices, and has some application in the theory of optimal experimental design. This family of problems tends to a generalization of the classical maximum coverage problem as $p$ goes to $0$, and to a trivial instance of the knapsack problem as $p$ goes to $1$. In this article, we establish a matrix inequality which shows that the objective function is submodular for all $p\in[0,1]$, from which it follows that the greedy approach, which has often been used for this problem, always gives a design within $1-1/e$ of the optimum. We next study the design found by rounding the solution of the continuous relaxed problem, an approach which has been applied by several authors. We prove an inequality which generalizes a classical result from the theory of optimal designs, and allows us to give a rounding procedure with an approximation factor which tends to $1$ as $p$ goes to $1$. Y1 - 2013 U6 - https://doi.org/10.1016/j.dam.2012.07.016 VL - 161 IS - 1-2 SP - 258 EP - 276 ER - TY - JOUR A1 - Sagnol, Guillaume T1 - A class of Semidefinite Programs with rank-one solutions JF - Linear Algebra and its Applications N2 - We show that a class of semidefinite programs (SDP) admits a solution that is a positive semidefinite matrix of rank at most $r$, where $r$ is the rank of the matrix involved in the objective function of the SDP. The optimization problems of this class are semidefinite packing problems, which are the SDP analogs to vector packing problems. Of particular interest is the case in which our result guarantees the existence of a solution of rank one: we show that the computation of this solution actually reduces to a Second Order Cone Program (SOCP). We point out an application in statistics, in the optimal design of experiments. Y1 - 2011 U6 - https://doi.org/10.1016/j.laa.2011.03.027 VL - 435 IS - 6 SP - 1446 EP - 1463 ER - TY - JOUR A1 - Gertzen, Thomas L. A1 - Grötschel, Martin ED - Grötschel, Martin T1 - Flinders Petrie, the Travelling Salesman Problem, and the Beginning of Mathematical Modeling in Archaeology JF - Optimization Stories Y1 - 2012 UR - http://www.mathematik.uni-bielefeld.de/documenta/vol-ismp/35_gertzen-thomas-groetschel-martin.pdf VL - Extra Vol.: Optim. Stories SP - 199 EP - 210 PB - Documenta Mathematica CY - Bielefeld ER - TY - JOUR A1 - Grötschel, Martin A1 - Yuan, Ya-xiang ED - Grötschel, Martin T1 - Euler, Mei-Ko Kwan, Königsberg, and a Chinese Postman JF - Documenta Mathematica - Optimization Stories Y1 - 2012 UR - http://www.mathematik.uni-bielefeld.de/documenta/vol-ismp/16_groetschel-martin-yuan-ya-xiang.pdf VL - Extra Vol.: Optim. Stories SP - 43 EP - 50 PB - Documenta Mathematica CY - Bielefeld ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Hellweg, D. A1 - Kottke, M. A1 - Dettmer, S. A1 - Rinkleff, T. A1 - Cacciapuoti, L. A1 - Arlt, J. A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang T1 - Spectroscopy of Dark Soliton States in Bose-Einstein Condensates JF - J. Opt. B: Quantum Semiclass. Opt. Y1 - 2003 U6 - https://doi.org/10.1088/1464-4266/5/2/369 VL - 5 SP - S124 ER - TY - JOUR A1 - Ahufinger, Verònica A1 - Corbalán, R. A1 - Cataliotti, F. S. A1 - Burger, Sven A1 - Minardi, F. A1 - Fort, C. T1 - Electromagnetically induced transparency in a Bose-Einstein condensate JF - Opt. Comm. Y1 - 2002 U6 - https://doi.org/10.1016/S0030-4018(02)01826-6 VL - 211 SP - 159 ER - TY - JOUR A1 - Plattner, A. A1 - Maurer, H. A1 - Vorloeper, J. A1 - Blome, Mark T1 - 3-D electrical resistivity tomography using adaptive wavelet parameter grids JF - Geophysical Journal International Y1 - 2012 VL - 189 SP - 317 EP - 330 ER - TY - JOUR A1 - Reimund, V. A1 - Blome, Mark A1 - Pelkner, M. A1 - Kreutzbruck, M. T1 - Fast defect parameter estimation based on magnetic flux leakage measurements with GMR sensors JF - International Journal of Applied Electromagnetics and Mechanics Y1 - 2011 U6 - https://doi.org/10.3233/JAE-2011-1391 VL - 37 IS - 2-3 SP - 199 EP - 205 ER - TY - JOUR A1 - Weiser, Martin T1 - Faster SDC convergence on non-equidistant grids by DIRK sweeps JF - BIT Numerical Mathematics N2 - Spectral deferred correction methods for solving stiff ODEs are known to converge rapidly towards the collocation limit solution on equidistant grids, but show a much less favourable contraction on non-equidistant grids such as Radau-IIa points. We interprete SDC methods as fixed point iterations for the collocation system and propose new DIRK-type sweeps for stiff problems based on purely linear algebraic considerations. Good convergence is recovered also on non-equidistant grids. The properties of different variants are explored on a couple of numerical examples. Y1 - 2015 U6 - https://doi.org/10.1007/s10543-014-0540-y VL - 55 IS - 4 SP - 1219 EP - 1241 ER - TY - JOUR A1 - Weiser, Martin A1 - Götschel, Sebastian T1 - State Trajectory Compression for Optimal Control with Parabolic PDEs JF - SIAM J. Sci. Comput. N2 - In optimal control problems with nonlinear time-dependent 3D PDEs, full 4D discretizations are usually prohibitive due to the storage requirement. For this reason gradient and quasi-Newton methods working on the reduced functional are often employed. The computation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. The state enters into the adjoint equation, again requiring the storage of a full 4D data set. We propose a lossy compression algorithm using an inexact but cheap predictor for the state data, with additional entropy coding of prediction errors. As the data is used inside a discretized, iterative algorithm, lossy coding maintaining an error bound is sufficient. Y1 - 2012 U6 - https://doi.org/10.1137/11082172X VL - 34 IS - 1 SP - A161 EP - A184 ER - TY - JOUR A1 - Weiser, Martin A1 - Röllig, Mathias A1 - Arndt, Ralf A1 - Erdmann, Bodo T1 - Development and test of a numerical model for pulse thermography in civil engineering JF - Heat and Mass Transfer N2 - Pulse thermography of concrete structures is used in civil engineering for detecting voids, honeycombing and delamination. The physical situation is readily modeled by Fourier's law. Despite the simplicity of the PDE structure, quantitatively realistic numerical 3D simulation faces two major obstacles. First, the short heating pulse induces a thin boundary layer at the heated surface which encapsulates all information and therefore has to be resolved faithfully. Even with adaptive mesh refinement techniques, obtaining useful accuracies requires an unsatisfactorily fine discretization. Second, bulk material parameters and boundary conditions are barely known exactly. We address both issues by a semi-analytic reformulation of the heat transport problem and by parameter identification. Numerical results are compared with measurements of test specimens. Y1 - 2010 VL - 46 IS - 11-12 SP - 1419 EP - 1428 ER - TY - JOUR A1 - Blome, Mark A1 - Maurer, H R A1 - Schmidt, K. T1 - Advances in three-dimensional geoelectric forward solver techniques JF - Geophysical Journal International Y1 - 2009 U6 - https://doi.org/10.1111/j.1365-246X.2008.04006.x VL - 176 IS - 3 SP - 740 EP - 752 ER - TY - JOUR A1 - Blome, Mark A1 - Maurer, HR A1 - Greenhalgh, S. T1 - Geoelectric experimental design — Efficient acquisition and exploitation of complete pole-bipole data sets JF - GEOPHYSICS Y1 - 2011 U6 - https://doi.org/10.1190/1.3511350 VL - 76 IS - 1 SP - F15 EP - F26 ER - TY - JOUR A1 - Grötschel, Martin A1 - Neumann, Gerald T1 - 10 Jahre TELOTA JF - Jahrbuch 2011 / Berlin-Brandenburgische Akademie der Wissenschaften N2 - Das TELOTA-Projekt - zunächst nur für zwei Jahre gestartet - feierte am 15. Juni 2011 sein 10-jähriges Bestehen im Rahmen eines Workshops mit einem abschließenden Festvortrag von Richard Stallmann zum Thema „Copyright versus community in the age of computer networks“. Diese Veranstaltung zeigte, wie aktuell die TELOTA-Themen weiterhin sind und dass diese eine große Resonanz in der allgemeinen Öffentlichkeit finden. Die TELOTA-Aktivitäten haben sich als wichtiger Bestandteil der IT-Infrastruktur der BBAW erwiesen, gehen aber weit über reinen Service hinaus. Sie beeinflussen die Forschung selbst und führen zu neuen interessanten wissenschaftlichen Fragestellungen. Der Rückblick auf die ersten zehn Jahre der TELOTA-Initiative in diesem Artikel soll einen kleinen Eindruck von dem geben, was bisher geleistet wurde. Y1 - 2012 SN - 978-3-05-005641-8 SP - 202 EP - 215 ER - TY - JOUR A1 - Wilhelms, Mathias A1 - Seemann, Gunnar A1 - Weiser, Martin A1 - Dössel, Olaf T1 - Benchmarking Solvers of the Monodomain Equation in Cardiac Electrophysiological Modeling JF - Biomed. Engineer. Y1 - 2010 U6 - https://doi.org/10.1515/BMT.2010.712 VL - 55 SP - 99 EP - 102 ER - TY - JOUR A1 - Grötschel, Martin T1 - Einblicke in die diskrete Mathematik JF - Der Mathematikunterricht N2 - „Diskrete Mathematik, was ist das?“, ist eine typische Frage von Lehrern mit traditioneller Mathematikausbildung, denn dort kam und kommt diskrete Mathematik kaum vor. Die etwas Aufgeschlosseneren fragen: „Wenn (schon wieder) etwas Neues unterrichtet werden soll, was soll denn dann im Lehrplan gestrichen werden?“ Auf die zweite Frage wird hier nicht eingegangen. Das Ziel dieses Aufsatzes ist es, in diskrete Mathematik einzuführen, Interesse an diesem Fachgebiet zu wecken und dazu anzuregen, dieses auch im Schulunterricht (ein wenig) zu berücksichtigen. Die Schüler und Schülerinnen werden dafür dankbar sein – eine Erfahrung, die in vielen Unterrichtsreihen gemacht wurde. Y1 - 2012 VL - 58 IS - 2 SP - 4 EP - 17 ER - TY - JOUR A1 - Hoang, Nam-Dung A1 - Koch, Thorsten T1 - Steiner tree packing revisited JF - Mathematical Methods of Operations Research N2 - The Steiner tree packing problem (STPP) in graphs is a long studied problem in combinatorial optimization. In contrast to many other problems, where there have been tremendous advances in practical problem solving, STPP remains very difficult. Most heuristics schemes are ineffective and even finding feasible solutions is already NP-hard. What makes this problem special is that in order to reach the overall optimal solution non-optimal solutions to the underlying NP-hard Steiner tree problems must be used. Any non-global approach to the STPP is likely to fail. Integer programming is currently the best approach for computing optimal solutions. In this paper we review some “classical” STPP instances which model the underlying real world application only in a reduced form. Through improved modelling, including some new cutting planes, and by emplyoing recent advances in solver technology we are for the first time able to solve those instances in the original 3D grid graphs to optimimality. Y1 - 2012 U6 - https://doi.org/10.1007/s00186-012-0391-8 VL - 76 IS - 1 SP - 95 EP - 123 ER - TY - JOUR A1 - Berthold, Timo A1 - Gleixner, Ambros T1 - Undercover: a primal MINLP heuristic exploring a largest sub-MIP JF - Mathematical Programming N2 - We present Undercover, a primal heuristic for nonconvex mixed-integer nonlinear programming (MINLP) that explores a mixed-integer linear subproblem (sub-MIP) of a given MINLP. We solve a vertex covering problem to identify a minimal set of variables that need to be fixed in order to linearize each constraint, a so-called cover. Subsequently, these variables are fixed to values obtained from a reference point, e.g., an optimal solution of a linear relaxation. We apply domain propagation and conflict analysis to try to avoid infeasibilities and learn from them, respectively. Each feasible solution of the sub-MIP corresponds to a feasible solution of the original problem. We present computational results on a test set of mixed-integer quadratically constrained programs (MIQCPs) and general MINLPs from MINLPLib. It turns out that the majority of these instances allow for small covers. Although general in nature, the heuristic appears most promising for MIQCPs, and complements nicely with existing root node heuristics in different state-of-the-art solvers. Y1 - 2014 U6 - https://doi.org/10.1007/s10107-013-0635-2 VL - 144 IS - 1-2 SP - 315 EP - 346 ER - TY - JOUR A1 - Heinz, Stefan A1 - Schlechte, Thomas A1 - Stephan, Rüdiger A1 - Winkler, Michael T1 - Solving steel mill slab design problems JF - Constraints N2 - The steel mill slab design problem from the CSPLIB is a combinatorial optimization problem motivated by an application of the steel industry. It has been widely studied in the constraint programming community. Several methods were proposed to solve this problem. A steel mill slab library was created which contains 380 instances. A closely related binpacking problem called the multiple knapsack problem with color constraints, originated from the same industrial problem, was discussed in the integer programming community. In particular, a simple integer program for this problem has been given by Forrest et al. (INFORMS J Comput 18:129–134, 2006). The aim of this paper is to bring these different studies together. Moreover, we adapt the model of Forrest et al. (INFORMS J Comput 18:129–134, 2006) for the steel mill slab design problem. Using this model and a state-of-the-art integer program solver all instances of the steel mill slab library can be solved efficiently to optimality. We improved, thereby, the solution values of 76 instances compared to previous results (Schaus et al., Constraints 16:125–147, 2010). Finally, we consider a recently introduced variant of the steel mill slab design problem, where within all solutions which minimize the leftover one is interested in a solution which requires a minimum number of slabs. For that variant we introduce two approaches and solve all instances of the steel mill slab library with this slightly changed objective function to optimality. Y1 - 2012 U6 - https://doi.org/10.1007/s10601-011-9113-8 VL - 17 IS - 1 SP - 39 EP - 50 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - State Trajectory Compression in Optimal Control JF - PAMM N2 - In optimal control problems with nonlinear time-dependent 3D PDEs, the computation of the reduced gradient by adjoint methods requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. Since the state enters into the adjoint equation, the storage of a 4D discretization is necessary. We propose a lossy compression algorithm using a cheap predictor for the state data, with additional entropy coding of prediction errors. Analytical and numerical results indicate that compression factors around 30 can be obtained without exceeding the FE discretization error. Y1 - 2010 U6 - https://doi.org/10.1002/pamm.201010282 VL - 10 IS - 1 SP - 579 EP - 580 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Friedow, Isabel A1 - Karbstein, Marika T1 - Optimierung des Linienplans 2010 in Potsdam JF - Der Nahverkehr Y1 - 2012 VL - 30 IS - 4 SP - 34 EP - 39 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Geißler, Björn A1 - Gollmer, Ralf A1 - Hayn, Christine A1 - Henrion, René A1 - Hiller, Benjamin A1 - Humpola, Jesco A1 - Koch, Thorsten A1 - Lehmann, Thomas A1 - Martin, Alexander A1 - Mirkov, Radoslava A1 - Morsi, Antonio A1 - Römisch, Werner A1 - Rövekamp, Jessica A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schultz, Rüdiger A1 - Schwarz, Robert A1 - Schweiger, Jonas A1 - Stangl, Claudia A1 - Steinbach, Marc A1 - Willert, Bernhard T1 - Mathematical optimization for challenging network planning problems in unbundled liberalized gas markets JF - Energy Systems N2 - The recently imposed new gas market liberalization rules in Germany lead to a change of business of gas network operators. While previously network operator and gas vendor were united, they were forced to split up into independent companies. The network has to be open to any other gas trader at the same conditions, and free network capacities have to be identified and publicly offered in a non-discriminatory way. We discuss how these changing paradigms lead to new and challenging mathematical optimization problems. This includes the validation of nominations, that asks for the decision if the network’s capacity is sufficient to transport a specific amount of flow, the verification of booked capacities and the detection of available freely allocable capacities, and the topological extension of the network with new pipelines or compressors in order to increase its capacity. In order to solve each of these problems and to provide meaningful results for the practice, a mixture of different mathematical aspects have to be addressed, such as combinatorics, stochasticity, uncertainty, and nonlinearity. Currently, no numerical solver is available that can deal with such blended problems out-of-the-box. The main goal of our research is to develop such a solver, that moreover is able to solve instances of realistic size. In this article, we describe the main ingredients of our prototypical software implementations. Y1 - 2013 U6 - https://doi.org/10.1007/s12667-013-0099-8 VL - 5 IS - 3 SP - 449 EP - 473 PB - Springer Berlin Heidelberg CY - Berlin ER - TY - JOUR A1 - Shan, Min A1 - Carlson, Kathryn E. A1 - Bujotzek, Alexander A1 - Wellner, Anja A1 - Gust, Ronald A1 - Weber, Marcus A1 - Katzenellenbogen, John A. A1 - Haag, Rainer T1 - Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor JF - ACS Chem. Biol. Y1 - 2013 VL - 8 IS - 4 SP - 707 EP - 715 ER - TY - JOUR A1 - Weber, Marcus T1 - Adaptive Spectral Clustering in Molecular Simulation. In: Studies in Classification, Data Analysis, and Knowledge Organization JF - XIV: Classification and Data Mining, A. Giusti, G. Ritter, M. Vichi (Eds.), Springer Series Y1 - 2013 SP - 147 EP - 157 ER - TY - JOUR A1 - Shan, Min A1 - Bujotzek, Alexander A1 - Abendroth, Frank A1 - Seitz, Oliver A1 - Weber, Marcus A1 - Haag, Rainer T1 - Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding JF - ChemBioChem, 12(17) Y1 - 2011 U6 - https://doi.org/10.1002/cbic.201100529 SP - 2587 EP - 2598 ER - TY - JOUR A1 - Günther, Andreas A1 - Lamecker, Hans A1 - Weiser, Martin T1 - Flexible Shape Matching with Finite Element Based LDDMM JF - International Journal of Computer Vision N2 - We consider Large Deformation Diffeomorphic Metric Mapping of general $m$-currents. After stating an optimization algorithm in the function space of admissable morph generating velocity fields, two innovative aspects in this framework are presented and numerically investigated: First, we spatially discretize the velocity field with conforming adaptive finite elements and discuss advantages of this new approach. Second, we directly compute the temporal evolution of discrete $m$-current attributes. Y1 - 2013 U6 - https://doi.org/10.1007/s11263-012-0599-3 VL - 105 IS - 2 SP - 128 EP - 143 ER - TY - JOUR A1 - Weiser, Martin T1 - On goal-oriented adaptivity for elliptic optimal control problems JF - Opt. Meth. Softw. N2 - The paper proposes goal-oriented error estimation and mesh refinement for optimal control problems with elliptic PDE constraints using the value of the reduced cost functional as quantity of interest. Error representation, hierarchical error estimators, and greedy-style error indicators are derived and compared to their counterparts when using the all-at-once cost functional as quantity of interest. Finally, the efficiency of the error estimator and generated meshes are demonstrated on numerical examples. Y1 - 2013 VL - 28 IS - 13 SP - 969 EP - 992 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Schiela, Anton A1 - Weiser, Martin T1 - Mathematical Cancer Therapy Planning in Deep Regional Hyperthermia JF - Acta Numerica N2 - This paper surveys the required mathematics for a typical challenging problem from computational medicine, the cancer therapy planning in deep regional hyperthermia. In the course of many years of close cooperation with clinics, the medical problem gave rise to quite a number of subtle mathematical problems, part of which had been unsolved when the common project started. Efficiency of numerical algorithms, i.e. computational speed and monitored reliability, play a decisive role for the medical treatment. Off-the-shelf software had turned out to be not sufficient to meet the requirements of medicine. Rather, new mathematical theory as well as new numerical algorithms had to be developed. In order to make our algorithms useful in the clinical environment, new visualization software, a virtual lab, including 3D geometry processing of individual virtual patients had to be designed and implemented. Moreover, before the problems could be attacked by numerical algorithms, careful mathematical modelling had to be done. Finally, parameter identification and constrained optimization for the PDEs had to be newly analyzed and realized over the individual patient's geometry. Our new techniques had an impact on the specificity of the individual patients' treatment and on the construction of an improved hyperthermia applicator. Y1 - 2012 VL - 21 SP - 307 EP - 378 ER - TY - JOUR A1 - Anco, Stephen A1 - Mohiuddin, Mohammad A1 - Wolf, Thomas T1 - Traveling waves and conservation laws for complex mKdV-type equations Y1 - 2012 U6 - https://doi.org/10.1016/j.amc.2012.06.061 VL - 219 IS - 2 SP - 679 EP - 698 ER - TY - JOUR A1 - Anco, Stephen A1 - Ali, Sajid A1 - Wolf, Thomas T1 - Exact Solutions of Nonlinear Partial Differential Equations by the Method of Group Foliation Reduction JF - SIGMA 7 N2 - A novel symmetry method for finding exact solutions to nonlinear PDEs is illustrated by applying it to a semilinear reaction-diffusion equation in multi-dimensions. The method uses a separation ansatz to solve an equivalent first-order group foliation system whose independent and dependent variables respectively consist of the invariants and differential invariants of a given one-dimensional group of point symmetries for the reaction-diffusion equation. With this group-foliation reduction method, solutions of the reaction-diffusion equation are obtained in an explicit form, including group-invariant similarity solutions and travelling-wave solutions, as well as dynamically interesting solutions that are not invariant under any of the point symmetries admitted by this equation. Y1 - 2011 U6 - https://doi.org/10.3842/SIGMA.2011.066 ER - TY - JOUR A1 - Wolf, Thomas A1 - Efimovskaya, Olga T1 - On Integrability of the Kontsevich Non-Abelian ODE System JF - Letters in Mathematical Physics Y1 - 2012 U6 - https://doi.org/10.1007/s11005-011-0527-4 VL - 100 IS - 2 SP - 161 EP - 170 ER - TY - JOUR A1 - Anco, Stephen A1 - Ali, Sajid A1 - Wolf, Thomas T1 - Symmetry analysis and exact solutions of semilinear heat flow in multi-dimensions JF - Journal of Mathematical Analysis and Applications Y1 - 2011 U6 - https://doi.org/10.1016/j.jmaa.2011.01.073 VL - 379 IS - 2 SP - 748 EP - 763 ER - TY - JOUR A1 - Wolf, Thomas T1 - A Dynamical Systems Approach for Static Evaluation in Go JF - Computational Intelligence and AI in Games, IEEE Transactions on N2 - In the paper, arguments are given as to why the concept of static evaluation has the potential to be a useful extension to Monte Carlo tree search. A new concept of modeling static evaluation through a dynamical system is introduced and strengths and weaknesses are discussed. The general suitability of this approach is demonstrated. Y1 - 2011 U6 - https://doi.org/10.1109/TCIAIG.2011.2141669 VL - 3 IS - 2 SP - 129 EP - 141 ER - TY - JOUR A1 - Hussin, V. A1 - Kiselev, A. V. A1 - Krutov, A.O. A1 - Wolf, Thomas T1 - N=2 Supersymmetric a=4 - Korteweg-de Vries hierarchy derived via Gardner's deformation of Kaup-Bousinesq equation JF - Journal of Mathematical Physics Y1 - 2010 U6 - https://doi.org/10.1063/1.3447731 VL - 51 ER - TY - JOUR A1 - Wolf, Thomas T1 - Positions in the Game of Go as Complex Systems JF - Proceedings of 2009 IEEE Toronto International Conference (TIC-STH 2009) - Science and Technology for Humanity Y1 - 2009 SN - 978-1-4244-3878-5 ER - TY - JOUR A1 - Neun, Winfried A1 - Sturm, Thomas A1 - Vigerske, Stefan T1 - Supporting Global Numerical Optimization of Rational Functions by Generic Symbolic Convexity Tests JF - Computer Algebra in Scientific Computing Y1 - 2010 SN - 978-3-642-15273-3 VL - LNCS 6244 SP - 205 EP - 219 ER - TY - JOUR A1 - Tsarev, Sergey A1 - Wolf, Thomas T1 - Hyperdeterminants as integrable discrete systems JF - Journal of Physics A: Mathematical and Theoretical Y1 - 2009 U6 - https://doi.org//10.1088/1751-8113/42/45/454023 VL - 42 ER - TY - JOUR A1 - Scharkoi, Olga A1 - Esslinger, Susanne A1 - Becker, Roland A1 - Weber, Marcus A1 - Nehls, Irene T1 - Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane JF - Molecular Simulation Y1 - 2014 U6 - https://doi.org/10.1080/08927022.2014.898845 ER - TY - JOUR A1 - Lubkoll, Lars A1 - Schiela, Anton A1 - Weiser, Martin T1 - An optimal control problem in polyconvex hyperelasticity JF - SIAM J. Control Opt. N2 - We consider a shape implant design problem that arises in the context of facial surgery. We introduce a reformulation as an optimal control problem, where the control acts as a boundary force. The state is modelled as a minimizer of a polyconvex hyperelastic energy functional. We show existence of optimal solutions and derive - on a formal level - first order optimality conditions. Finally, preliminary numerical results are presented. Y1 - 2014 U6 - https://doi.org/10.1137/120876629 VL - 52 IS - 3 SP - 1403 EP - 1422 ER - TY - JOUR A1 - Scharkoi, O. A1 - Esslinger, Susanne A1 - Becker, Roland A1 - Weber, Marcus A1 - Nehls, Irene T1 - Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the stereoisomerism of hydroxylated metabolites JF - Organohalogen Compounds Y1 - 2011 VL - 73 SP - 730 EP - 733 ER - TY - JOUR A1 - Durmaz, Vedat A1 - Schmidt, Sebastian A1 - Sabri, Peggy A1 - Piechotta, Christian A1 - Weber, Marcus T1 - A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens JF - Journal of Chemical Information and Modeling Y1 - 2013 VL - 53 IS - 10 SP - 2681 EP - 2688 ER - TY - JOUR A1 - Tyagi, Rahul A1 - Malhotra, Shashwat A1 - Thünemann, Andreas F. A1 - Sedighi, Amir A1 - Weber, Marcus A1 - Schäfer, Andreas A1 - Haag, Rainer T1 - Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles JF - J. Phys. Chem. C Y1 - 2013 VL - 117 IS - 23 SP - 12307 EP - 12317 ER - TY - JOUR A1 - Weber, Marcus A1 - Zoschke, Christian A1 - Sedighi, Amir A1 - Fleige, Emanuel A1 - Haag, Rainer A1 - Schäfer-Korting, Monika T1 - Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters JF - J Nanomed Nanotechnol Y1 - 2014 U6 - https://doi.org/10.4172/2157-7439.1000234 VL - 5 IS - 5 SP - 234 ER - TY - JOUR A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - De Pol-Holz, Ricardo A1 - López Correa, Matthias A1 - Forster, Nina A1 - Flögel, Sascha A1 - Hebbeln, Dierk A1 - Freiwald, André T1 - Aggradation and carbonate accumulation of Holocene Norwegian cold-water coral reefs JF - Sedimentology Y1 - 2015 U6 - https://doi.org/10.1111/sed.12206 VL - 62 IS - 7 SP - 1873 EP - 1898 PB - Wiley ER - TY - JOUR A1 - Cournia, Zoe A1 - Allen, Toby W. A1 - Andricioaei, Ioan A1 - Antonny, Bruno A1 - Baum, Daniel A1 - Brannigan, Grace A1 - Buchete, Nicolae-Viorel A1 - Deckman, Jason T. A1 - Delemotte, Lucie A1 - del Val, Coral A1 - Friedman, Ran A1 - Gkeka, Paraskevi A1 - Hege, Hans-Christian A1 - Hénin, Jérôme A1 - Kasimova, Marina A. A1 - Kolocouris, Antonios A1 - Klein, Michael L. A1 - Khalid, Syma A1 - Lemieux, Joanne A1 - Lindow, Norbert A1 - Roy, Mahua A1 - Selent, Jana A1 - Tarek, Mounir A1 - Tofoleanu, Florentina A1 - Vanni, Stefano A1 - Urban, Sinisa A1 - Wales, David J. A1 - Smith, Jeremy C. A1 - Bondar, Ana-Nicoleta T1 - Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory JF - Journal of Membrane Biology Y1 - 2015 U6 - https://doi.org/10.1007/s00232-015-9802-0 VL - 248 IS - 4 SP - 611 EP - 640 ER - TY - JOUR A1 - Karbstein, Marika T1 - Ohne Umsteigen ans Ziel JF - OR News N2 - Die Anforderungen an das Liniennetz eines Verkehrsunternehmens sind vielfältig: kurze Fahrzeiten, viele Direktverbindungen und geringe Kosten. Mathematische Optimierungsmethoden können die Planung von Liniennetzen unterstützen und beste Kompromisse bzgl. aller Anforderungen berechnen. Y1 - 2014 VL - 52 SP - 12 EP - 14 ER - TY - JOUR A1 - Mücklich, Frank A1 - Webel, Johannes A1 - Aboulfadl, Hisham A1 - Lindow, Norbert A1 - Hege, Hans-Christian T1 - Correlative Tomography – Extraction of Reliable Information with Adequate Resolution from mm Scale Down to Sub-nm Scale JF - Microsc. Microanal. Y1 - 2014 U6 - https://doi.org/10.1017/S1431927614005911 VL - 20 IS - Suppl 3 SP - 838 EP - 839 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Heismann, Olga T1 - The hypergraph assignment problem JF - Discrete Optimization Y1 - 2015 U6 - https://doi.org/10.1016/j.disopt.2014.11.002 VL - 15 SP - 15 EP - 25 ER - TY - JOUR A1 - Beckenbach, Isabel A1 - Borndörfer, Ralf A1 - Knoben, Loes A1 - Kretz, David A1 - Uetz, Marc J. T1 - The S-Bahn Challenge in Berlin JF - OR News Y1 - 2015 UR - https://gor.uni-paderborn.de/index.php?id=362 IS - 53 SP - 10 EP - 14 ER - TY - JOUR A1 - Hoppmann, Heide T1 - Linienplanung und Minimale Konfigurationen JF - OR News Y1 - 2015 VL - 55 SP - 22 EP - 23 ER - TY - JOUR A1 - Poulikakos, Lisa A1 - Gutsche, Philipp A1 - McPeak, Kevin A1 - Burger, Sven A1 - Niegemann, Jens A1 - Hafner, Christian A1 - Norris, David T1 - The Optical Chirality Flux as a Useful Far-Field Probe of Chiral Near Fields JF - ACS Photonics Y1 - 2016 U6 - https://doi.org/10.1021/acsphotonics.6b00201 VL - 3 SP - 1619 ER - TY - JOUR A1 - Blanco, Marco A1 - Borndörfer, Ralf A1 - Brückner, Michael A1 - Hoang, Nam-Dung A1 - Schlechte, Thomas T1 - On the Path Avoiding Forbidden Pairs Polytope JF - Electronic Notes in Discrete Mathematics N2 - Given a directed, acyclic graph, a source and a sink node, and a set of forbidden pairs of arcs, the path avoiding forbidden pairs (PAFP) problem is to find a path that connects the source and sink nodes and contains at most one arc from each forbidden pair. The general version of the problem is NP-hard, but it becomes polynomially solvable for certain topological configurations of the pairs. We present the first polyhedral study of the PAFP problem. We introduce a new family of valid inequalities for the PAFP polytope and show that they are sufficient to provide a complete linear description in the special case where the forbidden pairs satisfy a disjointness property. Furthermore, we show that the number of facets of the PAFP polytope is exponential in the size of the graph, even for the case of a single forbidden pair. Y1 - 2015 U6 - https://doi.org/10.1016/j.endm.2015.07.057 VL - 50 SP - 343 EP - 348 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Waas, Kerstin A1 - Weider, Steffen T1 - Integrated Optimization of Rolling Stock Rotations for Intercity Railways JF - Transportation Science N2 - This paper proposes a highly integrated solution approach for rolling stock planning problems in the context of long distance passenger traffic between cities. The main contributions are a generic hypergraph-based mixed-integer programming model for the considered rolling stock rotation problem and an integrated algorithm for its solution. The newly developed algorithm is able to handle a large spectrum of industrial railway requirements, such as vehicle composition, maintenance constraints, infrastructure capacities, and regularity aspects. We show that our approach has the power to produce rolling stock rotations that can be implemented in practice. In this way, the rolling stock rotations at the largest German long distance operator Deutsche Bahn Fernverkehr AG could be optimized by an automated system utilizing advanced mathematical programming techniques. Y1 - 2016 U6 - https://doi.org/10.1287/trsc.2015.0633 VL - 50 IS - 3 SP - 863 EP - 877 ER - TY - JOUR A1 - Färber, Claudia A1 - Titschack, Jürgen A1 - Schönberg, Christine H. L. A1 - Ehrig, Karsten A1 - Boos, Karin A1 - Baum, Daniel A1 - Illerhaus, Bernd A1 - Asgaard, Ulla A1 - Bromley, Richard G. A1 - Freiwald, André A1 - Wisshak, Max T1 - Long-term macrobioerosion in the Mediterranean Sea assessed by micro-computed tomography JF - Biogeosciences N2 - Biological erosion is a key process for the recycling of carbonate and the formation of calcareous sediments in the oceans. Experimental studies showed that bioerosion is subject to distinct temporal variability, but previous long-term studies were restricted to tropical waters. Here, we present results from a 14-year bioerosion experiment that was carried out along the rocky limestone coast of the island of Rhodes, Greece, in the Eastern Mediterranean Sea, in order to monitor the pace at which bioerosion affects carbonate substrate and the sequence of colonisation by bioeroding organisms. Internal macrobioerosion was visualised and quantified by micro-computed tomography and computer-algorithm-based segmentation procedures. Analysis of internal macrobioerosion traces revealed a dominance of bioeroding sponges producing eight types of characteristic Entobia cavity networks, which were matched to five different clionaid sponges by spicule identification in extracted tissue. The morphology of the entobians strongly varied depending on the species of the producing sponge, its ontogenetic stage, available space, and competition by other bioeroders. An early community developed during the first 5 years of exposure with initially very low macrobioerosion rates and was followed by an intermediate stage when sponges formed large and more diverse entobians and bioerosion rates increased. After 14 years, 30 % of the block volumes were occupied by boring sponges, yielding maximum bioerosion rates of 900 g m^−2 yr^−1. A high spatial variability in macrobioerosion prohibited clear conclusions about the onset of macrobioerosion equilibrium conditions. This highlights the necessity of even longer experimental exposures and higher replication at various factor levels in order to better understand and quantify temporal patterns of macrobioerosion in marine carbonate environments. Y1 - 2016 U6 - https://doi.org/10.5194/bg-13-3461-2016 VL - 13 IS - 11 SP - 3461 EP - 3474 CY - http://www.biogeosciences.net/13/3461/2016/ ER - TY - JOUR A1 - Gutsche, Philipp A1 - Poulikakos, Lisa A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Schmidt, Frank T1 - Time-harmonic optical chirality in inhomogeneous space JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2209551 VL - 9756 SP - 97560X ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Pumberger, Matthias A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Influence of pelvic tilt on functional acetabular orientation JF - Technology and Health Care Y1 - 2016 U6 - https://doi.org/10.3233/THC-161281 VL - 25 IS - 3 SP - 557 EP - 565 PB - IOS Press ER - TY - JOUR A1 - Lemanis, Robert A1 - Korn, Dieter A1 - Zachow, Stefan A1 - Rybacki, Erik A1 - Hoffmann, René T1 - The Evolution and Development of Cephalopod Chambers and Their Shape JF - PLOS ONE N2 - The Ammonoidea is a group of extinct cephalopods ideal to study evolution through deep time. The evolution of the planispiral shell and complexly folded septa in ammonoids has been thought to have increased the functional surface area of the chambers permitting enhanced metabolic functions such as: chamber emptying, rate of mineralization and increased growth rates throughout ontogeny. Using nano-computed tomography and synchrotron radiation based micro-computed tomography, we present the first study of ontogenetic changes in surface area to volume ratios in the phragmocone chambers of several phylogenetically distant ammonoids and extant cephalopods. Contrary to the initial hypothesis, ammonoids do not possess a persistently high relative chamber surface area. Instead, the functional surface area of the chambers is higher in earliest ontogeny when compared to Spirula spirula. The higher the functional surface area the quicker the potential emptying rate of the chamber; quicker chamber emptying rates would theoretically permit faster growth. This is supported by the persistently higher siphuncular surface area to chamber volume ratio we collected for the ammonite Amauroceras sp. compared to either S. spirula or nautilids. We demonstrate that the curvature of the surface of the chamber increases with greater septal complexity increasing the potential refilling rates. We further show a unique relationship between ammonoid chamber shape and size that does not exist in S. spirula or nautilids. This view of chamber function also has implications for the evolution of the internal shell of coleoids, relating this event to the decoupling of soft-body growth and shell growth. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0151404 VL - 11 IS - 3 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Weber, Marcus A1 - Schütte, Christof T1 - Finding dominant structures of nonreversible Markov processes JF - Multiscale Modeling and Simulation Y1 - 2016 U6 - https://doi.org/10.1137/15M1032272 VL - 14 IS - 4 SP - 1319 EP - 1340 ER - TY - JOUR A1 - Humpola, Jesco A1 - Joormann, Imke A1 - Oucherif, Djamal A1 - Pfetsch, Marc A1 - Schewe, Lars A1 - Schmidt, Martin A1 - Schwarz, Robert T1 - GasLib - A Library of Gas Network Instances JF - Optimization Online N2 - The development of mathematical simulation and optimization models and algorithms for solving gas transport problems is an active field of research. In order to test and compare these models and algorithms, gas network instances together with demand data are needed. The goal of GasLib is to provide a set of publicly available gas network instances that can be used by researchers in the field of gas transport. The advantages are that researchers save time by using these instances and that different models and algorithms can be compared on the same specified test sets. The library instances are encoded in an XML format. In this paper, we explain this format and present the instances that are available in the library. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57950 ER - TY - JOUR A1 - Fodor, Bálint A1 - Kozma, Peter A1 - Burger, Sven A1 - Fried, Miklos A1 - Petrik, Peter T1 - Effective medium approximation of ellipsometric response from random surface roughness simulated by finite-element method JF - Thin Solid Films Y1 - 2016 U6 - https://doi.org/10.1016/j.tsf.2016.01.054 VL - 617 SP - 20 ER - TY - JOUR A1 - Wohlfeil, Benjamin A1 - Rademacher, Georg A1 - Stamatiadis, Christos A1 - Voigt, Karsten A1 - Zimmermann, Lars A1 - Petermann, Klaus T1 - A Two Dimensional Fiber Grating Coupler on SOI for Mode Division Multiplexing JF - IEEE Photon. Technol. Lett. Y1 - 2016 U6 - https://doi.org/10.1109/LPT.2016.2514712 VL - 28 SP - 1241 ER - TY - JOUR A1 - Berthold, Timo A1 - Hendel, Gregor T1 - Shift-and-Propagate JF - Journal of Heuristics N2 - In recent years, there has been a growing interest in the design of general purpose primal heuristics for use inside complete mixed integer programming solvers. Many of these heuristics rely on an optimal LP solution, which may take a significant amount of time to find. In this paper, we address this issue by introducing a pre-root primal heuristic that does not require a previously found LP solution. This heuristic, named Shift-and-Propagate , applies domain propagation techniques to quickly drive a variable assignment towards feasibility. Computational experiments indicate that this heuristic is a powerful supplement to existing rounding and propagation heuristics. Y1 - 2014 U6 - https://doi.org/10.1007/s10732-014-9271-0 VL - 21 IS - 1 SP - 73 EP - 106 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Fügenschuh, Armin A1 - Klug, Torsten A1 - Schang, Thilo A1 - Schlechte, Thomas A1 - Schülldorf, Hanno T1 - The Freight Train Routing Problem for Congested Railway Networks with Mixed Traffic JF - Transportation Science N2 - We consider the following freight train routing problem (FTRP). Given is a transportation network with fixed routes for passenger trains and a set of freight trains (requests), each defined by an origin and destination station pair. The objective is to calculate a feasible route for each freight train such that the sum of all expected delays and all running times is minimal. Previous research concentrated on microscopic train routings for junctions or inside major stations. Only recently approaches were developed to tackle larger corridors or even networks. We investigate the routing problem from a strategic perspective, calculating the routes in a macroscopic transportation network of Deutsche Bahn AG. In this context, macroscopic refers to an aggregation of complex and large real-world structures into fewer network elements. Moreover, the departure and arrival times of freight trains are approximated. The problem has a strategic character since it asks only for a coarse routing through the network without the precise timings. We provide a mixed-integer nonlinear programming (MINLP) formulation for the FTRP, which is a multicommodity flow model on a time-expanded graph with additional routing constraints. The model’s nonlinearities originate from an algebraic approximation of the delays of the trains on the arcs of the network by capacity restraint functions. The MINLP is reduced to a mixed-integer linear model (MILP) by piecewise linear approximation. The latter is solved by a state-of-the art MILP solver for various real-world test instances. Y1 - 2016 U6 - https://doi.org/10.1287/trsc.2015.0656 VL - 50 IS - 2 SP - 408 EP - 423 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Barth, Carlo A1 - Pomplun, Jan A1 - Burger, Sven A1 - Becker, Christiane A1 - Schmidt, Frank T1 - Reconstruction of photonic crystal geometries using a reduced basis method for nonlinear outputs JF - Proc. SPIE N2 - Maxwell solvers based on the hp-adaptive finite element method allow for accurate geometrical modeling and high numerical accuracy. These features are indispensable for the optimization of optical properties or reconstruction of parameters through inverse processes. High computational complexity prohibits the evaluation of the solution for many parameters. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem allowing to compute solutions for a parameter configuration orders of magnitude faster. The RBM allows to evaluate linear and nonlinear outputs of interest like Fourier transform or the enhancement of the electromagnetic field in milliseconds. We apply the RBM to compute light-scattering off two dimensional photonic crystal structures made of silicon and reconstruct geometrical parameters. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58187 VL - 9756 SP - 97561R ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Model order reduction for the time-harmonic Maxwell equation applied to complex nanostructures JF - Proc. SPIE N2 - Fields such as optical metrology and computational lithography require fast and efficient methods for solving the time-harmonic Maxwell's equation. Highly accurate geometrical modelling and numerical accuracy at low computational costs are a prerequisite for any simulation study of complex nano-structured photonic devices. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem based on the hp-adaptive finite element solver JCMsuite capable of handling geometric and non-geometric parameter dependencies allowing for online evaluations in milliseconds. We apply the RBM to compute light-scattering at optical wavelengths of periodic arrays of fin field-effect transistors (FinFETs) where geometrical properties such as the width and height of the fin and gate can vary in a large range. Y1 - 2016 U6 - https://doi.org/10.1117/12.2212367 VL - 9742 SP - 97420M ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Pomplun, Jan A1 - Burger, Sven A1 - Schmidt, Frank T1 - Reduced basis method for electromagnetic scattering problem: a case study for FinFETs JF - Optical and Quantum Electronics N2 - Optical 3D simulations in many-query and real-time contexts require new solution strategies. We study an adaptive, error controlled reduced basis method for solving parametrized time-harmonic optical scattering problems. Application fields are, among others, design and optimization problems of nano-optical devices as well as inverse problems for parameter reconstructions occurring e. g. in optical metrology. The reduced basis method pre- sented here relies on a finite element modeling of the scattering problem with parametrization of materials, geometries and sources. Y1 - 2016 U6 - https://doi.org/10.1007/s11082-016-0530-1 VL - 48 SP - 250 ER - TY - JOUR A1 - Knight, James C A1 - Tully, Philip J A1 - Kaplan, Bernhard A1 - Lansner, Anders A1 - Furber, Steve T1 - Large-scale simulations of plastic neural networks on neuromorphic hardware JF - Frontiers in Neuroanatomy N2 - SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Rather than using bespoke analog or digital hardware, the basic computational unit of a SpiNNaker system is a general-purpose ARM processor, allowing it to be programmed to simulate a wide variety of neuron and synapse models. This flexibility is particularly valuable in the study of biological plasticity phenomena. A recently proposed learning rule based on the Bayesian Confidence Propagation Neural Network (BCPNN) paradigm offers a generic framework for modeling the interaction of different plasticity mechanisms using spiking neurons. However, it can be computationally expensive to simulate large networks with BCPNN learning since it requires multiple state variables for each synapse, each of which needs to be updated every simulation time-step. We discuss the trade-offs in efficiency and accuracy involved in developing an event-based BCPNN implementation for SpiNNaker based on an analytical solution to the BCPNN equations, and detail the steps taken to fit this within the limited computational and memory resources of the SpiNNaker architecture. We demonstrate this learning rule by learning temporal sequences of neural activity within a recurrent attractor network which we simulate at scales of up to 2.0 × 10^4 neurons and 5.1 × 10^7 plastic synapses: the largest plastic neural network ever to be simulated on neuromorphic hardware. We also run a comparable simulation on a Cray XC-30 supercomputer system and find that, if it is to match the run-time of our SpiNNaker simulation, the super computer system uses approximately 45× more power. This suggests that cheaper, more power efficient neuromorphic systems are becoming useful discovery tools in the study of plasticity in large-scale brain models. Y1 - 2016 U6 - https://doi.org/10.3389/fnana.2016.00037 VL - 10:37 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Sagnol, Guillaume A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Optimal duty rostering for toll enforcement inspectors JF - Annals of Operations Research N2 - We present the problem of planning mobile tours of inspectors on German motorways to enforce the payment of the toll for heavy good trucks. This is a special type of vehicle routing problem with the objective to conduct as good inspections as possible on the complete network. In addition, we developed a personalized crew rostering model, to schedule the crews of the tours. The planning of daily tours and the rostering are combined in a novel integrated approach and formulated as a complex and large scale Integer Program. The main focus of this paper extends our previous publications on how different requirements for the rostering can be modeled in detail. The second focus is on a bi-criteria analysis of the planning problem to find the balance between the control quality and the roster acceptance. Finally, computational results on real-world instances show the practicability of our method and how different input parameters influence the problem complexity. Y1 - 2016 U6 - https://doi.org/10.1007/s10479-016-2152-1 VL - 252(2) SP - 383 EP - 406 PB - Springer US ET - 252 ER - TY - JOUR A1 - Kasten, Jens A1 - Reininghaus, Jan A1 - Hotz, Ingrid A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Daviller, Guillaume A1 - Morzyński, Marek T1 - Acceleration feature points of unsteady shear flows JF - Archives of Mechanics N2 - A framework is proposed for extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance. The minima of the acceleration magnitude, i.e. a superset of the acceleration zeros, are extracted and discriminated into vortices and saddle points --- based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These features are tracked in time with a robust algorithm for tracking features. Thus a space-time hierarchy of the minima is built and vortex merging events are detected. The acceleration feature extraction strategy is applied to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of pressure field and minima of λ2. Y1 - 2016 VL - 68 IS - 1 SP - 55 EP - 80 ER - TY - JOUR A1 - Lubkoll, Lars A1 - Schiela, Anton A1 - Weiser, Martin T1 - An affine covariant composite step method for optimization with PDEs as equality constraints JF - Optimization Methods and Software N2 - We propose a composite step method, designed for equality constrained optimization with partial differential equations. Focus is laid on the construction of a globalization scheme, which is based on cubic regularization of the objective and an affine covariant damped Newton method for feasibility. We show finite termination of the inner loop and fast local convergence of the algorithm. We discuss preconditioning strategies for the iterative solution of the arising linear systems with projected conjugate gradient. Numerical results are shown for optimal control problems subject to a nonlinear heat equation and subject to nonlinear elastic equations arising from an implant design problem in craniofacial surgery. Y1 - 2017 U6 - https://doi.org/10.1080/10556788.2016.1241783 VL - 32 IS - 5 SP - 1132 EP - 1161 ER - TY - JOUR A1 - Bienefeld, Kaspar A1 - Zautke, Fred A1 - Gupta, Pooja T1 - A novel method for undisturbed long-term observation of the honey bee (Apis mellifera) behaviour – illustrated by the hygienic behaviour towards Varroa infestation JF - Journal of Apicultural Research Y1 - 2016 VL - 54(5) SP - 541 EP - 547 ER - TY - JOUR A1 - Durmaz, Vedat T1 - Markov model-based polymer assembly from force field-parameterized building blocks JF - Journal of Computer-Aided Molecular Design N2 - A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very workintensive and time-consuming. Using the example of polyglycerol, I present a polymer decompostion strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantumchemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers. Y1 - 2015 U6 - https://doi.org/10.1007/s10822-014-9817-0 VL - 29 SP - 225 EP - 232 ER - TY - JOUR A1 - Heye, Katharina A1 - Becker, Dennis A1 - Lütke-Eversloh, Christian A1 - Durmaz, Vedat A1 - Ternes, Thomas A1 - Oetken, Matthias A1 - Oehlmann, Jörg T1 - Effects of carbamazepine and two of its metabolites on the non-biting midge Chironomus riparius in a sediment full life cycle toxicity test JF - Water Research N2 - The antiepileptic drug carbamazepine (CBZ) and its main metabolites carbamazepine-10,11-epoxide (EP-CBZ) and 10,11-dihydro-10,11-dihydroxy-carbamazepine (DiOH-CBZ) were chosen as test substances to assess chronic toxicity on the non-biting midge Chironomus riparius. All three substances were tested in a 40-day sediment full life cycle test (according to OECD 233) in which mortality, emergence, fertility, and clutch size were evaluated. In addition, these parameters were integrated into the population growth rate to reveal population relevant effects. With an LC50 of 0.203 mg/kg (time-weighted mean), the metabolite EP-CBZ was significantly more toxic than the parent substance CBZ (LC50: 1.11 mg/kg). Especially mortality, emergence, and fertility showed to be sensitive parameters under the exposure to CBZ and EP-CBZ. By using classical molecular dynamics (MD) simulations, the binding of CBZ to the ecdysone receptor was investigated as one possible mode of action but showed to be unlikely. The second metabolite DiOH-CBZ did not show any effects within the tested concentration rage (0.171 – 1.22 mg/kg). Even though CBZ was less toxic compared to EP-CBZ, CBZ is found in the environment at much higher concentrations and causes therefore a higher potential risk for sediment dwelling organisms compared to its metabolites. Nevertheless, the current study illustrates the importance of including commonly found metabolites into the risk assessment of parent substances. Y1 - 2016 VL - 98 SP - 19 EP - 27 ER - TY - JOUR A1 - Owhadi, Houman A1 - Scovel, Clint A1 - Sullivan, T. J. T1 - On the Brittleness of Bayesian Inference JF - SIAM Review N2 - With the advent of high-performance computing, Bayesian methods are becoming increasingly popular tools for the quantification of uncertainty throughout science and industry. Since these methods can impact the making of sometimes critical decisions in increasingly complicated contexts, the sensitivity of their posterior conclusions with respect to the underlying models and prior beliefs is a pressing question to which there currently exist positive and negative answers. We report new results suggesting that, although Bayesian methods are robust when the number of possible outcomes is finite or when only a finite number of marginals of the data-generating distribution are unknown, they could be generically brittle when applied to continuous systems (and their discretizations) with finite information on the data-generating distribution. If closeness is defined in terms of the total variation (TV) metric or the matching of a finite system of generalized moments, then (1) two practitioners who use arbitrarily close models and observe the same (possibly arbitrarily large amount of) data may reach opposite conclusions; and (2) any given prior and model can be slightly perturbed to achieve any desired posterior conclusion. The mechanism causing brittleness/robustness suggests that learning and robustness are antagonistic requirements, which raises the possibility of a missing stability condition when using Bayesian inference in a continuous world under finite information. Y1 - 2015 U6 - https://doi.org/10.1137/130938633 VL - 57 IS - 4 SP - 566 EP - 582 ER - TY - JOUR A1 - Jäger, Klaus A1 - Barth, Carlo A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Burger, Sven A1 - Schmidt, Frank A1 - Becker, Christiane T1 - Simulations of sinusoidal nanotextures for coupling light into c-Si thin-film solar cells JF - Opt. Express Y1 - 2016 U6 - https://doi.org/10.1364/OE.24.00A569 VL - 24 SP - A569 ER - TY - JOUR A1 - Ledentsov, Jr., Nikolay A1 - Shchukin, Vitaly A1 - Kropp, Jörg-R. A1 - Burger, Sven A1 - Schmidt, Frank A1 - Ledentsov, Jr., Nikolay T1 - Direct visualization of the in-plane leakage of high-order transverse modes in vertical-cavity surface-emitting lasers mediated by oxide-aperture engineering JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2208909 VL - 9766 SP - 976608 ER - TY - JOUR A1 - Pomplun, Jan A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Gutsche, Philipp A1 - Schmidt, Frank T1 - Method for fast computation of angular light scattering spectra from 2D periodic arrays JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2219666 VL - 9778 SP - 977839 ER - TY - JOUR A1 - Landau, Itamar D. A1 - Egger, Robert A1 - Dercksen, Vincent J. A1 - Oberlaender, Marcel A1 - Sompolinsky, Haim T1 - The Impact of Structural Heterogeneity on Excitation-Inhibition Balance in Cortical Networks JF - Neuron N2 - Models of cortical dynamics often assume a homogeneous connectivity structure. However, we show that heterogeneous input connectivity can prevent the dynamic balance between excitation and inhibition, a hallmark of cortical dynamics, and yield unrealistically sparse and temporally regular firing. Anatomically based estimates of the connectivity of layer 4 (L4) rat barrel cortex and numerical simulations of this circuit indicate that the local network possesses substantial heterogeneity in input connectivity, sufficient to disrupt excitation-inhibition balance. We show that homeostatic plasticity in inhibitory synapses can align the functional connectivity to compensate for structural heterogeneity. Alternatively, spike-frequency adaptation can give rise to a novel state in which local firing rates adjust dynamically so that adaptation currents and synaptic inputs are balanced. This theory is supported by simulations of L4 barrel cortex during spontaneous and stimulus-evoked conditions. Our study shows how synaptic and cellular mechanisms yield fluctuation-driven dynamics despite structural heterogeneity in cortical circuits. Y1 - 2016 U6 - https://doi.org/10.1016/j.neuron.2016.10.027 VL - 92 IS - 5 SP - 1106 EP - 1121 ER - TY - JOUR A1 - Nielsen, Adam T1 - The Monte Carlo Computation Error of Transition Probabilities JF - Statistics & Probability Letters N2 - In many applications one is interested to compute transition probabilities of a Markov chain. This can be achieved by using Monte Carlo methods with local or global sampling points. In this article, we analyze the error by the difference in the $L^2$ norm between the true transition probabilities and the approximation achieved through a Monte Carlo method. We give a formula for the error for Markov chains with locally computed sampling points. Further, in the case of reversible Markov chains, we will deduce a formula for the error when sampling points are computed globally. We will see that in both cases the error itself can be approximated with Monte Carlo methods. As a consequence of the result, we will derive surprising properties of reversible Markov chains. Y1 - 2016 U6 - https://doi.org/10.1016/j.spl.2016.06.011 VL - 118 SP - 163 EP - 170 PB - Elsevier ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika T1 - Passenger routing for periodic timetable optimization BT - Planning and Operations JF - Public Transport N2 - The task of periodic timetabling is to determine trip arrival and departure times in a public transport system such that travel and transfer times are minimized. This paper investigates periodic timetabling models with integrated passenger routing. We show that different routing models can have a huge influence on the quality of the entire system: Whatever metric is applied, the performance ratios of timetables w.r.t. different routing models can be arbitrarily large. Computations on a real-world instance for the city of Wuppertal substantiate the theoretical findings. These results indicate the existence of untapped optimization potentials that can be used to improve the efficiency of public transport systems by integrating passenger routing. Y1 - 2016 U6 - https://doi.org/10.1007/s12469-016-0132-0 PB - Springer-Verlag Berlin Heidelberg ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Cameron--Martin theorems for sequences of Cauchy-distributed random variables JF - arXiv N2 - Given a sequence of Cauchy-distributed random variables defined by a sequence of location parameters and a sequence of scale parameters, we consider another sequence of random variables that is obtained by perturbing the location or scale parameter sequences. Using a result of Kakutani on equivalence of infinite product measures, we provide sufficient conditions for the equivalence of laws of the two sequences. Y1 - 2016 SP - 1608.03784 ER - TY - JOUR A1 - Abass, Aimi A1 - Gutsche, Philipp A1 - Maes, Bjorn A1 - Rockstuhl, Carsten A1 - Martins, Emiliano R T1 - Insights into directional scattering: from coupled dipoles to asymmetric dimer nanoantennas JF - Opt. Express N2 - Strong and directionally specific forward scattering from optical nanoantennas is of utmost importance for various applications in the broader context of photovoltaics and integrated light sources. Here, we outline a simple yet powerful design principle to perceive a nanoantenna that provides directional scattering into a higher index substrate based on the interference of multiple electric dipoles. A structural implementation of the electric dipole distribution is possible using plasmonic nanoparticles with a fairly simple geometry, i.e. two coupled rectangular nanoparticles, forming a dimer, on top of a substrate. The key to achieve directionality is to choose a sufficiently large size for the nanoparticles. This promotes the excitation of vertical electric dipole moments due to the bi-anisotropy of the nanoantenna. In turn, asymmetric scattering is obtained by ensuring the appropriate phase relation between the vertical electric dipole moments. The scattering strength and angular spread for an optimized nanoantenna can be shown to be broadband and robust against changes in the incidence angle. The scattering directionality is maintained even for an array configuration of the dimer. It only requires the preferred scattering direction of the isolated nanoantenna not to be prohibited by interference. Y1 - 2016 U6 - https://doi.org/10.1364/OE.24.019638 VL - 24 IS - 17 SP - 19638 EP - 19650 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Berthold, Timo A1 - Müller, Benjamin A1 - Weltge, Stefan T1 - Three Enhancements for Optimization-Based Bound Tightening JF - Journal of Global Optimization N2 - Optimization-based bound tightening (OBBT) is one of the most effective procedures to reduce variable domains of nonconvex mixed-integer nonlinear programs (MINLPs). At the same time it is one of the most expensive bound tightening procedures, since it solves auxiliary linear programs (LPs)—up to twice the number of variables many. The main goal of this paper is to discuss algorithmic techniques for an efficient implementation of OBBT. Most state-of-the-art MINLP solvers apply some restricted version of OBBT and it seems to be common belief that OBBT is beneficial if only one is able to keep its computational cost under control. To this end, we introduce three techniques to increase the efficiency of OBBT: filtering strategies to reduce the number of solved LPs, ordering heuristics to exploit simplex warm starts, and the generation of Lagrangian variable bounds (LVBs). The propagation of LVBs during tree search is a fast approximation to OBBT without the need to solve auxiliary LPs. We conduct extensive computational experiments on MINLPLib2. Our results indicate that OBBT is most beneficial on hard instances, for which we observe a speedup of 17% to 19% on average. Most importantly, more instances can be solved when using OBBT. Y1 - 2017 U6 - https://doi.org/10.1007/s10898-016-0450-4 VL - 67 IS - 4 SP - 731 EP - 757 ER - TY - JOUR A1 - Reimers, Jeffrey R. A1 - Biczysko, Malgorzata A1 - Bruce, Douglas A1 - Coker, David F. A1 - Frankcombe, Terry J. A1 - Hashimoto, Hideki A1 - Hauer, Jürgen A1 - Jankowiak, Ryszard A1 - Kramer, Tobias A1 - Linnanto, Juha A1 - Mamedov, Fikret A1 - Müh, Frank A1 - Rätsep, Margus A1 - Renger, Thomas A1 - Styring, Stenbjörn A1 - Wan, Jian A1 - Wang, Zhuan A1 - Wang-Otomo, Zheng-Yu A1 - Weng, Yu-Xiang A1 - Yang, Chunhong A1 - Zhang, Jian-Ping A1 - Freiberg, Arvi A1 - Krausz, Elmars T1 - Challenges facing an understanding of the nature of low-energy excited states in photosynthesis JF - BBA Bioenergetics N2 - While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding. Y1 - 2016 U6 - https://doi.org/10.1016/j.bbabio.2016.06.010 VL - 1857 IS - 9 SP - 1627 EP - 1640 ER - TY - JOUR A1 - Dunlop, Jason A1 - Apanaskevich, Dmitry A1 - Lehmann, Jens A1 - Hoffmann, Rene A1 - Fusseis, Florian A1 - Ehlke, Moritz A1 - Zachow, Stefan A1 - Xiao, Xianghui T1 - Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus JF - BMC Evolutionary Biology N2 - Background: Fossil ticks are extremely rare, whereby Ixodes succineus Weidner, 1964 from Eocene (ca. 44-49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). Results: Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil's referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. Conclusions: Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner's amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases. Y1 - 2016 U6 - https://doi.org/10.1186/s12862-016-0777-y VL - 16 IS - 1 ER - TY - JOUR A1 - Soltwisch, Victor A1 - Haase, Anton A1 - Wernecke, Jan A1 - Probst, Jürgen A1 - Schoengen, Max A1 - Burger, Sven A1 - Krumrey, Michael A1 - Scholze, Frank T1 - Correlated diffuse x-ray scattering from periodically nanostructured surfaces JF - Phys. Rev. B Y1 - 2016 U6 - https://doi.org/10.1103/PhysRevB.94.035419 VL - 94 SP - 035419 ER - TY - JOUR A1 - Humpola, Jesco A1 - Serrano, Felipe T1 - Sufficient pruning conditions for MINLP in gas network design JF - EURO Journal on Computational Optimization N2 - One-quarter of Europe’s energy demand is provided by natural gas distributed through a vast pipeline network covering the whole of Europe. At a cost of 1 million Euros per kilometer the extension of the European pipeline network is already a multi-billion Euro business. Therefore, automatic planning tools that support the decision process are desired. We model the topology optimization problem in gas networks by a mixed-integer nonlinear program (MINLP). This gives rise to a so-called active transmission problem, a continuous nonlinear non-convex feasibility problem which emerges from the MINLP model by fixing all integral variables. We offer novel sufficient conditions for proving the infeasibility of this active transmission problem. These conditions can be expressed in the form of a mixed-integer program (MILP), i.e., the infeasibility of a non-convex continuous nonlinear program (NLP) can be certified by solving an MILP. This result provides an efficient pruning procedure in a branch-and-bound algorithm. Our computational results demonstrate a substantial speedup for the necessary computations. Y1 - 2017 U6 - https://doi.org/10.1007/s13675-016-0077-8 VL - 5 IS - 1-2 SP - 239 EP - 261 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Villatoro, José A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Weber, Marcus A1 - Riedel, Jens A1 - Löhmannsröben, Hans-Gerd T1 - IR-MALDI ion mobility spectrometry: physical source characterization and application as HPLC detector JF - International Journal for Ion Mobility Spectrometry Y1 - 2016 U6 - https://doi.org/10.1007/s12127-016-0208-1 IS - 19/4 SP - 197 EP - 297 ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse Data JF - arXiv N2 - The reconstruction of an object's shape or surface from a set of 3D points is a common topic in materials and life sciences, computationally handled in computer graphics. Such points usually stem from optical or tactile 3D coordinate measuring equipment. Surface reconstruction also appears in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or the alignment of intra-operative navigation and preoperative planning data. In contrast to mere 3D point clouds, medical imaging yields contextual information on the 3D point data that can be used to adopt prior information on the shape that is to be reconstructed from the measurements. In this work we propose to use a statistical shape model (SSM) as a prior for surface reconstruction. The prior knowledge is represented by a point distribution model (PDM) that is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we reformulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given measurements are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are oriented according to the surface normals at the PDM points, a surface-based tting is accomplished. By estimating the parameters of the GMM in a maximum a posteriori manner, the reconstruction of the surface from the given measurements is achieved. Extensive experiments suggest that our proposed approach leads to superior surface reconstructions compared to Iterative Closest Point (ICP) methods. Y1 - 2016 SP - 1602.08425v1 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Klug, Torsten A1 - Lamorgese, Leonardo A1 - Mannino, Carlo A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Recent success stories on integrated optimization of railway systems JF - Transportation Research Part C: Emerging Technologies N2 - Planning and operating railway transportation systems is an extremely hard task due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. Because of that, however, mathematical models and optimization techniques can result in large gains for both railway customers and operators, e.g., in terms of cost reductions or service quality improvements. In the last years a large and growing group of researchers in the OR community have devoted their attention to this domain developing mathematical models and optimization approaches to tackle many of the relevant problems in the railway planning process. However, there is still a gap to bridge between theory and practice (e.g. Cacchiani et al., 2014; Borndörfer et al., 2010), with a few notable exceptions. In this paper we address three individual success stories, namely, long-term freight train routing (part I), mid-term rolling stock rotation planning (part II), and real-time train dispatching (part III). In each case, we describe real-life, successful implementations. We will discuss the individual problem setting, survey the optimization literature, and focus on particular aspects addressed by the mathematical models. We demonstrate on concrete applications how mathematical optimization can support railway planning and operations. This gives proof that mathematical optimization can support the planning of railway resources. Thus, mathematical models and optimization can lead to a greater efficiency of railway operations and will serve as a powerful and innovative tool to meet recent challenges of the railway industry. Y1 - 2017 U6 - https://doi.org/10.1016/j.trc.2016.11.015 VL - 74 IS - 1 SP - 196 EP - 211 ER - TY - JOUR A1 - Lemanis, Robert A1 - Zachow, Stefan A1 - Hoffmann, René T1 - Comparative cephalopod shell strength and the role of septum morphology on stress distribution JF - PeerJ N2 - The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio used to characterize septal morphology in the septal strength index and in calculations of tensile strength of nacre are likely insufficient. A better understanding of the material properties of cephalopod nacre may allow the estimation of maximum depth limits of shelled cephalopods through finite element analysis. Y1 - 2016 U6 - https://doi.org/10.7717/peerj.2434 VL - 4 SP - e2434 ER - TY - JOUR A1 - Lange, Alexander T1 - Reconstruction of disease transmission rates: applications to measles, dengue, and influenza JF - Journal of Theoretical Biology Y1 - 2016 U6 - https://doi.org/10.1016/j.jtbi.2016.04.017 VL - 400 SP - 138 EP - 153 ER - TY - JOUR A1 - Bauer, Gernot A1 - Gribova, Nadezhda A1 - Lange, Alexander A1 - Holm, Christian A1 - Gross, Joachim T1 - Three-body effects in triplets of capped gold nanocrystals JF - Molecular Physics Y1 - 2017 U6 - https://doi.org/10.1080/00268976.2016.1213909 VL - 115 SP - 1031 EP - 1040 ER - TY - JOUR A1 - Winkelmann, Stefanie T1 - Markov Control with Rare State Observation: Average Optimality JF - Markov Processes and Related Fields N2 - This paper investigates the criterion of long-term average costs for a Markov decision process (MDP) which is not permanently observable. Each observation of the process produces a fixed amount of information costs which enter the considered performance criterion and preclude from arbitrarily frequent state testing. Choosing the rare observation times is part of the control procedure. In contrast to the theory of partially observable Markov decision processes, we consider an arbitrary continuous-time Markov process on a finite state space without further restrictions on the dynamics or the type of interaction. Based on the original Markov control theory, we redefine the control model and the average cost criterion for the setting of information costs. We analyze the constant of average costs for the case of ergodic dynamics and present an optimality equation which characterizes the optimal choice of control actions and observation times. For this purpose, we construct an equivalent freely observable MDP and translate the well-known results from the original theory to the new setting. Y1 - 2017 VL - 23 SP - 1 EP - 34 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - The Spatiotemporal Master Equation: Approximation of Reaction-Diffusion Dynamics via Markov State Modeling JF - Journal of Chemical Physics N2 - Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest.We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method. We present the theory of Markov state models (MSM) as a theoretical foundation of this intuitive approach. By means of Markov state modeling, both the number and shape of compartments and the transition rates between them can be determined. We consider the ST-CME for two reaction-diffusion systems and compare it to more detailed models. Moreover, a rigorous formal justification of the ST-CME by Galerkin projection methods is presented. Y1 - 2016 U6 - https://doi.org/10.1063/1.4971163 VL - 145 IS - 21 ER - TY - JOUR A1 - Duwal, Sulav A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV/1 in Resource-Poor Settings JF - PloS Computational Biology N2 - An estimated 2.7 million new HIV-1 infections occurred in 2010. `Treatment-for-prevention’ may strongly prevent HIV-1 transmission. The basic idea is that immediate treatment initiation rapidly decreases virus burden, which reduces the number of transmittable viruses and thereby the probability of infection. However, HIV inevitably develops drug resistance, which leads to virus rebound and nullifies the effect of `treatment-for-prevention’ for the time it remains unrecognized. While timely conducted treatment changes may avert periods of viral rebound, necessary treatment options and diagnostics may be lacking in resource-constrained settings. Within this work, we provide a mathematical platform for comparing different treatment paradigms that can be applied to many medical phenomena. We use this platform to optimize two distinct approaches for the treatment of HIV-1: (i) a diagnostic-guided treatment strategy, based on infrequent and patient-specific diagnostic schedules and (ii) a pro-active strategy that allows treatment adaptation prior to diagnostic ascertainment. Both strategies are compared to current clinical protocols (standard of care and the HPTN052 protocol) in terms of patient health, economic means and reduction in HIV-1 onward transmission exemplarily for South Africa. All therapeutic strategies are assessed using a coarse-grained stochastic model of within-host HIV dynamics and pseudo-codes for solving the respective optimal control problems are provided. Our mathematical model suggests that both optimal strategies (i)-(ii) perform better than the current clinical protocols and no treatment in terms of economic means, life prolongation and reduction of HIV-transmission. The optimal diagnostic-guided strategy suggests rare diagnostics and performs similar to the optimal pro-active strategy. Our results suggest that ‘treatment-for-prevention’ may be further improved using either of the two analyzed treatment paradigms. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pcbi.1004200 VL - 11 IS - 4 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Mäusle, Raquel A1 - Burger, Sven T1 - Locally Enhanced and Tunable Optical Chirality in Helical Metamaterials JF - Photonics Y1 - 2016 U6 - https://doi.org/10.3390/photonics3040060 VL - 3 SP - 60 ER - TY - JOUR A1 - Hengartner, Michael A1 - Krüger, Tillmann H. C. A1 - Geraedts, Kirsten A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Ille, Fabian A1 - Egli, Marcel A1 - Röblitz, Susanna A1 - Ehrig, Rainald A1 - Saleh, Lanja A1 - Spanaus, Katharina A1 - Schippert, Cordula A1 - Zhang, Yuanyuan A1 - Leeners, Brigitte T1 - Negative affect is unrelated to fluctuations in hormone levels across the menstrual cycle: evidence from a multisite observational study across two successive cycles JF - Journal of Psychosomatic Research Y1 - 2017 U6 - https://doi.org/10.1016/j.jpsychores.2017.05.018 VL - 99 SP - 21 EP - 27 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Seasonal changes of the volatile density in the coma and on the surface of comet 67P/Churyumov-Gerasimenko JF - Monthly Notices of the Royal Astronomical Society N2 - Starting from several monthly data sets of Rosetta’s COmetary Pressure Sensor we reconstruct the gas density in the coma around comet 67P/Churyumov-Gerasimenko. The underlying inverse gas model is constructed by fitting ten thousands of measurements to thousands of potential gas sources distributed across the entire nucleus surface. The ensuing self-consistent solution for the entire coma density and surface activity reproduces the temporal and spatial variations seen in the data for monthly periods with Pearson correlation coefficients of 0.93 and higher. For different seasonal illumination conditions before and after perihelion we observe a systematic shift of gas sources on the nucleus. Y1 - 2017 U6 - https://doi.org/10.1093/mnras/stx866 VL - 469 SP - S20 EP - S28 ER - TY - JOUR A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Theisel, Holger T1 - MCFTLE: Monte Carlo Rendering of Finite-Time Lyapunov Exponent Fields JF - Computer Graphics Forum Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12914 N1 - By mistake the fourth author Hans-Christian Hege has been ommitted in the journal publication VL - 35 IS - 3 SP - 381 EP - 390 ER - TY - JOUR A1 - Rohr, Ulrich-Peter A1 - Herrmann, Pia A1 - Ilm, Katharina A1 - Zhang, Hai A1 - Lohmann, Sabine A1 - Reiser, Astrid A1 - Muranyi, Andrea A1 - Smith, Janice A1 - Burock, Susen A1 - Osterland, Marc A1 - Leith, Katherine A1 - Singh, Shalini A1 - Brunhoeber, Patrick A1 - Bowermaster, Rebecca A1 - Tie, Jeanne A1 - Christie, Michael A1 - Wong, Hui-Li A1 - Waring, Paul A1 - Shanmugam, Kandavel A1 - Gibbs, Peter A1 - Stein, Ulrike T1 - Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies JF - Annals of Oncology N2 - Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charité 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charité 2 comparison cohort was used to translate MACC1 qRT-PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-naïve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92% and 67% versus 100% and 68%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100% versus 90%, respectively). In the pooled dataset, 6.5% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17% higher 5-year RFS (95% CI (12.6-21.3%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100% and 96%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy. Y1 - 2017 U6 - https://doi.org/10.1093/annonc/mdx207 VL - 28 IS - 8 SP - 1869 EP - 1875 ER - TY - JOUR A1 - Brüning, Jan A1 - Goubergrits, Leonid A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Hildebrandt, Thomas T1 - Numerical Analysis of Nasal Breathing - A Pilot Study JF - Facial Plastic Surgery N2 - Background: Currently, there is no fully sufficient way to differentiate between symptomatic and normal nasal breathing. Using the nose’s total resistance is disputed as a valid means to objectify nasal airflow, and the need for a more comprehensive diagnostic method is increasing. This work’s aim was to test a novel approach considering intranasal wall shear stress as well as static pressure maps obtained by computational fluid dynamics (CFD). Methods: X-ray computed tomography (CT) scan data of six symptom-free subjects and seven symptomatic patients were used. Patient-specific geometries of the nasal cavity were segmented from these data sets. Inspiratory and expiratory steady airflow simulations were performed using CFD. Calculated static pressures and wall shear stresses (WSS) were mapped onto a common template of the nasal septum, allowing for comparison of these parameters between the two patient groups. Results: Significant differences in wall shear stress distributions during the inspiratory phase could be identified between the two groups, whereas no differences were found for the expiratory phase. It is assumed that one essential feature of normal nasal breathing probably consists in distinctively different intranasal flow fields for inspiration and expiration. This is in accordance with previous investigations. Conclusion: The proposed method seems to be a promising tool for developing a new kind of patient-specific assessment of nasal breathing. However, more studies and a greater case number of data with an expanded focus, would be ideal. Y1 - 2017 U6 - https://doi.org/doi:10.1055/s-0037-1603789 VL - 33 IS - 4 SP - 388 EP - 395 ER - TY - JOUR A1 - Vigerske, Stefan A1 - Gleixner, Ambros T1 - SCIP: Global Optimization of Mixed-Integer Nonlinear Programs in a Branch-and-Cut Framework JF - Optimization Methods & Software N2 - This paper describes the extensions that were added to the constraint integer programming framework SCIP in order to enable it to solve convex and nonconvex mixed-integer nonlinear programs (MINLPs) to global optimality. SCIP implements a spatial branch-and-bound algorithm based on a linear outer-approximation, which is computed by convex over- and underestimation of nonconvex functions. An expression graph representation of nonlinear constraints allows for bound tightening, structure analysis, and reformulation. Primal heuristics are employed throughout the solving process to find feasible solutions early. We provide insights into the performance impact of individual MINLP solver components via a detailed computational study over a large and heterogeneous test set. Y1 - 2018 U6 - https://doi.org/10.1080/10556788.2017.1335312 VL - 33 IS - 3 SP - 563 EP - 593 ER - TY - JOUR A1 - Redemann, Stefanie A1 - Baumgart, Johannes A1 - Lindow, Norbert A1 - Shelley, Michael A1 - Nazockdast, Ehssan A1 - Kratz, Andrea A1 - Prohaska, Steffen A1 - Brugués, Jan A1 - Fürthauer, Sebastian A1 - Müller-Reichert, Thomas T1 - C. elegans chromosomes connect to centrosomes by anchoring into the spindle network JF - Nature Communications N2 - The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient. Y1 - 2017 U6 - https://doi.org/10.1038/ncomms15288 VL - 8 IS - 15288 ER - TY - JOUR A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Günster, Jens A1 - Krauß-Schüler, Stefanie T1 - Adapting trabecular structures for 3D printing: an image processing approach based on µCT data JF - Biomedical Physics & Engineering Express N2 - Materials with a trabecular structure notably combine advantages such as lightweight, reasonable strength, and permeability for fluids. This combination of advantages is especially interesting for tissue engineering in trauma surgery and orthopedics. Bone-substituting scaffolds for instance are designed with a trabecular structure in order to allow cell migration for bone ingrowth and vascularization. An emerging and recently very popular technology to produce such complex, porous structures is 3D printing. However, several technological aspects regarding the scaffold architecture, the printable resolution, and the feature size have to be considered when fabricating scaffolds for bone tissue replacement and regeneration. Here, we present a strategy to assess and prepare realistic trabecular structures for 3D printing using image analysis with the aim of preserving the structural elements. We discuss critical conditions of the printing system and present a 3-stage approach to adapt a trabecular structure from $\mu$CT data while incorporating knowledge about the printing system. In the first stage, an image-based extraction of solid and void structures is performed, which results in voxel- and graph-based representations of the extracted structures. These representations not only allow us to quantify geometrical properties such as pore size or strut geometry and length. But, since the graph represents the geometry and the topology of the initial structure, it can be used in the second stage to modify and adjust feature size, volume and sample size in an easy and consistent way. In the final reconstruction stage, the graph is then converted into a voxel representation preserving the topology of the initial structure. This stage generates a model with respect to the printing conditions to ensure a stable and controlled voxel placement during the printing process. Y1 - 2017 U6 - https://doi.org/10.1088/2057-1976/aa7611 VL - 3 IS - 3 PB - IOP Publishing ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Transformations for the Prize-Collecting Steiner Tree Problem and the Maximum-Weight Connected Subgraph Problem to SAP JF - Journal of Computational Mathematics N2 - Transformations of Steiner tree problem variants have been frequently discussed in the literature. Besides allowing to easily transfer complexity results, they constitute a central pillar of exact state-of-the-art solvers for well-known variants such as the Steiner tree problem in graphs. In this paper transformations for both the prize-collecting Steiner tree problem and the maximum-weight connected subgraph problem to the Steiner arborescence problem are introduced for the first time. Furthermore, we demonstrate the considerable implications for practical solving approaches, including the computation of strong upper and lower bounds. Y1 - 2018 U6 - https://doi.org/10.4208/jcm.1709-m2017-0002 VL - 36 IS - 3 SP - 459 EP - 468 ER - TY - JOUR A1 - Koltai, Peter A1 - Ciccotti, Giovanni A1 - Schütte, Christof T1 - On Markov state models for non-equilibrium molecular dynamics JF - The Journal of Chemical Physics Y1 - 2016 U6 - https://doi.org/10.1063/1.4966157 N1 - 2016 Editor's Choice of The Journal of Chemical Physics VL - 145 IS - 174103 ER - TY - JOUR A1 - Eisenhauer, David A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Rech, Bernd A1 - Becker, Christiane T1 - Optical Properties of Smooth Anti-reflective Three-dimensional Textures for Silicon Thin-film Solar Cells JF - Energy Procedia Y1 - 2016 U6 - https://doi.org/10.1016/j.egypro.2016.11.314 VL - 102 SP - 27 EP - 35 ER - TY - JOUR A1 - Eisenhauer, David A1 - Köppel, Grit A1 - Jäger, Klaus A1 - Chen, Duote A1 - Shargaieva, Oleksandra A1 - Sonntag, Paul A1 - Armkreutz, Daniel A1 - Rech, Bernd A1 - Becker, Christiane T1 - Smooth anti-reflective three-dimensional textures for liquid phase crystallized silicon thin-film solar cells on glass JF - Sci. Rep. Y1 - 2017 U6 - https://doi.org/10.1038/s41598-017-02874-y VL - 7 SP - 2658 ER - TY - JOUR A1 - Kadow, Christopher A1 - Illing, Sebastian A1 - Kunst, Oliver A1 - Rust, Henning A1 - Pohlmann, Holger A1 - Müller, Wolfgang A. A1 - Cubasch, Ulrich T1 - Evaluation of forecasts by accuracy and spread in the MiKlip decadal climate prediction system JF - Meteorologische Zeitschrift N2 - We present the evaluation of temperature and precipitation forecasts obtained with the MiKlip decadal climate prediction system. These decadal hindcast experiments are verified with respect to the accuracy of the ensemble mean and the ensemble spread as a representative for the forecast uncertainty. The skill assessment follows the verification framework already used by the decadal prediction community, but enhanced with additional evaluation techniques like the logarithmic ensemble spread score. The core of the MiKlip system is the coupled Max Planck Institute Earth System Model. An ensemble of 10 members is initialized annually with ocean and atmosphere reanalyses of the European Centre for Medium-Range Weather Forecasts. For assessing the effect of the initialization, we compare these predictions to uninitialized climate projections with the same model system. Initialization improves the accuracy of temperature and precipitation forecasts in year 1, particularly in the Pacific region. The ensemble spread well represents the forecast uncertainty in lead year 1, except in the tropics. This estimate of prediction skill creates confidence in the respective 2014 forecasts, which depict less precipitation in the tropics and a warming almost everywhere. However, large cooling patterns appear in the Northern Hemisphere, the Pacific South America and the Southern Ocean. Forecasts for 2015 to 2022 show even warmer temperatures than for 2014, especially over the continents. The evaluation of lead years 2 to 9 for temperature shows skill globally with the exception of the eastern Pacific. The ensemble spread can again be used as an estimate of the forecast uncertainty in many regions: It improves over the tropics compared to lead year 1. Due to a reduction of the conditional bias, the decadal predictions of the initialized system gain skill in the accuracy compared to the uninitialized simulations in the lead years 2 to 9. Furthermore, we show that increasing the ensemble size improves the MiKlip decadal climate prediction system for all lead years. Y1 - 2016 U6 - https://doi.org/10.1127/metz/2015/0639 VL - 25 IS - 6 SP - 631 EP - 643 ER - TY - JOUR A1 - Burger, Sven A1 - Bongs, Kai A1 - Sengstock, Klaus A1 - Ertmer, Wolfgang ED - Martellucci, Sergio ED - Chester, Arthur N. ED - Aspect, Alain ED - Inguscio, Massimo T1 - Atom Optics With Bose-Einstein Condensates JF - Bose-Einstein Condensates and Atom Lasers Y1 - 2002 U6 - https://doi.org/10.1007/0-306-47103-5_7 SP - 97 EP - 115 PB - Springer US ER - TY - JOUR A1 - Berthold, Timo A1 - Gleixner, Ambros A1 - Heinz, Stefan A1 - Vigerske, Stefan T1 - Analyzing the computational impact of MIQCP solver components JF - Numerical Algebra, Control and Optimization N2 - We provide a computational study of the performance of a state-of-the-art solver for nonconvex mixed-integer quadratically constrained programs (MIQCPs). Since successful general-purpose solvers for large problem classes necessarily comprise a variety of algorithmic techniques, we focus especially on the impact of the individual solver components. The solver SCIP used for the experiments implements a branch-and-cut algorithm based on a linear relaxation to solve MIQCPs to global optimality. Our analysis is based on a set of 86 publicly available test instances. Y1 - 2012 U6 - https://doi.org/10.3934/naco.2012.2.739 VL - 2 IS - 4 SP - 739 EP - 748 ER - TY - JOUR A1 - Poss, Michael A1 - Raack, Christian T1 - Affine recourse for the robust network design problem: Between static and dynamic routing JF - Networks - Special Issue: INOC 2011 Conference, June 13–16, 2011, Hamburg, Germany N2 - Affinely-Adjustable Robust Counterparts provide tractable alternatives to (two-stage) robust programs with arbitrary recourse. We apply them to robust network design with polyhedral demand uncertainty, introducing the affine routing principle. We compare the affine routing to the well-studied static and dynamic routing schemes for robust network design. All three schemes are embedded into the general framework of two-stage network design with recourse. It is shown that affine routing can be seen as a generalization of the widely used static routing still being tractable and providing cheaper solutions. We investigate properties on the demand polytope under which affine routings reduce to static routings and also develop conditions on the uncertainty set leading to dynamic routings being affine. We show however that affine routings suffer from the drawback that (even totally) dominated demand vectors are not necessarily supported by affine solutions. Uncertainty sets have to be designed accordingly. Finally, we present computational results on networks from SNDlib. We conclude that for these instances the optimal solutions based on affine routings tend to be as cheap as optimal network designs for dynamic routings. In this respect the affine routing principle can be used to approximate the cost for two-stage solutions with free recourse which are hard to compute. Y1 - 2013 U6 - https://doi.org/10.1002/net.21482 VL - 61 IS - 2 SP - 180 EP - 198 ER - TY - JOUR A1 - Brandt, Manfred A1 - Brandt, Andreas T1 - Additive functionals with application to sojourn times in infinite-server and processor sharing systems JF - Queueing Systems N2 - We deal with an infinite-server system where the service speed is governed by a stationary and ergodic process with countably many states. Applying a random time transformation such that the service speed becomes one, the sojourn time of a class of virtual requests with given required service time is equal in distribution to an additive functional defined via a stationary version of the time-changed process. Thus bounds for the expectation of functions of additive functionals yield bounds for the expectation of functions of virtual sojourn times, in particular bounds for fractional moments and the distribution function. Interpreting the $GI(n)/GI(n)/\infty$ system or equivalently the $GI(n)/GI$ system under state-dependent processor sharing as an infinite-server system with random states given by the number $n$ of requests in the system provides results for sojourn times of virtual requests. In case of $M(n)/GI(n)/\infty$, the sojourn times of arriving and added requests are equal in distribution to sojourn times of virtual requests in modified systems, which yields many results for the sojourn times of arriving and added requests. In case of integer moments, the bounds generalize earlier results for $M/GI(n)/\infty$. In particular, the mean sojourn times of arriving and added requests in $M(n)/GI(n)/\infty$ are proportional to the required service time, generalizing Cohen's famous result for $M/GI(n)/\infty$. Y1 - 2012 U6 - https://doi.org/10.1007/s11134-012-9282-1 VL - 70 IS - 4 SP - 369 EP - 409 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Workload and busy period for M/GI/1 with a general impatience mechanism JF - Queueing Systems N2 - The paper deals with the workload and busy period for the M/GI/1 system under FCFS discipline, where the customers may become impatient during their waiting for service with generally distributed maximal waiting times and also during their service with generally distributed maximal service times depending on the time waited for service. This general impatience mechanism, originally introduced by Kovalenko (1961) and considered by Daley (1965), too, covers the special cases of impatience on waiting times as well as impatience on sojourn times, for which Boxma et al. (2010), (2011) gave new results and outlined special cases recently. Our unified approach bases on the vector process of workload and busy time. Explicit representations for the LSTs of workload and busy period are given in case of phase-type distributed impatience. Y1 - 2013 U6 - https://doi.org/10.1007/s11134-013-9373-7 VL - 75 IS - 2-4 SP - 189 EP - 209 ER - TY - JOUR A1 - Schlechte, Thomas A1 - Borndörfer, Ralf A1 - Erol, Berkan A1 - Graffagnino, Thomas A1 - Swarat, Elmar T1 - Micro–macro transformation of railway networks JF - Journal of Rail Transport Planning & Management N2 - In this paper a bottom-up approach of automatic simplification of a railway network is presented. Starting from a very detailed, microscopic level, as it is used in railway simulation, the network is transformed by an algorithm to a less detailed level (macroscopic network), that is sufficient for long-term planning and optimization. In addition running and headway times are rounded to a pre-chosen time discretization by a special cumulative method, which we will present and analyse in this paper. After the transformation we fill the network with given train requests to compute an optimal slot allocation. Then the optimized schedule is re-transformed into the microscopic level and can be simulated without any conflicts occuring between the slots. The algorithm is used to transform the network of the very dense Simplon corridor between Swiss and Italy. With our aggregation it is possible for the first time to generate a profit maximal and conflict free timetable for the corridor across a day by a simultaneously optimization run. Y1 - 2011 U6 - https://doi.org/10.1016/j.jrtpm.2011.09.001 VL - 1 IS - 1 SP - 38 EP - 48 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - Insensitive bounds for the moments of the sojourn times in M/GI systems under state-dependent processor sharing JF - Advances in Applied Probability N2 - We consider a system with Poisson arrivals and i.i.d. service times and where the requests are served according to the state-dependent (Cohen's generalized) processor sharing discipline, where each request in the system receives a service capacity which depends on the actual number of requests in the system. For this system we derive asymptotically tight upper bounds for the moments of the conditional sojourn time of a request with given required service time. The bounds generalize corresponding results, recently given for the single-server processor sharing system by Cheung et al. and for the state-dependent processor sharing system with exponential service times by the authors. Analogous results hold for the waiting times. Y1 - 2010 U6 - https://doi.org/10.1239/aap/1269611152 VL - 42 IS - 1 SP - 246 EP - 267 ER - TY - JOUR A1 - Berthold, Timo T1 - Measuring the impact of primal heuristics JF - Operations Research Letters N2 - In modern MIP solvers, primal heuristics play a major role in finding and improving feasible solutions early in the solution process. However, classical performance measures such as time to optimality or number of branch-and-bound nodes reflect the impact of primal heuristics on the overall solving process badly. This article discusses the question of how to evaluate the effect of primal heuristics. Therefore, we introduce a new performance measure, the "primal integral" which depends on the quality of solutions found during the solving process as well as on the points in time when they are found. Our computational results reveal that heuristics improve the performance of MIP solvers in terms of the primal bound by around 80%. Further, we compare five state-of-the-art MIP solvers w.r.t. the newly proposed measure. Y1 - 2013 U6 - https://doi.org/10.1016/j.orl.2013.08.007 VL - 41 IS - 6 SP - 611 EP - 614 ER - TY - JOUR A1 - Harrod, Steven A1 - Schlechte, Thomas T1 - A Direct Comparison of Physical Block Occupancy Versus Timed Block Occupancy in Train Timetabling Formulations JF - Transportation Research Part E: Logistics and Transportation Review N2 - Two fundamental mathematical formulations for railway timetabling are compared on a common set of sample problems, representing both multiple track high density services in Europe and single track bidirectional operations in North America. One formulation, ACP, enforces against conflicts by constraining time intervals between trains, while the other formulation, RCHF, monitors physical occupation of controlled track segments. The results demonstrate that both ACP and RCHF return comparable solutions in the aggregate, with some significant differences in select instances, and a pattern of significant differences in performance and constraint enforcement overall. Y1 - 2013 U6 - https://doi.org/10.1016/j.tre.2013.04.003 VL - 54 SP - 50 EP - 66 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen T1 - A Hypergraph Model for Railway Vehicle Rotation Planning JF - 11th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems N2 - We propose a model for the integrated optimization of vehicle rotations and vehicle compositions in long distance railway passenger transport. The main contribution of the paper is a hypergraph model that is able to handle the challenging technical requirements as well as very general stipulations with respect to the ``regularity'' of a schedule. The hypergraph model directly generalizes network flow models, replacing arcs with hyperarcs. Although NP-hard in general, the model is computationally well-behaved in practice. High quality solutions can be produced in reasonable time using high performance Integer Programming techniques, in particular, column generation and rapid branching. We show that, in this way, large-scale real world instances of our cooperation partner DB Fernverkehr can be solved. Y1 - 2011 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2011.146 VL - OpenAccess Series in Informatics (OASIcs) IS - 20 SP - 146 EP - 155 ER - TY - JOUR A1 - Schlechte, Thomas T1 - Railway Track Allocation - Simulation and Optimization JF - Proceedings of 4th International Seminar on Railway Operations Modelling and Analysis (IAROR) N2 - Today the railway timetabling process and the track allocation is one of the most challenging problems to solve by a railway infrastructure provider. Especially due to the deregulation of the transport market in the recent years several suppliers of railway traffic have entered the market. This leads to an increase of slot requests and then it is natural that conflicts occur among them. Furthermore, railway infrastructure networks consist of very expensive assets, even more they are rigid due to the long-term upgrade process. In order to make best use of these valuable infrastructure and to ensure economic operation, efficient planning of the railway operation is indispensable. Mathematical optimization models and algorithmic methodology can help to automatize and tackle these challenges. Our contribution in this paper is to present a renewed planning process due to the liberalization in Europe and a general framework to support the integration of simulation and optimization for railway capacity allocation. Y1 - 2011 VL - 4 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Schlechte, Thomas A1 - Swarat, Elmar T1 - Railway Track Allocation -- Simulation, Aggregation, and Optimization JF - Proc. 1st International Workshop on High-speed and Intercity Railways (IWHIR 2011) N2 - Today the railway timetabling process and the track allocation is one of the most challenging problems to solve by a railway company. Especially due to the deregulation of the transport market in the recent years several suppliers of railway traffic have entered the market in Europe. This leads to more potential conflicts between trains caused by an increasing demand of train paths. Planning and operating railway transportation systems is extremely hard due to the combinatorial complexity of the underlying discrete optimization problems, the technical intricacies, and the immense size of the problem instances. In order to make best use of the infrastructure and to ensure economic operation, efficient planning of the railway operation is indispensable. Mathematical optimization models and algorithms can help to automatize and tackle these challenges. Our contribution in this paper is to present a renewed planning process due to the liberalization in Europe and an associated concept for track allocation, that consists of three important parts, simulation, aggregation, and optimization. Furthermore, we present results of our general framework for real world data. Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-27963-8 VL - 2 IS - 148 SP - 53 EP - 70 ER - TY - JOUR A1 - Bleiholder, Jens A1 - Szott, Sascha A1 - Herschel, Melanie A1 - Kaufer, Frank A1 - Naumann, Felix T1 - Subsumption and Complementation As Data Fusion Operators JF - Proceedings of the 13th International Conference on Extending Database Technology N2 - The goal of data fusion is to combine several representations of one real world object into a single, consistent representation, e.g., in data integration. A very popular operator to perform data fusion is the minimum union operator. It is defined as the outer union and the subsequent removal of subsumed tuples. Minimum union is used in other applications as well, for instance in database query optimization to rewrite outer join queries, in the semantic web community in implementing Sparql's optional operator, etc. Despite its wide applicability, there are only few efficient implementations, and until now, minimum union is not a relational database primitive. This paper fills this gap as we present implementations of subsumption that serve as a building block for minimum union. Furthermore, we consider this operator as database primitive and show how to perform optimization of query plans in presence of subsumption and minimum union through rule-based plan transformations. Experiments on both artificial and real world data show that our algorithms outperform existing algorithms used for subsumption in terms of runtime and they scale to large volumes of data. In the context of data integration, we observe that performing data fusion calls for more than subsumption and minimum union. Therefore, another contribution of this paper is the definition of the complementation and complement union operators. Intuitively, these allow to merge tuples that have complementing values and thus eliminate unnecessary null-values. Y1 - 2010 U6 - https://doi.org/10.1145/1739041.1739103 SP - 513 EP - 524 ER - TY - JOUR A1 - Hiller, Benjamin A1 - Klug, Torsten A1 - Tuchscherer, Andreas T1 - An Exact Reoptimization Algorithm for the Scheduling of Elevator Groups JF - Flexible Services and Manufacturing Journal Y1 - 2013 U6 - https://doi.org/10.1007/s10696-013-9175-6 SP - 1 EP - 24 ER - TY - JOUR A1 - Eisenblätter, Andreas A1 - Schweiger, Jonas T1 - Multistage Stochastic Programming in Strategic Telecommunication Network Planning JF - Computational Management Science N2 - Mobile communication is nowadays taken for granted. Having started primarily as a service for speech communication, data service and mobile Internet access are now driving the evolution of network infrastructure. Operators are facing the challenge to match the demand by continuously expanding and upgrading the network infrastructure. However, the evolution of the customer's demand is uncertain. We introduce a novel (long-term) network planning approach based on multistage stochastic programming, where demand evolution is considered as a stochastic process and the network is extended as to maximize the expected profit. The approach proves capable of designing large-scale realistic UMTS networks with a time-horizon of several years. Our mathematical optimization model, the solution approach, and computational results are presented in this paper. Y1 - 2012 U6 - https://doi.org/10.1007/s10287-012-0143-5 VL - 9 IS - 3 SP - 303 EP - 321 PB - Springer ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Karbstein, Marika A1 - Pfetsch, Marc T1 - The Steiner connectivity problem JF - Mathematical Programming A Y1 - 2013 U6 - https://doi.org/10.1007/s10107-012-0564-5 VL - 142 IS - 1 SP - 133 EP - 167 ER - TY - JOUR A1 - Bleiholder, Jens A1 - Szott, Sascha A1 - Herschel, M. A1 - Naumann, Felix T1 - Complement union for data integration JF - Data Engineering Workshops (ICDEW), 2010 IEEE 26th International Conference on N2 - A data integration process consists of mapping source data into a target representation (schema mapping), identifying multiple representations of the same real-word object (duplicate detection), and finally combining these representations into a single consistent representation (data fusion). Clearly, as multiple representations of an object are generally not exactly equal, during data fusion, we have to take special care in handling data conflicts. This paper focuses on the definition and implementation of complement union, an operator that defines a new semantics for data fusion. Y1 - 2010 U6 - https://doi.org/10.1109/ICDEW.2010.5452760 SP - 183 EP - 186 ER - TY - JOUR A1 - Herschel, Melanie A1 - Naumann, Felix A1 - Szott, Sascha A1 - Taubert, Maik T1 - Scalable Iterative Graph Duplicate Detection JF - IEEE Transactions on Knowledge and Data Engineering N2 - Duplicate detection determines different representations of real-world objects in a database. Recent research has considered the use of relationships among object representations to improve duplicate detection. In the general case where relationships form a graph, research has mainly focused on duplicate detection quality/effectiveness. Scalability has been neglected so far, even though it is crucial for large real-world duplicate detection tasks. We scale-up duplicate detection in graph data (ddg) to large amounts of data and pairwise comparisons, using the support of a relational database management system. To this end, we first present a framework that generalizes the ddg process. We then present algorithms to scale ddg in space (amount of data processed with bounded main memory) and in time. Finally, we extend our framework to allow batched and parallel ddg, thus further improving efficiency. Experiments on data of up to two orders of magnitude larger than data considered so far in ddg show that our methods achieve the goal of scaling ddg to large volumes of data. Y1 - 2012 U6 - https://doi.org/10.1109/TKDE.2011.99 VL - 24 IS - 11 SP - 2094 EP - 2108 ER - TY - JOUR A1 - Thiede, Doreen T1 - Bericht zum 78. World Library and Information Congress (WLIC) Y1 - 2012 UR - http://www.bi-international.de/download/berichte/224_bericht_wlic2012.pdf ER - TY - JOUR A1 - Bertelmann, Roland A1 - Szott, Sascha A1 - Höhnow, Tobias T1 - Discovery jenseits von “all you can eat” und “one size fits all” JF - Bibliothek Forschung und Praxis Y1 - 2012 U6 - https://doi.org/10.1515/bfp-2012-0050 VL - 36 IS - 3 SP - 369 EP - 376 ER - TY - JOUR A1 - Szott, Sascha T1 - Vom Prototypen zum nachhaltigen Hosting-Service: die Resource Discovery Lösung ALBERT JF - Bibliotheksdienst Y1 - 2012 UR - http://digital.zlb.de/viewer/image/019591853_2012/683/ VL - 46 IS - 8/9 SP - 683 EP - 686 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio A1 - Mannino, Carlo A1 - Sassano, Antonio T1 - GUB Covers and Power-Indexed Formulations for Wireless Network Design JF - Management Science Y1 - 2013 U6 - https://doi.org/10.1287/mnsc.1120.1571 VL - 59 IS - 1 SP - 142 EP - 156 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio T1 - Pure 0-1 programming approaches to wireless network design JF - 4OR Y1 - 2012 U6 - https://doi.org/10.1007/s10288-011-0162-z VL - 10 IS - 2 SP - 211 EP - 212 ER - TY - JOUR A1 - Dely, Peter A1 - D'Andreagiovanni, Fabio A1 - Kassler, Andreas T1 - Fair Optimization of Mesh-Connected WLAN Hotspots JF - Wireless Communications and Mobile Computing Y1 - 2013 U6 - https://doi.org/10.1002/wcm.2393 VL - 15 IS - 5 SP - 924 EP - 946 ER - TY - JOUR A1 - Bauschert, Thomas A1 - Büsing, Christina A1 - D'Andreagiovanni, Fabio A1 - Koster, Arie M.C.A. A1 - Kutschka, Manuel A1 - Steglich, Uwe T1 - Network planning under demand uncertainty with robust optimization JF - IEEE Communications Magazine Y1 - 2014 U6 - https://doi.org/10.1109/MCOM.2014.6736760 VL - 52 IS - 2 SP - 178 EP - 185 ER - TY - JOUR A1 - Powell, Gary A1 - Weiser, Martin T1 - Views, A new form of container adaptors JF - C/C++ Users Journal N2 - The C++ standard template library has many useful containers for data. The standard library includes two adpators, queue, and stack. The authors have extended this model along the lines of relational database semantics. Sometimes the analogy is striking, and we will point it out occasionally. An adaptor allows the standard algorithms to be used on a subset or modification of the data without having to copy the data elements into a new container. The authors provide many useful adaptors which can be used together to produce interesting views of data in a container. Y1 - 2000 VL - 18 IS - 4 SP - 40 EP - 51 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Löbel, Andreas A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen ED - Muñoz, J. C. ED - Voß, S. T1 - Rapid Branching JF - Public Transport N2 - We propose rapid branching (RB) as a general branch-and-bound heuristic for solving large scale optimization problems in traffic and transport. The key idea is to combine a special branching rule and a greedy node selection strategy in order to produce solutions of controlled quality rapidly and efficiently. We report on three successful applications of the method for integrated vehicle and crew scheduling, railway track allocation, and railway vehicle rotation planning. Y1 - 2013 VL - 5 IS - 1 SP - 3 EP - 23 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Reuther, Markus A1 - Schlechte, Thomas A1 - Weider, Steffen ED - Muñoz, J. C. ED - Voß, S. T1 - Vehicle Rotation Planning for Intercity Railways JF - Proceedings of Conference on Advanced Systems for Public Transport 2012 (CASPT12) N2 - This paper provides a generic formulation for rolling stock planning problems in the context of intercity passenger traffic. The main contributions are a graph theoretical model and a Mixed-Integer-Programming formulation that integrate all main requirements of the considered Vehicle-Rotation-Planning problem (VRPP). We show that it is possible to solve this model for real-world instances provided by our industrial partner DB Fernverkehr AG using modern algorithms and computers. Y1 - 2012 ER - TY - JOUR A1 - Gamrath, Gerald T1 - Improving strong branching by domain propagation JF - EURO Journal on Computational Optimization N2 - One of the essential components of a branch-and-bound based mixed-integer linear programming (MIP) solver is the branching rule. Strong branching is a method used by many state-of-the-art branching rules to select the variable to branch on. It precomputes the dual bounds of potential child nodes by solving auxiliary linear programs (LPs) and thereby helps to take good branching decisions that lead to a small search tree. In this paper, we describe how these dual bound predictions can be improved by including domain propagation into strong branching. Domain propagation is a technique MIP solvers usually apply at every node of the branch-and-bound tree to tighten the local domains of variables. Computational experiments on standard MIP instances indicate that our improved strong branching method significantly improves the quality of the predictions and causes almost no additional effort. For a full strong branching rule, we are able to obtain substantial reductions of the branch-and-bound tree size as well as the solving time. Moreover, the state-of-the-art hybrid branching rule can be improved this way as well. This paper extends previous work by the author published in the proceedings of the CPAIOR 2013. Y1 - 2014 U6 - https://doi.org/10.1007/s13675-014-0021-8 VL - 2 IS - 3 SP - 99 EP - 122 PB - Springer CY - Berlin Heidelberg ER - TY - JOUR A1 - Grötschel, Martin A1 - Stephan, Rüdiger T1 - Characterization of Facets of the Hop Constrained Chain Polytope via Dynamic Programming JF - Discrete Applied Mathematics Y1 - 2014 U6 - https://doi.org/10.1016/j.dam.2013.08.015 VL - 162 SP - 229 EP - 246 ER - TY - JOUR A1 - Grötschel, Martin T1 - Vertrauen in die/in der Wissenschaft: Einführung in das Thema JF - DEBATTE Y1 - 2013 SN - 978-3-939818-41-0 IS - Heft 12, Erster Teil SP - 9 EP - 16 PB - Berlin-Brandenburgische Akademie der Wissenschaften ER - TY - JOUR A1 - Grötschel, Martin T1 - Vertrauen in die/in der Wissenschaft: Einführung JF - DEBATTE Y1 - 2013 SN - 978-3-939818-41-0 IS - Heft 12, Zweiter Teil SP - 63 EP - 69 PB - Berlin-Brandenburgische Akademie der Wissenschaften ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grötschel, Martin A1 - Jäger, Ulrich T1 - Planning Problems in Public Transit JF - Production Factor Mathematics Y1 - 2010 SN - 978-3-642-11247-8 U6 - https://doi.org/10.1007/978-3-642-11248-5 SP - 95 EP - 122 PB - acatech and Springer CY - Berlin Heidelberg ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Karbstein, Marika A1 - Pfetsch, Marc T1 - Models for Fare Planning in Public Transport JF - Discrete Applied Mathematics Y1 - 2012 U6 - https://doi.org/10.1016/j.dam.2012.02.027 VL - 160 IS - 18 SP - 2591 EP - 2605 ER - TY - JOUR A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Ehrig, Karsten A1 - Ebell, Gino A1 - Meinel, Dietmar A1 - Heyn, Andreas T1 - Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben JF - DGZfP-Jahrestagung 2014 Konferenzband Y1 - 2014 ER - TY - JOUR A1 - Ruprecht, Daniel A1 - Schädle, Achim A1 - Schmidt, Frank T1 - Transparent boundary conditions based on the pole condition for time-dependent, two-dimensional problems JF - Numerical Methods for Partial Differential Equations Y1 - 2013 U6 - https://doi.org/10.1002/num.21759 VL - 29 IS - 4 SP - 1367 EP - 1390 ER - TY - JOUR A1 - Menzel, Christoph A1 - Hebestreit, Erik A1 - Alaee, Rasoul A1 - Albooyeh, Mohammad A1 - Mühlig, Stefan A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Simovski, Constantin A1 - Tretyakov, Sergei A1 - Lederer, Falk A1 - Pertsch, Thomas T1 - Extreme Coupling: a route towards local magnetic metamaterials JF - Phys. Rev. B Y1 - 2014 U6 - https://doi.org/10.1103/PhysRevB.89.155125 VL - 89 SP - 155125 ER - TY - JOUR A1 - Menzel, Christoph A1 - Hebestreit, Erik A1 - Mühlig, Stefan A1 - Rockstuhl, Carsten A1 - Burger, Sven A1 - Lederer, Falk A1 - Pertsch, Thomas T1 - The spectral shift between near- and far-field resonances of optical nano-antennas JF - Opt. Expr. Y1 - 2014 U6 - https://doi.org/10.1364/OE.22.009971 VL - 22 IS - 8 SP - 9971 EP - 9982 ER - TY - JOUR A1 - McPeak, Kevin A1 - van Engers, Christian D. A1 - Blome, Mark A1 - Park, Jong Hyuk A1 - Burger, Sven A1 - Gosalvez, Miguel A. A1 - Faridi, Ava A1 - Ries, Yasmina A1 - Sahu, Ayaskanta A1 - Norris, David T1 - Complex Chiral Colloids and Surfaces via High-Index Off-Cut Silicon JF - Nano Lett. Y1 - 2014 U6 - https://doi.org/10.1021/nl501032j VL - 14 IS - 5 SP - 2934 EP - 2940 ER - TY - JOUR A1 - Shinano, Yuji A1 - Inui, Nobuo A1 - Fukagawa, Youzou A1 - Takakura, Noburu T1 - Optimizing Movement Sequences for Step-and-Scan Lithography Equipment JF - Journal of Advanced Mechanical Design, Systems, and Manufacturing N2 - The purpose of this work is to improve the throughput of step-and-scan lithography equipment to shorten the production time of a wafer. For this purpose, we propose a method for solving the MSOP (Movement Sequence Optimization Problem), which is the problem of computing the fastest schedule for visiting all shots on a wafer. It is well-known that the MSOP on step-and-repeat lithography equipment can be modeled as a traveling salesman problem. In contrast to step-and-repeat lithography equipment, a schedule for step-and-scan lithography equipment must also indicate the scanning direction of each shot, in addition to the sequence of the shots. For this reason, the traveling salesman problem formulation for step-and-repeat lithography equipment cannot be applied to solve the MSOP on step-and-scan lithography equipment directly. We overcame this difficulty by introducing auxiliary vertices to model the scanning directions in the traveling salesman problem formulation. By this method, we were able to compute exact optimal sequences considering the scanning directions of shots for several MSOP instances. Our numerical experiments demonstrated that our proposed method was capable of computing exact optimal solutions for real-world MSOP instances having up to 232 shots on a wafer. These optimal solutions gave a 0.25% to 4.66% improvement in productivity over solutions computed by previously known methods. Y1 - 2013 U6 - https://doi.org/10.1299/jamdsm.7.608 VL - 7 IS - 4 SP - 608 EP - 618 ER - TY - JOUR A1 - Paulus, Florian A1 - Weiss, Maximilian A1 - Steinhilber, Dirk A1 - Nikitin, Anatoly A1 - Schütte, Christof A1 - Haag, Rainer T1 - Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights JF - Macromolecules Y1 - 2013 U6 - https://doi.org/10.1021/ma401712w VL - 46 IS - 21 SP - 8458 EP - 8466 ER - TY - JOUR A1 - Nikitin, B. A. A1 - Wulkow, Michael A1 - Schütte, Christof T1 - Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique JF - Macromolecular Theory and Simulation Y1 - 2013 U6 - https://doi.org/10.1002/mats.201300125 VL - 22 IS - 9 SP - 475 EP - 489 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study JF - Molecular Physics Y1 - 2013 U6 - https://doi.org/10.1080/00268976.2013.827254 VL - 111 IS - 22-23 SP - 3363 EP - 3371 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Ciccotti, Giovanni A1 - Delle Site, Luigi T1 - Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation JF - Journal of Chemical Theory and Computation Y1 - 2014 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 10 IS - 4 SP - 1376 EP - 1386 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Held, Harald A1 - Huang, Wei A1 - Vigerske, Stefan T1 - Towards globally optimal operation of water supply networks JF - Numerical Algebra, Control and Optimization N2 - This paper is concerned with optimal operation of pressurized water supply networks at a fixed point in time. We use a mixed-integer nonlinear programming (MINLP) model incorporating both the nonlinear physical laws and the discrete decisions such as switching pumps on and off. We demonstrate that for instances from our industry partner, these stationary models can be solved to ε-global optimality within small running times using problem-specific presolving and state-of-the-art MINLP algorithms. In our modeling, we emphasize the importance of distinguishing between what we call real and imaginary flow, i.e., taking into account that the law of Darcy-Weisbach correlates pressure difference and flow along a pipe if and only if water is available at the high pressure end of a pipe. Our modeling solution extends to the dynamic operative planning problem. Y1 - 2012 U6 - https://doi.org/10.3934/naco.2012.2.695 VL - 2 IS - 4 SP - 695 EP - 711 ER - TY - JOUR A1 - Moewis, Philippe A1 - Boeth, Heide A1 - Heller, Markus O. A1 - Yntema, Caroline A1 - Jung, Tobias A1 - Doyscher, Ralf A1 - Ehrig, Rainald A1 - Zhong, Yanlin A1 - Taylor, William R. T1 - Towards understanding knee joint laxity: Errors in non-invasive assessment of joint rotation can be corrected JF - Medical Engineering and Physics Y1 - 2014 U6 - https://doi.org/doi.org/10.1016/j.medengphy.2014.03.017 VL - 36 IS - 7 SP - 889 EP - 895 ER - TY - JOUR A1 - Duarte, Belmiro P.M. A1 - Sagnol, Guillaume A1 - Wong, Weng Kee T1 - An algorithm based on Semidefinite Programming for finding minimax optimal designs JF - Computational Statistics & Data Analysis Y1 - 2018 U6 - https://doi.org/10.1016/j.csda.2017.09.008 VL - 119 SP - 99 EP - 117 ER - TY - JOUR A1 - Knötel, David A1 - Seidel, Ronald A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage JF - PLOS ONE N2 - Introduction – Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays. Methods – Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size. Results – Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0188018 ER - TY - JOUR A1 - Schmidt, Martin A1 - Assmann, Denis A1 - Burlacu, Robert A1 - Humpola, Jesco A1 - Joormann, Imke A1 - Kanelakis, Nikolaos A1 - Koch, Thorsten A1 - Oucherif, Djamal A1 - Pfetsch, Marc A1 - Schewe, Lars A1 - Schwarz, Robert A1 - Sirvent, Matthias T1 - GasLib – A Library of Gas Network Instances JF - Data Y1 - 2017 U6 - https://doi.org/10.3390/data2040040 VL - 2 IS - 4 ER - TY - JOUR A1 - Schnauber, Peter A1 - Schall, Johannes A1 - Bounouar, Samir A1 - Höhne, Theresa A1 - Park, Suk-In A1 - Ryu, Geun-Hwan A1 - Heindel, Tobias A1 - Burger, Sven A1 - Song, Jin-Dong A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Deterministic integration of quantum dots into on-chip multi-mode interference beamsplitters using in-situ electron beam lithography JF - Nano Lett. Y1 - 2018 U6 - https://doi.org/10.1021/acs.nanolett.7b05218 VL - 18 SP - 2336 ER - TY - JOUR A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - On accurate simulations of thin-film solar cells with a thick glass superstrate JF - Opt. Express Y1 - 2018 U6 - https://doi.org/10.1364/OE.26.000A99 VL - 26 SP - A99 ER - TY - JOUR A1 - Cockayne, Jon A1 - Oates, Chris A1 - Sullivan, T. J. A1 - Girolami, Mark T1 - Bayesian Probabilistic Numerical Methods JF - SIAM Review N2 - Over forty years ago average-case error was proposed in the applied mathematics literature as an alternative criterion with which to assess numerical methods. In contrast to worst-case error, this criterion relies on the construction of a probability measure over candidate numerical tasks, and numerical methods are assessed based on their average performance over those tasks with respect to the measure. This paper goes further and establishes Bayesian probabilistic numerical methods as solutions to certain inverse problems based upon the numerical task within the Bayesian framework. This allows us to establish general conditions under which Bayesian probabilistic numerical methods are well defined, encompassing both the non-linear and non-Gaussian context. For general computation, a numerical approximation scheme is proposed and its asymptotic convergence established. The theoretical development is extended to pipelines of computation, wherein probabilistic numerical methods are composed to solve more challenging numerical tasks. The contribution highlights an important research frontier at the interface of numerical analysis and uncertainty quantification, and a challenging industrial application is presented. Y1 - 2019 U6 - https://doi.org/10.1137/17M1139357 VL - 61 IS - 4 SP - 756 EP - 789 ER - TY - JOUR A1 - Ehrig, Rainald A1 - Heller, Markus O. T1 - On intrinsic equivalences of the finite helical axis, the instantaneous helical axis, and the SARA approach. A mathematical perspective. JF - Journal of Biomechanics Y1 - 2019 U6 - https://doi.org/10.1016/j.jbiomech.2018.12.034 VL - 84 SP - 4 EP - 10 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Koltai, Péter A1 - Klus, Stefan A1 - Banisch, Ralf A1 - Dellnitz, Michael A1 - Schütte, Christof T1 - Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics JF - Jounal of Nonlinear Science N2 - We consider complex dynamical systems showing metastable behavior but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics. Y1 - 2018 U6 - https://doi.org/10.1007/s00332-017-9415-0 VL - 28 IS - 2 SP - 471 EP - 512 ER - TY - JOUR A1 - Schweiger, Jonas A1 - Liers, Frauke T1 - A Decomposition Approach for Optimal Gas Network Extension with a Finite Set of Demand Scenarios JF - Optimization and Engineering N2 - Today's gas markets demand more flexibility from the network operators which in turn have to invest into their network infrastructure. As these investments are very cost-intensive and long-living, network extensions should not only focus on a single bottleneck scenario, but should increase the flexibility to fulfill different demand scenarios. In this work, we formulate a model for the network extension problem for multiple demand scenarios and propose a scenario decomposition in order to solve the arising challenging optimization tasks. In fact, each subproblem consists of a mixed-integer nonlinear optimization problem (MINLP). Valid bounds on the objective value are derived even without solving the subproblems to optimality. Furthermore, we develop heuristics that prove capable of improving the initial solutions substantially. Results of computational experiments on realistic network topologies are presented. It turns out that our method is able to solve these challenging instances to optimality within a reasonable amount of time. Y1 - 2018 VL - 19 IS - 2 SP - 297 EP - 326 PB - Springer ER - TY - JOUR A1 - Gilg, Brady A1 - Klug, Torsten A1 - Martienssen, Rosemarie A1 - Paat, Joseph A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Seymen, Senan A1 - Tesch, Alexander T1 - Conflict-free railway track assignment at depots JF - Journal of Rail Transport Planning & Management N2 - Managing rolling stock with no passengers aboard is a critical component of railway operations. One aspect of managing rolling stock is to park the rolling stock on a given set of tracks at the end of a day or service. Depending on the parking assignment, shunting may be required in order for a parked train to depart or for an incoming train to park. Given a collection of tracks M and a collection of trains T with a fixed arrival-departure timetable, the train assignment problem (TAP) is to determine the maximum number of trains from T that can be parked on M according to the timetable and without the use of shunting. Hence, efficiently solving the TAP allows to quickly compute feasible parking schedules that do not require further shunting adjustments. In this paper, we show that the TAP is NP-hard and present two integer programming models for solving the TAP. We compare both models on a theoretical level. Moreover, to our knowledge, we consider the first approach that integrates track lengths along with the three most common types of parking tracks FIFO, LIFO and FREE tracks in a common model. Furthermore, to optimize against uncertainty in the arrival times of the trains we extend our models by stochastic and robust modeling techniques. We conclude by giving computational results for both models, observing that they perform well on real timetables. Y1 - 2018 U6 - https://doi.org/10.1016/j.jrtpm.2017.12.004 ER - TY - JOUR A1 - Lang, Annemarie A1 - Volkamer, Andrea A1 - Behm, Laura A1 - Röblitz, Susanna A1 - Ehrig, Rainald A1 - Schneider, Marlon A1 - Geris, Lisbet A1 - Wichard, Joerg A1 - Buttgereit, Frank T1 - In silico Methods - Computational Alternatives to Animal Testing JF - ALTEX N2 - A seminar and interactive workshop on “In silico Methods – Computational Alternatives to Animal Testing” was held in Berlin, Germany, organized by Annemarie Lang, Frank Butt- gereit and Andrea Volkamer at the Charité-Universitätsmedizin Berlin, on August 17-18, 2017. During the half-day seminar, the variety and applications of in silico methods as alternatives to animal testing were presented with room for scientific discus- sions with experts from academia, industry and the German fed- eral ministry (Fig. 1). Talks on computational systems biology were followed by detailed information on predictive toxicology in order to display the diversity of in silico methods and the potential to embrace them in current approaches (Hartung and Hoffmann, 2009; Luechtefeld and Hartung, 2017). The follow- ing interactive one-day Design Thinking Workshop was aimed at experts, interested researchers and PhD-students interested in the use of in silico as alternative methods to promote the 3Rs (Fig. 2). Forty participants took part in the seminar while the workshop was restricted to sixteen participants. Y1 - 2018 U6 - https://doi.org/10.14573/altex.1712031 VL - 35 IS - 1 SP - 126 EP - 128 ER - TY - JOUR A1 - Banisch, Ralf A1 - Djurdjevac Conrad, Natasa T1 - Cycle-flow-based module detection in directed recurrence networks JF - EPL (Europhysics Letters) Y1 - 2014 U6 - https://doi.org/10.1209/0295-5075/108/68008 VL - 108 IS - 6 ER - TY - JOUR A1 - Villatoro, Jose A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Riedel, Jens A1 - Beitz, Toralf A1 - Löhmannsröben, Hans-Gerd T1 - IR-MALDI ion mobility spectrometry JF - Analytical and Bioanalytical Chemistry Y1 - 2016 U6 - https://doi.org/10.1007/s00216-016-9739-x VL - 408 IS - 23 SP - 6259 EP - 6268 ER - TY - JOUR A1 - Igde, Sinaida A1 - Röblitz, Susanna A1 - Müller, Anne A1 - Kolbe, Katharina A1 - Boden, Sophia A1 - Fessele, Claudia A1 - Lindhorst, Thisbe A1 - Weber, Marcus A1 - Hartmann, Laura T1 - Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH JF - Marcomolecular Bioscience Y1 - 2017 U6 - https://doi.org/10.1002/mabi.201700198 VL - 17 IS - 12 SP - 1700198 ER - TY - JOUR A1 - Chen, Duote A1 - Manley, Phillip A1 - Tockhorn, Philipp A1 - Eisenhauer, David A1 - Köppel, Grit A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Albrecht, Steve A1 - Becker, Christiane A1 - Jäger, Klaus T1 - Nanophotonic Light Management for Perovskite-Silicon Tandem Solar Cells JF - J. Photonics Energy Y1 - 2018 U6 - https://doi.org/10.1117/1.JPE.8.022601 VL - 8 SP - 022601 ER - TY - JOUR A1 - Koltai, Peter A1 - Wu, Hao A1 - Noé, Frank A1 - Schütte, Christof T1 - Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics JF - Computation Y1 - 2018 U6 - https://doi.org/10.3390/computation6010022 VL - 6 IS - 1 PB - MDPI CY - Basel, Switzerland ER - TY - JOUR A1 - Dibak, Manuel A1 - del Razo, Mauricio J. A1 - de Sancho, David A1 - Schütte, Christof A1 - Noé, Frank T1 - MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations JF - Journal of Chemical Physics N2 - Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long time-scale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large length scales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time and length scales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step toward MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B ⇌ C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported. Y1 - 2018 U6 - https://doi.org/10.1063/1.5020294 VL - 148 IS - 21 ER - TY - JOUR A1 - Weber, Marcus T1 - Implications of PCCA+ in Molecular Simulation JF - Computation N2 - Upon ligand binding or during chemical reactions the state of a molecular system changes in time. Usually we consider a finite set of (macro-) states of the system (e.g., ’bound’ vs. ’unbound’), although the process itself takes place in a continuous space. In this context, the formula chi=XA connects the micro-dynamics of the molecular system to its macro-dynamics. Chi can be understood as a clustering of micro-states of a molecular system into a few macro-states. X is a basis of an invariant subspace of a transfer operator describing the micro-dynamics of the system. The formula claims that there is an unknown linear relation A between these two objects. With the aid of this formula we can understand rebinding effects, the electron flux in pericyclic reactions, and systematic changes of binding rates in kinetic ITC experiments. We can also analyze sequential spectroscopy experiments and rare event systems more easily. This article provides an explanation of the formula and an overview of some of its consequences. Y1 - 2018 U6 - https://doi.org/10.3390/computation6010020 VL - 6 IS - 1 SP - 20 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko JF - Advances in Physics: X N2 - Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending. Y1 - 2018 U6 - https://doi.org/10.1080/23746149.2017.1404436 VL - 3 IS - 1 SP - 1404436 ER - TY - JOUR A1 - Schmidtke, Robert A1 - Erleben, Kenny T1 - Chunked Bounding Volume Hierarchies for Fast Digital Prototyping using Volumetric Meshes JF - IEEE Transactions on Visualization and Computer Graphics N2 - We present a novel approach to using Bounding Volume Hierarchies (BVHs) for collision detection of volumetric meshes for digital prototyping based on accurate simulation. In general, volumetric meshes contain more primitives than surface meshes, which in turn means larger BVHs. To manage these larger BVHs, we propose an algorithm for splitting meshes into smaller chunks with a limited-size BVH each. Limited-height BVHs make guided, all-pairs testing of two chunked meshes well-suited for GPU implementation. This is because the dynamically generated work during BVH traversal becomes bounded. Chunking is simple to implement compared to dynamic load balancing methods and can result in an overall two orders of magnitude speedup on GPUs. This indicates that dynamic load balancing may not be a well suited scheme for the GPU. The overall application timings showed that data transfers were not the bottleneck. Instead, the conversion to and from OpenCL friendly data structures was causing serious performance impediments. Still, a simple OpenMP acceleration of the conversion allowed the GPU solution to beat the CPU solution by 20%. We demonstrate our results using rigid and deformable body scenes of varying complexities on a variety of GPUs. Y1 - 2018 U6 - https://doi.org/10.1109/TVCG.2017.2784441 SN - 1941-0506 VL - 24 IS - 12 SP - 3044 EP - 3057 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. A1 - Stuart, Andrew T1 - Strong convergence rates of probabilistic integrators for ordinary differential equations JF - Statistics and Computing N2 - Probabilistic integration of a continuous dynamical system is a way of systematically introducing model error, at scales no larger than errors inroduced by standard numerical discretisation, in order to enable thorough exploration of possible responses of the system to inputs. It is thus a potentially useful approach in a number of applications such as forward uncertainty quantification, inverse problems, and data assimilation. We extend the convergence analysis of probabilistic integrators for deterministic ordinary differential equations, as proposed by Conrad et al.\ (\textit{Stat.\ Comput.}, 2016), to establish mean-square convergence in the uniform norm on discrete- or continuous-time solutions under relaxed regularity assumptions on the driving vector fields and their induced flows. Specifically, we show that randomised high-order integrators for globally Lipschitz flows and randomised Euler integrators for dissipative vector fields with polynomially-bounded local Lipschitz constants all have the same mean-square convergence rate as their deterministic counterparts, provided that the variance of the integration noise is not of higher order than the corresponding deterministic integrator. Y1 - 2019 U6 - https://doi.org/10.1007/s11222-019-09898-6 VL - 29 IS - 6 SP - 1265 EP - 1283 ER - TY - JOUR A1 - Schäfer, Florian A1 - Sullivan, T. J. A1 - Owhadi, Houman T1 - Compression, inversion, and approximate PCA of dense kernel matrices at near-linear computational complexity JF - Multiscale Modeling and Simulation Y1 - 2021 U6 - https://doi.org/10.1137/19M129526X VL - 19 IS - 2 SP - 688 EP - 730 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Equivalence of weak and strong modes of measures on topological vector spaces JF - Inverse Problems N2 - Modes of a probability measure on an infinite-dimensional Banach space X are often defined by maximising the small-radius limit of the ratio of measures of norm balls. Helin and Burger weakened the definition of such modes by considering only balls with centres in proper subspaces of X, and posed the question of when this restricted notion coincides with the unrestricted one. We generalise these definitions to modes of arbitrary measures on topological vector spaces, defined by arbitrary bounded, convex, neighbourhoods of the origin. We show that a coincident limiting ratios condition is a necessary and sufficient condition for the equivalence of these two types of modes, and show that the coincident limiting ratios condition is satisfied in a wide range of topological vector spaces. Y1 - 2018 U6 - https://doi.org/10.1088/1361-6420/aadef2 VL - 34 IS - 11 SP - 115013 ER - TY - JOUR A1 - Schuster, Ingmar A1 - Constantine, Paul A1 - Sullivan, T. J. T1 - Exact active subspace Metropolis–Hastings, with applications to the Lorenz-96 system N2 - We consider the application of active subspaces to inform a Metropolis-Hastings algorithm, thereby aggressively reducing the computational dimension of the sampling problem. We show that the original formulation, as proposed by Constantine, Kent, and Bui-Thanh (SIAM J. Sci. Comput., 38(5):A2779-A2805, 2016), possesses asymptotic bias. Using pseudo-marginal arguments, we develop an asymptotically unbiased variant. Our algorithm is applied to a synthetic multimodal target distribution as well as a Bayesian formulation of a parameter inference problem for a Lorenz-96 system. Y1 - 2017 ER - TY - JOUR A1 - Schrade, Katharina A1 - Tröger, Jessica A1 - Eldashan, Adeep A1 - Zühlke, Kerstin A1 - Abdul Azees, Kamal R. A1 - Elkins, Jonathan M. A1 - Neuenschwander, Martin A1 - Oder, Andreas A1 - Elkewedi, Mohamed A1 - Jaksch, Sarah A1 - Andrae, Karsten A1 - Li, Jinliang A1 - Fernandes, Jaoa A1 - Müller, Paul Markus A1 - Grunwald, Stephan A1 - Marino, Stephen F. A1 - Vukicevic, Tanja A1 - Eichhorst, Jenny A1 - Wiesner, Burkhard A1 - Weber, Marcus A1 - Kapiloff, Michael A1 - Rocks, Oliver A1 - Daumke, Oliver A1 - Wieland, Thomas A1 - Knapp, Stefan A1 - von Kries, Jens Peter A1 - Klussmann, Enno T1 - An AKAP-Lbc-RhoA interaction inhibitor promotes the translocation of aquaporin-2 to the plasma membrane of renal collecting duct principal cells JF - PLOS ONE N2 - Stimulation of renal collecting duct principal cells with antidiuretic hormone (arginine-vasopressin, AVP) results in inhibition of the small GTPase RhoA and the enrichment of the water channel aquaporin-2 (AQP2) in the plasma membrane. The membrane insertion facilitates water reabsorption from primary urine and fine-tuning of body water homeostasis. Rho guanine nucleotide exchange factors (GEFs) interact with RhoA, catalyze the exchange of GDP for GTP and thereby activate the GTPase. However, GEFs involved in the control of AQP2 in renal principal cells are unknown. The A-kinase anchoring protein, AKAP-Lbc, possesses GEF activity, specifically activates RhoA, and is expressed in primary renal inner medullary collecting duct principal (IMCD) cells. Through screening of 18,431 small molecules and synthesis of a focused library around one of the hits, we identified an inhibitor of the interaction of AKAP-Lbc and RhoA. This molecule, Scaff10-8, bound to RhoA, inhibited the AKAP-Lbc-mediated RhoA activation but did not interfere with RhoA activation through other GEFs or activities of other members of the Rho family of small GTPases, Rac1 and Cdc42. Scaff10-8 promoted the redistribution of AQP2 from intracellular vesicles to the periphery of IMCD cells. Thus, our data demonstrate an involvement of AKAP-Lbc-mediated RhoA activation in the control of AQP2 trafficking. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0191423 VL - 13 IS - 1 SP - e0191423 EP - e0191423 ER - TY - JOUR A1 - Tierney, Nicholas J. A1 - Mira, Antonietta A1 - Reinhold, J. Jost A1 - Weiser, Martin A1 - Burkart, Roman A1 - Benvenuti, Claudio A1 - Auricchio, Angelo T1 - Novel relocation methods for automatic external defibrillator improve out-of-hospital cardiac arrest coverage under limited resources JF - Resuscitation N2 - Background Mathematical optimisation models have recently been applied to identify ideal Automatic External Defibrillator (AED) locations that maximise coverage of Out of Hospital Cardiac Arrest (OHCA). However, these fixed location models cannot relocate existing AEDs in a flexible way, and have nearly exclusively been applied to urban regions. We developed a flexible location model for AEDs, compared its performance to existing fixed location and population models, and explored how these perform across urban and rural regions. Methods Optimisation techniques were applied to AED deployment and OHCA coverage was assessed. A total of 2802 geolocated OHCAs occurred in Canton Ticino, Switzerland, from January 1st 2005 to December 31st 2015. Results There were 719 AEDs in Canton Ticino. 635 (23%) OHCA events occurred within 100m of an AED, with 306 (31%) in urban, and 329 (18%) in rural areas. Median distance from OHCA events to the nearest AED was 224m (168m urban vs. 269m rural). Flexible location models performed better than fixed location and population models, with the cost to deploy 20 new AEDs instead relocating 171 existing AEDs to new locations, improving OHCA coverage to 38%, compared to 26% using fixed models, and 24% with the population based model. Conclusions Optimisation models for AEDs placement are superior to population models and should be strongly considered by communities when selecting areas for AED deployment. Compared to other models, flexible location models increase overall OHCA coverage, and decreases the distance to nearby AEDs, even in rural areas, while saving significant financial resources. Y1 - 2018 U6 - https://doi.org/10.1016/j.resuscitation.2018.01.055 IS - 125 SP - 83 EP - 89 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Zschiedrich, Lin A1 - Reitzenstein, Stephan A1 - Burger, Sven T1 - Numerical optimization of the extraction efficiency of a quantum-dot based single-photon emitter into a single-mode fiber JF - Opt. Express Y1 - 2018 U6 - https://doi.org/10.1364/OE.26.008479 VL - 26 SP - 8479 ER - TY - JOUR A1 - Santiago, Xavier Garcia A1 - Schneider, Philipp-Immanuel A1 - Rockstuhl, Carsten A1 - Burger, Sven T1 - Shape design of a reflecting surface using Bayesian Optimization JF - J. Phys.: Conf. Ser. Y1 - 2018 U6 - https://doi.org/10.1088/1742-6596/963/1/012003 VL - 963 SP - 012003 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Schneider, Philipp-Immanuel A1 - Burger, Sven A1 - Nieto-Vesperinas, Manuel T1 - Chiral scatterers designed by Bayesian optimization JF - J. Phys.: Conf. Ser. Y1 - 2018 U6 - https://doi.org/10.1088/1742-6596/963/1/012004 VL - 963 SP - 012004 ER - TY - JOUR A1 - Gutsche, Philipp A1 - Nieto-Vesperinas, Manuel T1 - Optical Chirality of Time-Harmonic Wavefields for Classification of Scatterers JF - Sci. Rep. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-27496-w VL - 8 SP - 9416 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Pabisiak, Jakub A1 - Perez-Gea, Ana Cristina A1 - Julian, Nicolas A1 - Hon, Sean A1 - Burger, Sven T1 - Efficient finite-element-based numerical modelling of large sub-wavelength patterned optical structures JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2292438 VL - 10542 SP - 105421G ER - TY - JOUR A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita A1 - Zachow, Stefan T1 - Uncertainty in Temperature-Based Determination of Time of Death JF - Heat and Mass Transfer N2 - Temperature-based estimation of time of death (ToD) can be per- formed either with the help of simple phenomenological models of corpse cooling or with detailed mechanistic (thermodynamic) heat transfer mod- els. The latter are much more complex, but allow a higher accuracy of ToD estimation as in principle all relevant cooling mechanisms can be taken into account. The potentially higher accuracy depends on the accuracy of tissue and environmental parameters as well as on the geometric resolution. We in- vestigate the impact of parameter variations and geometry representation on the estimated ToD based on a highly detailed 3D corpse model, that has been segmented and geometrically reconstructed from a computed to- mography (CT) data set, differentiating various organs and tissue types. Y1 - 2018 U6 - https://doi.org/10.1007/s00231-018-2324-4 VL - 54 IS - 9 SP - 2815 EP - 2826 PB - Springer ER - TY - JOUR A1 - Klus, Stefan A1 - Schuster, Ingmar A1 - Muandet, Krikamol T1 - Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces JF - Journal of Machine Learning Research N2 - Transfer operators such as the Perron-Frobenius or Koopman operator play an important role in the global analysis of complex dynamical systems. The eigenfunctions of these operators can be used to detect metastable sets, to project the dynamics onto the dominant slow processes, or to separate superimposed signals. We extend transfer operator theory to reproducing kernel Hilbert spaces and show that these operators are related to Hilbert space representations of conditional distributions, known as conditional mean embeddings in the machine learning community. Moreover, numerical methods to compute empirical estimates of these embeddings are akin to data-driven methods for the approximation of transfer operators such as extended dynamic mode decomposition and its variants. In fact, most of the existing methods can be derived from our framework, providing a unifying view on the approximation of transfer operators. One main benefit of the presented kernel-based approaches is that these methods can be applied to any domain where a similarity measure given by a kernel is available. We illustrate the results with the aid of guiding examples and highlight potential applications in molecular dynamics as well as video and text data analysis. Y1 - 2017 ER - TY - JOUR A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Gross, Markus A1 - Theisel, Holger T1 - Progressive Monte Carlo rendering of atmospheric flow features across scales JF - Physical Review Fluids N2 - To improve existing weather prediction and reanalysis capabilities, high-resolution and multi-modal climate data becomes an increasingly important topic. The advent of increasingly dense numerical simulation of atmospheric phenomena, provides new means to better understand dynamic processes and to visualize structural flow patterns that remain hidden otherwise. In the presented illustrations we demonstrate an advanced technique to visualize multiple scales of dense flow fields and Lagrangian patterns therein, simulated by state-of-the-art simulation models for each scale. They provide a deeper insight into the structural differences and patterns that occur on each scale and highlight the complexity of flow phenomena in our atmosphere. This paper is associated with a poster winner of a 2016 APS/DFD Milton van Dyke Award for work presented at the DFD Gallery of Fluid Motion. The original poster is available from the Gallery of Fluid Motion, https://doi.org/10.1103/APS.DFD.2016.GFM.P0030 Y1 - 2017 U6 - https://doi.org/10.1103/PhysRevFluids.2.090502 VL - 2 SP - 09050-1 EP - 09050-3 ER - TY - JOUR A1 - Zschiedrich, Lin A1 - Binkowski, Felix A1 - Nikolay, Niko A1 - Benson, Oliver A1 - Kewes, Günter A1 - Burger, Sven T1 - Riesz-projection-based theory of light-matter interaction in dispersive nanoresonators JF - Phys. Rev. A Y1 - 2018 U6 - https://doi.org/10.1103/PhysRevA.98.043806 VL - 98 SP - 043806 ER - TY - JOUR A1 - Spahn, Viola A1 - Del Vecchio, Giovanna A1 - Labuz, Dominika A1 - Rodriguez-Gaztelumendi, Antonio A1 - Massaly, N. A1 - Temp, Julia A1 - Durmaz, Vedat A1 - Sabri, P. A1 - Reidelbach, Marco A1 - Machelska, Halina A1 - Weber, Marcus A1 - Stein, Christoph T1 - A nontoxic pain killer designed by modeling of pathological receptor conformations JF - Science Y1 - 2017 U6 - https://doi.org/10.1126/science.aai8636 VL - 355 IS - 6328 SP - 966 EP - 969 ER - TY - JOUR A1 - Kreisbeck, Christoph A1 - Kramer, Tobias A1 - Molina, Rafael T1 - Time-dependent wave packet simulations of transport through Aharanov–Bohm rings with an embedded quantum dot JF - Journal of Physics: Condensed Matter N2 - We have performed time-dependent wave packet simulations of realistic Aharonov-Bohm (AB) devices with a quantum dot embedded in one of the arms of the interferometer. The AB ring can function as a measurement device for the intrinsic transmission phase through the quantum dot, however, care has to be taken in analyzing the influence of scattering processes in the junctions of the interferometer arms. We consider a harmonic quantum dot and show how the Darwin–Fock spectrum emerges as a unique pattern in the interference fringes of the AB oscillations. Y1 - 2017 U6 - https://doi.org/10.1088/1361-648X/aa605d VL - 29 IS - 15 SP - 155301 ER - TY - JOUR A1 - Zander, Thomas A1 - Dreischarf, Marcel A1 - Timm, Anne-Katrin A1 - Baumann, Wolfgang A1 - Schmidt, Hendrik T1 - Impact of material and morphological parameters on the mechanical response of the lumbar spine - A finite element sensitivity study JF - Journal of Biomechanics KW - finite element modelling KW - lumbar spine KW - sensitivity analysis KW - model validation KW - coefficient of determination Y1 - 2016 U6 - https://doi.org/10.1016/j.jbiomech.2016.12.014 VL - 53 SP - 185 EP - 190 ER - TY - JOUR A1 - Ritter, Zully A1 - Belavy, Daniel A1 - Baumann, Wolfgang A1 - Felsenberg, Dieter T1 - In vivo bone remodeling rates determination and compressive stiffness variations before, during 60 days bed rest and two years follow up: a micro-FE-analysis from HR-pQCT measurements of the Berlin bed rest study-2 JF - Acta Astronautica KW - finite-element analysis KW - bone structure KW - compressive stiffness KW - bed rest KW - HR-pQCT measurement Y1 - 2017 U6 - https://doi.org/10.1016/j.actaastro.2016.12.002 VL - 132 SP - 67 EP - 77 ER - TY - JOUR A1 - Kramer, Tobias A1 - Rodriguez, Mirta A1 - Zelinskyi, Yaroslav T1 - Modeling of Transient Absorption Spectra in Exciton Charge-Transfer Systems JF - Journal of Physical Chemistry B N2 - Time-resolved spectroscopy provides the main tool for analyzing the dynamics of excitonic energy transfer in light-harvesting complexes. To infer time-scales and effective coupling parameters from experimental data requires to develop numerical exact theoretical models. The finite duration of the laser-molecule interactions and the reorganization process during the exciton migration affect the location and strength of spectroscopic signals. We show that the non-perturbative hierarchical equations of motion (HEOM) method captures these processes in a model exciton system, including the charge transfer state. Y1 - 2017 U6 - https://doi.org/10.1021/acs.jpcb.6b09858 VL - 121 SP - 463 EP - 470 ER - TY - JOUR A1 - Tesch, Alexander T1 - Kompakte MIP Modelle für das Ressourcenbeschränkte Projektplanungsproblem JF - OR News Y1 - 2016 VL - 58 SP - 19 EP - 21 ER - TY - JOUR A1 - Kickhöfer, Benjamin A1 - Kern, Julia T1 - Pricing local emission exposure of road traffic: An agent-based approach JF - Transportation Research Part D: Transport and Environment N2 - This paper proposes a new approach to iteratively calculate local air pollution exposure tolls in large-scale urban settings by taking the exposure times and locations of individuals into consideration. It explicitly avoids detailed air pollution concentration calculations and is therefore characterized by little data requirements, reasonable computation times for iterative calculations, and open-source compatibility. In a first step, the paper shows how to derive time-dependent vehicle-specific exposure tolls in an agent-based model. It closes the circle from the polluting entity, to the receiving entity, to damage costs, to tolls, and back to the behavioral change of the polluting entity. In a second step, the approach is applied to a large-scale real-world scenario of the Munich metropolitan area in Germany. Changes in emission levels, exposure costs, and user benefits are calculated. These figures are compared to a flat emission toll, and to a regulatory measure (a speed reduction in the inner city), respectively. The results indicate that the flat emission toll reduces overall emissions more significantly than the exposure toll, but its exposure cost reductions are rather small. For the exposure toll, overall emissions increase for freight traffic which implies a potential conflict between pricing schemes to optimize local emission exposure and others to abate climate change. Regarding the mitigation of exposure costs caused by urban travelers, the regulatory measure is found to be an effective strategy, but it implies losses in user benefits. Y1 - 2015 U6 - https://doi.org/10.1016/j.trd.2015.04.019 VL - 37 SP - 14 EP - 28 ER - TY - JOUR A1 - Weiser, Martin A1 - Ghosh, Sunayana T1 - Theoretically optimal inexact SDC methods JF - Communications in Applied Mathematics and Computational Science N2 - In several inital value problems with particularly expensive right hand side evaluation or implicit step computation, there is a trade-off between accuracy and computational effort. We consider inexact spectral deferred correction (SDC) methods for solving such initial value problems. SDC methods are interpreted as fixed point iterations and, due to their corrective iterative nature, allow to exploit the accuracy-work-tradeoff for a reduction of the total computational effort. On one hand we derive error models bounding the total error in terms of the evaluation errors. On the other hand, we define work models describing the computational effort in terms of the evaluation accuracy. Combining both, a theoretically optimal local tolerance selection is worked out by minimizing the total work subject to achieving the requested tolerance. The properties of optimal local tolerances and the predicted efficiency gain compared to simpler heuristics, and a reasonable practical performance, are illustrated on simple numerical examples. Y1 - 2018 U6 - https://doi.org/10.2140/camcos.2018.13.53 IS - 13-1 SP - 53 EP - 86 ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse 3D Point-Clouds JF - Medical Image Analysis N2 - The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process of aligning intra-operative navigation and preoperative planning data. In such scenarios, one usually has to deal with sparse data, which significantly aggravates the problem of reconstruction. However, medical applications often provide contextual information about the 3D point data that allow to incorporate prior knowledge about the shape that is to be reconstructed. To this end, we propose the use of a statistical shape model (SSM) as a prior for surface reconstruction. The SSM is represented by a point distribution model (PDM), which is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we formulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given points are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are “oriented” according to the surface normals at the PDM points, a surface-based fitting is accomplished. Estimating the parameters of the GMM in a maximum a posteriori manner yields the reconstruction of the surface from the given data points. We compare our method to the extensively used Iterative Closest Points method on several different anatomical datasets/SSMs (brain, femur, tibia, hip, liver) and demonstrate superior accuracy and robustness on sparse data. Y1 - 2017 UR - http://www.sciencedirect.com/science/article/pii/S1361841517300233 U6 - https://doi.org/10.1016/j.media.2017.02.005 VL - 38 SP - 77 EP - 89 ER - TY - JOUR A1 - Ledentsov, Jr., Nikolay A1 - Shchukin, Vitaly A1 - Kropp, Jörg-R. A1 - Zschiedrich, Lin A1 - Schmidt, Frank A1 - Ledentsov, Jr., Nikolay T1 - Resonant cavity light–emitting diodes based on dielectric passive cavity structures JF - Proc. SPIE Y1 - 2017 U6 - https://doi.org/10.1117/12.2253089 VL - 10124 SP - 101240O ER - TY - JOUR A1 - Zhukova, Yulia A1 - Hiepen, Christian A1 - Knaus, Petra A1 - Osterland, Marc A1 - Prohaska, Steffen A1 - Dunlop, John W. C. A1 - Fratzl, Peter A1 - Skorb, Ekaterina V. T1 - The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration JF - Advanced Healthcare Materials N2 - Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair. Y1 - 2017 U6 - https://doi.org/10.1002/adhm.201601244 ER - TY - JOUR A1 - Lube, Juliane A1 - Flack, Natasha A1 - Cotofana, Sebastian A1 - Özkurtul, Orkun A1 - Woodley, Stephanie A1 - Zachow, Stefan A1 - Hammer, Niels T1 - Pelvic and lower extremity physiological cross-sectional areas: An MRI study of the living young and comparison to published research literature JF - Surgical and Radiologic Anatomy N2 - Purpose: Morphological data pertaining to the pelvis and lower extremity muscles are increasingly being used in biomechanical modeling to compare healthy and pathological conditions. Very few data sets exist that encompass all of the muscles of the lower limb, allowing for comparisons between regions. The aims of this study were to (a) provide physiological cross-sectional area (PCSA) data for the pelvic, thigh, and leg muscles in young, healthy participants, using magnetic resonance imaging (MRI), and (b) to compare these data with summarized PCSAs obtained from the literature. Materials and Methods: Six young and healthy volunteers participated and were scanned using 3 T MRI. PCSAs were calculated from volumetric segmentations obtained bilaterally of 28 muscles/muscle groups of the pelvis, thigh, and leg. These data were compared to published, summarized PCSA data derived from cadaveric, computed tomography, MRI and ultrasound studies. Results: The PCSA of the pelvis, thigh, and leg muscles tended to be 20–130% larger in males than in females, except for the gemelli which were 34% smaller in males, and semitendinosus and triceps surae which did not differ (<20% different). The dominant and the non-dominant sides showed similar and minutely different PCSA with less than 18% difference between sides. Comparison to other studies revealed wide ranges within, and large differences between, the cadaveric and imaging PCSA data. Comparison of the PCSA of this study and published literature revealed major differences in the iliopsoas, gluteus minimus, tensor fasciae latae, gemelli, obturator internus, biceps femoris, quadriceps femoris, and the deep leg flexor muscles. Conclusions: These volume-derived PCSAs of the pelvic and lower limb muscles alongside the data synthesised from the literature may serve as a basis for comparative and biomechanical studies of the living and healthy young, and enable calculation of muscle forces. Comparison of the literature revealed large variations in PCSA from each of the different investigative modalities, hampering omparability between studies. Sample size, age, post-mortem changes of muscle tone, chemical fixation of cadaveric tissues, and the underlying physics of the imaging techniques may potentially influence PCSA calculations. Y1 - 2017 U6 - https://doi.org/10.1007/s00276-016-1807-6 VL - 39 IS - 8 SP - 849 EP - 857 ER - TY - JOUR A1 - Mukhopadhyay, Anirban A1 - Bhandarkar, Suchendra T1 - Biharmonic Density Estimate - a scale space descriptor for 3D deformable surfaces JF - Pattern Analysis and Application Y1 - 2017 U6 - https://doi.org/10.1007/s10044-017-0610-2 SP - 1 EP - 13 ER - TY - JOUR A1 - Kramer, Tobias A1 - Rodriguez, Mirta T1 - Two-dimensional electronic spectra of the photosynthetic apparatus of green sulfur bacteria JF - Scientific Reports N2 - Advances in time resolved spectroscopy have provided new insight into the energy transmission in natural photosynthetic complexes. Novel theoretical tools and models are being developed in order to explain the experimental results. We provide a model calculation for the two-dimensional electronic spectra of Cholorobaculum tepidum which correctly describes the main features and transfer time scales found in recent experiments. From our calculation one can infer the coupling of the antenna chlorosome with the environment and the coupling between the chlorosome and the Fenna-Matthews-Olson complex. We show that environment assisted transport between the subunits is the required mechanism to reproduce the experimental two-dimensional electronic spectra. Y1 - 2017 U6 - https://doi.org/10.1038/srep45245 VL - 7 SP - 45245 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Quasi-invariance of countable products of Cauchy measures under non-unitary dilations JF - Electronic Communications in Probability Y1 - 2018 U6 - https://doi.org/10.1214/18-ECP113 VL - 23 IS - 8 SP - 1 EP - 6 ER - TY - JOUR A1 - Sahu, Manish A1 - Mukhopadhyay, Anirban A1 - Szengel, Angelika A1 - Zachow, Stefan T1 - Addressing multi-label imbalance problem of Surgical Tool Detection using CNN JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose: A fully automated surgical tool detection framework is proposed for endoscopic video streams. State-of-the-art surgical tool detection methods rely on supervised one-vs-all or multi-class classification techniques, completely ignoring the co-occurrence relationship of the tools and the associated class imbalance. Methods: In this paper, we formulate tool detection as a multi-label classification task where tool co-occurrences are treated as separate classes. In addition, imbalance on tool co-occurrences is analyzed and stratification techniques are employed to address the imbalance during Convolutional Neural Network (CNN) training. Moreover, temporal smoothing is introduced as an online post-processing step to enhance run time prediction. Results: Quantitative analysis is performed on the M2CAI16 tool detection dataset to highlight the importance of stratification, temporal smoothing and the overall framework for tool detection. Conclusion: The analysis on tool imbalance, backed by the empirical results indicates the need and superiority of the proposed framework over state-of-the-art techniques. Y1 - 2017 UR - https://link.springer.com/article/10.1007/s11548-017-1565-x U6 - https://doi.org/10.1007/s11548-017-1565-x N1 - Selected for final oral presentation VL - 12 IS - 6 SP - 1013 EP - 1020 PB - Springer ER - TY - JOUR A1 - Klus, Stefan A1 - Schütte, Christof T1 - Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator JF - Journal of Computational Dynamics N2 - The global behavior of dynamical systems can be studied by analyzing the eigenvalues and corresponding eigenfunctions of linear operators associated with the system. Two important operators which are frequently used to gain insight into the system's behavior are the Perron-Frobenius operator and the Koopman operator. Due to the curse of dimensionality, computing the eigenfunctions of high-dimensional systems is in general infeasible. We will propose a tensor-based reformulation of two numerical methods for computing finite-dimensional approximations of the aforementioned infinite-dimensional operators, namely Ulam's method and Extended Dynamic Mode Decomposition (EDMD). The aim of the tensor formulation is to approximate the eigenfunctions by low-rank tensors, potentially resulting in a significant reduction of the time and memory required to solve the resulting eigenvalue problems, provided that such a low-rank tensor decomposition exists. Typically, not all variables of a high-dimensional dynamical system contribute equally to the system's behavior, often the dynamics can be decomposed into slow and fast processes, which is also reflected in the eigenfunctions. Thus, the weak coupling between different variables might be approximated by low-rank tensor cores. We will illustrate the efficiency of the tensor-based formulation of Ulam's method and EDMD using simple stochastic differential equations. Y1 - 2016 U6 - https://doi.org/10.3934/jcd.2016007 VL - 3 IS - 2 SP - 139 EP - 161 ER - TY - JOUR A1 - Klus, Stefan A1 - Koltai, Peter A1 - Schütte, Christof T1 - On the numerical approximation of the Perron-Frobenius and Koopman operator JF - Journal of Computational Dynamics N2 - Information about the behavior of dynamical systems can often be obtained by analyzing the eigenvalues and corresponding eigenfunctions of linear operators associated with a dynamical system. Examples of such operators are the Perron-Frobenius and the Koopman operator. In this paper, we will review di� fferent methods that have been developed over the last decades to compute � infinite-dimensional approximations of these in� finite-dimensional operators - in particular Ulam's method and Extended Dynamic Mode Decomposition (EDMD) - and highlight the similarities and di� fferences between these approaches. The results will be illustrated using simple stochastic di� fferential equations and molecular dynamics examples. Y1 - 2016 U6 - https://doi.org/10.3934/jcd.2016003 VL - 3 IS - 1 SP - 51 EP - 77 ER - TY - JOUR A1 - Suinesiaputra, Avan A1 - Albin, Pierre A1 - Alba, Xenia A1 - Alessandrini, Martino A1 - Allen, Jack A1 - Bai, Wenjia A1 - Cimen, Serkan A1 - Claes, Peter A1 - Cowan, Brett A1 - D'hooge, Jan A1 - Duchateau, Nicolas A1 - Ehrhardt, Jan A1 - Frangi, Alejandro A1 - Gooya, Ali A1 - Grau, Vicente A1 - Lekadir, Karim A1 - Lu, Allen A1 - Mukhopadhyay, Anirban A1 - Oksuz, Ilkay A1 - Parajuli, Nripesh A1 - Pennec, Xavier A1 - Pereanez, Marco A1 - Pinto, Catarina A1 - Piras, Paolo A1 - Rohe, Marc-Michael A1 - Rueckert, Daniel A1 - Saring, Dennis A1 - Sermesant, Maxime A1 - Siddiqi, Kaleem A1 - Tabassian, Mahdi A1 - Teresi, Lusiano A1 - Tsaftaris, Sotirios A1 - Wilms, Matthias A1 - Young, Alistair A1 - Zhang, Xingyu A1 - Medrano-Gracia, Pau T1 - Statistical shape modeling of the left ventricle: myocardial infarct classification challenge JF - IEEE Journal of Biomedical and Health Informatics N2 - Statistical shape modeling is a powerful tool for visualizing and quantifying geometric and functional patterns of the heart. After myocardial infarction (MI), the left ventricle typically remodels in response to physiological challenges. Several methods have been proposed in the literature to describe statistical shape changes. Which method best characterizes left ventricular remodeling after MI is an open research question. A better descriptor of remodeling is expected to provide a more accurate evaluation of disease status in MI patients. We therefore designed a challenge to test shape characterization in MI given a set of three-dimensional left ventricular surface points. The training set comprised 100 MI patients, and 100 asymptomatic volunteers (AV). The challenge was initiated in 2015 at the Statistical Atlases and Computational Models of the Heart workshop, in conjunction with the MICCAI conference. The training set with labels was provided to participants, who were asked to submit the likelihood of MI from a different (validation) set of 200 cases (100 AV and 100 MI). Sensitivity, specificity, accuracy and area under the receiver operating characteristic curve were used as the outcome measures. The goals of this challenge were to (1) establish a common dataset for evaluating statistical shape modeling algorithms in MI, and (2) test whether statistical shape modeling provides additional information characterizing MI patients over standard clinical measures. Eleven groups with a wide variety of classification and feature extraction approaches participated in this challenge. All methods achieved excellent classification results with accuracy ranges from 0.83 to 0.98. The areas under the receiver operating characteristic curves were all above 0.90. Four methods showed significantly higher performance than standard clinical measures. The dataset and software for evaluation are available from the Cardiac Atlas Project website1. Y1 - 2017 U6 - https://doi.org/10.1109/JBHI.2017.2652449 IS - 99 ER - TY - JOUR A1 - Rusch, Beate A1 - Albrecht, Rita A1 - Meßmer, Gabriele A1 - Thiessen, Peter T1 - Katalogisierung in der Datenwolke JF - Zeitschrift für Bibliothekswesen und Bibliographie Y1 - 2016 U6 - https://doi.org/10.3196/1864295016635631 VL - Jahrgang 63 IS - Heft 5-6 SP - 258 EP - 264 ER - TY - JOUR A1 - Lohrum, Stefan A1 - Kratzer, Mathias A1 - Risch, Uwe A1 - Thiessen, Peter T1 - Zum Stand des Projektes "Cloudbasierte Infrastruktur für Bibliotheksdaten" (CIB) JF - Zeitschrift für Bibliothekswesen und Bibliographie Y1 - 2016 U6 - https://doi.org/10.3196/1864295016635627 VL - Jahrgang 63 IS - Heft 5-6 SP - 250 EP - 257 ER - TY - JOUR A1 - Baum, Daniel A1 - Lindow, Norbert A1 - Hege, Hans-Christian A1 - Lepper, Verena A1 - Siopi, Tzulia A1 - Kutz, Frank A1 - Mahlow, Kristin A1 - Mahnke, Heinz-Eberhard T1 - Revealing hidden text in rolled and folded papyri JF - Applied Physics A N2 - Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds. Y1 - 2017 U6 - https://doi.org/10.1007/s00339-017-0808-6 VL - 123 IS - 3 SP - 171 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Template-based Re-optimization of Rolling Stock Rotations JF - Public Transport N2 - Rolling stock, i.e., the set of railway vehicles, is among the most expensive and limited assets of a railway company and must be used efficiently. We consider in this paper the re-optimization problem to recover from unforeseen disruptions. We propose a template concept that allows to recover cost minimal rolling stock rotations from reference rotations under a large variety of operational requirements. To this end, connection templates as well as rotation templates are introduced and their application within a rolling stock rotation planning model is discussed. We present an implementation within the rolling stock rotation optimization framework rotor and computational results for scenarios provided by DB Fernverkehr AG, one of the leading railway operators in Europe. Y1 - 2017 U6 - https://doi.org/10.1007/s12469-017-0152-4 SP - 1 EP - 19 PB - Springer ER - TY - JOUR A1 - Chrapary, Hagen A1 - Dalitz, Wolfgang A1 - Sperber, Wolfram T1 - swMATH - Challenges, Next Steps, and Outlook JF - CICM-WS-WIP 2016, Workshop and Work in Progress Papers at CICM 2016 N2 - swMATH is currently one of the most comprehensive specialized information services and search engines for Mathematical SoftWare (MSW). It was the intention of the project to support the user community by providing infor- mation about MSW and searching relevant MSW. Currently swMATH lists infor- mation of more than 13,000 items and 120,000 publications which refer to MSW. Maintaining and updating of the service is mainly done automatically, the num- ber of requests is permanently increasing. This sounds like a perfect solution. But swMATH is only a first step to a powerful information system on mathematical research data. This talk addresses some open problems for the further develop- ment of the swMATH service. It is shown that some problems for swMATH lead to central questions for the information management of mathematical research data, especially for MSW. This contains an extended content analysis of MSW, versioning and citation standard of MSW, a typing of the swMATH resources and the presentation of context information and high-quality control within the swMATH service. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0074-1785-8 VL - Vol-1785 SP - 107 EP - 116 ER - TY - JOUR A1 - Orgis, Thomas A1 - Läuter, Matthias A1 - Handorf, Dörthe A1 - Dethloff, Klaus T1 - Baroclinic waves on the β plane using low-order Discontinuous Galerkin discretisation JF - Journal of Computational Physics N2 - A classic Discontinuous Galerkin Method with low-order polynomials and explicit as well as semi-implicit time-stepping is applied to an atmospheric model employing the Euler equations on the β plane. The method, which was initially proposed without regard for the source terms and their balance with the pressure gradient that dominates atmospheric dynamics, needs to be adapted to be able to keep the combined geostrophic and hydrostatic balance in three spatial dimensions. This is achieved inside the discretisation through a polynomial mapping of both source and flux terms without imposing filters between time steps. After introduction and verification of this balancing, the realistic development of barotropic and baroclinic waves in the model is demonstrated, including the formation of a retrograde Rossby wave pattern. A prerequesite is the numerical solution of the thermal wind equation to construct geostrophically balanced initial states in z coordinates with arbitrary prescribed zonal wind profile, offering a new set of test cases for atmospheric models employing z coordinates. The resulting simulations demonstrate that the balanced low-order Discontinous Galerkin discretisation with polynomial degrees down to k=1 can be a viable option for atmospheric modelling. Y1 - 2017 U6 - https://doi.org/10.1016/j.jcp.2017.03.029 VL - 339 SP - 461 EP - 481 ER - TY - JOUR A1 - Rüdrich, S. A1 - Sarich, Marco A1 - Schütte, Christof T1 - Utilizing hitting times for finding metastable sets in non-reversible Markov chains JF - Journal of Comp. Dynamics Y1 - 2017 ER - TY - JOUR A1 - Gupta, Pooja A1 - Gramatke, Annika A1 - Einspanier, Ralf A1 - Schütte, Christof A1 - von Kleist, Max A1 - Sharbati, Jutta T1 - In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements JF - Toxicology in Vitro N2 - Early and reliable identification of chemical toxicity is of utmost importance. At the same time, reduction of animal testing is paramount. Therefore, methods that improve the interpretability and usability of in vitro assays are essential. xCELLigence’s real-time cell analyzer (RTCA) provides a novel, fast and cost effective in vitro method to probe compound toxicity. We developed a simple mathematical framework for the qualitative and quantitative assessment of toxicity for RTCA measurements. Compound toxicity, in terms of its 50% inhibitory concentration IC50 on cell growth, and parameters related to cell turnover were estimated on cultured IEC-6 cells exposed to 10 chemicals at varying concentrations. Our method estimated IC50 values of 113.05, 7.16, 28.69 and 725.15 μM for the apparently toxic compounds 2-acetylamino-fluorene, aflatoxin B1, benzo-[a]-pyrene and chloramphenicol in the tested cell line, in agreement with literature knowledge. IC50 values of all apparent in vivo non-toxic compounds were estimated to be non-toxic by our method. Corresponding estimates from RTCA’s in-built model gave false positive (toxicity) predictions in 5/10 cases. Taken together, our proposed method reduces false positive predictions and reliably identifies chemical toxicity based on impedance measurements. The source code for the developed method including instructions is available at https://git.zib.de/bzfgupta/toxfit/tree/master. KW - Real-time cell analyzer KW - Toxicity KW - Mathematical modeling Y1 - 2017 SN - 1438-0064 VL - 41 SP - 179 EP - 188 ER - TY - JOUR A1 - von Kleist, Max A1 - Schütte, Christof A1 - Zhang, Wei T1 - Statistical analysis of the first passage path ensemble of jump processes JF - Journal of Statistical Physics N2 - The transition mechanism of jump processes between two different subsets in state space reveals important dynamical information of the processes and therefore has attracted considerable attention in the past years. In this paper, we study the first passage path ensemble of both discrete-time and continuous-time jump processes on a finite state space. The main approach is to divide each first passage path into nonreactive and reactive segments and to study them separately. The analysis can be applied to jump processes which are non-ergodic, as well as continuous-time jump processes where the waiting time distributions are non-exponential. In the particular case that the jump processes are both Markovian and ergodic, our analysis elucidates the relations between the study of the first passage paths and the study of the transition paths in transition path theory. We provide algorithms to numerically compute statistics of the first passage path ensemble. The computational complexity of these algorithms scales with the complexity of solving a linear system, for which efficient methods are available. Several examples demonstrate the wide applicability of the derived results across research areas. Y1 - 2018 U6 - https://doi.org/10.1007/s10955-017-1949-x VL - 170 SP - 809 EP - 843 ER - TY - JOUR A1 - Huttary, Rudolf A1 - Goubergrits, Leonid A1 - Schütte, Christof A1 - Bernhard, Stefan T1 - Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling JF - Computers in Biology and Medicine Y1 - 2017 U6 - https://doi.org/10.1016/j.compbiomed.2017.05.021 VL - 87 SP - 104 EP - 123 ER - TY - JOUR A1 - Klus, Stefan A1 - Nüske, Feliks A1 - Koltai, Peter A1 - Wu, Hao A1 - Kevrekidis, Ioannis A1 - Schütte, Christof A1 - Noé, Frank T1 - Data-driven model reduction and transfer operator approximation JF - Journal of Nonlinear Science Y1 - 2018 UR - https://link.springer.com/article/10.1007/s00332-017-9437-7 U6 - https://doi.org/10.1007/s00332-017-9437-7 VL - 28 IS - 3 SP - 985 EP - 1010 ER - TY - JOUR A1 - Heinze, Rieke A1 - Dipankar, Anurag A1 - Henken, Cintia Carbajal A1 - Moseley, Christopher A1 - Sourdeval, Odran A1 - Trömel, Silke A1 - Xie, Xinxin A1 - Adamidis, Panos A1 - Ament, Felix A1 - Baars, Holger A1 - Barthlott, Christian A1 - Behrendt, Andreas A1 - Blahak, Ulrich A1 - Bley, Sebastian A1 - Brdar, Slavko A1 - Brueck, Matthias A1 - Crewell, Susanne A1 - Deneke, Hartwig A1 - Di Girolamo, Paolo A1 - Evaristo, Raquel A1 - Fischer, Jürgen A1 - Frank, Christopher A1 - Friederichs, Petra A1 - Göcke, Tobias A1 - Gorges, Ksenia A1 - Hande, Luke A1 - Hanke, Moritz A1 - Hansen, Akio A1 - Hege, Hans-Christian A1 - Hose, Corinna A1 - Jahns, Thomas A1 - Kalthoff, Norbert A1 - Klocke, Daniel A1 - Kneifel, Stefan A1 - Knippertz, Peter A1 - Kuhn, Alexander A1 - van Laar, Thriza A1 - Macke, Andreas A1 - Maurer, Vera A1 - Mayer, Bernhard A1 - Meyer, Catrin I. A1 - Muppa, Shravan K. A1 - Neggers, Roeland A. J. A1 - Orlandi, Emiliano A1 - Pantillon, Florian A1 - Pospichal, Bernhard A1 - Röber, Niklas A1 - Scheck, Leonhard A1 - Seifert, Axel A1 - Seifert, Patric A1 - Senf, Fabian A1 - Siligam, Pavan A1 - Simmer, Clemens A1 - Steinke, Sandra A1 - Stevens, Bjorn A1 - Wapler, Kathrin A1 - Weniger, Michael A1 - Wulfmeyer, Volker A1 - Zängl, Günther A1 - Zhang, Dan A1 - Quaas, Johannes T1 - Large-eddy simulations over Germany using ICON: a comprehensive evaluation JF - Quarterly Journal of the Royal Meteorological Society N2 - Large-eddy simulations (LES) with the new ICOsahedral Non-hydrostatic atmosphere model (ICON) covering Germany are evaluated for four days in spring 2013 using observational data from various sources. Reference simulations with the established Consortium for Small-scale Modelling (COSMO) numerical weather prediction model and further standard LES codes are performed and used as a reference. This comprehensive evaluation approach covers multiple parameters and scales, focusing on boundary-layer variables, clouds and precipitation. The evaluation points to the need to work on parametrizations influencing the surface energy balance, and possibly on ice cloud microphysics. The central purpose for the development and application of ICON in the LES configuration is the use of simulation results to improve the understanding of moist processes, as well as their parametrization in climate models. The evaluation thus aims at building confidence in the model's ability to simulate small- to mesoscale variability in turbulence, clouds and precipitation. The results are encouraging: the high-resolution model matches the observed variability much better at small- to mesoscales than the coarser resolved reference model. In its highest grid resolution, the simulated turbulence profiles are realistic and column water vapour matches the observed temporal variability at short time-scales. Despite being somewhat too large and too frequent, small cumulus clouds are well represented in comparison with satellite data, as is the shape of the cloud size spectrum. Variability of cloud water matches the satellite observations much better in ICON than in the reference model. In this sense, it is concluded that the model is fit for the purpose of using its output for parametrization development, despite the potential to improve further some important aspects of processes that are also parametrized in the high-resolution model. Y1 - 2017 U6 - https://doi.org/10.1002/qj.2947 VL - 143 IS - 702 SP - 69 EP - 100 ER - TY - JOUR A1 - Seidel, Ronald A1 - Blumer, Michael A1 - Zaslansky, Paul A1 - Knötel, David A1 - Huber, Daniel R. A1 - Weaver, James C. A1 - Fratzl, Peter A1 - Omelon, Sidney A1 - Bertinetti, Luca A1 - Dean, Mason N. T1 - Ultrastructural, material and crystallographic description of endophytic masses – a possible damage response in shark and ray tessellated calcified cartilage JF - Journal of Structural Biology N2 - The cartilaginous endoskeletons of Elasmobranchs (sharks and rays) are reinforced superficially by minute, mineralized tiles, called tesserae. Unlike the bony skeletons of other vertebrates, elasmobranch skeletons have limited healing capability and their tissues’ mechanisms for avoiding damage or managing it when it does occur are largely unknown. Here we describe an aberrant type of mineralized elasmobranch skeletal tissue called endophytic masses (EPMs), which grow into the uncalcified cartilage of the skeleton, but exhibit a strikingly different morphology compared to tesserae and other elasmobranch calcified tissues. We use biological and materials characterization techniques, including computed tomography, electron and light microscopy, x-ray and Raman spectroscopy and histology to characterize the morphology, ultrastructure and chemical composition of tesserae-associated EPMs in different elasmobranch species. EPMs appear to develop between and in intimate association with tesserae, but lack the lines of periodic growth and varying mineral density characteristic of tesserae. EPMs are mineral-dominated (high mineral and low organic content), comprised of birefringent bundles of large monetite or brushite crystals aligned end to end in long strings. Both Unusual skeletal mineralization in elasmobranchs tesserae and EPMs appear to develop in a type-2 collagen-based matrix, but in contrast to tesserae, all chondrocytes embedded or in contact with EPMs are dead and mineralized. The differences outlined between EPMs and tesserae demonstrate them to be distinct tissues. We discuss several possible reasons for EPM development, including tissue reinforcement, repair, and disruptions of mineralization processes, within the context of elasmobranch skeletal biology as well as descriptions of damage responses of other vertebrate mineralized tissues. Y1 - 2017 U6 - https://doi.org/10.1016/j.jsb.2017.03.004 ER - TY - JOUR A1 - Ablyazimov, T. A1 - Abuhoza, A. A1 - Adak, R. P. A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - et al., T1 - Challenges in QCD matter physics – The scientific programme of the Compressed Baryonic Matter experiment at FAIR JF - The European Physical Journal A Y1 - 2017 U6 - https://doi.org/10.1140/epja/i2017-12248-y N1 - This paper has 587 authors. For the complete list of authors use the DOI, please. ER - TY - JOUR A1 - Kozlíková, Barbora A1 - Krone, Michael A1 - Falk, Martin A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Viola, Ivan A1 - Parulek, Julius A1 - Hege, Hans-Christian T1 - Visualization of Biomolecular Structures: State of the Art Revisited JF - Computer Graphics Forum N2 - Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.13072 VL - 36 IS - 8 SP - 178 EP - 204 ER - TY - JOUR A1 - Wust, Peter A1 - Nadobny, Johanna A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Gellermann, Johanna A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Influence of patient models and numerical methods on predicted power deposition patterns JF - Int. J. Hyperthermia Y1 - 1999 VL - 15 IS - 6 SP - 519 EP - 540 ER - TY - JOUR A1 - Wust, Peter A1 - Seebass, Martin A1 - Nadobny, Johanna A1 - Deuflhard, Peter A1 - Mönich, Gerhard A1 - Felix, Roland T1 - Simulation studies promote technological development of radiofrequency phased array hyperthermia JF - Int J Hyperthermia Y1 - 1996 VL - 12 IS - 4 SP - 477 EP - 494 ER - TY - JOUR A1 - Yan, Hong-Dan A1 - Lemmens, Peter A1 - Ahrens, Johannes A1 - Bröring, Martin A1 - Burger, Sven A1 - Daum, Winfried A1 - Lilienkamp, Gerhard A1 - Korte, Sandra A1 - Lak, Aidin A1 - Schilling, Meinhard T1 - High-density array of Au nanowires coupled by plasmon modes JF - Acta Phys. Sin. Y1 - 2012 U6 - https://doi.org/10.7498/aps.61.237105 VL - 61 IS - 23 SP - 237105 ER - TY - JOUR A1 - Yevick, David A1 - Friese, T. A1 - Schmidt, Frank T1 - A Comparison of Transparent Boundary Conditions for the Fresnel Equation JF - J. Comput. Phys. Y1 - 2001 VL - 168 IS - 2 SP - 433 EP - 444 ER - TY - JOUR A1 - Yevick, David A1 - Yu, J. A1 - Schmidt, Frank T1 - Analytic Studies of Absorbing and Impedance-Matched Boundary Layers JF - IEEE Photonics Technology Letters Y1 - 1997 U6 - https://doi.org/10.1109/68.554499 VL - 9 SP - 73 EP - 75 ER - TY - JOUR A1 - Röblitz, Susanna A1 - Stötzel, Claudia A1 - Deuflhard, Peter A1 - Jones, Hannah M. A1 - Azulay, David-Olivier A1 - van der Graaf, Piet A1 - Martin, Steven T1 - A mathematical model of the human menstrual cycle for the administration of GnRH analogues JF - Journal of Theoretical Biology Y1 - 2013 U6 - https://doi.org/10.1016/j.jtbi.2012.11.020 VL - 321 SP - 8 EP - 27 ER - TY - JOUR A1 - Schlosser, Felix A1 - Schoth, Mario A1 - Burger, Sven A1 - Schmidt, Frank A1 - Knorr, Andreas A1 - Mukamel, S. A1 - Richter, Marten T1 - Ultrafast nonlinear spectroscopy with spatially confined fields JF - AIP Conference Proceedings Y1 - 2011 U6 - https://doi.org/10.1063/1.3644223 VL - 1398 SP - 94 EP - 96 PB - AIP ER - TY - JOUR A1 - Siegel, D. A1 - Andrae, Karsten A1 - Proske, Matthias A1 - Kochan, C. A1 - Koch, Matthias A1 - Weber, Marcus A1 - Nehls, Irene T1 - Dynamic covalent hydrazine chemistry as a specific extraction and cleanup technique for the quantification of the Fusarium mycotoxin zearalenone in edible oils JF - Journal of Chromatography A Y1 - 2010 VL - 1217(15) SP - 2206 EP - 15 ER - TY - JOUR A1 - Wust, Peter A1 - Fahling, Horst A1 - Wlodarczyk, Waldemar A1 - Seebass, Martin A1 - Gellermann, Johanna A1 - Deuflhard, Peter A1 - Nadobny, Johanna T1 - Antenna arrays in the SIGMA-eye applicator JF - Med Phys Y1 - 2001 VL - 28 IS - 8 SP - 1793 EP - 1805 ER - TY - JOUR A1 - Wust, Peter A1 - Gellermann, Johanna A1 - Beier, Jürgen A1 - Wegner, S. A1 - Tilly, Wolfgang A1 - Troger, J. A1 - Stalling, Detlev A1 - Oswald, H. A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Evaluation of segmentation algorithms for generation of patient models in radiofrequency hyperthermia JF - Phys Med Biol Y1 - 1998 VL - 43 SP - 3295 EP - 3307 ER - TY - JOUR A1 - Wust, Peter A1 - Nadobny, Johanna A1 - Felix, Roland A1 - Deuflhard, Peter A1 - John, W. A1 - Louis, Alfred T1 - Numerical approaches to treatment planning in deep RF-hyperthermia JF - Strahlenther Onkol Y1 - 1989 VL - 165 IS - 10 SP - 751 EP - 757 ER - TY - JOUR A1 - Wust, Peter A1 - Nadobny, Johanna A1 - Felix, Roland A1 - Deuflhard, Peter A1 - Louis, Alfred A1 - John, W. T1 - Strategies for optimized application of annular-phased-array systems in clinical hyperthermia JF - Int J Hyperthermia Y1 - 1991 VL - 7 SP - 157 EP - 173 ER - TY - JOUR A1 - Teschke, G. A1 - Görsdorf, U. A1 - Körner, P. A1 - Trede, D. T1 - A New Approach for Target Classification in Ka-Band Radar Data JF - Proc. ERAD Barcelona Y1 - 2006 ER - TY - JOUR A1 - Lehmann, V. A1 - Teschke, G. T1 - Wavelet based methods for improved wind profiler signal processing JF - Annales Geophysicae Y1 - 2001 IS - 19 SP - 825 EP - 836 ER - TY - JOUR A1 - Schmidt, Frank A1 - Nolting, Hans-Peter T1 - Adaptive Multilevel Beam Propagation Method JF - IEEE Photonics Technology Letter Y1 - 1992 VL - 4 SP - 1381 EP - 1383 ER - TY - JOUR A1 - Schaber, Karlheinz A1 - Ofenloch, Oliver A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Aerosolbildung in Gas/Flüssigkeits-Kontaktapparaten - Modellierungsstrategien und Simulation JF - Chemie Ingenieur Technik Y1 - 2004 VL - 76 IS - 9 SP - 1358 EP - 1359 ER - TY - JOUR A1 - Schmidt, Frank A1 - Yevick, David T1 - Discrete Transparent Boundary Conditions for Schrödinger-Type Equations JF - J. Comput. Phys. Y1 - 1997 U6 - https://doi.org/10.1006/jcph.1997.5675 VL - 134 IS - 1 SP - 96 EP - 107 ER - TY - JOUR A1 - Schädle, Achim A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Klose, Roland A1 - Schmidt, Frank T1 - Domain Decomposition Method for Maxwell’s Equations JF - J. Comput. Phys. Y1 - 2007 U6 - https://doi.org/10.1016/j.jcp.2007.04.017 VL - 226 SP - 477 EP - 493 ER - TY - JOUR A1 - Scheibe, Ch. A1 - Bujotzek, Alexander A1 - Dernedde, Jens A1 - Weber, Marcus A1 - Seitz, O. T1 - DNA-programmed spatial screening of carbohydrate-lectin interactions JF - Chem. Sci. Y1 - 2011 VL - 2 SP - 770 EP - 775 ER - TY - JOUR A1 - Weiser, Martin A1 - Schiela, Anton T1 - Function space interior point methods for PDE constrained optimization JF - PAMM Y1 - 2004 VL - 4 IS - 1 SP - 43 EP - 46 ER - TY - JOUR A1 - Weber, Marcus A1 - Andrae, Karsten T1 - A simple method for the estimation of entropy differences JF - MATCH Commun. Math. Comp. Chem. 2010 Y1 - 2010 VL - 63(2) SP - 319 EP - 332 ER - TY - JOUR A1 - Weber, Marcus A1 - Becker, Roland A1 - Köppen, Robert A1 - Durmaz, Vedat T1 - Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane JF - Journal of Molecular Simulation Y1 - 2008 VL - 34 IS - 7 SP - 727 EP - 736 ER - TY - JOUR A1 - Weber, Marcus A1 - Bujotzek, Alexander A1 - Andrae, Karsten A1 - Weinhart, M. A1 - Haag, Rainer T1 - Computational entropy estimation of linear polyether modified surfaces and correlation with protein resistant properties of such surfaces JF - J. Mol. Sim. Y1 - 2011 ER - TY - JOUR A1 - Förster, C. A1 - Brauer, Arnd B. E. A1 - Fürste, J. A1 - Betzel, C. A1 - Weber, Marcus A1 - Cordes, Frank A1 - Erdmann, V. T1 - Visualization of the tRNA(Ser) acceptor step binding site in the seryl-tRNA synthetase JF - BBRC Y1 - 2007 VL - 362 IS - 2 SP - 415 EP - 418 ER - TY - JOUR A1 - Soares, M. A1 - Teschke, G. A1 - Zhariy, M. T1 - A Wavelet Regularization for Nonlinear Diffusion Equations JF - Technical Report 04-12, ISSN 1435-7968 Y1 - 2004 ER - TY - JOUR A1 - Soares, M. A1 - Teschke, G. A1 - Zhariy, M. T1 - A Regularization for Nonlinear Diffusion Equations in a Multiresolution Framework JF - Mathematical Methods in Applied Sciences Y1 - 2007 ER - TY - JOUR A1 - Sreenivasa, G. A1 - Gellermann, Johanna A1 - Nadobny, Johanna A1 - Schlag, P. A1 - Deuflhard, Peter A1 - Felix, Roland A1 - Wust, Peter T1 - Clinical Use of the Hyperthermia Treatment Planning System Hyperplan to Predict Effectiveness and Toxicity JF - Int. J. Oncology Biol. Phys. Y1 - 2003 VL - 55 IS - 2 SP - 407 EP - 419 ER - TY - JOUR A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Schell, H. A1 - Klein, P. A1 - Duda, G. T1 - On the Influence of Soft Tissue Coverage in the Determination of Bone Kinematics using Bone Markers JF - Journal of Orthopedic Research Y1 - 2005 IS - 23 SP - 726 EP - 734 ER - TY - JOUR A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Schell, H. A1 - Seebeck, P. A1 - Duda, G. T1 - Tibio-femoral Joint Contact Forces in Sheep JF - Journal of Biomechanics Y1 - 2006 IS - 39 SP - 791 EP - 798 ER - TY - JOUR A1 - Lehmann, V. A1 - Teschke, G. T1 - Advanced Intermittent Clutter Filtering for Radar Wind Profiler JF - under review Y1 - 2007 ER - TY - JOUR A1 - Lehmann, V. A1 - Teschke, G. T1 - A new intermittent clutter filtering algorithm for radar wind profiler JF - Proc. ISTP Boulder Y1 - 2006 ER - TY - JOUR A1 - Teschke, G. A1 - Ramlau, R. T1 - An Iterative Algorithm for Nonlinear InverseProblems with Joint Sparsity Constraints in Vector Valued Regimes and an Application to Color Image Inpainting JF - under review Y1 - 2007 ER - TY - JOUR A1 - Teschke, G. T1 - A new frame-based statistical strategy for bird migration clutter removal in wind profiler radar data JF - preprint Y1 - 2006 ER - TY - JOUR A1 - Teschke, G. T1 - Frames, Sparsity, and Nonlinear InverseProblems JF - Oberwolfach Reports Y1 - 2006 ER - TY - JOUR A1 - Volkwein, S. A1 - Weiser, Martin T1 - Affine Invariant Convergence Analysis for Inexact Augmented Lagrangian SQP Methods JF - SIAM J. Control Optim. Y1 - 2002 VL - 41 IS - 3 SP - 875 EP - 899 ER - TY - JOUR A1 - Weiser, Martin A1 - Gänzler, Tobias A1 - Schiela, Anton T1 - A control reduced primal interior point method for a class of control constrained optimal control problems JF - Comput. Optim. Appl. Y1 - 2007 VL - 41 IS - 1 SP - 127 EP - 145 ER - TY - JOUR A1 - Weber, Marcus A1 - Kube, Susanna A1 - Walter, Lionel A1 - Deuflhard, Peter T1 - Stable Computation of Probability Densities of Metastable Dynamical Systems JF - SIAM J. Multiscale Model. Simul. Y1 - 2007 VL - 6 IS - 2 SP - 396 EP - 416 ER - TY - JOUR A1 - Weiser, Martin A1 - Schiela, Anton A1 - Deuflhard, Peter T1 - Asymptotic Mesh Independence of Newton’s Method Revisited JF - SIAM J. Num. Anal. Y1 - 2005 VL - 42 IS - 5 SP - 1830 EP - 1845 ER - TY - JOUR A1 - Weiser, Martin T1 - Optimization and Identification in Regional Hyperthermia JF - Int. J. Appl. Electromagn. and Mech. Y1 - 2009 VL - 30 SP - 265 EP - 275 ER - TY - JOUR A1 - Weiser, Martin T1 - Pointwise Nonlinear Scaling for Reaction-Diffusion Equations JF - Appl. Num. Math. Y1 - 2009 VL - 59 IS - 8 SP - 1858 EP - 1869 ER - TY - JOUR A1 - Weiser, Martin A1 - Deuflhard, Peter A1 - Erdmann, Bodo T1 - Affine conjugate adaptive Newton methods for nonlinear elastomechanics JF - Opt. Meth. Softw. Y1 - 2007 VL - 22 IS - 3 SP - 413 EP - 431 ER - TY - JOUR A1 - Weihrauch, Mirko A1 - Wust, Peter A1 - Weiser, Martin A1 - Nadobny, Johanna A1 - Eisenhardt, Steffen A1 - Budach, Volker A1 - Gellermann, Johanna T1 - Adaptation of antenna profiles for control of MR guided hyperthermia (HT) in a hybrid MR-HT system JF - Medical Physics Y1 - 2007 VL - 34 IS - 12 SP - 4717 EP - 4725 ER - TY - JOUR A1 - Weiser, Martin T1 - Interior point methods in function space JF - SIAM J. Control Optimization Y1 - 2005 VL - 44 IS - 5 SP - 1766 EP - 1786 ER - TY - JOUR A1 - Wix, A. A1 - Schaber, Karlheinz A1 - Ofenloch, O. A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Simulation of Aerosol Formation in Gas-Liquid Contact Devices JF - Chem. Eng. Comm. Y1 - 2007 VL - 194 SP - 565 EP - 577 ER - TY - JOUR A1 - Dür, Mirjam A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Schabel, Samuel A1 - Schönberger, Christine A1 - Villforth, Klaus T1 - Steuerung einer Sortieranlage, z.B. für Altpapier JF - Europäische Patentanmeldung Y1 - 2010 VL - EP 09 718 564.9 ER - TY - JOUR A1 - Dür, Mirjam A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Schabel, Samuel A1 - Schönberger, Christine A1 - Villforth, Klaus T1 - Verfahren zum Einstellen und/oder Optimieren einer einen Gutstoff von einem Schlechtstoff trennenden Sortieranlage und Sortieranlage JF - Deutsches Patent Y1 - 2008 VL - DE 10 2008 013 034 ER - TY - JOUR A1 - Dür, Mirjam A1 - Fügenschuh, Armin A1 - Martin, Alexander A1 - Ulbrich, Stefan T1 - Verfahren und Vorrichtung zum Auswuchten von wellenelastischen Rotoren JF - Deutsche Patentanmeldung Y1 - 2006 VL - DE 10 2006 060 583.7 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Stanczak, Slawomir T1 - Retransmission Aware Congestion Control and Distributed Power Allocation in MANETs JF - Proc. 5th Int. Workshop on Resource Allocation, Cooperation and Competition in Wireless Networks (RAWNET/WNC3), Seoul, Korea Y1 - 2009 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Stanczak, Slawomir T1 - Stability and Distributed Power Control in MANETs with per Hop Retransmissions JF - IEEE Trans. on Communications Y1 - 2011 ER - TY - JOUR A1 - Giovanidis, Anastasios A1 - Wunder, Gerhard A1 - Boche, Holger T1 - A short-term throughput measure for communications using ARQ protocols JF - Proc. 7th ITG Conf. on SCC Y1 - 2008 ER - TY - JOUR A1 - Frank, Martin A1 - Fügenschuh, Armin A1 - Herty, Michael A1 - Schewe, Lars T1 - The Coolest Path Problem JF - Networks and Heterogeneous Media Y1 - 2010 VL - 5 IS - 1 SP - 143 EP - 162 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Göttlich, Simone A1 - Kirchner, Claus A1 - Herty, Michael A1 - Martin, Alexander T1 - Efficient Reformulation and Solution of a Nonlinear PDE-Controlled Flow Network Model JF - Computing Y1 - 2009 VL - 85 IS - 3 SP - 245 EP - 265 ER - TY - JOUR A1 - Dittel, Agnes A1 - Fügenschuh, Armin A1 - Göttlich, Simone A1 - Herty, Michael T1 - MIP Presolve Techniques for a PDE-based Supply Chain Model JF - Optimization Methods & Software Y1 - 2009 VL - 24 IS - 3 SP - 427 EP - 445 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - A note on the stability of the many-queue head-of-the-line processor-sharing system with permanent customers JF - Queueing Syst. Y1 - 1999 VL - 32 SP - 363 EP - 381 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On a two-queue priority system with impatience and its application to a call center JF - Methodol. Comput. Appl. Probab. Y1 - 1999 VL - 1 SP - 191 EP - 210 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the $M(n)/M(n)/s$ queue with impatient calls JF - Perform. Eval. Y1 - 1999 VL - 35 SP - 1 EP - 18 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the sojourn times for many-queue head-of-the-line processor-sharing systems with permanent customers JF - Math. Methods Oper. Res. Y1 - 1998 VL - 47 SP - 181 EP - 220 ER - TY - JOUR A1 - Brandt, Andreas A1 - Brandt, Manfred T1 - On the distribution of the number of packets in the fluid flow approximation of packet arrival streams JF - Queueing Syst. Y1 - 1994 VL - 17 SP - 275 EP - 315 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - Solving a School Bus Scheduling Problem with Integer Programming JF - European Journal of Operational Research Y1 - 2009 VL - 193 IS - 3 SP - 867 EP - 884 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Homfeld, Henning A1 - Huck, Andreas A1 - Martin, Alexander A1 - Yuan, Zhi T1 - Scheduling Locomotives and Car Transfers in Freight Transport JF - Transportation Science Y1 - 2008 VL - 42 IS - 4 SP - 1 EP - 14 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Fügenschuh, Marzena T1 - Integer Linear Programming Models for Topology Optimization in Sheet Metal Design JF - Mathematical Methods of Operations Research Y1 - 2008 VL - 68 IS - 2 SP - 313 EP - 331 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Göttlich, Simone A1 - Herty, Michael A1 - Klar, Alexander A1 - Martin, Alexander T1 - A Discrete Optimization Approach to Large Scale Supply Networks Based on Partial Differential Equations JF - SIAM Journal on Scientific Computing Y1 - 2008 VL - 30 IS - 3 SP - 1490 EP - 1507 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Martin, Alexander T1 - A Multicriterial Approach for Optimizing Bus Schedules and School Starting Times JF - Annals of Operations Research Y1 - 2006 VL - 147 IS - 1 SP - 199 EP - 216 ER - TY - JOUR A1 - Fügenschuh, Armin T1 - The Vehicle Routing Problem with Coupled Time Windows JF - Central European Journal of Operations Research Y1 - 2006 VL - 14 IS - 2 SP - 157 EP - 176 ER - TY - JOUR A1 - Fügenschuh, Armin A1 - Martin, Alexander T1 - Welche Gemeinsamkeiten haben Jugendliche und Groß banken? 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A1 - Meuldijk, J. A1 - Drinkenburg, B. A1 - Iedema, P. A1 - Wulkow, Michael T1 - A Novel Method to Model Emulsion Polymerization Kinetics JF - Polymer-Plastics Tech. Eng. Y1 - 2005 VL - 44 IS - 4 SP - 707 EP - 740 ER - TY - JOUR A1 - Schmidt, Christian-Ulrich A1 - Busch, Markus A1 - Lilge, Dieter A1 - Wulkow, Michael T1 - Detailed Molecular Structure Modeling – A Path Forward to Designing Application Properties of ldPE JF - Macromolecular Materials and Engineering Y1 - 2005 VL - 290 SP - 404 ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - A hybrid Galerkin-Monte-Carlo approach to higher-dimensional population balances in polymerization kinetics JF - Macromol. React. Eng. Y1 - 2010 VL - 4 SP - 562 EP - 577 ER - TY - JOUR A1 - Brüggemann, Stefan A1 - Bauer, Nanette A1 - Fuchs, Eberhard A1 - Polt, Axel A1 - Wagner, Bernhard A1 - Wulkow, Michael T1 - Support of Strategic Business Decisions at BASF’s Largest Integrated Production Site Based on Site-Wide Verbund Simulation JF - Computer Aided Chem. Eng. Y1 - 2008 VL - 25 SP - 925 EP - 930 ER - TY - JOUR A1 - Busch, Markus A1 - Müller, M. A1 - Wulkow, Michael T1 - The use of Simulation Techniques in Developing Kinetic Models for Polymerizations JF - Chem. Eng. Technol. Y1 - 2003 VL - 26 SP - 1031 ER - TY - JOUR A1 - Busch, Markus A1 - Wulkow, Michael T1 - Modellierung differenzierter mikrostruktureller Eigenschaften JF - Chem. Ing. Tech. Y1 - 2003 VL - 75 SP - 1027 ER - TY - JOUR A1 - Grosch, R. A1 - Briesen, Heiko A1 - Wulkow, Michael A1 - Marquardt, Wolfgang T1 - Generalization and numerical investigation of QMOM for crystallization processes JF - AIChE J. Y1 - 2007 VL - 53 SP - 207 EP - 227 ER - TY - JOUR A1 - Horn, H. A1 - Neu, T. A1 - Wulkow, Michael T1 - Modelling the Structure and Function of Extracellular Polymeric Substances in Biofilms with new Numerical Techniques JF - Wat. Sci. Techn. Y1 - 2001 VL - 43 IS - ´6 SP - 121 EP - 127 ER - TY - JOUR A1 - Horn, H. A1 - Wulkow, Michael T1 - Simulation von Wachstum und Abtrag der Biomasse – Eine exemplarische Betrachtung für eine 2D-Modellierung JF - Chem. Ing. Technik Y1 - 2005 VL - 77 IS - 4 SP - 418 EP - 424 ER - TY - JOUR A1 - Horn, H. A1 - Wulkow, Michael T1 - Modellierung von Einleitungen in kleine Fließgewässer JF - gwf Wasser Abwasser Y1 - 1996 VL - 137 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Telgmann, R. A1 - Wulkow, Michael T1 - The virtual lab approach to pharmacokinetic JF - Drug Discov Today Y1 - 2006 VL - 11 SP - 800 EP - 805 ER - TY - JOUR A1 - Hungenberg, K.-D. A1 - Chen, C.-C. A1 - Zhang, F. A1 - Wulkow, Michael A1 - Stubbe, G. A1 - Nieken, U. T1 - Design of Polymer Processes Using the Coupling of Commercial Simulation Packages Polymers Plus and PREDICI JF - DECHEMA Monographs Y1 - 2001 VL - 137 SP - 237 EP - 245 ER - TY - JOUR A1 - Hungenberg, K.-D. A1 - Knoll, K. A1 - Wulkow, Michael T1 - Absolute Propagation Rate Coefficients in Radical Polymerization from Gel Permeation Chromatography of Polymers Produced by Intermittent Initiation JF - Macromol. Theory Simul. Y1 - 1997 VL - 6 ER - TY - JOUR A1 - Berthold, Timo T1 - Heuristiken im Branch-and-Cut-Framework SCIP JF - OR News Y1 - 2008 IS - 32 SP - 24 EP - 25 ER - TY - JOUR A1 - Allen, Gabrielle A1 - Davis, K. A1 - Goodale, Tom A1 - Hutanu, Andrei A1 - Kaiser, Hartmut A1 - Kielmann, Thilo A1 - Merzky, Andre A1 - Nieuwpoort, R. A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Seidel, Edward A1 - Ullmer, Brygg T1 - The Grid Application Toolkit: Toward Generic and Easy Appliction Programming Interfaces for the Grid JF - Procceedings of the IEEE Y1 - 2005 U6 - https://doi.org/10.1109/JPROC.2004.842755 VL - 93 IS - 3 SP - 534 EP - 550 PB - IEEE Computer Society Press ER - TY - JOUR A1 - Röblitz, Thomas A1 - Schintke, Florian A1 - Reinefeld, Alexander A1 - Bärring, Olof A1 - Lopez, Maite Barroso A1 - Cancio, German A1 - Chapeland, Sylvain A1 - Chouikh, Karim A1 - Cons, Lionel A1 - Poznanski, Piotr A1 - Defert, Philippe A1 - Iven, Jan A1 - Kleinwort, Thorsten A1 - Panzer-Steindel, Bernd A1 - Polok, Jaroslaw A1 - Rafflin, Catherine A1 - Silverman, Alan A1 - Smith, Tim A1 - van Eldik, Jan A1 - Front, David A1 - Biasotto, Massimo A1 - Aiftimiei, Cristina A1 - Ferro, Enrico A1 - Maron, Gaetano A1 - Chierici, Andrea A1 - dell’Agnello, Luca A1 - Serra, Marco A1 - Michelotto, Michele A1 - Hess, Lord A1 - Lindenstruth, Volker A1 - Pister, Frank A1 - Steinbeck, Timm A1 - Groep, David A1 - Steenbakkers, Martijn A1 - Koeroo, Oscar A1 - de Cerff, Wim A1 - Venekamp, Gerben A1 - Anderson, Paul A1 - Colles, Tim A1 - Holt, Alexander A1 - Scobie, Alastair A1 - George, Michael A1 - Washbrook, Andrew A1 - Leiva, Rafael T1 - Autonomic Management of Large Clusters and Their Integration into the Grid JF - J. Grid Comput. Y1 - 2004 U6 - https://doi.org/10.1007/s10723-004-7647-3 VL - 2 IS - 3 SP - 247 EP - 260 ER - TY - JOUR A1 - Xiao, Li A1 - Zhang, Xiaodong A1 - Andrzejak, Artur A1 - Chen, Songqing T1 - Building a Large and Efficient Hybrid Peer-to-Peer Internet Caching System JF - IEEE Trans. Knowl. Data Eng. Y1 - 2004 U6 - https://doi.org/10.1109/TKDE.2004.1 VL - 16 IS - 6 SP - 754 EP - 769 ER - TY - JOUR A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Grid Services: Web Services zur Nutzung verteilter Ressourcen JF - Informatik Spektrum Y1 - 2004 U6 - https://doi.org/10.1007/s00287-004-0379-8 VL - 27 IS - 2 SP - 129 EP - 135 ER - TY - JOUR A1 - May, Patrick A1 - Barthel, Stefan A1 - Koch, Ina T1 - PTGL - a web-based database application for protein topologies JF - Bioinformatics Y1 - 2004 U6 - https://doi.org/10.1093/bioinformatics/bth367 VL - 20 IS - 17 SP - 3277 EP - 3279 ER - TY - JOUR A1 - Hupfeld, Felix A1 - Gordon, M. T1 - Using distributed consistent branching for efficient reconciliation of mobile workspaces JF - International Conference on Collaborative Computing Y1 - 2006 U6 - https://doi.org/10.1109/COLCOM.2006.361837 VL - 0 SP - 8 PB - IEEE Computer Society CY - Los Alamitos, CA, USA ER - TY - JOUR A1 - Andrzejak, Artur A1 - Ceyran, Mehmet T1 - Characterizing and Predicting Resource Demand by Periodicity Mining JF - J. Network Syst. Manage., Special Issue on Self-Managing Systems and Networks Y1 - 2005 VL - 13 IS - 2 ER - TY - JOUR A1 - Trißl, Silke A1 - Rother, Kristian A1 - Müller, Heiko A1 - Steinke, Thomas A1 - Koch, Ina A1 - Preissner, Robert A1 - Frömmel, Cornelius A1 - Leser, Ulf T1 - Columba: an integrated database of proteins, structures, and annotations JF - BMC Bioinformatics Y1 - 2005 U6 - https://doi.org/10.1186/1471-2105-6-81 VL - 6 SP - 81 EP - 92 ER - TY - JOUR A1 - Wendler, Jan A1 - Schintke, Florian T1 - Executing and observing CFD applications on the Grid JF - Future Generation Computer Systems the International Journal of Grid Computing: Theory, Methods and Applications Y1 - 2005 U6 - https://doi.org/10.1016/j.future.2004.09.026 VL - 21 IS - 1 SP - 11 EP - 18 PB - Elsevier Science Publishers ER - TY - JOUR A1 - Herrmann, Christoph A1 - Langhammer, Tobias T1 - Combining partial evaluation and staged interpretation in the implementation of domain-specific languages JF - Sci. Comput. Program. Y1 - 2006 U6 - https://doi.org/10.1016/j.scico.2006.02.002 VL - 62 IS - 1 SP - 47 EP - 65 ER - TY - JOUR A1 - Kolbeck, Björn A1 - May, Patrick A1 - Schmidt-Goenner, T. A1 - Steinke, Thomas A1 - Knapp, E. T1 - Connectivity independent protein-structure alignment: a hierarchical approach JF - BMC Bioinformatics Y1 - 2006 VL - 7 SP - 510 ER - TY - JOUR A1 - Andrzejak, Artur A1 - Reinefeld, Alexander T1 - Paradigms for Scalable and Dependable Grids JF - Future Generation Computer Systems (FGCS) Y1 - 2007 VL - 23 IS - 7 ER - TY - JOUR A1 - Rolia, Jerry A1 - Zhu, Xiaoyun A1 - Arlitt, Martin A1 - Andrzejak, Artur T1 - Statistical service assurances for applications in utility Grid environments JF - Performance Evaluation Y1 - 2004 U6 - https://doi.org/10.1016/j.peva.2004.07.015 VL - 58 IS - 2-3 SP - 319 EP - 339 ER - TY - JOUR A1 - Reinefeld, Alexander A1 - Schintke, Florian T1 - Grid Computing in Deutschland JF - Spektrum der Wissenschaft Y1 - 2003 SP - 72 EP - 73 PB - Spektrum der Wissenschaft Verlagsgesellschaft, Heidelberg ER - TY - JOUR A1 - Röblitz, Thomas A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Resource reservations with fuzzy requests JF - Concurrency and Computation: Practice and Experience Y1 - 2006 UR - http://dx.doi.org/10.1002/cpe.1023 U6 - https://doi.org/10.1002/cpe.1023 VL - 18 IS - 13 SP - 1681 EP - 1703 ER - TY - JOUR A1 - Meyer, Michael A1 - Steinke, Thomas A1 - Sühnel, Jürgen T1 - Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions JF - Journal of Molecular Modeling Y1 - 2007 UR - http://dx.doi.org/10.1007/s00894-006-0148-5 VL - 13 IS - 2 SP - 335 EP - 345 PB - Springer Berlin / Heidelberg ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Homogeneous dust emission and jet structure near active cometary nuclei: the case of 67P/Churyumov-Gerasimenko N2 - We compute trajectories of dust grains starting from a homogeneous surface activity-profile on a irregularly shaped cometary nucleus. Despite the initially homogeneous dust distribution a collimation in jet-like structures becomes visible. The fine structure is caused by concave topographical features with similar bundles of normal vectors. The model incorporates accurately determined gravitational forces, rotation of the nucleus, and gas-dust interaction. Jet-like dust structures are obtained for a wide range of gas-dust interactions. For the comet 67P/Churyumov-Gerasimenko, we derive the global dust distribution around the nucleus and find several areas of agreement between the homogeneous dust emission model and the Rosetta observation of dust jets, including velocity-dependent bending of trajectories. Y1 - 2015 ER - TY - JOUR A1 - Barth, Carlo A1 - Burger, Sven A1 - Becker, Christiane T1 - Symmetry-Dependency of Anticrossing Phenomena in Slab-Type Photonic Crystals JF - Opt. Express Y1 - 2016 U6 - https://doi.org/10.1364/OE.24.010931 VL - 24 SP - 10931 ER - TY - JOUR A1 - Barth, Carlo A1 - Probst, Jürgen A1 - Herrmann, Sven A1 - Hammerschmidt, Martin A1 - Becker, Christiane T1 - Numerical characterization of symmetry properties for photonic crystals with hexagonal lattice JF - Proc. SPIE N2 - We present a numerical method to characterize the symmetry properties of photonic crystal (PhC) modes based on field distributions, which themselves can be obtained numerically. These properties can be used to forecast specific features of the optical response of such systems, e.g. which modes are allowed to couple to external radiation fields. We use 2D PhCs with a hexagonal lattice of holes in dielectric as an example and apply our technique to reproduce results from analytical considerations. Further, the method is extended to fully vectorial problems in view of 3D PhCs and PhC slabs, its functionality is demonstrated using test cases and, finally, we provide an efficient implementation. The technique can thus readily be applied to output data of all band structure computation methods or even be embedded – gaining additional information about the mode symmetry. Y1 - 2016 U6 - https://doi.org/10.1117/12.2227094 VL - 9885 SP - 988506 ER - TY - JOUR A1 - Jäger, Klaus A1 - Köppel, Grit A1 - Barth, Carlo A1 - Hammerschmidt, Martin A1 - Herrmann, Sven A1 - Burger, Sven A1 - Schmidt, Frank A1 - Becker, Christiane T1 - Sinusoidal gratings for optimized light management in c-Si thin-film solar cells JF - Proc. SPIE Y1 - 2016 U6 - https://doi.org/10.1117/12.2225459 VL - 9898 SP - 989808 ER - TY - JOUR A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Erdmann, Bodo A1 - Weiser, Martin A1 - Zachow, Stefan A1 - Heinrich, Andreas A1 - Güttler, Felix Victor A1 - Teichgräber, Ulf A1 - Mall, Gita T1 - Automatic CT-based finite element model generation for temperature-based death time estimation: feasibility study and sensitivity analysis JF - International Journal of Legal Medicine N2 - Temperature based death time estimation is based either on simple phenomenological models of corpse cooling or on detailed physical heat transfer models. The latter are much more complex, but allow a higher accuracy of death time estimation as in principle all relevant cooling mechanisms can be taken into account. Here, a complete work flow for finite element based cooling simulation models is presented. The following steps are demonstrated on CT-phantoms: • CT-scan • Segmentation of the CT images for thermodynamically relevant features of individual geometries • Conversion of the segmentation result into a Finite Element (FE) simulation model • Computation of the model cooling curve • Calculation of the cooling time For the first time in FE-based cooling time estimation the steps from the CT image over segmentation to FE model generation are semi-automatically performed. The cooling time calculation results are compared to cooling measurements performed on the phantoms under controlled conditions. In this context, the method is validated using different CTphantoms. Some of the CT phantoms thermodynamic material parameters had to be experimentally determined via independent experiments. Moreover the impact of geometry and material parameter uncertainties on the estimated cooling time is investigated by a sensitivity analysis. KW - temperature based death time estimation KW - finite element method KW - CT segmentation KW - sensitivity analysis Y1 - 2017 U6 - https://doi.org/doi:10.1007/s00414-016-1523-0 VL - 131 IS - 3 SP - 699 EP - 712 ER - TY - JOUR A1 - Titschack, Jürgen A1 - Fink, Hiske G. A1 - Baum, Daniel A1 - Wienberg, Claudia A1 - Hebbeln, Dierk A1 - Freiwald, André T1 - Mediterranean cold-water corals - an important regional carbonate factory? JF - The Depositional Record Y1 - 2016 U6 - https://doi.org/10.1002/dep2.14 VL - 2 IS - 1 SP - 74 EP - 96 ER - TY - JOUR A1 - Kramer, Tobias A1 - Kreisbeck, Christoph A1 - Riha, Christian A1 - Chiatti, Olivio A1 - Buchholz, Sven A1 - Wieck, Andreas A1 - Reuter, Dirk A1 - Fischer, Saskia T1 - Thermal energy and charge currents in multi-terminal nanorings JF - AIP Advances N2 - We study in experiment and theory thermal energy and charge transfer close to the quantum limit in a ballistic nanodevice, consisting of multiply connected one-dimensional electron waveguides. The fabricated device is based on an AlGaAs/GaAs heterostructure and is covered by a global top-gate to steer the thermal energy and charge transfer in the presence of a temperature gradient, which is established by a heating current. The estimate of the heat transfer by means of thermal noise measurements shows the device acting as a switch for charge and thermal energy transfer. The wave-packet simulations are based on the multi-terminal Landauer-Büttiker approach and confirm the experimental finding of a mode-dependent redistribution of the thermal energy current, if a scatterer breaks the device symmetry. Y1 - 2016 U6 - https://doi.org/10.1063/1.4953812 VL - 6 SP - 065306 ER - TY - JOUR A1 - Krone, Michael A1 - Kozlíková, Barbora A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Parulek, Julius A1 - Hege, Hans-Christian A1 - Viola, Ivan T1 - Visual Analysis of Biomolecular Cavities: State of the Art JF - Computer Graphics Forum N2 - In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12928 SN - 1467-8659 VL - 35 IS - 3 SP - 527 EP - 551 ER - TY - JOUR A1 - Costa, Marta A1 - Manton, James D. A1 - Ostrovsky, Aaron D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases JF - Neuron N2 - Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. Y1 - 2016 U6 - https://doi.org/10.1016/j.neuron.2016.06.012 VL - 91 IS - 2 SP - 293 EP - 311 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias T1 - On the origin of inner coma structures observed by Rosetta during a diurnal rotation of comet 67P/Churyumov-Gerasimenko JF - The Astrophysical Journal Letters N2 - The Rosetta probe around comet 67P/Churyumov–Gerasimenko (67P) reveals an anisotropic dust distribution of the inner coma with jet-like structures. The physical processes leading to jet formation are under debate, with most models for cometary activity focusing on localized emission sources, such as cliffs or terraced regions. Here we suggest, by correlating high-resolution simulations of the dust environment around 67P with observations, that the anisotropy and the background dust density of 67P originate from dust released across the entire sunlit surface of the nucleus rather than from few isolated sources. We trace back trajectories from coma regions with high local dust density in space to the non-spherical nucleus and identify two mechanisms of jet formation: areas with local concavity in either two dimensions or only one. Pits and craters are examples of the first case; the neck region of the bi-lobed nucleus of 67P is an example of the latter case. The conjunction of multiple sources, in addition to dust released from all other sunlit areas, results in a high correlation coefficient (~0.8) of the predictions with observations during a complete diurnal rotation period of 67P. Y1 - 2016 U6 - https://doi.org/10.3847/2041-8205/823/1/L11 VL - 823 IS - 1 SP - L11 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Harman, Radoslav T1 - Computing exact D-optimal designs by mixed integer second-order cone programming JF - The Annals of Statistics N2 - Let the design of an experiment be represented by an $s-$dimensional vector $w$ of weights with nonnegative components. Let the quality of $w$ for the estimation of the parameters of the statistical model be measured by the criterion of $D-$optimality, defined as the $m$th root of the determinant of the information matrix $M(w)=\sum_{i=1}^s w_i A_i A_i^T$, where $A_i$,$i=1,\ldots,s$ are known matrices with $m$ rows. In this paper, we show that the criterion of $D-$optimality is second-order cone representable. As a result, the method of second-order cone programming can be used to compute an approximate $D-$optimal design with any system of linear constraints on the vector of weights. More importantly, the proposed characterization allows us to compute an exact $D-$optimal design, which is possible thanks to high-quality branch-and-cut solvers specialized to solve mixed integer second-order cone programming problems. Our results extend to the case of the criterion of $D_K-$optimality, which measures the quality of $w$ for the estimation of a linear parameter subsystem defined by a full-rank coefficient matrix $K$. We prove that some other widely used criteria are also second-order cone representable, for instance, the criteria of $A-$, $A_K$-, $G-$ and $I-$optimality. We present several numerical examples demonstrating the efficiency and general applicability of the proposed method. We show that in many cases the mixed integer second-order cone programming approach allows us to find a provably optimal exact design, while the standard heuristics systematically miss the optimum. Y1 - 2015 U6 - https://doi.org/10.1214/15-AOS1339 VL - 43 IS - 5 SP - 2198 EP - 2224 ER - TY - JOUR A1 - Sahu, Manish A1 - Moerman, Daniil A1 - Mewes, Philip A1 - Mountney, Peter A1 - Rose, Georg T1 - Instrument State Recognition and Tracking for Effective Control of Robotized Laparoscopic Systems JF - International Journal of Mechanical Engineering and Robotics Research N2 - Surgical robots are an important component for delivering advanced paradigm shifting technology such as image guided surgery and navigation. However, for robotic systems to be readily adopted into the operating room they must be easy and convenient to control and facilitate a smooth surgical workflow. In minimally invasive surgery, the laparoscope may be held by a robot but controlling and moving the laparoscope remains challenging. It is disruptive to the workflow for the surgeon to put down the tools to move the robot in particular for solo surgery approaches. This paper proposes a novel approach for naturally controlling the robot mounted laparoscope’s position by detecting a surgical grasping tool and recognizing if its state is open or close. This approach does not require markers or fiducials and uses a machine learning framework for tool and state recognition which exploits naturally occurring visual cues. Furthermore a virtual user interface on the laparoscopic image is proposed that uses the surgical tool as a pointing device to overcome common problems in depth perception. Instrument detection and state recognition are evaluated on in-vivo and ex-vivo porcine datasets. To demonstrate the practical surgical application and real time performance the system is validated in a simulated surgical environment. Y1 - 2016 U6 - https://doi.org/10.18178/ijmerr.5.1.33-38 VL - 5 IS - 1 SP - 33 EP - 38 ER - TY - JOUR A1 - Fournier, David A1 - Palidwor, Gareth A. A1 - Shcherbinin, Sergey A1 - Szengel, Angelika A1 - Schaefer, Martin H. A1 - Perez-Iratxeta, Carol A1 - Andrade-Navarro, Miguel A. T1 - Functional and Genomic Analyses of Alpha-Solenoid Proteins JF - PLoS ONE Journal N2 - Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0079894 ER - TY - JOUR A1 - Spötter, Andreas A1 - Gupta, Pooja A1 - Mayer, Manfred A1 - Reinsch, Norbert A1 - Bienefeld, Kaspar T1 - Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera) JF - Journal of Heredity Y1 - 2016 VL - 107 IS - 3 SP - 220 EP - 227 ER - TY - JOUR A1 - Domschke, Pia A1 - Groß, Martin A1 - Hante, Falk M. A1 - Hiller, Benjamin A1 - Schewe, Lars A1 - Schmidt, Martin T1 - Mathematische Modellierung, Simulation und Optimierung von Gastransportnetzwerken JF - gwf - Gas+Energie Y1 - 2015 VL - 156 IS - 11 SP - 880 EP - 885 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - Optimization of energy supply systems by MILP branch and bound method in consideration of hierarchical relationship between design and operation JF - Energy Conversion and Management N2 - To attain the highest performance of energy supply systems, it is necessary to rationally determine types, capacities, and numbers of equipment in consideration of their operational strategies corresponding to seasonal and hourly variations in energy demands. In the combinatorial optimization method based on the mixed-integer linear programming (MILP), integer variables are used to express the selection, numbers, and on/off status of operation of equipment, and the number of these variables increases with those of equipment and periods for variations in energy demands, and affects the computation efficiency significantly. In this paper, a MILP method utilizing the hierarchical relationship between design and operation variables is proposed to solve the optimal design problem of energy supply systems efficiently: At the upper level, the optimal values of design variables are searched by the branch and bound method; At the lower level, the values of operation variables are optimized independently at each period by the branch and bound method under the values of design variables given tentatively during the search at the upper level; Lower bounds for the optimal value of the objective function to be minimized are evaluated, and are utilized for the bounding operations at both the levels. This method is implemented into open and commercial MILP solvers. Illustrative and practical case studies on the optimal design of cogeneration systems are conducted, and the validity and effectiveness of the proposed method are clarified. Y1 - 2015 U6 - https://doi.org/10.1016/j.enconman.2014.12.020 VL - 92 SP - 92 EP - 104 ER - TY - JOUR A1 - Hermann, Gunter A1 - Pohl, Vincent A1 - Tremblay, Jean Christophe A1 - Paulus, Beate A1 - Hege, Hans-Christian A1 - Schild, Axel T1 - ORBKIT – A modular Python toolbox for cross-platform post-processing of quantum chemical wavefunction data JF - Journal of Computational Chemistry N2 - ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wave function, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT offers routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations. Y1 - 2016 U6 - https://doi.org/10.1002/jcc.24358 VL - 37 IS - 16 SP - 1511 EP - 1520 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Osman, Jan A1 - Mevert, Ricardo A1 - Kertzscher, Ulrich A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Turbulence in blood damage modeling JF - The International Journal of Artificial Organs N2 - Purpose: To account for the impact of turbulence in blood damage modeling, a novel approach based on the generation of instantaneous flow fields from RANS simulations is proposed. Methods: Turbulent flow in a bileaflet mechanical heart valve was simulated using RANS-based (SST k-ω) flow solver using FLUENT 14.5. The calculated Reynolds shear stress (RSS) field is transformed into a set of divergence-free random vector fields representing turbulent velocity fluctuations using procedural noise functions. To consider the random path of the blood cells, instantaneous flow fields were computed for each time step by summation of RSS-based divergence-free random and mean velocity fields. Using those instantaneous flow fields, instantaneous pathlines and corresponding point-wise instantaneous shear stresses were calculated. For a comparison, averaged pathlines based on mean velocity field and respective viscous shear stresses together with RSS values were calculated. Finally, the blood damage index (hemolysis) was integrated along the averaged and instantaneous pathlines using a power law approach and then compared. Results: Using RSS in blood damage modeling without a correction factor overestimates damaging stress and thus the blood damage (hemolysis). Blood damage histograms based on both presented approaches differ. Conclusions: A novel approach to calculate blood damage without using RSS as a damaging parameter is established. The results of our numerical experiment support the hypothesis that the use of RSS as a damaging parameter should be avoided. Y1 - 2016 U6 - https://doi.org/10.5301/ijao.5000476 VL - 39 IS - 4 SP - 147 EP - 210 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Steffy, Daniel A1 - Wolter, Kati T1 - Iterative Refinement for Linear Programming JF - INFORMS Journal on Computing N2 - We describe an iterative refinement procedure for computing extended precision or exact solutions to linear programming problems (LPs). Arbitrarily precise solutions can be computed by solving a sequence of closely related LPs with limited precision arithmetic. The LPs solved share the same constraint matrix as the original problem instance and are transformed only by modification of the objective function, right-hand side, and variable bounds. Exact computation is used to compute and store the exact representation of the transformed problems, while numeric computation is used for solving LPs. At all steps of the algorithm the LP bases encountered in the transformed problems correspond directly to LP bases in the original problem description. We show that this algorithm is effective in practice for computing extended precision solutions and that it leads to a direct improvement of the best known methods for solving LPs exactly over the rational numbers. Our implementation is publically available as an extension of the academic LP solver SoPlex. Y1 - 2016 U6 - https://doi.org/10.1287/ijoc.2016.0692 VL - 28 IS - 3 SP - 449 EP - 464 ER - TY - JOUR A1 - Leitner, Markus A1 - Ljubic, Ivana A1 - Sinnl, Markus A1 - Werner, Axel T1 - ILP heuristics and a new exact method for bi-objective 0/1 ILPs: Application to FTTx-network design JF - Computers & Operations Research Y1 - 2016 U6 - https://doi.org/10.1016/j.cor.2016.02.006 ER - TY - JOUR A1 - Krebek, von, Larissa K. S. A1 - Achazi, Andreas J. A1 - Solleder, Marthe A1 - Weber, Marcus A1 - Paulus, Beate A1 - Schalley, Christoph A. T1 - Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements JF - Chem. Eur. J. Y1 - 2016 U6 - https://doi.org/10.1002/chem.201603098 N1 - Has been announced under the title: Cooperativity in Multivalent Binding: A Detailed Experimental and Theoretical Thermochemical Study of Divalent Crown Ether-Ammonium Complexes VL - 22 IS - 43 SP - 15475 EP - 15484 ER - TY - JOUR A1 - Brandt, Christopher A1 - Tycowicz, Christoph von A1 - Hildebrandt, Klaus T1 - Geometric Flows of Curves in Shape Space for Processing Motion of Deformable Objects JF - Computer Graphics Forum N2 - We introduce techniques for the processing of motion and animations of non-rigid shapes. The idea is to regard animations of deformable objects as curves in shape space. Then, we use the geometric structure on shape space to transfer concepts from curve processing in Rn to the processing of motion of non-rigid shapes. Following this principle, we introduce a discrete geometric flow for curves in shape space. The flow iteratively replaces every shape with a weighted average shape of a local neighborhood and thereby globally decreases an energy whose minimizers are discrete geodesics in shape space. Based on the flow, we devise a novel smoothing filter for motions and animations of deformable shapes. By shortening the length in shape space of an animation, it systematically regularizes the deformations between consecutive frames of the animation. The scheme can be used for smoothing and noise removal, e.g., for reducing jittering artifacts in motion capture data. We introduce a reduced-order method for the computation of the flow. In addition to being efficient for the smoothing of curves, it is a novel scheme for computing geodesics in shape space. We use the scheme to construct non-linear Bézier curves by executing de Casteljau's algorithm in shape space. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12832 VL - 35 IS - 2 ER - TY - JOUR A1 - McPeak, Kevin A1 - van Engers, Christian D. A1 - Bianchi, Sarah A1 - Rossinelli, Aurelio A1 - Poulikakos, Lisa A1 - Bernard, Laetitia A1 - Herrmann, Sven A1 - Kim, David K. A1 - Burger, Sven A1 - Blome, Mark A1 - Jayanti, Sriharsha V. A1 - Norris, David T1 - Ultraviolet Plasmonic Chirality from Colloidal Aluminum Nanoparticles Exhibiting Charge-Selective Protein Detection JF - Adv. Mater. Y1 - 2015 U6 - https://doi.org/10.1002/adma.201503493 VL - 27 SP - 6244 ER - TY - JOUR A1 - Wolff, Christian A1 - Gutsche, Philipp A1 - Steel, Michael J. A1 - Eggleton, Benjamin J. A1 - Poulton, Christopher G. T1 - Power limits and a figure of merit for stimulated Brillouin scattering in the presence of third and fifth order loss JF - Opt. Express N2 - We derive a set of design guidelines and a figure of merit to aid the engineering process of on-chip waveguides for strong Stimulated Brillouin Scattering (SBS). To this end, we examine the impact of several types of loss on the total amplification of the Stokes wave that can be achieved via SBS. We account for linear loss and nonlinear loss of third order (two-photon absorption, 2PA) and fifth order, most notably 2PA-induced free carrier absorption (FCA). From this, we derive an upper bound for the output power of continuous-wave Brillouin-lasers and show that the optimal operating conditions and maximal realisable Stokes amplification of any given waveguide structure are determined by a dimensionless parameter ℱ involving the SBS-gain and all loss parameters. We provide simple expressions for optimal pump power, waveguide length and realisable amplification and demonstrate their utility in two example systems. Notably, we find that 2PA-induced FCA is a serious limitation to SBS in silicon and germanium for wavelengths shorter than 2200nm and 3600nm, respectively. In contrast, three-photon absorption is of no practical significance. Y1 - 2015 U6 - https://doi.org/10.1364/OE.23.026628 VL - 23 IS - 20 SP - 26628 EP - 26638 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - Neue Planungsinstrumente nutzen: Das Verkehrsangebot verbessern und Kosten sparen JF - Verkehr und Technik N2 - Wir illustrieren anhand des Liniennetzes der Stadt Potsdam das Potenzial mathematischer Methoden der Angebotsplanung. Wir zeigen, dass das "bestmögliche" Verkehrsangebot stark von planerischen Vorgaben beeinflusst wird, mit denen man die Erreichung unterschiedlicher und teilweise gegenläufiger Ziele steuern kann. Die Komplexität des Systems führt zum Auftreten von Rückkoppelungseffekten, die man nicht mit Hilfe von Daumenregeln beherrschen kann. Vielmehr ist der Einsatz moderner Planungsverfahren in einer interdisziplinären Zusammenarbeit von politischen Entscheidungsträgern, Verkehrsingenieuren und Mathematikern notwendig, um die aktuellen Herausforderungen in der Verkehrsplanung zu meistern. Der Artikel dokumentiert einen Beitrag zum 7. ÖPNV Innovationskongress des Ministeriums für Verkehr und Infrastruktur des Landes Baden-Württemberg, der vom 9.-11. März 2015 in Freiburg stattfand. Y1 - 2015 VL - 68 IS - 7 SP - 239 EP - 243 ER - TY - JOUR A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Martin, Alexander A1 - Miltenberger, Matthias A1 - Weninger, Dieter T1 - Progress in presolving for mixed integer programming JF - Mathematical Programming Computation N2 - This paper describes three presolving techniques for solving mixed integer programming problems (MIPs) that were implemented in the academic MIP solver SCIP. The task of presolving is to reduce the problem size and strengthen the formulation, mainly by eliminating redundant information and exploiting problem structures. The first method fixes continuous singleton columns and extends results known from duality fixing. The second analyzes and exploits pairwise dominance relations between variables, whereas the third detects isolated subproblems and solves them independently. The performance of the presented techniques is demonstrated on two MIP test sets. One contains all benchmark instances from the last three MIPLIB versions, while the other consists of real-world supply chain management problems. The computational results show that the combination of all three presolving techniques almost halves the solving time for the considered supply chain management problems. For the MIPLIB instances we obtain a speedup of 20 % on affected instances while not degrading the performance on the remaining problems. Y1 - 2015 U6 - https://doi.org/10.1007/s12532-015-0083-5 VL - 7 IS - 4 SP - 367 EP - 398 ER - TY - JOUR A1 - Zachow, Stefan T1 - Computational Planning in Facial Surgery JF - Facial Plastic Surgery N2 - This article reflects the research of the last two decades in computational planning for cranio-maxillofacial surgery. Model-guided and computer-assisted surgery planning has tremendously developed due to ever increasing computational capabilities. Simulators for education, planning, and training of surgery are often compared with flight simulators, where maneuvers are also trained to reduce a possible risk of failure. Meanwhile, digital patient models can be derived from medical image data with astonishing accuracy and thus can serve for model surgery to derive a surgical template model that represents the envisaged result. Computerized surgical planning approaches, however, are often still explorative, meaning that a surgeon tries to find a therapeutic concept based on his or her expertise using computational tools that are mimicking real procedures. Future perspectives of an improved computerized planning may be that surgical objectives will be generated algorithmically by employing mathematical modeling, simulation, and optimization techniques. Planning systems thus act as intelligent decision support systems. However, surgeons can still use the existing tools to vary the proposed approach, but they mainly focus on how to transfer objectives into reality. Such a development may result in a paradigm shift for future surgery planning. Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1564717 VL - 31 IS - 5 SP - 446 EP - 462 ER - TY - JOUR A1 - Kryven, Ivan A1 - Röblitz, Susanna A1 - Schütte, Christof T1 - Solution of the chemical master equation by radial basis functions approximation with interface tracking JF - BMC Systems Biology N2 - Background. The chemical master equation is the fundamental equation of stochastic chemical kinetics. This differential-difference equation describes temporal evolution of the probability density function for states of a chemical system. A state of the system, usually encoded as a vector, represents the number of entities or copy numbers of interacting species, which are changing according to a list of possible reactions. It is often the case, especially when the state vector is high-dimensional, that the number of possible states the system may occupy is too large to be handled computationally. One way to get around this problem is to consider only those states that are associated with probabilities that are greater than a certain threshold level. Results. We introduce an algorithm that significantly reduces computational resources and is especially powerful when dealing with multi-modal distributions. The algorithm is built according to two key principles. Firstly, when performing time integration, the algorithm keeps track of the subset of states with significant probabilities (essential support). Secondly, the probability distribution that solves the equation is parametrised with a small number of coefficients using collocation on Gaussian radial basis functions. The system of basis functions is chosen in such a way that the solution is approximated only on the essential support instead of the whole state space. Discussion. In order to demonstrate the effectiveness of the method, we consider four application examples: a) the self-regulating gene model, b) the 2-dimensional bistable toggle switch, c) a generalisation of the bistable switch to a 3-dimensional tristable problem, and d) a 3-dimensional cell differentiation model that, depending on parameter values, may operate in bistable or tristable modes. In all multidimensional examples the manifold containing the system states with significant probabilities undergoes drastic transformations over time. This fact makes the examples especially challenging for numerical methods. Conclusions. The proposed method is a new numerical approach permitting to approximately solve a wide range of problems that have been hard to tackle until now. A full representation of multi-dimensional distributions is recovered. The method is especially attractive when dealing with models that yield solutions of a complex structure, for instance, featuring multi-stability. Electronic version: http://www.biomedcentral.com/1752-0509/9/67 Y1 - 2015 U6 - https://doi.org/10.1186/s12918-015-0210-y VL - 9 IS - 67 SP - 1 EP - 12 ER - TY - JOUR A1 - Schütte, Christof A1 - Sarich, Marco T1 - A Critical Appraisal of Markov State Models JF - The European Physical Journal Special Topics N2 - Markov State Modelling as a concept for a coarse grained description of the essential kinetics of a molecular system in equilibrium has gained a lot of atten- tion recently. The last 10 years have seen an ever increasing publication activity on how to construct Markov State Models (MSMs) for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecu- lar sensors to molecular aggregation. Simultaneously the accompanying theory behind MSM building and approximation quality has been developed well be- yond the concepts and ideas used in practical applications. This article reviews the main theoretical results, provides links to crucial new developments, outlines the full power of MSM building today, and discusses the essential limitations still to overcome. Y1 - 2015 U6 - https://doi.org/10.1140/epjst/e2015-02421-0 VL - 224 IS - 12 SP - 2445 EP - 2462 ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Pelvic tilt compensates for increased acetabular anteversion JF - International Orthopaedics N2 - Pelvic tilt determines functional orientation of the acetabulum. In this study, we investigated the interaction of pelvic tilt and functional acetabular anteversion (AA) in supine position. Y1 - 2015 U6 - https://doi.org/10.1007/s00264-015-2949-6 VL - 40 IS - 8 SP - 1571 EP - 1575 ER - TY - JOUR A1 - Grötschel, Martin T1 - Die IMU und ihr Sekretariat JF - Mitteilungen der DMV N2 - Was macht die International Mathematical Union (IMU) eigentlich, und wozu ist das IMU-Sekretariat da? ... Y1 - 2015 U6 - https://doi.org/10.1515/dmvm-2015-0012 VL - 23 IS - 1 SP - 24 EP - 29 ER - TY - JOUR A1 - Ledentsov, Jr., Nikolay A1 - Shchukin, Vitaly A1 - Ledentsov, Jr., Nikolay A1 - Kropp, Jörg-R. A1 - Burger, Sven A1 - Schmidt, Frank T1 - Direct Evidence of the Leaky Emission in Oxide-Confined Vertical Cavity Lasers JF - IEEE J. Quant. Electron. Y1 - 2016 U6 - https://doi.org/10.1109/JQE.2016.2518081 VL - 52 IS - 3 SP - 2400207 ER - TY - JOUR A1 - Tycowicz, Christoph von A1 - Schulz, Christian A1 - Seidel, Hans-Peter A1 - Hildebrandt, Klaus T1 - Real-time Nonlinear Shape Interpolation JF - ACM Transactions on Graphics N2 - We introduce a scheme for real-time nonlinear interpolation of a set of shapes. The scheme exploits the structure of the shape interpolation problem, in particular, the fact that the set of all possible interpolated shapes is a low-dimensional object in a high-dimensional shape space. The interpolated shapes are defined as the minimizers of a nonlinear objective functional on the shape space. Our approach is to construct a reduced optimization problem that approximates its unreduced counterpart and can be solved in milliseconds. To achieve this, we restrict the optimization to a low-dimensional subspace that is specifically designed for the shape interpolation problem. The construction of the subspace is based on two components: a formula for the calculation of derivatives of the interpolated shapes and a Krylov-type sequence that combines the derivatives and the Hessian of the objective functional. To make the computational cost for solving the reduced optimization problem independent of the resolution of the example shapes, we combine the dimensional reduction with schemes for the efficient approximation of the reduced nonlinear objective functional and its gradient. In our experiments, we obtain rates of 20-100 interpolated shapes per second even for the largest examples which have 500k vertices per example shape. Y1 - 2015 U6 - https://doi.org/10.1145/2729972 VL - 34 IS - 3 SP - 34:1 EP - 34:10 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Karbstein, Marika T1 - Metric inequalities for routings on direct connections with application to line planning JF - Discrete Optimization N2 - We consider multi-commodity flow problems in which capacities are installed on paths. In this setting, it is often important to distinguish between flows on direct connection routes, using single paths, and flows that include path switching. We derive a feasibility condition for path capacities supporting such direct connection flows similar to the well-known feasibility condition for arc capacities in ordinary multi-commodity flows. The condition can be expressed in terms of a class of metric inequalities for routings on direct connections. We illustrate the concept on the example of the line planning problem in public transport and present an application to large-scale real-world problems. Y1 - 2015 VL - 18 SP - 56 EP - 73 ER - TY - JOUR A1 - Schnauber, Peter A1 - Thoma, Alexander A1 - Heine, Christoph V. A1 - Schlehahn, Alexander A1 - Gantz, Liron A1 - Gschrey, Manuel A1 - Schmidt, Ronny A1 - Hopfmann, Caspar A1 - Wohlfeil, Benjamin A1 - Schulze, Jan-Hindrick A1 - Strittmatter, Andre A1 - Heindel, Tobias A1 - Rodt, Sven A1 - Woggon, Ulrike A1 - Gershoni, David A1 - Reitzenstein, Stephan T1 - Bright Single-Photon Sources Based on Anti-Reflection Coated Deterministic Quantum Dot Microlenses JF - Technologies Y1 - 2016 U6 - https://doi.org/10.3390/technologies4010001 VL - 4 IS - 1 SP - 1 ER - TY - JOUR A1 - Härtig, Hermann A1 - Matsuoka, Satoshi A1 - Mueller, Frank A1 - Reinefeld, Alexander T1 - Resilience in Exascale Computing (Dagstuhl Seminar 14402) JF - Dagstuhl Reports Y1 - 2015 U6 - https://doi.org/10.4230/DagRep.4.9.124 VL - 4 IS - 9 SP - 124 EP - 139 ER - TY - JOUR A1 - Tuma, Christian A1 - Sauer, Joachim T1 - Quantum chemical ab initio prediction of proton exchange barriers between CH4 and different H-zeolites JF - The Journal of Chemical Physics Y1 - 2015 U6 - https://doi.org/10.1063/1.4923086 VL - 143 IS - 10 SP - 102810-1 EP - 102810-13 ER - TY - JOUR A1 - Zachow, Stefan A1 - Heppt, Werner T1 - The Facial Profile JF - Facial Plastic Surgery N2 - Facial appearance in our societies is often associated with notions of attractiveness, juvenileness, beauty, success, and so forth. Hence, the role of facial plastic surgery is highly interrelated to a patient's desire to feature many of these positively connoted attributes, which of course, are subject of different cultural perceptions or social trends. To judge about somebody's facial appearance, appropriate quantitative measures as well as methods to obtain and compare individual facial features are required. This special issue on facial profile is intended to provide an overview on how facial characteristics are surgically managed in an interdisciplinary way based on experience, instrumentation, and modern technology to obtain an aesthetic facial appearance with harmonious facial proportions. The facial profile will be discussed within the context of facial aesthetics. Latest concepts for capturing facial morphology in high speed and impressive detail are presented for quantitative analysis of even subtle changes, aging effects, or facial expressions. In addition, the perception of facial profiles is evaluated based on eye tracking technology. Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1566132 VL - 31 IS - 5 SP - 419 EP - 420 ER - TY - JOUR A1 - Stötzel, Claudia A1 - Röblitz, Susanna A1 - Siebert, Heike T1 - Complementing ODE-based System Analysis Using Boolean Networks Derived from an Euler-like Transformation JF - PLOS ONE Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0140954 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias T1 - Prevailing Dust-transport Directions on Comet 67P/Churyumov–Gerasimenko JF - The Astrophysical Journal Letters N2 - Dust transport and deposition behind larger boulders on the comet 67P/Churyumov–Gerasimenko (67P/C–G) have been observed by the Rosetta mission. We present a mechanism for dust-transport vectors based on a homogeneous surface activity model incorporating in detail the topography of 67P/C–G. The combination of gravitation, gas drag, and Coriolis force leads to specific dust transfer pathways, which for higher dust velocities fuel the near-nucleus coma. By distributing dust sources homogeneously across the whole cometary surface, we derive a global dust-transport map of 67P/C–G. The transport vectors are in agreement with the reported wind-tail directions in the Philae descent area. Y1 - 2015 U6 - https://doi.org/10.1088/2041-8205/813/2/L33 VL - 813 IS - 2 SP - L33 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Influence of pH and sequence in peptide aggregation via molecular simulation JF - Journal of Chemical Physics Y1 - 2015 U6 - https://doi.org/https://doi.org/10.1063/1.4935707 VL - 143 IS - 24 ER - TY - JOUR A1 - Schäfer, Patrick T1 - Scalable time series classification JF - Data Mining and Knowledge Discovery N2 - Time series classification tries to mimic the human understanding of similarity. When it comes to long or larger time series datasets, state-of-the-art classifiers reach their limits because of unreasonably high training or testing times. One representative example is the 1-nearest-neighbor dynamic time warping classifier (1-NN DTW) that is commonly used as the benchmark to compare to. It has several shortcomings: it has a quadratic time complexity in the time series length and its accuracy degenerates in the presence of noise. To reduce the computational complexity, early abandoning techniques, cascading lower bounds, or recently, a nearest centroid classifier have been introduced. Still, classification times on datasets of a few thousand time series are in the order of hours. We present our Bag-Of-SFA-Symbols in Vector Space classifier that is accurate, fast and robust to noise. We show that it is significantly more accurate than 1-NN DTW while being multiple orders of magnitude faster. Its low computational complexity combined with its good classification accuracy makes it relevant for use cases like long or large amounts of time series or real-time analytics. Y1 - 2015 U6 - https://doi.org/10.1007/s10618-015-0441-y SP - 1 EP - 26 ER - TY - JOUR A1 - Wolff, Christian A1 - Gutsche, Philipp A1 - Steel, Michael J. A1 - Eggleton, Benjamin J. A1 - Poulton, Christopher G. T1 - Impact of nonlinear loss on stimulated Brillouin scattering JF - J. Opt. Soc. Am. B N2 - We study the impact of two-photon absorption (2PA) and fifth-order nonlinear loss such as 2PA-induced free-carrier absorption in semiconductors on the performance of stimulated Brillouin scattering devices. We formulate the equations of motion including effective loss coefficients, whose explicit expressions are provided for numerical evaluation in any waveguide geometry. We find that 2PA results in a monotonic, algebraic relationship between amplification, waveguide length, and pump power, whereas fifth-order losses lead to a nonmonotonic relationship. We define a figure of merit for materials and waveguide designs in the presence of fifth-order losses. From this, we determine the optimal waveguide length for the case of 2PA alone and upper bounds for the total Stokes amplification for the case of 2PA as well as fifth-order losses. The analysis is performed analytically using a small-signal approximation and is compared to numerical solutions of the full nonlinear modal equations. Y1 - 2015 U6 - https://doi.org/10.1364/JOSAB.32.001968 VL - 32 IS - 9 SP - 1968 EP - 1978 ER - TY - JOUR A1 - Abendroth, Frank A1 - Solleder, Marthe A1 - Welker, Pia A1 - Licha, Kai A1 - Weber, Marcus A1 - Seitz, Oliver A1 - Mangoldt, Dorothea T1 - High affinity flourescence labelled ligands for the estrogen receptor JF - Eur. J. Org. Chem. Y1 - 2015 VL - 2015 IS - 10 SP - 2157 EP - 2166 ER - TY - JOUR A1 - Koschek, A1 - Durmaz, Vedat A1 - Krylova, A1 - Wieczorek, A1 - Gupta, Pooja A1 - Richter, A1 - Bujotzek, Alexander A1 - Fischer, A1 - Haag, Rainer A1 - Freund, A1 - Weber, Marcus A1 - Rademann, T1 - Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands JF - Beilstein J. Org. Chem. Y1 - 2015 VL - 11 SP - 837 EP - 847 ER - TY - JOUR A1 - Durmaz, Vedat A1 - Weber, Marcus A1 - Meyer, A1 - Mückter, T1 - Computergestützte Simulationen zur Abschätzung gesundheitlicher Risiken durch anthropogene Spurenstoffe der Wassermatrix JF - KA Korrespondenz Abwasser, Abfall Y1 - 2015 VL - 3/15 SP - 264 EP - 267 ER - TY - JOUR A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology JF - NeuroInformatics Y1 - 2014 U6 - https://doi.org/10.1007/s12021-013-9213-2 VL - 12 IS - 2 SP - 325 EP - 339 PB - Springer US ER - TY - JOUR A1 - Gamrath, Gerald ED - Gomes, Carla ED - Sellmann, Meinolf T1 - Improving strong branching by propagation JF - Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems N2 - Strong branching is an important component of most variable selection rules in branch-and-bound based mixed-integer linear programming solvers. It predicts the dual bounds of potential child nodes by solving auxiliary LPs and thereby helps to keep the branch-and-bound tree small. In this paper, we describe how these dual bound predictions can be improved by including domain propagation into strong branching. Computational experiments on standard MIP instances indicate that this is beneficial in three aspects: It helps to reduce the average number of LP iterations per strong branching call, the number of branch-and-bound nodes, and the overall solving time. Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38171-3_25 VL - 7874 SP - 347 EP - 354 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Gamrath, Gerald A1 - Lübbecke, Marco ED - Festa, P. T1 - Experiments with a Generic Dantzig-Wolfe Decomposition for Integer Programs JF - Experimental Algorithms Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-13193-6_21 VL - 6049 SP - 239 EP - 252 PB - Springer-Verlag CY - Berlin ER - TY - JOUR A1 - Vincens, Eric A1 - Witt, Karl Josef A1 - Homberg, Ulrike T1 - Approaches to Determine the Constriction Size Distribution for Understanding Filtration Phenomena in Granular Materials JF - Acta Geotechnica Y1 - 2015 U6 - https://doi.org/10.1007/s11440-014-0308-1 VL - 10 IS - 3 SP - 291 EP - 303 PB - Springer ER - TY - JOUR A1 - Oeltze, Steffen A1 - Lehmann, Dirk J. A1 - Kuhn, Alexander A1 - Janiga, Gábor A1 - Theisel, Holger A1 - Preim, Bernhard T1 - Blood Flow Clustering and Applications in Virtual Stenting of Intracranial Aneurysms JF - IEEE Transactions on Visualization and Computer Graphics, 2014 Y1 - 2013 U6 - https://doi.org/10.1109/TVCG.2013.2297914 SN - 0934-5892 VL - 20 IS - 5 SP - 686 EP - 701 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Heller, Markus O. A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Omnidirectional Displacements for Deformable Surfaces JF - Medical Image Analysis Y1 - 2013 U6 - https://doi.org/10.1016/j.media.2012.11.006 VL - 17 IS - 4 SP - 429 EP - 441 PB - Elsevier ER - TY - JOUR A1 - Lamas-Rodríguez, Julián A1 - Heras, Dora Blanco A1 - Argüello, Francisco A1 - Kainmüller, Dagmar A1 - Zachow, Stefan A1 - Bóo, Montserrat T1 - GPU-accelerated level-set segmentation JF - Journal of Real-Time Image Processing Y1 - 2013 UR - http://dx.doi.org/10.1007/s11554-013-0378-6 U6 - https://doi.org/10.1007/s11554-013-0378-6 SN - 1861-8200 SP - 1 EP - 15 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Hoffmann, René A1 - Schultz, Julia A. A1 - Schellhorn, Rico A1 - Rybacki, Erik A1 - Keupp, Helmut A1 - Gerden, S. R. A1 - Lemanis, Robert A1 - Zachow, Stefan T1 - Non-invasive imaging methods applied to neo- and paleontological cephalopod research JF - Biogeosciences N2 - Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum/maximum size of objects that can be studied, the degree of post-processing needed and availability. The main application of the methods is seen in morphometry and volumetry of cephalopod shells. In particular we present a method for precise buoyancy calculation. Therefore, cephalopod shells were scanned together with different reference bodies, an approach developed in medical sciences. It is necessary to know the volume of the reference bodies, which should have similar absorption properties like the object of interest. Exact volumes can be obtained from surface scanning. Depending on the dimensions of the study object different computed tomography techniques were applied. Y1 - 2014 U6 - https://doi.org/10.5194/bg-11-2721-2014 N1 - To access the corresponding discussion paper go to www.biogeosciences-discuss.net/10/18803/2013/ - Biogeosciences Discuss., 10, 18803-18851, 2013 VL - 11 IS - 10 SP - 2721 EP - 2739 ER - TY - JOUR A1 - Bongs, Kai A1 - Burger, Sven A1 - Dettmer, S. A1 - Hellweg, D. A1 - Arlt, J. A1 - Ertmer, Wolfgang A1 - Sengstock, Klaus ED - Aspect, Alain ED - Dalibard, J. T1 - Coherent manipulation and guiding of Bose-Einstein condensates by optical dipole potentials JF - Dossier Optique et interférometrie atomiques Y1 - 2001 VL - 2 SP - 671 PB - C. R. Acad. Sci. Paris - Series IV ER - TY - JOUR A1 - Burger, Sven A1 - Cataliotti, F. S. A1 - Fort, C. A1 - Maddaloni, P. A1 - Minardi, F. A1 - Inguscio, Massimo T1 - Quasi 2D Bose-Einstein condensation in an optical lattice JF - EPL Y1 - 2002 U6 - https://doi.org/10.1209/epl/i2002-00532-1 VL - 57 IS - 1 SP - 1 EP - 6 ER - TY - JOUR A1 - Hoch, Hannelore A1 - Wessel, Andreas A1 - Asche, Manfred A1 - Baum, Daniel A1 - Beckmann, Felix A1 - Bräunig, Peter A1 - Ehrig, Karsten A1 - Mühlethaler, Roland A1 - Riesemeier, Heinrich A1 - Staude, Andreas A1 - Stelbrink, Björn A1 - Wachmann, Ekkehard A1 - Weintraub, Phyllis A1 - Wipfler, Benjamin A1 - Wolff, Carsten A1 - Zilch, Mathias T1 - Non-Sexual Abdominal Appendages in Adult Insects Challenge a 300 Million Year Old Bauplan JF - Current Biology Y1 - 2014 U6 - https://doi.org/10.1016/j.cub.2013.11.040 VL - 24 IS - 1 SP - R16 EP - R17 ER - TY - JOUR A1 - Grötschel, Martin A1 - Raack, Christian A1 - Werner, Axel T1 - Towards optimizing the deployment of optical access networks JF - EURO Journal on Computational Optimization Y1 - 2013 U6 - https://doi.org/10.1007/s13675-013-0016-x VL - 2 SP - 17 EP - 53 PB - Springer ER - TY - JOUR A1 - Raack, Christian A1 - Raymond, Annie A1 - Schlechte, Thomas A1 - Werner, Axel T1 - Standings in sports competitions using integer programming JF - Journal of Quantitative Analysis in Sports Y1 - 2013 U6 - https://doi.org/10.1515/jqas-2013-0111 VL - 10 IS - 2 SP - 131 EP - 137 PB - De Gruyter ER - TY - JOUR A1 - Betker, Andreas A1 - Kosiankowski, Dirk A1 - Lange, Christoph A1 - Pfeuffer, Frank A1 - Raack, Christian A1 - Werner, Axel ED - Helber, Stefan ED - Breitner, Michael ED - Rösch, Daniel ED - Schön, Cornelia ED - Graf von der Schulenburg, Johann-Matthias ED - Sibbertsen, Philipp ED - Steinbach, Marc ED - Weber, Stefan ED - Wolter, Anja T1 - Energy efficiency in extensive IP-over-WDM networks with protection JF - Operations Research Proceedings 2012 Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-00795-3_14 SP - 93 EP - 99 PB - Springer ER - TY - JOUR A1 - Leitner, Markus A1 - Ljubić, Ivana A1 - Sinnl, Markus A1 - Werner, Axel T1 - On the Two-Architecture Connected Facility Location Problem JF - Electronic Notes in Discrete Mathematics Y1 - 2013 U6 - https://doi.org//10.1016/j.endm.2013.05.113 VL - 41 SP - 359 EP - 366 CY - Costa Adeje ER - TY - JOUR A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Positional Uncertainty of Isocontours: Condition Analysis and Probabilistic Measures JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2011 U6 - https://doi.org/10.1109/TVCG.2010.247 VL - 17 IS - 10 SP - 1393 EP - 1406 ER - TY - JOUR A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Christian A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - J. Wygnanski, Israel T1 - Three-dimensional Coherent Structures of the Swirling Jet Undergoing Vortex breakdown: Stability Analysis and Empirical Mode Construction JF - J. Fluid Mech. Y1 - 2011 U6 - https://doi.org/10.1017/jfm.2011.141 VL - 679 SP - 383 EP - 414 ER - TY - JOUR A1 - Andrae, Dirk A1 - Barth, Ingo A1 - Bredtmann, Timm A1 - Hege, Hans-Christian A1 - Manz, Jörn A1 - Marquardt, Falko A1 - Paulus, Beate T1 - Electronic Quantum Fluxes During Pericyclic Reactions Exemplified for the Cope Rearrangement of Semibullvalene JF - J. Phys. Chem. B Y1 - 2011 U6 - https://doi.org/10.1021/jp110365g VL - 115 IS - 18 SP - 5476 EP - 5483 ER - TY - JOUR A1 - Zobel, Valentin A1 - Reininghaus, Jan A1 - Hotz, Ingrid T1 - Generalized Heat Kernel Signature JF - Journal of WSCG, International Conference on Computer Graphics, Visualization and Computer Vision Y1 - 2011 SP - 93 EP - 100target ER - TY - JOUR A1 - Diederichs, Gerd A1 - Seim, Heiko A1 - Meyer, Henning A1 - Issever, Ahi A1 - M. Link, Thomas A1 - J. Schröder, Ralf A1 - Scheibel, Markus T1 - CT-based patient-specific modeling of glenoid rim defects: A feasibility study JF - AJR Am J Roentgenol Y1 - 2008 U6 - https://doi.org/10.2214/AJR.08.1091 VL - 191 IS - 5 SP - 1406 EP - 1411 ER - TY - JOUR A1 - Shi, Kuangyu A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Visualizing Transport Structures of Time-Dependent Flow Fields JF - IEEE Computer Graphics and Applications Y1 - 2008 U6 - https://doi.org/10.1109/MCG.2008.106 SP - 24 EP - 35 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Kertzscher, Ulrich A1 - Schöneberg, Bastian A1 - Wellnhofer, Ernst A1 - Petz, Christoph T1 - CFD analysis in an anatomically realistic coronary artery model based on non-invasive 3D imaging JF - Int. J. Cardiovasc. Imaging Y1 - 2008 U6 - https://doi.org/10.1007/s10554-007-9275-z VL - 24(4) SP - 411 EP - 421 ER - TY - JOUR A1 - Sahner, Jan A1 - Weber, Britta A1 - Lamecker, Hans A1 - Prohaska, Steffen T1 - Extraction of feature Lines on surface meshes based on discrete Morse theory JF - Computer Graphics Forum Y1 - 2008 U6 - https://doi.org/10.1111/j.1467-8659.2008.01202.x VL - 27 IS - 3 SP - 735 EP - 742 CY - Eindhoven, Netherlands ER - TY - JOUR A1 - Laramee, Robert S. A1 - Erlebacher, Gordon A1 - Garth, Christoph A1 - Schafhitzel, Tobias A1 - Theisel, Holger A1 - Tricoche, Xavier A1 - Weinkauf, Tino A1 - Weiskopf, Daniel T1 - Applications of Texture-Based Flow Visualization JF - Engineering Applications of Computational Fluid Mechanics Y1 - 2008 UR - http://www.cs.swan.ac.uk/~csbob/research/application/ VL - 2 IS - 3 SP - 264 EP - 274 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Manz, Jörn A1 - Marquardt, Falko A1 - Paulus, Beate A1 - Schild, Axel T1 - Electron Flux during Pericyclic Reactions in the Tunneling Limit: Quantum Simulation for Cyclooctatetraene JF - Chem. Phys Y1 - 2010 U6 - https://doi.org/10.1016/j.chemphys.2010.07.033 N1 - Festschrift in Chem. Phys. in honour of Professor Horst Koeppel VL - 376 IS - 1-3 SP - 46 EP - 55 ER - TY - JOUR A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Christian A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Wygnanski, Israel T1 - Self Excited Oscillations in Swirling Jets: Stability Analysis and Empirical Mode Construction JF - Bulletin of the American Physical Society Y1 - 2010 UR - http://meetings.aps.org/link/BAPS.2010.DFD.GE.8 N1 - 63rd Annual Meeting of the APS Division of Fluid Dynamics, November 21-23, 2010, Long Beach, CA VL - 55 IS - 16 SP - GE.00008 ER - TY - JOUR A1 - Lamecker, Hans A1 - Pennec, Xavier T1 - Atlas to Image-with-Tumor Registration based on Demons and Deformation Inpainting JF - Proc. MICCAI Workshop on Computational Imaging Biomarkers for Tumors - From Qualitative to Quantitative (CIBT’2010) Y1 - 2010 CY - Beijing, China ER - TY - JOUR A1 - Kasten, Jens A1 - Petz, Christoph A1 - Hotz, Ingrid A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Tadmor, Gilead T1 - Lagrangian Feature Extraction of the Cylinder Wake JF - Physics of Fluids Y1 - 2010 U6 - https://doi.org/10.1063/1.3483220 VL - 22 IS - 9 SP - 091108 ER - TY - JOUR A1 - Torsney-Weir, Thomas A1 - Saad, Ahmed A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Weber, Britta A1 - Verbavatz, Jean-Marc T1 - Tuner: Principled Parameter Finding for Image Segmentation Algorithms Using Visual Response Surface Exploration JF - IEEE Trans. Vis. Comput. Graph. Y1 - 2011 VL - 17 IS - 12 SP - 1892 EP - 1901 ER - TY - JOUR A1 - Reininghaus, Jan A1 - Löwen, Christian A1 - Hotz, Ingrid T1 - Fast Combinatorial Vector Field Topology JF - IEEE Trans. Computer Graphics and Visualization Y1 - 2011 VL - 17 IS - 10 SP - 1433 EP - 1443 ER - TY - JOUR A1 - Ramm, Heiko A1 - Kahnt, Max A1 - Zachow, Stefan T1 - Patientenspezifische Simulationsmodelle für die funktionelle Analyse von künstlichem Gelenkersatz JF - Computer Aided Medical Engineering (CaMe) Y1 - 2012 VL - 3 IS - 2 SP - 30 EP - 36 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Perceptually Linear Parameter Variations JF - Computer Graphics Forum Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03054.x target VL - 31 IS - 2 SP - 535 EP - 544 ER - TY - JOUR A1 - Wiebel, Alexander A1 - Vos, Frans A1 - Foerster, David A1 - Hege, Hans-Christian T1 - WYSIWYP: What You See Is What You Pick JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2012 U6 - https://doi.org/10.1109/TVCG.2012.292 VL - 18 IS - 12 SP - 2236 EP - 2244 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Interactive Rendering of Materials and Biological Structures on Atomic and Nanoscopic Scale JF - Computer Graphics Forum Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03128.x target VL - 31 IS - 3 SP - 1325 EP - 1334 ER - TY - JOUR A1 - Petz, Christoph A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Probabilistic Local Features in Uncertain Vector Fields with Spatial Correlation JF - Computer Graphics Forum Y1 - 2012 VL - 31 IS - 3 SP - 1045 EP - 1054 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Schaller, Jens A1 - Kertzscher, Ulrich A1 - van den Bruck, Nils A1 - Pöthkow, Kai A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Spuler, Andreas T1 - Statistical wall shear stress maps of ruptured and unruptured middle cerebral artery aneurysms JF - J. R. Soc. Interface Y1 - 2012 U6 - https://doi.org/10.1098/rsif.2011.0490 VL - 9 IS - 69 SP - 677 EP - 688 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zachow, Stefan T1 - Multi-object segmentation of head bones JF - MIDAS Journal Y1 - 2009 ER - TY - JOUR A1 - Bischof, Horst A1 - Rau, Anne-Mareike A1 - Raicu, Daniela S. T1 - Comparison and Evaluation of Methods for Liver Segmentation from CT Datasets JF - IEEE Transactions on Medical Imaging Y1 - 2009 VL - 28(8) SP - 1251 EP - 1265 ER - TY - JOUR A1 - Barth, Ingo A1 - Hege, Hans-Christian A1 - Ikeda, Hiroshi A1 - Kenfack, Anatole A1 - Koppitz, Michael A1 - Manz, Jörn A1 - Marquardt, Falko A1 - K. Paramonov, Guennaddi T1 - Concerted Quantum Effects of Electronic and Nuclear Fluxes in Molecules JF - Chem. Phys. Lett. Y1 - 2009 U6 - https://doi.org/10.1016/j.cplett.2009.09.011 VL - 481 IS - 1-3 SP - 118 EP - 123 PB - Elsevier ER - TY - JOUR A1 - Petz, Christoph A1 - Kasten, Jens A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Hierarchical Vortex Regions in Swirling Flow JF - Computer Graphics Forum Y1 - 2009 VL - 28 IS - 3 SP - 863 EP - 870 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Multi-object Segmentation with Coupled Deformable Models JF - Annals of the British Machine Vision Association (BMVA) Y1 - 2009 VL - 5 SP - 1 EP - 10 ER - TY - JOUR A1 - Weinkauf, Tino A1 - Günther, David T1 - Separatrix Persistence: Extraction of Salient Edges on Surfaces Using Topological Methods JF - Computer Graphics Forum (Proc. SGP’09) Y1 - 2009 U6 - https://doi.org/10.1111/j.1467-8659.2009.01528.x VL - 28 IS - 5 SP - 1519 EP - 1528 ER - TY - JOUR A1 - Zachow, Stefan A1 - Muigg, Philipp A1 - Hildebrandt, Thomas A1 - Doleisch, Helmut A1 - Hege, Hans-Christian T1 - Visual Exploration of Nasal Airflow JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2009 U6 - https://doi.org/10.1109/TVCG.2009.198 VL - 15 IS - 8 SP - 1407 EP - 1414 ER - TY - JOUR A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Computergestützte Planung in der kraniofazialen Chirurgie JF - Face 01/08, Int. Mag. of Orofacial Esthetics Y1 - 2008 SP - 43 EP - 49 PB - Oemus Journale Leipzig ER - TY - JOUR A1 - Steinmann, Alexander A1 - Bartsch, Peter A1 - Zachow, Stefan A1 - Hildebrandt, Thomas T1 - Breathing Easily: Simulation of airflow in human noses can become a useful rhinosurgery planning tool JF - ANSYS Advantage Y1 - 2008 VL - Vol. II, No. 1 SP - 30 EP - 31 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Kertzscher, Ulrich A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Stalling, Detlev T1 - Numerical Dye Washout Method as a Tool for Characterizing the Heart Valve Flow JF - ASAIO Journal Y1 - 2008 U6 - https://doi.org/10.1097/MAT.0b013e31815c5e38 VL - 54(1) SP - 50 EP - 57 ER - TY - JOUR A1 - Cordes, Frank A1 - Preissner, Robert A1 - Steinke, Thomas T1 - How Does a Protein Work? JF - BioTOPics J. of Biotechnology Berlin-Brandenburg Y1 - 2003 VL - 18 IS - 2 SP - 4 EP - 5 ER - TY - JOUR A1 - Andrzejak, Artur A1 - Welzl, Emo T1 - In between k-Sets, j-Facets, and i-Faces: (i , j) - Partition JF - Discrete & Computational Geometry Y1 - 2003 U6 - https://doi.org/s00454-002-2778-4 VL - 29 IS - 1 SP - 105 EP - 131 ER - TY - JOUR A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Modeling Replica Availability in Large Data Grids JF - J. Grid Computing Y1 - 2003 U6 - https://doi.org/10.1023/B:GRID.0000024086.50333.0d VL - 1 IS - 2 SP - 219 EP - 227 ER - TY - JOUR A1 - Graupner, Sven A1 - Kotov, Vadim A1 - Andrzejak, Artur A1 - Trinks, Holger T1 - Service-Centric Globally Distributed Computing JF - IEEE Internet Computing Y1 - 2003 U6 - https://doi.org/10.1109/MIC.2003.1215658 VL - 7 IS - 4 SP - 36 EP - 43 CY - Los Alamitos, CA, USA ER - TY - JOUR A1 - Günther, David A1 - Reininghaus, Jan A1 - Wagner, Hubert A1 - Hotz, Ingrid T1 - Efficient Computation of 3D Morse-Smale Complexes and Persistent Homology using Discrete Morse Theory JF - The Visual Computer Y1 - 2012 U6 - https://doi.org/10.1007/s00371-012-0726-8 VL - 28 IS - 10 SP - 959 EP - 969 ER - TY - JOUR A1 - Reininghaus, Jan A1 - Kasten, Jens A1 - Weinkauf, Tino A1 - Hotz, Ingrid T1 - Efficient Computation of Combinatorial Feature Flow Fields JF - Transactions on Visualization and Computer Graphics Y1 - 2012 U6 - https://doi.org/10.1109/TVCG.2011.269 VL - 18 IS - 9 SP - 1563 EP - 1573 ER - TY - JOUR A1 - Weiser, Martin A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Craniofacial Surgery Planning Based on Virtual Patient Models JF - it - Information Technology Y1 - 2010 U6 - https://doi.org/10.1524/itit.2010.0600 VL - 52 IS - 5 SP - 258 EP - 263 PB - Oldenbourg Verlagsgruppe ER - TY - JOUR A1 - Ziegler, Alexander A1 - Ogurreck, Malte A1 - Steinke, Thomas A1 - Beckmann, Felix A1 - Prohaska, Steffen A1 - Ziegler, Andreas T1 - Opportunities and challenges for digital morphology JF - Biology Direct Y1 - 2010 U6 - https://doi.org/10.1186/1745-6150-5-45 VL - 5 IS - 1 SP - 45 ER - TY - JOUR A1 - Kenfack, Anatole A1 - Marquardt, Falko A1 - K. Paramonov, Gennadij A1 - Barth, Ingo A1 - Lasser, Caroline A1 - Paulus, Beate T1 - Initial-state dependence of coupled electronic and nuclear fluxes in molecules JF - Phys. Rev. A Y1 - 2010 U6 - https://doi.org/10.1103/PhysRevA.81.052502 VL - 81 IS - 5 SP - 052502 PB - American Physical Society ER - TY - JOUR A1 - Dworzak, Jalda A1 - Lamecker, Hans A1 - von Berg, Jens A1 - Klinder, Tobias A1 - Lorenz, Cristian A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - 3D Reconstruction of the Human Rib Cage from 2D Projection Images using a Statistical Shape Model JF - Int. J. Comput. Assist. Radiol. Surg. Y1 - 2010 U6 - https://doi.org/10.1007/s11548-009-0390-2 SN - 1861-6410 VL - 5 IS - 2 SP - 111 EP - 124 PB - Springer ER - TY - JOUR A1 - Hutanu, Andrei A1 - Allen, Gabrielle A1 - Beck, Stephen A1 - Holub, Petr A1 - Kaiser, Hartmut A1 - Kulshrestha, Archit A1 - Liska, Milos A1 - MacLaren, Jon A1 - Matyska, Ludek A1 - Paruchuri, Ravi A1 - Prohaska, Steffen A1 - Seidel, Edward A1 - Ullmer, Brygg A1 - Venkataraman, Shalini T1 - Distributed and collaborative visualization of large data sets using high-speed networks JF - Future Generation Comp. Syst Y1 - 2006 U6 - https://doi.org/10.1016/j.future.2006.03.026 VL - 22(8) SP - 1004 EP - 1010 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Timmel, Tobias A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Characterization of an artificial valve flow using the numerical dye washout visualization technique JF - Artificial Organs Y1 - 2006 VL - 30(8) SP - 642 EP - 650 ER - TY - JOUR A1 - Heller, Markus O. A1 - Matziolis, Georg A1 - König, Christian A1 - Taylor, William R. A1 - Hinterwimmer, S. A1 - Graichen, H. A1 - Hege, Hans-Christian A1 - Bergmann, G. A1 - Perka, Carsten A1 - Duda, G. N. T1 - Muskuloskelettale Biomechanik des Kniegelenks - Grundlagen für die präoperative Planung von Umstellung und Gelenkersatz JF - Der Orthopäde Y1 - 2007 U6 - https://doi.org/10.1007/s00132-007-1115-2 VL - 36 IS - 7 SP - 628 EP - 634 ER - TY - JOUR A1 - Paar, Philip A1 - Clasen, Malte T1 - Earth, Landscape, Biotope, Plant. Interactive visualisation with Biosphere3D JF - Proceedings of CORP - 12th International Conference on Urban Planning and Spatial Development in the Information Society, May 20th - 23rd Y1 - 2007 SP - 207 EP - 214 ER - TY - JOUR A1 - Lange, Thomas A1 - Hünerbein, Michael A1 - Eulenstein, Sebastian A1 - Beller, Sigfried A1 - Schlag, Peter A1 - Lamecker, Hans T1 - A Distance Measure for Non-Rigid Registration of Geometrical Models to Intensity Data JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2007 VL - 2, Suppl. 1 SP - 204 EP - 206 PB - Springer ER - TY - JOUR A1 - Heppt, Werner A1 - Hildebrandt, Thomas A1 - Steinmann, Alexander A1 - Zachow, Stefan T1 - Aesthetic and Function in Rhinoplasty JF - Springer Journal Y1 - 2007 VL - 264 (Suppl 1), RL 126 SP - 307 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lange, Thomas A1 - Lamecker, Hans T1 - Shape constrained automatic segmentation of the liver based on a heuristic intensity model JF - Proc. MICCAI Workshop 3D Segmentation in the Clinic Y1 - 2007 SP - 109 EP - 116 ER - TY - JOUR A1 - Gessat, Michael A1 - Zachow, Stefan A1 - Burgert, Oliver A1 - Lemke, Heinz T1 - Geometric Meshes in Medical Applications - Steps towards a specification of Geometric Models in DICOM JF - Int. J. of Computer Assisted Radiology and Surgery (CARS) Y1 - 2007 U6 - https://doi.org/10.1007/s11548-007-0112-6 SP - 440 EP - 442 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Heppt, Werner T1 - Innovation in der Funktionell-Ästhetischen Nasenchirurgie: Rhino-CFD JF - Face, Int. Mag. of Orofacial Esthetics Y1 - 2007 SP - 20 EP - 23 PB - Oemus Journale Leipzig ER - TY - JOUR A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Hildebrandt, Thomas A1 - Heppt, Werner T1 - Understanding nasal airflow via CFD simulation and visualization JF - Proc. Computer Aided Surgery around the Head Y1 - 2007 SP - 173 EP - 176 ER - TY - JOUR A1 - Lamecker, Hans A1 - Kamer, Lukas A1 - Wittmers, Antonia A1 - Zachow, Stefan A1 - Kaup, Thomas A1 - Schramm, Alexander A1 - Noser, Hansrudi A1 - Hammer, Beat T1 - A method for the three-dimensional statistical shape analysis of the bony orbit JF - Proc. Computer Aided Surgery around the Head Y1 - 2007 SP - 94 EP - 97 ER - TY - JOUR A1 - Kälberer, Felix A1 - Polthier, Konrad A1 - Reitebuch, Ulrich A1 - Wardetzky, Max T1 - Free Lence - Coding with free valences JF - Computer Graphics Forum Y1 - 2005 U6 - https://doi.org/10.1111/j.1467-8659.2005.00872.x VL - 24 IS - Issue 3 SP - 469 EP - 478 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Weinkauf, Tino A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Towards distributed visualization and analysis of large flow data JF - JSME International Journal, Series B Y1 - 2005 VL - 48 (2) SP - 241 EP - 246 ER - TY - JOUR A1 - Brandt, Robert A1 - Rohlfing, Torsten A1 - Rybak, Jürgen A1 - Krofczik, Sabine A1 - Maye, Alexander A1 - Westerhoff, Malte A1 - Hege, Hans-Christian A1 - Menzel, Randolf T1 - A three-dimensional average-shape atlas of the honeybee brain and its applications JF - Journal of Comparative Neurology Y1 - 2005 VL - 492(1) SP - 1 EP - 19 ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Haberl, Hannes A1 - Stiller, Michael T1 - Medical applications for statistical shape models JF - Computer Aided Surgery around the Head, Fortschritt-Berichte VDI - Biotechnik/Medizintechnik Y1 - 2005 VL - 17 (258) SP - 61 ER - TY - JOUR A1 - Thomsen, Jesper A1 - Laib, Andreas A1 - Koller, Bruno A1 - Prohaska, Steffen A1 - Mosekilde, L. A1 - Gowin, Wolfgang T1 - Stereological measures of trabecular bone structure: Comparison of 3D micro computed tomography with 2D histological sections in human proximal tibial bone biopsies JF - Journal of Microscopy Y1 - 2005 VL - 218 SP - 171 EP - 179 ER - TY - JOUR A1 - Weinkauf, Tino A1 - Sahner, Jan A1 - Theisel, Holger A1 - Hege, Hans-Christian T1 - Cores of Swirling Particle Motion in Unsteady Flows JF - IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization 2007) Y1 - 2007 U6 - https://doi.org/10.1109/TVCG.2007.70545 VL - 13 IS - 6 SP - 1759 EP - 1766 ER - TY - JOUR A1 - Gubatz, Sabine A1 - Dercksen, Vincent J. A1 - Brüß, Cornelia A1 - Weschke, Winfriede A1 - Wobus, Ulrich T1 - Analysis of barley (hordeum vulgare) grain development using three-dimensional digital models JF - The Plant Journal Y1 - 2007 U6 - https://doi.org/10.1111/j.1365-313X.2007.03260.x VL - 52 IS - 4 SP - 779 EP - 790 ER - TY - JOUR A1 - Dornheim, Jana A1 - Seim, Heiko A1 - Preim, Bernhard A1 - Hertel, Ilka A1 - Strauß, Gero T1 - Segmentation of neck lymph nodes in CT datasets with stable 3D mass-spring models JF - Academic Radiology (2) Y1 - 2007 U6 - https://doi.org/10.1016/j.acra.2007.09.001 VL - 14(2) SP - 1389 EP - 1399 ER - TY - JOUR A1 - Weinkauf, Tino A1 - Theisel, Holger A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Topological structures in two-parameter-dependent 2D vector fields JF - Computer Graphics Forum Y1 - 2006 U6 - https://doi.org/10.1111/j.1467-8659.2006.00980.x VL - 25 (3) SP - 607 EP - 616 ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Wittmers, Antonia A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Automatic segmentation of mandibles in low-dose CT-data JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2006 VL - 1(1) SP - 393 EP - 395 ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Zöckler, Maja T1 - Surgical treatment of craniosynostosis based on a statistical 3D-shape model JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2006 U6 - https://doi.org/10.1007/s11548-006-0024-x VL - 1(1) SP - 253 EP - 254 ER - TY - JOUR A1 - Benger, Werner A1 - Hege, Hans-Christian T1 - Strategies for direct visualization of second-rank tensor fields JF - Visualization and Processing of Tensor Fields Y1 - 2006 U6 - https://doi.org/10.1007/3-540-31272-2_11 SP - 191 EP - 214 PB - Springer Verlag ER - TY - JOUR A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Computer assisted planning in cranio-maxillofacial surgery JF - Journal of Computing and Information Technology Y1 - 2006 VL - 14(1) SP - 53 EP - 64 ER - TY - JOUR A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Is the course of the mandibular nerve deducible from the shape of the mandible? JF - Int. J. of Computer Assisted Radiology and Surgery Y1 - 2006 SP - 415 EP - 417 PB - Springer ER - TY - JOUR A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Hildebrandt, Thomas A1 - Weber, Rainer A1 - Heppt, Werner T1 - CFD simulation of nasal airflow: Towards treatment planning for functional rhinosurgery JF - Int. J. of Computer Assisted Radiology and Surgery Y1 - 2006 SP - 165 EP - 167 PB - Springer ER - TY - JOUR A1 - Benger, Werner A1 - Bartsch, Hauke A1 - Hege, Hans-Christian A1 - Kitzler, Hagen A1 - Shumilina, Anna A1 - Werner, Annett T1 - Visualizing neuronal structures in the human brain via Diffusion Tensor MRI JF - Int. Journal of Neuroscience Y1 - 2006 VL - 116(4) SP - 461 EP - 514 ER - TY - JOUR A1 - Maye, Alexander A1 - Wenckebach, Thomas A1 - Hege, Hans-Christian T1 - Visualization, reconstruction, and integration of neuronal structures in digital brain atlases JF - Int. Journal of Neuroscience Y1 - 2006 VL - 116(4) SP - 431 EP - 459 ER - TY - JOUR A1 - Cassot, Francis A1 - Lauwers, Frederic A1 - Fouard, Céline A1 - Prohaska, Steffen A1 - Lauwer-Cances, Valerie T1 - A novel three-dimensional computer assisted method for a quantitative study of microvascular networks of the human cerebral cortex JF - Microcirculation Y1 - 2006 VL - 13 SP - 15 EP - 32 ER - TY - JOUR A1 - Fouard, Céline A1 - Malandain, Grégoire A1 - Prohaska, Steffen A1 - Westerhoff, Malte T1 - Blockwise processing applied to brain micro-vascular network study JF - IEEE Transactions on Medical Imaging Y1 - 2006 U6 - https://doi.org/10.1109/TMI.2006.880670 VL - 25 IS - 10 SP - 1319 EP - 1328 ER - TY - JOUR A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Kurths, Jürgen A1 - Prohaska, Steffen A1 - Gowin, Wolfgang T1 - Modeling resorption in 2D-CT and 3D μ-CT bone images JF - Int. J. of Bif. and Chaos Y1 - 2005 VL - 15(9) SP - 2995 EP - 3009 ER - TY - JOUR A1 - Ziegler, Günter M. A1 - Hege, Hans-Christian A1 - Duda, Georg T1 - Neue Bilder für die Medizin? JF - DFN-Mitteilungen Y1 - 2005 VL - 13(3) SP - 163 EP - 167 ER - TY - JOUR A1 - Lange, Carsten A1 - Polthier, Konrad T1 - Anisotropic fairing of point sets JF - Special Issue of CAGD 2005 Y1 - 2005 U6 - https://doi.org/10.1016/j.cagd.2005.06.010 ER - TY - JOUR A1 - Werner, Armin A1 - Deussen, Oliver A1 - Döllner, Jürgen A1 - Hege, Hans-Christian A1 - Paar, Philip A1 - Rekittke, Jörg ED - Buhmann, Erich ED - Paar, Philip ED - Bishop, Ian ED - Lange, Eckart T1 - Lenné 3D walking through landscape plan JF - Trends in Real-Time Landscape Visualization and Participation Y1 - 2005 SP - 48 EP - 59 PB - Wichmann Verlag ER - TY - JOUR A1 - Grötschel, Martin A1 - Lügger, Joachim T1 - Veränderungen der Publikations- und Kommunikationswelt: Open Access, Google, etc. JF - Gegenworte: Hefte für den Disput über Wissen N2 - Beim Schreiben dieses Artikels, der auf Veränderungen der Kommunikations- und Publikationstechniken und ihre Bedeutung hinweist, ist uns mehr als je zuvor bewusst geworden, wie beschränkt das Medium Papier ist. Es gibt z. B. keine Hyperlinks, durch die man unmittelbar das Erwähnte erleben oder überprüfen kann. Ein schneller Wechsel vom Wort zum Bild, zum Ton oder Video ist nicht möglich. Wer will schon lange URLs abtippen und Medienbrüche erleiden? Wir haben uns daher entschlossen, eine textidentische Version dieses Artikels mit allen URLs – sie liegt Ihnen hier vor – elektronisch anzubieten und in der für die "Gegenworte" (BBAW) gekürzten Fassung nur durch [URL] anzudeuten, dass der Leser an dieser Stelle einfach in der elektronischen Version einen Klick ins Internet machen sollte. Und damit sind wir bereits mitten im Thema. Y1 - 2009 VL - 21 IS - 21 SP - 69 EP - 72 ER - TY - JOUR A1 - Lügger, Joachim T1 - Zum Nutzen des Web 2.0 für „Die kleine Kollaboration“ in den Wissenschaften JF - ABI Technik -- Zeitschrift für Automation, Bau und Technik im Archiv-, Bibliotheks- und Informationswesen N2 - Gemeinsame Web-Auftritte zu organisieren, die sich über mehrere Institutionen und Fachgebiete erstrecken, ist eine anspruchsvolle und faszinierende Aufgabe, die auf verschiedene Weise gelingen, aber auch scheitern kann. Wer sich daran versucht, tut gut daran, sich über bestimmte Prinzipien und technische Mittel zu informieren, die das fortgeschrittene Web ihm heute bietet. Das Internet, das World Wide Web und das moderne Web 2.0 sind in einer fast zwanzig Jahre dauernden Kollaboration einer globalen Gemeinschaft von Entwicklern und Anwendern entstanden. Es enthält heute eine Fülle sofort einsetzbarer Komponenten, von der „Benutzerdefinierten Google-Suche Beta“ mit Google‘s PageRanking auf ausgewählten Web-Seiten bis hin zum automatisierten Web-Server mit Content-Management für das „Mitmach-Web“. Der Artikel stellt nur eine kleine Auswahl solcher Lösungen vor und macht den Versuch, einige Prinzipien des Web 2.0 so herauszuarbeiten, dass die notwendige Kommunikation zwischen Managern, Technikern, Redakteuren und Organisatoren in der kleinen Kollaboration unterstützt wird. „Kleine Kollaboration“ bedeutet hier, dass es nicht um die globale Vernetzung von technischen Großgeräten der e-Science gehen soll, auch nicht um die Super-Suchmaschine in Europa, sondern um die Unterstützung der Zusammenarbeit und Kommunikation von Wissenschaftlern und Museumsfachleuten mit Ihren Nutzern. Y1 - 2009 SN - 2191-4664 VL - 29 IS - 1 SP - 1 EP - 11 ER - TY - JOUR A1 - Deuflhard, Peter A1 - Röblitz, Susanna A1 - Stötzel, Claudia T1 - Mathematical Systems Biology at Zuse Institute Berlin (ZIB) JF - BioTOPics - Journal of Biotechnology in Berlin-Brandenburg Y1 - 2010 VL - 39 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Nagaiah, Chamakuri A1 - Kunisch, Karl A1 - Weiser, Martin T1 - Lossy Compression in Optimal Control of Cardiac Defibrillation JF - J. Sci. Comput. N2 - This paper presents efficient computational techniques for solving an optimization problem in cardiac defibrillation governed by the monodomain equations. Time-dependent electrical currents injected at different spatial positions act as the control. Inexact Newton-CG methods are used, with reduced gradient computation by adjoint solves. In order to reduce the computational complexity, adaptive mesh refinement for state and adjoint equations is performed. To reduce the high storage and bandwidth demand imposed by adjoint gradient and Hessian-vector evaluations, a lossy compression technique for storing trajectory data is applied. An adaptive choice of quantization tolerance based on error estimates is developed in order to ensure convergence. The efficiency of the proposed approach is demonstrated on numerical examples. Y1 - 2014 U6 - https://doi.org/10.1007/s10915-013-9785-x VL - 60 IS - 1 SP - 35 EP - 59 ER - TY - JOUR A1 - Schmid, Martina A1 - Andrae, Patrick A1 - Manley, Phillip T1 - Plasmonic and photonic scattering and near fields of nanoparticles JF - Nanoscale Research Letters Y1 - 2014 U6 - https://doi.org/10.1186/1556-276X-9-50 VL - 9 SP - 50 ER - TY - JOUR A1 - Preidel, Veit A1 - Lockau, Daniel A1 - Sontheimer, Tobias A1 - Back, Franziska A1 - Rudigier-Voigt, Eveline A1 - Rech, Bernd A1 - Becker, Christiane T1 - Analysis of absorption enhancement in tailor-made periodic polycrystalline silicon microarrays JF - physica status solidi (RRL)-Rapid Research Letters Y1 - 2013 U6 - https://doi.org/10.1002/pssr.201308098 VL - 7 IS - 12 SP - 1045 EP - 1049 PB - WILEY-VCH Verlag ER - TY - JOUR A1 - Becker, Christiane A1 - Amkreutz, Daniel A1 - Sontheimer, Tobias A1 - Preidel, Veit A1 - Lockau, Daniel A1 - Haschke, Jan A1 - Jogschies, Lisa A1 - Klimm, Carola A1 - Merkel, Janis J. A1 - Plocica, Paul A1 - Steffens, Simon A1 - Rech, Bernd T1 - Polycrystalline silicon thin-film solar cells: Status and perspectives JF - Solar Energy Materials and Solar Cells Y1 - 2013 U6 - https://doi.org/10.1016/j.solmat.2013.05.043 VL - 119 SP - 112 EP - 123 ER - TY - JOUR A1 - Sontheimer, Tobias A1 - Preidel, Veit A1 - Lockau, Daniel A1 - Back, Franziska A1 - Rudigier-Voigt, Eveline A1 - Löchel, Bernd A1 - Erko, Alexei A1 - Schmidt, Frank A1 - Schnegg, Alexander A1 - Lips, Klaus A1 - Becker, Christiane A1 - Rech, Bernd T1 - Correlation between structural and opto-electronic characteristics of crystalline Si microhole arrays for photonic light management JF - Journal of Applied Physics Y1 - 2013 U6 - https://doi.org/10.1063/1.4829008 VL - 114 IS - 17 SP - 173513 PB - AIP Publishing ER - TY - JOUR A1 - Lockau, Daniel A1 - Sontheimer, Tobias A1 - Preidel, Veit A1 - Ruske, Florian A1 - Hammerschmidt, Martin A1 - Becker, Christiane A1 - Schmidt, Frank A1 - Rech, Bernd T1 - Advanced microhole arrays for light trapping in thin film silicon solar cells JF - Solar Energy Materials and Solar Cells Y1 - 2014 U6 - https://doi.org/10.1016/j.solmat.2013.11.024 VL - 125 SP - 298 EP - 304 ER - TY - JOUR A1 - Kirner, Simon A1 - Hammerschmidt, Martin A1 - Schwanke, Christoph A1 - Lockau, Daniel A1 - Calnan, Sonya A1 - Frijnts, Tim A1 - Neubert, Sebastian A1 - Schöpke, Andreas A1 - Schmidt, Frank A1 - Zollondz, Jens-Hendrik A1 - Heidelberg, Andreas A1 - Stannowski, Bernd A1 - Rech, Bernd A1 - Schlatmann, Rutger T1 - Implications of TCO Topography on Intermediate Reflector Design for a-Si/μc-Si Tandem Solar Cells — Experiments and Rigorous Optical Simulations JF - IEEE Journal of Photovoltaics Y1 - 2014 U6 - https://doi.org/10.1109/JPHOTOV.2013.2279204 VL - 4 IS - 1 SP - 10 EP - 15 ER - TY - JOUR A1 - Röblitz, Susanna A1 - Weber, Marcus T1 - Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification JF - Advances in Data Analysis and Classification Y1 - 2013 U6 - https://doi.org/10.1007/s11634-013-0134-6 VL - 7 IS - 2 SP - 147 EP - 179 ER - TY - JOUR A1 - Albrecht, Rita A1 - Ceynowa, Klaus A1 - Degkwitz, Andreas A1 - Kende, Jiri A1 - Koch, Thorsten A1 - Messmer, Gabriele A1 - Risch, Uwe A1 - Rusch, Beate A1 - Scheuerl, Robert A1 - Voß, Michael T1 - Cloudbasierte Infrastruktur für Bibliotheksdaten – auf dem Weg zu einer Neuordnung der deutschen Verbundlandschaft JF - Bibliothek Forschung und Praxis N2 - Im Oktober 2012 hatte die Deutsche Forschungsgemeinschaft (DFG) ein Förderprogramm zur Neuausrichtung überregionaler Informationsservices ausgeschrieben, um eine umfassende Reorganisation bestehender Infrastrukturen anzustoßen, die mit den Empfehlungen des Wissenschaftsrates zur Zukunft der bibliothekarischen Verbundsysteme in Deutschland gefordert wurde. Im Themenfeld „Bibliotheksdateninfrastruktur und Lokale Systeme“ der DFG-Ausschreibung wurde das vom Hessischen Bibliotheksinformationssystem (HeBIS), vom Bibliotheksverbund Bayern (BVB) und vom Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) beantragte Vorhaben „Cloudbasierte Infrastruktur für Bibliotheksdaten“ (CIB) bewilligt. Das Projekt zielt auf die Überführung bibliothekarischer Workflows und Dienste in cloudbasierte Arbeitsumgebungen und die sukzessive Ablösung traditioneller Verbund- und Lokalsysteme durch internationale Systemplattformen. Zu den Arbeitspaketen des Vorhabens gehört u. a. die Einbindung von Norm- und Fremddatenangeboten und von weiteren Services in diese Plattformen. Y1 - 2013 U6 - https://doi.org/10.1515/bfp-2013-0044 VL - 37 IS - 3 SP - 279 EP - 287 ER - TY - JOUR A1 - Müller, Anja A1 - Rusch, Beate A1 - Amrhein, Kilian A1 - Klindt, Marco T1 - Unfertige Dialoge – Das Berliner Förderprogramm Digitalisierung JF - Bibliotheksdienst N2 - Das Förderprogramm Digitalisierung des Landes Berlin fördert Digitalisierungsprojekte in Berliner Kulturerbeeinrichtungen und hat parallel dazu die Servicestelle Digitalisierung (digiS) als zentrale Beratungs- und Koordinierungsstelle eingerichtet. Ziel ist dabei, eine technische und organisatorische Infrastruktur für die Projekte sowie zur Sicherung der Langzeitverfügbarkeit digitalen Kulturguts vorzuhalten. Der Artikel beschreibt das Förderprogramm, das Aufgabenspektrum von digiS und die Herausforderungen, die sich für Kulturerbeinstitutionen ergeben, wenn sie sich auf den offenen Dialog mit ihren Nutzern einlassen und ihre Objekte digital langzeitverfügbar halten wollen. Y1 - 2013 U6 - https://doi.org/10.1515/bd-2013-0104 VL - 47 IS - 12 SP - 931 EP - 942 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Weiser, Martin T1 - Lossy Compression for PDE-constrained Optimization: Adaptive Error Control JF - Comput. Optim. Appl. N2 - For the solution of optimal control problems governed by nonlinear parabolic PDEs, methods working on the reduced objective functional are often employed to avoid a full spatio-temporal discretization of the problem. The evaluation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the ad-joint equation. The state enters into the adjoint equation, requiring the storage of a full 4D data set. If Newton-CG methods are used, two additional trajectories have to be stored. To get numerical results which are accurate enough, in many case very fine discretizations in time and space are necessary, which leads to a significant amount of data to be stored and transmitted to mass storage. Lossy compression methods were developed to overcome the storage problem by reducing the accuracy of the stored trajectories. The inexact data induces errors in the reduced gradient and reduced Hessian. In this paper, we analyze the influence of such a lossy trajectory compression method on Newton-CG methods for optimal control of parabolic PDEs and design an adaptive strategy for choosing appropriate quantization tolerances. Y1 - 2015 VL - 62 IS - 1 SP - 131 EP - 155 PB - Springer ER - TY - JOUR A1 - Schöneich, Marc A1 - Stommel, Markus A1 - Kratz, Andrea A1 - Zobel, Valentin A1 - Scheuermann, Gerik A1 - Hotz, Ingrid A1 - Burgeth, Bernhard T1 - Optimization strategy for the design of ribbed plastic components JF - International Journal of Plastics Technology Y1 - 2014 IS - 10 SP - 160 EP - 175 ER - TY - JOUR A1 - Petrik, Peter A1 - Kumar, Nitish A1 - Fried, Miklos A1 - Fodor, Bálint A1 - Juhász, György A1 - Pereira, Silvania A1 - Burger, Sven A1 - Urbach, H. Paul T1 - Fourier ellipsometry – an ellipsometric approach to Fourier scatterometry JF - J. Eur. Opt. Soc.-Rapid Y1 - 2015 U6 - https://doi.org/10.2971/jeos.2015.15002 VL - 10 SP - 15002 ER - TY - JOUR A1 - Betker, Andreas A1 - Gamrath, Inken A1 - Kosiankowski, Dirk A1 - Lange, Christoph A1 - Lehmann, Heiko A1 - Pfeuffer, Frank A1 - Simon, Felix A1 - Werner, Axel T1 - Comprehensive Topology and Traffic Model of a Nationwide Telecommunication Network JF - Journal of Optical Communications and Networking N2 - As a basis for meaningful simulation and optimization efforts with regard to traffic engineering or energy consumption in telecommunication networks, suitable models are indispensable. This concerns not only realistic network topologies but also models for the geographical distribution and the temporal dynamics of traffic, as well as the assumptions on network components and technology. This paper derives such a model from the practice of a large national carrier. Applying the network and traffic model, we demonstrate its use by presenting various optimization cases related to energy-efficient telecommunication. Here, we focus on load adaptivity by employing sleep modes to the network hardware, where several constraints on the reconfigurability of the network over time are considered. Y1 - 2014 U6 - https://doi.org/10.1364/JOCN.6.001038 VL - 6 IS - 11 SP - 1038 EP - 1047 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio A1 - Krolikowski, Jonatan A1 - Pulaj, Jonad T1 - A fast hybrid primal heuristic for multiband robust capacitated network design with multiple time periods JF - Applied Soft Computing N2 - We investigate the Robust Multiperiod Network Design Problem, a generalization of the Capacitated Network Design Problem (CNDP) that, besides establishing flow routing and network capacity installation as in a canonical CNDP, also considers a planning horizon made up of multiple time periods and protection against fluctuations in traffic volumes. As a remedy against traffic volume uncertainty, we propose a Robust Optimization model based on Multiband Robustness (Büsing and D'Andreagiovanni, 2012), a refinement of classical Gamma-Robustness by Bertsimas and Sim (2004) that uses a system of multiple deviation bands. Since the resulting optimization problem may prove very challenging even for instances of moderate size solved by a state-of-the-art optimization solver, we propose a hybrid primal heuristic that combines a randomized fixing strategy inspired by ant colony optimization and an exact large neighbourhood search. Computational experiments on a set of realistic instances from the SNDlib (2010) show that our original heuristic can run fast and produce solutions of extremely high quality associated with low optimality gaps. Y1 - 2014 U6 - https://doi.org/10.1016/j.asoc.2014.10.016 VL - 26 SP - 497 EP - 507 ER - TY - JOUR A1 - Schmid, Martina A1 - Manley, Phillip T1 - Nano- and microlenses as concepts for enhanced performance of solar cells JF - J. Photon. Energy Y1 - 2014 U6 - https://doi.org/10.1117/1.JPE.5.057003 VL - 5 SP - 057003 ER - TY - JOUR A1 - Nielsen, Adam A1 - Weber, Marcus T1 - Computing the nearest reversible Markov chain JF - Numerical Linear Algebra with Applications N2 - Reversible Markov chains are the basis of many applications. However, computing transition probabilities by a finite sampling of a Markov chain can lead to truncation errors. Even if the original Markov chain is reversible, the approximated Markov chain might be non-reversible and will lose important properties, like the real valued spectrum. In this paper, we show how to find the closest reversible Markov chain to a given transition matrix. It turns out that this matrix can be computed by solving a convex minimization problem. KW - Reversible Markov Chain KW - Convex Optimization KW - MSM Y1 - 2015 U6 - https://doi.org/10.1002/nla.1967 VL - 22 IS - 3 SP - 483 EP - 499 ER - TY - JOUR A1 - Kossick, Regine A1 - Schulte (Fotos), Philip A1 - Kuiper (Fotos), Jens-Hendrik T1 - Die Bibliothek des Konrad-Zuse-Zentrums für Informationstechnik "Überall ist Mathematik drin" JF - One Person Libraries Berlin. 10 Jahre Arbeitskreis OPL Berlin/Brandenburg Y1 - 2010 SP - 18 EP - 23 ER - TY - JOUR A1 - Schäfer, Patrick T1 - Experiencing the Shotgun Distance for Time Series Analysis JF - Transactions on Machine Learning and Data Mining Y1 - 2014 SN - 1864-9734 VL - 7 IS - 1 SP - 3 EP - 25 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Dittbrenner, Bastian A1 - Langenhan, Andreas A1 - Seidl, Stephan A1 - Weider, Steffen T1 - Integrierte Dienst- und Dienstreihenfolgeplanung zur Erhöhung der Fahrerzufriedenheit JF - Straßenverkehrstechnik Y1 - 2014 IS - 9 SP - 583 EP - 591 ER - TY - JOUR A1 - Humpola, Jesco A1 - Lehmann, Thomas A1 - Fügenschuh, Armin T1 - A primal heuristic for optimizing the topology of gas networks based on dual information JF - EURO Journal on Computational Optimization N2 - We present a novel heuristic to identify feasible solutions of a mixed-integer nonlinear programming problem arising in natural gas transportation: the selection of new pipelines to enhance the network's capacity to a desired level in a cost-efficient way. We solve this problem in a linear programming based branch-and-cut approach, where we deal with the nonlinearities by linear outer approximation and spatial branching. At certain nodes of the branching tree, we compute a KKT point of a nonlinear relaxation. Based on the information from the KKT point we alter some of the binary variables in a locally promising way exploiting our problem-specific structure. On a test set of real-world instances, we are able to increase the chance of identifying feasible solutions by some order of magnitude compared to standard MINLP heuristics that are already built in the general-purpose MINLP solver SCIP. Y1 - 2015 U6 - https://doi.org/10.1007/s13675-014-0029-0 VL - 3 IS - 1 SP - 53 EP - 78 ER - TY - JOUR A1 - Shchukin, Vitaly A1 - Ledentsov, Jr., Nikolay A1 - Kropp, Jörg-R. A1 - Steinle, Gunther A1 - Ledentsov, Jr., Nikolay A1 - Burger, Sven A1 - Schmidt, Frank T1 - Single-Mode Vertical Cavity Surface Emitting Laser via Oxide-Aperture-Engineering of Leakage of High Order Transverse Modes JF - IEEE J. Quant. Electron. Y1 - 2014 U6 - https://doi.org/10.1109/JQE.2014.2364544 VL - 50 IS - 12 SP - 990 EP - 995 ER - TY - JOUR A1 - Weber, Britta A1 - Tranfield, Erin M. A1 - Höög, Johanna L. A1 - Baum, Daniel A1 - Antony, Claude A1 - Hyman, Tony A1 - Verbavatz, Jean-Marc A1 - Prohaska, Steffen T1 - Automated stitching of microtubule centerlines across serial electron tomograms JF - PLoS ONE Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0113222 SP - e113222 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Hoang, Nam-Dung T1 - Fair ticket pricing in public transport as a constrained cost allocation game JF - Annals of Operations Research N2 - Ticket pricing in public transport usually takes a welfare maximization point of view. Such an approach, however, does not consider fairness in the sense that users of a shared infrastructure should pay for the costs that they generate. We propose an ansatz to determine fair ticket prices that combines concepts from cooperative game theory and linear and integer programming. The ticket pricing problem is considered to be a constrained cost allocation game, which is a generalization of cost allocation games that allows to deal with constraints on output prices and on the formation of coalitions. An application to pricing railway tickets for the intercity network of the Netherlands is presented. The results demonstrate that the fairness of prices can be improved substantially in this way. A preliminary version of this paper appeared in the Proceedings of HPSC 2009 (Borndörfer and Hoang 2012). This journal article introduces better model and algorithms. Y1 - 2014 U6 - https://doi.org/10.1007/s10479-014-1698-z VL - 226 SP - 51 EP - 68 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Schaller, Jens A1 - Kertzscher, Ulrich A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Spuler, Andreas T1 - Reproducibility of Image-Based Analysis of Cerebral Aneurysm Geometry and Hemodynamics: An In-Vitro Study of Magnetic Resonance Imaging, Computed Tomography, and Three-Dimensional Rotational Angiography JF - Journal of Neurological Surgery, Part A: Central European Neurosurgery Y1 - 2013 U6 - https://doi.org/10.1055/s-0033-1342937 VL - 74 IS - 5 SP - 294 EP - 302 ER - TY - JOUR A1 - Sips, Mike A1 - Kothur, Patrick A1 - Unger, Andrea A1 - Hege, Hans-Christian A1 - Dransch, Doris T1 - A Visual Analytics Approach to Multiscale Exploration of Environmental Time Series JF - IEEE Transactions on Visualization and Computer Graphics N2 - We present a Visual Analytics approach that addresses the detection of interesting patterns in numerical time series, specifically from environmental sciences. Crucial for the detection of interesting temporal patterns are the time scale and the starting points one is looking at. Our approach makes no assumption about time scale and starting position of temporal patterns and consists of three main steps: an algorithm to compute statistical values for all possible time scales and starting positions of intervals, visual identification of potentially interesting patterns in a matrix visualization, and interactive exploration of detected patterns. We demonstrate the utility of this approach in two scientific scenarios and explain how it allowed scientists to gain new insight into the dynamics of environmental systems. Y1 - 2012 U6 - https://doi.org/10.1109/TVCG.2012.191 VL - 18 IS - 12 SP - 2899 EP - 2907 ER - TY - JOUR A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Theisel, Holger T1 - Advected Tangent Curves: A General Scheme for Characteristic Curves of Flow Fields JF - Computer Graphics Forum N2 - We present the first general scheme to describe all four types of characteristic curves of flow fields – stream, path, streak, and time lines – as tangent curves of a derived vector field. Thus, all these lines can be obtained by a simple integration of an autonomous ODE system. Our approach draws on the principal ideas of the recently introduced tangent curve description of streak lines. We provide the first description of time lines as tangent curves of a derived vector field, which could previously only be constructed in a geometric manner. Furthermore, our scheme gives rise to new types of curves. In particular, we introduce advected stream lines as a parameter-free variant of the time line metaphor. With our novel mathematical description of characteristic curves, a large number of feature extraction and analysis tools becomes available for all types of characteristic curves, which were previously only available for stream and path lines. We will highlight some of these possible applications including the computation of time line curvature fields and the extraction of cores of swirling advected stream lines. Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03063.x VL - 31 IS - 2pt4 SP - 825 EP - 834 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - A pH-dependent coarse-grained model for peptides JF - Soft Matter N2 - We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving interactions. We use reference data from atomistic simulations and experimental databases and transfer their main physical features to the coarse-grained resolution according to the principle of “consistency across the scales”. The coarse-grained model is refined by finding a set of parameters that, when applied to peptides with different sequences and experimental properties, reproduces the experimental and atomistic data of reference. We use such a parameterized model for performing several numerical tests to check its transferability to other systems and to prove the universality of the related modeling strategy. We have tried systems with rather different responses to pH variations, showing a highly satisfactory performance of the model. Y1 - 2013 U6 - https://doi.org/10.1039/C3SM27893J VL - 9 IS - 26 SP - 6118 EP - 6127 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1 JF - International Journal of Biomathematics and Biostatistics N2 - We present the theory of “Markov decision processes (MDP) with rare state observation” and apply it to optimal treatment scheduling and diagnostic testing to mitigate HIV-1 drug resistance development in resource-poor countries. The developed theory assumes that the state of the process is hidden and can only be determined by making an examination. Each examination produces costs which enter into the considered cost functional so that the resulting optimization problem includes finding optimal examination times. This is a realistic ansatz: In many real world applications, like HIV-1 treatment scheduling, the information about the disease evolution involves substantial costs, such that examination and control are intimately connected. However, a perfect compliance with the optimal strategy can rarely be achieved. This may be particularly true for HIV-1 resistance testing in resource-constrained countries. In the present work, we therefore analyze the sensitivity of the costs with respect to deviations from the optimal examination times both analytically and for the considered application. We discover continuity in the cost-functional with respect to the examination times. For the HIV-application, moreover, sensitivity towards small deviations from the optimal examination rule depends on the disease state. Furthermore, we compare the optimal rare-control strategy to (i) constant control strategies (one action for the remaining time) and to (ii) the permanent control of the original, fully observed MDP. This comparison is done in terms of expected costs and in terms of life-prolongation. The proposed rare-control strategy offers a clear benefit over a constant control, stressing the usefulness of medical testing and informed decision making. This indicates that lower-priced medical tests could improve HIV treatment in resource-constrained settings and warrants further investigation. Y1 - 2013 VL - 2 IS - 1 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Ciccotti, Giovanni A1 - von Kleist, Max T1 - Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation JF - Journal of Chemical Theory and Computation N2 - In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context, we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and nontrivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes. Y1 - 2014 U6 - https://doi.org/10.1021/ct400993e VL - 10 IS - 4 SP - 1376 EP - 1386 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1 JF - Communications in Mathematical Sciences N2 - Markov Decision Processes (MDP) or Partially Observable MDPs (POMDP) are used for modelling situations in which the evolution of a process is partly random and partly controllable. These MDP theories allow for computing the optimal control policy for processes that can continuously or frequently be observed, even if only partially. However, they cannot be applied if state observation is very costly and therefore rare (in time). We present a novel MDP theory for rare, costly observations and derive the corresponding Bellman equation. In the new theory, state information can be derived for a particular cost after certain, rather long time intervals. The resulting information costs enter into the total cost and thus into the optimization criterion. This approach applies to many real world problems, particularly in the medical context, where the medical condition is examined rather rarely because examination costs are high. At the same time, the approach allows for efficient numerical realization. We demonstrate the usefulness of the novel theory by determining, from the national economic perspective, optimal therapeutic policies for the treatment of the human immunodeficiency virus (HIV) in resource-rich and resource-poor settings. Based on the developed theory and models, we discover that available drugs may not be utilized efficiently in resource-poor settings due to exorbitant diagnostic costs. Y1 - 2014 U6 - https://doi.org/10.4310/CMS.2014.v12.n5.a4 VL - 12 IS - 5 SP - 859 EP - 877 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Spuler, Andreas A1 - Schaller, Jens A1 - Wiegmann, Nils A1 - Berthe, Andre A1 - Hege, Hans-Christian A1 - Affeld, Klaus A1 - Kertzscher, Ulrich T1 - In vitro study of hemodynamic treatment improvement: Hunterian ligation of a fenestrated basilar artery aneurysm after coiling JF - The International Journal of Artificial Organs N2 - Hunterian ligation affecting hemodynamics in vessels was proposed to avoid rebleeding in a case of a fenestrated basilar artery aneurysm after incomplete coil occlusion. We studied the hemodynamics in vitro to predict the hemodynamic changes near the aneurysm remnant caused by Hunterian ligation. A transparent model was fabricated based on three-dimensional rotational angiography imaging. Arteries were segmented and reconstructed. Pulsatile flow in the artery segments near the partially occluded (coiled) aneurysm was investigated by means of particle image velocimetry. The hemodynamic situation was investigated before and after Hunterian ligation of either the left or the right vertebral artery (LVA/RVA). Since post-ligation flow rate in the basilar artery was unknown, reduced and retained flow rates were simulated for both ligation options. Flow in the RVA and in the corresponding fenestra vessel is characterized by a vortex at the vertebrobasilar junction, whereas the LVA exhibits undisturbed laminar flow. Both options (RVA or LVA ligation) cause a significant flow reduction near the aneurysm remnant with a retained flow rate. The impact of RVA ligation is, however, significantly higher. This in vitro case study shows that flow reduction near the aneurysm remnant can be achieved by Hunterian ligation and that this effect depends largely on the selection of the ligated vessel. Thus the ability of the proposed in vitro pipe-line to improve hemodynamic impact of the proposed therapy was successfully proved. Y1 - 2014 U6 - https://doi.org/10.5301/ijao.5000314 VL - 37 IS - 4 SP - 325 EP - 335 ER - TY - JOUR A1 - Röblitz, Susanna A1 - Weber, Marcus T1 - Fuzzy Spectral Clustering by PCCA+ JF - Classification and Clustering: Models, Software and Applications Y1 - 2009 UR - http://www.wias-berlin.de/publications/wias-publ/run.jsp?template=abstract&type=Report&year=2009&number=26 IS - WIAS Report No. 26 SP - 73 EP - 79 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Weiser, Martin A1 - Maierhofer, Christiane A1 - Richter, Regina A1 - Röllig, Mathias T1 - Fast Defect Shape Reconstruction Based on the Travel Time in Pulse Thermography JF - Nondestructive Testing of Materials and Structures Y1 - 2013 VL - 6 SP - 83 EP - 89 ER - TY - JOUR A1 - Odesskii, Alexander A1 - Wolf, Thomas T1 - Compatible quadratic Poisson brackets related to a family of elliptic curves JF - Journal of Geometry and Physics Y1 - 2013 SN - 0393-0440 VL - 63 IS - 0 SP - 107 EP - 117 ER - TY - JOUR A1 - Anco, Stephen A1 - MacNaughton, Steven A. A1 - Wolf, Thomas T1 - Conservation laws and symmetries of quasilinear radial wave equations in multi-dimensions JF - Journal of Mathematical Physics Y1 - 2012 U6 - https://doi.org/10.1063/1.4711814 VL - 53 IS - 5 ER - TY - JOUR A1 - Wolf, Thomas A1 - Schrüfer, Eberhard A1 - Webster, Kenneth T1 - Solving large linear algebraic systems in the context of integrable non-abelian Laurent ODEs JF - Programming and Computer Software Y1 - 2012 U6 - https://doi.org/10.1134/S0361768812020065 SN - 0361-7688 VL - 38 IS - 2 SP - 73 EP - 83 ER - TY - JOUR A1 - Euler, Marianna A1 - Euler, Norbert A1 - Wolf, Thomas T1 - The Two-Component Camassa-Holm Equations CH(2,1) and CH(2,2): First-Order Integrating Factors and Conservation Laws JF - Journal of Nonlinear Mathematical Physics N2 - Recently, Holm and Ivanov, proposed and studied a class of multi-component generalizations of the Camassa–Holm equations [D. D. Holm and R. I. Ivanov, Multi-component generalizations of the CH equation: geometrical aspects, peakons and numerical examples, J. Phys A: Math. Theor. 43 (2010) 492001 (20pp)]. We consider two of those systems, denoted by Holm and Ivanov by CH(2,1) and CH(2,2), and report a class of integrating factors and its corresponding conservation laws for these two systems. In particular, we obtain the complete set of first-order integrating factors for the systems in Cauchy–Kovalevskaya form and evaluate the corresponding sets of conservation laws for CH(2,1) and CH(2,2). Y1 - 2013 U6 - https://doi.org/10.1142/S1402925112400025 VL - 19 IS - 1 SP - 13 EP - 22 ER - TY - JOUR A1 - Grunzke, Richard A1 - Breuers, Sebastian A1 - Gesing, Sandra A1 - Herres-Pawlis, Sonja A1 - Kruse, Martin A1 - Blunk, Dirk A1 - de la Garza, Luis A1 - Packschies, Lars A1 - Schäfer, Patrick A1 - Schärfe, Charlotta A1 - Schlemmer, Tobias A1 - Steinke, Thomas A1 - Schuller, Bernd A1 - Müller-Pfefferkorn, Ralph A1 - Jäkel, René A1 - Nagel, Wolfgang A1 - Atkinson, Malcolm A1 - Krüger, Jens T1 - Standards-based metadata management for molecular simulations JF - Concurrency and Computation: Practice and Experience Y1 - 2013 U6 - https://doi.org/10.1002/cpe.3116 ER - TY - JOUR A1 - Moualeu-Ngangue, Dany Pascal A1 - Röblitz, Susanna A1 - Ehrig, Rainald A1 - Deuflhard, Peter T1 - Parameter Identification in a Tuberculosis Model for Cameroon JF - PLOS ONE N2 - A deterministic model of tuberculosis in Cameroon is designed and analyzed with respect to its transmission dynamics. The model includes lack of access to treatment and weak diagnosis capacity as well as both frequency- and density-dependent transmissions. It is shown that the model is mathematically well-posed and epidemiologically reasonable. Solutions are non-negative and bounded whenever the initial values are non-negative. A sensitivity analysis of model parameters is performed and the most sensitive ones are identified by means of a state-of-the-art Gauss-Newton method. In particular, parameters representing the proportion of individuals having access to medical facilities are seen to have a large impact on the dynamics of the disease. The model predicts that a gradual increase of these parameters could significantly reduce the disease burden on the population within the next 15 years. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0120607 ER - TY - JOUR A1 - Quitzsch, Nicole T1 - Vorbei die Zeiten von Gebrauchsanweisungen für Bibliotheksportale : Nutzerbeteiligung und Co-Design am Beispiel des neuen KOBV-Portals T1 - Gone are the times of operating instructions for library portals : User participation and co-design, exemplified by the new KOBV Portal JF - Bibliotheksdienst N2 - Bibliotheken stehen heute mehr denn je vor der Frage, wie sie ihre Dienste attraktiv gestalten können. Da liegt es nahe, Nutzerinnen und Nutzer aktiv in den Designprozess einzubinden. Die Neuentwicklung des KOBV-Portals (http://portal.kobv.de), einer regionalen Suche über die Bestände der Bibliotheken in Berlin und Brandenburg, geht konsequent den Weg des Co-Designs. Nutzerinnen und Nutzer werden als Entwicklungspartner verstanden. Als Projektpartner wurde das Institut für Bibliotheks- und Informationswissenschaft (IBI) der Humboldt-Universität zu Berlin gewonnen. N2 - More than ever, libraries today are faced with the question of how to make their services more attractive. Thus, it only seems logical to actively integrate users into the design process. The re-implementation of the KOBV Portal (http://portal.kobv.de), a regional search in the holdings of libraries in Berlin and Brandenburg, consistently follows the path of co-design. Users are regarded as development partners. The Berlin School of Library and Information Science acts as a project partner. Y1 - 2014 U6 - https://doi.org/10.1515/bd-2014-0097 VL - 48 IS - 10 SP - 795 EP - 806 ER - TY - JOUR A1 - Humpola, Jesco A1 - Fügenschuh, Armin T1 - Convex reformulations for solving a nonlinear network design problem JF - Computational Optimization and Applications N2 - We consider a nonlinear nonconvex network design problem that arises, for example, in natural gas or water transmission networks. Given is such a network with active and passive components, that is, valves, compressors, control valves (active) and pipelines (passive), and a desired amount of flow at certain specified entry and exit nodes in the network. The active elements are associated with costs when used. Besides flow conservation constraints in the nodes, the flow must fulfill nonlinear nonconvex pressure loss constraints on the arcs subject to potential values (i.e., pressure levels) in both end nodes of each arc. The problem is to compute a cost minimal setting of the active components and numerical values for the flow and node potentials. We examine different (convex) relaxations for a subproblem of the design problem and benefit from them within a branch-and-bound approach. We compare different approaches based on nonlinear optimization numerically on a set of test instances. Y1 - 2015 U6 - https://doi.org/10.1007/s10589-015-9756-2 VL - 62 IS - 3 SP - 717 EP - 759 PB - Springer US ER - TY - JOUR A1 - Moualeu-Ngangue, Dany Pascal A1 - Bowong, Samuel A1 - Kurths, Jürgen T1 - Parameter Estimation of a Tuberculosis Model in a Patchy Environment: Case of Cameroon JF - BIOMAT - Proceedings of the 12th International Symposium on Mathematical and Computational Biology, Toronto, 2013 Y1 - 2014 U6 - https://doi.org/10.1142/9789814602228_0021 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio T1 - Revisiting wireless network jamming by SIR-based considerations and Multiband Robust Optimization JF - Optimization Letters N2 - We revisit the mathematical models for wireless network jamming introduced by Commander et al. (2007,2008): we first point out the strong connections with classical wireless network design and then we propose a new model based on the explicit use of signal-to-interference quantities. Moreover, to address the uncertain nature of the jamming problem and tackle the peculiar right-hand-side uncertainty of the corresponding model, we propose an original robust cutting-plane algorithm drawing inspiration from multiband robust optimization. Finally, we assess the performance of the proposed cutting plane algorithm by experiments on realistic network instances. Y1 - 2014 U6 - https://doi.org/10.1007/s11590-014-0839-2 VL - 9 SP - 1495 EP - 1510 PB - Springer ER - TY - JOUR A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Seidel, Hans-Peter A1 - Hildebrandt, Klaus T1 - Animating Deformable Objects Using Sparse Spacetime Constraints JF - ACM Transactions on Graphics N2 - We propose a scheme for animating deformable objects based on spacetime optimization. The main feature is that it robustly and quickly (within a few seconds) generates interesting motion from a sparse set of spacetime constraints. Providing only partial (as opposed to full) keyframes for positions and velocities is sufficient. The computed motion satisfies the constraints and the remaining degrees of freedom are determined by physical principles using elasticity and the spacetime constraints paradigm. Our modeling of the spacetime optimization problem combines dimensional reduction, modal coordinates, wiggly splines, and rotation strain warping. Controlling the warped motion requires the derivative of the warp map. We derive a representation of the derivative that can be efficiently and robustly evaluated. Our solver is based on a theorem that characterizes the solutions of the optimization problem and allows us to restrict the optimization to very low-dimensional search spaces. This treatment of the optimization problem avoids a time discretization and the resulting method can robustly deal with sparse input and wiggly motion. Y1 - 2014 U6 - https://doi.org/10.1145/2601097.2601156 VL - 33 IS - 4 SP - 109:1 EP - 109:10 ER - TY - JOUR A1 - Matsuyama, Kei A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - Freiwald, André T1 - Two new species of erect Bryozoa (Gymnolaemata: Cheilostomata) and the application of non-destructive imaging methods for quantitative taxonomy JF - Zootaxa N2 - Two new species of cheilostome Bryozoa are described from continental-slope habitats off Mauritania, including canyon and coldwater-coral (mound) habitats. Internal structures of both species were visualised and quantified using micro-computed tomographic (micro-CT) methods. Cellaria bafouri n. sp. is characterised by the arrangement of zooids in alternating longitudinal rows, a smooth cryptocyst, and the presence of an ooecial plate with denticles. Smittina imragueni n. sp. exhibits many similarities with Smittina cervicornis (Pallas, 1766), but differs especially in the shape and orientation of the suboral avicularium. Observations on Smittina imragueni and material labelled as Smittina cervicornis suggest that the latter represents a species group, members of which have not yet been discriminated, possibly because of high intracolony variation and marked astogenetic changes in surface morphology. Both new species are known only from the habitats where they were collected, probably reflecting the paucity of bryozoan sampling from this geographic area and depth range. Both species are able to tolerate low oxygen concentration, which is assumed to be compensated by the high nutrient supply off Mauritania. The application of micro-CT for the semiautomatic quantification of zooidal skeletal characters was successfully tested. We were able to automatically distinguish individual zooidal cavities and acquire corresponding morphological datasets. Comparing the obtained results with conventional SEM measurements allowed ascertaining the reliability of this new method. The employment of micro-CT allows the observation and quantification of previously un- seen characters that can be used in describing and differentiating species that were previously indistinguishable. Further- more, this method might help elucidate processes of colony growth and the function of individual zooids during this process. Y1 - 2015 U6 - https://doi.org/10.11646/zootaxa.4020.1.3 VL - 4020 IS - 1 SP - 81 EP - 100 ER - TY - JOUR A1 - Gschrey, Manuel A1 - Thoma, Alexander A1 - Schnauber, Peter A1 - Seifried, Marc A1 - Schmidt, Ronny A1 - Wohlfeil, Benjamin A1 - Krüger, Luzy A1 - Schulze, Jan-Hindrick A1 - Heindel, Tobias A1 - Burger, Sven A1 - Schmidt, Frank A1 - Strittmatter, Andre A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Highly indistinguishable photons from deterministic quantum-dot microlenses utilizing three-dimensional in situ electron-beam lithography JF - Nature Communications Y1 - 2015 U6 - https://doi.org/10.1038/ncomms8662 VL - 6 SP - 7662 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio A1 - Nardin, Antonella T1 - Towards the fast and robust optimal design of Wireless Body Area Networks JF - Applied Soft Computing N2 - Wireless body area networks are wireless sensor networks whose adoption has recently emerged and spread in important healthcare applications, such as the remote monitoring of health conditions of patients. A major issue associated with the deployment of such networks is represented by energy consumption: in general, the batteries of the sensors cannot be easily replaced and recharged, so containing the usage of energy by a rational design of the network and of the routing is crucial. Another issue is represented by traffic uncertainty: body sensors may produce data at a variable rate that is not exactly known in advance, for example because the generation of data is event-driven. Neglecting traffic uncertainty may lead to wrong design and routing decisions, which may compromise the functionality of the network and have very bad effects on the health of the patients. In order to address these issues, in this work we propose the first robust optimization model for jointly optimizing the topology and the routing in body area networks under traffic uncertainty. Since the problem may result challenging even for a state-of-the-art optimization solver, we propose an original optimization algorithm that exploits suitable linear relaxations to guide a randomized fixing of the variables, supported by an exact large variable neighborhood search. Experiments on realistic instances indicate that our algorithm performs better than a state-of-the-art solver, fast producing solutions associated with improved optimality gaps. Y1 - 2015 U6 - https://doi.org/10.1016/j.asoc.2015.04.037 VL - 37 SP - 971 EP - 982 PB - Elsevier ER - TY - JOUR A1 - Banisch, Ralf A1 - Djurdjevac Conrad, Natasa A1 - Schütte, Christof T1 - Reactive flows and unproductive cycles for random walks on complex networks JF - The European Physical Journal Special Topics, vol. 224, iss. 12 (2015) pp. 2369-2387 Y1 - 2015 U6 - https://doi.org/10.1140/epjst/e2015-02417-8 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Buwaya, Julia A1 - Sagnol, Guillaume A1 - Swarat, Elmar T1 - Network spot-checking games: Theory and application to toll enforcing in transportation networks JF - Networks N2 - We introduce the class of spot-checking games (SC games). These games model problems where the goal is to distribute fare inspectors over a toll network. In an SC game, the pure strategies of network users correspond to paths in a graph, and the pure strategies of the inspectors are subset of arcs to be controlled. Although SC games are not zero-sum, we show that a Nash equilibrium can be computed by linear programming. The computation of a strong Stackelberg equilibrium (SSE) is more relevant for this problem and we give a mixed integer programming (MIP) formulation for this problem. We show that the computation of such an equilibrium is NP-hard. More generally, we prove that it is NP-hard to compute a SSE in a polymatrix game, even if the game is pairwise zero-sum. Then, we give some bounds on the price of spite, which measures how the payoff of the inspector degrades when committing to a Nash equilibrium. Finally, we report computational experiments on instances constructed from real data, for an application to the enforcement of a truck toll in Germany. These numerical results show the efficiency of the proposed methods, as well as the quality of the bounds derived in this article. Y1 - 2015 U6 - https://doi.org/10.1002/net.21596 VL - 65 SP - 312 EP - 328 PB - Wiley Periodicals, Inc. ER - TY - JOUR A1 - Humpola, Jesco A1 - Fügenschuh, Armin A1 - Koch, Thorsten T1 - Valid inequalities for the topology optimization problem in gas network design JF - OR Spectrum N2 - One quarter of Europe's energy demand is provided by natural gas distributed through a vast pipeline network covering the whole of Europe. At a cost of 1 million Euro per km extending the European pipeline network is already a multi-billion Euro business. Therefore, automatic planning tools that support the decision process are desired. Unfortunately, current mathematical methods are not capable of solving the arising network design problems due to their size and complexity. In this article, we will show how to apply optimization methods that can converge to a proven global optimal solution. By introducing a new class of valid inequalities that improve the relaxation of our mixed-integer nonlinear programming model, we are able to speed up the necessary computations substantially. Y1 - 2016 U6 - https://doi.org/https://doi.org/10.1007/s00291-015-0390-2 VL - 38 IS - 3 SP - 597 EP - 631 PB - Springer CY - Berlin Heidelberg ER - TY - JOUR A1 - Lemanis, Robert A1 - Zachow, Stefan A1 - Fusseis, Florian A1 - Hoffmann, René T1 - A new approach using high-resolution computed tomography to test the buoyant properties of chambered cephalopod shells JF - Paleobiology N2 - The chambered shell of modern cephalopods functions as a buoyancy apparatus, allowing the animal to enter the water column without expending a large amount of energy to overcome its own weight. Indeed, the chambered shell is largely considered a key adaptation that allowed the earliest cephalopods to leave the ocean floor and enter the water column. It has been argued by some, however, that the iconic chambered shell of Paleozoic and Mesozoic ammonoids did not provide a sufficiently buoyant force to compensate for the weight of the entire animal, thus restricting ammonoids to a largely benthic lifestyle reminiscent of some octopods. Here we develop a technique using high-resolution computed tomography to quantify the buoyant properties of chambered shells without reducing the shell to ideal spirals or eliminating inherent biological variability by using mathematical models that characterize past work in this area. This technique has been tested on Nautilus pompilius and is now extended to the extant deep-sea squid Spirula spirula and the Jurassic ammonite Cadoceras sp. hatchling. Cadoceras is found to have possessed near-neutral to positive buoyancy if hatched when the shell possessed between three and five chambers. However, we show that the animal could also overcome degrees of negative buoyancy through swimming, similar to the paralarvae of modern squids. These calculations challenge past inferences of benthic life habits based solely on calculations of negative buoyancy. The calculated buoyancy of Cadoceras supports the possibility of planktonic dispersal of ammonite hatchlings. This information is essential to understanding ammonoid ecology as well as biotic interactions and has implications for the interpretation of geochemical data gained from the isotopic analysis of the shell. Y1 - 2015 U6 - https://doi.org/10.1017/pab.2014.17 VL - 41 IS - 2 SP - 313 EP - 329 PB - Cambridge University Press CY - Cambridge ER - TY - JOUR A1 - Tycowicz, Christoph von A1 - Schulz, Christian A1 - Seidel, Hans-Peter A1 - Hildebrandt, Klaus T1 - An Efficient Construction of Reduced Deformable Objects JF - ACM Transactions on Graphics N2 - Many efficient computational methods for physical simulation are based on model reduction. We propose new model reduction techniques for the approximation of reduced forces and for the construction of reduced shape spaces of deformable objects that accelerate the construction of a reduced dynamical system, increase the accuracy of the approximation, and simplify the implementation of model reduction. Based on the techniques, we introduce schemes for real-time simulation of deformable objects and interactive deformation-based editing of triangle or tet meshes. We demonstrate the effectiveness of the new techniques in different experiments with elastic solids and shells and compare them to alternative approaches. Y1 - 2013 U6 - https://doi.org/10.1145/2508363.2508392 VL - 32 IS - 6 SP - 213:1 EP - 213:10 PB - ACM ER - TY - JOUR A1 - Hildebrandt, Klaus A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Polthier, Konrad T1 - Interactive spacetime control of deformable objects JF - ACM Transactions on Graphics N2 - Creating motions of objects or characters that are physically plausible and follow an animator’s intent is a key task in computer animation. The spacetime constraints paradigm is a valuable approach to this problem, but it suffers from high computational costs. Based on spacetime constraints, we propose a technique that controls the motion of deformable objects and offers an interactive response. This is achieved by a model reduction of the underlying variational problem, which combines dimension reduction, multipoint linearization, and decoupling of ODEs. After a preprocess, the cost for creating or editing a motion is reduced to solving a number of one-dimensional spacetime problems, whose solutions are the wiggly splines introduced by Kass and Anderson [2008]. We achieve interactive response using a new fast and robust numerical scheme for solving a set of one-dimensional problems based on an explicit representation of the wiggly splines. Y1 - 2012 U6 - https://doi.org/10.1145/2185520.2185567 VL - 31 IS - 4 SP - 71:1 EP - 71:8 PB - ACM ER - TY - JOUR A1 - Hildebrandt, Klaus A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Polthier, Konrad T1 - Interactive surface modeling using modal analysis JF - ACM Transactions on Graphics N2 - We propose a framework for deformation-based surface modeling that is interactive, robust and intuitive to use. The deformations are described by a non-linear optimization problem that models static states of elastic shapes under external forces which implement the user input. Interactive response is achieved by a combination of model reduction, a robust energy approximation, and an efficient quasi-Newton solver. Motivated by the observation that a typical modeling session requires only a fraction of the full shape space of the underlying model, we use second and third derivatives of a deformation energy to construct a low-dimensional shape space that forms the feasible set for the optimization. Based on mesh coarsening, we propose an energy approximation scheme with adjustable approximation quality. The quasi-Newton solver guarantees superlinear convergence without the need of costly Hessian evaluations during modeling. We demonstrate the effectiveness of the approach on different examples including the test suite introduced in [Botsch and Sorkine 2008]. Y1 - 2011 U6 - https://doi.org/10.1145/2019627.2019638 VL - 30 IS - 5 SP - 119:1 EP - 119:11 ER - TY - JOUR A1 - Hildebrandt, Klaus A1 - Schulz, Christian A1 - Tycowicz, Christoph von A1 - Polthier, Konrad T1 - Modal Shape Analysis beyond Laplacian JF - Computer Aided Geometric Design N2 - In recent years, substantial progress in shape analysis has been achieved through methods that use the spectra and eigenfunctions of discrete Laplace operators. In this work, we study spectra and eigenfunctions of discrete differential operators that can serve as an alternative to the discrete Laplacians for applications in shape analysis. We construct such operators as the Hessians of surface energies, which operate on a function space on the surface, or of deformation energies, which operate on a shape space. In particular, we design a quadratic energy such that, on the one hand, its Hessian equals the Laplace operator if the surface is a part of the Euclidean plane, and, on the other hand, the Hessian eigenfunctions are sensitive to the extrinsic curvature (e.g. sharp bends) on curved surfaces. Furthermore, we consider eigenvibrations induced by deformation energies, and we derive a closed form representation for the Hessian (at the rest state of the energy) for a general class of deformation energies. Based on these spectra and eigenmodes, we derive two shape signatures. One that measures the similarity of points on a surface, and another that can be used to identify features of surfaces. Y1 - 2012 U6 - https://doi.org/10.1016/j.cagd.2012.01.001 VL - 29 IS - 5 SP - 204 EP - 2018 ER - TY - JOUR A1 - Tycowicz, Christoph von A1 - Kälberer, Felix A1 - Polthier, Konrad T1 - Context-based Coding of Adaptive Multiresolution Meshes JF - Computer Graphics Forum N2 - Multiresolution meshes provide an efficient and structured representation of geometric objects. To increase the mesh resolution only at vital parts of the object, adaptive refinement is widely used. We propose a lossless compression scheme for these adaptive structures that exploits the parent-child relationships inherent to the mesh hierarchy. We use the rules that correspond to the adaptive refinement scheme and store bits only where some freedom of choice is left, leading to compact codes that are free of redundancy. Moreover, we extend the coder to sequences of meshes with varying refinement. The connectivity compression ratio of our method exceeds that of state-of-the-art coders by a factor of 2 to 7. For efficient compression of vertex positions we adapt popular wavelet-based coding schemes to the adaptive triangular and quadrangular cases to demonstrate the compatibility with our method. Akin to state-of-the-art coders, we use a zerotree to encode the resulting coefficients. Using improved context modeling we enhanced the zerotree compression, cutting the overall geometry data rate by 7% below those of the successful Progressive Geometry Compression. More importantly, by exploiting the existing refinement structure we achieve compression factors that are 4 times greater than those of coders which can handle irregular meshes. Y1 - 2011 U6 - https://doi.org/10.1111/j.1467-8659.2011.01972.x VL - 30 IS - 8 SP - 2231 EP - 2245 ER - TY - JOUR A1 - Höhne, Theresa A1 - Schnauber, Peter A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Burger, Sven T1 - Numerical Investigation of Light Emission from Quantum Dots Embedded into On-Chip, Low Index Contrast Optical Waveguides JF - Phys. Status Solidi B Y1 - 2019 U6 - https://doi.org/10.1002/pssb.201800437 VL - 256 SP - 1800437 ER - TY - JOUR A1 - Rodríguez, Mirta A1 - Kramer, Tobias T1 - Machine Learning of Two-Dimensional Spectroscopic Data JF - Chemical Physics N2 - Two-dimensional electronic spectroscopy has become one of the main experimental tools for analyzing the dynamics of excitonic energy transfer in large molecular complexes. Simplified theoretical models are usually employed to extract model parameters from the experimental spectral data. Here we show that computationally expensive but exact theoretical methods encoded into a neural network can be used to extract model parameters and infer structural information such as dipole orientation from two dimensional electronic spectra (2DES) or reversely, to produce 2DES from model parameters. We propose to use machine learning as a tool to predict unknown parameters in the models underlying recorded spectra and as a way to encode computationally expensive numerical methods into efficient prediction tools. We showcase the use of a trained neural network to efficiently compute disordered averaged spectra and demonstrate that disorder averaging has non-trivial effects for polarization controlled 2DES. Y1 - 2019 U6 - https://doi.org/10.1016/j.chemphys.2019.01.002 VL - 520 SP - 52 EP - 60 ER - TY - JOUR A1 - Mrowinski, Paweł A1 - Schnauber, Peter A1 - Gutsche, Philipp A1 - Kaganskiy, Arsenty A1 - Schall, Johannes A1 - Burger, Sven A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Directional emission of a deterministically fabricated quantum dot – Bragg reflection multi-mode waveguide system JF - ACS Photonics Y1 - 2019 U6 - https://doi.org/10.1021/acsphotonics.9b00369 VL - 6 SP - 2231 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Dispersion-engineered nanocomposites enable achromatic diffractive optical elements JF - Optica Y1 - 2019 U6 - https://doi.org/10.1364/OPTICA.6.001031 VL - 6 SP - 1031 ER - TY - JOUR A1 - Baum, Daniel A1 - Weaver, James C. A1 - Zlotnikov, Igor A1 - Knötel, David A1 - Tomholt, Lara A1 - Dean, Mason N. T1 - High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms JF - Integrative And Comparative Biology N2 - Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e. poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e. structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, this random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—stingray tessellated cartilage, starfish dermal endoskeleton, and the prismatic layer of bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized and analyzed. Y1 - 2019 U6 - https://doi.org/10.1093/icb/icz117 ER - TY - JOUR A1 - Weber, Marie-Christin A1 - Fischer, Lisa A1 - Damerau, Alexandra A1 - Ponomarev, Igor A1 - Pfeiffenberger, Moritz A1 - Gaber, Timo A1 - Götschel, Sebastian A1 - Lang, Jens A1 - Röblitz, Susanna A1 - Buttgereit, Frank A1 - Ehrig, Rainald A1 - Lang, Annemarie T1 - In vitro and in silico modeling of cellular and matrix-related changes during the early phase of osteoarthritis JF - BioRxiv N2 - Understanding the pathophysiological processes of osteoarthritis (OA) require adequate model systems. Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific parts of the disease. This study aimed to combine in vitro and in silico modeling to describe cellular and matrix-related changes during the early phase of OA. We developed an in vitro OA model based on scaffold-free cartilage-like constructs (SFCCs), which was mathematically modeled using a partial differential equation (PDE) system to resemble the processes during the onset of OA. SFCCs were produced from mesenchymal stromal cells and analyzed weekly by histology and qPCR to characterize the cellular and matrix-related composition. To simulate the early phase of OA, SFCCs were treated with interleukin-1β (IL-1β), tumor necrosis factor α (TNFα) and examined after 3 weeks or cultivated another 3 weeks without inflammatory cytokines to validate the regeneration potential. Mathematical modeling was performed in parallel to the in vitro experiments. SFCCs expressed cartilage-specific markers, and after stimulation an increased expression of inflammatory markers, matrix degrading enzymes, a loss of collagen II (Col-2) and a reduced cell density was observed which could be partially reversed by retraction of stimulation. Based on the PDEs, the distribution processes within the SFCCs, including those of IL-1β, Col-2 degradation and cell number reduction was simulated. By combining in vitro and in silico methods, we aimed to develop a valid, efficient alternative approach to examine and predict disease progression and new therapeutic strategies. Y1 - 2019 U6 - https://doi.org/10.1101/725317 ER - TY - JOUR A1 - D'Andreagiovanni, Fabio A1 - Mett, Fabian A1 - Nardin, Antonella A1 - Pulaj, Jonad T1 - Integrating LP-guided variable fixing with MIP heuristics in the robust design of hybrid wired-wireless FTTx access networks JF - Applied Soft Computing N2 - This study investigates how to model and solve the problem of optimally designing FTTx telecommunications access networks integrating wired and wireless technologies, while taking into account the uncertainty of wireless signal propagation. We propose an original robust optimization model for the related robust 3-architecture Connected Facility Location problem, which includes additional variables and constraints to model wireless signal coverage represented through signal-to-interference ratios. Since the resulting robust problem can prove very challenging even for a modern state-of-the art optimization solver, we propose to solve it by an original primal heuristic that combines a probabilistic variable fixing procedure, guided by peculiar Linear Programming relaxations, with a Mixed Integer Programming heuristic, based on an exact very large neighborhood search. A numerical study carried out on a set of realistic instances show that our heuristic can find solutions of much higher quality than a state-of-the-art solver. Y1 - 2017 U6 - https://doi.org/10.1016/j.asoc.2017.07.018 VL - 61 SP - 1074 EP - 1087 ER - TY - JOUR A1 - Barth, Carlo A1 - Becker, Christiane T1 - Machine learning classification for field distributions of photonic modes JF - Commun. Phys. Y1 - 2018 U6 - https://doi.org/10.1038/s42005-018-0060-1 VL - 1 SP - 58 ER - TY - JOUR A1 - Krämer, Martin A1 - Maggioni, Marta A1 - Brisson, Nicholas A1 - Zachow, Stefan A1 - Teichgräber, Ulf A1 - Duda, Georg A1 - Reichenbach, Jürgen T1 - T1 and T2* mapping of the human quadriceps and patellar tendons using ultra-short echo-time (UTE) imaging and bivariate relaxation parameter-based volumetric visualization JF - Magnetic Resonance Imaging N2 - Quantification of magnetic resonance (MR)-based relaxation parameters of tendons and ligaments is challenging due to their very short transverse relaxation times, requiring application of ultra-short echo-time (UTE) imaging sequences. We quantify both T1 and T2⁎ in the quadriceps and patellar tendons of healthy volunteers at a field strength of 3 T and visualize the results based on 3D segmentation by using bivariate histogram analysis. We applied a 3D ultra-short echo-time imaging sequence with either variable repetition times (VTR) or variable flip angles (VFA) for T1 quantification in combination with multi-echo acquisition for extracting T2⁎. The values of both relaxation parameters were subsequently binned for bivariate histogram analysis and corresponding cluster identification, which were subsequently visualized. Based on manually-drawn regions of interest in the tendons on the relaxation parameter maps, T1 and T2⁎ boundaries were selected in the bivariate histogram to segment the quadriceps and patellar tendons and visualize the relaxation times by 3D volumetric rendering. Segmentation of bone marrow, fat, muscle and tendons was successfully performed based on the bivariate histogram analysis. Based on the segmentation results mean T2⁎ relaxation times, over the entire tendon volumes averaged over all subjects, were 1.8 ms ± 0.1 ms and 1.4 ms ± 0.2 ms for the patellar and quadriceps tendons, respectively. The mean T1 value of the patellar tendon, averaged over all subjects, was 527 ms ± 42 ms and 476 ms ± 40 ms for the VFA and VTR acquisitions, respectively. The quadriceps tendon had higher mean T1 values of 662 ms ± 97 ms (VFA method) and 637 ms ± 40 ms (VTR method) compared to the patellar tendon. 3D volumetric visualization of the relaxation times revealed that T1 values are not constant over the volume of both tendons, but vary locally. This work provided additional data to build upon the scarce literature available on relaxation times in the quadriceps and patellar tendons. We were able to segment both tendons and to visualize the relaxation parameter distributions over the entire tendon volumes. Y1 - 2019 U6 - https://doi.org/10.1016/j.mri.2019.07.015 VL - 63 IS - 11 SP - 29 EP - 36 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Reuther, Markus A1 - Schlechte, Thomas T1 - Optimization of handouts for rolling stock rotations JF - Journal of Rail Transport Planning & Management N2 - A railway operator creates (rolling stock) rotations in order to have a precise master plan for the operation of a timetable by railway vehicles. A rotation is considered as a cycle that multiply traverses a set of operational days while covering trips of the timetable. As it is well known, the proper creation of rolling stock rotations by, e.g., optimization algorithms is challenging and still a topical research subject. Nevertheless, we study a completely different but strongly related question in this paper, i.e.: How to visualize a rotation? For this purpose, we introduce a basic handout concept, which directly leads to the visualization, i.e., handout of a rotation. In our industrial application at DB Fernverkehr AG, the handout is exactly as important as the rotation itself. Moreover, it turns out that also other European railway operators use exactly the same methodology (but not terminology). Since a rotation can have many handouts of different quality, we show how to compute optimal ones through an integer program (IP) by standard software. In addition, a construction as well as an improvement heuristic are presented. Our computational results show that the heuristics are a very reliable standalone approach to quickly find near-optimal and even optimal handouts. The efficiency of the heuristics is shown via a computational comparison to the IP approach. Y1 - 2019 U6 - https://doi.org/10.1016/j.jrtpm.2019.02.001 IS - 10 SP - 1 EP - 8 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Hellmeier, Florian A1 - Bruening, Jan Joris A1 - Spuler, Andreas A1 - Hege, Hans-Christian A1 - Voss, Samuel A1 - Janiga, Gábor A1 - Saalfeld, Sylvia A1 - Beuing, Oliver A1 - Berg, Philipp T1 - Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH): Uncertainty Quantification of Geometric Rupture Risk Parameters JF - BioMedical Engineering OnLine N2 - Background Geometric parameters have been proposed for prediction of cerebral aneurysm rupture risk. Predicting the rupture risk for incidentally detected unruptured aneurysms could help clinicians in their treatment decision. However, assessment of geometric parameters depends on several factors, including the spatial resolution of the imaging modality used and the chosen reconstruction procedure. The aim of this study was to investigate the uncertainty of a variety of previously proposed geometric parameters for rupture risk assessment, caused by variability of reconstruction procedures. Materials 26 research groups provided segmentations and surface reconstructions of five cerebral aneurysms as part of the Multiple Aneurysms AnaTomy CHallenge (MATCH) 2018. 40 dimensional and non-dimensional geometric parameters, describing aneurysm size, neck size, and irregularity of aneurysm shape, were computed. The medians as well as the absolute and relative uncertainties of the parameters were calculated. Additionally, linear regression analysis was performed on the absolute uncertainties and the median parameter values. Results A large variability of relative uncertainties in the range between 3.9 and 179.8% was found. Linear regression analysis indicates that some parameters capture similar geometric aspects. The lowest uncertainties < 6% were found for the non-dimensional parameters isoperimetric ratio, convexity ratio, and ellipticity index. Uncertainty of 2D and 3D size parameters was significantly higher than uncertainty of 1D parameters. The most extreme uncertainties > 80% were found for some curvature parameters. Conclusions Uncertainty analysis is essential on the road to clinical translation and use of rupture risk prediction models. Uncertainty quantification of geometric rupture risk parameters provided by this study may help support development of future rupture risk prediction models. Y1 - 2019 U6 - https://doi.org/10.1186/s12938-019-0657-y VL - 18 IS - 35 ER - TY - JOUR A1 - Breuer, Thomas A1 - Bussieck, Michael A1 - Fiand, Frederik A1 - Cao, Karl-Kiên A1 - Gils, Hans Christian A1 - Wetzel, Manuel A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Khabi, Dmitry T1 - BEAM-ME: Ein interdisziplinärer Beitrag zur Erreichung der Klimaziele JF - OR-News : das Magazin der GOR Y1 - 2019 IS - 66 SP - 6 EP - 8 ER - TY - JOUR A1 - Fröhler, Bernhard A1 - Elberfeld, Tim A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Weissenböck, Johannes A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Kastner, Johann A1 - Heinzl, Christoph T1 - A Visual Tool for the Analysis of Algorithms for Tomographic Fiber Reconstruction in Materials Science JF - Computer Graphics Forum N2 - We present visual analysis methods for the evaluation of tomographic fiber reconstruction algorithms by means of analysis, visual debugging and comparison of reconstructed fibers in materials science. The methods are integrated in a tool (FIAKER) that supports the entire workflow. It enables the analysis of various fiber reconstruction algorithms, of differently parameterized fiber reconstruction algorithms and of individual steps in iterative fiber reconstruction algorithms. Insight into the performance of fiber reconstruction algorithms is obtained by a list‐based ranking interface. A 3D view offers interactive visualization techniques to gain deeper insight, e.g., into the aggregated quality of the examined fiber reconstruction algorithms and parameterizations. The tool was designed in close collaboration with researchers who work with fiber‐reinforced polymers on a daily basis and develop algorithms for tomographic reconstruction and characterization of such materials. We evaluate the tool using synthetic datasets as well as tomograms of real materials. Five case studies certify the usefulness of the tool, showing that it significantly accelerates the analysis and provides valuable insights that make it possible to improve the fiber reconstruction algorithms. The main contribution of the paper is the well‐considered combination of methods and their seamless integration into a visual tool that supports the entire workflow. Further findings result from the analysis of (dis‐)similarity measures for fibers as well as from the discussion of design decisions. It is also shown that the generality of the analytical methods allows a wider range of applications, such as the application in pore space analysis. Y1 - 2019 U6 - https://doi.org/10.1111/cgf.13688 VL - 38 IS - 3 SP - 273 EP - 283 ER - TY - JOUR A1 - Żołnacz, Kinga A1 - Musiał, Anna A1 - Srocka, Nicole A1 - Große, Jan A1 - Schlösinger, Maximilian A1 - Schneider, Philipp-Immanuel A1 - Kravets, Oleh A1 - Mikulicz, Monika A1 - Olszewski, Jacek A1 - Poturaj, Krzysztof A1 - Wójcik, Grzegorz A1 - Mergo, Paweł A1 - Dybka, Kamil A1 - Dyrkacz, Mariusz A1 - Dłubek, Michał A1 - Rodt, Sven A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Sęk, Grzegorz A1 - Reitzenstein, Stephan A1 - Urbańczyk, Wacław T1 - Method for direct coupling of a semiconductor quantum dot to an optical fiber for single-photon source applications JF - Opt. Express Y1 - 2019 U6 - https://doi.org/10.1364/OE.27.026772 VL - 27 SP - 26772 ER - TY - JOUR A1 - Gotzes, Uwe T1 - Ein neuer Ansatz zur Optimierung des Bilanzausgleichs in einem Gasmarktgebiet JF - Zeitschrift für Energiewirtschaft N2 - Im BDEW/VKU/GEODE-Leitfaden Krisenvorsorge Gas ist zu lesen, dass als oberster Grundsatz zur Vermeidung von Versorgungsengpässen in Gasversorgungssystemen gilt, möglichst laufend einen Bilanzausgleich in allen Teilen des Netzes zu erreichen. Wir entwickeln Modelle zur Optimierung des laufenden Bilanzausgleichs. Als Gasversorgungssystem betrachten wir modellhaft die Fernleitungsnetze eines Marktgebiets. Als Teile des Gasversorgungssystems fassen wir vereinfachend die jeweiligen Netze der Fernleitungsnetzbetreiber auf. Die Optimierung erfolgt in zwei Schritten. Im ersten Schritt wird der optimale Einsatz netzbezogener Maßnahmen ermittelt. Beispiele für netzbezogene Maßnahmen sind die Nutzung von Netzpuffer und Mengenverlagerungen mit anderen Infrastrukturbetreibern. Falls sich die Bilanzen durch netzbezogene Maßnahmen nicht vollständig ausgleichen lassen, werden Fehlmengen angesetzt, die so gleichmäßig wie möglich auf die Teile des Netzes verteilt werden. Im zweiten Schritt werden die verbliebenen Fehlmengen, welche in der Regel durch marktbezogene Maßnahmen bereinigt werden, regulierungskonform auf möglichst große Teile des Gasversorgungssystems verteilt. Im Ergebnis erhalten wir ein transparentes, gerechtes, flexibel parametrier- und erweiterbares Verfahren, welches zyklisch im Dispatchingprozess eingesetzt werden kann, um die Integrität der Netze zu unterstützen. Dies wird an Beispielen verdeutlicht. Y1 - 2019 U6 - https://doi.org/10.1007/s12398-019-00257-6 ER - TY - JOUR A1 - Pulaj, Jonad T1 - Cutting planes for families implying Frankl's conjecture JF - Mathematics of Computation N2 - We find previously unknown families of sets which ensure Frankl's conjecture holds for all families that contain them using an algorithmic framework. The conjecture states that for any nonempty finite union-closed (UC) family there exists an element of the ground set in at least half the sets of the considered UC family. Poonen's Theorem characterizes the existence of weights which determine whether a given UC family implies the conjecture for all UC families which contain it. We design a cutting-plane method that computes the explicit weights which satisfy the existence conditions of Poonen's Theorem. This method enables us to answer several open questions regarding structural properties of UC families, including the construction of a counterexample to a conjecture of Morris from 2006. Y1 - 2019 U6 - https://doi.org/10.1090/mcom/3461 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Hoppmann, Heide A1 - Karbstein, Marika A1 - Lindner, Niels T1 - Separation of cycle inequalities in periodic timetabling JF - Discrete Optimization N2 - Cycle inequalities play an important role in the polyhedral study of the periodic timetabling problem in public transport. We give the first pseudo-polynomial time separation algorithm for cycle inequalities, and we contribute a rigorous proof for the pseudo-polynomial time separability of the change-cycle inequalities. Moreover, we provide several NP-completeness results, indicating that pseudo-polynomial time is best possible. The efficiency of these cutting planes is demonstrated on real-world instances of the periodic timetabling problem. Y1 - 2020 U6 - https://doi.org/10.1016/j.disopt.2019.100552 IS - 35 SP - 100552 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Lindner, Niels A1 - Roth, Sarah T1 - A Concurrent Approach to the Periodic Event Scheduling Problem JF - Journal of Rail Transport Planning & Management N2 - We introduce a concurrent solver for the periodic event scheduling problem (PESP). It combines mixed integer programming techniques, the modulo network simplex method, satisfiability approaches, and a new heuristic based on maximum cuts. Running these components in parallel speeds up the overall solution process. This enables us to significantly improve the current upper and lower bounds for all benchmark instances of the library PESPlib. Y1 - 2020 U6 - https://doi.org/10.1016/j.jrtpm.2019.100175 SN - 2210-9706 IS - 15 SP - 100175 ER - TY - JOUR A1 - Heller, Eric J. A1 - Fleischmann, Ragnar A1 - Kramer, Tobias T1 - Branched Flow N2 - In many physical situations involving diverse length scales, waves or rays representing them travel through media characterized by spatially smooth, random, modest refractive index variations. "Primary" diffraction (by individual sub-wavelength features) is absent. Eventually the weak refraction leads to imperfect focal "cusps". Much later, a statistical regime characterized by momentum diffusion is manifested. An important intermediate regime is often overlooked, one that is diffusive only in an ensemble sense. Each realization of the ensemble possesses dramatic ray limit structure that guides the waves (in the same sense that ray optics is used to design lens systems). This structure is a universal phenomenon called branched flow. Many important phenomena develop in this intermediate regime. Here we give examples and some of the physics of this emerging field. Y1 - 2019 ER - TY - JOUR A1 - Lang, Annemarie A1 - Fischer, Lisa A1 - Weber, Marie-Christin A1 - Gaber, Timo A1 - Ehrig, Rainald A1 - Röblitz, Susanna A1 - Buttgereit, Frank T1 - Combining in vitro simulation and in silico modelling towards a sophisticated human osteoarthritis model JF - Osteoarthritis and Cartilage N2 - Our project aimed at building an in silico model based on our recently developed in vitro osteoarthritis (OA) model seeking for refinement of the model to enhance validity and translatability towards the more sophisticated simulation of OA. In detail, the previously 3D in vitro model is based on 3D chondrogenic constructs generated solely from human bone marrow derived mesenchymal stromal cells (hMSCs). Besides studying the normal state of the model over 3 weeks, the in vitro model was treated with interleukin-1β (IL-1β) and tumor necrosis factor alpha (TNFα) to mimic an OA-like environment. Y1 - 2019 U6 - https://doi.org/10.1016/j.joca.2019.02.277 VL - 27 SP - S183 ER - TY - JOUR A1 - Girolami, Mark A. A1 - Ipsen, Ilse C. F. A1 - Oates, Chris A1 - Owen, Art B. A1 - Sullivan, T. J. T1 - Editorial: Special edition on probabilistic numerics JF - Statistics and Computing Y1 - 2019 U6 - https://doi.org/doi:10.1007/s11222-019-09892-y VL - 29 IS - 6 SP - 1181 EP - 1183 ER - TY - JOUR A1 - Oltmanns, Elias A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang A1 - Kuper, Heinz-Günter T1 - Different Preservation Levels: The Case of Scholarly Digital Editions JF - Data Science Journal N2 - Ensuring the long-term availability of research data forms an integral part of data management services. Where OAIS compliant digital preservation has been established in recent years, in almost all cases the services aim at the preservation of file-based objects. In the Digital Humanities, research data is often represented in highly structured aggregations, such as Scholarly Digital Editions. Naturally, scholars would like their editions to remain functionally complete as long as possible. Besides standard components like webservers, the presentation typically relies on project specific code interacting with client software like webbrowsers. Especially the latter being subject to rapid change over time invariably makes such environments awkward to maintain once funding has ended. Pragmatic approaches have to be found in order to balance the curation effort and the maintainability of access to research data over time. A sketch of four potential service levels aiming at the long-term availability of research data in the humanities is outlined: (1) Continuous Maintenance, (2) Application Conservation, (3) Application Data Preservation, and (4) Bitstream Preservation. The first being too costly and the last hardly satisfactory in general, we suggest that the implementation of services by an infrastructure provider should concentrate on service levels 2 and 3. We explain their strengths and limitations considering the example of two Scholarly Digital Editions. KW - Digital Preservation Y1 - 2019 U6 - https://doi.org/10.5334/dsj-2019-051 VL - 18 IS - 1(51) ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Hijazi, Hassan A1 - Coffrin, Carleton T1 - Convex Relaxations for Quadratic On/Off Constraints and Applications to Optimal Transmission Switching JF - INFORMS Journal on Computing N2 - This paper studies mixed-integer nonlinear programs featuring disjunctive constraints and trigonometric functions and presents a strengthened version of the Convex Quadratic relaxation of the Optimal Transmission Switching problem. We first characterize the convex hull of univariate quadratic on/off constraints in the space of original variables using perspective functions. We then introduce new tight quadratic relaxations for trigonometric functions featuring variables with asymmetrical bounds. These results are used to further tighten recent convex relaxations introduced for the Optimal Transmission Switching problem in Power Systems. Using the proposed improvements, along with bound propagation, on 23 medium-size test cases in the PGLib benchmark library with a relaxation gap of more than 1%, we reduce the gap to less than 1% on 5 instances. The tightened model has promising computational results when compared to state-of-the-art formulations. Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1287/ijoc.2019.0900 VL - 32 IS - 3 SP - 682 EP - 696 PB - INFORMS Institute for Operations Research and the Management Sciences CY - 5521 Research Park Drive, Suite 200, Catonsville, MD 21228 USA ER - TY - JOUR A1 - Kostre, Margarita A1 - Schütte, Christof A1 - Noé, Frank A1 - del Razo Sarmina, Mauricio T1 - Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs JF - Multiscale Modeling & Simulation N2 - Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small to be relevant for life processes. Alternatively, particle-based reaction-diffusion models are currently the most accurate and computationally feasible approach at these scales. Their efficiency lies in modeling entire molecules as particles that can diffuse and interact with each other. In this work, we develop modeling and numerical schemes for particle-based reaction-diffusion in an open setting, where the reservoirs are mediated by reaction-diffusion PDEs. We derive two important theoretical results. The first one is the mean-field for open systems of diffusing particles; the second one is the mean-field for a particle-based reaction-diffusion system with second-order reactions. We employ these two results to develop a numerical scheme that consistently couples particle-based reaction-diffusion processes with reaction-diffusion PDEs. This allows modeling open biochemical systems in contact with reservoirs that are time-dependent and spatially inhomogeneous, as in many relevant real-world applications. Y1 - 2021 U6 - https://doi.org/10.1137/20M1352739 VL - 19 IS - 4 SP - 1659 EP - 1683 PB - Society for Industrial and Applied Mathematics ER - TY - JOUR A1 - Pakhomov, Anton A1 - Löchner, Franz A1 - Zschiedrich, Lin A1 - Saravi, Sina A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Pertsch, Thomas A1 - Setzpfand, Frank T1 - Far-field polarization signatures of surface optical nonlinearity in noncentrosymmetric semiconductors JF - Sci. Rep. Y1 - 2020 U6 - https://doi.org/10.1038/s41598-020-67186-0 VL - 10 SP - 10545 ER - TY - JOUR A1 - Weber, Marie-Christin A1 - Fischer, Lisa A1 - Damerau, Alexandra A1 - Ponomarev, Igor A1 - Pfeiffenberger, Moritz A1 - Gaber, Timo A1 - Götschel, Sebastian A1 - Lang, Jens A1 - Röblitz, Susanna A1 - Buttgereit, Frank A1 - Ehrig, Rainald A1 - Lang, Annemarie T1 - Macroscale mesenchymal condensation to study cytokine-driven cellular and matrix-related changes during cartilage degradation JF - Biofabrication N2 - Understanding the pathophysiological processes of cartilage degradation requires adequate model systems to develop therapeutic strategies towards osteoarthritis (OA). Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific disease aspects. This study aimed to combine in vitro and in silico modeling based on a tissue-engineering approach using mesenchymal condensation to mimic cytokine-induced cellular and matrix-related changes during cartilage degradation. Thus, scaffold-free cartilage-like constructs (SFCCs) were produced based on self-organization of mesenchymal stromal cells (mesenchymal condensation) and i) characterized regarding their cellular and matrix composition or secondly ii) treated with interleukin-1β (IL-1β) and tumor necrosis factor α (TNFα) for 3 weeks to simulate OA-related matrix degradation. In addition, an existing mathematical model based on partial differential equations was optimized and transferred to the underlying settings to simulate distribution of IL-1β, type II collagen degradation and cell number reduction. By combining in vitro and in silico methods, we aim to develop a valid, efficient alternative approach to examine and predict disease progression and effects of new therapeutics. Y1 - 2020 U6 - https://doi.org/10.1088/1758-5090/aba08f VL - 12 IS - 4 ER - TY - JOUR A1 - Serrano, Felipe A1 - Schwarz, Robert A1 - Gleixner, Ambros T1 - On the relation between the extended supporting hyperplane algorithm and Kelley’s cutting plane algorithm JF - Journal of Global Optimization N2 - Recently, Kronqvist et al. (J Global Optim 64(2):249–272, 2016) rediscovered the supporting hyperplane algorithm of Veinott (Oper Res 15(1):147–152, 1967) and demonstrated its computational benefits for solving convex mixed integer nonlinear programs. In this paper we derive the algorithm from a geometric point of view. This enables us to show that the supporting hyperplane algorithm is equivalent to Kelley’s cutting plane algorithm (J Soc Ind Appl Math 8(4):703–712, 1960) applied to a particular reformulation of the problem. As a result, we extend the applicability of the supporting hyperplane algorithm to convex problems represented by a class of general, not necessarily convex nor differentiable, functions. Y1 - 2020 U6 - https://doi.org/10.1007/s10898-020-00906-y VL - 78 SP - 161 EP - 179 ER - TY - JOUR A1 - Shi, Liping A1 - Evlyukhin, Andrey B. A1 - Reinhardt, Carsten A1 - Babushkin, Ihar A1 - Zenin, Vladimir A. A1 - Burger, Sven A1 - Malureanu, Radu A1 - Chichkov, Boris N. A1 - Morgner, Uwe A1 - Kovacev, Milutin T1 - Progressive Self-Boosting Anapole-Enhanced Deep-Ultraviolet Third Harmonic During Few-Cycle Laser Radiation JF - ACS Photonics Y1 - 2020 U6 - https://doi.org/10.1021/acsphotonics.0c00753 VL - 7 SP - 1655 ER - TY - JOUR A1 - Scholtz, Gerhard A1 - Knötel, David A1 - Baum, Daniel T1 - D’Arcy W. Thompson’s Cartesian transformations: a critical evaluation JF - Zoomorphology N2 - The images of D’Arcy Wentworth Thompson’s book “On Growth and Form” got an iconic status and became influential for biometrics and other mathematical approaches to organismic form. In particular, this is true for those of the chapter on the theory of transformation, which even has an impact on art and humanities. Based on his approach, Thompson formulated far-reaching conclusions with a partly anti-Darwinian stance. Here, we use the example of Thompson’s transformation of crab carapaces to test to what degree the transformation of grids, landmarks, and shapes result in congruent images. For comparison, we applied the same series of tests to digitized carapaces of real crabs. Both approaches show similar results. Only the simple transformations show a reasonable form of congruence. In particular, the transformations to majoid spider crabs reveal a complicated transformation of grids with partly crossing lines. By contrast, the carapace of the lithodid species is relatively easily created despite the fact that it is no brachyuran, but evolved a spider crab-like shape convergently from a hermit crab ancestor. Y1 - 2020 U6 - https://doi.org/10.1007/s00435-020-00494-1 VL - 139 SP - 293 EP - 308 ER - TY - JOUR A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Colom, Rémi A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Quasinormal mode expansion of optical far-field quantities JF - Phys. Rev. B Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevB.102.035432 VL - 102 SP - 035432 ER - TY - JOUR A1 - Musiał, Anna A1 - Żołnacz, Kinga A1 - Srocka, Nicole A1 - Kravets, Oleh A1 - Große, Jan A1 - Olszewski, Jacek A1 - Poturaj, Krzysztof A1 - Wojcik, Grzegorz A1 - Mergo, Paweł A1 - Kamil, Dybka A1 - Dyrkacz, Mariusz A1 - Dlubek, Michal A1 - Lauritsen, Kristian A1 - Bülter, Andreas A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Rodt, Sven A1 - Urbanczyk, Wacław A1 - Sek, Grzegorz A1 - Reitzenstein, Stephan T1 - Plug&play fibre-coupled 73 kHz single-photon source operating in the telecom O-band JF - Adv. Quantum Technol. Y1 - 2020 U6 - https://doi.org/10.1002/qute.202000018 VL - 3 SP - 2000018 ER - TY - JOUR A1 - Skrzypczak, Jan A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - RMWPaxos: Fault-Tolerant In-Place Consensus Sequences JF - IEEE Transactions on Parallel and Distributed Systems Y1 - 2020 U6 - https://doi.org/10.1109/TPDS.2020.2981891 SN - 1045-9219 VL - 31 IS - 10 SP - 2392 EP - 2405 ER - TY - JOUR A1 - Colom, Rémi A1 - Stout, Brian A1 - Bonod, Nicolas T1 - Modal Expansion of the Impulse Response Function for Predicting the Time Dynamics of Open Optical Cavities JF - arXiv Y1 - 2020 ER - TY - JOUR A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae JF - MethodsX N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. Y1 - 2020 U6 - https://doi.org/10.1016/j.mex.2020.100905 VL - 7 SP - 100905 ER - TY - JOUR A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Lindow, Norbert A1 - Powers, James A. A1 - Cota, Vanessa A1 - Quintanilla, Luis J. A1 - Brugués, Jan A1 - Prohaska, Steffen A1 - Chu, Diana S. A1 - Müller-Reichert, Thomas T1 - Sperm-specific meiotic chromosome segregation in C. elegans JF - eLife Y1 - 2020 U6 - https://doi.org/10.7554/eLife.50988 VL - 9 SP - e50988 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Hendel, Gregor A1 - Gamrath, Gerald A1 - Achterberg, Tobias A1 - Bastubbe, Michael A1 - Berthold, Timo A1 - Christophel, Philipp M. A1 - Jarck, Kati A1 - Koch, Thorsten A1 - Linderoth, Jeff A1 - Lübbecke, Marco A1 - Mittelmann, Hans A1 - Ozyurt, Derya A1 - Ralphs, Ted A1 - Salvagnin, Domenico A1 - Shinano, Yuji T1 - MIPLIB 2017: Data-Driven Compilation of the 6th Mixed-Integer Programming Library JF - Mathematical Programming Computation N2 - We report on the selection process leading to the sixth version of the Mixed Integer Programming Library. Selected from an initial pool of over 5,000 instances, the new MIPLIB 2017 collection consists of 1,065 instances. A subset of 240 instances was specially selected for benchmarking solver performance. For the first time, the compilation of these sets was done using a data-driven selection process supported by the solution of a sequence of mixed integer optimization problems, which encoded requirements on diversity and balancedness with respect to instance features and performance data. Y1 - 2021 U6 - https://doi.org/10.1007/s12532-020-00194-3 VL - 13 IS - 3 SP - 443 EP - 490 ER - TY - JOUR A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Koch, Thorsten A1 - Miltenberger, Matthias A1 - Kniasew, Dimitri A1 - Schlögel, Dominik A1 - Martin, Alexander A1 - Weninger, Dieter T1 - Tackling Industrial-Scale Supply Chain Problems by Mixed-Integer Programming JF - Journal of Computational Mathematics N2 - The modeling flexibility and the optimality guarantees provided by mixed-integer programming greatly aid the design of robust and future-proof decision support systems. The complexity of industrial-scale supply chain optimization, however, often poses limits to the application of general mixed-integer programming solvers. In this paper we describe algorithmic innovations that help to ensure that MIP solver performance matches the complexity of the large supply chain problems and tight time limits encountered in practice. Our computational evaluation is based on a diverse set, modeling real-world scenarios supplied by our industry partner SAP. Y1 - 2019 U6 - https://doi.org/10.4208/jcm.1905-m2019-0055 VL - 37 SP - 866 EP - 888 ER - TY - JOUR A1 - Siefke, Thomas A1 - Hurtado, Carol A1 - Dickmann, Johannes A1 - Dickmann, Walter A1 - Käseberg, Tim A1 - Meyer, Jan A1 - Burger, Sven A1 - Zeitner, Uwe A1 - Bodermann, Bernd A1 - Kroker, Stefanie T1 - Quasi-bound states in the continuum for deep subwavelength structural information retrieval for DUV nano-optical polarizers JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.396044 VL - 28 SP - 23122 ER - TY - JOUR A1 - Sahu, Manish A1 - Szengel, Angelika A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Surgical phase recognition by learning phase transitions JF - Current Directions in Biomedical Engineering (CDBME) N2 - Automatic recognition of surgical phases is an important component for developing an intra-operative context-aware system. Prior work in this area focuses on recognizing short-term tool usage patterns within surgical phases. However, the difference between intra- and inter-phase tool usage patterns has not been investigated for automatic phase recognition. We developed a Recurrent Neural Network (RNN), in particular a state-preserving Long Short Term Memory (LSTM) architecture to utilize the long-term evolution of tool usage within complete surgical procedures. For fully automatic tool presence detection from surgical video frames, a Convolutional Neural Network (CNN) based architecture namely ZIBNet is employed. Our proposed approach outperformed EndoNet by 8.1% on overall precision for phase detection tasks and 12.5% on meanAP for tool recognition tasks. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1515/cdbme-2020-0037 N1 - Nomination for the Best-Paper Award VL - 6 IS - 1 SP - 20200037 PB - De Gruyter ER - TY - JOUR A1 - Tockhorn, Philipp A1 - Sutter, Johannes A1 - Colom, Rémi A1 - Kegelmann, Lukas A1 - Al-Ashouri, Amran A1 - Roß, Marcel A1 - Jäger, Klaus A1 - Unold, Thomas A1 - Burger, Sven A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Improved Quantum Efficiency by Advanced Light Management in Nanotextured Solution-Processed Perovskite Solar Cells JF - ACS Photonics Y1 - 2020 U6 - https://doi.org/10.1021/acsphotonics.0c00935 VL - 7 SP - 2589 ER - TY - JOUR A1 - Feis, Joshua A1 - Beutel, Dominik A1 - Köpfler, Julian A1 - Santiago, Xavier Garcia A1 - Rockstuhl, Carsten A1 - Wegener, Martin A1 - Fernandez-Corbaton, Ivan T1 - Helicity-Preserving Optical Cavity Modes for Enhanced Sensing of Chiral Molecules JF - Phys. Rev. Lett. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevLett.124.033201 VL - 124 SP - 033201 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Flat optics in high numerical aperture broadband imaging systems JF - J. Opt. Y1 - 2020 U6 - https://doi.org/10.1088/2040-8986/ab8ea2 VL - 22 SP - 065607 ER - TY - JOUR A1 - Farchmin, Nando A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Wurm, Matthias A1 - Bodermann, Bernd A1 - Bär, Markus A1 - Heidenreich, Sebastian T1 - Efficient Bayesian inversion for shape reconstruction of lithography masks JF - J. Micro/Nanolith. MEMS MOEMS Y1 - 2020 U6 - https://doi.org/10.1117/1.JMM.19.2.024001 VL - 19 SP - 024001 ER - TY - JOUR A1 - Willsch, Maraike A1 - Friedrich, Frank A1 - Baum, Daniel A1 - Jurisch, Ivo A1 - Ohl, Michael T1 - A comparative description of the mesosomal musculature in Sphecidae and Ampulicidae (Hymenoptera, Apoidea) using 3D techniques JF - Deutsche Entomologische Zeitschrift N2 - Conflicting hypotheses about the relationships among the major lineages of aculeate Hymenoptera clearly show the necessity of detailed comparative morphological studies. Using micro-computed tomography and 3D reconstructions, the skeletal musculature of the meso- and metathorax and the first and second abdominal segment in Apoidea are described. Females of Sceliphron destillatorium, Sphex (Fernaldina) lucae (both Sphecidae), and Ampulex compressa (Ampulicidae) were examined. The morphological terminology provided by the Hymenoptera Anatomy Ontology is used. Up to 42 muscles were found. The three species differ in certain numerical and structural aspects. Ampulicidae differs significantly from Sphecidae in the metathorax and the anterior abdomen. The metapleural apodeme and paracoxal ridge are weakly developed in Ampulicidae, which affect some muscular structures. Furthermore, the muscles that insert on the coxae and trochanters are broader and longer in Ampulicidae. A conspicuous characteristic of Sphecidae is the absence of the metaphragma. Overall, we identified four hitherto unrecognized muscles. Our work suggests additional investigations on structures discussed in this paper. Y1 - 2020 U6 - https://doi.org/10.3897/dez.67.49493 VL - 67 IS - 1 SP - 51 EP - 67 ER - TY - JOUR A1 - Hoang, Margaux A1 - Garnier, Philippe A1 - Lasue, Jeremie A1 - Rème, Henri A1 - Capria, Maria Teresa A1 - Altwegg, Kathrin A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin T1 - Investigating the Rosetta/RTOF observations of comet 67P/Churyumov-Gerasimenko using a comet nucleus model: Influence of dust mantle and trapped CO JF - Astronomy & Astrophysics N2 - Context. Cometary outgassing is induced by the sublimation of ices and the ejection of dust originating from the nucleus. Therefore measuring the composition and dynamics of the cometary gas provides information concerning the interior composition of the body. Nevertheless, the bulk composition differs from the coma composition, and numerical models are required to simulate the main physical processes induced by the illumination of the icy body. Aims. The objectives of this study are to bring new constraints on the interior composition of the nucleus of comet 67P/Churyumov-Gerasimenko (hereafter 67P) by comparing the results of a thermophysical model applied to the nucleus of 67P and the coma measurements made by the Reflectron-type Time-Of-Flight (RTOF) mass spectrometer. This last is one of the three instruments of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA), used during the Rosetta mission. Methods. Using a thermophysical model of the comet nucleus, we studied the evolution of the stratigraphy (position of the sublimation and crystallisation fronts), the temperature of the surface and subsurface, and the dynamics and spatial distribution of the volatiles (H2O, CO2 and CO). We compared them with the in situ measurements from ROSINA/RTOF and an inverse coma model. Results. We observed the evolution of the surface and near surface temperature, and the deepening of sublimation fronts. The thickness of the dust layer covering the surface strongly influences the H2O outgassing but not the more volatiles species. The CO outgassing is highly sensitive to the initial CO/H2O ratio, as well as to the presence of trapped CO in the amorphous ice. Conclusions. The study of the influence of the initial parameters on the computed volatile fluxes and the comparison with ROSINA/RTOF measurements provide a range of values for an initial dust mantle thickness and a range of values for the volatile ratio. These imply the presence of trapped CO. Nevertheless, further studies are required to reproduce the strong change of behaviour observed in RTOF measurements between September 2014 and February 2015. Y1 - 2020 U6 - https://doi.org/10.1051/0004-6361/201936655 VL - 638 SP - A106 ER - TY - JOUR A1 - Mrowiński, Paweł A1 - Schnauber, Peter A1 - Kaganskiy, Arsenty A1 - Schall, Johannes A1 - Burger, Sven A1 - Rodt, Sven A1 - Reitzenstein, Stephan T1 - Directional single-photon emission from deterministic quantum dot waveguide structures JF - Phys. Status Solidi RRL Y1 - 2020 U6 - https://doi.org/10.1002/pssr.202000115 VL - 14 SP - 2000115 ER - TY - JOUR A1 - Zhang, Wei T1 - Some new results on relative entropy production, time reversal, and optimal control of time-inhomogeneous diffusion processes JF - Journal of Mathematical Physics N2 - This paper studies time-inhomogeneous nonequilibrium diffusion processes, including both Brownian dynamics and Langevin dynamics. We derive upper bounds of the relative entropy production of the time-inhomogeneous process with respect to the transient invariant probability measures. We also study the time reversal of the reverse process in Crooks' fluctuation theorem. We show that the time reversal of the reverse process coincides with the optimally controlled forward process that leads to zero variance importance sampling estimator based on Jarzynski's equality. Y1 - 2021 U6 - https://doi.org/10.1063/5.0038740 VL - 62 IS - 4 ER - TY - JOUR A1 - Anzt, H. A1 - Bach, F. A1 - Druskat, S. A1 - Löffler, F. A1 - Loewe, A. A1 - Renard, B. Y. A1 - Seemann, G. A1 - Struck, A. A1 - Achhammer, E. A1 - Appell, F. A1 - Bader, M. A1 - Brusch, L. A1 - Busse, C. A1 - Chourdakis, G. A1 - Dabrowski, P. W. A1 - Ebert, P. A1 - Flemisch, B. A1 - Friedl, S. A1 - Fritzsch, B. A1 - Funk, M. D. A1 - Gast, V. A1 - Goth, F. A1 - Grad, J.-N. A1 - Hermann, Sibylle A1 - Hohmann, F. A1 - Janosch, S. A1 - Kutra, D. A1 - Linxweiler, J. A1 - Muth, T. A1 - Peters-Kottig, Wolfgang A1 - Rack, F. A1 - Raters, F. H. C. A1 - Rave, S. A1 - Reina, G. A1 - Reißig, M. A1 - Ropinski, T. A1 - Schaarschmidt, J. A1 - Seibold, H. A1 - Thiele, J. P. A1 - Uekermann, B. A1 - Unger, S. A1 - Weeber, R. T1 - An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 1; peer review: 1 approved, 1 approved with reservations] JF - F1000Research N2 - Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin. KW - Sustainable Software Development KW - Research Software Y1 - 2020 U6 - https://doi.org/10.12688/f1000research.23224.1 IS - 9:295 ER - TY - JOUR A1 - Straube, Arthur A1 - Kowalik, Bartosz G. A1 - Netz, Roland R. A1 - Höfling, Felix T1 - Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures JF - Commun. Phys. N2 - Friction in liquids arises from conservative forces between molecules and atoms. Although the hydrodynamics at the nanoscale is subject of intense research and despite the enormous interest in the non-Markovian dynamics of single molecules and solutes, the onset of friction from the atomistic scale so far could not be demonstrated. Here, we fill this gap based on frequency-resolved friction data from high-precision simulations of three prototypical liquids, including water. Combining with theory, we show that friction in liquids emerges abruptly at a characteristic frequency, beyond which viscous liquids appear as non-dissipative, elastic solids. Concomitantly, the molecules experience Brownian forces that display persistent correlations. A critical test of the generalised Stokes–Einstein relation, mapping the friction of single molecules to the visco-elastic response of the macroscopic sample, disproves the relation for Newtonian fluids, but substantiates it exemplarily for water and a moderately supercooled liquid. The employed approach is suitable to yield insights into vitrification mechanisms and the intriguing mechanical properties of soft materials. Y1 - 2020 U6 - https://doi.org/10.1038/s42005-020-0389-0 VL - 3 SP - 126 PB - Nature ER - TY - JOUR A1 - Haase, Tobias A1 - Sunkara, Vikram A1 - Kohl, Benjamin A1 - Meier, Carola A1 - Bußmann, Patricia A1 - Becker, Jessica A1 - Jagielski, Michal A1 - von Kleist, Max A1 - Ertel, Wolfgang T1 - Discerning the spatio-temporal disease patterns of surgically induced OA mouse models JF - PLOS One N2 - Osteoarthritis (OA) is the most common cause of disability in ageing societies, with no effective therapies available to date. Two preclinical models are widely used to validate novel OA interventions (MCL-MM and DMM). Our aim is to discern disease dynamics in these models to provide a clear timeline in which various pathological changes occur. OA was surgically induced in mice by destabilisation of the medial meniscus. Analysis of OA progression revealed that the intensity and duration of chondrocyte loss and cartilage lesion formation were significantly different in MCL-MM vs DMM. Firstly, apoptosis was seen prior to week two and was narrowly restricted to the weight bearing area. Four weeks post injury the magnitude of apoptosis led to a 40–60% reduction of chondrocytes in the non-calcified zone. Secondly, the progression of cell loss preceded the structural changes of the cartilage spatio-temporally. Lastly, while proteoglycan loss was similar in both models, collagen type II degradation only occurred more prominently in MCL-MM. Dynamics of chondrocyte loss and lesion formation in preclinical models has important implications for validating new therapeutic strategies. Our work could be helpful in assessing the feasibility and expected response of the DMM- and the MCL-MM models to chondrocyte mediated therapies. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0213734 VL - 14 IS - 4 PB - PLOS One ER - TY - JOUR A1 - Sunkara, Vikram T1 - On the Properties of the Reaction Counts Chemical Master Equation JF - Entropy N2 - The reaction counts chemical master equation (CME) is a high-dimensional variant of the classical population counts CME. In the reaction counts CME setting, we count the reactions which have fired over time rather than monitoring the population state over time. Since a reaction either fires or not, the reaction counts CME transitions are only forward stepping. Typically there are more reactions in a system than species, this results in the reaction counts CME being higher in dimension, but simpler in dynamics. In this work, we revisit the reaction counts CME framework and its key theoretical results. Then we will extend the theory by exploiting the reactions counts’ forward stepping feature, by decomposing the state space into independent continuous-time Markov chains (CTMC). We extend the reaction counts CME theory to derive analytical forms and estimates for the CTMC decomposition of the CME. This new theory gives new insights into solving hitting times-, rare events-, and a priori domain construction problems. Y1 - 2019 U6 - https://doi.org/10.3390/e21060607 VL - 21 IS - 6 SP - 607 ER - TY - JOUR A1 - Temp, Julia A1 - Labuz, Dominika A1 - Negrete, Roger A1 - Sunkara, Vikram A1 - Machelska, Halina T1 - Pain and knee damage in male and female mice in the medial meniscal transection-induced osteoarthritis JF - Osteoarthritis and Cartilage Y1 - 2019 U6 - https://doi.org/10.1016/j.joca.2019.11.003 ER - TY - JOUR A1 - Ege, Yannic A1 - Foth, Christian A1 - Baum, Daniel A1 - Wirkner, Christian S. A1 - Richter, Stefan T1 - Making spherical-harmonics-based Geometric Morphometrics (SPHARM) approachable for 3D images containing large cavity openings using Ambient Occlusion - a study using hermit crab claw shape variability JF - Zoomorphology N2 - An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time. Y1 - 2020 U6 - https://doi.org/10.1007/s00435-020-00488-z VL - 139 SP - 421 EP - 432 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Steffy, Daniel T1 - Linear Programming using Limited-Precision Oracles JF - Mathematical Programming N2 - Since the elimination algorithm of Fourier and Motzkin, many different methods have been developed for solving linear programs. When analyzing the time complexity of LP algorithms, it is typically either assumed that calculations are performed exactly and bounds are derived on the number of elementary arithmetic operations necessary, or the cost of all arithmetic operations is considered through a bit-complexity analysis. Yet in practice, implementations typically use limited-precision arithmetic. In this paper we introduce the idea of a limited-precision LP oracle and study how such an oracle could be used within a larger framework to compute exact precision solutions to LPs. Under mild assumptions, it is shown that a polynomial number of calls to such an oracle and a polynomial number of bit operations, is sufficient to compute an exact solution to an LP. This work provides a foundation for understanding and analyzing the behavior of the methods that are currently most effective in practice for solving LPs exactly. Y1 - 2020 U6 - https://doi.org/10.1007/s10107-019-01444-6 VL - 183 IS - 1-2 SP - 525 EP - 554 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Schuster, Ingmar A1 - Sullivan, T. J. T1 - A rigorous theory of conditional mean embeddings JF - SIAM Journal on Mathematics of Data Science Y1 - 2020 U6 - https://doi.org/10.1137/19M1305069 VL - 2 IS - 3 SP - 583 EP - 606 ER - TY - JOUR A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms JF - Photoacoustics N2 - Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies. Y1 - 2020 U6 - https://doi.org/10.1016/j.pacs.2019.100157 VL - 17 SP - 100157 ER - TY - JOUR A1 - Kramer, Tobias A1 - Rodríguez, Mirta T1 - Effect of disorder and polarization sequences on two-dimensional spectra of light harvesting complexes JF - Photosynthesis Research N2 - Two-dimensional electronic spectra (2DES) provide unique ways to track the energy transfer dynamics in light-harvesting complexes. The interpretation of the peaks and structures found in experimentally recorded 2DES is often not straightforward, since several processes are imaged simultaneously. The choice of specific pulse polarization sequences helps to disentangle the sometimes convoluted spectra, but brings along other disturbances. We show by detailed theoretical calculations how 2DES of the Fenna-Matthews-Olson complex are affected by rotational and conformational disorder of the chromophores. Y1 - 2020 U6 - https://doi.org/10.1007/s11120-019-00699-6 VL - 144 SP - 147 EP - 154 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Minion, Michael L. T1 - An Efficient Parallel-in-Time Method for Optimization with Parabolic PDEs JF - SIAM J. Sci. Comput. N2 - To solve optimization problems with parabolic PDE constraints, often methods working on the reduced objective functional are used. They are computationally expensive due to the necessity of solving both the state equation and a backward-in-time adjoint equation to evaluate the reduced gradient in each iteration of the optimization method. In this study, we investigate the use of the parallel-in-time method PFASST in the setting of PDE-constrained optimization. In order to develop an efficient fully time-parallel algorithm, we discuss different options for applying PFASST to adjoint gradient computation, including the possibility of doing PFASST iterations on both the state and the adjoint equations simultaneously. We also explore the additional gains in efficiency from reusing information from previous optimization iterations when solving each equation. Numerical results for both a linear and a nonlinear reaction-diffusion optimal control problem demonstrate the parallel speedup and efficiency of different approaches. Y1 - 2019 U6 - https://doi.org/10.1137/19M1239313 VL - 41 IS - 6 SP - C603 EP - C626 ER - TY - JOUR A1 - Mohr, Gunther A1 - Altenburg, Simon J. A1 - Ulbricht, Alexander A1 - Heinrich, Philipp A1 - Baum, Daniel A1 - Maierhofer, Christiane A1 - Hilgenberg, Kai T1 - In-situ defect detection in laser powder bed fusion by using thermography and optical tomography – comparison to computed tomography JF - Metals Y1 - 2020 U6 - https://doi.org/10.3390/met10010103 VL - 10 IS - 1 SP - 103 ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Döpking, Sandra A1 - Burger, Sven A1 - Matera, Sebastian T1 - Field Heterogeneities and Their Impact on Photocatalysis: Combining Optical and Kinetic Monte Carlo Simulations on the Nanoscale JF - J. Phys. Chem. C Y1 - 2020 U6 - https://doi.org/10.1021/acs.jpcc.9b11469 VL - 124 SP - 3177 ER - TY - JOUR A1 - Dibak, Manuel A1 - Fröhner, Christoph A1 - Noé, Frank A1 - Höfling, Felix T1 - Diffusion-influenced reaction rates in the presence of pair interactions JF - The Journal of Chemical Physics N2 - The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi’s volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction–diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction–diffusion equation in the steady state and derive semi- analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions. Y1 - 2019 U6 - https://doi.org/10.1063/1.5124728 VL - 151 SP - 164105 ER - TY - JOUR A1 - Erlekam, Franziska A1 - Igde, Sinaida A1 - Röblitz, Susanna A1 - Hartmann, Laura A1 - Weber, Marcus T1 - Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC JF - Computation N2 - In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting of two separate kinetic steps, such as protein folding or sequential binding processes. The ITC method alone cannot deliver kinetic parameters, especially not for multivalent bindings. This paper describes how to solve the problem using kinITC and an invariant subspace projection. The algorithm is tested for multivalent systems with different valencies. Y1 - 2019 U6 - https://doi.org/10.3390/computation7030046 VL - 7 IS - 3 SP - 46 ER - TY - JOUR A1 - Weber, Marcus T1 - Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung JF - KA Korrespondenz Abwasser, Abfall Y1 - 2019 VL - 7 SP - 551 EP - 557 ER - TY - JOUR A1 - Venkatareddy, Narendra Lagumaddepalli A1 - Wilke, Patrick A1 - Ernst, Natalia A1 - Horch, Justus A1 - Weber, Marcus A1 - Dallmann, Andre A1 - Börner, Hans G. T1 - Mussel-glue inspired adhesives: A study on the relevance of L-Dopa and the function of the sequence at nanomaterial-peptide interfaces JF - Advanced Materials Interfaces N2 - Mussel glue‐proteins undergo structural transitions at material interfaces to optimize adhesive surface contacts. Those intriguing structure responses are mimicked by a mussel‐glue mimetic peptide (HSY*SGWSPY*RSG (Y* = l‐Dopa)) that was previously selected by phage‐display to adhere to Al2O3 after enzymatic activation. Molecular level insights into the full‐length adhesion domain at Al2O3 surfaces are provided by a divergent‐convergent analysis, combining nuclear Overhauser enhancement based 2D NOESY and saturation transfer difference NMR analysis of submotifs along with molecular dynamics simulations of the full‐length peptide. The peptide is divided into two submotifs, each containing one Dopa “anchor” (Motif‐1 and 2). The analysis proves Motif‐1 to constitute a dynamic Al2O3 binder and adopting an “M”‐structure with multiple surface contacts. Motif‐2 binds stronger by two surface contacts, forming a compact “C”‐structure. Taking these datasets as constraints enables to predict the structure and propose a binding process model of the full‐length peptide adhering to Al2O3. Y1 - 2019 U6 - https://doi.org/10.1002/admi.201900501 VL - 6 IS - 13 SP - 1900501 ER - TY - JOUR A1 - Christgau, Steffen A1 - Schnor, Bettina T1 - Comparing MPI Passive Target Synchronization on a Non-Cache-Coherent Shared-Memory Processor JF - Mitteilungen - Gesellschaft für Informatik e. V., Parallel-Algorithmen und Rechnerstrukturen, ISSN 0177-0454, 28. PARS-Workshop Y1 - 2020 IS - 35 SP - 121 EP - 132 ER - TY - JOUR A1 - Del Vecchio, Giovanna A1 - Labuz, Dominika A1 - Temp, Julia A1 - Seitz, Viola A1 - Kloner, Michael A1 - Negrete, Roger A1 - Rodriguez-Gaztelumendi, Antonio A1 - Weber, Marcus A1 - Machelska, Halina A1 - Stein, Christoph T1 - pKa of opioid ligands as a discriminating factor for side effects JF - Scientific Reports N2 - The non-selective activation of central and peripheral opioid receptors is a major shortcoming of currently available opioids. Targeting peripheral opioid receptors is a promising strategy to preclude side effects. Recently, we showed that fentanyl-derived μ-opioid receptor (MOR) agonists with reduced acid dissociation constants (pKa) due to introducing single fluorine atoms produced injury-restricted antinociception in rat models of inflammatory, postoperative and neuropathic pain. Here, we report that a new double-fluorinated compound (FF6) and fentanyl show similar pKa, MOR affinity and [35S]-GTPγS binding at low and physiological pH values. In vivo, FF6 produced antinociception in injured and non-injured tissue, and induced sedation and constipation. The comparison of several fentanyl derivatives revealed a correlation between pKa values and pH-dependent MOR activation, antinociception and side effects. An opioid ligand's pKa value may be used as discriminating factor to design safer analgesics. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-55886-1 VL - 9 SP - 19344 ER - TY - JOUR A1 - Banyassady, Bahareh A1 - Chiu, Man-Kwun A1 - Korman, Matias A1 - Mulzer, Wolfgang A1 - van Renssen, André A1 - Roeloffzen, Marcel A1 - Seiferth, Paul A1 - Stein, Yannik A1 - Vogtenhuber, Birgit A1 - Willert, Max T1 - Routing in polygonal domains JF - Computational Geometry, Theory and Applications N2 - We consider the problem of routing a data packet through the visibility graph of a polygonal domain P with n vertices and h holes. We may preprocess P to obtain a "label" and a "routing table" for each vertex of P. Then, we must be able to route a data packet between any two vertices p and q of P, where each step must use only the label of the target node q and the routing table of the current node. For any fixed epsilon > 0, we present a routing scheme that always achieves a routing path whose length exceeds the shortest path by a factor of at most 1 + epsilon. The labels have O(log n) bits, and the routing tables are of size O(((epsilon^-1)+h)log n). The preprocessing time is O((n^2)log n). It can be improved to O(n^2) for simple polygons. Y1 - 2019 U6 - https://doi.org/10.1016/j.comgeo.2019.101593 VL - 87 PB - Elsevier ER - TY - JOUR A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - Sullivan, T. J. A1 - von Tycowicz, Christoph T1 - Geodesic Analysis in Kendall's Shape Space with Epidemiological Applications JF - Journal of Mathematical Imaging and Vision N2 - We analytically determine Jacobi fields and parallel transports and compute geodesic regression in Kendall’s shape space. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and thereby reduce the computational expense by several orders of magnitude over common, nonlinear constrained approaches. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As an example application we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative (OAI). Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data alone. Y1 - 2020 U6 - https://doi.org/10.1007/s10851-020-00945-w VL - 62 IS - 4 SP - 549 EP - 559 ER - TY - JOUR A1 - Becker, Fabian A1 - Djurdjevac Conrad, Natasa A1 - Eser, Raphael A. A1 - Helfmann, Luzie A1 - Schütt, Brigitta A1 - Schütte, Christof A1 - Zonker, Johannes T1 - The Furnace and the Goat—A spatio-temporal model of the fuelwood requirement for iron metallurgy on Elba Island, 4th century BCE to 2nd century CE JF - PLOS ONE Y1 - 2020 UR - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241133 U6 - https://doi.org/10.1371/journal.pone.0241133 VL - 15 SP - 1 EP - 37 PB - Public Library of Science ER - TY - JOUR A1 - Banyassady, Bahareh A1 - Barba, Luis A1 - Mulzer, Wolfgang T1 - Time-Space Trade-Offs for Computing Euclidean Minimum Spanning Trees JF - Journal of Computational Geometry (JoCG) N2 - We present time-space trade-offs for computing the Euclidean minimum spanning tree of a set S of n point-sites in the plane. More precisely, we assume that S resides in a random-access memory that can only be read. The edges of the Euclidean minimum spanning tree EMST(S) have to be reported sequentially, and they cannot be accessed or modified afterwards. There is a parameter s in {1, ..., n} so that the algorithm may use O(s) cells of read-write memory (called the workspace) for its computations. Our goal is to find an algorithm that has the best possible running time for any given s between 1 and n. We show how to compute EMST(S) in O(((n^3)/(s^2)) log s) time with O(s) cells of workspace, giving a smooth trade-off between the two best-known bounds O(n^3) for s = 1 and O(n log n) for s = n. For this, we run Kruskal's algorithm on the "relative neighborhood graph" (RNG) of S. It is a classic fact that the minimum spanning tree of RNG(S) is exactly EMST(S). To implement Kruskal's algorithm with O(s) cells of workspace, we define s-nets, a compact representation of planar graphs. This allows us to efficiently maintain and update the components of the current minimum spanning forest as the edges are being inserted. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?https://jocg.org/index.php/jocg/article/view/473 VL - 11(1) SP - 525 EP - 547 ER - TY - JOUR A1 - Manley, Phillip A1 - Walde, Sebastian A1 - Hagedorn, Sylvia A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Becker, Christiane T1 - Nanopatterned Sapphire Substrates in Deep-UV LEDs: Is there an Optical Benefit? JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.379438 VL - 28 SP - 3619 ER - TY - JOUR A1 - Omari, Mohamed A1 - Lange, Alexander A1 - Plöntzke, Julia A1 - Röblitz, Susanna T1 - Model-based exploration of the impact of glucose metabolism on the estrous cycle dynamics in dairy cows JF - Biology Direct Y1 - 2019 U6 - https://doi.org/10.1186/s13062-019-0256-7 VL - 15 ER - TY - JOUR A1 - Schulz, Robert A1 - Yamamoto, Kenji A1 - Klossek, André A1 - Rancan, Fiorenza A1 - Vogt, Annika A1 - Schütte, Christof A1 - Rühl, Eckart A1 - Netz, Roland R. T1 - Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin JF - Biophysical Journal N2 - Based on experimental drug concentration profiles in healthy as well as tape-stripped ex vivo human skin, we model the penetration of the antiinflammatory drug dexamethasone into the skin layers by the one-dimensional generalized diffusion equation. We estimate the position-dependent free-energy and diffusivity profiles by solving the conjugated minimization problem, in which the only inputs are concentration profiles of dexamethasone in skin at three consecutive penetration times. The resulting free-energy profiles for damaged and healthy skin show only minor differences. In contrast, the drug diffusivity in the first 10 μm of the upper skin layer of damaged skin is 200-fold increased compared to healthy skin, which reflects the corrupted barrier function of tape-stripped skin. For the case of healthy skin, we examine the robustness of our method by analyzing the behavior of the extracted skin parameters when the number of input and output parameters are reduced. We also discuss techniques for the regularization of our parameter extraction method. Y1 - 2019 U6 - https://doi.org/10.1016/j.bpj.2019.07.027 VL - 117 IS - 5 SP - 998 EP - 1008 ER - TY - JOUR A1 - Rössig, Ansgar A1 - Petkovic, Milena T1 - Advances in Verification of ReLU Neural Networks JF - Journal of Global Optimization N2 - We consider the problem of verifying linear properties of neural networks. Despite their success in many classification and prediction tasks, neural networks may return unexpected results for certain inputs. This is highly problematic with respect to the application of neural networks for safety-critical tasks, e.g. in autonomous driving. We provide an overview of algorithmic approaches that aim to provide formal guarantees on the behavior of neural networks. Moreover, we present new theoretical results with respect to the approximation of ReLU neural networks. On the other hand, we implement a solver for verification of ReLU neural networks which combines mixed integer programming (MIP) with specialized branching and approximation techniques. To evaluate its performance, we conduct an extensive computational study. For that we use test instances based on the ACAS Xu System and the MNIST handwritten digit data set. Our solver is publicly available and able to solve the verification problem for instances which do not have independent bounds for each input neuron. Y1 - 2020 U6 - https://doi.org/10.1007/s10898-020-00949-1 PB - Springer ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Strüngmann, L. T1 - The Chase radical and reduced products JF - Journal of Pure and Applied Algebra Y1 - 2007 N1 - Additional Note: doi:10.1016/j.jpaa.2007.02.007 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.jpaa.2007.02.007 VL - 211 SP - 532 EP - 540 ER - TY - JOUR A1 - Droste, M. A1 - Göbel, R. A1 - Pokutta, Sebastian T1 - Absolute graphs with prescribed endomorphism monoid JF - Semigroup Forum Y1 - 2008 N1 - URL of the PDF: http://dx.doi.org/doi:10.1007/s00233-007-9029-1 VL - 76 SP - 256 EP - 267 ER - TY - JOUR A1 - Göbel, R. A1 - Pokutta, Sebastian T1 - Construction of dual modules using Martin’s axiom JF - Journal of Algebra Y1 - 2008 N1 - Additional Note: doi:10.1016/j.jalgebra.2008.06.017 N1 - URL of the PDF: https://www.sciencedirect.com/science/article/pii/S0021869308003153 VL - 320 SP - 2388 EP - 2404 ER - TY - JOUR A1 - Heldt, D. A1 - Kreuzer, M. A1 - Pokutta, Sebastian A1 - Poulisse, H. T1 - Approximate Computation of zero-dimensional polynomial ideals JF - Journal of Symbolic Computation Y1 - 2009 N1 - Additional Note: doi:10.1016/j.jsc.2008.11.010 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.jsc.2008.11.010 VL - 44 SP - 1566 EP - 1591 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Stauffer, G. T1 - France Telecom Workforce Scheduling Problem: a challenge JF - RAIRO-Operations Research Y1 - 2009 N1 - Additional Note: DOI: 10.1051/ro/2009025 N1 - URL of the PDF: http://dx.doi.org/10.1051/ro/2009025 IS - 43 SP - 375 EP - 386 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - Random half-integral polytopes JF - Operations Research Letters Y1 - 2011 UR - http://www.optimization-online.org/DB_HTML/2010/11/2813.html N1 - Additional Note: doi:10.1016/j.orl.2011.03.003 VL - 39 IS - 3 SP - 204 EP - 207 ER - TY - JOUR A1 - Haus, Utz-Uwe A1 - Hemmecke, R. A1 - Pokutta, Sebastian T1 - Reconstructing biochemical cluster networks JF - Journal of Mathematical Chemistry Y1 - 2011 N1 - URL of the PDF: http://dx.doi.org/10.1007/s10910-011-9892-6 VL - 49 IS - 10 SP - 2441 EP - 2456 ER - TY - JOUR A1 - Letchford, A.N. A1 - Pokutta, Sebastian A1 - Schulz, A.S. T1 - On the membership problem for the 0,1/2-closure JF - Operations Research Letters Y1 - 2011 UR - http://www.box.net/shared/zxx88q38l3 N1 - Additional Note: doi:10.1016/j.orl.2011.07.003 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.orl.2011.07.003 VL - 39 IS - 5 SP - 301 EP - 304 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Schulz, A.S. T1 - Integer-empty polytopes in the 0/1-cube with maximal Gomory-Chvátal rank JF - Operations Research Letters Y1 - 2011 UR - http://www.optimization-online.org/DB_HTML/2010/12/2850.html N1 - Additional Note: doi:10.1016/j.orl.2011.09.004 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.orl.2011.09.004 VL - 39 IS - 6 SP - 457 EP - 460 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Schmaltz, Christian T1 - Managing liquidity: Optimal degree of centralization JF - Journal of Banking and Finance KW - Real options Y1 - 2011 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1458963 U6 - https://doi.org/DOI: 10.1016/j.jbankfin.2010.07.001 SN - 0378-4266 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.jbankfin.2010.07.001 VL - 35 SP - 627 EP - 638 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Stauffer, G. T1 - Lower bounds for the Chvátal-Gomory rank in the 0/1 cube JF - Operations Research Letters Y1 - 2011 UR - http://www.optimization-online.org/DB_HTML/2010/09/2748.html N1 - Additional Note: doi:10.1016/j.orl.2011.03.001 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.orl.2011.03.001 VL - 39 IS - 3 SP - 200-203 ER - TY - JOUR A1 - Schienle, Adam A1 - Maristany de las Casas, Pedro A1 - Blanco, Marco T1 - A Priori Search Space Pruning in the Flight Planning Problem N2 - We study the Flight Planning Problem for a single aircraft, where we look for a minimum cost path in the airway network, a directed graph. Arc evaluation, such as weather computation, is computationally expensive due to non-linear functions, but required for exactness. We propose several pruning methods to thin out the search space for Dijkstra's algorithm before the query commences. We do so by using innate problem characteristics such as an aircraft's tank capacity, lower and upper bounds on the total costs, and in particular, we present a method to reduce the search space even in the presence of regional crossing costs. We test all pruning methods on real-world instances, and show that incorporating crossing costs into the pruning process can reduce the number of nodes by 90\% in our setting. T3 - ZIB-Report - 20-32 Y1 - 2019 U6 - https://doi.org/https://doi.org/10.4230/OASIcs.ATMOS.2019.8 SN - 1438-0064 ER - TY - JOUR A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Rigid Motion Invariant Statistical Shape Modeling based on Discrete Fundamental Forms JF - Medical Image Analysis N2 - We present a novel approach for nonlinear statistical shape modeling that is invariant under Euclidean motion and thus alignment-free. By analyzing metric distortion and curvature of shapes as elements of Lie groups in a consistent Riemannian setting, we construct a framework that reliably handles large deformations. Due to the explicit character of Lie group operations, our non-Euclidean method is very efficient allowing for fast and numerically robust processing. This facilitates Riemannian analysis of large shape populations accessible through longitudinal and multi-site imaging studies providing increased statistical power. Additionally, as planar configurations form a submanifold in shape space, our representation allows for effective estimation of quasi-isometric surfaces flattenings. We evaluate the performance of our model w.r.t. shape-based classification of hippocampus and femur malformations due to Alzheimer's disease and osteoarthritis, respectively. In particular, we achieve state-of-the-art accuracies outperforming the standard Euclidean as well as a recent nonlinear approach especially in presence of sparse training data. To provide insight into the model's ability of capturing biological shape variability, we carry out an analysis of specificity and generalization ability. Y1 - 2021 U6 - https://doi.org/10.1016/j.media.2021.102178 VL - 73 ER - TY - JOUR A1 - Zakiyeva, Nazgul A1 - Xu, X. T1 - Nonlinear network autoregressive model with application to natural gas network forecasting JF - Mathematics Japonica T3 - ZIB-Report - 21-24 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81025 ER - TY - JOUR A1 - Gotzes, Uwe A1 - Hoppmann-Baum, Kai T1 - Bounding the final rank during a round robin tournament with integer programming JF - Operational Research N2 - This article is mainly motivated by the urge to answer two kinds of questions regarding the Bundesliga, which is Germany’s primary football (soccer) division having the highest average stadium attendance worldwide: “At any point in the season, what is the lowest final rank a certain team can achieve?” and “At any point in the season, what is the highest final rank a certain team can achieve?”. Although we focus on the Bundesliga in particular, the integer programming formulations we introduce to answer these questions can easily be adapted to a variety of other league systems and tournaments. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/s12351-020-00546-w VL - 1866-1505 ER - TY - JOUR A1 - Sahu, Manish A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Simulation-to-Real domain adaptation with teacher-student learning for endoscopic instrument segmentation JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose Segmentation of surgical instruments in endoscopic video streams is essential for automated surgical scene understanding and process modeling. However, relying on fully supervised deep learning for this task is challenging because manual annotation occupies valuable time of the clinical experts. Methods We introduce a teacher–student learning approach that learns jointly from annotated simulation data and unlabeled real data to tackle the challenges in simulation-to-real unsupervised domain adaptation for endoscopic image segmentation. Results Empirical results on three datasets highlight the effectiveness of the proposed framework over current approaches for the endoscopic instrument segmentation task. Additionally, we provide analysis of major factors affecting the performance on all datasets to highlight the strengths and failure modes of our approach. Conclusions We show that our proposed approach can successfully exploit the unlabeled real endoscopic video frames and improve generalization performance over pure simulation-based training and the previous state-of-the-art. This takes us one step closer to effective segmentation of surgical instrument in the annotation scarce setting. Y1 - 2021 U6 - https://doi.org/10.1007/s11548-021-02383-4 N1 - Honorary Mention: Machine Learning for Computer-Assisted Intervention (CAI) Award @IPCAI2021 N1 - Honorary Mention: Audience Award for Best Innovation @IPCAI2021 VL - 16 SP - 849 EP - 859 PB - Springer Nature ER - TY - JOUR A1 - Pronzato, Luc A1 - Sagnol, Guillaume T1 - Removing inessential points in c- and A-optimal design JF - Journal of Statistical Planning and Inference N2 - A design point is inessential when it does not contribute to an optimal design, and can therefore be safely discarded from the design space. We derive three inequalities for the detection of such inessential points in c-optimal design: the first two are direct consequences of the equivalence theorem for c-optimality; the third one is derived from a second-order cone programming formulation of c-optimal design. Elimination rules for A-optimal design are obtained as a byproduct. When implemented within an optimization algorithm, each inequality gives a screening test that may provide a substantial acceleration by reducing the size of the problem online. Several examples are presented with a multiplicative algorithm to illustrate the effectiveness of the approach. Y1 - 2021 UR - https://hal.archives-ouvertes.fr/hal-02868664 U6 - https://doi.org/10.1016/j.jspi.2020.11.011 VL - 213 SP - 233 EP - 252 ER - TY - JOUR A1 - Höfling, Felix A1 - Dietrich, Siegfried T1 - Finite-size corrections for the static structure factor of a liquid slab with open boundaries JF - The Journal of Chemical Physics N2 - The presence of a confining boundary can modify the local structure of a liquid markedly. In addition, small samples of finite size are known to exhibit systematic deviations of thermodynamic quantities relative to their bulk values. Here, we consider the static structure factor of a liquid sample in slab geometry with open boundaries at the surfaces, which can be thought of as virtually cutting out the sample from a macroscopically large, homogeneous fluid. This situation is a relevant limit for the interpretation of grazing-incidence diffraction experiments at liquid interfaces and films. We derive an exact, closed expression for the slab structure factor, with the bulk structure factor as the only input. This shows that such free boundary conditions cause significant differences between the two structure factors, in particular, at small wavenumbers. An asymptotic analysis of this result yields the scaling exponent and an accurate, useful approximation of these finite-size corrections. Furthermore, the open boundaries permit the interpretation of the slab as an open system, supporting particle exchange with a reservoir. We relate the slab structure factor to the particle number fluctuations and discuss conditions under which the subvolume of the slab represents a grand canonical ensemble with chemical potential μ and temperature T. Thus, the open slab serves as a test-bed for the small-system thermodynamics in a μT reservoir. We provide a microscopically justified and exact result for the size dependence of the isothermal compressibility. Our findings are corroborated by simulation data for Lennard-Jones liquids at two representative temperatures. Y1 - 2020 U6 - https://doi.org/10.1063/5.0017923 VL - 153 SP - 054119 ER - TY - JOUR A1 - Ebrahimi Viand, Roya A1 - Höfling, Felix A1 - Klein, Rupert A1 - Delle Site, Luigi T1 - Theory and simulation of open systems out of equilibrium JF - The Journal of Chemical Physics N2 - We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations. Y1 - 2020 U6 - https://doi.org/10.1063/5.0014065 VL - 153 SP - 101102 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Schuster, Ingmar T1 - Markov Chain Importance Sampling - a highly efficient estimator for MCMC JF - Journal of Computational and Graphical Statistics N2 - Markov chain (MC) algorithms are ubiquitous in machine learning and statistics and many other disciplines. Typically, these algorithms can be formulated as acceptance rejection methods. In this work we present a novel estimator applicable to these methods, dubbed Markov chain importance sampling (MCIS), which efficiently makes use of rejected proposals. For the unadjusted Langevin algorithm, it provides a novel way of correcting the discretization error. Our estimator satisfies a central limit theorem and improves on error per CPU cycle, often to a large extent. As a by-product it enables estimating the normalizing constant, an important quantity in Bayesian machine learning and statistics. Y1 - 2020 U6 - https://doi.org/10.1080/10618600.2020.1826953 ER - TY - JOUR A1 - Scott, Philip A1 - Santiago, Xavier Garcia A1 - Beutel, Dominik A1 - Rockstuhl, Carsten A1 - Wegener, Martin A1 - Fernandez-Corbaton, Ivan T1 - On enhanced sensing of chiral molecules in optical cavities JF - Appl. Phys. Rev. Y1 - 2020 U6 - https://doi.org/10.1063/5.0025006 VL - 7 SP - 041413 ER - TY - JOUR A1 - del Razo, Mauricio J. A1 - Dibak, Manuel A1 - Schütte, Christof A1 - Noé, Frank T1 - Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics JF - The Journal of Chemical Physics Y1 - 2021 U6 - https://doi.org/10.1063/5.0060314 VL - 155 IS - 12 ER - TY - JOUR A1 - Jäger, Klaus A1 - Sutter, Johannes A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Becker, Christiane T1 - Prospects of light management in perovskite/silicon tandem solar cells JF - Nanophotonics Y1 - 2021 U6 - https://doi.org/10.1515/nanoph-2020-0674 VL - 10 SP - 1991 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - On the exact solution of prize-collecting Steiner tree problems JF - INFORMS Journal on Computing Y1 - 2021 U6 - https://doi.org/10.1287/ijoc.2021.1087 ER - TY - JOUR A1 - Sunkara, Vikram A1 - Heinz, Gitta A. A1 - Heinrich, Frederik F. A1 - Durek, Pawel A1 - Mobasheri, Ali A1 - Mashreghi, Mir-Farzin A1 - Lang, Annemarie T1 - Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint JF - Osteoarthritis and Cartilage Y1 - 2021 U6 - https://doi.org/10.1016/j.joca.2021.03.007 VL - 29 IS - 6 SP - 905 EP - 914 ER - TY - JOUR A1 - Pakhomov, Anton V. A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Pertsch, Thomas A1 - Setzpfand, Frank T1 - Modeling of surface-induced second-harmonic generation from multilayer structures by the transfer matrix method JF - Opt. Express Y1 - 2021 U6 - https://doi.org/10.1364/OE.417066 VL - 29 SP - 9098 ER - TY - JOUR A1 - Binkowski, Felix A1 - Wu, Tong A1 - Lalanne, Philippe A1 - Burger, Sven A1 - Govorov, Alexander O. T1 - Hot Electron Generation through Near-Field Excitation of Plasmonic Nanoresonators JF - ACS Photonics Y1 - 2021 U6 - https://doi.org/10.1021/acsphotonics.1c00231 VL - 8 SP - 1243 ER - TY - JOUR A1 - Lindner, Niels T1 - Hypersurfaces with defect JF - Journal of Algebra N2 - A projective hypersurface X⊆P^n has defect if h^i(X) ≠ h^i(P^n) for some i∈{n,…,2n−2} in a suitable cohomology theory. This occurs for example when X⊆P^4 is not Q-factorial. We show that hypersurfaces with defect tend to be very singular: In characteristic 0, we present a lower bound on the Tjurina number, where X is allowed to have arbitrary isolated singularities. For X with mild singularities, we prove a similar result in positive characteristic. As an application, we obtain an estimate on the asymptotic density of hypersurfaces without defect over a finite field. Y1 - 2020 U6 - https://doi.org/10.1016/j.jalgebra.2020.02.022 VL - 555 SP - 1 EP - 35 ER - TY - JOUR A1 - Tack, Alexander A1 - Preim, Bernhard A1 - Zachow, Stefan T1 - Fully automated Assessment of Knee Alignment from Full-Leg X-Rays employing a "YOLOv4 And Resnet Landmark regression Algorithm" (YARLA): Data from the Osteoarthritis Initiative JF - Computer Methods and Programs in Biomedicine N2 - We present a method for the quantification of knee alignment from full-leg X-Rays. A state-of-the-art object detector, YOLOv4, was trained to locate regions of interests (ROIs) in full-leg X-Ray images for the hip joint, the knee, and the ankle. Residual neural networks (ResNets) were trained to regress landmark coordinates for each ROI.Based on the detected landmarks the knee alignment, i.e., the hip-knee-ankle (HKA) angle, was computed. The accuracy of landmark detection was evaluated by a comparison to manually placed landmarks for 360 legs in 180 X-Rays. The accuracy of HKA angle computations was assessed on the basis of 2,943 X-Rays. Results of YARLA were compared to the results of two independent image reading studies(Cooke; Duryea) both publicly accessible via the Osteoarthritis Initiative. The agreement was evaluated using Spearman's Rho, and weighted kappa as well as regarding the correspondence of the class assignment (varus/neutral/valgus). The average difference between YARLA and manually placed landmarks was less than 2.0+- 1.5 mm for all structures (hip, knee, ankle). The average mismatch between HKA angle determinations of Cooke and Duryea was 0.09 +- 0.63°; YARLA resulted in a mismatch of 0.10 +- 0.74° compared to Cooke and of 0.18 +- 0.64° compared to Duryea. Cooke and Duryea agreed almost perfectly with respect to a weighted kappa value of 0.86, and showed an excellent reliability as measured by a Spearman's Rho value of 0.99. Similar values were achieved by YARLA, i.e., a weighted kappa value of0.83 and 0.87 and a Spearman's Rho value of 0.98 and 0.99 to Cooke and Duryea,respectively. Cooke and Duryea agreed in 92% of all class assignments and YARLA did so in 90% against Cooke and 92% against Duryea. In conclusion, YARLA achieved results comparable to those of human experts and thus provides a basis for an automated assessment of knee alignment in full-leg X-Rays. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.cmpb.2021.106080 VL - 205 IS - 106080 ER - TY - JOUR A1 - Hoppmann-Baum, Kai A1 - Hennings, Felix A1 - Zittel, Janina A1 - Gotzes, Uwe A1 - Spreckelsen, Eva-Maria A1 - Spreckelsen, Klaus A1 - Koch, Thorsten T1 - An Optimization Approach for the Transient Control of Hydrogen Transport Networks JF - Mathematical Methods of Operations Research Y1 - 2021 IS - Special Issue on Energy Networks ER - TY - JOUR A1 - Hembus, Jessica A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - Bader, Rainer T1 - Establishment of a rolling-sliding test bench to analyze abrasive wear propagation of different bearing materials for knee implants JF - Applied Sciences N2 - Currently, new materials for knee implants need to be extensively and expensive tested in a knee wear simulator in a realized design. However, using a rolling-sliding test bench, these materials can be examined under the same test conditions but with simplified geometries. In the present study, the test bench was optimized, and forces were adapted to the physiological contact pressure in the knee joint using the available geometric parameters. Various polymers made of polyethylene and polyurethane articulating against test wheels made of cobalt-chromium and aluminum titanate were tested in the test bench using adapted forces based on ISO 14243-1. Polyurethane materials showed distinctly higher wear rates than polyethylene materials and showed inadequate wear resistance for use as knee implant material. Thus, the rolling-sliding test bench is an adaptable test setup for evaluating newly developed bearing materials for knee implants. It combines the advantages of screening and simulator tests and allows testing of various bearing materials under physiological load and tribological conditions of the human knee joint. The wear behavior of different material compositions and the influence of surface geometry and quality can be initially investigated without the need to produce complex implant prototypes of total knee endoprosthesis or interpositional spacers. Y1 - 2021 U6 - https://doi.org/10.3390/app11041886 VL - 11 IS - 4 ER - TY - JOUR A1 - Andrle, Anna A1 - Hönicke, Philipp A1 - Gwalt, Grzegorz A1 - Schneider, Philipp-Immanuel A1 - Kayser, Yves A1 - Siewert, Frank A1 - Soltwisch, Victor T1 - GIXRF and machine learning as metrological tools for shape and element sensitive reconstructions of periodic nanostructures JF - Proc. SPIE Y1 - 2021 U6 - https://doi.org/10.1117/12.2586082 VL - 11611 SP - 116110R ER - TY - JOUR A1 - Manley, Phillip A1 - Segantini, Michele A1 - Ahiboz, Doguscan A1 - Hammerschmidt, Martin A1 - Arnaoutakis, Georgios A1 - MacQueen, Rowan W. A1 - Burger, Sven A1 - Becker, Christiane T1 - Double-layer metasurface for enhanced photon up-conversion JF - APL Photon. Y1 - 2021 U6 - https://doi.org/10.1063/5.0040839 VL - 6 SP - 036103 ER - TY - JOUR A1 - Csizmadia, Zsolt A1 - Berthold, Timo T1 - The confined primal integral: a measure to benchmark heuristic MINLP solvers against global MINLP solvers JF - Mathematical Programming N2 - It is a challenging task to fairly compare local solvers and heuristics against each other and against global solvers. How does one weigh a faster termination time against a better quality of the found solution? In this paper, we introduce the confined primal integral, a new performance measure that rewards a balance of speed and solution quality. It emphasizes the early part of the solution process by using an exponential decay. Thereby, it avoids that the order of solvers can be inverted by choosing an arbitrarily large time limit. We provide a closed analytic formula to compute the confined primal integral a posteriori and an incremental update formula to compute it during the run of an algorithm. For the latter, we show that we can drop one of the main assumptions of the primal integral, namely the knowledge of a fixed reference solution to compare against. Furthermore, we prove that the confined primal integral is a transitive measure when comparing local solves with different final solution values. Finally, we present a computational experiment where we compare a local MINLP solver that uses certain classes of cutting planes against a solver that does not. Both versions show very different tendencies w.r.t. average running time and solution quality, and we use the confined primal integral to argue which of the two is the preferred setting. Y1 - 2020 U6 - https://doi.org/10.1007/s10107-020-01547-5 ER - TY - JOUR A1 - Gamrath, Gerald A1 - Berthold, Timo A1 - Salvagnin, Domenico T1 - An exploratory computational analysis of dual degeneracy in mixed-integer programming JF - EURO Journal on Computational Optimization N2 - Dual degeneracy, i.e., the presence of multiple optimal bases to a linear programming (LP) problem, heavily affects the solution process of mixed integer programming (MIP) solvers. Different optimal bases lead to different cuts being generated, different branching decisions being taken and different solutions being found by primal heuristics. Nevertheless, only a few methods have been published that either avoid or exploit dual degeneracy. The aim of the present paper is to conduct a thorough computational study on the presence of dual degeneracy for the instances of well-known public MIP instance collections. How many instances are affected by dual degeneracy? How degenerate are the affected models? How does branching affect degeneracy: Does it increase or decrease by fixing variables? Can we identify different types of degenerate MIPs? As a tool to answer these questions, we introduce a new measure for dual degeneracy: the variable–constraint ratio of the optimal face. It provides an estimate for the likelihood that a basic variable can be pivoted out of the basis. Furthermore, we study how the so-called cloud intervals—the projections of the optimal face of the LP relaxations onto the individual variables—evolve during tree search and the implications for reducing the set of branching candidates. Y1 - 2020 U6 - https://doi.org/10.1007/s13675-020-00130-z IS - 8 SP - 241 EP - 246 ER - TY - JOUR A1 - Liu, Yongtao A1 - Zhou, Zhiguang A1 - Wang, Fan A1 - Kewes, Günter A1 - Wen, Shihui A1 - Burger, Sven A1 - Wakiani, Majid Ebrahimi A1 - Xi, Peng A1 - Yang, Jiong A1 - Yang, Xusan A1 - Benson, Oliver A1 - Jin, Dayong T1 - Axial localization and tracking of self-interference nanoparticles by lateral point spread functions JF - Nat. Commun. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-22283-0 VL - 12 SP - 2019 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Borndörfer, Ralf A1 - Kraus, Luitgard A1 - Sedeño-Noda, Antonio T1 - An FPTAS for Dynamic Multiobjective Shortest Path Problems JF - Algorithms N2 - The Dynamic Multiobjective Shortest Path problem features multidimensional costs that can depend on several variables and not only on time; this setting is motivated by flight planning applications and the routing of electric vehicles. We give an exact algorithm for the FIFO case and derive from it an FPTAS for both, the static Multiobjective Shortest Path (MOSP) problems and, under mild assumptions, for the dynamic problem variant. The resulting FPTAS is computationally efficient and beats the known complexity bounds of other FPTAS for MOSP problems. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/a14020043 VL - 14 IS - 2 SP - 1 EP - 22 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Zimmer, Max T1 - Deep Neural Network Training with Frank-Wolfe N2 - This paper studies the empirical efficacy and benefits of using projection-free first-order methods in the form of Conditional Gradients, a.k.a. Frank-Wolfe methods, for training Neural Networks with constrained parameters. We draw comparisons both to current state-of-the-art stochastic Gradient Descent methods as well as across different variants of stochastic Conditional Gradients. In particular, we show the general feasibility of training Neural Networks whose parameters are constrained by a convex feasible region using Frank-Wolfe algorithms and compare different stochastic variants. We then show that, by choosing an appropriate region, one can achieve performance exceeding that of unconstrained stochastic Gradient Descent and matching state-of-the-art results relying on L2-regularization. Lastly, we also demonstrate that, besides impacting performance, the particular choice of constraints can have a drastic impact on the learned representations. Y1 - 2020 ER - TY - JOUR A1 - Cryille W., Combettes A1 - Spiegel, Christoph A1 - Pokutta, Sebastian T1 - Projection-Free Adaptive Gradients for Large-Scale Optimization N2 - The complexity in large-scale optimization can lie in both handling the objective function and handling the constraint set. In this respect, stochastic Frank-Wolfe algorithms occupy a unique position as they alleviate both computational burdens, by querying only approximate first-order information from the objective and by maintaining feasibility of the iterates without using projections. In this paper, we improve the quality of their first-order information by blending in adaptive gradients. We derive convergence rates and demonstrate the computational advantage of our method over the state-of-the-art stochastic Frank-Wolfe algorithms on both convex and nonconvex objectives. The experiments further show that our method can improve the performance of adaptive gradient algorithms for constrained optimization. Y1 - 2020 ER - TY - JOUR A1 - Chaumel, Júlia A1 - Schotte, Merlind A1 - Bizzarro, Joseph J. A1 - Zaslansky, Paul A1 - Fratzl, Peter A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage JF - Bone N2 - In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone. Y1 - 2020 U6 - https://doi.org/10.1016/j.bone.2020.115264 VL - 134 SP - 115264 ER - TY - JOUR A1 - Villatoro, José A1 - Zühlke, Martin A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Weber, Marcus A1 - Löhmannsröben, Hans-Gerd T1 - Sub-ambient pressure IR-MALDI ion mobility spectrometer for the determination of low and high field mobilities JF - Analytical and Bioanalytical Chemistry N2 - A new ion mobility (IM) spectrometer, enabling mobility measurements in the pressure range between 5 and 500 mbar and in the reduced field strength range E/N of 5–90 Td, was developed and characterized. Reduced mobility (K0) values were studied under low E/N (constant value) as well as high E/N (deviation from low field K0) for a series of molecular ions in nitrogen. Infrared matrix-assisted laser desorption ionization (IR-MALDI) was used in two configurations: a source working at atmospheric pressure (AP) and, for the first time, an IR-MALDI source working with a liquid (aqueous) matrix at sub-ambient/reduced pressure (RP). The influence of RP on IR-MALDI was examined and new insights into the dispersion process were gained. This enabled the optimization of the IM spectrometer for best analytical performance. While ion desolvation is less efficient at RP, the transport of ions is more efficient, leading to intensity enhancement and an increased number of oligomer ions. When deciding between AP and RP IR-MALDI, a trade-off between intensity and resolving power has to be considered. Here, the low field mobility of peptide ions was first measured and compared with reference values from ESI-IM spectrometry (at AP) as well as collision cross sections obtained from molecular dynamics simulations. The second application was the determination of the reduced mobility of various substituted ammonium ions as a function of E/N in nitrogen. The mobility is constant up to a threshold at high E/N. Beyond this threshold, mobility increases were observed. This behavior can be explained by the loss of hydrated water molecules. Y1 - 2020 U6 - https://doi.org/10.1007/s00216-020-02735-0 VL - 412 SP - 5247 EP - 5260 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Sprungk, Björn A1 - Sullivan, T. J. T1 - The linear conditional expectation in Hilbert space JF - Bernoulli Y1 - 2021 U6 - https://doi.org/10.3150/20-BEJ1308 VL - 27 IS - 4 SP - 2299 EP - 2299 ER - TY - JOUR A1 - Miron, Philippe A1 - Beron-Vera, Francisco A1 - Helfmann, Luzie A1 - Koltai, Péter T1 - Transition paths of marine debris and the stability of the garbage patches JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - We used transition path theory (TPT) to infer "reactive" pathways of floating marine debris trajectories. The TPT analysis was applied on a pollution-aware time-homogeneous Markov chain model constructed from trajectories produced by satellite-tracked undrogued buoys from the NOAA Global Drifter Program. The latter involved coping with the openness of the system in physical space, which further required an adaptation of the standard TPT setting. Directly connecting pollution sources along coastlines with garbage patches of varied strengths, the unveiled reactive pollution routes represent alternative targets for ocean cleanup efforts. Among our specific findings we highlight: constraining a highly probable pollution source for the Great Pacific Garbage Patch; characterizing the weakness of the Indian Ocean gyre as a trap for plastic waste; and unveiling a tendency of the subtropical gyres to export garbage toward the coastlines rather than to other gyres in the event of anomalously intense winds. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1063/5.0030535 VL - 31 IS - 3 ER - TY - JOUR A1 - Fischer, Sophie A1 - Ehrig, Rainald A1 - Schäfer, Stefan A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Egli, Marcel A1 - Ille, Fabian A1 - Krüger, Tillmann H. C. A1 - Leeners, Brigitte A1 - Röblitz, Susanna T1 - Mathematical Modelling and Simulation Provides Evidence for New Strategies of Ovarian Stimulation JF - Frontiers in Endocrinology N2 - New approaches to ovarian stimulation protocols, such as luteal start, random start or double stimulation, allow for flexibility in ovarian stimulation at different phases of the menstrual cycle which is especially useful when time for assisted reproductive technology is limited, e.g. for emergency fertility preservation in cancer patients. It has been proposed that the success of these methods is based on the continuous growth of multiple cohorts ("waves") of follicles throughout the menstrual cycle which leads to the availability of ovarian follicles for ovarian controlled stimulation at several time points. Though several preliminary studies have been published, their scientific evidence has not been considered as being strong enough to integrate these results into routine clinical practice. This work aims at adding further scientific evidence about the efficiency of variable-start protocols and underpinning the theory of follicular waves by using mathematical modelling and numerical simulations. For this purpose, we have modified and coupled two previously published models, one describing the time course of hormones and one describing competitive follicular growth in a normal menstrual cycle. The coupled model is used to test stimulation protocols in silico. Simulation results show the occurrence of follicles in a wave-like manner during a normal menstrual cycle and qualitatively predict the outcome of ovarian stimulation initiated at different time points of the menstrual cycle. Y1 - 2021 U6 - https://doi.org/10.3389/fendo.2021.613048 VL - 12 ER - TY - JOUR A1 - Sharma, Upanshu A1 - Zhang, Wei T1 - Non-reversible sampling schemes on submanifolds JF - SIAM Journal on Numerical Analysis N2 - Calculating averages with respect to probability measures on submanifolds is often necessary in various application areas such as molecular dynamics, computational statistical mechanics and Bayesian statistics. In recent years, various numerical schemes have been proposed in the literature to study this problem based on appropriate reversible constrained stochastic dynamics. In this paper we present and analyse a non-reversible generalisation of the projection-based scheme developed by one of the authors [ESAIM: M2AN, 54 (2020), pp. 391-430]. This scheme consists of two steps - starting from a state on the submanifold, we first update the state using a non-reversible stochastic differential equation which takes the state away from the submanifold, and in the second step we project the state back onto the manifold using the long-time limit of a ordinary differential equation. We prove the consistency of this numerical scheme and provide quantitative error estimates for estimators based on finite-time running averages. Furthermore, we present theoretical analysis which shows that this scheme outperforms its reversible counterpart in terms of asymptotic variance. We demonstrate our findings on an illustrative test example. Y1 - 2020 U6 - https://doi.org/10.1137/20M1378752 VL - 59 IS - 6 SP - 2989 EP - 3031 ER - TY - JOUR A1 - Martens, Kevin A1 - Binkowski, Felix A1 - Nguyen, Linh A1 - Hu, Li A1 - Govorov, Alexander O. A1 - Burger, Sven A1 - Liedl, Tim T1 - Long- and Short-Ranged Chiral Interactions in DNA Assembled Plasmonic Chains JF - Nat. Commun. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-22289-8 VL - 12 SP - 2025 ER - TY - JOUR A1 - Hoppmann-Baum, Kai A1 - Hennings, Felix A1 - Lenz, Ralf A1 - Gotzes, Uwe A1 - Heinecke, Nina A1 - Spreckelsen, Klaus A1 - Koch, Thorsten T1 - Optimal Operation of Transient Gas Transport Networks JF - Optimization and Engineering N2 - In this paper, we describe an algorithmic framework for the optimal operation of transient gas transport networks consisting of a hierarchical MILP formulation together with a sequential linear programming inspired post-processing routine. Its implementation is part of the KOMPASS decision support system, which is currently used in an industrial setting. Real-world gas transport networks are controlled by operating complex pipeline intersection areas, which comprise multiple compressor units, regulators, and valves. In the following, we introduce the concept of network stations to model them. Thereby, we represent the technical capabilities of a station by hand-tailored artificial arcs and add them to network. Furthermore, we choose from a predefined set of flow directions for each network station and time step, which determines where the gas enters and leaves the station. Additionally, we have to select a supported simple state, which consists of two subsets of artificial arcs: Arcs that must and arcs that cannot be used. The goal is to determine a stable control of the network satisfying all supplies and demands. The pipeline intersections, that are represented by the network stations, were initially built centuries ago. Subsequently, due to updates, changes, and extensions, they evolved into highly complex and involved topologies. To extract their basic properties and to model them using computer-readable and optimizable descriptions took several years of effort. To support the dispatchers in controlling the network, we need to compute a continuously updated list of recommended measures. Our motivation for the model presented here is to make fast decisions on important transient global control parameters, i.e., how to route the flow and where to compress the gas. Detailed continuous and discrete technical control measures realizing them, which take all hardware details into account, are determined in a subsequent step. In this paper, we present computational results from the KOMPASS project using detailed real-world data. Y1 - 2020 U6 - https://doi.org/10.1007/s11081-020-09584-x VL - 22 SP - 735 EP - 781 ER - TY - JOUR A1 - Bonnet, Luc A1 - Akian, Jean-Luc A1 - Savin, Éric A1 - Sullivan, T. J. T1 - Adaptive reconstruction of imperfectly-observed monotone functions, with applications to uncertainty quantification JF - Algorithms N2 - Motivated by the desire to numerically calculate rigorous upper and lower bounds on deviation probabilities over large classes of probability distributions, we present an adaptive algorithm for the reconstruction of increasing real-valued functions. While this problem is similar to the classical statistical problem of isotonic regression, the optimisation setting alters several characteristics of the problem and opens natural algorithmic possibilities. We present our algorithm, establish sufficient conditions for convergence of the reconstruction to the ground truth, and apply the method to synthetic test cases and a real-world example of uncertainty quantification for aerodynamic design. Y1 - 2020 U6 - https://doi.org/10.3390/a13080196 VL - 13 IS - 8 SP - 196 ER - TY - JOUR A1 - Würth, Christian A1 - Manley, Phillip A1 - Voigt, Robert A1 - Ahiboz, Doguscan A1 - Becker, Christiane A1 - Resch-Genger, Ute T1 - Metasurface enhanced sensitized photon upconversion: towards highly efficient low power upconversion applications and nano-scale E-field sensors JF - Nano Lett. Y1 - 2020 U6 - https://doi.org/10.1021/acs.nanolett.0c02548 VL - 20 SP - 6682 ER - TY - JOUR A1 - Ramin, Elham A1 - Bestuzheva, Ksenia A1 - Gargalo, Carina A1 - Ramin, Danial A1 - Schneider, Carina A1 - Ramin, Pedram A1 - Flores-Alsina, Xavier A1 - Andersen, Maj M. A1 - Gernaey, Krist V. T1 - Incremental design of water symbiosis networks with prior knowledge: The case of an industrial park in Kenya JF - Science of the Total Environment N2 - Industrial parks have a high potential for recycling and reusing resources such as water across companies by creating symbiosis networks. In this study, we introduce a mathematical optimization framework for the design of water network integration in industrial parks formulated as a large-scale standard mixed-integer non-linear programming (MINLP) problem. The novelty of our approach relies on i) developing a multi-level incremental optimization framework for water network synthesis, ii) including prior knowledge of demand growth and projected water scarcity to evaluate the significance of water-saving solutions, iii) incorporating a comprehensive formulation of water network synthesis problem including multiple pollutants and different treatment units and iv) performing a multi-objective optimization of the network including freshwater savings and relative cost of the network. The significance of the proposed optimization framework is illustrated by applying it to an existing industrial park in a water-scarce region in Kenya. Firstly, we illustrated the benefits of including prior knowledge to prevent an over-design of the network at the early stages. In the case study, we achieved a more flexible and expandable water network with 36% lower unit cost at the early stage and 15% lower unit cost at later stages for the overall maximum freshwater savings of 25%. Secondly, multi-objective analysis suggests an optimum freshwater savings of 14% to reduce the unit cost of network by half. Moreover, the significance of symbiosis networks is highlighted by showing that intra-company connections can only achieve a maximum freshwater savings of 17% with significantly higher unit cost (+45%). Finally, we showed that the values of symbiosis connectivity index in the Pareto front correspond to higher freshwater savings, indicating the significant role of the symbiosis network in the industrial park under study. This is the first study, where all the above elements have been taken into account simultaneously for the design of a water reuse network. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.scitotenv.2020.141706 VL - 751 ER - TY - JOUR A1 - Pimentel, Pedro A1 - Szengel, Angelika A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Estacio, Laura A1 - Doenitz, Christian A1 - Ramm, Heiko ED - Li, Jianning ED - Egger, Jan T1 - Automated Virtual Reconstruction of Large Skull Defects using Statistical Shape Models and Generative Adversarial Networks BT - First Challenge, AutoImplant 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 8, 2020, Proceedings JF - Towards the Automatization of Cranial Implant Design in Cranioplasty N2 - We present an automated method for extrapolating missing regions in label data of the skull in an anatomically plausible manner. The ultimate goal is to design patient-speci� c cranial implants for correcting large, arbitrarily shaped defects of the skull that can, for example, result from trauma of the head. Our approach utilizes a 3D statistical shape model (SSM) of the skull and a 2D generative adversarial network (GAN) that is trained in an unsupervised fashion from samples of healthy patients alone. By � tting the SSM to given input labels containing the skull defect, a First approximation of the healthy state of the patient is obtained. The GAN is then applied to further correct and smooth the output of the SSM in an anatomically plausible manner. Finally, the defect region is extracted using morphological operations and subtraction between the extrapolated healthy state of the patient and the defective input labels. The method is trained and evaluated based on data from the MICCAI 2020 AutoImplant challenge. It produces state-of-the art results on regularly shaped cut-outs that were present in the training and testing data of the challenge. Furthermore, due to unsupervised nature of the approach, the method generalizes well to previously unseen defects of varying shapes that were only present in the hidden test dataset. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-64327-0_3 N1 - Best Paper Award VL - 12439 SP - 16 EP - 27 PB - Springer International Publishing ET - 1 ER - TY - JOUR A1 - Soares, Ana Prates A1 - Baum, Daniel A1 - Hesse, Bernhard A1 - Kupsch, Andreas A1 - Müller, Bernd A1 - Zaslansky, Paul T1 - Scattering and phase-contrast X-ray methods reveal damage to glass fibers in endodontic posts following dental bur trimming JF - Dental Materials Y1 - 2020 U6 - https://doi.org/10.1016/j.dental.2020.10.018 VL - 37 IS - 2 SP - 201 EP - 211 ER - TY - JOUR A1 - Skrzypczak, Jan A1 - Schintke, Florian T1 - Towards Log-Less, Fine-Granular State Machine Replication JF - Datenbank Spektrum Y1 - 2020 U6 - https://doi.org/10.1007/s13222-020-00358-4 VL - 20 IS - 3 SP - 231 EP - 241 ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - The gas production of 14 species from comet 67P/Churyumov-Gerasimenko based on DFMS/COPS data from 2014-2016 JF - Monthly Notices of the Royal Astronomical Society N2 - The coma of comet 67P/Churyumov-Gerasimenko has been probed by the Rosetta spacecraft and shows a variety of different molecules. The ROSINA COmet Pressure Sensor and the Double Focusing Mass Spectrometer provide in-situ densities for many volatile compounds including the 14 gas species H2O, CO2, CO, H2S, O2, C2H6, CH3OH, H2CO, CH4, NH3, HCN, C2H5OH, OCS, and CS2. We fit the observed densities during the entire comet mission between August 2014 and September 2016 to an inverse coma model. We retrieve surface emissions on a cometary shape with 3996 triangular elements for 50 separated time intervals. For each gas we derive systematic error bounds and report the temporal evolution of the production, peak production, and the time-integrated total production. We discuss the production for the two lobes of the nucleus and for the northern and southern hemispheres. Moreover we provide a comparison of the gas production with the seasonal illumination. Y1 - 2020 U6 - https://doi.org/10.1093/mnras/staa2643 VL - 498 IS - 3 SP - 3995 EP - 4004 PB - Monthly Notices of the Royal Astronomical Society ER - TY - JOUR A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen A1 - Baum, Daniel T1 - Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography JF - bioRxiv N2 - We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. Y1 - 2020 U6 - https://doi.org/10.1101/2020.05.28.120899 ER - TY - JOUR A1 - Santiago, Xavier Garcia A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Schneider, Philipp-Immanuel T1 - Bayesian optimization with improved scalability and derivative information for efficient design of nanophotonic structures JF - J. Light. Technol. Y1 - 2021 U6 - https://doi.org/10.1109/JLT.2020.3023450 VL - 39 SP - 167 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Santiago, Xavier Garcia A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Rockstuhl, Carsten A1 - Decker, Manuel T1 - Modeling Optical Materials at the Single Scatterer Level: The Transition from Homogeneous to Heterogeneous Materials JF - Adv. Theory Simul. Y1 - 2020 U6 - https://doi.org/10.1002/adts.202000192 VL - 3 SP - 2000192 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Weber, Marcus A1 - Schütte, Christof T1 - The Augmented Jump Chain JF - Advanced Theory and Simulations N2 - Modern methods of simulating molecular systems are based on the mathematical theory of Markov operators with a focus on autonomous equilibrated systems. However, non-autonomous physical systems or non-autonomous simulation processes are becoming more and more important. A representation of non-autonomous Markov jump processes is presented as autonomous Markov chains on space-time. Augmenting the spatial information of the embedded Markov chain by the temporal information of the associated jump times, the so-called augmented jump chain is derived. The augmented jump chain inherits the sparseness of the infinitesimal generator of the original process and therefore provides a useful tool for studying time-dependent dynamics even in high dimensions. Furthermore, possible generalizations and applications to the computation of committor functions and coherent sets in the non-autonomous setting are discussed. After deriving the theoretical foundations, the concepts with a proof-of-concept Galerkin discretization of the transfer operator of the augmented jump chain applied to simple examples are illustrated. Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000274 VL - 4 IS - 4 PB - Wiley-VCH ER - TY - JOUR A1 - Stein, Lewin A1 - Straube, Florian A1 - Weinzierl, Stefan A1 - Lemke, Mathias T1 - Directional sound source modeling using the adjoint Euler equations in a finite-difference time-domain approach JF - Acoustical Society of America N2 - An adjoint-based approach for synthesizing complex sound sources by discrete, grid-based monopoles in finite-difference time-domain simulations is presented. Previously [Stein et al., 2019a, J. Acoust. Soc. Am. 146(3), 1774–1785] demonstrated that the approach allows to consider unsteady and non-uniform ambient conditions such as wind flow and thermal gradient in contrast to standard methods of numerical sound field simulation. In this work, it is proven that not only ideal monopoles but also realistic sound sources with complex directivity characteristics can be synthesized. In detail, an oscillating circular piston and a real 2-way near-field monitor are modeled. The required number of monopoles in terms of the SPL deviation between the directivity of the original and the synthesized source is analyzed. Since the computational effort is independent of the number of monopoles used for the synthesis, also more complex sources can be reproduced by increasing the number of monopoles utilized. In contrast to classical least-square problem solvers, this does not increase the computational effort, which makes the method attractive for predicting the effect of sound reinforcement systems with highly directional sources under difficult acoustic boundary conditions. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1121/10.0002425 VL - 148 IS - 5 SP - 3075 EP - 3085 PB - The Journal of the Acoustical Society of America ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Eßer, Thomas A1 - Frankenberger, Patrick A1 - Huck, Andreas A1 - Jobmann, Christoph A1 - Krostitz, Boris A1 - Kuchenbecker, Karsten A1 - Moorhagen, Kai A1 - Nagl, Philipp A1 - Peterson, Michael A1 - Reuther, Markus A1 - Schang, Thilo A1 - Schoch, Michael A1 - Schülldorf, Hanno A1 - Schütz, Peter A1 - Therolf, Tobias A1 - Waas, Kerstin A1 - Weider, Steffen T1 - Deutsche Bahn Schedules Train Rotations Using Hypergraph Optimization JF - Informs Journal on Applied Analytics N2 - Deutsche Bahn (DB) operates a large fleet of rolling stock (locomotives, wagons, and train sets) that must be combined into trains to perform rolling stock rotations. This train composition is a special characteristic of railway operations that distinguishes rolling stock rotation planning from the vehicle scheduling problems prevalent in other industries. DB models train compositions using hyperarcs. The resulting hypergraph models are ad-dressed using a novel coarse-to-fine method that implements a hierarchical column genera-tion over three levels of detail. This algorithm is the mathematical core of DB’s fleet em-ployment optimization (FEO) system for rolling stock rotation planning. FEO’s impact within DB’s planning departments has been revolutionary. DB has used it to support the company’s procurements of its newest high-speed passenger train fleet and its intermodal cargo locomotive fleet for cross-border operations. FEO is the key to successful tendering in regional transport and to construction site management in daily operations. DB’s plan-ning departments appreciate FEO’s high-quality results, ability to reoptimize (quickly), and ease of use. Both employees and customers benefit from the increased regularity of operations. DB attributes annual savings of 74 million euro, an annual reduction of 34,000 tons of CO2 emissions, and the elimination of 600 coupling operations in cross-border operations to the implementation of FEO. Y1 - 2021 U6 - https://doi.org/10.1287/inte.2020.1069 VL - 51 IS - 1 SP - 42 EP - 62 ER - TY - JOUR A1 - Anari, N. A1 - Haghtalab, N. A1 - Naor, S. A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - Structured Robust Submodular Maximization: Offline and Online Algorithms JF - INFORMS Journal on Computing Y1 - 2020 ER - TY - JOUR A1 - Laydon, Daniel J. A1 - Sunkara, Vikram A1 - Boelen, Lies A1 - Bangham, Charles R. M. A1 - Asquith, Becca T1 - The relative contributions of infectious and mitotic spread to HTLV-1 persistence JF - PLOS Computational Biology Y1 - 2020 U6 - https://doi.org/10.1371/journal.pcbi.1007470 ER - TY - JOUR A1 - Sunkara, Vikram A1 - Heinz, Gitta A. A1 - Heinrich, Frederik F. A1 - Durek, Pawel A1 - Mobasheri, Ali A1 - Mashreghi, Mir-Farzin A1 - Lang, Annemarie T1 - Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint JF - bioarxiv (Accepted in Osteoarthr. Cartil.) Y1 - 2020 U6 - https://doi.org/10.1101/2020.06.13.148056 ER - TY - JOUR A1 - Dibak, Manuel A1 - J. del Razo, Mauricio A1 - De Sancho, David A1 - Schütte, Christof A1 - Noé, Frank T1 - MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations JF - Journal of Chemical Physics N2 - Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long-timescale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large lengthscales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time- and lengthscales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step towards MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B <--> C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported. Y1 - 2018 U6 - https://doi.org/10.1063/1.5020294 VL - 148 IS - 214107 ER - TY - JOUR A1 - Manley, Phillip A1 - Song, Min A1 - Burger, Sven A1 - Schmid, Martina T1 - Efficient determination of bespoke optically active nanoparticle distributions JF - J. Opt. Y1 - 2018 U6 - https://doi.org/10.1088/2040-8986/aad114 VL - 20 SP - 085003 ER - TY - JOUR A1 - Peters-Kottig, Wolfgang T1 - Anwendung von OPUS für Forschungsdaten – das Beispiel eines außeruniversitären Forschungsinstituts JF - o-bib. Das offene Bibliotheksjournal N2 - OPUS wurde als Dokumentenserver konzipiert und ursprünglich nicht für den Nachweis von Forschungsdaten angelegt. Mit vergleichsweise geringem Aufwand können dennoch Forschungsdaten als Supplementary Material zu Zeitschriftenbeiträgen publiziert werden. Auch reine Forschungsdatenpublikationen können via OPUS veröffentlicht werden, selbst wenn die gegenwärtig auf Textpublikationen zugeschnittene Metadatenerfassung weniger gut für die Beschreibung reiner Forschungsdaten geeignet ist. Ein Unterschied zu anderen Systemen und Anwendungsszenarien besteht in der Beschränkung, großvolumige Daten nicht innerhalb von OPUS selbst vorzuhalten. Der für das institutionelle Repository des Zuse-Instituts Berlin konzipierte pragmatische Lösungsansatz ist in OPUS ohne zusätzliche Programmierung umsetzbar und skaliert für beliebig große Forschungsdatensätze. Y1 - 2018 U6 - https://doi.org/10.5282/o-bib/2018h2s79-91 VL - 5 IS - 2 SP - 79 EP - 91 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Helfmann, Luzie A1 - Zonker, Johannes A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach JF - EPJ Data Science N2 - Human mobility always had a great influence on the spreading of cultural, social and technological ideas. Developing realistic models that allow for a better understanding, prediction and control of such coupled processes has gained a lot of attention in recent years. However, the modeling of spreading processes that happened in ancient times faces the additional challenge that available knowledge and data is often limited and sparse. In this paper, we present a new agent-based model for the spreading of innovations in the ancient world that is governed by human movements. Our model considers the diffusion of innovations on a spatial network that is changing in time, as the agents are changing their positions. Additionally, we propose a novel stochastic simulation approach to produce spatio-temporal realizations of the spreading process that are instructive for studying its dynamical properties and exploring how different influences affect its speed and spatial evolution. Y1 - 2018 U6 - https://doi.org/10.1140/epjds/s13688-018-0153-9 VL - 7 IS - 1 PB - EPJ Data Science ET - EPJ Data Science ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Barner, Christoph A1 - Borndörfer, Ralf A1 - Grima, Mickaël A1 - Seeling, Mathes A1 - Spies, Claudia A1 - Wernecke, Klaus T1 - Robust Allocation of Operating Rooms: a Cutting Plane Approach to handle Lognormal Case Durations JF - European Journal of Operational Research N2 - The problem of allocating operating rooms (OR) to surgical cases is a challenging task, involving both combinatorial aspects and uncertainty handling. We formulate this problem as a parallel machines scheduling problem, in which job durations follow a lognormal distribution, and a fixed assignment of jobs to machines must be computed. We propose a cutting-plane approach to solve the robust counterpart of this optimization problem. To this end, we develop an algorithm based on fixed-point iterations that identifies worst-case scenarios and generates cut inequalities. The main result of this article uses Hilbert's projective geometry to prove the convergence of this procedure under mild conditions. We also propose two exact solution methods for a similar problem, but with a polyhedral uncertainty set, for which only approximation approaches were known. Our model can be extended to balance the load over several planning periods in a rolling horizon. We present extensive numerical experiments for instances based on real data from a major hospital in Berlin. In particular, we find that: (i) our approach performs well compared to a previous model that ignored the distribution of case durations; (ii) compared to an alternative stochastic programming approach, robust optimization yields solutions that are more robust against uncertainty, at a small price in terms of average cost; (iii) the \emph{longest expected processing time first} (LEPT) heuristic performs well and efficiently protects against extreme scenarios, but only if a good prediction model for the durations is available. Finally, we draw a number of managerial implications from these observations. Y1 - 2018 U6 - https://doi.org/10.1016/j.ejor.2018.05.022 VL - 271 IS - 2 SP - 420 EP - 435 ER - TY - JOUR A1 - Agudo Jácome, Leonardo A1 - Hege, Hans-Christian A1 - Paetsch, Olaf A1 - Pöthkow, Kai T1 - Three-dimensional reconstruction and quantification of dislocation substructures from transmission electron microscopy stereo pairs JF - Ultramicroscopy N2 - A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (>300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3% and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed. Y1 - 2018 U6 - https://doi.org/10.1016/j.ultramic.2018.08.015 VL - 195 SP - 157 EP - 170 ER - TY - JOUR A1 - Oeltze-Jaffra, Steffen A1 - Meuschke, Monique A1 - Neugebauer, Mathias A1 - Saalfeld, Sylvia A1 - Lawonn, Kai A1 - Janiga, Gabor A1 - Hege, Hans-Christian A1 - Zachow, Stefan A1 - Preim, Bernhard T1 - Generation and Visual Exploration of Medical Flow Data: Survey, Research Trends, and Future Challenges JF - Computer Graphics Forum N2 - Simulations and measurements of blood and air flow inside the human circulatory and respiratory system play an increasingly important role in personalized medicine for prevention, diagnosis, and treatment of diseases. This survey focuses on three main application areas. (1) Computational Fluid Dynamics (CFD) simulations of blood flow in cerebral aneurysms assist in predicting the outcome of this pathologic process and of therapeutic interventions. (2) CFD simulations of nasal airflow allow for investigating the effects of obstructions and deformities and provide therapy decision support. (3) 4D Phase-Contrast (4D PC) Magnetic Resonance Imaging (MRI) of aortic hemodynamics supports the diagnosis of various vascular and valve pathologies as well as their treatment. An investigation of the complex and often dynamic simulation and measurement data requires the coupling of sophisticated visualization, interaction, and data analysis techniques. In this paper, we survey the large body of work that has been conducted within this realm. We extend previous surveys by incorporating nasal airflow, addressing the joint investigation of blood flow and vessel wall properties, and providing a more fine-granular taxonomy of the existing techniques. From the survey, we extract major research trends and identify open problems and future challenges. The survey is intended for researchers interested in medical flow but also more general, in the combined visualization of physiology and anatomy, the extraction of features from flow field data and feature-based visualization, the visual comparison of different simulation results, and the interactive visual analysis of the flow field and derived characteristics. Y1 - 2019 U6 - https://doi.org/10.1111/cgf.13394 VL - 38 IS - 1 SP - 87 EP - 125 PB - Wiley ER - TY - JOUR A1 - Jin, Eugene Jennifer A1 - Kiral, Ferdi Ridvan A1 - Ozel, Mehmet Neset A1 - Burchardt, Lara Sophie A1 - Osterland, Marc A1 - Epstein, Daniel A1 - Wolfenberg, Heike A1 - Prohaska, Steffen A1 - Hiesinger, Peter Robin T1 - Live Observation of Two Parallel Membrane Degradation Pathways at Axon Terminals JF - Current Biology N2 - Neurons are highly polarized cells that require continuous turnover of membrane proteins at axon terminals to develop, function, and survive. Yet, it is still unclear whether membrane protein degradation requires transport back to the cell body or whether degradation also occurs locally at the axon terminal, where live observation of sorting and degradation has remained a challenge. Here, we report direct observation of two cargo-specific membrane protein degradation mechanisms at axon terminals based on a live-imaging approach in intact Drosophila brains. We show that different acidification-sensing cargo probes are sorted into distinct classes of degradative ‘‘hub’’ compartments for synaptic vesicle proteins and plasma membrane proteins at axon terminals. Sorting and degradation of the two cargoes in the separate hubs are molecularly distinct. Local sorting of synaptic vesicle proteins for degradation at the axon terminal is, surprisingly, Rab7 independent, whereas sorting of plasma membrane proteins is Rab7 dependent. The cathepsin-like protease CP1 is specific to synaptic vesicle hubs, and its delivery requires the vesicle SNARE neuronal synaptobrevin. Cargo separation only occurs at the axon terminal, whereas degradative compartments at the cell body are mixed. These data show that at least two local, molecularly distinct pathways sort membrane cargo for degradation specifically at the axon terminal, whereas degradation can occur both at the terminal and en route to the cell body. Y1 - 2018 U6 - https://doi.org/10.1016/j.cub.2018.02.032 VL - 28 IS - 7 SP - 1027 EP - 1038.e4 ER - TY - JOUR A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - Matsuyama, Kei A1 - Boos, Karin A1 - Färber, Claudia A1 - Kahl, Wolf-Achim A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Soriano, Carmen A1 - Stock, Stuart R. T1 - Ambient occlusion – a powerful algorithm to segment shell and skeletal intrapores in computed tomography data JF - Computers and Geosciences N2 - During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). The segmentation accuracy is evaluated as a function of (i) changes in the ray length input variable, and (ii) the usage of AO (scalar) field and other AO-derived (scalar) fields. The results clearly indicate that the AO field itself outperforms all other AO-derived fields in terms of segmentation accuracy and robustness against variations in the ray length input variable. The newly implemented optimisations improved the AO field-based segmentation only slightly, while the segmentations based on the AO-derived fields improved considerably. Additionally, we evaluated the potential of the AO field and AO-derived fields for the separation and classification of cavities as well as skeletal structures by comparing them with commonly used distance-map-based segmentations. For this, we tested the zooid separation within a bryozoan colony, the stereom classification of an ophiuroid tooth, the separation of bioerosion traces within a marble block and the calice (central cavity)-pore separation within a dendrophyllid coral. The obtained results clearly indicate that the ideal input field depends on the three-dimensional morphology of the object of interest. The segmentations based on the AO-derived fields often provided cavity separations and skeleton classifications that were superior to or impossible to obtain with commonly used distance- map-based segmentations. The combined usage of various AO-derived fields by supervised or unsupervised segmentation algorithms might provide a promising target for future research to further improve the results for this kind of high-end data segmentation and classification. Furthermore, the application of the developed segmentation algorithm is not restricted to X-ray (micro-)computed tomographic data but may potentially be useful for the segmentation of 3D volume data from other sources. Y1 - 2018 U6 - https://doi.org/10.1016/j.cageo.2018.03.007 VL - 115 SP - 75 EP - 87 ER - TY - JOUR A1 - Munguia, Lluis-Miquel A1 - Oxberry, Geoffrey A1 - Rajan, Deepak A1 - Shinano, Yuji T1 - Parallel PIPS-SBB: Multi-Level Parallelism For Stochastic Mixed-Integer Programs JF - Computational Optimization and Applications N2 - PIPS-SBB is a distributed-memory parallel solver with a scalable data distribution paradigm. It is designed to solve MIPs with a dual-block angular structure, which is characteristic of deterministic-equivalent Stochastic Mixed-Integer Programs (SMIPs). In this paper, we present two different parallelizations of Branch & Bound (B&B), implementing both as extensions of PIPS-SBB, thus adding an additional layer of parallelism. In the first of the proposed frameworks, PIPS-PSBB, the coordination and load-balancing of the different optimization workers is done in a decentralized fashion. This new framework is designed to ensure all available cores are processing the most promising parts of the B&B tree. The second, ug[PIPS-SBB,MPI], is a parallel implementation using the Ubiquity Generator (UG), a universal framework for parallelizing B&B tree search that has been successfully applied to other MIP solvers. We show the effects of leveraging multiple levels of parallelism in potentially improving scaling performance beyond thousands of cores. Y1 - 2019 U6 - https://doi.org/10.1007/s10589-019-00074-0 ER - TY - JOUR A1 - Chrapary, Hagen A1 - Dalitz, Wolfgang A1 - Neun, Winfried A1 - Sperber, Wolfram T1 - Design, Concepts, and State of the Art of the swMATH Service JF - Mathematics in Computer Science N2 - In this paper, the concepts and design for an efficient information service for mathematical software and further mathematical research data are presented. The publication-based approach and the web-based approach are the main building blocks of the service and will be discussed. Heuristic methods are used for identification, extraction, and ranking of information about software and other mathematical research data. The methods provide not only information about the research data but also link software and mathematical research data to the scientific context. Y1 - 2017 U6 - https://doi.org/10.1007/s11786-017-0305-5 VL - 11 IS - 3-4 SP - 469 EP - 481 ER - TY - JOUR A1 - Achterberg, Tobias A1 - Bixby, Robert E. A1 - Gu, Zonghao A1 - Rothberg, Edward A1 - Weninger, Dieter T1 - Presolve Reductions in Mixed Integer Programming JF - INFORMS Journal on Computing N2 - Mixed integer programming has become a very powerful tool for modeling and solving real-world planning and scheduling problems, with the breadth of applications appearing to be almost unlimited. A critical component in the solution of these mixed-integer programs is a set of routines commonly referred to as presolve. Presolve can be viewed as a collection of preprocessing techniques that reduce the size of and, more importantly, improve the ``strength'' of the given model formulation, that is, the degree to which the constraints of the formulation accurately describe the underlying polyhedron of integer-feasible solutions. As our computational results will show, presolve is a key factor in the speed with which we can solve mixed-integer programs, and is often the difference between a model being intractable and solvable, in some cases easily solvable. In this paper we describe the presolve functionality in the Gurobi commercial mixed-integer programming code. This includes an overview, or taxonomy of the different methods that are employed, as well as more-detailed descriptions of several of the techniques, with some of them appearing, to our knowledge, for the first time in the literature. Y1 - 2019 ER - TY - JOUR A1 - Rettig, Anika A1 - Haase, Tobias A1 - Pletnyov, Alexandr A1 - Kohl, Benjamin A1 - Ertel, Wolfgang A1 - von Kleist, Max A1 - Sunkara, Vikram T1 - SLCV – A Supervised Learning - Computer Vision combined strategy for automated muscle fibre detection in cross sectional images JF - PeerJ N2 - Muscle fibre cross sectional area (CSA) is an important biomedical measure used to determine the structural composition of skeletal muscle, and it is relevant for tackling research questions in many different fields of research. To date, time consuming and tedious manual delineation of muscle fibres is often used to determine the CSA. Few methods are able to automatically detect muscle fibres in muscle fibre cross sections to quantify CSA due to challenges posed by variation of bright- ness and noise in the staining images. In this paper, we introduce SLCV, a robust semi-automatic pipeline for muscle fibre detection, which combines supervised learning (SL) with computer vision (CV). SLCV is adaptable to different staining methods and is quickly and intuitively tunable by the user. We are the first to perform an error analysis with respect to cell count and area, based on which we compare SLCV to the best purely CV-based pipeline in order to identify the contribution of SL and CV steps to muscle fibre detection. Our results obtained on 27 fluorescence-stained cross sectional images of varying staining quality suggest that combining SL and CV performs signifi- cantly better than both SL based and CV based methods with regards to both the cell separation- and the area reconstruction error. Furthermore, applying SLCV to our test set images yielded fibre detection results of very high quality, with average sensitivity values of 0.93 or higher on different cluster sizes and an average Dice Similarity Coefficient (DSC) of 0.9778. T3 - ZIB-Report - 19-10 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72639 PB - PeerJ CY - PeerJ ER - TY - JOUR A1 - Berthold, Timo A1 - Farmer, James A1 - Heinz, Stefan A1 - Perregaard, Michael T1 - Parallelization of the FICO Xpress Optimizer JF - Optimization Methods and Software N2 - Computing hardware has mostly thrashed out the physical limits for speeding up individual computing cores. Consequently, the main line of progress for new hardware is growing the number of computing cores within a single CPU. This makes the study of efficient parallelization schemes for computation-intensive algorithms more and more important. A natural precondition to achieving reasonable speedups from parallelization is maintaining a high workload of the available computational resources. At the same time, reproducibility and reliability are key requirements for software that is used in industrial applications. In this paper, we present the new parallelization concept for the state-of-the-art MIP solver FICO Xpress-Optimizer. MIP solvers like Xpress are expected to be deterministic. This inevitably results in synchronization latencies which render the goal of a satisfying workload a challenge in itself. We address this challenge by following a partial information approach and separating the concepts of simultaneous tasks and independent threads from each other. Our computational results indicate that this leads to a much higher CPU workload and thereby to an improved, almost linear, scaling on modern high-performance CPUs. As an added value, the solution path that Xpress takes is not only deterministic in a fixed environment, but also, to a certain extent, thread-independent. This paper is an extended version of Berthold et al. [Parallelization of the FICO Xpress-Optimizer, in Mathematical Software – ICMS 2016: 5th International Conference, G.-M. Greuel, T. Koch, P. Paule, and A. Sommere, eds., Springer International Publishing, Berlin, 2016, pp. 251–258] containing more detailed technical descriptions, illustrative examples and updated computational results. Y1 - 2018 U6 - https://doi.org/10.1080/10556788.2017.1333612 VL - 33 IS - 3 SP - 518 EP - 529 ER - TY - JOUR A1 - Sullivan, T. J. T1 - Contributed discussion on the article "A Bayesian conjugate gradient method" JF - Bayesian Analysis N2 - The recent article "A Bayesian conjugate gradient method" by Cockayne, Oates, Ipsen, and Girolami proposes an approximately Bayesian iterative procedure for the solution of a system of linear equations, based on the conjugate gradient method, that gives a sequence of Gaussian/normal estimates for the exact solution. The purpose of the probabilistic enrichment is that the covariance structure is intended to provide a posterior measure of uncertainty or confidence in the solution mean. This note gives some comments on the article, poses some questions, and suggests directions for further research. Y1 - 2019 U6 - https://doi.org/10.1214/19-BA1145 VL - 14 IS - 3 SP - 985 EP - 989 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Using Gaussian process regression for efficient parameter reconstruction JF - Proc. SPIE Y1 - 2019 U6 - https://doi.org/10.1117/12.2513268 VL - 10959 SP - 1095911 ER - TY - JOUR A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - An auxiliary field approach for computing optical resonances in dispersive media JF - J. Eur. Opt. Soc.-Rapid Y1 - 2019 U6 - https://doi.org/10.1186/s41476-019-0098-z VL - 15 SP - 3 ER - TY - JOUR A1 - Graf, Florian A1 - Feis, Joshua A1 - Santiago, Xavier Garcia A1 - Wegener, Martin A1 - Rockstuhl, Carsten A1 - Fernandez-Corbaton, Ivan T1 - Achiral, Helicity Preserving, and Resonant Structures for Enhanced Sensing of Chiral Molecules JF - ACS Photonics Y1 - 2019 U6 - https://doi.org/10.1021/acsphotonics.8b01454 VL - 6 SP - 482 ER - TY - JOUR A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - 3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent JF - Journal of Biomedical Optics N2 - Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori. Y1 - 2019 U6 - https://doi.org/10.1117/1.JBO.24.6.066001 VL - 24 IS - 6 SP - 066001 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Djurdjevac Conrad, Natasa A1 - Djurdjevac, Ana A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - From interacting agents to density-based modeling with stochastic PDEs JF - Communications in Applied Mathematics and Computational Science N2 - Many real-world processes can naturally be modeled as systems of interacting agents. However, the long-term simulation of such agent-based models is often intractable when the system becomes too large. In this paper, starting from a stochastic spatio-temporal agent-based model (ABM), we present a reduced model in terms of stochastic PDEs that describes the evolution of agent number densities for large populations. We discuss the algorithmic details of both approaches; regarding the SPDE model, we apply Finite Element discretization in space which not only ensures efficient simulation but also serves as a regularization of the SPDE. Illustrative examples for the spreading of an innovation among agents are given and used for comparing ABM and SPDE models. Y1 - 2021 U6 - https://doi.org/10.2140/camcos.2021.16.1 VL - 16 IS - 1 SP - 1 EP - 32 ER - TY - JOUR A1 - Thiel, Denise A1 - Djurdjevac Conrad, Natasa A1 - Ntini, Evgenia A1 - Peschutter, Ria A1 - Siebert, Heike A1 - Marsico, Annalisa T1 - Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis JF - BMC Bioinformatics N2 - Background: Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromatin interactions in transcriptional regulation. Although network-based methods, mainly exploiting gene-lncRNA co-expression, have been applied to characterize lncRNA of unknown function by means of ’guilt-by-association’, no strategy exists so far which identifies mRNA-lncRNA functional modules based on the 3D chromatin interaction graph. Results: To better understand the function of chromatin interactions in the context of lncRNA-mediated gene regulation, we have developed a multi-step graph analysis approach to examine the RNA polymerase II ChIA-PET chromatin interaction network in the K562 human cell line. We have annotated the network with gene and lncRNA coordinates, and chromatin states from the ENCODE project. We used centrality measures, as well as an adaptation of our previously developed Markov State Models (MSM) clustering method, to gain a better understanding of lncRNAs in transcriptional regulation. The novelty of our approach resides in the detection of fuzzy regulatory modules based on network properties and their optimization based on co-expression analysis between genes and gene-lncRNA pairs. This results in our method returning more bona fide regulatory modules than other state-of-the art approaches for clustering on graphs. Conclusions: Interestingly, we find that lncRNA network hubs tend to be significantly enriched in evolutionary conserved lncRNAs and enhancer-like functions. We validated regulatory functions for well known lncRNAs, such as MALAT1 and the enhancer-like lncRNA FALEC. In addition, by investigating the modular structure of bigger components we mine putative regulatory functions for uncharacterized lncRNAs. Y1 - 2019 U6 - https://doi.org/10.1186/s12859-019-2900-8 VL - 20 IS - 1471-2105 ER - TY - JOUR A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Hammerschmidt, Martin A1 - Burger, Sven T1 - Modal analysis for nanoplasmonics with nonlocal material properties JF - Phys. Rev. B Y1 - 2019 U6 - https://doi.org/10.1103/PhysRevB.100.155406 VL - 100 SP - 155406 ER - TY - JOUR A1 - Andrle, Anna A1 - Hönicke, Philipp A1 - Schneider, Philipp-Immanuel A1 - Kayser, Yves A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Scholze, Frank A1 - Beckhoff, Burkhard A1 - Soltwisch, Victor T1 - Grazing incidence x-ray fluorescence based characterization of nanostructures for element sensitive profile reconstruction JF - Proc. SPIE Y1 - 2019 U6 - https://doi.org/10.1117/12.2526082 VL - 11057 SP - 110570M ER - TY - JOUR A1 - Farchmin, Nando A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Wurm, Matthias A1 - Bär, Markus A1 - Heidenreich, Sebastian T1 - Efficient global sensitivity analysis for silicon line gratings using polynomial chaos JF - Proc. SPIE Y1 - 2019 U6 - https://doi.org/10.1117/12.2525978 VL - 11057 SP - 110570J ER - TY - JOUR A1 - Hendel, Gregor T1 - Adaptive Large Neighborhood Search for Mixed Integer Programming JF - Mathematical Programming Computation N2 - Large Neighborhood Search (LNS) heuristics are among the most powerful but also most expensive heuristics for mixed integer programs (MIP). Ideally, a solver learns adaptively which LNS heuristics work best for the MIP problem at hand in order to concentrate its limited computational budget. To this end, this work introduces Adaptive Large Neighborhood Search (ALNS) for MIP, a primal heuristic that acts a framework for eight popular LNS heuristics such as Local Branching and Relaxation Induced Neighborhood Search (RINS). We distinguish the available LNS heuristics by their individual search domains, which we call neighborhoods. The decision which neighborhood should be executed is guided by selection strategies for the multi armed bandit problem, a related optimization problem during which suitable actions have to be chosen to maximize a reward function. In this paper, we propose an LNS-specific reward function to learn to distinguish between the available neighborhoods based on successful calls and failures. A second, algorithmic enhancement is a generic variable fixing priorization, which ALNS employs to adjust the subproblem complexity as needed. This is particularly useful for some neighborhoods which do not fix variables by themselves. The proposed primal heuristic has been implemented within the MIP solver SCIP. An extensive computational study is conducted to compare different LNS strategies within our ALNS framework on a large set of publicly available MIP instances from the MIPLIB and Coral benchmark sets. The results of this simulation are used to calibrate the parameters of the bandit selection strategies. A second computational experiment shows the computational benefits of the proposed ALNS framework within the MIP solver SCIP. Y1 - 2018 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Bruening, Jan Joris A1 - Schmidt, Nora Laura A1 - Lamecker, Hans A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Goubergrits, Leonid T1 - The Healthy Nasal Cavity - Characteristics of Morphology and Related Airflow Based on a Statistical Shape Model Viewed from a Surgeon’s Perspective JF - Facial Plastic Surgery N2 - Functional surgery on the nasal framework requires referential criteria to objectively assess nasal breathing for indication and follow-up. Thismotivated us to generate amean geometry of the nasal cavity based on a statistical shape model. In this study, the authors could demonstrate that the introduced nasal cavity’s mean geometry features characteristics of the inner shape and airflow, which are commonly observed in symptom-free subjects. Therefore, the mean geometry might serve as a reference-like model when one considers qualitative aspects. However, to facilitate quantitative considerations and statistical inference, further research is necessary. Additionally, the authorswere able to obtain details about the importance of the isthmus nasi and the inferior turbinate for the intranasal airstream. KW - statistical shape model KW - nasal cavity KW - nasal breathing KW - nasal airflow KW - isthmus nasi KW - inferior turbinate Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1677721 VL - 35 IS - 1 SP - 9 EP - 13 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Bruening, Jan Joris A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Heppt, Werner A1 - Schmidt, Nora A1 - Goubergrits, Leonid T1 - Digital Analysis of Nasal Airflow Facilitating Decision Support in Rhinosurgery JF - Facial Plastic Surgery N2 - Successful functional surgery on the nasal framework requires reliable and comprehensive diagnosis. In this regard, the authors introduce a new methodology: Digital Analysis of Nasal Airflow (diANA). It is based on computational fluid dynamics, a statistical shape model of the healthy nasal cavity and rhinologic expertise. diANA necessitates an anonymized tomographic dataset of the paranasal sinuses including the complete nasal cavity and, when available, clinical information. The principle of diANA is to compare the morphology and the respective airflow of an individual nose with those of a reference. This enablesmorphometric aberrations and consecutive flow field anomalies to localize and quantify within a patient’s nasal cavity. Finally, an elaborated expert opinion with instructive visualizations is provided. Using diANA might support surgeons in decision-making, avoiding unnecessary surgery, gaining more precision, and target-orientation for indicated operations. KW - nasal airflow simulation KW - nasal breathing KW - statistical shape model KW - diANA KW - nasal obstruction KW - rhinorespiratory homeostasis Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1677720 VL - 35 IS - 1 SP - 1 EP - 8 ER - TY - JOUR A1 - Hettich, G. A1 - Schierjott, R. A. A1 - Schilling, C. A1 - Maas, A. A1 - Ramm, Heiko A1 - Bindernagel, Matthias A1 - Lamecker, Hans A1 - Grupp, T. M. T1 - Validation of a Statistical Shape Model for Acetabular Bone Defect Analysis JF - ISTA 2018 London Abstract Book N2 - Acetabular bone defects are still challenging to quantify. Numerous classification schemes have been proposed to categorize the diverse kinds of defects. However, these classification schemes are mainly descriptive and hence it remains difficult to apply them in pre-clinical testing, implant development and pre-operative planning. By reconstructing the native situation of a defect pelvis using a Statistical Shape Model (SSM), a more quantitative analysis of the bone defects could be performed. The aim of this study is to develop such a SSM and to validate its accuracy using relevant clinical scenarios and parameters. Y1 - 2018 ER - TY - JOUR A1 - Delle Site, Luigi A1 - Krekeler, Christian A1 - Whittaker, John A1 - Agarwal, Animesh A1 - Klein, Rupert A1 - Höfling, Felix T1 - Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir JF - Advanced Theory and Simulations N2 - The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed. Y1 - 2019 U6 - https://doi.org/10.1002/adts.201900014 VL - 2 SP - 1900014 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Pauwels, Edouard T1 - An unexpected connection between Bayes A-optimal designs and the group lasso JF - Statistical Papers N2 - We show that the A-optimal design optimization problem over m design points in R^n is equivalent to minimizing a quadratic function plus a group lasso sparsity inducing term over n x m real matrices. This observation allows to describe several new algorithms for A-optimal design based on splitting and block coordinate decomposition. These techniques are well known and proved powerful to treat large scale problems in machine learning and signal processing communities. The proposed algorithms come with rigorous convergence guarantees and convergence rate estimate stemming from the optimization literature. Performances are illustrated on synthetic benchmarks and compared to existing methods for solving the optimal design problem. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73059 VL - 60 IS - 2 SP - 215 EP - 234 ER - TY - JOUR A1 - Becker, Christiane A1 - Burger, Sven A1 - Jäger, Klaus T1 - Nanooptische Simulationen für optoelektronische Anwendungen JF - Photonik: Fachzeitschrift für die optischen Technologien Y1 - 2019 SN - 1432-9778 VL - 2019 IS - 2 SP - 42 EP - 45 ER - TY - JOUR A1 - Kewes, Günter A1 - Binkowski, Felix A1 - Burger, Sven A1 - Zschiedrich, Lin A1 - Benson, Oliver T1 - Heuristic Modeling of Strong Coupling in Plasmonic Resonators JF - ACS Photonics Y1 - 2018 U6 - https://doi.org/10.1021/acsphotonics.8b00766 VL - 5 SP - 4089 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Santiago, Xavier Garcia A1 - Soltwisch, Victor A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Rockstuhl, Carsten T1 - Benchmarking five global optimization approaches for nano-optical shape optimization and parameter reconstruction JF - ACS Photonics Y1 - 2019 U6 - https://doi.org/10.1021/acsphotonics.9b00706 VL - 6 SP - 2726 ER - TY - JOUR A1 - Sunkara, Vikram T1 - Algebraic Expressions of Conditional Expectations in Gene Regulatory Networks JF - Journal of Mathematical Biology N2 - Gene Regulatory Networks are powerful models for describing the mechanisms and dynamics inside a cell. These networks are generally large in dimension and seldom yield analytical formulations. It was shown that studying the conditional expectations between dimensions (vertices or species) of a network could lead to drastic dimension reduction. These conditional expectations were classically given by solving equations of motions derived from the Chemical Master Equation. In this paper we deviate from this convention and take an Algebraic approach instead. That is, we explore the consequences of conditional expectations being described by a polynomial function. There are two main results in this work. Firstly: if the conditional expectation can be described by a polynomial function, then coefficients of this polynomial function can be reconstructed using the classical moments. And secondly: there are dimensions in Gene Regulatory Networks which inherently have conditional expectations with algebraic forms. We demonstrate through examples, that the theory derived in this work can be used to develop new and effective numerical schemes for forward simulation and parameter inference. The algebraic line of investigation of conditional expectations has considerable scope to be applied to many different aspects of Gene Regulatory Networks; this paper serves as a preliminary commentary in this direction. T3 - ZIB-Report - 18-52 KW - Markov Chains KW - Chemical Master Equations KW - Dimension Reduction Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70526 SN - 1438-0064 IS - 79 SP - 1779 EP - 1829 PB - Journal of Mathematical Biology ER - TY - JOUR A1 - Reidelbach, Marco A1 - Weber, Marcus A1 - Imhof, Petra T1 - Prediction of perturbed proton transfer networks JF - PLoS ONE N2 - The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain conformations in a transition network calculation provide an efficient, bias-free description. In principle, a new transition network calculation is required for every unsampled change in the system of interest, e.g. an unsampled protonation state change, which is associated with significant computational costs. Transition networks void of or including an unsampled change are termed unperturbed or perturbed, respectively. Here, we present a prediction method, which is based on an extensive coarse-graining of the underlying transition networks to speed up the calculations. It uses the minimum spanning tree and a corresponding sensitivity analysis of an unperturbed transition network as initial guess and refinement parameter for the determination of an unknown, perturbed transition network. Thereby, the minimum spanning tree defines a sub-network connecting all nodes without cycles and minimal edge weight sum, while the sensitivity analysis analyzes the stability of the minimum spanning tree towards individual edge weight reductions. Using the prediction method, we are able to reduce the calculation costs in a model system by up to 80%, while important network properties are maintained in most predictions. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1371/journal.pone.0207718 VL - 13 IS - 12 SP - e0207718 EP - e0207718 ER - TY - JOUR A1 - Villatoro, José A1 - Weber, Marcus A1 - Zühlke, Martin A1 - Lehmann, Andreas A1 - Zechiowski, Karl A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Löhmannsröben, Hans-Gerd A1 - Kreuzer, Oliver T1 - Structural characterization of synthetic peptides using electronspray ion mobility spectrometry and molecular dynamics simulations JF - International Journal of Mass Spectrometry N2 - Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540–3310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF). Y1 - 2019 U6 - https://doi.org/10.1016/j.ijms.2018.10.036 VL - 436 SP - 108 EP - 117 ER - TY - JOUR A1 - Weiser, Martin A1 - Freytag, Yvonne A1 - Erdmann, Bodo A1 - Hubig, Michael A1 - Mall, Gita T1 - Optimal Design of Experiments for Estimating the Time of Death in Forensic Medicine JF - Inverse Problems N2 - Estimation of time of death based on a single measurement of body core temperature is a standard procedure in forensic medicine. Mechanistic models using simulation of heat transport promise higher accuracy than established phenomenological models in particular in nonstandard situations, but involve many not exactly known physical parameters. Identifying both time of death and physical parameters from multiple temperature measurements is one possibility to reduce the uncertainty significantly. In this paper, we consider the inverse problem in a Bayesian setting and perform both local and sampling-based uncertainty quantification, where proper orthogonal decomposition is used as model reduction for fast solution of the forward model. Based on the local uncertainty quantification, optimal design of experiments is performed in order to minimize the uncertainty in the time of death estimate for a given number of measurements. For reasons of practicability, temperature acquisition points are selected from a set of candidates in different spatial and temporal locations. Applied to a real corpse model, a significant accuracy improvement is obtained already with a small number of measurements. Y1 - 2018 U6 - https://doi.org/10.1088/1361-6420/aae7a5 VL - 34 IS - 12 SP - 125005 ER - TY - JOUR A1 - Spötter, Andreas A1 - Gupta, Pooja A1 - Nürnberg, A1 - Reinsch, Norbert A1 - Bienefeld, Kaspar T1 - Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica) N2 - Honey bees are exposed to a number of damaging pathogens and parasites. The most destructive among them, affecting mainly the brood, is Varroa destructor. A promising approach to prevent its spread is to breed for Varroa‐tolerant honey bees. A trait that has been shown to provide significant resistance against the Varroa mite is hygienic behaviour, a behavioural response of honey bee workers to brood diseases in general. This study reports the development of a 44K SNP assay, specifically designed for the analysis of hygienic behaviour of individual worker bees (Apis mellifera carnica) directed against V. destructor. Initially, 70 000 SNPs chosen from a large set of SNPs published by the Honey Bee Genome Project were validated for their suitability in the analysis of the Varroa resistance trait ‘uncapping of Varroa‐infested brood’. This was achieved by genotyping of pooled DNA samples of trait bearers and two trait‐negative controls using next‐generation sequencing. Approximately 36 000 of these validated SNPs and another 8000 SNPs not validated in this study were selected for the construction of a SNP assay. This assay will be employed in following experiments to analyse individualized DNA samples in order to identify quantitative trait loci (QTL) involved in the control of the investigated trait and to evaluate and possibly confirm QTL found in other studies. However, this assay is not just suitable to study Varroa tolerance, it is as well applicable to analyse any other trait in honey bees. In addition, because of its high density, this assay provides access into genomic selection with respect to several traits considered in honey bee breeding. It will become publicly available via AROS Applied Biotechnology AS, Aarhus, Denmark, before the end of the year 2011. Y1 - 2012 U6 - https://doi.org/10.1111/j.1755-0998.2011.03106.x VL - 12 IS - 2 SP - 323 EP - 332 ER - TY - JOUR A1 - Srocka, Nicole A1 - Musiał, Anna A1 - Schneider, Philipp-Immanuel A1 - Mrowiński, Paweł A1 - Holewa, Paweł A1 - Burger, Sven A1 - Quandt, David A1 - Strittmatter, André A1 - Rodt, Sven A1 - Reitzenstein, Stephan A1 - Sęk, Grzegorz T1 - Enhanced photon-extraction efficiency from InGaAs/GaAs quantum dots in deterministic photonic structures at 1.3 μm fabricated by in-situ electron-beam lithography JF - AIP Adv. Y1 - 2018 U6 - https://doi.org/10.1063/1.5038137 VL - 8 SP - 085205 ER - TY - JOUR A1 - Nava-Yazdani, Esfandiar A1 - Polthier, Konrad T1 - De Casteljau's Algotithm on Manifolds JF - Computer Aided Geometric Design N2 - This paper proposes a generalization of the ordinary de Casteljau algorithm to manifold-valued data including an important special case which uses the exponential map of a symmetric space or Riemannian manifold. We investigate some basic properties of the corresponding Bézier curves and present applications to curve design on polyhedra and implicit surfaces as well as motion of rigid body and positive definite matrices. Moreover, we apply our approach to construct canal and developable surfaces. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69096 VL - 30 IS - 7 SP - 722 EP - 732 PB - CAGD ER - TY - JOUR A1 - Seblany, Feda A1 - Homberg, Ulrike A1 - Vincens, Eric A1 - Winkler, Paul A1 - Witt, Karl Josef T1 - Merging criteria for defining pores and constrictions in numerical packing of spheres JF - Granular Matter N2 - The void space of granular materials is generally divided into larger local volumes denoted as pores and throats connecting pores. The smallest section in a throat is usually denoted as constriction. A correct description of pores and constrictions may help to understand the processes related to the transport of fluid or fine particles through granular materials, or to build models of imbibition for unsaturated granular media. In the case of numerical granular materials involving packings of spheres, different methods can be used to compute the pore space properties. However, these methods generally induce an over-segmentation of the pore network and a merging step is usually applied to mitigate such undesirable artifacts even if a precise delineation of a pore is somewhat subjective. This study provides a comparison between different merging criteria for pores in packing of spheres and a discussion about their implication on both the pore size distribution and the constriction size distribution of the material. A correspondence between these merging techniques is eventually proposed as a guide for the user. Y1 - 2018 U6 - https://doi.org/10.1007/s10035-018-0808-z SN - 1434-5021 SN - 1434-7636 VL - 20 IS - 37 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Al Hajj, Hassan A1 - Sahu, Manish A1 - Lamard, Mathieu A1 - Conze, Pierre-Henri A1 - Roychowdhury, Soumali A1 - Hu, Xiaowei A1 - Marsalkaite, Gabija A1 - Zisimopoulos, Odysseas A1 - Dedmari, Muneer Ahmad A1 - Zhao, Fenqiang A1 - Prellberg, Jonas A1 - Galdran, Adrian A1 - Araujo, Teresa A1 - Vo, Duc My A1 - Panda, Chandan A1 - Dahiya, Navdeep A1 - Kondo, Satoshi A1 - Bian, Zhengbing A1 - Bialopetravicius, Jonas A1 - Qiu, Chenghui A1 - Dill, Sabrina A1 - Mukhopadyay, Anirban A1 - Costa, Pedro A1 - Aresta, Guilherme A1 - Ramamurthy, Senthil A1 - Lee, Sang-Woong A1 - Campilho, Aurelio A1 - Zachow, Stefan A1 - Xia, Shunren A1 - Conjeti, Sailesh A1 - Armaitis, Jogundas A1 - Heng, Pheng-Ann A1 - Vahdat, Arash A1 - Cochener, Beatrice A1 - Quellec, Gwenole T1 - CATARACTS: Challenge on Automatic Tool Annotation for cataRACT Surgery JF - Medical Image Analysis N2 - Surgical tool detection is attracting increasing attention from the medical image analysis community. The goal generally is not to precisely locate tools in images, but rather to indicate which tools are being used by the surgeon at each instant. The main motivation for annotating tool usage is to design efficient solutions for surgical workflow analysis, with potential applications in report generation, surgical training and even real-time decision support. Most existing tool annotation algorithms focus on laparoscopic surgeries. However, with 19 million interventions per year, the most common surgical procedure in the world is cataract surgery. The CATARACTS challenge was organized in 2017 to evaluate tool annotation algorithms in the specific context of cataract surgery. It relies on more than nine hours of videos, from 50 cataract surgeries, in which the presence of 21 surgical tools was manually annotated by two experts. With 14 participating teams, this challenge can be considered a success. As might be expected, the submitted solutions are based on deep learning. This paper thoroughly evaluates these solutions: in particular, the quality of their annotations are compared to that of human interpretations. Next, lessons learnt from the differential analysis of these solutions are discussed. We expect that they will guide the design of efficient surgery monitoring tools in the near future. Y1 - 2019 U6 - https://doi.org/10.1016/j.media.2018.11.008 N1 - Best paper award - Computer Graphics Night 2020 (TU Darmstadt) VL - 52 IS - 2 SP - 24 EP - 41 PB - Elsevier ER - TY - JOUR A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - A Riesz-projection-based method for nonlinear eigenvalue problems JF - J. Comput. Phys. Y1 - 2020 U6 - https://doi.org/10.1016/j.jcp.2020.109678 VL - 419 SP - 109678 ER - TY - JOUR A1 - Lalanne, P. A1 - Yan, W. A1 - Gras, A. A1 - Sauvan, C. A1 - Hugonin, J.-P. A1 - Besbes, M. A1 - Demésy, G. A1 - Truong, M. D. A1 - Gralak, B. A1 - Zolla, F. A1 - Nicolet, A. A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Zimmerling, J. A1 - Remis, R. A1 - Urbach, H. Paul A1 - Liu, H. T. A1 - Weiss, T. T1 - Quasinormal mode solvers for resonators with dispersive materials JF - J. Opt. Soc. Am. A Y1 - 2019 U6 - https://doi.org/10.1364/JOSAA.36.000686 VL - 36 SP - 686 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Erratum: Equivalence of weak and strong modes of measures on topological vector spaces (2018 Inverse Problems 34 115013) JF - Inverse Problems Y1 - 2018 U6 - https://doi.org/10.1088/1361-6420/aae55b VL - 34 IS - 12 SP - 129601 ER - TY - JOUR A1 - Klus, Stefan A1 - Bittracher, Andreas A1 - Schuster, Ingmar A1 - Schütte, Christof T1 - A kernel-based approach to molecular conformation analysis JF - Journal of Chemical Physics N2 - We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for analyzing dynamical systems in order to identify conformation dynamics based on molecular dynamics simulation data. We show that many of the prominent methods like Markov State Models, EDMD, and TICA can be regarded as special cases of this approach and that new efficient algorithms can be constructed based on this derivation. The results of these new powerful methods will be illustrated with several examples, in particular the alanine dipeptide and the protein NTL9. Y1 - 2018 U6 - https://doi.org/10.1063/1.5063533 VL - 149 IS - 24 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias A1 - Hviid, Stubbe A1 - Jorda, Laurent A1 - Keller, Horst Uwe A1 - Kührt, Ekkehard T1 - Comet 67P/Churyumov-Gerasimenko rotation changes derived from sublimation induced torques JF - Astronomy & Astrophysics N2 - Context. The change of the rotation period and the orientation of the rotation axis of comet 67P/Churyumov-Gerasimenko (67P/C-G) is deducible from images taken by the scientific imaging instruments on-board the Rosetta mission with high precision. Non gravitational forces are a natural explanation for these data. Aims. We describe observed changes for the orientation of the rotation axis and the rotation period of 67P/C-G. For these changes we give an explanation based on a sublimation model with a best-fit for the surface active fraction (model P). Torque effects of periodically changing gas emissions on the surface are considered. Methods. We solve the equation of state for the angular momentum in the inertial and the body- fixed frames and provide an analytic theory of the rotation changes in terms of Fourier coefficients, generally applicable to periodically forced rigid body dynamics. Results. The torque induced changes of the rotation state constrain the physical properties of the surface, the sublimation rate and the local active fraction of the surface. Conclusions. We determine a distribution of the local surface active fraction in agreement with the rotation properties, period and orientation, of 67P/C-G. The torque movement confirms that the sublimation increases faster than the insolation towards perihelion. The derived relatively uniform activity pattern is discussed in terms of related surface features. Y1 - 2019 U6 - https://doi.org/10.1051/0004-6361/201834349 VL - 630 SP - A3 ER - TY - JOUR A1 - Wilson, Jon A1 - Gutsche, Philipp A1 - Herrmann, Sven A1 - Burger, Sven A1 - McPeak, Kevin T1 - Correlation of circular differential optical absorption with geometric chirality in plasmonic meta-atoms JF - Opt. Express Y1 - 2019 U6 - https://doi.org/10.1364/OE.27.005097 VL - 27 SP - 5097 ER - TY - JOUR A1 - Dartsch, Maria A1 - Dulski, Sebastian A1 - Engels, Frauke A1 - Gran, Meike A1 - Kende, Jiri A1 - Lohrum, Stefan A1 - Porth, Robert A1 - Ristau, Ute A1 - Rüter, Christian A1 - Sabisch, Andreas A1 - Stumm, Birgit A1 - Taylor, Viola A1 - Voß, Michael T1 - Einführung des cloudbasierten Bibliothekssystems Alma in Berlin – ein Erfahrungsbericht JF - ABI Technik - Zeitschrift für Automation, Bau und Technik im Archiv-, Bibliotheks- und Informationswesen N2 - Die enge Zusammenarbeit der vier Berliner Universitätsbibliotheken1 reicht weit zurück. Bereits vor der Jahrtausendwende haben die Berliner Universitätsbibliotheken (UBs) gemeinsam das Bibliothekssystem Aleph 500 ausgewählt und implementiert, danach folgten weitere Systeme – das Linking System SFX, die Digitale Bibliothek MetaLib und das Bibliotheksportal Primo. Es war daher folgerichtig und selbstverständlich, dass auch die Auswahl und Implementierung eines neuen Bibliothekssystems in enger Abstimmung und Zusammenarbeit erfolgte. Die Erfahrungen bei Vertragsverhandlungen und Implementierung von Alma sind Gegenstand des folgenden Berichtes. N2 - As regards implementing new library technology, the Berlin University libraries have been working closely together for more than 20 years. It was the case for the implementation of the legacy system Aleph 500, the linking system SFX, the digital library MetaLib and the library portal Primo, and therefore it was a matter of course to continue the close cooperation during the implementation of the new cloud-based library system, too. The experience gained during the contract negotiations and the implementation project, and lessons learned are the focus of this report. Y1 - 2018 U6 - https://doi.org/10.1515/abitech-2018-2002 VL - 38 IS - 2 SP - 128 EP - 141 ER - TY - JOUR A1 - Oates, Chris A1 - Sullivan, T. J. T1 - A modern retrospective on probabilistic numerics JF - Statistics and Computing N2 - This article attempts to place the emergence of probabilistic numerics as a mathematical-statistical research field within its historical context and to explore how its gradual development can be related to modern formal treatments and applications. We highlight in particular the parallel contributions of Sul'din and Larkin in the 1960s and how their pioneering early ideas have reached a degree of maturity in the intervening period, mediated by paradigms such as average-case analysis and information-based complexity. We provide a subjective assessment of the state of research in probabilistic numerics and highlight some difficulties to be addressed by future works. Y1 - 2019 U6 - https://doi.org/10.1007/s11222-019-09902-z VL - 29 IS - 6 SP - 1335 EP - 1351 ER - TY - JOUR A1 - Kersting, Hans A1 - Sullivan, T. J. A1 - Hennig, Philipp T1 - Convergence rates of Gaussian ODE filters JF - Statistics and Computing Y1 - 2020 U6 - https://doi.org/10.1007/s11222-020-09972-4 VL - 30 SP - 1791 EP - 1816 PB - Springer CY - Statistics and Computing ER - TY - JOUR A1 - Gupta, Pooja A1 - Peter, Sarah A1 - Jung, Markus A1 - Lewin, Astrid A1 - Hemmrich-Stanisak, Georg A1 - Franke, Andre A1 - von Kleist, Max A1 - Schütte, Christof A1 - Einspanier, Ralf A1 - Sharbati, Soroush A1 - zur Bruegge, Jennifer T1 - Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel 2 aspects of Mycobacterium avium subspecies paratuberculosis infections JF - Scientific Reports in Nature N2 - Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-018-38141-x VL - 9 ER - TY - JOUR A1 - Deuflhard, Peter T1 - The Grand Four. Affine Invariant Globalizations of Newton's Method JF - Vietnam Journal of Mathematics Y1 - 2018 U6 - https://doi.org/10.1007/s10013-018-0301-3 VL - 46 IS - 4 SP - 761 EP - 777 ER - TY - JOUR A1 - Lelièvre, Tony A1 - Zhang, Wei T1 - Pathwise estimates for effective dynamics: the case of nonlinear vectorial reaction coordinates JF - Multiscale Modeling and Simulation N2 - Effective dynamics using conditional expectation was proposed in [F. Legoll and T. Lelièvre, Nonlinearity, 2010] to approximate the essential dynamics of high-dimensional diffusion processes along a given reaction coordinate. The approximation error of the effective dynamics when it is used to approximate the behavior of the original dynamics has been considered in recent years. As a continuation of the previous work [F. Legoll, T. Lelièvre, and S. Olla, Stoch. Process. Appl, 2017], in this paper we obtain pathwise estimates for effective dynamics when the reaction coordinate function is either nonlinear or vector-valued. Y1 - 2018 U6 - https://doi.org/10.1137/18M1186034 IS - 17 SP - 1019 EP - 1051 ER - TY - JOUR A1 - Zhang, Wei T1 - Ergodic SDEs on submanifolds and related numerical sampling schemes JF - ESAIM: Mathematical Modelling and Numerical Analysis N2 - In many applications, it is often necessary to sample the mean value of certain quantity with respect to a probability measure $\mu$ on the level set of a smooth function ξ:R^d→R^k, 1≤k SEE > OOE for their linear programming (LP) relaxations, meaning that IEE has the strongest linear relaxation among the event-based models. We further show that the popular DDT formulation can be retrieved from IEE by certain polyhedral operations, thus giving a unifying view on a complete branch of MIP formulations for the RCPSP. In addition, we analyze the computational performance of all presented models on test instances of the PSPLIB (Kolisch and Sprecher 1997). Y1 - 2020 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Burger, Sven A1 - Staude, Isabelle A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - General design formalism for highly efficient flat optics for broadband applications JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.386573 VL - 28 SP - 6452 ER - TY - JOUR A1 - Götschel, Sebastian A1 - Schiela, Anton A1 - Weiser, Martin T1 - Kaskade 7 - a Flexible Finite Element Toolbox JF - Computers and Mathematics with Applications N2 - Kaskade 7 is a finite element toolbox for the solution of stationary or transient systems of partial differential equations, aimed at supporting application-oriented research in numerical analysis and scientific computing. The library is written in C++ and is based on the \textsc{Dune} interface. The code is independent of spatial dimension and works with different grid managers. An important feature is the mix-and-match approach to discretizing systems of PDEs with different ansatz and test spaces for all variables. We describe the mathematical concepts behind the library as well as its structure, illustrating its use at several examples on the way. Y1 - 2021 U6 - https://doi.org/10.1016/j.camwa.2020.02.011 VL - 81 SP - 444 EP - 458 ER - TY - JOUR A1 - Bärmann, Andreas A1 - Heidt, Andreas A1 - Martin, Alex A1 - er, A1 - Pokutta, Sebastian A1 - Thurner, Christoph T1 - Polyhedral Approximation of Ellipsoidal Uncertainty Sets via Extended Formulations - a computational case study JF - Computational Management Science Y1 - 2016 UR - http://www.optimization-online.org/DB_HTML/2014/02/4245.html N1 - Additional Note: http://link.springer.com/article/10.1007/s10287-015-0243-0 DOI:10.1007/s10287-015-0243-0 N1 - URL of the PDF: http://link.springer.com/article/10.1007/s10287-015-0243-0 VL - 13 IS - 2 SP - 151 EP - 193 ER - TY - JOUR A1 - Roy, Aurko A1 - Pokutta, Sebastian T1 - Hierarchical Clustering via Spreading Metrics JF - Journal of Machine Learning Research (JMLR) Y1 - 2017 N1 - Additional Note: http://https://papers.nips.cc/paper/by-source-2016-1199 N1 - URL of the PDF: http://jmlr.org/papers/v18/17-081.html VL - 18 SP - 1 EP - 35 ER - TY - JOUR A1 - Bodur, Merve A1 - Del Pia, Alberto A1 - Dey, Santanu Sabush A1 - Molinaro, Marco A1 - Pokutta, Sebastian T1 - Aggregation-based cutting-planes for packing and covering Integer Programs JF - to appear in Mathematical Programming A Y1 - 2017 N1 - Additional Note: doi:10.1007/s10107-017-1192-x N1 - URL of the PDF: http://dx.doi.org/10.1007/s10107-017-1192-x ER - TY - JOUR A1 - Bazzi, Abbas A1 - Fiorini, Samuel A1 - Pokutta, Sebastian A1 - Svensson, Ola T1 - Small linear programs cannot approximate Vertex Cover within a factor of 2 - epsilon JF - to appear in Mathematics of Operations Research Y1 - 2017 N1 - URL of the Slides: https://app.box.com/s/00aqupo722bbpmdcyzwt8xmfqzyu14iy ER - TY - JOUR A1 - Braun, Gábor A1 - Guzmán, C. A1 - Pokutta, Sebastian T1 - Unifying Lower Bounds on the Oracle Complexity of Nonsmooth Convex Optimization JF - IEEE Transactions of Information Theory Y1 - 2017 N1 - Additional Note: doi:10.1109/TIT.2017.2701343 http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7919238 N1 - URL of the PDF: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7919238 VL - 63 IS - 7 SP - 4709 EP - 4724 ER - TY - JOUR A1 - Braun, Gábor A1 - Jain, R. A1 - Lee, T. A1 - Pokutta, Sebastian T1 - Information-theoretic approximations of the nonnegative rank JF - Computational Complexity Y1 - 2017 UR - http://eccc.hpi-web.de/report/2013/158 VL - 26 IS - 1 SP - 147 EP - 197 ER - TY - JOUR A1 - Christensen, H. A1 - Khan, A. A1 - Pokutta, Sebastian A1 - Tetali, P. T1 - Multidimensional Bin Packing and Other Related Problems: A survey JF - to appear in Computer Science Review Y1 - 2017 N1 - Additional Note: http://www.sciencedirect.com/science/article/pii/S1574013716301356 http://www.sciencedirect.com/science/article/pii/S1574013716301356 N1 - URL of the PDF: http://www.sciencedirect.com/science/article/pii/S1574013716301356 ER - TY - JOUR A1 - Martin, Alex A1 - Müller, J. A1 - Pape, S. A1 - Peter, A. A1 - Pokutta, Sebastian A1 - Winter, T. T1 - Pricing and clearing combinatorial markets with singleton and swap orders JF - Mathematical Methods of Operations Research Y1 - 2017 VL - 85 IS - 2 SP - 155 EP - 177 ER - TY - JOUR A1 - Knueven, B. A1 - Ostrowski, J. A1 - Pokutta, Sebastian T1 - Detecting Almost Symmetries in Graphs JF - to appear in Mathematical Programming C Y1 - 2017 UR - http://www.optimization-online.org/DB_HTML/2015/09/5117.html N1 - URL of the PDF: http://link.springer.com/article/10.1007/s12532-017-0124-3 ER - TY - JOUR A1 - Braun, Gábor A1 - Brown-Cohen, Jonah A1 - Huq, Arefin A1 - Pokutta, Sebastian A1 - Raghavendra, Prasad A1 - Weitz, Benjamin A1 - Zink, Daniel T1 - The matching problem has no small symmetric SDP JF - Mathematical Programming A Y1 - 2017 N1 - Additional Note: DOI 10.1007/s10107-016-1098-z N1 - URL of the PDF: http://dx.doi.org/10.1007/s10107-016-1098-z VL - 165 IS - 2 SP - 643 EP - 662 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - Rigid abelian groups and the probabilistic method JF - Contemporary Mathematics Y1 - 2012 N1 - Additional Note: doi:/10.1090/conm/576 N1 - URL of the PDF: http://dx.doi.org/10.1090/conm/576 VL - 576 SP - 17 EP - 30 ER - TY - JOUR A1 - Göbel, R. A1 - Pokutta, Sebastian T1 - Absolutely rigid fields and Shelah’s absolutely rigid trees JF - Contemporary Mathematics Y1 - 2012 UR - http://www.box.net/shared/numjyo0qxmpsz9dposyt N1 - Additional Note: doi:/10.1090/conm/576 N1 - URL of the PDF: http://dx.doi.org/10.1090/conm/576 VL - 576 SP - 105 EP - 128 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - Schmaltz, Christian T1 - Optimal Planning under Basel III Regulations JF - Cass-Capco Institute Paper Series on Risk Y1 - 2012 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1914800 N1 - Additional Note: http://www.capco.com/capco-institute/capco-journal/journal-34-cass-capco-institute-paper-series-on-risk N1 - URL of the PDF: http://www.capco.com/capco-institute/capco-journal/journal-34-cass-capco-institute-paper-series-on-risk VL - 34 ER - TY - JOUR A1 - Kroll, C. A1 - Pokutta, Sebastian T1 - Just a perfect day: developing a happiness optimised day schedule JF - Journal of Economic Psychology Y1 - 2013 N1 - Additional Note: doi:/10.1016/j.joep.2012.09.015 N1 - URL of the PDF: http://www.sciencedirect.com/science/article/pii/S0167487012001158 VL - 34 SP - 210 EP - 217 ER - TY - JOUR A1 - Pokutta, Sebastian A1 - VanVyve, M. T1 - A note on the extension complexity of the knapsack polytope JF - Operations Research Letters Y1 - 2013 UR - http://www.optimization-online.org/DB_HTML/2013/02/3787.html N1 - Additional Note: DOI information: 10.1016/j.orl.2013.03.010 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.orl.2013.03.010 VL - 41 SP - 347 EP - 350 ER - TY - JOUR A1 - Schmaltz, Christian A1 - Pokutta, Sebastian A1 - Heidorn, Thomas A1 - Andrae, Silvio T1 - How to make regulators and shareholders happy under Basel III JF - Journal of Banking and Finance Y1 - 2014 UR - http://ssrn.com/abstract=2179490 N1 - Additional Note: 10.1016/j.jbankfin.2014.05.031 N1 - URL of the PDF: http://dx.doi.org/10.1016/j.jbankfin.2014.05.031 SP - 311 EP - 325 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - A short proof for the polyhedrality of the Chvátal-Gomory closure of a compact convex set JF - Operations Research Letters Y1 - 2014 N1 - Additional Note: 10.1016/j.orl.2014.05.004 VL - 42 SP - 307 EP - 310 ER - TY - JOUR A1 - Drewes, S. A1 - Pokutta, Sebastian T1 - Computing discrete expected utility maximizing portfolios JF - Journal of Investing Y1 - 2014 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1662729 VL - 23 IS - 4 SP - 121 EP - 132 ER - TY - JOUR A1 - Drewes, S. A1 - Pokutta, Sebastian T1 - Symmetry-exploiting cuts for a class of mixed-0/1 second order cone programs JF - Discrete Optimization Y1 - 2014 UR - http://www.optimization-online.org/DB_HTML/2010/06/2652.html N1 - Additional Note: doi:10.1016/j.disopt.2014.04.002 VL - 13 SP - 23 EP - 35 ER - TY - JOUR A1 - Martin, Alexander A1 - Müller, J. A1 - Pokutta, Sebastian T1 - Strict linear prices in non-convex European day-ahead electricity markets JF - Optimization Methods and Software Y1 - 2014 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1660528 N1 - Additional Note: 10.1080/10556788.2013.823544 N1 - URL of the PDF: http://dx.doi.org/10.1080/10556788.2013.823544 VL - 29 IS - 1 SP - 189 EP - 221 ER - TY - JOUR A1 - Briët, Jop A1 - Dadush, Daniel A1 - Pokutta, Sebastian T1 - On the existence of 0/1 polytopes with high semidefinite extension complexity JF - Mathematical Programming B Y1 - 2015 VL - 153 IS - 1 SP - 179 EP - 199 ER - TY - JOUR A1 - Braun, Gábor A1 - Fiorini, Samuel A1 - Pokutta, Sebastian A1 - Steurer, D. T1 - Approximation Limits of Linear Programs (Beyond Hierarchies) JF - Mathematics of Operations Research Y1 - 2015 VL - 40 IS - 3 SP - 179 EP - 199 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - The matching polytope does not admit fully-polynomial size relaxation schemes JF - IEEE Transactions on Information Theory Y1 - 2015 N1 - Additional Note: doi:10.1109/TIT.2015.2465864 N1 - URL of the PDF: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7182355 VL - 61 IS - 10 SP - 1 EP - 11 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian A1 - Xie, Y. T1 - Info-Greedy Sequential Adaptive Compressed Sensing JF - IEEE Journal of Selected Topics in Signal Processing Y1 - 2015 VL - 9 IS - 4 SP - 601 EP - 611 ER - TY - JOUR A1 - Fiorini, Samuel A1 - Massar, S. A1 - Pokutta, Sebastian A1 - Tiwary, H.R. A1 - de Wolf, R. T1 - Exponential Lower Bounds for Polytopes in Combinatorial Optimization JF - Journal of the ACM Y1 - 2015 N1 - URL of the PDF: https://doi.org/10.1145/2716307 VL - 62 IS - 2 SP - 1 EP - 17 ER - TY - JOUR A1 - Braun, Gábor A1 - Fiorini, Samuel A1 - Pokutta, Sebastian T1 - Average case polyhedral complexity of the maximum stable set problem JF - Mathematical Programming A Y1 - 2016 N1 - Additional Note: http://www.dagstuhl.de/dagpub/978-3-939897-74-3 N1 - URL of the PDF: https://rdcu.be/7uOy VL - 160 IS - 1 SP - 407 EP - 431 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - A polyhedral characterization of Border Bases JF - SIAM Journal on Discrete Mathematics Y1 - 2016 VL - 30 IS - 1 SP - 239 EP - 265 ER - TY - JOUR A1 - Braun, Gábor A1 - Pokutta, Sebastian T1 - Common information and unique disjointness JF - Algorithmica Y1 - 2016 UR - http://eccc.hpi-web.de/report/2013/056 N1 - URL of the PDF: https://rdcu.be/6b9u VL - 76 IS - 3 SP - 597 EP - 629 ER - TY - JOUR A1 - Gatzert, Nadine A1 - Pokutta, Sebastian A1 - Vogl, Nikolai T1 - Convergence of Capital and Insurance Markets: Pricing Aspects of Index-Linked Catastrophic Loss Instruments JF - to appear in Journal of Risk and Insurance Y1 - 2016 UR - http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2320370 ER - TY - JOUR A1 - Brüning, Jan A1 - Hildebrandt, Thomas A1 - Heppt, Werner A1 - Schmidt, Nora A1 - Lamecker, Hans A1 - Szengel, Angelika A1 - Amiridze, Natalja A1 - Ramm, Heiko A1 - Bindernagel, Matthias A1 - Zachow, Stefan A1 - Goubergrits, Leonid T1 - Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity JF - Scientific Reports N2 - This study’s objective was the generation of a standardized geometry of the healthy nasal cavity. An average geometry of the healthy nasal cavity was generated using a statistical shape model based on 25 symptom-free subjects. Airflow within the average geometry and these geometries was calculated using fluid simulations. Integral measures of the nasal resistance, wall shear stresses (WSS) and velocities were calculated as well as cross-sectional areas (CSA). Furthermore, individual WSS and static pressure distributions were mapped onto the average geometry. The average geometry featured an overall more regular shape that resulted in less resistance, reduced wall shear stresses and velocities compared to the median of the 25 geometries. Spatial distributions of WSS and pressure of average geometry agreed well compared to the average distributions of all individual geometries. The minimal CSA of the average geometry was larger than the median of all individual geometries (83.4 vs. 74.7 mm²). The airflow observed within the average geometry of the healthy nasal cavity did not equal the average airflow of the individual geometries. While differences observed for integral measures were notable, the calculated values for the average geometry lay within the distributions of the individual parameters. Spatially resolved parameters differed less prominently. Y1 - 2020 UR - https://rdcu.be/b2irD U6 - https://doi.org/10.1038/s41598-020-60755-3 VL - 3755 IS - 10 ER - TY - JOUR A1 - Nyakatura, John A1 - Baumgarten, Roxane A1 - Baum, Daniel A1 - Stark, Heiko A1 - Youlatos, Dionisios T1 - Muscle internal structure revealed by contrast-enhanced μCT and fibre recognition: The hindlimb extensors of an arboreal and a fossorial squirrel JF - Mammalian Biology N2 - In individuals of similar body mass representing closely related species with different lifestyles, muscle architectural properties can be assumed to reflect adaptation to differing, lifestyle-related functional demands. We here employ a fiber recognition algorithm on contrast-enhanced micro-computed tomography (μCT) scans of one specimen each of an arboreal (Sciurus vulgaris) and a fossorial (Spermophilus citellus) sciuromorph rodent. The automated approach accounts for potential heterogeneity of architectural properties within a muscle by analyzing all fascicles that compose a muscle. Muscle architectural properties (volume, fascicle length, and orientation, and force-generating capacity) were quantified in 14 hindlimb (hip, knee, and ankle) extensor muscles and compared between specimens. We expected the arboreal squirrel to exhibit greater force-generating capacity and a greater capacity for length change allowing more powerful hindlimb extension. Generally and mostly matching our expectations, the S. vulgaris specimen had absolutely and relatively larger extensor muscles than the S. citellus specimen which were thus metabolically more expensive and demonstrate the relatively larger investment into powerful hindlimb extension necessary in the arboreal context. We conclude that detailed quantitative data on hindlimb muscle internal structure as was gathered here for a very limited sample further lends support to the notion that muscle architecture reflects adaptation to differential functional demands in closely related species with different locomotor behaviors and lifestyles. Y1 - 2019 U6 - https://doi.org/10.1016/j.mambio.2019.10.007 VL - 99 SP - 71 EP - 80 ER - TY - JOUR A1 - Schwieger, Robert A1 - Siebert, Heike A1 - Röblitz, Susanna T1 - Correspondence of Trap Spaces in Different Models of Bioregulatory Networks JF - SIAM Journal on Applied Dynamical Systems N2 - Mathematical models for bioregulatory networks can be based on different formalisms, depending on the quality of available data and the research question to be answered. Discrete boolean models can be constructed based on qualitative data, which are frequently available. On the other hand, continuous models in terms of ordinary differential equations (ODEs) can incorporate time-series data and give more detailed insight into the dynamics of the underlying system. A few years ago, a method based on multivariate polynomial interpolation and Hill functions has been developed for an automatic conversion of boolean models to systems of ordinary differential equations. This method is frequently used by modellers in systems biology today, but there are only a few results available about the conservation of mathematical structures and properties across the formalisms. Here, we consider subsets of the phase space where some components stay fixed, called trap spaces, and demonstrate how boolean trap spaces can be linked to invariant sets in the continuous state space. This knowledge is of practical relevance since finding trap spaces in the boolean setting, which is relatively easy, allows for the construction of reduced ODE models. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1137/17M1155302 VL - 17 IS - 2 SP - 1742 EP - 1765 ER - TY - JOUR A1 - Lange, Alexander A1 - Schwieger, Robert A1 - Plöntzke, Julia A1 - Schäfer, Stefan A1 - Röblitz, Susanna T1 - Follicular competition in cows: the selection of dominant follicles as a synergistic effect JF - Journal of Mathematical Biology N2 - The reproductive cycle of mono-ovulatory species such as cows or humans is known to show two or more waves of follicular growth and decline between two successive ovulations. Within each wave, there is one dominant follicle escorted by subordinate follicles of varying number. Under the surge of the luteinizing hormone a growing dominant follicle ovulates. Rarely the number of ovulating follicles exceeds one. In the biological literature, the change of hormonal concentrations and individually varying numbers of follicular receptors are made responsible for the selection of exactly one dominant follicle, yet a clear cause has not been identified. In this paper, we suggest a synergistic explanation based on competition, formulated by a parsimoniously defined system of ordinary differential equations (ODEs) that quantifies the time evolution of multiple follicles and their competitive interaction during one wave. Not discriminating between follicles, growth and decline are given by fixed rates. Competition is introduced via a growth-suppressing term, equally supported by all follicles. We prove that the number of dominant follicles is determined exclusively by the ratio of follicular growth and competition. This number turns out to be independent of the number of subordinate follicles. The asymptotic behavior of the corresponding dynamical system is investigated rigorously, where we demonstrate that the ω-limit set only contains fixed points. When also including follicular decline, our ODEs perfectly resemble ultrasound data of bovine follicles. Implications for the involved but not explicitly modeled hormones are discussed. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1007/s00285-018-1284-0 ER - TY - JOUR A1 - Manley, Phillip A1 - Abdi, Fatwa F. A1 - Berglund, Sean P. A1 - Islam, A. T. M. Nazmul A1 - Burger, Sven A1 - van de Krol, Roel A1 - Schmid, Martina T1 - Absorption Enhancement for Ultra-Thin Solar Fuel Devices with Plasmonic Gratings JF - ACS Appl. Energy Mater. Y1 - 2018 U6 - https://doi.org/10.1021/acsaem.8b01070 VL - 1 SP - 5810 ER - TY - JOUR A1 - Tack, Alexander A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative JF - Osteoarthritis and Cartilage N2 - Abstract: Objective: To present a novel method for automated segmentation of knee menisci from MRIs. To evaluate quantitative meniscal biomarkers for osteoarthritis (OA) estimated thereof. Method: A segmentation method employing convolutional neural networks in combination with statistical shape models was developed. Accuracy was evaluated on 88 manual segmentations. Meniscal volume, tibial coverage, and meniscal extrusion were computed and tested for differences between groups of OA, joint space narrowing (JSN), and WOMAC pain. Correlation between computed meniscal extrusion and MOAKS experts' readings was evaluated for 600 subjects. Suitability of biomarkers for predicting incident radiographic OA from baseline to 24 months was tested on a group of 552 patients (184 incident OA, 386 controls) by performing conditional logistic regression. Results: Segmentation accuracy measured as Dice Similarity Coefficient was 83.8% for medial menisci (MM) and 88.9% for lateral menisci (LM) at baseline, and 83.1% and 88.3% at 12-month follow-up. Medial tibial coverage was significantly lower for arthritic cases compared to non-arthritic ones. Medial meniscal extrusion was significantly higher for arthritic knees. A moderate correlation between automatically computed medial meniscal extrusion and experts' readings was found (ρ=0.44). Mean medial meniscal extrusion was significantly greater for incident OA cases compared to controls (1.16±0.93 mm vs. 0.83±0.92 mm; p<0.05). Conclusion: Especially for medial menisci an excellent segmentation accuracy was achieved. Our meniscal biomarkers were validated by comparison to experts' readings as well as analysis of differences w.r.t groups of OA, JSN, and WOMAC pain. It was confirmed that medial meniscal extrusion is a predictor for incident OA. Y1 - 2018 U6 - https://doi.org/10.1016/j.joca.2018.02.907 VL - 26 IS - 5 SP - 680 EP - 688 ER - TY - JOUR A1 - Vierhaus, Ingmar A1 - Fügenschuh, Armin A1 - Gottwald, Robert Lion A1 - Grösser, Stefan T1 - Using white-box nonlinear optimization methods in system dynamics policy improvement JF - System Dynamics Review N2 - We present a new strategy for the direct optimization of the values of policy functions. This approach is particularly well suited to model actors with a global perspective on the system and relies heavily on modern mathematical white-box optimization methods. We demonstrate our strategy on two classical models: market growth and World2. Each model is first transformed into an optimization problem by defining how the actor can influence the models' dynamics and by choosing objective functions to measure improvements. To improve comparability between different runs, we also introduce a comparison measure for possible interventions. We solve the optimization problems, discuss the resulting policies and compare them to the existing results from the literature. In particular, we present a run of the World2 model which significantly improves the published “towards a global equilibrium” run with equal cost of intervention. Y1 - 2017 U6 - https://doi.org/10.1002/sdr.1583 VL - 33 IS - 2 SP - 138 EP - 168 ER - TY - JOUR A1 - Beckenbach, Isabel A1 - Borndörfer, Ralf T1 - Hall’s and Kőnig’s theorem in graphs and hypergraphs JF - Discrete Mathematics N2 - We investigate the relation between Hall’s theorem and Kőnig’s theorem in graphs and hypergraphs. In particular, we characterize the graphs satisfying a deficiency version of Hall’s theorem, thereby showing that this class strictly contains all Kőnig–Egerváry graphs. Furthermore, we give a generalization of Hall’s theorem to normal hypergraphs. Y1 - 2018 U6 - https://doi.org/10.1016/j.disc.2018.06.013 VL - 341 IS - 10 SP - 2753 EP - 2761 ER - TY - JOUR A1 - Koltai, Péter A1 - Schütte, Christof T1 - A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics JF - SIAM J. Multiscale Model. Simul. N2 - We investigate metastable dynamical systems subject to non-stationary forcing as they appear in molecular dynamics for systems driven by external fields. We show, that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation—a Markov state model—can be assembled by constructing two equilibrium Markov state models; one for the unforced system, and one for a slightly perturbed one. Y1 - 2018 U6 - https://doi.org/10.1137/17M1146403 VL - 16 IS - 4 SP - 1455 EP - 1485 PB - SIAM ER - TY - JOUR A1 - Apprich, Christian A1 - Dieterich, Annegret A1 - Höllig, Klaus A1 - Nava-Yazdani, Esfandiar T1 - Cubic spline approximation of a circle with maximal smoothness and accuracy JF - Computer Aided Geometric Design N2 - We construct cubic spline approximations of a circle which are four times continuously differentiable and converge with order six. Y1 - 2017 U6 - https://doi.org/10.1016/j.cagd.2017.05.001 VL - 56 SP - 1 EP - 3 PB - Elsevier B.V. ER - TY - JOUR A1 - Sullivan, T. J. T1 - Well-posed Bayesian inverse problems and heavy-tailed stable quasi-Banach space priors JF - Inverse Problems and Imaging Y1 - 2017 U6 - https://doi.org/10.3934/ipi.2017040 VL - 11 IS - 5 SP - 857 EP - 874 ER - TY - JOUR A1 - Löchner, Franz A1 - Fedotova, Anna A1 - Liu, Sheng A1 - Keeler, Gordon A1 - Peake, Gregory A1 - Saravi, Sina A1 - Shcherbakov, Maxim A1 - Burger, Sven A1 - Fedyanin, Andrey A1 - Brener, Igal A1 - Pertsch, Thomas A1 - Setzpfandt, Frank A1 - Staude, Isabelle T1 - Polarization-Dependent Second Harmonic Diffraction from Resonant GaAs Metasurfaces JF - ACS Photonics Y1 - 2018 U6 - https://doi.org/10.1021/acsphotonics.7b01533 VL - 5 SP - 1786 ER - TY - JOUR A1 - Weber, Tobias A1 - Sager, Sebastian A1 - Gleixner, Ambros T1 - Solving Quadratic Programs to High Precision using Scaled Iterative Refinement JF - Mathematical Programming Computation N2 - Quadratic optimization problems (QPs) are ubiquitous, and solution algorithms have matured to a reliable technology. However, the precision of solutions is usually limited due to the underlying floating-point operations. This may cause inconveniences when solutions are used for rigorous reasoning. We contribute on three levels to overcome this issue. First, we present a novel refinement algorithm to solve QPs to arbitrary precision. It iteratively solves refined QPs, assuming a floating-point QP solver oracle. We prove linear convergence of residuals and primal errors. Second, we provide an efficient implementation, based on SoPlex and qpOASES that is publicly available in source code. Third, we give precise reference solutions for the Maros and Mészáros benchmark library. Y1 - 2019 U6 - https://doi.org/10.1007/s12532-019-00154-6 VL - 11 SP - 421 EP - 455 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Gutsche, Philipp A1 - Santiago, Xavier Garcia A1 - Schneider, Philipp-Immanuel A1 - McPeak, Kevin A1 - Nieto-Vesperinas, Manuel A1 - Burger, Sven T1 - Role of Geometric Shape in Chiral Optics JF - Symmetry Y1 - 2020 U6 - https://doi.org/10.3390/sym12010158 VL - 12 SP - 158 ER - TY - JOUR A1 - Becker, Christiane A1 - Burger, Sven A1 - Barth, Carlo A1 - Manley, Phillip A1 - Jäger, Klaus A1 - Eisenhauer, David A1 - Köppel, Grit A1 - Chabera, Pavel A1 - Chen, Junsheng A1 - Zheng, Kaibo A1 - Pullerits, Tönu T1 - Nanophotonic enhanced two-photon excited photoluminescence of perovskite quantum dots JF - ACS Photonics Y1 - 2018 U6 - https://doi.org/10.1021/acsphotonics.8b01199 VL - 5 SP - 4668 ER - TY - JOUR A1 - Redemann, Stefanie A1 - Lantzsch, Ina A1 - Lindow, Norbert A1 - Prohaska, Steffen A1 - Srayko, Martin A1 - Müller-Reichert, Thomas T1 - A switch in microtubule orientation during C. elegans meiosis JF - Current Biology N2 - In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes. Y1 - 2018 U6 - https://doi.org/10.1016/j.cub.2018.07.012 SN - 0960-9822 ER - TY - JOUR A1 - Santiago, Xavier Garcia A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Rockstuhl, Carsten A1 - Fernandez-Corbaton, Ivan A1 - Zschiedrich, Lin T1 - Decomposition of scattered electromagnetic fields into vector spherical wave functions on surfaces with general shapes JF - Phys. Rev. B Y1 - 2019 U6 - https://doi.org/10.1103/PhysRevB.99.045406 VL - 99 SP - 045406 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Blanco, Marco A1 - Sauvage, Thibaut T1 - The Cone of Flow Matrices: Approximation Hierarchies and Applications JF - Networks N2 - Let G be a directed acyclic graph with n arcs, a source s and a sink t. We introduce the cone K of flow matrices, which is a polyhedral cone generated by the matrices $\vec{1}_P\vec{1}_P^T\in\RR^{n\times n}$, where $\vec{1}_P\in\RR^n$ is the incidence vector of the (s,t)-path P. We show that several hard flow (or path) optimization problems, that cannot be solved by using the standard arc-representation of a flow, reduce to a linear optimization problem over $\mathcal{K}$. This cone is intractable: we prove that the membership problem associated to $\mathcal{K}$ is NP-complete. However, the affine hull of this cone admits a nice description, and we give an algorithm which computes in polynomial-time the decomposition of a matrix $X\in \operatorname{span} \mathcal{K}$ as a linear combination of some $\vec{1}_P\vec{1}_P^T$'s. Then, we provide two convergent approximation hierarchies, one of them based on a completely positive representation of~K. We illustrate this approach by computing bounds for the quadratic shortest path problem, as well as a maximum flow problem with pairwise arc-capacities. Y1 - 2018 U6 - https://doi.org/10.1002/net.21820 VL - 72 IS - 1 SP - 128 EP - 150 ER - TY - JOUR A1 - Werdehausen, Daniel A1 - Staude, Isabelle A1 - Burger, Sven A1 - Petschulat, Jörg A1 - Scharf, Toralf A1 - Pertsch, Thomas A1 - Decker, Manuel T1 - Design rules for customizable optical materials based on nanocomposites JF - Opt. Mater. Express Y1 - 2018 U6 - https://doi.org/10.1364/OME.8.003456 VL - 8 SP - 3456 ER - TY - JOUR A1 - Abebe, Muluneh G. A1 - Abass, Aimi A1 - Gomard, Guillaume A1 - Zschiedrich, Lin A1 - Lemmer, Uli A1 - Richards, Bryce S. A1 - Rockstuhl, Carsten A1 - Paetzold, Ulrich W. T1 - Rigorous wave-optical treatment of photon recycling in thermodynamics of photovoltaics: Perovskite thin-film solar cells JF - Phys. Rev. B Y1 - 2018 U6 - https://doi.org/10.1103/PhysRevB.98.075141 VL - 98 SP - 075141 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Reinefeld, Alexander A1 - Rodríguez, Mirta A1 - Zelinskyi, Yaroslav T1 - Efficient calculation of open quantum system dynamics and time-resolved spectroscopy with Distributed Memory HEOM (DM-HEOM) JF - Journal of Computational Chemistry N2 - Time- and frequency resolved optical signals provide insights into the properties of light harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the complex. The hierarchical equations of motion (HEOM) provide a unifying theory, which allows one to study the combined effects of system-environment dissipation and non-Markovian memory without making restrictive assumptions about weak or strong couplings or separability of vibrational and electronic degrees of freedom. With increasing system size the exact solution of the open quantum system dynamics requires memory and compute resources beyond a single compute node. To overcome this barrier, we developed a scalable variant of HEOM. Our distributed memory HEOM, DM-HEOM, is a universal tool for open quantum system dynamics. It is used to accurately compute all experimentally accessible time- and frequency resolved processes in light harvesting molecular complexes with arbitrary system-environment couplings for a wide range of temperatures and complex sizes. Y1 - 2018 U6 - https://doi.org/doi:10.1002/jcc.25354 VL - 39 IS - 22 SP - 1779 EP - 1794 PB - Wiley Periodicals, Inc. ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Reimers, Jeffrey R. A1 - Reinefeld, Alexander A1 - Rodríguez, Mirta A1 - Yin, Shiwei T1 - Energy flow in the Photosystem I supercomplex: comparison of approximative theories with DM-HEOM JF - Chemical Physics N2 - We analyze the exciton dynamics in PhotosystemI from Thermosynechococcus elongatus using the distributed memory implementation of the hierarchical equation of motion (DM-HEOM) for the 96 Chlorophylls in the monomeric unit. The exciton-system parameters are taken from a first principles calculation. A comparison of the exact results with Foerster rates and Markovian approximations allows one to validate the exciton transfer times within the complex and to identify deviations from approximative theories. We show the optical absorption, linear, and circular dichroism spectra obtained with DM-HEOM and compare them to experimental results. Y1 - 2018 U6 - https://doi.org/10.1016/j.chemphys.2018.05.028 VL - 515 SP - 262 EP - 271 PB - Elsevier B.V. ER - TY - JOUR A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Santiago, Xavier Garcia A1 - Zschiedrich, Lin A1 - Weiser, Martin A1 - Burger, Sven T1 - Solving inverse problems appearing in design and metrology of diffractive optical elements by using Bayesian optimization JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2315468 VL - 10694 SP - 1069407 ER - TY - JOUR A1 - Wagner, Sabine A1 - Zapata, Carlos A1 - Wan, Wei A1 - Gawlitza, Kornelia A1 - Weber, Marcus A1 - Rurack, Knut T1 - Role of Counterions in Molecularly Imprinted Polymers for Anionic Species JF - Langmuir N2 - Small-molecule oxoanions are often imprinted noncovalently as carboxylates into molecularly imprinted polymers (MIPs), requiring the use of an organic counterion. Popular species are either pentamethylpiperidine (PMP) as a protonatable cation or tetraalkylammonium (TXA) ions as permanent cations. The present work explores the influence of the TXA as a function of their alkyl chain length, from methyl to octyl, using UV/vis absorption, fluorescence titrations, and HPLC as well as MD simulations. Protected phenylalanines (Z-L/D-Phe) served as templates/analytes. While the influence of the counterion on the complex stability constants and anion-induced spectral changes shows a monotonous trend with increasing alkyl chain length at the prepolymerization stage, the cross-imprinting/rebinding studies showed a unique pattern that suggested the presence of adaptive cavities in the MIP matrix, related to the concept of induced fit of enzyme–substrate interaction. Larger cavities formed in the presence of larger counterions can take up pairs of Z-x-Phe and smaller TXA, eventually escaping spectroscopic detection. Correlation of the experimental data with the MD simulations revealed that counterion mobility, the relative distances between the three partners, and the hydrogen bond lifetimes are more decisive for the response features observed than actual distances between interacting atoms in a complex or the orientation of binding moieties. TBA has been found to yield the highest imprinting factor, also showing a unique dual behavior regarding the interaction with template and fluorescent monomer. Finally, interesting differences between both enantiomers have been observed in both theory and experiment, suggesting true control of enantioselectivity. The contribution concludes with suggestions for translating the findings into actual MIP development. Y1 - 2018 U6 - https://doi.org/10.1021/acs.langmuir.8b00500 VL - 34 IS - 23 SP - 6963 EP - 6975 ER - TY - JOUR A1 - Spahn, Viola A1 - Del Vecchio, Giovanna A1 - Rodriguez-Gaztelumendi, Antonio A1 - Temp, Julia A1 - Labuz, Dominika A1 - Kloner, Michael A1 - Reidelbach, Marco A1 - Machelska, Halina A1 - Weber, Marcus A1 - Stein, Christoph T1 - Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist JF - Scientific Reports N2 - Novel pain killers without adverse effects are urgently needed. Y1 - 2018 VL - 8 SP - 8965 PB - Springer Nature ER - TY - JOUR A1 - Weber, Marcus T1 - Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung JF - KA Korrespondenz Abwasser, Abfall Y1 - 2018 ER - TY - JOUR A1 - Seibert, Felix A1 - Peters, Mathias A1 - Schintke, Florian T1 - Improving I/O Performance Through Colocating Interrelated Input Data and Near-Optimal Load Balancing JF - Proceedings of the IPDPSW; Fourth IEEE International Workshop on High-Performance Big Data, Deep Learning, and Cloud Computing (HPBDC) N2 - Most distributed file systems assign new files to storage servers randomly. While working well in some situations, this does not help to optimize the input performance for most MapReduce computations’ data access patterns. In this work, we consider an access pattern where input files are partitioned into groups of heterogeneous size. Each group is accessed by exactly one process. We design and implement a data placement strategy that places these file groups together on the same storage server. This colocation approach is combined with near-optimal storage load balancing. To do so, we use a classical scheduling approximation algorithm to solve the NP hard group assignment problem. We argue that local processing is not only beneficial because of reduced network traffic, but especially because it imposes an even resource schedule. Our experiments, based on the parallel processing of remote sensing images, reveal an enormous reduction of network traffic and up to 39 % faster input read times. Further, simulations show that our approximate assignments limit storage server imbalances to less than 5 % above the theoretical minimum, in contrast to more than 85 % with random assignment. Y1 - 2018 U6 - https://doi.org/10.1109/IPDPSW.2018.00081 N1 - Best Paper Award VL - 2018 SP - 448 EP - 457 ER - TY - JOUR A1 - Hoffmann, Rene A1 - Lemanis, Robert A1 - Wulff, Lena A1 - Zachow, Stefan A1 - Lukeneder, Alexander A1 - Klug, Christian A1 - Keupp, Helmut T1 - Traumatic events in the life of the deep-sea cephalopod mollusc, the coleoid Spirula spirula JF - ScienceDirect: Deep Sea Research Part I - Oceanographic Research N2 - Here, we report on different types of shell pathologies of the enigmatic deep-sea (mesopelagic) cephalopod Spirula spirula. For the first time, we apply non-invasive imaging methods to: document trauma-induced changes in shell shapes, reconstruct the different causes and effects of these pathologies, unravel the etiology, and attempt to quantify the efficiency of the buoyancy apparatus. We have analysed 2D and 3D shell parameters from eleven shells collected as beach findings from the Canary Islands (Gran Canaria and Fuerteventura), West-Australia, and the Maldives. All shells were scanned with a nanotom-m computer tomograph. Seven shells were likely injured by predator attacks: fishes, cephalopods or crustaceans, one specimen was infested by an endoparasite (potentially Digenea) and one shell shows signs of inflammation and one shell shows large fluctuations of chamber volumes without any signs of pathology. These fluctuations are potential indicators of a stressed environment. Pathological shells represent the most deviant morphologies of a single species and can therefore be regarded as morphological end-members. The changes in the shell volume / chamber volume ratio were assessed in order to evaluate the functional tolerance of the buoyancy apparatus showing that these had little effect. Y1 - 2018 U6 - https://doi.org/10.1016/j.dsr.2018.10.007 VL - 142 IS - 12 SP - 127 EP - 144 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Combining NP-Hard Reduction Techniques and Strong Heuristics in an Exact Algorithm for the Maximum-Weight Connected Subgraph Problem JF - SIAM Journal on Optimization N2 - Borne out of a surprising variety of practical applications, the maximum-weight connected subgraph problem has attracted considerable interest during the past years. This interest has not only led to notable research on theoretical properties, but has also brought about several (exact) solvers-with steadily increasing performance. Continuing along this path, the following article introduces several new algorithms such as reduction techniques and heuristics and describes their integration into an exact solver. The new methods are evaluated with respect to both their theoretical and practical properties. Notably, the new exact framework allows to solve common problem instances from the literature faster than all previous approaches. Moreover, one large-scale benchmark instance from the 11th DIMACS Challenge can be solved for the first time to optimality and the primal-dual gap for two other ones can be significantly reduced. Y1 - 2019 U6 - https://doi.org/10.1137/17M1145963 VL - 29 IS - 1 SP - 369 EP - 398 PB - Society for Industrial and Applied Mathematics ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Surface localization of gas sources on comet 67P/Churyumov-Gerasimenko based on DFMS/COPS data JF - Monthly Notices of the Royal Astronomical Society N2 - We reconstruct the temporal evolution of the source distribution for the four major gas species H2O, CO2, CO, and O2 on the surface of comet 67P/Churyumov-Gerasimenko during its 2015 apparition. The analysis applies an inverse coma model and fits to data between August 6th 2014 and September 5th 2016 measured with the Double Focusing Mass Spectrometer (DFMS) of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) and the COmet Pressure Sensor (COPS). The spatial distribution of gas sources with their temporal variation allows one to construct surface maps for gas emissions and to evaluate integrated productions rates. For all species peak production rates and integrated productions rates per orbit are evaluated separately for the northern and the southern hemisphere. The nine most active emitting areas on the comet’s surface are defined and their correlation to emissions for each of the species is discussed. Y1 - 2018 U6 - https://doi.org/10.1093/mnras/sty3103 VL - 483 SP - 852 EP - 861 PB - Monthly Notices of the Royal Astronomical Society ER - TY - JOUR A1 - Peitz, Sebastian A1 - Gräler, Manuel A1 - Henke, Christian A1 - Hessel-von Molo, Mirko A1 - Dellnitz, Michael A1 - Trächtler, Ansgar T1 - Multiobjective Model Predictive Control of an Industrial Laundry JF - Procedia Technology N2 - In a wide range of applications, it is desirable to optimally control a system with respect to concurrent, potentially competing goals. This gives rise to a multiobjective optimal control problem where, instead of computing a single optimal solution, the set of optimal compromises, the so-called Pareto set, has to be approximated. When it is not possible to compute the entire control trajectory in advance, for instance due to uncertainties or unforeseeable events, model predictive control methods can be applied to control the system during operation in real time. In this article, we present an algorithm for the solution of multiobjective model predictive control problems. In an offline scenario, it can be used to compute the entire set of optimal compromises whereas in a real time scenario, one optimal compromise is computed according to an operator’s preference. The results are illustrated using the example of an industrial laundry. A logistics model of the laundry is developed and then utilized in the optimization routine. Results are presented for an offline as well as an online scenario Y1 - 2016 IS - 26 SP - 483 EP - 490 ER - TY - JOUR A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative JF - Medical Image Analysis N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs). The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures. The shape models and neural networks employed are trained using data of the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets of the SKI10 challenge. For the first time, an accuracy equivalent to the inter-observer variability of human readers has been achieved in this challenge. Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We made the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation. In conclusion, combining statistical anatomical knowledge via SSMs with the localized classification via CNNs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data. Y1 - 2019 U6 - https://doi.org/10.1016/j.media.2018.11.009 VL - 52 IS - 2 SP - 109 EP - 118 ER - TY - JOUR A1 - Hiller, Benjamin A1 - Koch, Thorsten A1 - Schewe, Lars A1 - Schwarz, Robert A1 - Schweiger, Jonas T1 - A System to Evaluate Gas Network Capacities: Concepts and Implementation JF - European Journal of Operational Research N2 - In 2005 the European Union liberalized the gas market with a disruptive change and decoupled trading of natural gas from its transport. The gas is now trans- ported by independent so-called transmissions system operators or TSOs. The market model established by the European Union views the gas transmission network as a black box, providing shippers (gas traders and consumers) the opportunity to transport gas from any entry to any exit. TSOs are required to offer the maximum possible capacities at each entry and exit such that any resulting gas flow can be realized by the network. The revenue from selling these capacities more than one billion Euro in Germany alone, but overestimating the capacity might compromise the security of supply. Therefore, evaluating the available transport capacities is extremely important to the TSOs. This is a report on a large project in mathematical optimization, set out to develop a new toolset for evaluating gas network capacities. The goals and the challenges as they occurred in the project are described, as well as the developments and design decisions taken to meet the requirements. Y1 - 2018 VL - 270 IS - 3 SP - 797 EP - 808 ER - TY - JOUR A1 - Shinano, Yuji A1 - Berthold, Timo A1 - Heinz, Stefan T1 - ParaXpress: An Experimental Extension of the FICO Xpress-Optimizer to Solve Hard MIPs on Supercomputers JF - Optimization Methods & Software N2 - The Ubiquity Generator (UG) is a general framework for the external parallelization of mixed integer programming (MIP) solvers. In this paper, we present ParaXpress, a distributed memory parallelization of the powerful commercial MIP solver FICO Xpress. Besides sheer performance, an important feature of Xpress is that it provides an internal parallelization for shared memory systems. When aiming for a best possible performance of ParaXpress on a supercomputer, the question arises how to balance the internal Xpress parallelization and the external parallelization by UG against each other. We provide computational experiments to address this question and we show computational results for running ParaXpress on a Top500 supercomputer, using up to 43,344 cores in parallel. Y1 - 2018 U6 - https://doi.org/10.1080/10556788.2018.1428602 VL - 33 IS - 3 SP - 530 EP - 539 ER - TY - JOUR A1 - Shinano, Yuji A1 - Heinz, Stefan A1 - Vigerske, Stefan A1 - Winkler, Michael T1 - FiberSCIP - A shared memory parallelization of SCIP JF - INFORMS Journal on Computing N2 - Recently, parallel computing environments have become significantly popular. In order to obtain the benefit of using parallel computing environments, we have to deploy our programs for these effectively. This paper focuses on a parallelization of SCIP (Solving Constraint Integer Programs), which is a mixed-integer linear programming solver and constraint integer programming framework available in source code. There is a parallel extension of SCIP named ParaSCIP, which parallelizes SCIP on massively parallel distributed memory computing environments. This paper describes FiberSCIP, which is yet another parallel extension of SCIP to utilize multi-threaded parallel computation on shared memory computing environments, and has the following contributions: First, we present the basic concept of having two parallel extensions, and the relationship between them and the parallelization framework provided by UG (Ubiquity Generator), including an implementation of deterministic parallelization. Second, we discuss the difficulties in achieving a good performance that utilizes all resources on an actual computing environment, and the difficulties of performance evaluation of the parallel solvers. Third, we present a way to evaluate the performance of new algorithms and parameter settings of the parallel extensions. Finally, we demonstrate the current performance of FiberSCIP for solving mixed-integer linear programs (MIPs) and mixed-integer nonlinear programs (MINLPs) in parallel. Y1 - 2018 U6 - https://doi.org/10.1287/ijoc.2017.0762 VL - 30 IS - 1 SP - 11 EP - 30 ER - TY - JOUR A1 - Furini, Fabio A1 - Traversi, Emiliano A1 - Belotti, Pietro A1 - Frangioni, Antonio A1 - Gleixner, Ambros A1 - Gould, Nick A1 - Liberti, Leo A1 - Lodi, Andrea A1 - Misener, Ruth A1 - Mittelmann, Hans A1 - Sahinidis, Nikolaos V. A1 - Vigerske, Stefan A1 - Wiegele, Angelika T1 - QPLIB: A Library of Quadratic Programming Instances JF - Mathematical Programming Computation N2 - This paper describes a new instance library for Quadratic Programming (QP), i.e., the family of continuous and (mixed)-integer optimization problems where the objective function, the constrains, or both are quadratic. QP is a very diverse class of problems, comprising sub-classes of problems ranging from trivial to undecidable. This diversity is reflected in the variety of solution methods for QP, ranging from entirely combinatorial ones to completely continuous ones, including many for which both aspects are fundamental. Selecting a set of instances of QP that is at the same time not overwhelmingly onerous but sufficiently challenging for the many different interested communities is therefore important. We propose a simple taxonomy for QP instances that leads to a systematic problem selection mechanism. We then briefly survey the field of QP, giving an overview of theory, methods and solvers. Finally, we describe how the library was put together, and detail its final contents. Y1 - 2019 U6 - https://doi.org/10.1007/s12532-018-0147-4 VL - 11 IS - 2 SP - 237 EP - 265 ER - TY - JOUR A1 - Gotzes, Uwe A1 - Gotzes, Claudia T1 - The Jeep Problem: A Flexible MIP Formulation JF - Journal of Nepal Mathematical Society N2 - This article deals with the Jeep Problem (also known as Desert Crossing Problem), which reads as follows: An unlimited supply of fuel is available at one edge of a desert, but there is no source on the desert itself. A vehicle can carry enough fuel to go a certain distance, and it can built up its own refuelling stations. What is the minimum amount of fuel the vehicle will require in order to cross the desert? Under these mild conditions this question is answered since the 1940s. But what is the answer if the caches are restricted to certain areas or if the fuel consumption does not depend linearly on the distance travelled? To answer these and similar questions we develop and solve a flexible mixed-integer programming (MIP) model for the classical problem and enhance it with new further aspects of practical relevance. Y1 - 2018 SN - 2616-0161 VL - 1 SP - 11 EP - 17 ER - TY - JOUR A1 - Shpak, Maksim A1 - Burger, Sven A1 - Byman, Ville A1 - Saastamoinen, Kimmo A1 - Haapalainen, Mertsi A1 - Lassila, Antti T1 - Online measurement of optical fibre geometry during manufacturing JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2314762 VL - 10683 SP - 1068318 ER - TY - JOUR A1 - Castagna, Natascia A1 - Morel, Jacques A1 - Testa, Luc A1 - Burger, Sven T1 - Modelling of standard and specialty fibre-based systems using finite element methods JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2307372 VL - 10683 SP - 1068336 ER - TY - JOUR A1 - Gregersen, Niels A1 - de Lasson, Jakob Rosenkrantz A1 - Frandsen, Lars Hagedorn A1 - Gutsche, Philipp A1 - Burger, Sven A1 - Kim, Oleksiy S. A1 - Breinbjerg, Olav A1 - Ivinskaya, Aliaksandra A1 - Wang, Fengwen A1 - Sigmund, Ole A1 - Häyrynen, Teppo A1 - Lavrinenko, Andrei T1 - Benchmarking state-of-the-art numerical simulation techniques for analyzing large photonic crystal membrane line defect cavities JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2304338 VL - 10672 SP - 106721C ER - TY - JOUR A1 - Höhne, Theresa A1 - Zschiedrich, Lin A1 - Haghighi, Nasibeh A1 - Lott, James A. A1 - Burger, Sven T1 - Validation of quasi-normal modes and of constant-flux modes for computing fundamental resonances of VCSELs JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2307200 VL - 10682 SP - 106821U ER - TY - JOUR A1 - Jäger, Klaus A1 - Manley, Phillip A1 - Chen, Duote A1 - Tockhorn, Philipp A1 - Eisenhauer, David A1 - Köppel, Grit A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Antireflective nanotextures for monolithic perovskite-silicon tandem solar cells JF - Proc. SPIE Y1 - 2018 U6 - https://doi.org/10.1117/12.2306142 VL - 10688 SP - 106880A ER - TY - JOUR A1 - Li, Jianning A1 - Pimentel, Pedro A1 - Szengel, Angelika A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Estacio, Laura A1 - Doenitz, Christian A1 - Ramm, Heiko A1 - Shi, Haochen A1 - Chen, Xiaojun A1 - Matzkin, Franco A1 - Newcombe, Virginia A1 - Ferrante, Enzo A1 - Jin, Yuan A1 - Ellis, David G. A1 - Aizenberg, Michele R. A1 - Kodym, Oldrich A1 - Spanel, Michal A1 - Herout, Adam A1 - Mainprize, James G. A1 - Fishman, Zachary A1 - Hardisty, Michael R. A1 - Bayat, Amirhossein A1 - Shit, Suprosanna A1 - Wang, Bomin A1 - Liu, Zhi A1 - Eder, Matthias A1 - Pepe, Antonio A1 - Gsaxner, Christina A1 - Alves, Victor A1 - Zefferer, Ulrike A1 - von Campe, Cord A1 - Pistracher, Karin A1 - Schäfer, Ute A1 - Schmalstieg, Dieter A1 - Menze, Bjoern H. A1 - Glocker, Ben A1 - Egger, Jan T1 - AutoImplant 2020 - First MICCAI Challenge on Automatic Cranial Implant Design JF - IEEE Transactions on Medical Imaging N2 - The aim of this paper is to provide a comprehensive overview of the MICCAI 2020 AutoImplant Challenge. The approaches and publications submitted and accepted within the challenge will be summarized and reported, highlighting common algorithmic trends and algorithmic diversity. Furthermore, the evaluation results will be presented, compared and discussed in regard to the challenge aim: seeking for low cost, fast and fully automated solutions for cranial implant design. Based on feedback from collaborating neurosurgeons, this paper concludes by stating open issues and post-challenge requirements for intra-operative use. Y1 - 2021 U6 - https://doi.org/10.1109/TMI.2021.3077047 SN - 0278-0062 VL - 40 IS - 9 SP - 2329 EP - 2342 ER - TY - JOUR A1 - Plock, Matthias A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel T1 - Recent advances in Bayesian optimization with applications to parameter reconstruction in optical nano-metrology JF - Proc. SPIE Y1 - 2021 U6 - https://doi.org/10.1117/12.2592266 VL - 11783 SP - 117830J ER - TY - JOUR A1 - Lantzsch, Ina A1 - Yu, Che-Hang A1 - Chen, Yu-Zen A1 - Zimyanin, Vitaly A1 - Yazdkhasti, Hossein A1 - Lindow, Norbert A1 - Szentgyoergyi, Erik A1 - Pani, Ariel M A1 - Prohaska, Steffen A1 - Srayko, Martin A1 - Fürthauer, Sebastian A1 - Redemann, Stefanie T1 - Microtubule reorganization during female meiosis in C. elegans JF - eLife N2 - Most female meiotic spindles undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of meiotic spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic \textit{Caenorhabditis elegans} spindles. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over within seconds. The results show that the metaphase to anaphase transition correlates with an increase in microtubule numbers and a decrease in their average length. Detailed analysis of the tomographic data revealed that the microtubule length changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the spindle reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe. This suggests that the most prominent drivers of spindle rearrangements are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on katanin. Y1 - 2021 U6 - https://doi.org/10.7554/eLife.58903 VL - 10 SP - e58903 ER - TY - JOUR A1 - Gao, Timm A1 - Rickert, Lucas A1 - Urban, Felix A1 - Große, Jan A1 - Srocka, Nicole A1 - Rodt, Sven A1 - Musial, Anna A1 - Zolnacz, Kinga A1 - Mergo, Pawel A1 - Dybka, Kamil A1 - Urbanczyk, Waclaw A1 - Sek, Grzegorz A1 - Burger, Sven A1 - Reitzenstein, Stephan A1 - Heindel, Tobias T1 - A quantum key distribution testbed using a plug&play telecom-wavelength single-photon source JF - Appl. Phys. Rev. Y1 - 2022 U6 - https://doi.org/10.1063/5.0070966 VL - 9 SP - 011412 ER - TY - JOUR A1 - Hoppmann-Baum, Kai T1 - On the Complexity of Computing Maximum and Minimum Min‐Cost‐Flows JF - Networks N2 - Consider a flow network, i.e., a directed graph where each arc has a nonnegative capacity value and an associated length, together with nonempty supply intervals for the sources and nonempty demand intervals for the sinks. The Maximum Min-Cost-Flow Problem (MaxMCF) is to find fixed supply and demand values within these intervals such that the optimal objective value of the induced Min-Cost-Flow Problem (MCF) is maximized. In this paper, we show that MaxMCF as well as its uncapacitated variant, the Maximum Transportation Problem (MaxTP), are NP-hard. Further, we prove that MaxMCF is APX-hard if a connectedness-condition regarding the sources and the sinks of the flow network is dropped. Finally, we show how the Minimum Min-Cost-Flow Problem (MinMCF) can be solved in polynomial time. Y1 - 2021 U6 - https://doi.org/10.1002/net.22060 ER - TY - JOUR A1 - Torun, Cem Güney A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Munns, Joseph H.D. A1 - Schröder, Tim T1 - Optimized diamond inverted nanocones for enhanced color center to fiber coupling JF - Appl. Phys. Lett. Y1 - 2021 U6 - https://doi.org/10.1063/5.0050338 VL - 118 SP - 234002 ER - TY - JOUR A1 - Toulkeridou, Evropi A1 - Gutierrez, Carlos Enrique A1 - Baum, Daniel A1 - Doya, Kenji A1 - Economo, Evan P. T1 - Automated segmentation of insect anatomy from micro-CT images using deep learning JF - bioRxiv Y1 - 2021 U6 - https://doi.org/10.1101/2021.05.29.446283 ER - TY - JOUR A1 - Doerffel, Tom A1 - Papke, Ariane A1 - Klein, Rupert A1 - Ernst, Natalia A1 - Smolarkiewicz, Piotr K. T1 - Dynamics of tilted atmospheric vortices under asymmetric diabatic heating JF - Theoretical and Computational Fluid Dynamics N2 - Päschke et al. (J Fluid Mech, 2012) studied the nonlinear dynamics of strongly tilted vortices subject to asymmetric diabatic heating by asymptotic methods. They found, inter alia, that an azimuthal Fourier mode 1 heating pattern can intensify or attenuate such a vortex depending on the relative orientation of the tilt and the heating asymmetries. The theory originally addressed the gradient wind regime which, asymptotically speaking, corresponds to vortex Rossby numbers of order unity in the limit. Formally, this restricts the applicability of the theory to rather weak vortices. It is shown below that said theory is, in contrast, uniformly valid for vanishing Coriolis parameter and thus applicable to vortices up to low hurricane strengths. An extended discussion of the asymptotics as regards their physical interpretation and their implications for the overall vortex dynamics is also provided in this context. The paper’s second contribution is a series of three-dimensional numerical simulations examining the effect of different orientations of dipolar diabatic heating on idealized tropical cyclones. Comparisons with numerical solutions of the asymptotic equations yield evidence that supports the original theoretical predictions of Päschke et al. In addition, the influence of asymmetric diabatic heating on the time evolution of the vortex centerline is further analyzed, and a steering mechanism that depends on the orientation of the heating dipole is revealed. Finally, the steering mechanism is traced back to the correlation of dipolar perturbations of potential temperature, induced by the vortex tilt, and vertical velocity, for which diabatic heating not necessarily needs to be responsible, but which may have other origins. Y1 - 2021 U6 - https://doi.org/10.1007/s00162-021-00591-x VL - 35 IS - 6 SP - 831 EP - 873 ER - TY - JOUR A1 - Hiller, Benjamin A1 - Saitenmacher, René A1 - Walther, Tom T1 - Improved models for operation modes of complex compressor stations JF - Mathematical Methods of Operations Research N2 - We study combinatorial structures in large-scale mixed-integer (nonlinear) programming problems arising in gas network optimization. We propose a preprocessing strategy exploiting the observation that a large part of the combinatorial complexity arises in certain subnetworks. Our approach analyzes these subnetworks and the combinatorial structure of the flows within these subnetworks in order to provide alternative models with a stronger combinatorial structure that can be exploited by off-the-shelve solvers. In particular, we consider the modeling of operation modes for complex compressor stations (i.e., ones with several in- or outlets) in gas networks. We propose a refined model that allows to precompute tighter bounds for each operation mode and a number of model variants based on the refined model exploiting these tighter bounds. We provide a procedure to obtain the refined model from the input data for the original model. This procedure is based on a nontrivial reduction of the graph representing the gas flow through the compressor station in an operation mode. We evaluate our model variants on reference benchmark data, showing that they reduce the average running time between 10% for easy instances and 46% for hard instances. Moreover, for three of four considered networks, the average number of search tree nodes is at least halved, showing the effectivity of our model variants to guide the solver’s search. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1007/s00186-021-00745-x VL - 94 SP - 171 EP - 195 ER - TY - JOUR A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Timetable merging for the Periodic Event Scheduling Problem JF - EURO Journal on Transportation and Logistics N2 - We propose a new mixed integer programming based heuristic for computing new benchmark primal solutions for instances of the PESPlib. The PESPlib is a collection of instances for the Periodic Event Scheduling Problem (PESP), comprising periodic timetabling problems inspired by real-world railway timetabling settings, and attracting several international research teams during the last years. We describe two strategies to merge a set of good periodic timetables. These make use of the instance structure and minimum weight cycle bases, finally leading to restricted mixed integer programming formulations with tighter variable bounds. Implementing this timetable merging approach in a concurrent solver, we improve the objective values of the best known solutions for the smallest and largest PESPlib instances by 1.7 and 4.3 percent, respectively. Y1 - 2022 U6 - https://doi.org/10.1016/j.ejtl.2022.100081 VL - 11 SP - 100081 ER - TY - JOUR A1 - Volkova, Kseniia A1 - Heupel, Julia A1 - Trofimov, Sergei A1 - Betz, Fridtjof A1 - Colom, Rémi A1 - MacQueen, Rowan W. A1 - Akhundzada, Sapida A1 - Reginka, Meike A1 - Ehresmann, Arno A1 - Reithmeier, Johann Peter A1 - Burger, Sven A1 - Popov, Cyril A1 - Naydenov, Boris T1 - Optical and Spin Properties of NV Center Ensembles in Diamond Nano-Pillars JF - Nanomaterials Y1 - 2022 U6 - https://doi.org/10.3390/nano12091516 VL - 12 SP - 1516 ER - TY - JOUR A1 - Andrle, Anna A1 - Hönicke, Philipp A1 - Gwalt, Grzegorz A1 - Schneider, Philipp-Immanuel A1 - Kayser, Yves A1 - Siewert, Frank A1 - Soltwisch, Victor T1 - Shape- and Element-Sensitive Reconstruction of Periodic Nanostructures with Grazing Incidence X-ray Fluorescence Analysis and Machine Learning JF - Nanomaterials Y1 - 2021 U6 - https://doi.org/10.3390/nano11071647 VL - 11 SP - 1647 ER - TY - JOUR A1 - Bremer, Lucas A1 - Jimenez, Carlos A1 - Thiele, Simon A1 - Weber, Ksenia A1 - Huber, Tobias A1 - Rodt, Sven A1 - Herkommer, Alois A1 - Burger, Sven A1 - Höfling, Sven A1 - Giessen, Harald A1 - Reitzenstein, Stephan T1 - Numerical optimization of single-mode fiber- coupled single-photon sources based on semiconductor quantum dots JF - Opt. Express Y1 - 2022 U6 - https://doi.org/10.1364/OE.456777 VL - 30 SP - 15913 ER - TY - JOUR A1 - Dass, Mihir A1 - Kuen, Lilli A1 - Posnjak, Gregor A1 - Burger, Sven A1 - Liedl, Tim T1 - Visible wavelength spectral tuning of absorption and circular dichroism of DNA-assembled Au/Ag core-shell nanorod assemblies JF - Mater. Adv. Y1 - 2022 U6 - https://doi.org/10.1039/D1MA01211H VL - 3 SP - 3438 ER - TY - JOUR A1 - Ahiboz, Doguscan A1 - Andresen, Elina A1 - Manley, Phillip A1 - Resch-Genger, Ute A1 - Würth, Christian A1 - Becker, Christiane T1 - Metasurface-Enhanced Photon Upconversion upon 1550 nm Excitation JF - Adv. Opt. Mater. Y1 - 2021 U6 - https://doi.org/10.1002/adom.202101285 VL - 9 SP - 2101285 ER - TY - JOUR A1 - Dai, Chengxin A1 - Füllgrabe, Anja A1 - Pfeuffer, Julianus A1 - Solovyeva, Elizaveta M. A1 - Deng, Jingwen A1 - Moreno, Pablo A1 - Kamatchinathan, Selvakumar A1 - Kundu, Deepti Jaiswal A1 - George, Nancy A1 - Fexovy, Silvie A1 - Grüning, Björn A1 - Föll, Melanie Christine A1 - Griss, Johannes A1 - Vaudel, Marc A1 - Audain, Enrique A1 - Locard-Paulet, Marie A1 - Turewicz, Michael A1 - Eisenacher, Martin A1 - Uszkoreit, Julian A1 - Van Den Bossche, Tim A1 - Schwämmle, Veit A1 - Webel, Henry A1 - Schulze, Stefan A1 - Bouyssié, David A1 - Jayaram, Savita A1 - Duggineni, Vinay Kumar A1 - Samaras, Patroklos A1 - Wilhelm, Mathias A1 - Choi, Meena A1 - Wang, Mingxun A1 - Kohlbacher, Oliver A1 - Brazma, Alvis A1 - Papatheodorou, Irene A1 - Bandeira, Nuno A1 - Deutsch, Eric W. A1 - Vizcaíno, Juan Antonio A1 - Bai, Mingze A1 - Sachsenberg, Timo A1 - Levitsky, Lev I. A1 - Perez-Riverol, Yasset T1 - A proteomics sample metadata representation for multiomics integration and big data analysis JF - Nature Communications N2 - The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1038/s41467-021-26111-3 VL - 12 IS - 5854 ER - TY - JOUR A1 - Umer, Husen M. A1 - Zhu, Yafeng A1 - Pfeuffer, Julianus A1 - Sachsenberg, Timo A1 - Lehtiö, Janne A1 - Branca, Rui A1 - Perez-Riverol, Yasset T1 - Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides JF - Bioinformatics N2 - We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512). Y1 - 2021 IS - 5 SP - 1470 EP - 1472 PB - Oxford Academic ET - 38 ER - TY - JOUR A1 - Ayanbayev, Birzhan A1 - Klebanov, Ilja A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Γ-convergence of Onsager–Machlup functionals: I. With applications to maximum a posteriori estimation in Bayesian inverse problems JF - Inverse Problems Y1 - 2022 U6 - https://doi.org/10.1088/1361-6420/ac3f81 VL - 38 IS - 2 ER - TY - JOUR A1 - Ayanbayev, Birzhan A1 - Klebanov, Ilja A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Γ-convergence of Onsager–Machlup functionals: II. Infinite product measures on Banach spaces JF - Inverse Problems Y1 - 2022 U6 - https://doi.org/10.1088/1361-6420/ac3f82 VL - 38 IS - 2 ER - TY - JOUR A1 - Tierno, Pietro A1 - Johansen, Tom H. A1 - Straube, Arthur T1 - Thermally active nanoparticle clusters enslaved by engineered domain wall traps JF - Nature Commun. N2 - The stable assembly of fluctuating nanoparticle clusters on a surface represents a technological challenge of widespread interest for both fundamental and applied research. Here we demonstrate a technique to stably confine in two dimensions clusters of interacting nanoparticles via size-tunable, virtual magnetic traps. We use cylindrical Bloch walls arranged to form a triangular lattice of ferromagnetic domains within an epitaxially grown ferrite garnet film. At each domain, the magnetic stray field generates an effective harmonic potential with a field tunable stifness. The experiments are combined with theory to show that the magnetic confinement is effectively harmonic and pairwise interactions are of dipolar nature, leading to central, strictly repulsive forces. For clusters of magnetic nanoparticles, the stationary collective states arise from the competition between repulsion, confinement and the tendency to fill the central potential well. Using a numerical simulation model as a quantitative map between the experiment and theory we explore the field-induced crystallization process for larger clusters and unveil the existence of three different dynamical regimes. The present method provides a model platform for investigations of the collective phenomena emerging when strongly confined nanoparticle clusters are forced to move in an idealized, harmonic-like potential. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-25931-7 VL - 12 SP - 5813 ER - TY - JOUR A1 - Garcia Santiago, Xavier A1 - Hammerschmidt, Martin A1 - Sachs, Johannes A1 - Burger, Sven A1 - Kwon, Hyunah A1 - Knöller, Marvin A1 - Arens, Tilo A1 - Fischer, Peer A1 - Fernandez-Corbaton, Ivan A1 - Rockstuhl, Carsten T1 - Toward maximally electromagnetically chiral scatterers at optical frequencies JF - ACS Photonics Y1 - 2022 U6 - https://doi.org/10.1021/acsphotonics.1c01887 VL - 9 SP - 1954 ER - TY - JOUR A1 - von Lindheim, Johannes A1 - Harikrishnan, Abhishek A1 - Dörffel, Tom A1 - Klein, Rupert A1 - Koltai, Peter A1 - Mikula, Natalia A1 - Müller, Annette A1 - Névir, Peter A1 - Pacey, George A1 - Polzin, Robert A1 - Vercauteren, Nikki T1 - Definition, detection and tracking of persistent structures in atmospheric flows JF - arXiv N2 - Long-lived flow patterns in the atmosphere such as weather fronts, mid-latitude blockings or tropical cyclones often induce extreme weather conditions. As a consequence, their description, detection, and tracking has received increasing attention in recent years. Similar objectives also arise in diverse fields such as turbulence and combustion research, image analysis, and medical diagnostics under the headlines of "feature tracking", "coherent structure detection" or "image registration" - to name just a few. A host of different approaches to addressing the underlying, often very similar, tasks have been developed and successfully used. Here, several typical examples of such approaches are summarized, further developed and applied to meteorological data sets. Common abstract operational steps form the basis for a unifying framework for the specification of "persistent structures" involving the definition of the physical state of a system, the features of interest, and means of measuring their persistence. Y1 - 2021 ER - TY - JOUR A1 - Stout, Brian A1 - Colom, Remi A1 - Bonod, Nicolas A1 - McPhedran, Ross C T1 - Spectral expansions of open and dispersive optical systems: Gaussian regularization and convergence JF - New J. Phys. Y1 - 2021 U6 - https://doi.org/10.1088/1367-2630/ac10a6 VL - 23 SP - 083004 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Sedeno-Noda, Antonio A1 - Borndörfer, Ralf T1 - An Improved Multiobjective Shortest Path Algorithm JF - Computers & Operations Research N2 - We present a new label-setting algorithm for the Multiobjective Shortest Path (MOSP) problem that computes a minimum complete set of efficient paths for a given instance. The size of the priority queue used in the algorithm is bounded by the number of nodes in the input graph and extracted labels are guaranteed to be efficient. These properties allow us to give a tight output-sensitive running time bound for the new algorithm that can almost be expressed in terms of the running time of Dijkstra’s algorithm for the Shortest Path problem. Hence, we suggest to call the algorithm Multiobjective Dijkstra Algorithm (MDA). The simplified label management in the MDA allows us to parallelize some subroutines. In our computational experiments, we compare the MDA and the classical label-setting MOSP algorithm by Martins, which we improved using new data structures and pruning techniques. On average, the MDA is 2 to 9 times faster on all used graph types. On some instances the speedup reaches an order of magnitude. Y1 - 2021 U6 - https://doi.org/10.1016/j.cor.2021.105424 VL - 135 ER - TY - JOUR A1 - Picht, Thomas A1 - Le Calve, Maxime A1 - Tomasello, Rosario A1 - Fekonja, Lucius A1 - Gholami, Mohammad Fardin A1 - Bruhn, Matthias A1 - Zwick, Carola A1 - Rabe, Jürgen P. A1 - Müller-Birn, Claudia A1 - Vajkoczy, Peter A1 - Sauer, Igor M. A1 - Zachow, Stefan A1 - Nyakatura, John A. A1 - Ribault, Patricia A1 - Pulvermüller, Friedemann T1 - A note on neurosurgical resection and why we need to rethink cutting JF - Neurosurgery Y1 - 2021 U6 - https://doi.org/10.1093/neuros/nyab326 VL - 89 IS - 5 SP - 289 EP - 291 ER - TY - JOUR A1 - Wu, Tong A1 - Arrivault, Denis A1 - Duruflé, Marc A1 - Gras, Alexandre A1 - Binkowski, Felix A1 - Burger, Sven A1 - Yan, Wei A1 - Lalanne, Philippe T1 - Efficient hybrid method for the modal analysis of optical microcavities and nanoresonators JF - J. Opt. Soc. Am. A Y1 - 2021 U6 - https://doi.org/10.1364/JOSAA.428224 VL - 38 SP - 1224 ER - TY - JOUR A1 - Hennings, Felix T1 - Large-scale empirical study on the momentum equation's inertia term JF - Journal of Natural Gas Science and Engineering N2 - A common approach to reduce the Euler equations' complexity for the simulation and optimization of gas networks is to neglect small terms that contribute little to the overall equations. An example is the inertia term of the momentum equation, which is said to be of negligible size under real-world operating conditions. However, this justification has always only been based on experience or single sets of artificial data points. This study closes this gap by presenting a large-scale empirical evaluation of the absolute and relative size of the inertia term when operating a real-world gas network. Our data consists of three years of fine-granular state data of one of the largest gas networks in Europe, featuring over 6,000 pipes with a total length of over 10,000 km. We found that there are only 120 events in which a subnetwork consisting of multiple pipes has an inertia term of high significance for more than three minutes. On average, such an event occurs less often than once every ten days. Therefore, we conclude that the inertia term is indeed negligible for real-world transient gas network control problems. Y1 - 2021 U6 - https://doi.org/10.1016/j.jngse.2021.104153 VL - 95 PB - Elsevier ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Burger, Sven T1 - RPExpand: Software for Riesz projection expansion of resonance phenomena JF - SoftwareX Y1 - 2021 U6 - https://doi.org/10.1016/j.softx.2021.100763 VL - 15 SP - 100763 ER - TY - JOUR A1 - Negrin-Montecelo, Yoel A1 - Movsesyan, Artur A1 - Gao, Jie A1 - Burger, Sven A1 - Wang, Zhiming A1 - Nlate, Sylvain A1 - Pouget, Emilie A1 - Oda, Reiko A1 - Comesana-Hermo, Miguel A1 - Govorov, Alexander O. A1 - Correa-Duarte, Miguel T1 - Chiral Generation of Hot Carriers for Polarization-Sensitive Plasmonic Photocatalysis with Hybrid Nanostructures JF - J. Am. Chem. Soc. Y1 - 2022 U6 - https://doi.org/10.1021/jacs.1c10526 VL - 144 SP - 1663 ER - TY - JOUR A1 - Wang, Junyang A1 - Cockayne, Jon A1 - Chkrebtii, Oksana A1 - Sullivan, T. J. A1 - Oates, Chris T1 - Bayesian numerical methods for nonlinear partial differential equations JF - Statistics and Computing Y1 - 2021 U6 - https://doi.org/10.1007/s11222-021-10030-w VL - 31 IS - 5 ER - TY - JOUR A1 - Movsesyan, Artur A1 - Santiago, Eva Yazmin A1 - Burger, Sven A1 - Correa-Duarte, Miguel A1 - Besteiro, Lucas V. A1 - Wang, Zhiming A1 - Govorov, Alexander O. T1 - Plasmonic nanocrystals with complex shapes for photocatalysis and growth: Contrasting anisotropic hot-electron generation with the photothermal effect JF - Adv. Opt. Mater. Y1 - 2022 U6 - https://doi.org/10.1002/adom.202102663 VL - 10 SP - 2102663 ER - TY - JOUR A1 - Schwartz, Stephan T1 - An overview of graph covering and partitioning JF - Discrete Mathematics N2 - While graph covering is a fundamental and well-studied problem, this field lacks a broad and unified literature review. The holistic overview of graph covering given in this article attempts to close this gap. The focus lies on a characterization and classification of the different problems discussed in the literature. In addition, notable results and common approaches are also included. Whenever appropriate, this review extends to the corresponding partitioning problems. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1016/j.disc.2022.112884 VL - 345 IS - 8 ER - TY - JOUR A1 - Sahin, Guvenc A1 - Digehsara, Amin Ahmadi A1 - Borndörfer, Ralf T1 - Efficient Algorithms for the Multi-Period Line Planning Problem in Public Transportation JF - Open Access Series in Informatics (OASIcs), 21st Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2021) N2 - In order to plan and schedule a demand-responsive public transportation system, both temporal and spatial changes in demand should be taken into account even at the line planning stage. We study the multi-period line planning problem with integrated decisions regarding dynamic allocation of vehicles among the lines. Given the NP-hard nature of the line planning problem, the multi-period version is clearly difficult to solve for large public transit networks even with advanced solvers. It becomes necessary to develop algorithms that are capable of solving even the very-large instances in reasonable time. For instances which belong to real public transit networks, we present results of a heuristic local branching algorithm and an exact approach based on constraint propagation. Y1 - 2021 U6 - https://doi.org/10.4230/OASIcs.ATMOS.2021.17 VL - 96 SP - 17:1 EP - 17:6 ER - TY - JOUR A1 - Schlechte, Thomas A1 - Borndörfer, Ralf A1 - Denißen, Jonas A1 - Heller, Simon A1 - Klug, Torsten A1 - Küpper, Michael A1 - Lindner, Niels A1 - Reuther, Markus A1 - Söhlke, Andreas A1 - Steadman, William T1 - Timetable Optimization for a Moving Block System JF - Journal of Rail Transport Planning & Management N2 - We present an optimization model which is capable of routing and ordering trains on a microscopic level under a moving block regime. Based on a general timetabling definition (GTTP) that allows the plug in of arbitrarily detailed methods to compute running and headway times, we describe a layered graph approach using velocity expansion, and develop a mixed integer linear programming formulation. Finally, we present promising results for a German corridor scenario with mixed traffic, indicating that applying branch-and-cut to our model is able to solve reasonably sized instances with up to hundred trains to optimality. Y1 - 2022 U6 - https://doi.org/10.1016/j.jrtpm.2022.100315 SN - 2210-9706 VL - 22 SP - 100315 ER - TY - JOUR A1 - Bienenstock, Daniel A1 - Muñoz, Gonzalo A1 - Pokutta, Sebastian T1 - Principled Deep Neural Network Training through Linear Programming N2 - Deep Learning has received significant attention due to its impressive performance in many state-of-the-art learning tasks. Unfortunately, while very powerful, Deep Learning is not well understood theoretically and in particular only recently results for the complexity of training deep neural networks have been obtained. In this work we show that large classes of deep neural networks with various architectures (e.g., DNNs, CNNs, Binary Neural Networks, and ResNets), activation functions (e.g., ReLUs and leaky ReLUs), and loss functions (e.g., Hinge loss, Euclidean loss, etc) can be trained to near optimality with desired target accuracy using linear programming in time that is exponential in the input data and parameter space dimension and polynomial in the size of the data set; improvements of the dependence in the input dimension are known to be unlikely assuming P≠NP, and improving the dependence on the parameter space dimension remains open. In particular, we obtain polynomial time algorithms for training for a given fixed network architecture. Our work applies more broadly to empirical risk minimization problems which allows us to generalize various previous results and obtain new complexity results for previously unstudied architectures in the proper learning setting. Y1 - 2018 ER - TY - JOUR A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - Second-order Conditional Gradient Sliding N2 - Constrained second-order convex optimization algorithms are the method of choice when a high accuracy solution to a problem is needed, due to their local quadratic convergence. These algorithms require the solution of a constrained quadratic subproblem at every iteration. We present the \emph{Second-Order Conditional Gradient Sliding} (SOCGS) algorithm, which uses a projection-free algorithm to solve the constrained quadratic subproblems inexactly. When the feasible region is a polytope the algorithm converges quadratically in primal gap after a finite number of linearly convergent iterations. Once in the quadratic regime the SOCGS algorithm requires O(log(log1/ε)) first-order and Hessian oracle calls and O(log(1/ε)log(log1/ε)) linear minimization oracle calls to achieve an ε-optimal solution. This algorithm is useful when the feasible region can only be accessed efficiently through a linear optimization oracle, and computing first-order information of the function, although possible, is costly. Y1 - 2020 ER - TY - JOUR A1 - Berthold, Timo A1 - Koch, Thorsten A1 - Shinano, Yuji T1 - MILP. Try. Repeat. JF - Proceedings of the 13th International Conference on the Practice and Theory of Automated Timetabling - PATAT 2021 Y1 - 2021 VL - 2 ER - TY - JOUR A1 - Kerdreux, Thomas A1 - d'Aspremont, Alexandre A1 - Pokutta, Sebastian T1 - Local and Global Uniform Convexity Conditions N2 - We review various characterizations of uniform convexity and smoothness on norm balls in finite-dimensional spaces and connect results stemming from the geometry of Banach spaces with scaling inequalities used in analysing the convergence of optimization methods. In particular, we establish local versions of these conditions to provide sharper insights on a recent body of complexity results in learning theory, online learning, or offline optimization, which rely on the strong convexity of the feasible set. While they have a significant impact on complexity, these strong convexity or uniform convexity properties of feasible sets are not exploited as thoroughly as their functional counterparts, and this work is an effort to correct this imbalance. We conclude with some practical examples in optimization and machine learning where leveraging these conditions and localized assumptions lead to new complexity results. Y1 - 2021 ER - TY - JOUR A1 - Bärmann, Andreas A1 - Martin, Alexander A1 - Pokutta, Sebastian A1 - Schneider, Oskar T1 - An Online-Learning Approach to Inverse Optimization Y1 - 2018 ER - TY - JOUR A1 - Sagnol, Guillaume A1 - Schmidt genannt Waldschmidt, Daniel T1 - Restricted Adaptivity in Stochastic Scheduling JF - 29th Annual European Symposium on Algorithms (ESA 2021) N2 - We consider the stochastic scheduling problem of minimizing the expected makespan on m parallel identical machines. While the (adaptive) list scheduling policy achieves an approximation ratio of 2, any (non-adaptive) fixed assignment policy has performance guarantee Ω(logm/loglogm). Although the performance of the latter class of policies are worse, there are applications in which non-adaptive policies are desired. In this work, we introduce the two classes of δ-delay and τ-shift policies whose degree of adaptivity can be controlled by a parameter. We present a policy - belonging to both classes - which is an O(loglogm)-approximation for reasonably bounded parameters. In other words, an exponential improvement on the performance of any fixed assignment policy can be achieved when allowing a small degree of adaptivity. Moreover, we provide a matching lower bound for any δ-delay and τ-shift policy when both parameters, respectively, are in the order of the expected makespan of an optimal non-anticipatory policy. Y1 - 2021 U6 - https://doi.org/10.4230/LIPIcs.ESA.2021.79 VL - 204 SP - 79:1 EP - 79:14 ER - TY - JOUR A1 - Beckenbach, Isabel T1 - Von Graphen zu Hypergraphen JF - OR News Y1 - 2020 SN - 1437-2045 IS - 70 ER - TY - JOUR A1 - Roth, Sarah T1 - SAT-Heuristiken für das Periodic Event Scheduling-Problem JF - OR News Y1 - 2021 SN - 1437-2045 IS - 71 ER - TY - JOUR A1 - Pathania, Yogyata A1 - Chakraborty, Dipanjan A1 - Höfling, Felix T1 - Continuous demixing transition of binary liquids: finite-size scaling from the analysis of sub-systems JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000235 VL - 4 SP - 2000235 ER - TY - JOUR A1 - Frömberg, Daniela A1 - Höfling, Felix T1 - Generalized master equation for first-passage problems in partitioned spaces JF - Journal of Physics A: Mathematical and Theoretical Y1 - 2021 U6 - https://doi.org/10.1088/1751-8121/abf2ec VL - 54 SP - 215601 ER - TY - JOUR A1 - Klein, Rupert A1 - Ebrahimi Viand, Roya A1 - Höfling, Felix A1 - Delle Site, Luigi T1 - Nonequilibrium induced by reservoirs: Physico-mathematical model and numerical tests JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202100071 VL - 4 SP - 2100071 ER - TY - JOUR A1 - Gholami, Abbas A1 - Höfling, Felix A1 - Klein, Rupert A1 - Delle Site, Luigi T1 - Thermodynamic relations at the coupling boundary in adaptive resolution simulations for open systems JF - Advances Theory and Simulation Y1 - 2021 U6 - https://doi.org/10.1002/adts.202000303 VL - 4 SP - 2000303 ER - TY - JOUR A1 - Mokhtari, Zahra A1 - Patterson, Robert I. A. A1 - Höfling, Felix T1 - Spontaneous trail formation in populations of auto-chemotactic walkers JF - New Journal of Physics Y1 - 2022 U6 - https://doi.org/10.1088/1367-2630/ac43ec VL - 24 SP - 013012 ER - TY - JOUR A1 - Le, Thi Thai A1 - Fukumoto, Yasuhide T1 - Effect of depth discontinuity on interfacial stability of tangential-velocity discontinuity in shallow-water flow JF - Physics Letters A N2 - It is well known as the Kelvin-Helmholtz instability (KHI) that an interface of tangential velocity discontinuity is necessarily unstable, regardless of the velocity difference's strength. However, the KHI is suppressed for shallow water flows if the Froude number, defined by the ratio of the velocity difference to the gravity wave's speed, is sufficiently large. In this investigation, we examine the effect of the depth difference of two fluid layers on the KHI. The depth difference enhances instability. Given the Froude number in the instability range, the growth rate sensitively depends on the depth ratio and increases monotonically with the depth ratio difference from unity. The critical value of the Froude number for stabilization varies with the depth ratio and attains the minimum value √8 for equal depth. This behavior is verified by asymptotic analysis. Y1 - 2022 U6 - https://doi.org/10.1016/j.physleta.2022.128073 VL - 436 SP - 128073 PB - ELSEVIER ER - TY - JOUR A1 - Hosada, Junko A1 - Maher, Stephen A1 - Shinano, Yuji A1 - Villumsen, Jonas Christoffer T1 - Location, transshipment and routing: An adaptive transportation network integrating long-haul and local vehicle routing JF - EURO Journal on Transportation and Logistics Y1 - 2022 U6 - https://doi.org/10.1016/j.ejtl.2022.100091 VL - 11 PB - Elsevier ER - TY - JOUR A1 - Petkovic, Milena A1 - Chen, Ying A1 - Gamrath, Inken A1 - Gotzes, Uwe A1 - Hadjidimitrou, Natalia Selini A1 - Zittel, Janina A1 - Xu, Xiaofei A1 - Koch, Thorsten T1 - A hybrid approach for high precision prediction of gas flows JF - Energy Systems N2 - About 23% of the German energy demand is supplied by natural gas. Additionally, for about the same amount Germany serves as a transit country. Thereby, the German network represents a central hub in the European natural gas transport network. The transport infrastructure is operated by transmissions system operators (TSOs). The number one priority of the TSOs is to ensure the security of supply. However, the TSOs have only very limited knowledge about the intentions and planned actions of the shippers (traders). Open Grid Europe (OGE), one of Germany’s largest TSO, operates a high-pressure transport network of about 12,000 km length. With the introduction of peak-load gas power stations, it is of great importance to predict in- and out-flow of the network to ensure the necessary flexibility and security of supply for the German Energy Transition (“Energiewende”). In this paper, we introduce a novel hybrid forecast method applied to gas flows at the boundary nodes of a transport network. This method employs an optimized feature selection and minimization. We use a combination of a FAR, LSTM and mathematical programming to achieve robust high-quality forecasts on real-world data for different types of network nodes. Y1 - 2022 U6 - https://doi.org/10.1007/s12667-021-00466-4 VL - 13 SP - 383 EP - 408 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Franz, Henriette A1 - Koch, Thorsten T1 - Optimal Connected Subgraphs: Integer Programming Formulations and Polyhedra JF - Networks Y1 - 2022 U6 - https://doi.org/10.1002/net.22101 VL - 80 IS - 3 SP - 314 EP - 332 PB - Wiley ER - TY - JOUR A1 - Lücke, Marvin A1 - Nüske, Feliks T1 - tgEDMD: Approximation of the Kolmogorov Operator in Tensor Train Format JF - Journal of Nonlinear Science N2 - Extracting information about dynamical systems from models learned off simulation data has become an increasingly important research topic in the natural and engineering sciences. Modeling the Koopman operator semigroup has played a central role in this context. As the approximation quality of any such model critically depends on the basis set, recent work has focused on deriving data-efficient representations of the Koopman operator in low-rank tensor formats, enabling the use of powerful model classes while avoiding over-fitting. On the other hand, detailed information about the system at hand can be extracted from models for the infinitesimal generator, also called Kolmogorov backward operator for stochastic differential equations. In this work, we present a data-driven method to efficiently approximate the generator using the tensor train (TT) format. The centerpiece of the method is a TT representation of the tensor of generator evaluations at all data sites. We analyze consistency and complexity of the method, present extensions to practically relevant settings, and demonstrate its applicability to benchmark numerical examples. Y1 - 2022 U6 - https://doi.org/10.1007/s00332-022-09801-0 VL - 32 ER - TY - JOUR A1 - Tockhorn, Philipp A1 - Sutter, Johannes A1 - Cruz, Alexandros A1 - Wagner, Philipp A1 - Jäger, Klaus A1 - Yoo, Danbi A1 - Lang, Felix A1 - Grischek, Max A1 - Li, Bor A1 - Li, Jinzhao A1 - Shargaieva, Oleksandra A1 - Unger, Eva A1 - Al-Ashouri, Amran A1 - Köhnen, Eike A1 - Stolterfoth, Martin A1 - Neher, Dieter A1 - Schlatmann, Rutger A1 - Rech, Bernd A1 - Stannowski, Bernd A1 - Albrecht, Steve A1 - Becker, Christiane T1 - Nano-optical designs for high-efficiency monolithic perovskite–silicon tandem solar cells JF - Nat. Nanotechnol. Y1 - 2022 U6 - https://doi.org/10.1038/s41565-022-01228-8 VL - 17 SP - 1214 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Klus, Stefan A1 - Hamzi, Boumediene A1 - Schütte, Christof T1 - Dimensionality Reduction of Complex Metastable Systems via Kernel Embeddings of Transition Manifolds JF - Journal of Nonlinear Science N2 - We present a novel kernel-based machine learning algorithm for identifying the low-dimensional geometry of the effective dynamics of high-dimensional multiscale stochastic systems. Recently, the authors developed a mathematical framework for the computation of optimal reaction coordinates of such systems that is based on learning a parameterization of a low-dimensional transition manifold in a certain function space. In this article, we enhance this approach by embedding and learning this transition manifold in a reproducing kernel Hilbert space, exploiting the favorable properties of kernel embeddings. Under mild assumptions on the kernel, the manifold structure is shown to be preserved under the embedding, and distortion bounds can be derived. This leads to a more robust and more efficient algorithm compared to the previous parameterization approaches. Y1 - 2021 U6 - https://doi.org/10.1007/s00332-020-09668-z VL - 31 ER - TY - JOUR A1 - Möller, Jan A1 - Isbilir, Ali A1 - Sungkaworn, Titiwat A1 - Osberg, Brenda A1 - Karathanasis, Christos A1 - Sunkara, Vikram A1 - Grushevsky, Eugene O A1 - Bock, Andreas A1 - Annibale, Paolo A1 - Heilemann, Mike A1 - Schütte, Christof A1 - Lohse, Martin J. T1 - Single molecule mu-opioid receptor membrane-dynamics reveal agonist-specific dimer formation with super-resolved precision JF - Nature Chemical Biology Y1 - 2020 U6 - https://doi.org/10.1038/s41589-020-0566-1 VL - 16 SP - 946 EP - 954 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Moschner, Johann A1 - Koksch, Beate A1 - Netz, Roland A1 - Schütte, Christof T1 - Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis JF - The European Physical Journal B Y1 - 2021 U6 - https://doi.org/10.1140/epjb/s10051-021-00200-0 VL - 94 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Schütte, Christof T1 - A probabilistic algorithm for aggregating vastly undersampled large Markov chains JF - Physica D: Nonlinear Phenomena Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75874 VL - 416 ER - TY - JOUR A1 - Klus, Stefan A1 - Husic, Brooke E. A1 - Mollenhauer, Mattes A1 - Noe, Frank T1 - Kernel methods for detecting coherent structures in dynamical data JF - Chaos: An Interdisciplinary Journal of Nonlinear Science Y1 - 2019 U6 - https://doi.org/10.1063/1.5100267 VL - 29 IS - 12 ER - TY - JOUR A1 - Sechi, Renata A1 - Fackeldey, Konstantin A1 - Chewle, Surahit A1 - Weber, Marcus T1 - SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data JF - Algorithms N2 - This work addresses the problem of determining the number of components from sequential spectroscopic data analyzed by non-negative matrix factorization without separability assumption (SepFree NMF). These data are stored in a matrix M of dimension “measured times” versus “measured wavenumbers” and can be decomposed to obtain the spectral fingerprints of the states and their evolution over time. SepFree NMF assumes a memoryless (Markovian) process to underline the dynamics and decomposes M so that M=WH, with W representing the components’ fingerprints and H their kinetics. However, the rank of this decomposition (i.e., the number of physical states in the process) has to be guessed from pre-existing knowledge on the observed process. We propose a measure for determining the number of components with the computation of the minimal memory effect resulting from the decomposition; by quantifying how much the obtained factorization is deviating from the Markovian property, we are able to score factorizations of a different number of components. In this way, we estimate the number of different entities which contribute to the observed system, and we can extract kinetic information without knowing the characteristic spectra of the single components. This manuscript provides the mathematical background as well as an analysis of computer generated and experimental sequentially measured Raman spectra. Y1 - 2022 U6 - https://doi.org/10.3390/a15090297 VL - 15 IS - 9 SP - 297 ER - TY - JOUR A1 - Bauer, Wolfgang A1 - Weber, Marcus A1 - Diehl-Wiesenecker, Eva A1 - Galtung, Noa A1 - Prpic, Monika A1 - Somasundaram, Rajan A1 - Tauber, Rudolf A1 - Schwenk, Jochen A1 - Micke, Patrick A1 - Kappert, Kai T1 - Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection JF - Viruses N2 - We evaluated how plasma proteomic signatures in patients with suspected COVID-19 can unravel the pathophysiology, and determine kinetics and clinical outcome of the infection. We identified distinct plasma proteins linked to the presence and course of COVID-19. These plasma proteomic findings may translate to a protein fingerprint, helping to assist clinical management decisions. Y1 - 2021 U6 - https://doi.org/10.3390/v13122456 VL - 13 IS - 12 SP - 2456 ER - TY - JOUR A1 - Koltai, Péter A1 - Lie, Han Cheng A1 - Plonka, Martin T1 - Fréchet differentiable drift dependence of Perron–Frobenius and Koopman operators for non-deterministic dynamics JF - Nonlinearity N2 - We prove the Fréchet differentiability with respect to the drift of Perron–Frobenius and Koopman operators associated to time-inhomogeneous ordinary stochastic differential equations. This result relies on a similar differentiability result for pathwise expectations of path functionals of the solution of the stochastic differential equation, which we establish using Girsanov's formula. We demonstrate the significance of our result in the context of dynamical systems and operator theory, by proving continuously differentiable drift dependence of the simple eigen- and singular values and the corresponding eigen- and singular functions of the stochastic Perron–Frobenius and Koopman operators. Y1 - 2019 U6 - https://doi.org/10.1088/1361-6544/ab1f2a VL - 32 IS - 11 SP - 4232 EP - 4257 ER - TY - JOUR A1 - Mollenhauer, Mattes A1 - Klus, Stefan A1 - Schütte, Christof A1 - Koltai, Péter T1 - Kernel Autocovariance Operators of Stationary Processes: Estimation and Convergence JF - Journal of Machine Learning Research N2 - We consider autocovariance operators of a stationary stochastic process on a Polish space that is embedded into a reproducing kernel Hilbert space. We investigate how empirical estimates of these operators converge along realizations of the process under various conditions. In particular, we examine ergodic and strongly mixing processes and obtain several asymptotic results as well as finite sample error bounds. We provide applications of our theory in terms of consistency results for kernel PCA with dependent data and the conditional mean embedding of transition probabilities. Finally, we use our approach to examine the nonparametric estimation of Markov transition operators and highlight how our theory can give a consistency analysis for a large family of spectral analysis methods including kernel-based dynamic mode decomposition. Y1 - 2022 UR - https://jmlr.org/papers/v23/20-442.html VL - 23 IS - 327 SP - 1 EP - 34 ER - TY - JOUR A1 - Boltze, Julia A1 - Höllerl, Annika A1 - Kuberek, Monika A1 - Lohrum, Stefan A1 - Pampel, Heinz A1 - Putnings, Markus A1 - Retter, Regina A1 - Rusch, Beate A1 - Schäffler, Hildegard A1 - Söllner, Konstanze T1 - DeepGreen: Eine Infrastruktur für die Open-Access-Transformation JF - O-Bib. Das Offene Bibliotheksjournal N2 - Mit DeepGreen wurde eine Infrastruktur aufgebaut und etabliert, die Zeitschriftenartikel von wissenschaftlichen Verlagen abholt und berechtigten Bibliotheken zur Veröffentlichung in ihren Repositorien sendet. DeepGreen unterstützt Bibliotheken als Dienstleister für Hochschulen, außeruniversitäre Einrichtungen und die dort tätigen Wissenschaftler*innen, Publikationen auf Open-Access-Repositorien frei zugänglich zu machen und fördert das Zusammenspiel von wissenschaftlichen Einrichtungen und Verlagen. DeepGreen wurde von Januar 2016 bis Juni 2021 von der Deutschen Forschungsgemeinschaft gefördert und wird nun vom Kooperativen Bibliotheksverbund Berlin-Brandenburg, von der Bayerischen Staatsbibliothek und von der Universitätsbibliothek Erlangen-Nürnberg in arbeitsteiliger Eigenleistung für zwei Jahre weiterbetrieben. Der vorliegende Beitrag beleuchtet vielfältige Aspekte bei der Realisierung von DeepGreen und geht auf die Perspektiven dieser zentralen Open-Access-Infrastruktur für deutsche Wissenschaftseinrichtungen ein. Y1 - 2022 U6 - https://doi.org/10.5282/o-bib/5764 VL - 9 IS - 1 ER - TY - JOUR A1 - Lang, Annemarie A1 - Vester, Antja A1 - Ferreira-Gomes, M. A1 - Guerra, G.M. A1 - Heinrich, Fredrich R. A1 - Götzke, C.C. A1 - Kurmies, Sebastian A1 - Sunkara, Vikram A1 - Durek, Pawel A1 - Boerckel, Joel D. A1 - Mashreghi, Mir-Farzin T1 - PIPELINE FOR SINGLE CELL SEQUENCING OF HUMAN CHONDROCYTE PELLET CULTURES TO DELINEATE IL-1β MODULATED CHANGES IN CELL HETEROGENEITY JF - Osteoarthritis and Cartilage Y1 - 2022 U6 - https://doi.org/10.1016/j.joca.2022.02.112 VL - 30 IS - Supplement 1 SP - S90 ER - TY - JOUR A1 - Skrzypczak, Jan A1 - Schintke, Florian A1 - Schütt, Thorsten T1 - Linearizable State Machine Replication of State-Based CRDTs without Logs JF - arXiv N2 - General solutions of state machine replication have to ensure that all replicas apply the same commands in the same order, even in the presence of failures. Such strict ordering incurs high synchronization costs caused by distributed consensus or by the use of a leader. This paper presents a protocol for linearizable state machine replication of conflict-free replicated data types (CRDTs) that neither requires consensus nor a leader. By leveraging the properties of state-based CRDTs - in particular the monotonic growth of a join semilattice - synchronization overhead is greatly reduced. In addition, updates just need a single round trip and modify the state `in-place' without the need for a log. Furthermore, the message size overhead for coordination consists of a single counter per message. While reads in the presence of concurrent updates are not wait-free without a coordinator, we show that more than 97% of reads can be handled in one or two round trips under highly concurrent accesses. Our protocol achieves high throughput without auxiliary processes like command log management or leader election. It is well suited for all practical scenarios that need linearizable access on CRDT data on a fine-granular scale. Y1 - 2019 ER - TY - JOUR A1 - Alhaddad, Samer A1 - Förstner, Jens A1 - Groth, Stefan A1 - Grünewald, Daniel A1 - Grynko, Yevgen A1 - Hannig, Frank A1 - Kenter, Tobias A1 - Pfreundt, F.J. A1 - Plessl, Christian A1 - Schotte, Merlind A1 - Steinke, Thomas A1 - Teich, J. A1 - Weiser, Martin A1 - Wende, Florian T1 - The HighPerMeshes Framework for Numerical Algorithms on Unstructured Grids JF - Concurrency and Computation: Practice and Experience N2 - Solving PDEs on unstructured grids is a cornerstone of engineering and scientific computing. Heterogeneous parallel platforms, including CPUs, GPUs, and FPGAs, enable energy-efficient and computationally demanding simulations. In this article, we introduce the HPM C++-embedded DSL that bridges the abstraction gap between the mathematical formulation of mesh-based algorithms for PDE problems on the one hand and an increasing number of heterogeneous platforms with their different programming models on the other hand. Thus, the HPM DSL aims at higher productivity in the code development process for multiple target platforms. We introduce the concepts as well as the basic structure of the HPM DSL, and demonstrate its usage with three examples. The mapping of the abstract algorithmic description onto parallel hardware, including distributed memory compute clusters, is presented. A code generator and a matching back end allow the acceleration of HPM code with GPUs. Finally, the achievable performance and scalability are demonstrated for different example problems. Y1 - 2022 U6 - https://doi.org/10.1002/cpe.6616 VL - 34 IS - 14 ER - TY - JOUR A1 - Lelievre, Tony A1 - Stoltz, Gabriel A1 - Zhang, Wei T1 - Multiple projection MCMC algorithms on submanifolds JF - IMA Journal of Numerical Analysis N2 - We propose new Markov Chain Monte Carlo algorithms to sample probability distributions on submanifolds, which generalize previous methods by allowing the use of set-valued maps in the proposal step of the MCMC algorithms. The motivation for this generalization is that the numerical solvers used to project proposed moves to the submanifold of interest may find several solutions. We show that the new algorithms indeed sample the target probability measure correctly, thanks to some carefully enforced reversibility property. We demonstrate the interest of the new MCMC algorithms on illustrative numerical examples. Y1 - 2022 U6 - https://doi.org/10.1093/imanum/drac006 ER - TY - JOUR A1 - Zhang, Wei A1 - Li, Tiejun A1 - Schütte, Christof T1 - Solving eigenvalue PDEs of metastable diffusion processes using artificial neural networks JF - Journal of Computational Physics N2 - In this paper, we consider the eigenvalue PDE problem of the infinitesimal generators of metastable diffusion processes. We propose a numerical algorithm based on training artificial neural networks for solving the leading eigenvalues and eigenfunctions of such high-dimensional eigenvalue problem. The algorithm is useful in understanding the dynamical behaviors of metastable processes on large timescales. We demonstrate the capability of our algorithm on a high-dimensional model problem, and on the simple molecular system alanine dipeptide. Y1 - 2021 U6 - https://doi.org/10.1016/j.jcp.2022.111377 VL - 465 ER - TY - JOUR A1 - Schütt, Thorsten A1 - Schintke, Florian A1 - Skrzypczak, Jan T1 - Transactions on Red-black and AVL trees in NVRAM JF - arXiv Y1 - 2020 ER - TY - JOUR A1 - Alhaddad, Samer A1 - Förstner, Jens A1 - Groth, Stefan A1 - Grünewald, Daniel A1 - Grynko, Yevgen A1 - Hannig, Frank A1 - Kenter, Tobias A1 - Pfreundt, Franz-Josef A1 - Plessl, Christian A1 - Schotte, Merlind A1 - Steinke, Thomas A1 - Teich, Jürgen A1 - Weiser, Martin A1 - Wende, Florian T1 - HighPerMeshes - A Domain-Specific Language for Numerical Algorithms on Unstructured Grids JF - Euro-Par 2020: Parallel Processing Workshops. N2 - Solving partial differential equations on unstructured grids is a cornerstone of engineering and scientific computing. Nowadays, heterogeneous parallel platforms with CPUs, GPUs, and FPGAs enable energy-efficient and computationally demanding simulations. We developed the HighPerMeshes C++-embedded Domain-Specific Language (DSL) for bridging the abstraction gap between the mathematical and algorithmic formulation of mesh-based algorithms for PDE problems on the one hand and an increasing number of heterogeneous platforms with their different parallel programming and runtime models on the other hand. Thus, the HighPerMeshes DSL aims at higher productivity in the code development process for multiple target platforms. We introduce the concepts as well as the basic structure of the HighPer-Meshes DSL, and demonstrate its usage with three examples, a Poisson and monodomain problem, respectively, solved by the continuous finite element method, and the discontinuous Galerkin method for Maxwell’s equation. The mapping of the abstract algorithmic description onto parallel hardware, including distributed memory compute clusters is presented. Finally, the achievable performance and scalability are demonstrated for a typical example problem on a multi-core CPU cluster. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-71593-9_15 SP - 185 EP - 196 PB - Springer ER - TY - JOUR A1 - Wende, Florian A1 - Marsman, Martijn A1 - Kim, Jeongnim A1 - Vasilev, Fedor A1 - Zhao, Zhengji A1 - Steinke, Thomas T1 - OpenMP in VASP: Threading and SIMD JF - International Journal of Quantum Chemistry N2 - The Vienna Ab initio Simulation Package (VASP) is a widely used electronic structure code that originally exploits process-level parallelism through the Message Passing Interface (MPI) for work distribution within and across nodes. Architectural changes of modern parallel processors urge programmers to address thread- and data-level parallelism as well to benefit most from the available compute resources within a node. We describe for VASP how to approach for an MPI + OpenMP parallelization including data-level parallelism through OpenMP SIMD constructs together with a generic high-level vector coding scheme. We can demonstrate an improved scalability of VASP and more than 20% gain over the MPI-only version, as well as a 2x increased performance of collective operations using the multiple-endpoint MPI feature. The high-level vector coding scheme applied to VASP's general gradient approximation routine gives up 9x performance gain on AVX512 platforms with the Intel compiler. Y1 - 2018 U6 - https://doi.org/10.1002/qua.25851 IS - Emerging Architectures in Computational Chemistry SP - e25851 PB - Wiley Online Library ER - TY - JOUR A1 - Kamčev, Nina A1 - Spiegel, Christoph T1 - Another note on intervals in the Hales-Jewett theorem JF - Electronic Journal of Combinatorics N2 - The Hales-Jewett Theorem states that any r-colouring of [m]ⁿ contains a monochromatic combinatorial line if n is large enough. Shelah's proof of the theorem implies that for m = 3 there always exists a monochromatic combinatorial line whose set of active coordinates is the union of at most r intervals. For odd r, Conlon and Kamčev constructed r–colourings for which it cannot be fewer than r intervals. However, we show that for even r and large n, any r–colouring of [3]ⁿ contains a monochromatic combinatorial line whose set of active coordinates is the union of at most r−1 intervals. This is optimal and extends a result of Leader and Räty for r=2. Y1 - 2022 U6 - https://doi.org/10.37236/6730 VL - 29 IS - 1 SP - P1.62 ER - TY - JOUR A1 - Hunkenschröder, Christoph A1 - Pokutta, Sebastian A1 - Weismantel, Robert T1 - Optimizing a low-dimensional convex function over a high-dimensional cub JF - SIAM Journal on Optimization Y1 - 2022 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus A1 - Keller, Bettina G. T1 - A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models JF - Journal of Mathematical Physics N2 - Dynamical reweighting methods permit to estimate kinetic observables of a stochastic process governed by a target potential U(x) from trajectories that have been generated at a different potential V(x). In this article, we present Girsanov reweighting and Square Root Approximation (SqRA): the first method reweights path probabilities exploiting the Girsanov theorem and can be applied to Markov State Models (MSMs) to reweight transition probabilities; the second method was originally developed to discretize the Fokker-Planck operator into a transition rate matrix, but here we implement it into a reweighting scheme for transition rates. We begin by reviewing the theoretical background of the methods, then present two applications relevant to Molecular Dynamics (MD), highlighting their strengths and weaknesses. Y1 - 2022 U6 - https://doi.org/10.1063/5.0127227 VL - 63 IS - 12 SP - 123306-1 EP - 123306-21 PB - AIP Publishing ER - TY - JOUR A1 - Fernandes, Rita A1 - Chaowdhary, Suvrat A1 - Saleh, Noureldin A1 - Mikula, Natalia A1 - Kanevche, Katerina A1 - Berlepsch, Hans A1 - Hosogi, Naoki A1 - Heberle, Joachim A1 - Weber, Marcus A1 - Böttcher, Christoph A1 - Koksch, Beate T1 - Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures JF - Angewandte Chemie N2 - A conjugated Cy5 dye-peptide system reveals the formation of two novel and structurally distinct supramolecular assemblies with photo-physical characteristics of H-type dimers or tetramers, respectively. The molecular ultrastructures are triggered by the complementary interplay of mutual chromophore coupling and pH induced changes in the peptide charge pattern. Y1 - 2022 VL - 61 IS - 48 SP - e202208647 ER - TY - JOUR A1 - Hoppmann-Baum, Kai A1 - Burdakov, Oleg A1 - Mexi, Gioni A1 - Casselgren, Carl Johan A1 - Koch, Thorsten T1 - Length-Constrained Cycle Partition with an Application to UAV Routing JF - Optimization Methods and Software N2 - This article discusses the Length-Constrained Cycle Partition Problem (LCCP), which constitutes a new generalization of the Travelling Salesperson Problem (TSP). Apart from nonnegative edge weights, the undirected graph in LCCP features a nonnegative critical length parameter for each vertex. A cycle partition, i.e., a vertex-disjoint cycle cover, is a feasible solution for LCCP if the length of each cycle is not greater than the critical length of each vertex contained in it. The goal is to find a feasible partition having a minimum number of cycles. Besides analyzing theoretical properties and developing preprocessing techniques, we propose an elaborate heuristic algorithm that produces solutions of good quality even for large-size instances. Moreover, we present two exact mixed-integer programming formulations (MIPs) for LCCP, which are inspired by well-known modeling approaches for TSP. Further, we introduce the concept of conflict hypergraphs, whose cliques yield valid constraints for the MIP models. We conclude with a discussion on computational experiments that we conducted using (A)TSPLIB-based problem instances. As a motivating example application, we describe a routing problem where a fleet of uncrewed aerial vehicles (UAVs) must patrol a given set of areas. Y1 - 2022 U6 - https://doi.org/10.1080/10556788.2022.2053972 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Maher, Stephen A1 - Müller, Benjamin A1 - Pedroso, João Pedro T1 - Price-and-verify: a new algorithm for recursive circle packing using Dantzig–Wolfe decomposition JF - Annals of Operations Research N2 - Packing rings into a minimum number of rectangles is an optimization problem which appears naturally in the logistics operations of the tube industry. It encompasses two major difficulties, namely the positioning of rings in rectangles and the recursive packing of rings into other rings. This problem is known as the Recursive Circle Packing Problem (RCPP). We present the first dedicated method for solving RCPP that provides strong dual bounds based on an exact Dantzig–Wolfe reformulation of a nonconvex mixed-integer nonlinear programming formulation. The key idea of this reformulation is to break symmetry on each recursion level by enumerating one-level packings, i.e., packings of circles into other circles, and by dynamically generating packings of circles into rectangles. We use column generation techniques to design a “price-and-verify” algorithm that solves this reformulation to global optimality. Extensive computational experiments on a large test set show that our method not only computes tight dual bounds, but often produces primal solutions better than those computed by heuristics from the literature. Y1 - 2018 U6 - https://doi.org/10.1007/s10479-018-3115-5 VL - 284 IS - 2 SP - 527 EP - 555 PB - Springer US ER - TY - JOUR A1 - Maher, Stephen J. T1 - A novel passenger recovery approach for the integrated airline recovery problem JF - Computers & Operations Research N2 - Schedule disruptions require airlines to intervene through the process of recovery; this involves modifications to the planned schedule, aircraft routings, crew pairings and passenger itineraries. Passenger recovery is generally considered as the final stage in this process, and hence passengers experience unnecessarily large impacts resulting from flight delays and cancellations. Most recovery approaches considering passengers involve a separately defined module within the problem formulation. However, this approach may be overly complex for recovery in many aviation and general transportation applications. This paper presents a unique description of the cancellation variables that models passenger recovery by prescribing the alternative travel arrangements for passengers in the event of flight cancellations. The results will demonstrate that this simple, but effective, passenger recovery approach significantly reduces the operational costs of the airline and increases passenger flow through the network. The integrated airline recovery problem with passenger reallocation is solved using column-and-row generation to achieve high quality solutions in short runtimes. An analysis of the column-and-row generation solution approach is performed, identifying a number of enhancement techniques to further improve the solution runtimes. Y1 - 2015 U6 - https://doi.org/10.1016/j.cor.2014.11.005 VL - 57 SP - 123 EP - 137 ER - TY - JOUR A1 - Maher, Stephen J. T1 - Solving the integrated airline recovery problem using column-and-row generation JF - Transportation Science N2 - Airline recovery presents very large and difficult problems requiring high quality solutions within very short time limits. To improve computational performance, the complete airline recovery problem is generally formulated as a series of sequential stages. While the sequential approach greatly simplifies the complete recovery problem, there is no guarantee of global optimality or solution quality. To address this, there has been increasing interest in the development of efficient solution techniques to solve an integrated recovery problem. In this paper, an integrated airline recovery problem is proposed by integrating the schedule, crew and aircraft recovery stages. To achieve short runtimes and high quality solutions, this problem is solved using column-and-row generation. Column-and-row generation achieves an improvement in solution runtimes by reducing the problem size and thereby achieving a faster execution of each LP solve. Further, the results demonstrate that a good upper bound achieved early in the solution process, indicating an improved solution quality with the early termination of the algorithm. This paper also details the integration of the row generation procedure with branch-and-price, which is used to achieve integral optimal solutions. The benefits of applying column-and-row generation to solve the integrated recovery problem are demonstrated with a comparison to a standard column generation technique. Y1 - 2015 U6 - https://doi.org/10.1287/trsc.2014.0552 VL - 50 IS - 1 SP - 216 EP - 239 ER - TY - JOUR A1 - Maher, Stephen J. A1 - Murray, John M. T1 - The unrooted set covering connected subgraph problem differentiating between HIV envelope sequences JF - European Journal of Operational Research N2 - This paper presents a novel application of operations research techniques to the analysis of HIV Env gene sequences, aiming to identify key features that are possible vaccine targets. These targets are identified as being critical to the transmission of HIV by being present in early transmitted (founder) sequences and absent in later chronic sequences. Identifying the key features of Env involves two steps: first, calculating the covariance of amino acid combinations and positions to form a network of related and compensatory mutations; and second, developing an integer program to identify the smallest connected subgraph of the constructed covariance network that exhibits a set covering property. The integer program developed for this analysis, labelled the unrooted set covering connected subgraph problem (USCCSP), integrates a set covering problem and connectivity evaluation, the latter formulated as a network flow problem. The resulting integer program is very large and complex, requiring the use of Benders' decomposition to develop an efficient solution approach. The results will demonstrate the necessity of applying acceleration techniques to the Benders' decomposition solution approach and the effectiveness of these techniques and heuristic approaches for solving the USCCSP. Y1 - 2016 U6 - https://doi.org/doi:10.1016/j.ejor.2015.07.011 VL - 248 IS - 2 SP - 668 EP - 680 ER - TY - JOUR A1 - Froyland, Gary A1 - Maher, Stephen J. A1 - Wu, Cheng-Lung T1 - The recoverable robust tail assignment problem JF - Transportation Science N2 - Schedule disruptions are commonplace in the airline industry with many flight-delaying events occurring each day. Recently there has been a focus on introducing robustness into airline planning stages to reduce the effect of these disruptions. We propose a recoverable robustness technique as an alternative to robust optimisation to reduce the effect of disruptions and the cost of recovery. We formulate the recoverable robust tail assignment problem (RRTAP) as a stochastic program, solved using column generation in the master and subproblems of the Benders' decomposition. We implement a two-phase algorithm for the Benders' decomposition and identify pareto-optimal cuts. The RRTAP includes costs due to flight delays, cancellation, and passenger rerouting, and the recovery stage includes cancellation, delay, and swapping options. To highlight the benefits of simultaneously solving planning and recovery problems in the RRTAP we compare our tail assignment solution against current approaches from the literature. Using airline data we demonstrate that by developing a better tail assignment plan via the RRTAP framework, one can reduce recovery costs in the event of a disruption. Y1 - 2014 U6 - https://doi.org/10.1287/trsc.2013.0463 VL - 48 IS - 3 SP - 351 EP - 372 ER - TY - JOUR A1 - Tack, Alexander A1 - Shestakov, Alexey A1 - Lüdke, David A1 - Zachow, Stefan T1 - A deep multi-task learning method for detection of meniscal tears in MRI data from the Osteoarthritis Initiative database JF - Frontiers in Bioengineering and Biotechnology, section Biomechanics N2 - We present a novel and computationally efficient method for the detection of meniscal tears in Magnetic Resonance Imaging (MRI) data. Our method is based on a Convolutional Neural Network (CNN) that operates on a complete 3D MRI scan. Our approach detects the presence of meniscal tears in three anatomical sub-regions (anterior horn, meniscal body, posterior horn) for both the Medial Meniscus (MM) and the Lateral Meniscus (LM) individually. For optimal performance of our method, we investigate how to preprocess the MRI data or how to train the CNN such that only relevant information within a Region of Interest (RoI) of the data volume is taken into account for meniscal tear detection. We propose meniscal tear detection combined with a bounding box regressor in a multi-task deep learning framework to let the CNN implicitly consider the corresponding RoIs of the menisci. We evaluate the accuracy of our CNN-based meniscal tear detection approach on 2,399 Double Echo Steady-State (DESS) MRI scans from the Osteoarthritis Initiative database. In addition, to show that our method is capable of generalizing to other MRI sequences, we also adapt our model to Intermediate-Weighted Turbo Spin-Echo (IW TSE) MRI scans. To judge the quality of our approaches, Receiver Operating Characteristic (ROC) curves and Area Under the Curve (AUC) values are evaluated for both MRI sequences. For the detection of tears in DESS MRI, our method reaches AUC values of 0.94, 0.93, 0.93 (anterior horn, body, posterior horn) in MM and 0.96, 0.94, 0.91 in LM. For the detection of tears in IW TSE MRI data, our method yields AUC values of 0.84, 0.88, 0.86 in MM and 0.95, 0.91, 0.90 in LM. In conclusion, the presented method achieves high accuracy for detecting meniscal tears in both DESS and IW TSE MRI data. Furthermore, our method can be easily trained and applied to other MRI sequences. Y1 - 2021 U6 - https://doi.org/10.3389/fbioe.2021.747217 SP - 28 EP - 41 ER - TY - JOUR A1 - Berg, Mascha A1 - Plöntzke, Julia A1 - Siebert, Heike A1 - Röblitz, Susanna T1 - Modelling Oscillatory Patterns in the Bovine Estrous Cycle with Boolean Delay Equations JF - Bulletin of Mathematical Biology N2 - Boolean delay equations (BDEs), with their relatively simple and intuitive mode of modelling, have been used in many research areas including, for example, climate dynamics and earthquake propagation. Their application to biological systems has been scarce and limited to the molecular level. Here, we derive and present two BDE models. One is directly derived from a previously published ordinary differential equation (ODE) model for the bovine estrous cycle, whereas the second model includes a modification of a particular biological mechanism. We not only compare the simulation results from the BDE models with the trajectories of the ODE model, but also validate the BDE models with two additional numerical experiments. One experiment induces a switch in the oscillatory pattern upon changes in the model parameters, and the other simulates the administration of a hormone that is known to shift the estrous cycle in time. The models presented here are the first BDE models for hormonal oscillators, and the first BDE models for drug administration. Even though automatic parameter estimation still remains challenging, our results support the role of BDEs as a framework for the systematic modelling of complex biological oscillators. Y1 - 2021 U6 - https://doi.org/10.1007/s11538-021-00942-z VL - 83 IS - 121 SP - 1 EP - 25 ER - TY - JOUR A1 - Zangerl, Lina Maria A1 - Peters-Kottig, Wolfgang A1 - Oßwald, Achim T1 - Personal Digital Archiving: Eine neue Aufgabe für Öffentliche und Wissenschaftliche Bibliotheken JF - Bibliothek Forschung und Praxis N2 - Die Sicherung und längerfristige Archivierung persönlich relevanter Dokumente und Dateien, in der Fachliteratur als Personal Digital Archiving (PDA) bezeichnet, ist eine für Privatpersonen zunehmend wichtiger werdende Aufgabe. Praktische Anleitungen und weiterführende Hinweise zur Umsetzung dieser Aufgabe gibt die auf unterschiedliche Nutzer:innenperspektiven ausgerichtete Webseite meinDigitalesArchiv.de, die seit 2020 von der nestor-AG PDA bereitgestellt wird. Mit den Informationen dieser Webseite können und sollten Bibliotheken und andere Einrichtungen, die Informationskompetenz vermitteln, Privatpersonen für die Sicherung ihrer persönlichen digitalen Daten sensibilisieren und schulen. Mit der Umsetzung dieser Aufgabe können Öffentliche wie Wissenschaftliche Bibliotheken zur Sicherung auch gesamtgesellschaftlich relevanter Erinnerungsbausteine beitragen. Y1 - 2022 U6 - https://doi.org/10.1515/bfp-2021-0058 VL - 46 IS - 1 SP - 152 EP - 161 ER - TY - JOUR A1 - Schneider, Philipp-Immanuel A1 - Manley, Phillip A1 - Krüger, Jan A1 - Zschiedrich, Lin A1 - Köning, Rainer A1 - Bodermann, Bernd A1 - Burger, Sven T1 - Reconstructing phase aberrations for high-precision dimensional microscopy JF - Proc. SPIE Y1 - 2022 U6 - https://doi.org/10.1117/12.2620762 VL - 12137 SP - 121370I ER - TY - JOUR A1 - Avalos-Ovando, Oscar A1 - Santiago, Eva Yazmin A1 - Movsesyan, Artur A1 - Kong, Xiang-Tian A1 - Yu, Peng A1 - Besteiro, Lucas V. A1 - Khosravi Khorashad, Larousse A1 - Okamoto, Hiromi A1 - Slocik, Joseph M. A1 - Correa-Duarte, Miguel A1 - Comesana-Hermo, Miguel A1 - Liedl, Tim A1 - Markovich, Gil A1 - Burger, Sven A1 - Govorov, Alexander O. T1 - Chiral Bioinspired Plasmonics: A Paradigm Shift for Optical Activity and Photochemistry JF - ACS Photon. Y1 - 2022 U6 - https://doi.org/10.1021/acsphotonics.2c00445 VL - 9 SP - 2219 ER - TY - JOUR A1 - Tack, Alexander A1 - Ambellan, Felix A1 - Zachow, Stefan T1 - Towards novel osteoarthritis biomarkers: Multi-criteria evaluation of 46,996 segmented knee MRI data from the Osteoarthritis Initiative JF - PLOS One N2 - Convolutional neural networks (CNNs) are the state-of-the-art for automated assessment of knee osteoarthritis (KOA) from medical image data. However, these methods lack interpretability, mainly focus on image texture, and cannot completely grasp the analyzed anatomies’ shapes. In this study we assess the informative value of quantitative features derived from segmentations in order to assess their potential as an alternative or extension to CNN-based approaches regarding multiple aspects of KOA. Six anatomical structures around the knee (femoral and tibial bones, femoral and tibial cartilages, and both menisci) are segmented in 46,996 MRI scans. Based on these segmentations, quantitative features are computed, i.e., measurements such as cartilage volume, meniscal extrusion and tibial coverage, as well as geometric features based on a statistical shape encoding of the anatomies. The feature quality is assessed by investigating their association to the Kellgren-Lawrence grade (KLG), joint space narrowing (JSN), incident KOA, and total knee replacement (TKR). Using gold standard labels from the Osteoarthritis Initiative database the balanced accuracy (BA), the area under the Receiver Operating Characteristic curve (AUC), and weighted kappa statistics are evaluated. Features based on shape encodings of femur, tibia, and menisci plus the performed measurements showed most potential as KOA biomarkers. Differentiation between non-arthritic and severely arthritic knees yielded BAs of up to 99%, 84% were achieved for diagnosis of early KOA. Weighted kappa values of 0.73, 0.72, and 0.78 were achieved for classification of the grade of medial JSN, lateral JSN, and KLG, respectively. The AUC was 0.61 and 0.76 for prediction of incident KOA and TKR within one year, respectively. Quantitative features from automated segmentations provide novel biomarkers for KLG and JSN classification and show potential for incident KOA and TKR prediction. The validity of these features should be further evaluated, especially as extensions of CNN- based approaches. To foster such developments we make all segmentations publicly available together with this publication. Y1 - 2021 U6 - https://doi.org/10.1371/journal.pone.0258855 VL - 16 IS - 10 ER - TY - JOUR A1 - Lindner, Niels A1 - Reisch, Julian T1 - An analysis of the parameterized complexity of periodic timetabling JF - Journal of Scheduling N2 - Public transportation networks are typically operated with a periodic timetable. The periodic event scheduling problem (PESP) is the standard mathematical modeling tool for periodic timetabling. PESP is a computationally very challenging problem: For example, solving the instances of the benchmarking library PESPlib to optimality seems out of reach. Since PESP can be solved in linear time on trees, and the treewidth is a rather small graph parameter in the networks of the PESPlib, it is a natural question to ask whether there are polynomial-time algorithms for input networks of bounded treewidth, or even better, fixed-parameter tractable algorithms. We show that deciding the feasibility of a PESP instance is NP-hard even when the treewidth is 2, the branchwidth is 2, or the carvingwidth is 3. Analogous results hold for the optimization of reduced PESP instances, where the feasibility problem is trivial. Moreover, we show W[1]-hardness of the general feasibility problem with respect to treewidth, which means that we can most likely only accomplish pseudo-polynomial-time algorithms on input networks with bounded tree- or branchwidth. We present two such algorithms based on dynamic programming. We further analyze the parameterized complexity of PESP with bounded cyclomatic number, diameter, or vertex cover number. For event-activity networks with a special—but standard—structure, we give explicit and sharp bounds on the branchwidth in terms of the maximum degree and the carvingwidth of an underlying line network. Finally, we investigate several parameters on the smallest instance of the benchmarking library PESPlib. Y1 - 2022 U6 - https://doi.org/10.1007/s10951-021-00719-1 VL - 25 SP - 157 EP - 176 ER - TY - JOUR A1 - Eigen, Lennart A1 - Baum, Daniel A1 - Dean, Mason N. A1 - Werner, Daniel A1 - Wölfer, Jan A1 - Nyakatura, John A. T1 - Ontogeny of a tessellated surface: carapace growth of the longhorn cowfish Lactoria cornuta JF - Journal of Anatomy N2 - Biological armors derive their mechanical integrity in part from their geometric architectures, often involving tessellations: individual structural elements tiled together to form surface shells. The carapace of boxfish, for example, is comprised of mineralized polygonal plates, called scutes, arranged in a complex geometric pattern and nearly completely encasing the body. In contrast to artificial armors, the boxfish exoskeleton grows with the fish; the relationship between the tessellation and the gross structure of the armor is therefore critical to sustained protection throughout growth. To clarify whether or how the boxfish tessellation is maintained or altered with age, we quantify architectural aspects of the tessellated carapace of the longhorn cowfish Lactoria cornuta through ontogeny (across nearly an order of magnitude in standard length) and in a high-throughput fashion, using high-resolution microCT data and segmentation algorithms to characterize the hundreds of scutes that cover each individual. We show that carapace growth is canalized with little variability across individuals: rather than continually adding scutes to enlarge the carapace surface, the number of scutes is surprisingly constant, with scutes increasing in volume, thickness, and especially width with age. As cowfish and their scutes grow, scutes become comparatively thinner, with the scutes at the edges (weak points in a boxy architecture) being some of the thickest and most reinforced in younger animals and thinning most slowly across ontogeny. In contrast, smaller scutes with more variable curvature were found in the limited areas of more complex topology (e.g. around fin insertions, mouth, and anus). Measurements of Gaussian and mean curvature illustrate that cowfish are essentially tessellated boxes throughout life: predominantly zero curvature surfaces comprised of mostly flat scutes, and with scutes with sharp bends used sparingly to form box edges. Since growth of a curved, tiled surface with a fixed number of tiles would require tile restructuring to accommodate the surface’s changing radius of curvature, our results therefore illustrate a previously unappreciated advantage of the odd boxfish morphology: by having predominantly flat surfaces, it is the box-like body form that in fact permits a relatively straightforward growth system of this tessellated architecture (i.e. where material is added to scute edges). Our characterization of the ontogeny and maintenance of the carapace tessellation provides insights into the potentially conflicting mechanical, geometric and developmental constraints of this species, but also perspectives into natural strategies for constructing mutable tiled architectures. Y1 - 2022 U6 - https://doi.org/10.1111/joa.13692 VL - 241 IS - 3 SP - 565 EP - 580 PB - Wiley ER - TY - JOUR A1 - Lenz, Ralf A1 - Serrano, Felipe T1 - Tight Convex Relaxations for the Expansion Planning Problem JF - Journal of Optimization Theory and Applications N2 - Secure energy transport is considered as highly relevant for the basic infrastructure of nowadays society and economy. To satisfy increasing demands and to handle more diverse transport situations, operators of energy networks regularly expand the capacity of their network by building new network elements, known as the expansion planning problem. A key constraint function in expansion planning problems is a nonlinear and nonconvex potential loss function. In order to improve the algorithmic performance of state-of-the-art MINLP solvers, this paper presents an algebraic description for the convex envelope of this function. Through a thorough computational study, we show that this tighter relaxation tremendously improves the performance of the MINLP solver SCIP on a large test set of practically relevant instances for the expansion planning problem. In particular, the results show that our achievements lead to an improvement of the solver performance for a development version by up to 58%. Y1 - 2022 U6 - https://doi.org/10.1007/s10957-022-02029-8 VL - 194 SP - 325 EP - 352 ER - TY - JOUR A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Computation of eigenfrequency sensitivities using Riesz projections for efficient optimization of nanophotonic resonators JF - Commun. Phys. Y1 - 2022 U6 - https://doi.org/10.1038/s42005-022-00977-1 VL - 5 SP - 202 ER - TY - JOUR A1 - Mahnke, Heinz-Eberhard A1 - Arlt, Tobias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Herter, Felix A1 - Lindow, Norbert A1 - Manke, Ingo A1 - Siopi, Tzulia A1 - Menei, Eve A1 - Etienne, Marc A1 - Lepper, Verena T1 - Virtual unfolding of folded papyri JF - Journal of Cultural Heritage N2 - The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Musée du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for “Lord”. Y1 - 2020 U6 - https://doi.org/10.1016/j.culher.2019.07.007 VL - 41 SP - 264 EP - 269 PB - Elsevier ER - TY - JOUR A1 - Baum, Daniel A1 - Herter, Felix A1 - Larsen, John Møller A1 - Lichtenberger, Achim A1 - Raja, Rubina T1 - Revisiting the Jerash Silver Scroll: a new visual data analysis approach JF - Digital Applications in Archaeology and Cultural Heritage N2 - This article revisits a complexly folded silver scroll excavated in Jerash, Jordan in 2014 that was digitally examined in 2015. In this article we apply, examine and discuss a new virtual unfolding technique that results in a clearer image of the scroll’s 17 lines of writing. We also compare it to the earlier unfolding and discuss progress in general analytical tools. We publish the original and the new images as well as the unfolded volume data open access in order to make these available to researchers interested in optimising unfolding processes of various complexly folded materials. Y1 - 2021 U6 - https://doi.org/10.1016/j.daach.2021.e00186 VL - 21 SP - e00186 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Zonker, Johannes A1 - Schütte, Christof A1 - Djurdjevac Conrad, Natasa T1 - Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading JF - Mathematical Biosciences N2 - Agent based models (ABMs) are a useful tool for modeling spatio-temporal population dynamics, where many details can be included in the model description. Their computational cost though is very high and for stochastic ABMs a lot of individual simulations are required to sample quantities of interest. Especially, large numbers of agents render the sampling infeasible. Model reduction to a metapopulation model leads to a significant gain in computational efficiency, while preserving important dynamical properties. Based on a precise mathematical description of spatio-temporal ABMs, we present two different metapopulation approaches (stochastic and piecewise deterministic) and discuss the approximation steps between the different models within this framework. Especially, we show how the stochastic metapopulation model results from a Galerkin projection of the underlying ABM onto a finite-dimensional ansatz space. Finally, we utilize our modeling framework to provide a conceptual model for the spreading of COVID-19 that can be scaled to real-world scenarios. Y1 - 2021 U6 - https://doi.org/10.1016/j.mbs.2021.108619 VL - 336 PB - Elsevier ER - TY - JOUR A1 - Plock, Matthias A1 - Andrle, Kas A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel T1 - Bayesian Target-Vector Optimization for Efficient Parameter Reconstruction JF - Adv. Theory Simul. Y1 - 2022 U6 - https://doi.org/10.1002/adts.202200112 VL - 5 SP - 2200112 ER - TY - JOUR A1 - Martens, Kevin A1 - Funck, Timon A1 - Santiago, Eva Y. A1 - Govorov, Alexander O. A1 - Burger, Sven A1 - Liedl, Tim T1 - Onset of Chirality in Plasmonic Meta-Molecules and Dielectric Coupling JF - ACS Nano Y1 - 2022 U6 - https://doi.org/10.1021/acsnano.2c04729 VL - 16 SP - 16143 ER - TY - JOUR A1 - Fischer-Holzhausen, Sophie A1 - Röblitz, Susanna T1 - Hormonal regulation of ovarian follicle growth in humans: Model-based exploration of cycle variability and parameter sensitivities JF - Journal of Theoretical Biology N2 - We present a modelling and simulation framework for the dynamics of ovarian follicles and key hormones along the hypothalamic-pituitary-gonadal axis throughout consecutive human menstrual cycles. All simulation results (hormone concentrations and ovarian follicle sizes) are in biological units and can easily be compared to clinical data. The model takes into account variability in follicles' response to stimulating hormones, which introduces variability between cycles. The growth of ovarian follicles in waves is an emergent property in our model simulations and further supports the hypothesis that follicular waves are also present in humans. We use Approximate Bayesian Computation and cluster analysis to construct a population of virtual subjects and to study parameter distributions and sensitivities. The model can be used to compare and optimize treatment protocols for ovarian hyperstimulation, thus potentially forming the integral part of a clinical decision support system in reproductive endocrinology. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1016/j.jtbi.2022.111150 ER - TY - JOUR A1 - Roux, Christophe A1 - Pokutta, Sebastian A1 - Wirth, Elias A1 - Kerdreux, Thomas T1 - Efficient Online-Bandit Strategies for Minimax Learning Problems N2 - Several learning problems involve solving min-max problems, e.g., empirical distributional robust learning [Namkoong and Duchi, 2016, Curi et al., 2020] or learning with non-standard aggregated losses [Shalev- Shwartz and Wexler, 2016, Fan et al., 2017]. More specifically, these problems are convex-linear problems where the minimization is carried out over the model parameters w ∈ W and the maximization over the empirical distribution p ∈ K of the training set indexes, where K is the simplex or a subset of it. To design efficient methods, we let an online learning algorithm play against a (combinatorial) bandit algorithm. We argue that the efficiency of such approaches critically depends on the structure of K and propose two properties of K that facilitate designing efficient algorithms. We focus on a specific family of sets Sn,k encompassing various learning applications and provide high-probability convergence guarantees to the minimax values. Y1 - 2021 ER - TY - JOUR A1 - Krüger, Tillmann A1 - Leeners, Brigitte A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Ille, Fabian A1 - Egli, Marcel A1 - Engler, Harald A1 - Röblitz, Susanna A1 - Frieling, Helge A1 - Sinke, Christopher A1 - Jahn, Kirsten T1 - The androgen system across the menstrual cycle: Hormonal, (epi-)genetic and psychometric alterations JF - Physiology and Behavior Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1016/j.physbeh.2022.114034 ER - TY - JOUR A1 - Colom, Remi A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Kivshar, Yuri A1 - Burger, Sven T1 - Enhanced Purcell factor for nanoantennas supporting interfering resonances JF - Phys. Rev. Research Y1 - 2022 U6 - https://doi.org/10.1103/PhysRevResearch.4.023189 VL - 4 SP - 023189 ER - TY - JOUR A1 - Fischer-Holzhausen, Sophie A1 - Röblitz, Susanna T1 - Mathematical modelling of follicular growth and ovarian stimulation JF - Current Opinion in Endocrine and Metabolic Research Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1016/j.coemr.2022.100385 ER - TY - JOUR A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - Höfling, Felix T1 - Stochastic pH oscillations in a model of the urea–urease reaction confined to lipid vesicles JF - J. Phys. Chem. Lett. N2 - The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We numerically study the confinement of the reaction to lipid vesicles, which permit the exchange with an external reservoir by differential transport, enabling the recovery of the pH level and yielding a constant supply of urea molecules. For microscopically small vesicles, the discreteness of the number of molecules requires a stochastic treatment of the reaction dynamics. Our analysis shows that intrinsic noise induces a significant statistical variation of the oscillation period, which increases as the vesicles become smaller. The mean period, however, is found to be remarkably robust for vesicle sizes down to approximately 200 nm, but the periodicity of the rhythm is gradually destroyed for smaller vesicles. The observed oscillations are explained as a canard-like limit cycle that differs from the wide class of conventional feedback oscillators. Y1 - 2021 U6 - https://doi.org/10.1021/acs.jpclett.1c03016 VL - 12 SP - 9888 EP - 9893 ER - TY - JOUR A1 - Dierkes, Thomas T1 - Construction of ODE systems from time series data by a highly flexible modelling approach JF - ArXiv e-prints N2 - In this paper, a down-to-earth approach to purely data-based modelling of unknown dynamical systems is presented. Starting from a classical, explicit ODE formulation y=f(t,y) of a dynamical system, a method determining the unknown right-hand side f(t,y) from some trajectory data y_k(t_j), possibly very sparse, is given. As illustrative examples, a semi-standard predator-prey model is reconstructed from a data set describing the population numbers of hares and lynxes over a period of twenty years, and a simple damped pendulum system with a highly non-linear right-hand side is recovered from some artificial but very sparse data. Y1 - 2015 VL - math.NA 1512.03357 ER - TY - JOUR A1 - Dierkes, Thomas T1 - Ist die Umsetzung der Open-Access-Komponente in Allianz-Lizenzverträgen wirklich so kompliziert? JF - ABI Technik N2 - Thomas Dierkes ist promovierter Mathematiker und als Entwickler beim Kooperativen Bibliotheksverbund Berlin-Brandenburg (KOBV) am Zuse-Institut Berlin (ZIB) tätig. Er arbeitet dort an der Entwicklung einer „Datendrehscheibe“ für die Umsetzung der Open-Access-Komponente in Allianz-Lizenzen. Er beantwortet die aktuelle Abi Technikfrage: „Ist die Umsetzung der Open-Access-Komponente in Allianz-Lizenzverträgen wirklich so kompliziert?“ Y1 - 2017 U6 - https://doi.org/10.1515/abitech-2017-0051 VL - 37 IS - 3 SP - 237 ER - TY - JOUR A1 - Rusch, Beate A1 - Boltze, Julia A1 - Dierkes, Thomas A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Staub, Hedda T1 - DeepGreen - DeepGold: Open-Access-Transformation - Entwicklung und Perspektiven JF - GMS Medizin - Bibliothek - Information N2 - Das deutsche Projekt DeepGreen (https://deepgreen.kobv.de/de/deepgreen/) arbeitet an einer automatisierten Lösung, um Artikeldaten (Volltexte und Metadaten) von wissenschaftlichen Verlagen abzuholen und an Repositorien zu liefern, die diese Artikel wiederum Open Access veröffentlichen können. Ausgangspunkt für das Projekt sind die überregional geförderten deutschen Allianz-Lizenzen. Diese enthalten eine Open-Access-Komponente, die es Autor*innen oder deren Institution erlaubt, ihre Artikel nach einer verkürzten Embargofrist in einem Repositorium ihrer Wahl Open Access zugänglich zu machen. DeepGreen wird seit 2016 von der Deutschen Forschungsgemeinschaft gefördert (1. Förderphase: 01.2016–12.2017; 2. Förderphase: 08.2018–07.2020) und besteht aus einem Konsortium aus 6 Institutionen: Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV), Bayerische Staatsbibliothek (BSB), Bibliotheksverbund Bayern (BVB), Universitätsbibliothek der Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum Potsdam (GFZ), Universitätsbibliothek der Technischen Universität Berlin (TUBB). Y1 - 2019 U6 - https://doi.org/10.3205/mbi000432 VL - 19 IS - 1-2 ER - TY - JOUR A1 - Maher, Stephen J. A1 - Desaulniers, Guy A1 - Soumis, Francois T1 - Recoverable robust single day aircraft maintenance routing problem JF - Computers & Operations Research N2 - Aircraft maintenance planning is of critical importance to the safe and efficient operations of an airline. It is common to solve the aircraft routing and maintenance planning problems many months in advance, with the solution spanning multiple days. An unfortunate consequence of this approach is the possible infeasibility of the maintenance plan due to frequent perturbations occurring in operations. There is an emerging concept that focuses on the generation of aircraft routes for a single day to ensure maintenance coverage that night, alleviating the effects of schedule perturbations from preceding days. In this paper, we present a novel approach to ensure that a sufficient number of aircraft routes are provided each day so maintenance critical aircraft receive maintenance that night. By penalising the under supply of routes terminating at maintenance stations from each overnight airport, we construct a single day routing to provide the best possible maintenance plan. This single day aircraft maintenance routing problem (SDAMRP) is further protected from disruptions by applying the recoverable robustness framework. To efficiently solve the recoverable robust SDAMRP acceleration techniques, such as identifying Pareto-optimal cuts and a trust region approach, have been applied. The SDAMRP is evaluated against a set of flight schedules and the results demonstrate a significantly improved aircraft maintenance plan. Further, the results demonstrate the magnitude of recoverability improvement that is achieved by employing recoverable robustness to the SDAMRP. Y1 - 2014 U6 - https://doi.org/10.1016/j.cor.2014.03.007 VL - 51 SP - 130 EP - 145 ER - TY - JOUR A1 - Djurdjevac, Ana T1 - Linear Parabolic Problems in Random Moving Domains N2 - We consider linear parabolic equations on a random non-cylindrical domain. Utilizing the domain mapping method, we write the problem as a partial differential equation with random coefficients on a cylindrical deterministic domain. Exploiting the deterministic results concerning equations on non-cylindrical domains, we state the necessary assumptions about the velocity filed and in addition, about the flow transformation that this field generates. In this paper we consider both cases, the uniformly bounded with respect to the sample and log-normal type transformation. In addition, we give an explicit example of a log-normal type transformation and prove that it does not satisfy the uniformly bounded condition. We define a general framework for considering linear parabolic problems on random non-cylindrical domains. As the first example, we consider the heat equation on a random tube domain and prove its well-posedness. Moreover, as the other example we consider the parabolic Stokes equation which illustrates the case when it is not enough just to study the plain-back transformation of the function, but instead to consider for example the Piola type transformation, in order to keep the divergence free property. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1137/19M1284889 VL - 9 IS - 2 SP - 848 EP - 879 ER - TY - JOUR A1 - Djurdjevac, Ana A1 - Gräser, Carsten A1 - Herbert, Philip J. T1 - Non-stationary incompressible linear fluid equations in a moving domain JF - arXiv N2 - This article considers non-stationary incompressible linear fluid equations in a moving domain. We demonstrate the existence and uniqueness of an appropriate weak formulation of the problem by making use of the theory of time-dependent Bochner spaces. It is not possible to directly apply established evolving Hilbert space theory due to the incompressibility constraint. After we have established the well-posedness, we derive and analyse a time discretisation of the system. Y1 - 2021 ER - TY - JOUR A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Thiede, Doreen T1 - Conference Report on the 20th BOBCATSSS Symposium JF - IFLA SET Bulletin Y1 - 2012 UR - http://www.ifla.org/files/set/Bulletin/_SET_Bulletin2012-July%202012%20Vol.13n2.pdf VL - 13 IS - 2 SP - 18 EP - 19 ER - TY - JOUR A1 - Chegini, Fatemeh A1 - Kopanicakova, Alena A1 - Krause, Rolf A1 - Weiser, Martin T1 - Efficient Identification of Scars using Heterogeneous Model Hierarchies JF - EP Europace N2 - Aims. Detection and quantification of myocardial scars are helpful both for diagnosis of heart diseases and for building personalized simulation models. Scar tissue is generally charac­terized by a different conduction of electrical excitation. We aim at estimating conductivity-related parameters from endocardial mapping data, in particular the conductivity tensor. Solving this inverse problem requires computationally expensive monodomain simulations on fine discretizations. Therefore, we aim at accelerating the estimation using a multilevel method combining electrophysiology models of different complexity, namely the mono­domain and the eikonal model. Methods. Distributed parameter estimation is performed by minimizing the misfit between simulated and measured electrical activity on the endocardial surface, subject to the mono­domain model and regularization, leading to a constrained optimization problem. We formulate this optimization problem, including the modeling of scar tissue and different regularizations, and design an efficient iterative solver. We consider monodomain grid hierarchies and monodomain-eikonal model hierarchies in a recursive multilevel trust-region method. Results. From several numerical examples, both the efficiency of the method and the estimation quality, depending on the data, are investigated. The multilevel solver is significantly faster than a comparable single level solver. Endocardial mapping data of realistic density appears to be just sufficient to provide quantitatively reasonable estimates of location, size, and shape of scars close to the endocardial surface. Conclusion. In several situations, scar reconstruction based on eikonal and monodomain models differ significantly, suggesting the use of the more accurate but more expensive monodomain model for this purpose. Still, eikonal models can be utilized to accelerate the computations considerably, enabling the use of complex electrophysiology models for estimating myocardial scars from endocardial mapping data. Y1 - 2021 U6 - https://doi.org/10.1093/europace/euaa402 VL - 23 SP - i113 EP - i122 ER - TY - JOUR A1 - Goltz-Fellgiebel, Julia Alexandra A1 - Groh, Melanie A1 - Kinstler, Till A1 - Kropf, Katrin A1 - Weiser, Evelyn T1 - Cycling for Libraries 2012 - The Baltic States JF - BuB Y1 - 2012 UR - http://www.b-u-b.de/pdfarchiv/Heft-BuB_10_2012.pdf IS - 10 SP - 670 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten T1 - Implications, Conflicts, and Reductions for Steiner Trees JF - Mathematical Programming Y1 - 2023 U6 - https://doi.org/10.1007/s10107-021-01757-5 VL - 197 SP - 903 EP - 966 PB - Springer ER - TY - JOUR A1 - Sekuboyina, Anjany A1 - Husseini, Malek E. A1 - Bayat, Amirhossein A1 - Löffler, Maximilian A1 - Liebl, Hans A1 - Li, Hongwei A1 - Tetteh, Giles A1 - Kukačka, Jan A1 - Payer, Christian A1 - Štern, Darko A1 - Urschler, Martin A1 - Chen, Maodong A1 - Cheng, Dalong A1 - Lessmann, Nikolas A1 - Hu, Yujin A1 - Wang, Tianfu A1 - Yang, Dong A1 - Xu, Daguang A1 - Ambellan, Felix A1 - Amiranashvili, Tamaz A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Lehnert, Sebastian A1 - Lirio, Marilia A1 - de Olaguer, Nicolás Pérez A1 - Ramm, Heiko A1 - Sahu, Manish A1 - Tack, Alexander A1 - Zachow, Stefan A1 - Jiang, Tao A1 - Ma, Xinjun A1 - Angerman, Christoph A1 - Wang, Xin A1 - Brown, Kevin A1 - Kirszenberg, Alexandre A1 - Puybareau, Élodie A1 - Chen, Di A1 - Bai, Yiwei A1 - Rapazzo, Brandon H. A1 - Yeah, Timyoas A1 - Zhang, Amber A1 - Xu, Shangliang A1 - Hou, Feng A1 - He, Zhiqiang A1 - Zeng, Chan A1 - Xiangshang, Zheng A1 - Liming, Xu A1 - Netherton, Tucker J. A1 - Mumme, Raymond P. A1 - Court, Laurence E. A1 - Huang, Zixun A1 - He, Chenhang A1 - Wang, Li-Wen A1 - Ling, Sai Ho A1 - Huynh, Lê Duy A1 - Boutry, Nicolas A1 - Jakubicek, Roman A1 - Chmelik, Jiri A1 - Mulay, Supriti A1 - Sivaprakasam, Mohanasankar A1 - Paetzold, Johannes C. A1 - Shit, Suprosanna A1 - Ezhov, Ivan A1 - Wiestler, Benedikt A1 - Glocker, Ben A1 - Valentinitsch, Alexander A1 - Rempfler, Markus A1 - Menze, Björn H. A1 - Kirschke, Jan S. T1 - VerSe: A Vertebrae labelling and segmentation benchmark for multi-detector CT images JF - Medical Image Analysis N2 - Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision support systems for diagnosis, surgery planning, and population-based analysis of spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms tackling the labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the results of this evaluation and further investigate the performance variation at the vertebra level, scan level, and different fields of view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top-performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The VerSe content and code can be accessed at: https://github.com/anjany/verse. Y1 - 2021 U6 - https://doi.org/10.1016/j.media.2021.102166 VL - 73 ER - TY - JOUR A1 - Glatzeder, Korbinian A1 - Komnik, Igor A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - Potthast, Wolfgang T1 - Dynamic pressure analysis of novel interpositional knee spacer implants in 3D-printed human knee models JF - Scientific Reports N2 - Alternative treatment methods for knee osteoarthritis (OA) are in demand, to delay the young (< 50 Years) patient’s need for osteotomy or knee replacement. Novel interpositional knee spacers shape based on statistical shape model (SSM) approach and made of polyurethane (PU) were developed to present a minimally invasive method to treat medial OA in the knee. The implant should be supposed to reduce peak strains and pain, restore the stability of the knee, correct the malalignment of a varus knee and improve joint function and gait. Firstly, the spacers were tested in artificial knee models. It is assumed that by application of a spacer, a significant reduction in stress values and a significant increase in the contact area in the medial compartment of the knee will be registered. Biomechanical analysis of the effect of novel interpositional knee spacer implants on pressure distribution in 3D-printed knee model replicas: the primary purpose was the medial joint contact stress-related biomechanics. A secondary purpose was a better understanding of medial/lateral redistribution of joint loading. Six 3D printed knee models were reproduced from cadaveric leg computed tomography. Each of four spacer implants was tested in each knee geometry under realistic arthrokinematic dynamic loading conditions, to examine the pressure distribution in the knee joint. All spacers showed reduced mean stress values by 84–88% and peak stress values by 524–704% in the medial knee joint compartment compared to the non-spacer test condition. The contact area was enlarged by 462–627% as a result of the inserted spacers. Concerning the appreciable contact stress reduction and enlargement of the contact area in the medial knee joint compartment, the premises are in place for testing the implants directly on human knee cadavers to gain further insights into a possible tool for treating medial knee osteoarthritis. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-20463-6 VL - 12 ER - TY - JOUR A1 - Sekuboyina, Anjany A1 - Bayat, Amirhossein A1 - Husseini, Malek E. A1 - Löffler, Maximilian A1 - Li, Hongwei A1 - Tetteh, Giles A1 - Kukačka, Jan A1 - Payer, Christian A1 - Štern, Darko A1 - Urschler, Martin A1 - Chen, Maodong A1 - Cheng, Dalong A1 - Lessmann, Nikolas A1 - Hu, Yujin A1 - Wang, Tianfu A1 - Yang, Dong A1 - Xu, Daguang A1 - Ambellan, Felix A1 - Amiranashvili, Tamaz A1 - Ehlke, Moritz A1 - Lamecker, Hans A1 - Lehnert, Sebastian A1 - Lirio, Marilia A1 - de Olaguer, Nicolás Pérez A1 - Ramm, Heiko A1 - Sahu, Manish A1 - Tack, Alexander A1 - Zachow, Stefan A1 - Jiang, Tao A1 - Ma, Xinjun A1 - Angerman, Christoph A1 - Wang, Xin A1 - Wei, Qingyue A1 - Brown, Kevin A1 - Wolf, Matthias A1 - Kirszenberg, Alexandre A1 - Puybareau, Élodie A1 - Valentinitsch, Alexander A1 - Rempfler, Markus A1 - Menze, Björn H. A1 - Kirschke, Jan S. T1 - VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images JF - arXiv Y1 - 2020 ER - TY - JOUR A1 - Berio, Fidji A1 - Bayle, Yann A1 - Baum, Daniel A1 - Goudemand, Nicolas A1 - Debiais-Thibaud, Mélanie T1 - Hide and seek shark teeth in Random Forests: Machine learning applied to Scyliorhinus canicula populations JF - PeerJ - Aquatic Biology N2 - Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula exhibits distinct genetic structures, life history traits, and body size differences between populations inhabiting the North Atlantic Ocean and the Mediterranean Sea. In this work, we sample more than 3,000 S. canicula teeth from 56 specimens and provide and use a dataset containing their shape coordinates. We investigate tooth shape and form differences between a Mediterranean and an Atlantic S. canicula population using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils. Y1 - 2022 U6 - https://doi.org/10.7717/peerj.13575 SP - 10:e13575 ER - TY - JOUR A1 - Laguillo-Diego, Alejandra A1 - Kiewisz, Robert A1 - Martí-Gómez, Carlos A1 - Baum, Daniel A1 - Müller-Reichert, Thomas A1 - Vernos, Isabelle T1 - MCRS1 modulates the heterogeneity of microtubule minus-end morphologies in mitotic spindles JF - Molecular Biology of the Cell N2 - Faithful chromosome segregation requires the assembly of a bipolar spindle, consisting of two antiparallel microtubule (MT) arrays having most of their minus ends focused at the spindle poles and their plus ends overlapping in the spindle midzone. Spindle assembly, chromosome alignment and segregation require highly dynamic MTs. The plus ends of MTs have been extensively investigated; instead, their minus end structure remains poorly characterized. Here, we used large-scale electron tomography to study the morphology of the MT minus ends in 3D-reconstructed metaphase spindles in HeLa cells. In contrast to the homogeneous open morphology of the MT plus ends at the kinetochores, we found that MT minus ends are heterogeneous showing either open or closed morphologies. Silencing the minus-end specific stabilizer, MCRS1 increased the proportion of open MT minus ends. Altogether, these data suggest a correlation between the morphology and the dynamic state of the MT ends. Taking this heterogeneity of the MT minus end morphologies into account, our work indicates an unsynchronized behavior of MTs at the spindle poles, thus laying the ground for further studies on the complexity of MT dynamics regulation. Y1 - 2022 U6 - https://doi.org/10.1091/mbc.E22-08-0306-T VL - 34 IS - 1 ER - TY - JOUR A1 - Becker, Kaitlyn P A1 - Teeple, Clark A1 - Charles, Nicholas A1 - Jung, Yeonsu A1 - Baum, Daniel A1 - Weaver, James C A1 - Mahadevan, L. A1 - Wood, Robert J T1 - Active entanglement enables stochastic, topological grasping JF - PNAS N2 - Grasping, in both biological and engineered mechanisms, can be highly sensitive to the gripper and object morphology, as well as perception and motion planning. Here we circumvent the need for feedback or precise planning by using an array of fluidically-actuated slender hollow elastomeric filaments to actively entangle with objects that vary in geometric and topological complexity. The resulting stochastic interactions enable a unique soft and conformable grasping strategy across a range of target objects that vary in size, weight, and shape. We experimentally evaluate the grasping performance of our strategy, and use a computational framework for the collective mechanics of flexible filaments in contact with complex objects to explain our findings. Overall, our study highlights how active collective entanglement of a filament array via an uncontrolled, spatially distributed scheme provides new options for soft, adaptable grasping. Y1 - 2022 U6 - https://doi.org/10.1073/pnas.2209819119 VL - 119 IS - 42 SP - e2209819119 ER - TY - JOUR A1 - Koch, Thorsten A1 - Berthold, Timo A1 - Pedersen, Jaap A1 - Vanaret, Charlie T1 - Progress in mathematical programming solvers from 2001 to 2020 JF - EURO Journal on Computational Optimization N2 - This study investigates the progress made in lp and milp solver performance during the last two decades by comparing the solver software from the beginning of the millennium with the codes available today. On average, we found out that for solving lp/milp, computer hardware got about 20 times faster, and the algorithms improved by a factor of about nine for lp and around 50 for milp, which gives a total speed-up of about 180 and 1,000 times, respectively. However, these numbers have a very high variance and they considerably underestimate the progress made on the algorithmic side: many problem instances can nowadays be solved within seconds, which the old codes are not able to solve within any reasonable time. Y1 - 2022 U6 - https://doi.org/10.1016/j.ejco.2022.100031 VL - 10 SP - 100031 ER - TY - JOUR A1 - Chen, Ying A1 - Koch, Thorsten A1 - Zakiyeva, Nazgul A1 - Liu, Kailiang A1 - Xu, Zhitong A1 - Chen, Chun-houh A1 - Nakano, Junji A1 - Honda, Keisuke T1 - Article’s scientific prestige: Measuring the impact of individual articles in the web of science JF - Journal of Informetrics N2 - We performed a citation analysis on the Web of Science publications consisting of more than 63 million articles and 1.45 billion citations on 254 subjects from 1981 to 2020. We proposed the Article’s Scientific Prestige (ASP) metric and compared this metric to number of citations (#Cit) and journal grade in measuring the scientific impact of individual articles in the large-scale hierarchical and multi-disciplined citation network. In contrast to #Cit, ASP, that is computed based on the eigenvector centrality, considers both direct and indirect citations, and provides steady-state evaluation cross different disciplines. We found that ASP and #Cit are not aligned for most articles, with a growing mismatch amongst the less cited articles. While both metrics are reliable for evaluating the prestige of articles such as Nobel Prize winning articles, ASP tends to provide more persuasive rankings than #Cit when the articles are not highly cited. The journal grade, that is eventually determined by a few highly cited articles, is unable to properly reflect the scientific impact of individual articles. The number of references and coauthors are less relevant to scientific impact, but subjects do make a difference. Y1 - 2023 U6 - https://doi.org/10.1016/j.joi.2023.101379 VL - 17 IS - 1 SP - 101379 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Scheduling data streams for low latency and high throughput on a Cray XC40 using Libfabric JF - Concurrency and Computation Practice and Experience Y1 - 2020 U6 - https://doi.org/10.1002/cpe.5563 VL - 32 IS - 20 SP - 1 EP - 14 ER - TY - JOUR A1 - Dierkes, Thomas A1 - Röblitz, Susanna A1 - Wade, Moritz A1 - Deuflhard, Peter T1 - Parameter identification in large kinetic networks with BioPARKIN JF - CoRR - Computing Research Repository - arXiv.org Y1 - 2013 UR - arxiv.org/abs/1303.4928v2 VL - abs/1303.4928 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Improving the throughput of a scalable FLESnet using the Data-Flow Scheduler JF - CBM Progress Report 2018 Y1 - 2019 SN - 978-3-9815227-6-1 U6 - https://doi.org/10.15120/GSI-2019-01018 SP - 149 EP - 150 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Supporting various interconnects in FLESnet using Libfabric JF - CBM Progress Report 2016 Y1 - 2017 UR - https://repository.gsi.de/record/201318 SN - 978-3-9815227-4-7 SP - 159 EP - 160 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Reinefeld, Alexander T1 - Handling Compute-Node Failures in FLESnet JF - CBM Progress Report 2019 Y1 - 2020 SN - 978-3-9815227-8-5 U6 - https://doi.org/10.15120/GSI-2020-00904 SP - 167 EP - 168 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Reinefeld, Alexander T1 - Data-flow scheduling for a scalable FLESnet JF - CBM Progress Report 2017 Y1 - 2018 SN - 978-3-9815227-5-4 U6 - https://doi.org/10.15120/GSI-2018-00485 SP - 130 EP - 131 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian T1 - Load balancing mechanism for FLESnet JF - CBM Progress Report 2020 Y1 - 2021 U6 - https://doi.org/10.15120/GSI-2021-00421 SP - 156 EP - 157 ER - TY - JOUR A1 - Boltz, Horst-Holger A1 - Sirbu, Alexei A1 - Stelzer, Nina A1 - de Lanerolle, Primal A1 - Winkelmann, Stefanie A1 - Annibale, Paolo T1 - The Impact of Membrane Protein Diffusion on GPCR Signaling JF - Cells N2 - Spatiotemporal signal shaping in G protein-coupled receptor (GPCR) signaling is now a well-established and accepted notion to explain how signaling specificity can be achieved by a superfamily sharing only a handful of downstream second messengers. Dozens of Gs-coupled GPCR signals ultimately converge on the production of cAMP, a ubiquitous second messenger. This idea is almost always framed in terms of local concentrations, the differences in which are maintained by means of spatial separation. However, given the dynamic nature of the reaction-diffusion processes at hand, the dynamics, in particular the local diffusional properties of the receptors and their cognate G proteins, are also important. By combining some first principle considerations, simulated data, and experimental data of the receptors diffusing on the membranes of living cells, we offer a short perspective on the modulatory role of local membrane diffusion in regulating GPCR-mediated cell signaling. Our analysis points to a diffusion-limited regime where the effective production rate of activated G protein scales linearly with the receptor–G protein complex’s relative diffusion rate and to an interesting role played by the membrane geometry in modulating the efficiency of coupling Y1 - 2022 U6 - https://doi.org/10.3390/cells11101660 VL - 11 IS - 10 SP - 1660 ER - TY - JOUR A1 - Boltz, Horst-Holger A1 - Kurchan, Jorge A1 - Liu, Andrea J. T1 - Fluctuation distributions of energy minima in complex landscapes JF - Physical Review Research N2 - We discuss the properties of the distributions of energies of minima obtained by gradient descent in complex energy landscapes. We find strikingly similar phenomenology across several prototypical models. We particularly focus on the distribution of energies of minima in the analytically well-understood p-spin-interaction spin-glass model. We numerically find non-Gaussian distributions that resemble the Tracy-Widom distributions often found in problems of random correlated variables, and nontrivial finite-size scaling. Based on this, we propose a picture of gradient-descent dynamics that highlights the importance of a first-passage process in the eigenvalues of the Hessian. This picture provides a concrete link to problems in which the Tracy-Widom distribution is established. Aspects of this first-passage view of gradient-descent dynamics are generic for nonconvex complex landscapes, rationalizing the commonality that we find across models. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevResearch.3.013061 VL - 3 IS - 1 SP - 013061 ER - TY - JOUR A1 - Dierkes, Thomas A1 - Ortmann, Karl Michael T1 - On the efficient utilisation of duration JF - Insurance: Mathematics and Economics N2 - In this article we present a new approach to estimate the change of the present value of a given cashflow pattern caused by an interest rate shift. Our approximation is based on analysing the evolution of the present value function through a linear differential equation. The outcome is far more accurate than the standard approach achieved by a Taylor expansion. Furthermore, we derive an approximation formula of second order that produces nearly accurate results. In particular, we prove that our method is superior to any known alternative approximation formula based on duration. In order to demonstrate the power of this improved approximation we apply it to coupon bonds, level annuities, and level perpetuities. We finally generalise the approach to a non-flat term structure. As for applications in insurance, we estimate the change of the discounted value of future liabilities due to a proportional shift in the set of capital accumulation factors. These findings are of particular importance to capital adequacy calculations with respect to interest rate stress scenarios that are part of regulatory solvency requirements. Y1 - 2015 U6 - https://doi.org/10.1016/j.insmatheco.2014.11.002 VL - 60 SP - 29 EP - 37 ER - TY - JOUR A1 - Boltz, Horst-Holger A1 - Sirbu, Alexei A1 - Stelzer, Nina A1 - Lohse, Martin J. A1 - Schütte, Christof A1 - Annibale, Paolo T1 - Quantitative spectroscopy of single molecule interaction times JF - Optic Letters N2 - Single molecule fluorescence tracking provides information at nanometer-scale and millisecond-temporal resolution about the dynamics and interaction of individual molecules in a biological environment. While the dynamic behavior of isolated molecules can be characterized well, the quantitative insight is more limited when interactions between two indistinguishable molecules occur. We address this aspect by developing a theoretical foundation for a spectroscopy of interaction times, i.e., the inference of interaction from imaging data. A non-trivial crossover between a power law to an exponential behavior of the distribution of the interaction times is highlighted, together with the dependence of the exponential term upon the microscopic reaction affinity. Our approach is validated with simulated and experimental datasets. Y1 - 2021 U6 - https://doi.org/10.1364/OL.413030 VL - 46 IS - 7 SP - 1538 EP - 1541 ER - TY - JOUR A1 - Petkovic, Milena A1 - Zakiyeva, Nazgul T1 - Mathematical Optimization for Analyzing and Forecasting Nonlinear Network Time Series JF - Operations Research Proceedings 2022 N2 - This work presents an innovative short to mid-term forecasting model that analyzes nonlinear complex spatial and temporal dynamics in energy networks under demand and supply balance constraints using Network Nonlinear Time Series (TS) and Mathematical Programming (MP) approach. We address three challenges simultaneously, namely, the adjacency matrix is unknown; the total amount in the network has to be balanced; dependence is unnecessarily linear. We use a nonparametric approach to handle the nonlinearity and estimate the adjacency matrix under the sparsity assumption. The estimation is conducted with the Mathematical Optimisation method. We illustrate the accuracy and effectiveness of the model on the example of the natural gas transmission network of one of the largest transmission system operators (TSOs) in Germany, Open Grid Europe. The obtained results show that, especially for shorter forecasting horizons, proposed method outperforms all considered benchmark models, improving the avarage nMAPE for 5.1% and average RMSE for 79.6% compared to the second-best model. The model is capable to capture the nonlinear dependencies in the complex spatial-temporal network dynamics and benefits from both sparsity assumption and the demand and supply balance constraint. Y1 - 2022 ER - TY - JOUR A1 - Heida, Martin A1 - Sikorski, Alexander A1 - Weber, Marcus T1 - Consistency and order 1 convergence of cell-centered finite volume discretizations of degenerate elliptic problems in any space dimension JF - SIAM Journal on Numerical Analysis N2 - We study consistency of cell-centered finite difference methods for elliptic equations with degenerate coefficients in any space dimension $d \geq 2$. This results in order of convergence estimates in the natural weighted energy norm and in the weighted discrete $L^2$-norm on admissible meshes. The cells of meshes under consideration may be very irregular in size. We particularly allow the size of certain cells to remain bounded from below even in the asymptotic limit. For uniform meshes we show that the order of convergence is at least 1 in the energy semi-norm, provided the discrete and continuous solutions exist and the continuous solution has $H^2$ regularity. Y1 - 2022 U6 - https://doi.org/10.20347/WIAS.PREPRINT.2913 ER - TY - JOUR A1 - Plöntzke, Julia A1 - Berg, Mascha A1 - Ehrig, Rainald A1 - Leonhard-Marek, Sabine A1 - Müller, Kerstin-Elisabeth A1 - Röblitz, Susanna T1 - Model Based Exploration of Hypokalemia in Dairy Cows JF - Scientific Reports N2 - Hypokalemia, characterized by too low serum potassium levels, is a severe mineral disorder which can be life threatening. It is increasingly diagnosed in veterinarian healthcare and a topic of ongoing research. In this paper, we explore the different originating conditions of hypokalemia: reduced potassium intake, increased excretion, acid-base disturbances, or increased insulin, by using a dynamic mathematical model for potassium balance in non-lactating and lactating cows. Simulations are compared with literature. The results give insights into the network dynamics and point to scenarios on which experimental effort should be focused. Application of mathematical models can assist in experimental planning as well as the reduction, refinement and replacement of animal experiments. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-22596-0 VL - 12, 19781 ER - TY - JOUR A1 - Ehlers, Sarah A1 - Baum, Daniel A1 - Mühlethaler, Roland A1 - Hoch, Hannelore A1 - Bräunig, Peter T1 - Large abdominal mechanoreceptive sense organs in small plant-dwelling insects JF - Biology Letters N2 - The Hemiptera is the largest non-endopterygote insect order comprising approximately 98,000 recent species. All species of the suborders Cicadomorpha (leafhoppers, spittlebugs, treehoppers and cicadas) and Fulgoromorpha (planthoppers) feed by sucking sap from plant tissues and are thus often vectors for economically important phytopathogens. Except for the cicadas (Cicadomorpha: Cicadoidea: Cicadidae) which produce air-borne sounds, all species of the suborders Cicadomorpha and Fulgoromorpha communicate by vibrational (substrate-borne) signals. While the generation of these signals has been extensively investigated, the mechanisms of perception are poorly understood. This study provides a full description and 3D reconstruction of a large and complex array of six paired chordotonal organs in the first abdominal segments of the Rhododendron leafhopper Graphocephala fennahi (Cicadomorpha: Membracoidea: Cicadellidae). Further we were able to identify homologous organs in the closely related spittlebug Philaenus spumarius (Cicadomorpha: Cercopoidea: Aphrophoridae) and the planthopper Issus coleoptratus (Fulgoromorpha: Fulgoroidea: Issidae). The configuration is congruent with the abdominal chordotonal organs in cicadas, where one of them is an elaborate tympanal organ. This indicates that these organs, together with the tymbal organ constitute a synapomorphy of the Tymbalia (Hemiptera excl. Sternorrhyncha). Our results contribute to the understanding of the evolution from substrate-borne to airborne communication in insects. Y1 - 2022 U6 - https://doi.org/10.1098/rsbl.2022.0078 VL - 18 IS - 4 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Prodanov, Dimiter T1 - The Active Segmentation Platform for Microscopic Image Classification and Segmentation JF - Brain Sciences. 2021 N2 - Image segmentation still represents an active area of research since no universal solution can be identified. Traditional image segmentation algorithms are problem-specific and limited in scope. On the other hand, machine learning offers an alternative paradigm where predefined features are combined into different classifiers, providing pixel-level classification and segmentation. However, machine learning only can not address the question as to which features are appropriate for a certain classification problem. The article presents an automated image segmentation and classification platform, called Active Segmentation, which is based on ImageJ. The platform integrates expert domain knowledge, providing partial ground truth, with geometrical feature extraction based on multi-scale signal processing combined with machine learning. The approach in image segmentation is exemplified on the ISBI 2012 image segmentation challenge data set. As a second application we demonstrate whole image classification functionality based on the same principles. The approach is exemplified using the HeLa and HEp-2 data sets. Obtained results indicate that feature space enrichment properly balanced with feature selection functionality can achieve performance comparable to deep learning approaches. In summary, differential geometry can substantially improve the outcome of machine learning since it can enrich the underlying feature space with new geometrical invariant objects. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/brainsci11121645 VL - 11 IS - 12 SP - 1645 ER - TY - JOUR A1 - Sunkara, Vikram A1 - Lewis, Angus A1 - Nguyen, Giang T. A1 - O'Reilly, Malgorzata M. A1 - Bean, Nigel T1 - A discontinuous Galerkin method for approximating the stationary distribution of stochastic fluid-fluid processes JF - Methodology and Computing in Applied Probability Y1 - 2022 U6 - https://doi.org/10.1007/s11009-022-09945-2 ER - TY - JOUR A1 - Kossen, Tabea A1 - Hirzel, Manuel A. A1 - Madai, Vince I. A1 - Boenisch, Franziska A1 - Hennemuth, Anja A1 - Hildebrand, Kristian A1 - Pokutta, Sebastian A1 - Sharma, Kartikey A1 - Hilbert, Adam A1 - Sobesky, Jan A1 - Galinovic, Ivana A1 - Khalil, Ahmed A. A1 - Fiebach, Jochen B. A1 - Frey, Dietmar T1 - Towards Sharing Brain Images: Differentially Private TOF-MRA Images with Segmentation Labels Using Generative Adversarial Networks JF - Frontiers in Artificial Intelligence N2 - Sharing labeled data is crucial to acquire large datasets for various Deep Learning applications. In medical imaging, this is often not feasible due to privacy regulations. Whereas anonymization would be a solution, standard techniques have been shown to be partially reversible. Here, synthetic data using a Generative Adversarial Network (GAN) with differential privacy guarantees could be a solution to ensure the patient's privacy while maintaining the predictive properties of the data. In this study, we implemented a Wasserstein GAN (WGAN) with and without differential privacy guarantees to generate privacy-preserving labeled Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) image patches for brain vessel segmentation. The synthesized image-label pairs were used to train a U-net which was evaluated in terms of the segmentation performance on real patient images from two different datasets. Additionally, the Fréchet Inception Distance (FID) was calculated between the generated images and the real images to assess their similarity. During the evaluation using the U-Net and the FID, we explored the effect of different levels of privacy which was represented by the parameter ϵ. With stricter privacy guarantees, the segmentation performance and the similarity to the real patient images in terms of FID decreased. Our best segmentation model, trained on synthetic and private data, achieved a Dice Similarity Coefficient (DSC) of 0.75 for ϵ = 7.4 compared to 0.84 for ϵ = ∞ in a brain vessel segmentation paradigm (DSC of 0.69 and 0.88 on the second test set, respectively). We identified a threshold of ϵ <5 for which the performance (DSC <0.61) became unstable and not usable. Our synthesized labeled TOF-MRA images with strict privacy guarantees retained predictive properties necessary for segmenting the brain vessels. Although further research is warranted regarding generalizability to other imaging modalities and performance improvement, our results mark an encouraging first step for privacy-preserving data sharing in medical imaging. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.3389/frai.2022.813842 ER - TY - JOUR A1 - Lenz, Ralf A1 - Becker, Kai-Helge T1 - Optimization of Capacity Expansion in Potential-driven Networks including Multiple Looping - A comparison of modelling approaches JF - OR Spectrum N2 - In commodity transport networks such as natural gas, hydrogen and water networks, flows arise from nonlinear potential differences between the nodes, which can be represented by so-called "potential-driven" network models. When operators of these networks face increasing demand or the need to handle more diverse transport situations, they regularly seek to expand the capacity of their network by building new pipelines parallel to existing ones ("looping"). The paper introduces a new mixed-integer non-linear programming (MINLP) model and a new non-linear programming (NLP) model and compares these with existing models for the looping problem and related problems in the literature, both theoretically and experimentally. On this basis, we give recommendations about the circumstances under which a certain model should be used. In particular, it turns out that one of our novel models outperforms the existing models. Moreover, the paper is the first to include the practically relevant option that a particular pipeline may be looped several times. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1007/s00291-021-00648-7 VL - 44 SP - 179 EP - 224 ER - TY - JOUR A1 - Reidelbach, Marco A1 - Bai, Mei A1 - Zöllner, Martin Sebastian A1 - Schneeberger, Michaela A1 - Kubicek, Katharina A1 - Kirchberg, Henning A1 - Bressler, Christian A1 - Thorwart, Michael A1 - Herrmann, Carmen T1 - Solvent dynamics of aqueous halides before and after photoionization JF - Journal of Physical Chemistry Y1 - 2022 ER - TY - JOUR A1 - Maher, Stephen J. A1 - Desaulniers, Guy A1 - Soumis, Francois T1 - The daily tail assignment problem under operational uncertainty using look-ahead maintenance constraints JF - European Journal of Operational Research N2 - The tail assignment problem is a critical part of the airline planning process that assigns specific aircraft to sequences of flights, called lines-of-flight, to satisfy operational constraints. The aim of this paper is to develop an operationally flexible method, based upon the one-day routes business model, to compute tail assignments that satisfy short-range—within the next three days—aircraft maintenance requirements. While maintenance plans commonly span multiple days, the methods used to compute tail assignments for the given plans can be overly complex and provide little recourse in the event of schedule perturbations. The presented approach addresses operational uncertainty by using solutions from the one-day routes aircraft maintenance routing approach as input. The daily tail assignment problem is solved with an objective to satisfy maintenance requirements explicitly for the current day and implicitly for the subsequent two days. A computational study will be performed to assess the performance of exact and heuristic solution algorithms that modify the input lines-of-flight to reduce maintenance misalignments. The daily tail assignment problem and the developed algorithms are demonstrated to compute solutions that effectively satisfy maintenance requirements when evaluated using input data collected from three different airlines. Y1 - 2018 U6 - https://doi.org/10.1016/j.ejor.2017.06.041 VL - 264 IS - 2 SP - 534 EP - 547 ER - TY - JOUR A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Maher, Stephen J. A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - SCIP-Jack – A solver for STP and variants with parallelization extensions JF - Mathematical Programming Computation N2 - The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problem-specific. In contrast, this paper introduces a general-purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-of-the-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances. Y1 - 2017 U6 - https://doi.org/10.1007/s12532-016-0114-x VL - 9 IS - 2 SP - 231 EP - 296 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten A1 - Maher, Stephen J. T1 - Reduction Techniques for the Prize-Collecting Steiner Tree Problem and the Maximum-Weight Connected Subgraph Problem JF - Networks N2 - The concept of reduction has frequently distinguished itself as a pivotal ingredient of exact solving approaches for the Steiner tree problem in graphs. In this paper we broaden the focus and consider reduction techniques for three Steiner problem variants that have been extensively discussed in the literature and entail various practical applications: The prize-collecting Steiner tree problem, the rooted prize-collecting Steiner tree problem and the maximum-weight connected subgraph problem. By introducing and subsequently deploying numerous new reduction methods, we are able to drastically decrease the size of a large number of benchmark instances, already solving more than 90 percent of them to optimality. Furthermore, we demonstrate the impact of these techniques on exact solving, using the example of the state-of-the-art Steiner problem solver SCIP-Jack. Y1 - 2019 U6 - https://doi.org/10.1002/net.21857 VL - 73 SP - 206 EP - 233 PB - Wiley ET - 2 ER - TY - JOUR A1 - Koch, Thorsten A1 - Schmidt, Martin A1 - Hiller, Benjamin A1 - Pfetsch, Marc A1 - Geißler, Björn A1 - Henrion, René A1 - Joormann, Imke A1 - Martin, Alexander A1 - Morsi, Antonio A1 - Römisch, Werner A1 - Schewe, Lars A1 - Schultz, Rüdiger T1 - Capacity Evaluation for Large-Scale Gas Networks JF - German Success Stories in Industrial Mathematics Y1 - 2020 SN - 978-3-030-81454-0 U6 - https://doi.org/10.1007/978-3-030-81455-7 VL - 35 SP - 23 EP - 28 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Evaluation of Design Alternatives for a Gas Turbine Cogeneration Plant Based on Multiobjective K-Best Solutions JF - International Conference on Power Engineering-2019 N2 - To realize the best performance in energy supply, it is an important task to determine types, capacities, and numbers of energy conversion equipment appropriately. It is also necessary to take account of seasonal and hourly variations in energy demands and corresponding operational strategies of equipment. The mixed-integer linear programming (MILP) method has been utilized widely to derive the optimal solution for such a design problem. From the design viewpoint, it is important to generate not only the optimal solution but also suboptimal ones which follow the optimal one without omission, what are called K-best solutions. In this paper, an MILP method utilizing the hierarchical relationship between design and operation variables is applied along with some strategies to efficiently drive K-best solutions of a multiobjective optimal design problem of a gas turbine cogeneration system for district energy supply. The annual total cost and primary energy consumption are adopted as the objective functions to be minimized. A case study is conducted, and K-best solutions with an allowable increase in the value of the combined objective function are derived for each value of the weight for the annual total cost. Through the study, it is clarified how the weight affects the computation time, the number of the K-best solutions, and the design specifications and the values of the objective functions for the K-best solutions. Y1 - 2019 SP - 1112 EP - 1117 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Wakui, Tetsuya T1 - Search for K-best solutions in optimal design of energy supply systems by an extended MILP hierarchical branch and bound method JF - Energy N2 - For the purpose of making a decision in the optimal design of an energy supply system, it is important to investigate not only the optimal solution but also suboptimal ones which follow the optimal one without any omissions, what are called K-best solutions. In this paper, a mixed-integer linear programming method utilizing the hierarchical relationship between design and operation variables proposed previ- ously is extended to search the K-best solutions very efficiently. In addition, methods for updating the incumbents are incorporated into the extended method for three options for the criterion set newly in deriving the K-best solutions. This extended method is implemented into open and commercial MILP solvers, and is applied to illustrative and practical case studies, respectively, on the optimal design of cogeneration systems. Through the studies, it turns out that the proposed method is much superior in terms of solution optimality and computation efficiency to a conventional method, and that the computation efficiency to derive one of the K-best solutions by the proposed method increases with the number of K-best solutions. In addition, features of the K-best solutions in the value of objective function are clarified. Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2018.02.077 VL - 184 SP - 45 EP - 57 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayama, Yuki A1 - Wakui, Tetsuya T1 - Model reduction by time aggregation for optimal design of energy supply systems by an MILP hierarchical branch and bound method JF - Energy N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accordance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies. Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2019.04.066 VL - 181 SP - 782 EP - 792 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Takeuchi, Kotaro A1 - Wakui, Tetsuya T1 - Operation-based time-period clustering for optimal design of energy supply systems by a hierarchical MILP method JF - THE 32ND INTERNATIONAL CONFERENCE ON EFFICIENCY, COST, OPTIMIZATION, SIMULATION AND ENVIRONMENTAL IMPACT OF ENERGY SYSTEMS(ECOS 2019) N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, a method of clustering periods has been proposed based on the optimal operational strategies of the systems to avoid a large decrease in the lower bound for the optimal value of the objective function by model reduction. This method has been realized only by solving the relaxed optimal design problem at the upper level in advance. The method can decrease the number of operation variables and constraints at the upper level, and thus can decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the proposed clustering method is effective to enhance the computation efficiency in comparison with the conventional one which clusters periods regularly in time series. Y1 - 2019 SP - 527 EP - 539 ER - TY - JOUR A1 - Griewank, Andreas A1 - Hasenfelder, Richard A1 - Radons, Manuel A1 - Lehmann, Lutz A1 - Streubel, Tom T1 - Integrating Lipschitzian dynamical systems using piecewise algorithmic differentiation JF - Optimization Methods and Software N2 - In this article we analyse a generalized trapezoidal rule for initial value problems with piecewise smooth right-hand side F : IR^n -> IR^n based on a generalization of algorithmic differentiation. When applied to such a problem, the classical trapezoidal rule suffers from a loss of accuracy if the solution trajectory intersects a nondifferentiability of F. The advantage of the proposed generalized trapezoidal rule is threefold: Firstly, we can achieve a higher convergence order than with the classical method. Moreover, the method is energy preserving for piecewise linear Hamiltonian systems. Finally, in analogy to the classical case we derive a third-order interpolation polynomial for the numerical trajectory. In the smooth case, the generalized rule reduces to the classical one. Hence, it is a proper extension of the classical theory. An error estimator is given and numerical results are presented. Y1 - 2018 U6 - https://doi.org/10.1080/10556788.2017.1378653 VL - 33 SP - 1089 EP - 1107 PB - Taylor & Francis ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakayama, Yuki A1 - Wakui, Tetsuya T1 - Model reduction by time aggregation for optimal design of energy supply systems by an MILP hierarchical branch and bound method JF - Energy N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of en- ergy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been pro- posed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accor- dance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies. Y1 - 2019 VL - 181 SP - 782 EP - 792 ER - TY - JOUR A1 - Griewank, Andreas A1 - Streubel, Tom A1 - Lehmann, Lutz A1 - Radons, Manuel A1 - Hasenfelder, Richard T1 - Piecewise linear secant approximation via algorithmic piecewise differentiation JF - Optimization Methods and Software N2 - It is shown how piecewise differentiable functions F : IR^n -> IR^m that are defined by evaluation programmes can be approximated locally by a piecewise linear model based on a pair of sample points \check x and \hat x. We show that the discrepancy between function and model at any point x is of the bilinear order O(||x - \check x||*||x - \hat x||). As an application of the piecewise linearization procedure we devise a generalized Newton's method based on successive piecewise linearization and prove for it sufficient conditions for convergence and convergence rates equalling those of semismooth Newton. We conclude with the derivation of formulas for the numerically stable implementation of the aforedeveloped piecewise linearization methods. Y1 - 2017 U6 - https://doi.org/10.1080/10556788.2017.1387256 VL - 33 IS - 4-6 SP - 1108 EP - 1126 PB - Taylor & Francis ER - TY - JOUR A1 - 品野, 勇治 T1 - 最適化研究における数値実験を中心とした アプリケーション駆動研究サイクル JF - 機関誌「オペレーションズ・リサーチ」 N2 - 最適化研究におけるアプリケーション駆動研究サイクルを紹介する.アプリケーション駆動研究サイクルは,学術機関での研究と企業における研究成果の利用とのつながりを良くする点では優れている.一方で,ソフトウェア開発・維持に多大な労力を要するため,日本の大学や研究機関における実施には困難さが伴う.ZIBにおいてアプリケーション駆動研究サイクルが,比較的うまく機能している背景を説明する.また,日本においてアプリケーション駆動研究サイクルを活性化するための第一歩として,論文投稿時に,論文中の数値実験に利用した全データ提出の義務化を提案したい. Y1 - 2014 UR - https://orsj.org/wp-content/corsj/or59-5/or59_5_247.pdf VL - 59 IS - 5 SP - 247 EP - 253 ER - TY - JOUR A1 - Wakayama, Yuki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の階層的関係を考慮した最適化(時間集約によるモデル縮約とその効果) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation(Model Reduction by Time Aggregation and Its Effect) JF - エネルギー・資源学会第34回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - A hierarchical mixed-integer linear programming method to solve optimal design problems of energy supply systems efficiently has been proposed. The original problem is solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of each other at the lower level. In this paper, a method of reducing model by time aggregation is proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. On one hand, the method may decrease the number of design variables and costraints at the upper level, and thus the computation time at the upper level. On the other hand, it may increase the numbers of generated design solution candidates and solved optimal operation problems, and thus the computation time at both the levels. Though a case study on the optimal design of a cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency. Y1 - 2018 SP - 401 EP - 404 ER - TY - JOUR A1 - Takeuchi, Kotaro A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの 設計と運用の階層的関係を考慮した最適化 (運用を考慮した期間クラスタリングによるモデル縮約) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Model Reduction by Clustering Periods in Consideration of Operation) JF - エネルギー・資源学会第35回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - To attain the highest performance of energy supply systems, it is necessary to determine design specifications optimally in consideration of operational strategies corresponding to seasonal and hourly variations in energy demands. Mixed-integer linear programming (MILP) methods have been applied widely to such multi-period optimal design problems. A hierarchical MILP method has been proposed to solve the problems very efficiently. In addition, by utilizing features of the hierarchical MILP method, a method of reducing model by clustering periods has also been proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, by utilizing features of the hierarchical MILP method, a method of clustering periods is proposed based on the optimal operational strategies of energy supply systems obtained by solving the relaxed optimal design problem. As a case study, the method is applied to the optimal design of a gas turbine cogeneration system, and it is clarified that the method is effective to enhance the computation efficiency in comparison with a conventional method of clustering periods regularly. Y1 - 2019 SP - 169 EP - 174 ER - TY - JOUR A1 - Kamada, Hiroki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 混合整数線形モデルによる エネルギー供給システムのロバスト最適設計 (階層的最適化手法の適用) T1 - Robust Optimal Design of Energy Supply Systems Based on a Mixed-Integer Linear Model (Application of a Hierarchical Optimization Method) JF - エネルギー・資源学会第35回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - A robust optimal design method of energy supply systems under uncertain energy demands has been proposed using a mixed- integer linear model for constituent equipment. A robust optimal design problem has been formulated as a three-level min-max- min optimization one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret criterion, and considering hierarchical relationships among design variables, uncertain energy demands, and operation variables. However, this method takes a long computation time, and thus it can be applied only to small-scale problems. In this paper, mixed-integer linear programming method in consideration of the hierarchical relationship between design and operation variables is applied to parts of the robust optimal design method which take long computation times to solve problems efficiently. In a case study, this revised method is applied to the robust optimal design of a cogeneration system with a simple configuration, and the validity and effectiveness of the method are ascertained. Y1 - 2019 SP - 163 EP - 168 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の階層的関係を考慮した最適化(手法の提案) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Proposal of Optimization Method) JF - 第33回エネルギー・資源学会研究発表会講演論文要旨集・講演論文集 N2 - A mixed-integer linear programming (MILP) method utilizing the hierarchical relationship between design and op- eration variables is proposed to solve the optimal design problem of energy supply systems efficiently: At the upper level, the optimal values of design variables are searched by the branch and bound method; At the lower level, the values of operation variables are optimized by the branch and bound method under the values of design variables given tentatively during the search at the upper level; Lower bounds for the optimal value of the objective function are evaluated, and are utilized for the bounding operations at both the levels. This method is implemented into open and commercial MILP solvers. Illustrative and practical case studies on the optimal design of cogeneration systems are conducted, and the validity and effectiveness of the proposed method are clarified. Y1 - 2014 SP - 183 EP - 188 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Taniguchi, Syusuke A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用階層的関係を考慮した最適化(K-ベスト解の探索) T1 - Optimization ofEnergy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Search for K-Best Solutions) JF - 日本機械学会第11回最適化シンポジウム2014講演論文集 N2 - A mixed-integer linear programming methodutilizing the hierarchical relationship between design and operation variables proposed ot solve the optimal design problem of energy supply systems efficiently is extended ot search K-best solutions: At the upper level, the optimal values ofdesign variables are searched with operation variables relaxed to continuous ones; At the lower level, the values of operation variables are optimized with the values of design variables given tentatively; The obtained solution is used to renew K-best incumbent solutions, and the upper bound for the value of the objective function for K-best solutions is replaced correspondingly. A practical case study is conducted, and the validity and effectiveness of the proposed method are clarified. Y1 - 2014 SP - 1 EP - 4 ER - TY - JOUR A1 - Wakayama, Yuki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 階層的最適化によるエネルギ ー供給システムの最適設計・運用 (期間のクラスタリングに よるモデル縮約とその効果) T1 - Optimal Design and Operation of Energy Supply Systems by Hierarchical Optimization (Model Reduction by Clustering Periods and Its Effect) JF - 日本機械学会関西支部第93期定時総会講演会講演論文集 N2 - Ahierarchical mixed-integer linear programmingmethod has been proposed to solve optimal design problems of energy supply systems efficiently. In this paper, a method of reducing model by clustering periods is proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Through acase study on the optimaldesign of a cogeneration system, ti is clarified how the model reduction si effective ot enhance the computation efficiency. Y1 - 2018 SP - 259 EP - 260 ER - TY - JOUR A1 - 品野, 勇治 T1 - MIPLIB と Hans Mittelmann’s benchmarks JF - 機関誌「オペレーションズ・リサーチ」 N2 - 混合整数計画法 (Mixed Integer Programming: MIP) は,MIP を解くソフトウェアである MIP ソルバが大規模な現実問題を解けるようになったこともあり,現実問題を解く有用な OR の手法として広く知られるようになった.しかしながら,MIP ソルバの開発に欠かせないベンチマーク・データセットおよび性能測定方法についてはそれほど広く知られているとは言い難い.ベンチマーク・データセットは注意を払って作成しないと,多くのバイアスがかかってしまう.それらのバイアスを可能な限りのぞき,真に有用なベンチマーク・テストの結果を得るためには複数の人数で多大な労力を割く必要がある.本稿では,そのような MIP ソルバ開発の背景として重要な役割を果たしてきた MIPLIB と Hans Mittelmann’s benchmarks について解説する.また,本稿において Hans Mittelmann’s benchmarks は,BENCHMARKS FOR OPTIMIZATION SOFTWAREのページ (http://plato.asu.edu/bench.html) に示されているベンチマークである. Y1 - 2020 UR - https://orsj.org/wp-content/corsj/or65-1/or65_1_49.pdf VL - 65 IS - 1 SP - 49 EP - 56 ER - TY - JOUR A1 - 藤澤, 克樹 A1 - 品野, 勇治 T1 - 最適化と計算の今後 ―大規模問題をどこまで解決できるのか?― JF - 機関誌「オペレーションズ・リサーチ」 N2 - 近年,大規模かつ複雑な最適化問題を高速に解く需要はさまざまな産業界や学術分野において急速に高まりつつある.これからの研究においては最先端理論 (Theory)+超大規模実データ (Practice)+最新計算技術(Computation) の三つを有機的に組み合わせることによって,実用に耐えうる解決策の提示と大規模最適化問題を扱う際の先例となることが求められている.本稿では最適化と計算に関する最新の傾向に触れるとともに,最適化の計算の今後についても考えていきたい. Y1 - 2014 UR - https://orsj.org/wp-content/corsj/or59-1/or59_1_11.pdf VL - 59 IS - 1 SP - 11 EP - 19 ER - TY - JOUR A1 - 品野, 勇治 A1 - 藤井, 浩一 T1 - 使ってみよう線形計画ソルバ JF - 機関誌「オペレーションズ・リサーチ」 N2 - 本稿では,線形計画問題を解くソフトウェアである線形計画ソルバの標準的な利用方法と,原稿執筆時点で利用可能なソルバを可能な限り紹介する.筆者らはソルバ開発コミュニティの中で仕事をしているので,この機会に現在のソルバ開発現場の様子も紹介するとともに,各ソルバの特徴として何を紹介するべきかは,できる限り開発者,または,開発者に近い研究者に問い合わせて記述した.本稿は,多くの線形計画ソルバの選択肢がある中で,読者がもつ問題を解くのに最も適当なソルバを選択するための指針を与えることを主たる目的としている. Y1 - 2019 UR - https://orsj.org/wp-content/corsj/or64-4/or64_4_238.pdf VL - 64 IS - 4 SP - 238 EP - 245 ER - TY - JOUR A1 - Taniguchi, Shusuke A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Ohkura, Masashi A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の階層的関係を考慮した最適化(多目的最適化におけるK-ベスト解の探索) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Search for K-Best Solutions in Multiobjective Optimization) JF - エネルギー・資源学会第31回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - A mixed-integer linear programming method utilizing the hierarchical relationship between design and operation variables proposed to solve the optimal design problem of energy supply systems efficiently is extended to search K-best solutions in multiobjective optimization: At the upper level, the optimal values of design variables are searched by the branch and bound method with operation variables relaxed to continuous ones; At the lower level, the values of operation variables are optimized independently at the respective periods set for variations in energy demands by the branch and bound method with the values of design variables given tentatively during the search at the upper level. A weighting method is employed for multiobjective optimization, and a weighted sum of the annual total cost and primary energy consumption is adopted as the objective function to be minimized. A practical case study on the optimal design of a cogeneration system is conducted. The validity and effectiveness of the proposed method are clarified, and the trade-off relationship between the annual total cost and primary energy consumption is confirmed. Y1 - 2015 SP - 267 EP - 272 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Resonance expansion of quadratic quantities with regularized quasinormal modes JF - Phys. Status Solidi A Y1 - 2023 U6 - https://doi.org/10.1002/pssa.202200892 VL - 220 SP - 2200892 ER - TY - JOUR A1 - Sipiran, Ivan A1 - Lazo, Patrick A1 - Lopez, Cristian A1 - Bagewadi, Nihar A1 - Bustos, Benjamin A1 - Dao, Hieu A1 - Gangisetty, Shankar A1 - Hanik, Martin A1 - Ho-Thi, Ngoc-Phuong A1 - Holenderski, Mike A1 - Jarnikov, Dmitri A1 - Labrada, Arniel A1 - Lengauer, Stefan A1 - Licandro, Roxane A1 - Nguyen, Dinh-Huan A1 - Nguyen-Ho, Thang-Long A1 - Pérez Rey, Luis A. A1 - Pham, Bang-Dang A1 - Pham, Minh-Khoi A1 - Preiner, Reinhold A1 - Schreck, Tobias A1 - Trinh, Quoc-Huy A1 - Tonnaer, Loek A1 - von Tycowicz, Christoph A1 - Vu-Le, The-Anh T1 - SHREC 2021: Retrieval of Cultural Heritage Objects JF - Computers and Graphics N2 - This paper presents the methods and results of the SHREC’21 contest on a dataset of cultural heritage (CH) objects. We present a dataset of 938 scanned models that have varied geometry and artistic styles. For the competition, we propose two challenges: the retrieval-by-shape challenge and the retrieval-by-culture challenge. The former aims at evaluating the ability of retrieval methods to discriminate cultural heritage objects by overall shape. The latter focuses on assessing the effectiveness of retrieving objects from the same culture. Both challenges constitute a suitable scenario to evaluate modern shape retrieval methods in a CH domain. Ten groups participated in the contest: thirty runs were submitted for the retrieval-by-shape task, and twenty-six runs were submitted for the retrieval-by-culture challenge. The results show a predominance of learning methods on image-based multi-view representations to characterize 3D objects. Nevertheless, the problem presented in our challenges is far from being solved. We also identify the potential paths for further improvements and give insights into the future directions of research. Y1 - 2021 U6 - https://doi.org/10.1016/j.cag.2021.07.010 VL - 100 SP - 1 EP - 20 ER - TY - JOUR A1 - Caputo, Ariel A1 - Emporio, Marco A1 - Giachetti, Andrea A1 - Cristani, Marco A1 - Borghi, Guido A1 - D'Eusanio, Andrea A1 - Le, Minh-Quan A1 - Nguyen, Hai-Dang A1 - Tran, Minh-Triet A1 - Ambellan, Felix A1 - Hanik, Martin A1 - Navayazdani, Esfandiar A1 - Tycowicz, Christoph von T1 - SHREC 2022 Track on Online Detection of Heterogeneous Gestures JF - Computers and Graphics N2 - This paper presents the outcomes of a contest organized to evaluate methods for the online recognition of heterogeneous gestures from sequences of 3D hand poses. The task is the detection of gestures belonging to a dictionary of 16 classes characterized by different pose and motion features. The dataset features continuous sequences of hand tracking data where the gestures are interleaved with non-significant motions. The data have been captured using the Hololens 2 finger tracking system in a realistic use-case of mixed reality interaction. The evaluation is based not only on the detection performances but also on the latency and the false positives, making it possible to understand the feasibility of practical interaction tools based on the algorithms proposed. The outcomes of the contest's evaluation demonstrate the necessity of further research to reduce recognition errors, while the computational cost of the algorithms proposed is sufficiently low. Y1 - 2022 U6 - https://doi.org/10.1016/j.cag.2022.07.015 VL - 107 SP - 241 EP - 251 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Schwartz, Stephan A1 - Surau, William T1 - Vertex Covering with Capacitated Trees JF - Networks N2 - The covering of a graph with (possibly disjoint) connected subgraphs is a funda-mental problem in graph theory. In this paper, we study a version to cover a graph’svertices by connected subgraphs subject to lower and upper weight bounds, and pro-pose a column generation approach to dynamically generate feasible and promisingsubgraphs. Our focus is on the solution of the pricing problem which turns out to bea variant of the NP-hard Maximum Weight Connected Subgraph Problem. We com-pare different formulations to handle connectivity, and find that a single-commodityflow formulation performs best. This is notable since the respective literature seemsto have widely dismissed this formulation. We improve it to a new coarse-to-fine flowformulation that is theoretically and computationally superior, especially for largeinstances with many vertices of degree 2 like highway networks, where it provides aspeed-up factor of 5 over the non-flow-based formulations. We also propose a pre-processing method that exploits a median property of weight-constrained subgraphs,a primal heuristic, and a local search heuristic. In an extensive computational studywe evaluate the presented connectivity formulations on different classes of instances,and demonstrate the effectiveness of the proposed enhancements. Their speed-upsessentially multiply to an overall factor of well over 10. Overall, our approach allowsthe reliable solution of instances with several hundreds of vertices in a few min-utes. These findings are further corroborated in a comparison to existing districtingmodels on a set of test instances from the literature Y1 - 2023 U6 - https://doi.org/10.1002/net.22130 VL - 81 IS - 2 SP - 253 EP - 277 ER - TY - JOUR A1 - Chen, Ying A1 - Chua, Wee Song A1 - Koch, Thorsten T1 - Forecasting day-ahead high-resolution natural-gas demand and supply in Germany JF - Applied Energy N2 - Forecasting natural gas demand and supply is essential for an efficient operation of the German gas distribution system and a basis for the operational decisions of the transmission system operators. The German gas market is moving towards more short-term planning, in particular, day-ahead contracts. This increases the difficulty that the operators in the dispatching centre are facing, as well as the necessity of accurate forecasts. This paper presents a novel predictive model that provides day-ahead forecasts of the high resolution gas flow by developing a Functional AutoRegressive model with eXogenous variables (FARX). The predictive model allows the dynamic patterns of hourly gas flows to be described in a wide range of historical profiles, while also taking the relevant determinants data into account. By taking into account a richer set of information, FARX provides stronger performance in real data analysis, with both accuracy and high computational efficiency. Compared to several alternative models in out-of-sample forecasts, the proposed model can improve forecast accuracy by at least 12% and up to 5-fold for one node, 3% to 2-fold and 2-fold to 4-fold for the other two nodes. The results show that lagged 1-day gas flow and nominations are important predictors, and with their presence in the forecast model, temperature becomes insignificant for short-term predictions. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1016/j.apenergy.2018.06.137 IS - Volume 228 SP - 1091 EP - 1110 ER - TY - JOUR A1 - Chen, Ying A1 - Xu, Xiuqin A1 - Koch, Thorsten T1 - Day-ahead high-resolution forecasting of natural gas demand and supply in Germany with a hybrid model JF - Applied Energy N2 - As the natural gas market is moving towards short-term planning, accurate and robust short-term forecasts of the demand and supply of natural gas is of fundamental importance for a stable energy supply, a natural gas control schedule, and transport operation on a daily basis. We propose a hybrid forecast model, Functional AutoRegressive and Convolutional Neural Network model, based on state-of-the-art statistical modeling and artificial neural networks. We conduct short-term forecasting of the hourly natural gas flows of 92 distribution nodes in the German high-pressure gas pipeline network, showing that the proposed model provides nice and stable accuracy for different types of nodes. It outperforms all the alternative models, with an improved relative accuracy up to twofold for plant nodes and up to fourfold for municipal nodes. For the border nodes with rather flat gas flows, it has an accuracy that is comparable to the best performing alternative model. KW - Natural gas flow forecasting KW - Neural network KW - Hybrid model KW - Functional autoregressive Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1016/j.apenergy.2019.114486 VL - 262 IS - 114486 ER - TY - JOUR A1 - Ben Soltane, Isam A1 - Colom, Rémi A1 - Stout, Brian A1 - Bonod, Nicolas T1 - Derivation of the Transient and Steady Optical States from the Poles of the S-Matrix JF - Laser Photon. Rev. Y1 - 2023 U6 - https://doi.org/10.1002/lpor.202200141 VL - 17 SP - 2200141 ER - TY - JOUR A1 - Chewle, Surahit A1 - Emmerling, Franziska A1 - Weber, Marcus T1 - Effect of choice of solvent on crystallization pathway of Paracetamol: An experimental and theoretical case study JF - Crystals N2 - The choice of solvents influences crystalline solid formed during the crystallization of active pharmaceutical ingredients (API). The underlying effects are not always well understood because of the complexity of the systems. Theoretical models are often insufficient to describe this phenomenon. In this study, the crystallization behavior of the model drug paracetamol in different solvents was studied based on experimental and molecular dynamics data. The crystallization process was followed in situ using time-resolved Raman spectroscopy. Molecular dynamics with simulated annealing algorithm was used for an atomistic understanding of the underlying processes. The experimental and theoretical data indicate that paracetamol molecules adopt a particular geometry in a given solvent predefining the crystallization of certain polymorphs. Y1 - 2020 U6 - https://doi.org/10.3390/cryst10121107 VL - 10 IS - 12 SP - 1107 ER - TY - JOUR A1 - Lopez-Fraguas, Eduardo A1 - Binkowski, Felix A1 - Burger, Sven A1 - Hagedorn, Sylvia A1 - Garcia-Camara, Braulio A1 - Vergaz, Ricardo A1 - Becker, Christiane A1 - Manley, Phillip T1 - Tripling the light extraction efficiency of a deep ultraviolet LED using a nanostructured p-contact JF - Sci. Rep. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-15499-7 VL - 12 SP - 11480 ER - TY - JOUR A1 - Wang, Yujing A1 - Vannucci, Luca A1 - Burger, Sven A1 - Gregersen, Niels T1 - Near-unity efficiency in ridge waveguide-based, on-chip single-photon sources JF - Mater. Quantum Technol. Y1 - 2022 U6 - https://doi.org/10.1088/2633-4356/aca8e8 VL - 2 SP - 045004 ER - TY - JOUR A1 - Ramos Leite, Tiago A1 - Zschiedrich, Lin A1 - Kizilkaya, Orhan A1 - McPeak, Kevin M. T1 - Resonant Plasmonic–Biomolecular Chiral Interactions in the Far-Ultraviolet: Enantiomeric Discrimination of sub-10 nm Amino Acid Films JF - Nano Lett. Y1 - 2022 UR - https://digitalcommons.lsu.edu/chem_engineering_pubs/34/ U6 - https://doi.org/10.1021/acs.nanolett.2c01724 VL - 22 SP - 7343 ER - TY - JOUR A1 - Rej, Sourav A1 - Santiago, Eva Yazmin A1 - Baturina, Olga A1 - Zhang, Yu A1 - Burger, Sven A1 - Kment, Stepan A1 - Govorov, Alexander O. A1 - Naldoni, Alberto T1 - Colloidal Titanium Nitride Nanobars for Broadband Inexpensive Plasmonics and Photochemistry from Visible to Mid-IR Wavelengths JF - Nano Energy Y1 - 2022 U6 - https://doi.org/10.1016/j.nanoen.2022.107989 VL - 104 SP - 107989 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Takeuchi, Kotaro A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の 階層的関係を考慮した最適化 (モデル縮約のための期間クラスタリング手法の比較) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Comparison of Time-Period Clustering Methods for Model Reduction) JF - 第38回エネルギー・資源学会研究発表会講演論文集 N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, three clustering methods are applied to time aggregation and compared with one another in terms of the computation efficiency. Especially, the k-medoids method is applied newly in addition to the time-series and operation-based methods applied previously. A case study is conducted on the optimal design of a gas turbine cogeneration system for district energy supply. Through the study, it turns out the k-medoids method is effective to shorten the computation time as compared with the time-series method, although it is necessary to set the number of clusters artifically in both the methods. It also turns out that the operation-based method is more effective than the k-medoids method in terms of the computation efficiency even with the number of clusters set automatically. Y1 - 2019 SP - 109 EP - 114 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の 階層的関係を考慮した最適化 (蓄エネルギー機器を有するシステムへの適用) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Application to Systems With Energy Storage Units) JF - 第40回エネルギー・資源学会研究発表会講演論文集 N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies has been extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of re- ducing model is extended by aggregating representative days and sampling times differently in consideration of the characteristics of storage units. A case study is conducted on the optimal design of a gas turbine cogeneration system with a thermal storage unit for district energy supply. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solution as compared with a conventional method. It also turns out that the model reduction with the special time aggregation is effective to shorten the computation time as compared with that without time aggregation in case that the number of candidates for equipment capacities is relatively small. Y1 - 2021 SP - 398 EP - 403 ER - TY - JOUR A1 - Bittracher, Andreas A1 - Mollenhauer, Mattes A1 - Koltai, Péter A1 - Schütte, Christof T1 - Optimal Reaction Coordinates: Variational Characterization and Sparse Computation JF - Multiscale Modelling & Simulation N2 - Reaction coordinates (RCs) are indicators of hidden, low-dimensional mechanisms that govern the long-term behavior of high-dimensional stochastic processes. We present a novel and general variational characterization of optimal RCs and provide conditions for their existence. Optimal RCs are minimizers of a certain loss function, and reduced models based on them guarantee a good approximation of the statistical long-term properties of the original high-dimensional process. We show that for slow-fast systems, metastable systems, and other systems with known good RCs, the novel theory reproduces previous insight. Remarkably, for reversible systems, the numerical effort required to evaluate the loss function scales only with the variability of the underlying, low-dimensional mechanism, and not with that of the full system. The theory provided lays the foundation for an efficient and data-sparse computation of RCs via modern machine learning techniques. Y1 - 2023 U6 - https://doi.org/10.1137/21M1448367 VL - 21 IS - 2 SP - 449 EP - 488 ER - TY - JOUR A1 - Rickert, Lucas A1 - Betz, Fridtjof A1 - Plock, Matthias A1 - Burger, Sven A1 - Heindel, Tobias T1 - High-performance designs for fiber-pigtailed quantum-light sources based on quantum dots in electrically-controlled circular Bragg gratings JF - Opt. Express Y1 - 2023 U6 - https://doi.org/10.1364/OE.486060 VL - 31 SP - 14750 ER - TY - JOUR A1 - Carderera, Alejandro A1 - Pokutta, Sebastian A1 - Schütte, Christof A1 - Weiser, Martin T1 - CINDy: Conditional gradient-based Identification of Non-linear Dynamics – Noise-robust recovery JF - Journal of Computational and Applied Mathematics N2 - Governing equations are essential to the study of nonlinear dynamics, often enabling the prediction of previously unseen behaviors as well as the inclusion into control strategies. The discovery of governing equations from data thus has the potential to transform data-rich fields where well-established dynamical models remain unknown. This work contributes to the recent trend in data-driven sparse identification of nonlinear dynamics of finding the best sparse fit to observational data in a large library of potential nonlinear models. We propose an efficient first-order Conditional Gradient algorithm for solving the underlying optimization problem. In comparison to the most prominent alternative algorithms, the new algorithm shows significantly improved performance on several essential issues like sparsity-induction, structure-preservation, noise robustness, and sample efficiency. We demonstrate these advantages on several dynamics from the field of synchronization, particle dynamics, and enzyme chemistry. Y1 - 2021 ER - TY - JOUR A1 - Wolf, Sarah A1 - Fürst, Steffen A1 - Geiges, Andreas A1 - Laublichler, Manfred A1 - Mielke, Jahel A1 - Steudle, Gesine A1 - Winter, Konstantin A1 - Jaeger, Carlo T1 - The Decision Theatre Triangle for societal challenges – an example case and research needs JF - Journal of Cleaner Production N2 - Tackling societal challenges relating to sustainability requires both an understanding of the underlying complex socio-ecological systems and participation of scientists as well as relevant stakeholders, such as practice experts, decision makers, and citizens. This paper introduces the Decision Theatre Triangle, a method which combines empirical information, mathematical modelling and simulation, and a format for dialogue between scientists and stakeholders. While it builds on previous Decision Theatre work, the new structuring into these three elements emphasizes what is needed for setting up a Decision Theatre for a given challenge. Based on experience with a specific example – sustainable mobility in Germany – it is argued that agent-based models are particularly suitable for Decision Theatres and that the method is useful not only for decision support but also for science communication and co-creation of a deeper knowledge of the system under discussion. As a step towards facilitating a broader use of the Decision Theatre Triangle method, the paper then sketches research needs for each of its three elements, with a focus on mathematical modelling and simulation. Y1 - 2023 U6 - https://doi.org/10.1016/j.jclepro.2023.136299 VL - 394 SP - 136299 ER - TY - JOUR A1 - Tomholt, Lara A1 - Baum, Daniel A1 - Wood, Robert J. A1 - Weaver, James C. T1 - High-throughput segmentation, data visualization, and analysis of sea star skeletal networks JF - Journal of Structural Biology N2 - The remarkably complex skeletal systems of the sea stars (Echinodermata, Asteroidea), consisting of hundreds to thousands of individual elements (ossicles), have intrigued investigators for more than 150 years. While the general features and structural diversity of isolated asteroid ossicles have been well documented in the literature, the task of mapping the spatial organization of these constituent skeletal elements in a whole-animal context represents an incredibly laborious process, and as such, has remained largely unexplored. To address this unmet need, particularly in the context of understanding structure-function relationships in these complex skeletal systems, we present an integrated approach that combines micro-computed tomography, semi-automated ossicle segmentation, data visualization tools, and the production of additively manufactured tangible models to reveal biologically relevant structural data that can be rapidly analyzed in an intuitive manner. In the present study, we demonstrate this high-throughput workflow by segmenting and analyzing entire skeletal systems of the giant knobby star, Pisaster giganteus, at four different stages of growth. The in-depth analysis, presented herein, provides a fundamental understanding of the three-dimensional skeletal architecture of the sea star body wall, the process of skeletal maturation during growth, and the relationship between skeletal organization and morphological characteristics of individual ossicles. The widespread implementation of this approach for investigating other species, subspecies, and growth series has the potential to fundamentally improve our understanding of asteroid skeletal architecture and biodiversity in relation to mobility, feeding habits, and environmental specialization in this fascinating group of echinoderms. Y1 - 2023 U6 - https://doi.org/10.1016/j.jsb.2023.107955 VL - 215 IS - 2 SP - 107955 ER - TY - JOUR A1 - Griewank, Andreas A1 - Streubel, Tom A1 - Tischendorf, Caren T1 - On the abs-polynomial expansion of piecewise smooth functions JF - Optimization Methods and Software N2 - Tom Streubel has observed that for functions in abs-normal form, generalized Taylor expansions of arbitrary order $\bar d-1$ can be generated by algorithmic piecewise differentiation. Abs-normal form means that the real or vector valued function is defined by an evaluation procedure that involves the absolute value function $|...|$ apart from arithmetic operations and $\bar d$ times continuously differentiable univariate intrinsic functions. The additive terms in Streubel's expansion are abs-polynomial, i.e. involve neither divisions nor intrinsics. When and where no absolute values occur, Moore's recurrences can be used to propagate univariate Taylor polynomials through the evaluation procedure with a computational effort of $\mathcal O({\bar d}^2)$, provided all univariate intrinsics are defined as solutions of linear ODEs. This regularity assumption holds for all standard intrinsics, but for irregular elementaries one has to resort to Faa di Bruno's formula, which has exponential complexity in $\bar d$. As already conjectured we show that the Moore recurrences can be adapted for regular intrinsics to the abs-normal case. Finally, we observe that where the intrinsics are real analytic the expansions can be extended to infinite series that converge absolutely on spherical domains. Y1 - 2020 U6 - https://doi.org/10.1080/10556788.2020.1817448 PB - Taylor & Francis ER - TY - JOUR A1 - Streubel, Tom A1 - Tischendorf, Caren A1 - Griewank, Andreas T1 - Piecewise Polynomial Taylor Expansions - The Generalization of Faà di Bruno's Formula JF - Modeling, Simulation and Optimization of Complex Processes HPSC 2018 N2 - We present an extension of Taylor's Theorem for the piecewise polynomial expansion of non-smooth evaluation procedures involving absolute value operations. Evaluation procedures are computer programs of mathematical functions in closed form expression and allow a different treatment of smooth operations or calls to the absolute value function. The well known classical Theorem of Taylor defines polynomial approximations of sufficiently smooth functions and is widely used for the derivation and analysis of numerical integrators for systems of ordinary differential- or differential-algebraic equations, for the construction of solvers for continuous non-linear optimization of finite dimensional objective functions and for root solving of non-linear systems of equations. The long term goal is the stabilization and acceleration of already known methods and the derivation of new methods by incorporating piecewise polynomial Taylor expansions. The herein provided proof of the higher order approximation quality of the new generalized expansions is constructive and allows efficiently designed algorithms for the execution and computation of the piecewise polynomial expansions. As a demonstration towards the ultimate goal we will derive a prototype of a {\$}{\$}k{\$}{\$}k-step method on the basis of polynomial interpolation and the proposed generalized expansions. Y1 - 2020 U6 - https://doi.org/10.1007/978-3-030-55240-4_3 IS - Modeling, Simulation and Optimization of Complex Processes HPSC 2018 SP - 63 EP - 82 PB - Springer International Publishing ER - TY - JOUR A1 - Donati, Luca A1 - Keller, Bettina G. T1 - Girsanov reweighting for metadynamics simulations JF - The Journal of Chemical Physics N2 - Metadynamics is a computational method to explore the phase space of a molecular system. Gaussian functions are added along relevant coordinates on the fly during a molecular-dynamics simulation to force the system to escape from minima in the potential energy function. The dynamics in the resulting trajectory are however unphysical and cannot be used directly to estimate dynamical properties of the system. Girsanov reweighting is a recent method used to construct the Markov State Model (MSM) of a system subjected to an external perturbation. With the combination of these two techniques—metadynamics/Girsanov-reweighting—the unphysical dynamics in a metadynamics simulation can be reweighted to obtain the MSM of the unbiased system. We demonstrate the method on a one-dimensional diffusion process, alanine dipeptide, and the hexapeptide Val-Gly-Val-Ala-Pro-Gly (VGVAPG). The results are in excellent agreement with the MSMs obtained from direct unbiased simulations of these systems. We also apply metadynamics/Girsanov-reweighting to a β-hairpin peptide, whose dynamics is too slow to efficiently explore its phase space by direct simulation Y1 - 2018 U6 - https://doi.org/10.1063/1.5027728 VL - 149 IS - 7 SP - 072335 ER - TY - JOUR A1 - Donati, Luca A1 - Heida, Martin A1 - Keller, Bettina G. A1 - Weber, Marcus T1 - Estimation of the infinitesimal generator by square-root approximation JF - J. Phys.: Condens. Matter N2 - In recent years, for the analysis of molecular processes, the estimation of time-scales and transition rates has become fundamental. Estimating the transition rates between molecular conformations is—from a mathematical point of view—an invariant subspace projection problem. We present a method to project the infinitesimal generator acting on function space to a low-dimensional rate matrix. This projection can be performed in two steps. First, we discretize the conformational space in a Voronoi tessellation, then the transition rates between adjacent cells is approximated by the geometric average of the Boltzmann weights of the Voronoi cells. This method demonstrates that there is a direct relation between the potential energy surface of molecular structures and the transition rates of conformational changes. We will show also that this approximation is correct and converges to the generator of the Smoluchowski equation in the limit of infinitely small Voronoi cells. We present results for a two dimensional diffusion process and alanine dipeptide as a high-dimensional system. Y1 - 2018 U6 - https://doi.org/10.1088/1361-648X/aadfc8 VL - 30 IS - 42 SP - 425201 EP - 425201 ER - TY - JOUR A1 - Hassan, Irtaza A1 - Donati, Luca A1 - Stensitzki, Till A1 - Keller, Bettina G A1 - Heyne, Karsten A1 - Imhof, Petra T1 - The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations JF - Chemical Physics Letters N2 - We have combined infrared (IR) experiments with molecular dynamics (MD) simulations in solution at finite temperature to analyse the vibrational signature of the small floppy peptide Alanine-Leucine. IR spectra computed from first-principles MD simulations exhibit no distinct differences between conformational clusters of -helix or -sheet-like folds with different orientations of the bulky leucine side chain. All computed spectra show two prominent bands, in good agreement with the experiment, that are assigned to the stretch vibrations of the carbonyl and carboxyl group, respectively. Variations in band widths and exact maxima are likely due to small fluctuations in the backbone torsion angles. Y1 - 2018 U6 - https://doi.org/10.1016/j.cplett.2018.03.026 VL - 698 SP - 227 EP - 233 ER - TY - JOUR A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Vigerske, Stefan A1 - Winkler, Michael T1 - 制約整数計画ソルバ SCIP の並列化 JF - 統計数理 N2 - 制約整数計画(CIP: Constraint Integer Programs)は,制約プログラミング(CP: Constraint Programming),混合整数計画(MIP: Mixed Integer Programming),充足可能性問題(SAT: Satisfability Problem)の研究分野におけるモデリング技術と解法を統合している.その結果,制約整数計画は,広いクラスの最適化問題を扱うことができる.SCIP(Solving Constraint Integer Programs)は,CIP を解くソルバとして実装され,Zuse Institute Berlin(ZIB)の研究者を中心として継続的に拡張が続けられている.本論文では,著者らによって開発された SCIP に対する2 種類の並列化拡張を紹介する.一つは,複数計算ノード間で大規模に並列動作する ParaSCIPである.もう一つは,複数コアと共有メモリを持つ 1 台の計算機上で(スレッド)並列で動作する FiberSCIP である.ParaSCIP は,HLRN II スーパーコンピュータ上で,一つのインスタンスを解くために最大 7,168 コアを利用した動作実績がある.また,統計数理研究所の Fujitsu PRIMERGY RX200S5 上でも,最大 512 コアを利用した動作実績がある.統計数理研究所のFujitsu PRIMERGY RX200S5 上では,これまでに最適解が得られていなかった MIPLIB2010のインスタンスである dg012142 に最適解を与えた. N2 - The paradigm of constraint integer programming (CIP) combines modeling and solving techniques from the fields of constraint programming (CP), mixed-integer programming (MIP) and satisfability problem (SAT). This paradigm allows us to address a wide range of optimization problems. SCIP is an implementation of the idea of CIP and is now being continuously extended by a group of researchers centered at Zuse Institute Berlin (ZIB). This paper introduces two parallel extensions of SCIP. One is ParaSCIP, which is intended to run on a large scale distributed memory computing environment, and the other is FiberSCIP, intended to run on a shared memory computing environment. ParaSCIP has been run successfully on the HLRN II supercomputer utilizing up to 7,168 cores to solve a single difficult MIP. It has also been tested on an ISM supercomputer (Fujitsu PRIMERGY RX200S5 using up to 512 cores). The previously unsolved instance dg012142 from MIPLIB2010 was solved by using the ISM supercomputer. Y1 - 2013 UR - https://www.ism.ac.jp/editsec/toukei/pdf/61-1-047.pdf VL - 61 IS - 1 SP - 47 EP - 78 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven T1 - Cover Picture: Resonance Expansion of Quadratic Quantities with Regularized Quasinormal Modes JF - Phys. Status Solidi A Y1 - 2023 U6 - https://doi.org/10.1002/pssa.202370013 VL - 220 SP - 2370013 ER - TY - JOUR A1 - Wulkow, Niklas A1 - Koltai, Péter A1 - Sunkara, Vikram A1 - Schütte, Christof T1 - Data-driven modelling of nonlinear dynamics by barycentric coordinates and memory JF - J. Stat. Phys. N2 - We present a numerical method to model dynamical systems from data. We use the recently introduced method Scalable Probabilistic Approximation (SPA) to project points from a Euclidean space to convex polytopes and represent these projected states of a system in new, lower-dimensional coordinates denoting their position in the polytope. We then introduce a specific nonlinear transformation to construct a model of the dynamics in the polytope and to transform back into the original state space. To overcome the potential loss of information from the projection to a lower-dimensional polytope, we use memory in the sense of the delay-embedding theorem of Takens. By construction, our method produces stable models. We illustrate the capacity of the method to reproduce even chaotic dynamics and attractors with multiple connected components on various examples. Y1 - 2021 ER - TY - JOUR A1 - Wulkow, Niklas A1 - Koltai, Péter A1 - Schütte, Christof T1 - Memory-Based Reduced Modelling and Data-Based Estimation of Opinion Spreading JF - Journal of Nonlinear Science N2 - We investigate opinion dynamics based on an agent-based model and are interested in predicting the evolution of the percentages of the entire agent population that share an opinion. Since these opinion percentages can be seen as an aggregated observation of the full system state, the individual opinions of each agent, we view this in the framework of the Mori–Zwanzig projection formalism. More specifically, we show how to estimate a nonlinear autoregressive model (NAR) with memory from data given by a time series of opinion percentages, and discuss its prediction capacities for various specific topologies of the agent interaction network. We demonstrate that the inclusion of memory terms significantly improves the prediction quality on examples with different network topologies. Y1 - 2021 U6 - https://doi.org/10.1007/s00332-020-09673-2 VL - 31 ER - TY - JOUR A1 - Driesen, Joshua A1 - El-Khatib, Ziad A1 - Wulkow, Niklas A1 - Joblin, Mitchell A1 - Vasileva, Iskriyana A1 - Glücker, Andreas A1 - Kruspel, Valentin A1 - Vogel, Catherine T1 - Data-Powered Positive Deviance during the SARS-CoV-2 Pandemic—An Ecological Pilot Study of German Districts JF - International Journal of Environmental Research and Public Health N2 - We introduced the mixed-methods Data-Powered Positive Deviance (DPPD) framework as a potential addition to the set of tools used to search for effective response strategies against the SARS-CoV-2 pandemic. For this purpose, we conducted a DPPD study in the context of the early stages of the German SARS-CoV-2 pandemic. We used a framework of scalable quantitative methods to identify positively deviant German districts that is novel in the scientific literature on DPPD, and subsequently employed qualitative methods to identify factors that might have contributed to their comparatively successful reduction of the forward transmission rate. Our qualitative analysis suggests that quick, proactive, decisive, and flexible/pragmatic actions, the willingness to take risks and deviate from standard procedures, good information flows both in terms of data collection and public communication, alongside the utilization of social network effects were deemed highly important by the interviewed districts. Our study design with its small qualitative sample constitutes an exploratory and illustrative effort and hence does not allow for a clear causal link to be established. Thus, the results cannot necessarily be extrapolated to other districts as is. However, the findings indicate areas for further research to assess these strategies’ effectiveness in a broader study setting. We conclude by stressing DPPD’s strengths regarding replicability, scalability, adaptability, as well asits focus on local solutions, which make it a promising framework to be applied in various contexts,e.g., in the context of the Global South. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/ijerph18189765 VL - 18 IS - 9765 SP - 1 EP - 29 ER - TY - JOUR A1 - Ragyanszki, Anita A1 - Fiser, Bela A1 - Lee-Ruff, Edward A1 - Liebman, Joel F. T1 - Strained Small Nitrogen Heterocycles-Azabicyclobutanes and Azirines JF - ChemistrySelect N2 - Small ring nitrogen heterocycles, azabicyclobutanes and azirines, were investigated by computational methods in order to address the discrepancy between their regioisomers 1- and 2-azabicyclobutane and 1H- and 2H-azirines. Both 1-azabicyclobutane and 2H-azirine are well known synthetic starting points to larger nitrogen heterocycles whereas 2-azabicyclobutane and 1H-azirine and their derivatives have yet to be reported as isolable compounds. Calculated parameters such as structure, base strength (proton affinities), NICS values and enthalpies of formation from which strain energies are derived are reported. The destabilization of the less stable regioisomers is attributed to homoantiaromaticity in 2-azabicyclobutane and antiaromaticity in 1H-azirine. Two stereoisomers exist for 2-azabicyclobutane with the endo- stereoisomer being more stable. This phenomenon is indicative of the hydrogen bond acceptor properties of the neighboring cyclpropane and the π-bond character of the central bond in 2-azabicyclobutane. Y1 - 2023 U6 - https://doi.org/10.1002/slct.202301405 VL - 8 IS - 26 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - An effective approach for deriving and evaluating approximate optimal design solutions of energy supply systems by time series aggregation JF - Frontiers in Energy Research N2 - It is important to design multi-energy supply systems optimally in consideration of their operations for variations in energy demands. An approach for efficiently solving such an optimal design problem with a large number of periods for variations in energy demands is to derive an approximate optimal design solution by time series aggregation. However, such an approach does not provide any information on the accuracy for the optimal value of the objective function. In this paper, an effective approach for time series aggregation is proposed to derive an approximate optimal design solution and evaluate a proper gap between the upper and lower bounds for the optimal value of the objective function based on a mixed-integer linear model. In accordance with aggregation, energy demands are relaxed to uncertain parameters and the problem for deriving an approximate optimal design solution and evaluating it is transformed to a three-level optimization problem, and it is solved by applying both the robust and hierarchical optimization methods. A case study is conducted on a cogeneration system with a practical configuration, and it turns out that the proposed approach enables one to derive much smaller gaps as compared with those obtained by a conventional approach. Y1 - 2023 U6 - https://doi.org/10.3389/fenrg.2023.1128681 VL - 11 SP - 1 EP - 14 ER - TY - JOUR A1 - Nohadani, Omid A1 - Sharma, Kartikey T1 - Optimization under Connected Uncertainty JF - INFORMS Journal on Optimization N2 - Robust optimization methods have shown practical advantages in a wide range of decision-making applications under uncertainty. Recently, their efficacy has been extended to multiperiod settings. Current approaches model uncertainty either independent of the past or in an implicit fashion by budgeting the aggregate uncertainty. In many applications, however, past realizations directly influence future uncertainties. For this class of problems, we develop a modeling framework that explicitly incorporates this dependence via connected uncertainty sets, whose parameters at each period depend on previous uncertainty realizations. To find optimal here-and-now solutions, we reformulate robust and distributionally robust constraints for popular set structures and demonstrate this modeling framework numerically on broadly applicable knapsack and portfolio-optimization problems. Y1 - 2022 U6 - https://doi.org/10.1287/ijoo.2021.0067 VL - 4 IS - 3 SP - 326 EP - 346 ER - TY - JOUR A1 - Masing, Berenike A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - The price of symmetric line plans in the Parametric City JF - Transportation Research Part B: Methodological N2 - We consider the line planning problem in public transport in the Parametric City, an idealized model that captures typical scenarios by a (small) number of parameters. The Parametric City is rotation symmetric, but optimal line plans are not always symmetric. This raises the question to quantify the symmetry gap between the best symmetric and the overall best solution. For our analysis, we formulate the line planning problem as a mixed integer linear program, that can be solved in polynomial time if the solutions are forced to be symmetric. We prove that the symmetry gap is small when a specific Parametric City parameter is fixed, and we give an approximation algorithm for line planning in the Parametric City in this case. While the symmetry gap can be arbitrarily large in general, we show that symmetric line plans are a good choice in most practical situations. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88613 VL - 166 SP - 419 EP - 443 ER - TY - JOUR A1 - Combettes, Cyrille A1 - Pokutta, Sebastian T1 - Revisiting the Approximate Carathéodory Problem via the Frank-Wolfe Algorithm JF - Mathematical Programming Y1 - 2023 U6 - https://doi.org/10.1007/s10107-021-01735-x VL - 197 SP - 191 EP - 214 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus A1 - Keller, Bettina G. T1 - Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux JF - Journal of Physics: Condensed Matter N2 - Molecular dynamics (MD) are extremely complex, yet understanding the slow components of their dynamics is essential to understanding their macroscopic properties. To achieve this, one models the MD as a stochastic process and analyses the dominant eigenfunctions of the associated Fokker–Planck operator, or of closely related transfer operators. So far, the calculation of the discretized operators requires extensive MD simulations. The square-root approximation of the Fokker–Planck equation is a method to calculate transition rates as a ratio of the Boltzmann densities of neighboring grid cells times a flux, and can in principle be calculated without a simulation. In a previous work we still used MD simulations to determine the flux. Here, we propose several methods to calculate the exact or approximate flux for various grid types, and thus estimate the rate matrix without a simulation. Using model potentials we test computational efficiency of the methods, and the accuracy with which they reproduce the dominant eigenfunctions and eigenvalues. For these model potentials, rate matrices with up to $\mathcal{O}\left(1{0}^{6}\right)$ states can be obtained within seconds on a single high-performance compute server if regular grids are used. Y1 - 2021 U6 - https://doi.org/10.1088/1361-648X/abd5f7 VL - 33 IS - 11 SP - 115902 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus T1 - Assessing transition rates as functions of environmental variables JF - The Journal of Chemical Physics N2 - We present a method to estimate the transition rates of molecular systems under different environmental conditions which cause the formation or the breaking of bonds and require the sampling of the Grand Canonical Ensemble. For this purpose, we model the molecular system in terms of probable "scenarios", governed by different potential energy functions, which are separately sampled by classical MD simulations. Reweighting the canonical distribution of each scenario according to specific environmental variables, we estimate the grand canonical distribution, then we use the Square Root Approximation (SqRA) method to discretize the Fokker-Planck operator into a rate matrix and the robust Perron Cluster Cluster Analysis (PCCA+) method to coarse-grain the kinetic model. This permits to efficiently estimate the transition rates of conformational states as functions of environmental variables, for example, the local pH at a cell membrane. In this work we formalize the theoretical framework of the procedure and we present a numerical experiment comparing the results with those provided by a constant-pH method based on non-equilibrium Molecular Dynamics Monte Carlo simulations. The method is relevant for the development of new drug design strategies which take into account how the cellular environment influences biochemical processes. Y1 - 2022 U6 - https://doi.org/10.1063/5.0109555 VL - 157 IS - 22 SP - 224103-1 EP - 224103-14 PB - AIP Publishing ER - TY - JOUR A1 - Kieninger, Stefanie A1 - Donati, Luca A1 - Keller, Bettina G. T1 - Dynamical reweighting methods for Markov models JF - Current Opinion in Structural Biology N2 - Conformational dynamics is essential to biomolecular processes. Markov State Models (MSMs) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations is still at an early stage of development. Several dynamical reweighing approaches have been proposed, which can be classified as approaches based on (i) Kramers rate theory, (ii) rescaling of the probability density flux, (iii) reweighting by formulating a likelihood function, (iv) path reweighting. We present the state-of-the-art and discuss the methodological differences of these methods, their limitations and recent applications. Y1 - 2020 U6 - https://doi.org/10.1016/j.sbi.2019.12.018 VL - 61 SP - 124 EP - 131 ER - TY - JOUR A1 - Duarte, Belmiro A1 - Sagnol, Guillaume T1 - Approximate and exact optimal designs for 2^k factorial experiments for generalized linear models via second order cone programming JF - Statistical Papers N2 - Model-based optimal designs of experiments (M-bODE) for nonlinear models are typically hard to compute. The literature on the computation of M-bODE for nonlinear models when the covariates are categorical variables, i.e. factorial experiments, is scarce. We propose second order cone programming (SOCP) and Mixed Integer Second Order Programming (MISOCP) formulations to find, respectively, approximate and exact A- and D-optimal designs for 2𝑘 factorial experiments for Generalized Linear Models (GLMs). First, locally optimal (approximate and exact) designs for GLMs are addressed using the formulation of Sagnol (J Stat Plan Inference 141(5):1684–1708, 2011). Next, we consider the scenario where the parameters are uncertain, and new formulations are proposed to find Bayesian optimal designs using the A- and log det D-optimality criteria. A quasi Monte-Carlo sampling procedure based on the Hammersley sequence is used for computing the expectation in the parametric region of interest. We demonstrate the application of the algorithm with the logistic, probit and complementary log–log models and consider full and fractional factorial designs. Y1 - 2020 U6 - https://doi.org/10.1007/s00362-018-01075-7 VL - 61 SP - 2737 EP - 2767 ER - TY - JOUR A1 - Berthold, Timo A1 - Mexi, Gioni A1 - Salvagnin, Domenico T1 - Using Multiple Reference Vectors and Objective Scaling in the Feasibility Pump JF - EURO Journal on Computational Optimization N2 - The Feasibility Pump (FP) is one of the best-known primal heuristics for mixed-integer programming (MIP): more than 15 papers suggested various modifications of all of its steps. So far, no variant considered information across multiple iterations, but all instead maintained the principle to optimize towards a single reference integer point. In this paper, we evaluate the usage of multiple reference vectors in all stages of the FP algorithm. In particular, we use LP-feasible vectors obtained during the main loop to tighten the variable domains before entering the computationally expensive enumeration stage. Moreover, we consider multiple integer reference vectors to explore further optimizing directions and introduce alternative objective scaling terms to balance the contributions of the distance functions and the original MIP objective. Our computational experiments demonstrate that the new method can improve performance on general MIP test sets. In detail, our modifications provide a 29.3% solution quality improvement and 4.0% running time improvement in an embedded setting, needing 16.0% fewer iterations over a large test set of MIP instances. In addition, the method’s success rate increases considerably within the first few iterations. In a standalone setting, we also observe a moderate performance improvement, which makes our version of FP suitable for the two main use-cases of the algorithm. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-87392 VL - 11 ER - TY - JOUR A1 - Sahin, Guvenc A1 - Ahmadi, Amin A1 - Borndörfer, Ralf A1 - Schlechte, Thomas T1 - Multi-period line planning with resource transfers JF - Transportation Research Part C: Emerging Technologies N2 - Urban transportation systems are subject to a high level of variation and fluctuation in demand over the day. When this variation and fluctuation are observed in both time and space, it is crucial to develop line plans that are responsive to demand. A multi-period line planning approach that considers a changing demand during the planning horizon is proposed. If such systems are also subject to limitations of resources, a dynamic transfer of resources from one line to another throughout the planning horizon should also be considered. A mathematical modelling framework is developed to solve the line planning problem with a cost-oriented approach considering transfer of resources during a finite length planning horizon of multiple periods. We use real-life public transportation network data for our computational results. We analyze whether or not multi-period solutions outperform single period solutions in terms of feasibility and relevant costs. The importance of demand variation on multi-period solutions is investigated. We evaluate the impact of resource transfer constraints on the effectiveness of solutions. We also study the effect of period lengths along with the problem parameters that are significant for and sensitive to the optimality of solutions. Y1 - 2020 U6 - https://doi.org/10.1016/j.trc.2020.102726 VL - 119 SP - 102726 ER - TY - JOUR A1 - Jung, Christian A1 - Nowacka, Anna A1 - Barisin, Tin A1 - Meinel, Dietmar A1 - Paetsch, Olaf A1 - Grzesiak, Szymon A1 - Salamon, Michael A1 - Schladitz, Katja A1 - Redenbach, Claudia A1 - Pahn, Matthias T1 - 3d imaging and analysis of cracks in loaded concrete samples. 12th Conference on Industrial Computed Tomography (iCT) 2023, 27 February - 2 March 2023 in Fürth, Germany JF - e-Journal of Nondestructive Testing N2 - Concrete plays a central role as the standard building material in civil engineering. Experimental characterization of the concrete microstructure and a description of failure mechanisms are important to understand the concrete’s mechanical properties. Computed tomography is a powerful source of information as it yields 3d images of concrete specimens. However, complete visual inspection is often infeasible due to very large image sizes. Hence, automatic methods for crack detection and segmentation are needed. A region-growing algorithm and a 3d U-Net showed promising results in a previous study. Cracks in normal concrete and high-performance concrete that were initiated via tensile tests were investigated. Here, the methods are validated on a more diverse set of concrete types and crack characteristics. Adequate adaptions of the methods are necessary to deal with the complex crack structures. The segmentation results are assessed qualitatively and compared to those of a template matching algorithm which is well-established in industry. Y1 - 2023 U6 - https://doi.org/10.58286/27721 VL - 28 IS - 3 ER - TY - JOUR A1 - Sterzik, Anna A1 - Lichtenberg, Nils A1 - Krone, Michael A1 - Baum, Daniel A1 - Cunningham, Douglas W. A1 - Lawonn, Kai T1 - Enhancing molecular visualization: Perceptual evaluation of line variables with application to uncertainty visualization JF - Computers & Graphics N2 - Data are often subject to some degree of uncertainty, whether aleatory or epistemic. This applies both to experimental data acquired with sensors as well as to simulation data. Displaying these data and their uncertainty faithfully is crucial for gaining knowledge. Specifically, the effective communication of the uncertainty can influence the interpretation of the data and the user’s trust in the visualization. However, uncertainty-aware visualization has gotten little attention in molecular visualization. When using the established molecular representations, the physicochemical attributes of the molecular data usually already occupy the common visual channels like shape, size, and color. Consequently, to encode uncertainty information, we need to open up another channel by using feature lines. Even though various line variables have been proposed for uncertainty visualizations, they have so far been primarily used for two-dimensional data and there has been little perceptual evaluation. Thus, we conducted two perceptual studies to determine the suitability of the line variables blur, dashing, grayscale, sketchiness, and width for distinguishing several values in molecular visualizations. While our work was motivated by uncertainty visualization, our techniques and study results also apply to other types of scalar data. Y1 - 2023 U6 - https://doi.org/10.1016/j.cag.2023.06.006 VL - 114 SP - 401 EP - 413 ER - TY - JOUR A1 - Turner, Mark A1 - Koch, Thorsten A1 - Serrano, Felipe A1 - Winkler, Michael T1 - Adaptive Cut Selection in Mixed-Integer Linear Programming JF - Open Journal of Mathematical Optimization N2 - Cutting plane selection is a subroutine used in all modern mixed-integer linear programming solvers with the goal of selecting a subset of generated cuts that induce optimal solver performance. These solvers have millions of parameter combinations, and so are excellent candidates for parameter tuning. Cut selection scoring rules are usually weighted sums of different measurements, where the weights are parameters. We present a parametric family of mixed-integer linear programs together with infinitely many family-wide valid cuts. Some of these cuts can induce integer optimal solutions directly after being applied, while others fail to do so even if an infinite amount are applied. We show for a specific cut selection rule, that any finite grid search of the parameter space will always miss all parameter values, which select integer optimal inducing cuts in an infinite amount of our problems. We propose a variation on the design of existing graph convolutional neural networks, adapting them to learn cut selection rule parameters. We present a reinforcement learning framework for selecting cuts, and train our design using said framework over MIPLIB 2017 and a neural network verification data set. Our framework and design show that adaptive cut selection does substantially improve performance over a diverse set of instances, but that finding a single function describing such a rule is difficult. Code for reproducing all experiments is available at https://github.com/Opt-Mucca/Adaptive-Cutsel-MILP. Y1 - 2023 U6 - https://doi.org/10.5802/ojmo.25 VL - 4 SP - 5 ER - TY - JOUR A1 - Wilson, David A1 - Anglin, Carolyn A1 - Ambellan, Felix A1 - Grewe, Carl Martin A1 - Tack, Alexander A1 - Lamecker, Hans A1 - Dunbar, Michael A1 - Zachow, Stefan T1 - Validation of three-dimensional models of the distal femur created from surgical navigation point cloud data for intraoperative and postoperative analysis of total knee arthroplasty JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose: Despite the success of total knee arthroplasty there continues to be a significant proportion of patients who are dissatisfied. One explanation may be a shape mismatch between pre and post-operative distal femurs. The purpose of this study was to investigate a method to match a statistical shape model (SSM) to intra-operatively acquired point cloud data from a surgical navigation system, and to validate it against the pre-operative magnetic resonance imaging (MRI) data from the same patients. Methods: A total of 10 patients who underwent navigated total knee arthroplasty also had an MRI scan less than 2 months pre-operatively. The standard surgical protocol was followed which included partial digitization of the distal femur. Two different methods were employed to fit the SSM to the digitized point cloud data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). The available MRI data were manually segmented and the reconstructed three-dimensional surfaces used as ground truth against which the statistical shape model fit was compared. Results: For both approaches, the difference between the statistical shape model-generated femur and the surface generated from MRI segmentation averaged less than 1.7 mm, with maximum errors occurring in less clinically important areas. Conclusion: The results demonstrated good correspondence with the distal femoral morphology even in cases of sparse data sets. Application of this technique will allow for measurement of mismatch between pre and post-operative femurs retrospectively on any case done using the surgical navigation system and could be integrated into the surgical navigation unit to provide real-time feedback. Y1 - 2017 UR - https://link.springer.com/content/pdf/10.1007%2Fs11548-017-1630-5.pdf U6 - https://doi.org/10.1007/s11548-017-1630-5 VL - 12 IS - 12 SP - 2097 EP - 2105 PB - Springer ER - TY - JOUR A1 - Witzig, Jakob A1 - Beckenbach, Isabel A1 - Eifler, Leon A1 - Fackeldey, Konstantin A1 - Gleixner, Ambros A1 - Grever, Andreas A1 - Weber, Marcus T1 - Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes JF - Multiscale Modeling and Simulation N2 - In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst. KW - Markov State Models KW - NESS KW - Non-reversible Markov Processes KW - Mixed-Integer Programming Y1 - 2018 U6 - https://doi.org/10.1137/16M1091162 SN - 1438-0064 VL - 16 IS - 1 SP - 248 EP - 265 ER - TY - JOUR A1 - Grewe, Carl Martin A1 - Schreiber, Lisa A1 - Zachow, Stefan T1 - Fast and Accurate Digital Morphometry of Facial Expressions JF - Facial Plastic Surgery Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1564720 VL - 31 IS - 05 SP - 431 EP - 438 PB - Thieme Medical Publishers CY - New York ER - TY - JOUR A1 - Ernst, Ariane A1 - Schütte, Christof A1 - Sigrist, Stephan A1 - Winkelmann, Stefanie T1 - Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics JF - Mathematical Biosciences N2 - Neurotransmission at chemical synapses relies on the calcium-induced fusion of synaptic vesicles with the presynaptic membrane. The distance to the calcium channels determines the release probability and thereby the postsynaptic signal. Suitable models of the process need to capture both the mean and the variance observed in electrophysiological measurements of the postsynaptic current. In this work, we propose a method to directly compute the exact first- and second-order moments for signals generated by a linear reaction network under convolution with an impulse response function, rendering computationally expensive numerical simulations of the underlying stochastic counting process obsolete. We show that the autocorrelation of the process is central for the calculation of the filtered signal’s second-order moments, and derive a system of PDEs for the cross-correlation functions (including the autocorrelations) of linear reaction networks with time-dependent rates. Finally, we employ our method to efficiently compare different spatial coarse graining approaches for a specific model of synaptic vesicle fusion. Beyond the application to neurotransmission processes, the developed theory can be applied to any linear reaction system that produces a filtered stochastic signal. Y1 - 2022 U6 - https://doi.org/10.1016/j.mbs.2021.108760 VL - 343 ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Gleixner, Ambros A1 - Vigerske, Stefan T1 - A Computational Study of Perspective Cuts JF - Mathematical Programming Computation N2 - The benefits of cutting planes based on the perspective function are well known for many specific classes of mixed-integer nonlinear programs with on/off structures. However, we are not aware of any empirical studies that evaluate their applicability and computational impact over large, heterogeneous test sets in general-purpose solvers. This paper provides a detailed computational study of perspective cuts within a linear programming based branch-and-cut solver for general mixed-integer nonlinear programs. Within this study, we extend the applicability of perspective cuts from convex to nonconvex nonlinearities. This generalization is achieved by applying a perspective strengthening to valid linear inequalities which separate solutions of linear relaxations. The resulting method can be applied to any constraint where all variables appearing in nonlinear terms are semi-continuous and depend on at least one common indicator variable. Our computational experiments show that adding perspective cuts for convex constraints yields a consistent improvement of performance, and adding perspective cuts for nonconvex constraints reduces branch-and-bound tree sizes and strengthens the root node relaxation, but has no significant impact on the overall mean time. Y1 - 2023 U6 - https://doi.org/10.1007/s12532-023-00246-4 VL - 15 SP - 703 EP - 731 ER - TY - JOUR A1 - Quer, Jannes A1 - Donati, Luca A1 - Keller, Bettina A1 - Weber, Marcus T1 - An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates JF - SIAM Journal on Scientific Computing N2 - In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov's theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a non-equilibrium dynamics which is used to sample the equilibrium quantities. Y1 - 2018 U6 - https://doi.org/10.1137/17m1124772 VL - 40 IS - 2 SP - A653 EP - A670 ER - TY - JOUR A1 - Hendel, Gregor A1 - Anderson, Daniel A1 - Le Bodic, Pierre A1 - Pfetsch, Marc T1 - Estimating the Size of Branch-And-Bound Trees JF - INFORMS Journal on Computing N2 - This paper investigates the estimation of the size of Branch-and-Bound (B&B) trees for solving mixed-integer programs. We first prove that the size of the B&B tree cannot be approximated within a factor of~2 for general binary programs, unless P equals NP. Second, we review measures of the progress of the B&B search, such as the gap, and propose a new measure, which we call leaf frequency. We study two simple ways to transform these progress measures into B&B tree size estimates, either as a direct projection, or via double-exponential smoothing, a standard time-series forecasting technique. We then combine different progress measures and their trends into nontrivial estimates using Machine Learning techniques, which yields more precise estimates than any individual measure. The best method we have identified uses all individual measures as features of a random forest model. In a large computational study, we train and validate all methods on the publicly available MIPLIB and Coral general purpose benchmark sets. On average, the best method estimates B&B tree sizes within a factor of 3 on the set of unseen test instances even during the early stage of the search, and improves in accuracy as the search progresses. It also achieves a factor 2 over the entire search on each out of six additional sets of homogeneous instances we have tested. All techniques are available in version 7 of the branch-and-cut framework SCIP. Y1 - 2021 U6 - https://doi.org/10.1287/ijoc.2021.1103 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros A1 - Pulaj, Jonad T1 - A Safe Computational Framework for Integer Programming applied to Chvátal's Conjecture JF - ACM Transactions on Mathematical Software N2 - We describe a general and safe computational framework that provides integer programming results with the degree of certainty that is required for machine-assisted proofs of mathematical theorems. At its core, the framework relies on a rational branch-and-bound certificate produced by an exact integer programming solver, SCIP, in order to circumvent floating-point roundoff errors present in most state-of-the-art solvers for mixed-integer programs.The resulting certificates are self-contained and checker software exists that can verify their correctness independently of the integer programming solver used to produce the certificate. This acts as a safeguard against programming errors that may be present in complex solver software. The viability of this approach is tested by applying it to finite cases of Chvátal's conjecture, a long-standing open question in extremal combinatorics. We take particular care to verify also the correctness of the input for this specific problem, using the Coq formal proof assistant. As a result we are able to provide a first machine-assisted proof that Chvátal's conjecture holds for all downsets whose union of sets contains seven elements or less. Y1 - 2022 U6 - https://doi.org/10.1145/3485630 VL - 48 IS - 2 ER - TY - JOUR A1 - Röhl, Susanne A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - Computing the minimal rebinding effect for non-reversible processes JF - Multiscale Modeling and Simulation N2 - The aim of this paper is to investigate the rebinding effect, a phenomenon describing a "short-time memory" which can occur when projecting a Markov process onto a smaller state space. For guaranteeing a correct mapping by the Markov State Model, we assume a fuzzy clustering in terms of membership functions, assigning degrees of membership to each state. The macro states are represented by the membership functions and may be overlapping. The magnitude of this overlap is a measure for the strength of the rebinding effect, caused by the projection and stabilizing the system. A minimal bound for the rebinding effect included in a given system is computed as the solution of an optimization problem. Based on membership functions chosen as a linear combination of Schur vectors, this generalized approach includes reversible as well as non-reversible processes. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1137/20M1334966 VL - 19 IS - 1 SP - 460 EP - 477 ER - TY - JOUR A1 - Reuter, Bernhard A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Generalized Markov modeling of nonreversible molecular kinetics JF - The Journal of Chemical Physics N2 - Markov state models are to date the gold standard for modeling molecular kinetics since they enable the identification and analysis of metastable states and related kinetics in a very instructive manner. The state-of-the-art Markov state modeling methods and tools are very well developed for the modeling of reversible processes in closed equilibrium systems. On the contrary, they are largely not well suited to deal with nonreversible or even nonautonomous processes of nonequilibrium systems. Thus, we generalized the common Robust Perron Cluster Cluster Analysis (PCCA+) method to enable straightforward modeling of nonequilibrium systems as well. The resulting Generalized PCCA (G-PCCA) method readily handles equilibrium as well as nonequilibrium data by utilizing real Schur vectors instead of eigenvectors. This is implemented in the G-PCCA algorithm that enables the semiautomatic coarse graining of molecular kinetics. G-PCCA is not limited to the detection of metastable states but also enables the identification and modeling of cyclic processes. This is demonstrated by three typical examples of nonreversible systems. Y1 - 2019 U6 - https://doi.org/10.1063/1.5064530 VL - 17 IS - 150 SP - 174103 ER - TY - JOUR A1 - Taylor, William R. A1 - Pöpplau, Berry M. A1 - König, Christian A1 - Ehrig, Rainald A1 - Zachow, Stefan A1 - Duda, Georg A1 - Heller, Markus O. T1 - The medial-lateral force distribution in the ovine stifle joint during walking JF - Journal of Orthopaedic Research Y1 - 2011 U6 - https://doi.org/10.1002/jor.21254 VL - 29 IS - 4 SP - 567 EP - 571 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Hobbie, Hannes A1 - Schönheit, David A1 - Koch, Thorsten A1 - Möst, Dominik A1 - Gleixner, Ambros T1 - A massively parallel interior-point solver for LPs with generalized arrowhead structure, and applications to energy system models JF - European Journal of Operational Research N2 - Linear energy system models are a crucial component of energy system design and operations, as well as energy policy consulting. If detailed enough, such models lead to large-scale linear programs, which can be intractable even for the best state-of-the-art solvers. This article introduces an interior-point solver that exploits common structures of energy system models to efficiently run in parallel on distributed-memory systems. The solver is designed for linear programs with doubly-bordered block-diagonal constraint matrix and makes use of a Schur complement based decomposition. In order to handle the large number of linking constraints and variables commonly observed in energy system models, a distributed Schur complement preconditioner is used. In addition, the solver features a number of more generic techniques such as parallel matrix scaling and structure-preserving presolving. The implementation is based on the solver PIPS-IPM. We evaluate the computational performance on energy system models with up to four billion nonzero entries in the constraint matrix—and up to one billion columns and one billion rows. This article mainly concentrates on the energy system model ELMOD, which is a linear optimization model representing the European electricity markets by the use of a nodal pricing market-clearing. It has been widely applied in the literature on energy system analyses in recent years. However, it will be demonstrated that the new solver is also applicable to other energy system models. Y1 - 2022 U6 - https://doi.org/10.1016/j.ejor.2021.06.063 VL - 296 IS - 1 SP - 60 EP - 71 ER - TY - JOUR A1 - Weber, Marcus A1 - Fackeldey, Konstantin A1 - Schütte, Christof T1 - Set-Free Markov State Model Building JF - Journal of Chemical Physics Y1 - 2017 U6 - https://doi.org/10.1063/1.4978501 VL - 146 IS - 12 ER - TY - JOUR A1 - Kiewisz, Robert A1 - Fabig, Gunar A1 - Conway, William A1 - Baum, Daniel A1 - Needleman, Daniel A1 - Müller-Reichert, Thomas T1 - Three-dimensional structure of kinetochore-fibers in human mitotic spindles JF - eLife N2 - During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variation in circumference and KMT density along their length, with the pole-proximal side showing a broadening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an interactive display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells. Y1 - 2022 U6 - https://doi.org/10.7554/eLife.75459 VL - 11 SP - e75459 ER - TY - JOUR A1 - Heller, Markus O. A1 - Kratzenstein, Stefan A1 - Ehrig, Rainald A1 - Wassilew, Georgi A1 - Duda, Georg A1 - Taylor, William R. T1 - The weighted optimal common shape technique improves identification of the hip joint centre of rotation in vivo JF - Journal of Orthopedic Research Y1 - 2011 VL - 29 SP - 1470 EP - 5 ER - TY - JOUR A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - Local Refinements in Classical Molecular Dynamics Simulations JF - J. Phys. Conf. Ser. Y1 - 2014 VL - 490 SP - 012016 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Das, Krishna M. Padmanabha A1 - Leigh, Kendra E A1 - Cespugli, Marco A1 - Fischer, Patrick D. A1 - Wang, Zi-Fu A1 - Tesseyre, Guilhem A1 - Pandita, Shreya A1 - Shnapir, Alex A1 - Calderaio, Anthony A1 - Hutcheson, Colin A1 - Gechev, Minko A1 - Rose, Alexander A1 - Lewis, Noam A1 - Yaffe, Erez A1 - Luxenburg, Roni A1 - Herce, Henry D. A1 - Durmaz, Vedat A1 - Halazonetis, Thanos D. A1 - Fackeldey, Konstantin A1 - Patten, Justin J. A1 - Chuprina, Alexander A1 - Dziuba, Igor A1 - Plekhova, Alla A1 - Moroz, Yurii A1 - Radchenko, Dmytro A1 - Tarkhanova, Olga A1 - Yavnyuk, Irina A1 - Gruber, Christian C. A1 - Yust, Ryan A1 - Payne, Dave A1 - Näär, Anders M. A1 - Namchuk, Mark N. A1 - Davey, Robert A. A1 - Wagner, Gerhard A1 - Kinney, Jamie A1 - Arthanari, Haribabu T1 - A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening JF - iScience N2 - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics. Here we leverage the power of our recently developed in silico screening platform, VirtualFlow, to identify inhibitors that target SARS-CoV-2. VirtualFlow is able to efficiently harness the power of computing clusters and cloud-based computing platforms to carry out ultra-large scale virtual screens. In this unprecedented structure-based multi-target virtual screening campaign, we have used VirtualFlow to screen an average of approximately 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets in the cloud. In addition to targeting the active sites of viral enzymes, we also target critical auxiliary sites such as functionally important protein-protein interaction interfaces. This multi-target approach not only increases the likelihood of finding a potent inhibitor, but could also help identify a collection of anti-coronavirus drugs that would retain efficacy in the face of viral mutation. Drugs belonging to different regimen classes could be combined to develop possible combination therapies, and top hits that bind at highly conserved sites would be potential candidates for further development as coronavirus drugs. Here, we present the top 200 in silico hits for each target site. While in-house experimental validation of some of these compounds is currently underway, we want to make this array of potential inhibitor candidates available to researchers worldwide in consideration of the pressing need for fast-tracked drug development. Y1 - 2021 U6 - https://doi.org/10.26434/chemrxiv.12682316 VL - 24 IS - 2 SP - 102021 PB - CellPress ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Boeszoermnyi, Andras A1 - Wang, Zi-Fu A1 - Fischer, Patrick D. A1 - Coote, Paul A1 - Das, Krishna M. Padmanabha A1 - Malets, Yehor S. A1 - Radchenko, Dmytro S. A1 - Moroz, Yurii A1 - Scott, David A. A1 - Fackeldey, Konstantin A1 - Hoffmann, Moritz A1 - Iavniuk, Iryna A1 - Wagner, Gerhard A1 - Arthanari, Haribabu T1 - An open-source drug discovery platform enables ultra-large virtual screens JF - Nature N2 - On average, an approved drug today costs $2-3 billion and takes over ten years to develop1. In part, this is due to expensive and time-consuming wet-lab experiments, poor initial hit compounds, and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening (SBVS) has the potential to mitigate these problems. With SBVS, the quality of the hits improves with the number of compounds screened2. However, despite the fact that large compound databases exist, the ability to carry out large-scale SBVSs on computer clusters in an accessible, efficient, and flexible manner has remained elusive. Here we designed VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large ligand libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we have prepared the largest and freely available ready-to-dock ligand library available, with over 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened over 1 billion compounds and discovered a small molecule inhibitor (iKeap1) that engages KEAP1 with nanomolar affinity (Kd = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. We also identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify binders with high affinity for target proteins. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1038/s41586-020-2117-z VL - 580 SP - 663 EP - 668 PB - Springer Nature ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Çınaroğlu, Süleyman A1 - Fischer, Patrick D. A1 - Fackeldey, Konstantin A1 - Wagner, Gerhard A1 - Arthanari, Haribabu T1 - VirtualFlow Ants—Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization JF - Special Issue Artificial Intelligence & Deep Learning Approaches for Structural Bioinformatics N2 - The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/ijms22115807 VL - 22 IS - 11 SP - 5807 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Sikorski, Alexander A1 - Weber, Marcus T1 - Spectral Clustering for Non-Reversible Markov Chains JF - Computational and Applied Mathematics N2 - Spectral clustering methods are based on solving eigenvalue problems for the identification of clusters, e.g., the identification of metastable subsets of a Markov chain. Usually, real-valued eigenvectors are mandatory for this type of algorithms. The Perron Cluster Analysis (PCCA+) is a well-known spectral clustering method of Markov chains. It is applicable for reversible Markov chains, because reversibility implies a real-valued spectrum. We also extend this spectral clustering method to non-reversible Markov chains and give some illustrative examples. The main idea is to replace the eigenvalue problem by a real-valued Schur decomposition. By this extension non-reversible Markov chains can be analyzed. Furthermore, the chains do not need to have a positive stationary distribution. In addition to metastabilities, dominant cycles and sinks can also be identified. This novel method is called GenPCCA (i.e., generalized PCCA), since it includes the case of non-reversible processes. We also apply the method to real-world eye-tracking data. KW - Spectral clustering KW - Markov chain KW - Non-reversible KW - Schur decomposition KW - GenPCCA Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1007/s40314-018-0697-0 VL - 37 IS - 5 SP - 6376 EP - 6391 ER - TY - JOUR A1 - Ernst, Natalia A1 - Fackeldey, Konstantin A1 - Volkamer, Andrea A1 - Opatz, Oliver A1 - Weber, Marcus T1 - Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes JF - Molecular Simulation N2 - Molecular simulations are often used to analyse the stability of protein–ligand complexes. The stability can be characterised by exit rates or using the exit time approach, i.e. by computing the expected holding time of the complex before its dissociation. However determining exit rates by straightforward molecular dynamics methods can be challenging for stochastic processes in which the exit event occurs very rarely. Finding a low variance procedure for collecting rare event statistics is still an open problem. In this work we discuss a novel method for computing exit rates which uses results of Robust Perron Cluster Analysis (PCCA+). This clustering method gives the possibility to define a fuzzy set by a membership function, which provides additional information of the kind ‘the process is being about to leave the set’. Thus, the derived approach is not based on the exit event occurrence and, therefore, is also applicable in case of rare events. The novel method can be used to analyse the temperature effect of protein–ligand systems through the differences in exit rates, and, thus, open up new drug design strategies and therapeutic applications. Y1 - 2019 U6 - https://doi.org/10.1080/08927022.2019.1610949 VL - 45 IS - 11 SP - 904 EP - 911 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Fackeldey, Konstantin A1 - Wagner, Gerhard A1 - Arthanari, Haribabu T1 - Accounting of Receptor Flexibility in Ultra-Large Virtual Screens with VirtualFlow Using a Grey Wolf Optimization Method JF - Supercomputing Frontiers and Innovations N2 - Structure-based virtual screening approaches have the ability to dramatically reduce the time and costs associated to the discovery of new drug candidates. Studies have shown that the true hit rate of virtual screenings improves with the scale of the screened ligand libraries. Therefore, we have recently developed an open source drug discovery platform (VirtualFlow), which is able to routinely carry out ultra-large virtual screenings. One of the primary challenges of molecular docking is the circumstance when the protein is highly dynamic or when the structure of the protein cannot be captured by a static pose. To accommodate protein dynamics, we report the extension of VirtualFlow to allow the docking of ligands using a grey wolf optimization algorithm using the docking program GWOVina, which substantially improves the quality and efficiency of flexible receptor docking compared to AutoDock Vina. We demonstrate the linear scaling behavior of VirtualFlow utilizing GWOVina up to 128 000 CPUs. The newly supported docking method will be valuable for drug discovery projects in which protein dynamics and flexibility play a significant role. Y1 - 2020 U6 - https://doi.org/10.14529/jsfi200301 VL - 7 IS - 3 SP - 4 EP - 12 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Röhm, Jonas A1 - Niknejad, Amir A1 - Chewle, Surahit A1 - Weber, Marcus T1 - Analyzing Raman Spectral Data without Separabiliy Assumption JF - Journal of Mathematical Chemistry N2 - Raman spectroscopy is a well established tool for the analysis of vibration spectra, which then allow for the determination of individual substances in a chemical sample, or for their phase transitions. In the Time-Resolved-Raman-Sprectroscopy the vibration spectra of a chemical sample are recorded sequentially over a time interval, such that conclusions for intermediate products (transients) can be drawn within a chemical process. The observed data-matrix M from a Raman spectroscopy can be regarded as a matrix product of two unknown matrices W and H, where the first is representing the contribution of the spectra and the latter represents the chemical spectra. One approach for obtaining W and H is the non-negative matrix factorization. We propose a novel approach, which does not need the commonly used separability assumption. The performance of this approach is shown on a real world chemical example. Y1 - 2021 U6 - https://doi.org/10.1007/s10910-020-01201-7 VL - 3 IS - 59 SP - 575 EP - 596 PB - Springer ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Oster, Mathias A1 - Sallandt, Leon A1 - Schneider, Reinhold T1 - Approximative Policy Iteration for Exit Time Feedback Control Problems driven by Stochastic Differential Equations using Tensor Train format JF - SIAM Journal on Multiscale Modeling and Simulation N2 - We consider a stochastic optimal exit time feedback control problem. The Bellman equation is solved approximatively via the Policy Iteration algorithm on a polynomial ansatz space by a sequence of linear equations. As high degree multi-polynomials are needed, the corresponding equations suffer from the curse of dimensionality even in moderate dimensions. We employ tensor-train methods to account for this problem. The approximation process within the Policy Iteration is done via a Least-Squares ansatz and the integration is done via Monte-Carlo methods. Numerical evidences are given for the (multi dimensional) double well potential and a three-hole potential. Y1 - 2022 U6 - https://doi.org/10.1137/20M1372500 VL - 20 IS - 1 SP - 379 EP - 403 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Koltai, Peter A1 - Nevir, Peter A1 - Rust, Henning A1 - Schild, Axel A1 - Weber, Marcus T1 - From metastable to coherent sets - Time-discretization schemes JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - In this article, we show that these well-established spectral algorithms (like PCCA+, Perron Cluster Cluster Analysis) also identify coherent sets of non-autonomous dynamical systems. For the identification of coherent sets, one has to compute a discretization (a matrix T) of the transfer operator of the process using a space-time-discretization scheme. The article gives an overview about different time-discretization schemes and shows their applicability in two different fields of application. Y1 - 2019 U6 - https://doi.org/10.1063/1.5058128 VL - 29 SP - 012101 EP - 012101 ER - TY - JOUR A1 - Moewis, Philippe A1 - Kaiser, René A1 - Trepczynski, Adam A1 - von Tycowicz, Christoph A1 - Krahl, Leonie A1 - Ilg, Ansgar A1 - Holz, Johannes A1 - Duda, Georg T1 - Patient specific resurfacing implant knee surgery in subjects with early osteoarthritis results in medial pivot and lateral femoral rollback during flexion: A retrospective pilot study JF - Knee Surgery, Sports Traumatology, Arthroscopy N2 - Purpose. Metallic resurfacing implants have been developed for the treatment of early, focal, small, condylar and trochlear osteoarthritis (OA) lesions. They represent an option for patients who are either too young to fulfill the criteria for total knee arthroplasty (TKA) or too old for biological treatment. Although relevant clinical evidence has been collected for different resurfacing types, the in vivo post-operative knee kinematics remains unknown. The present study aims to measure and analyse the knee joint kinematics in subjects with patient-specific Episealer implants Methods. Retrospective study design. Fluoroscopic analyses during high flexion activities (unloaded flexion-extension and loaded lunge) were conducted at >12 months post-surgery in ten Episealer knees. The post-operative knee joint kinematics was compared to equally assessed kinematic from ten healthy knees, twenty G-Curve TKA knees and 10 J-Curve knees. Pre- and postoperative clinical data of the Episealer knees were collected using a visual analog scale (VAS), the EQ 5d Health Questionnaire and the Knee Injury and Osteoarthritis Outcome Score (KOOS). Results. During unloaded flexion-extension and loaded lunge, the medial condyle in the Episealer knees remained relative stationary, indicating a medial pivot, while the lateral condyle translated consistently towards posterior. Similarly, reduced movement of the medial condyle and posterior translation of the lateral condyle was also observed in the healthy knees, although to a lesser extent. In contrast, the kinematics of both TKA cohorts during unloaded flexion-extension showed a tendency towards anterior displacement in the medial compartment, which led to significant differences in comparison with the Episealer knees. In the lateral compartment, a certain degree of femoral rollback was noted in the G-Curve TKA cohort. Improved scores were observed in the Episealer subjects between the preoperative and 1-year postoperative follow-up. Conclusion. At 12 months postsurgery, a physiological-like knee kinematics was observed in the group of patient-specific reconstructed chondral/osteochondral lesions by means of a resurfacing Episealer implant strategy. Considering that these patients are physically active and do not fulfill the criteria for TKA, the group is hard to be compared to TKA patients which usually are less active and more challenging. Nevertheless, the comparison to either healthy knee kinematics as well as to TKA reconstructed knees with different implant designs showed a more physiological-like kinematics in the resurfacing implants that seems more appropriate for such a patient group. Despite positive results, careful clinical follow-up of treated patients is recommended for the long-term OA progression. Further investigations need to be encouraged not only in larger patient groups but also in a prospective manner to assess the pre- to postoperative kinematic changes. Y1 - 2021 U6 - https://doi.org/10.1007/s00167-021-06749-8 ER - TY - JOUR A1 - Šofranac, Boro A1 - Gleixner, Ambros A1 - Pokutta, Sebastian T1 - An Algorithm-independent Measure of Progress for Linear Constraint Propagation JF - Constraints Y1 - 2022 U6 - https://doi.org/10.1007/s10601-022-09338-9 VL - 27 SP - 432 EP - 455 ER - TY - JOUR A1 - Ehrig, Rainald A1 - Taylor, William R. A1 - Duda, Georg A1 - Heller, Markus O. T1 - A Survey for Formal Methods for Determining Functional Joint Axes JF - Journal of Biomechanics Y1 - 2007 SP - 2150 EP - 2157 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - Safe and Verified Gomory Mixed Integer Cuts in a Rational MIP Framework JF - SIAM Journal on Optimization N2 - This paper is concerned with the exact solution of mixed-integer programs (MIPs) over the rational numbers, i.e., without any roundoff errors and error tolerances. Here, one computational bottleneck that should be avoided whenever possible is to employ large-scale symbolic computations. Instead it is often possible to use safe directed rounding methods, e.g., to generate provably correct dual bounds. In this work, we continue to leverage this paradigm and extend an exact branch-and-bound framework by separation routines for safe cutting planes, based on the approach first introduced by Cook, Dash, Fukasawa, and Goycoolea in 2009. Constraints are aggregated safely using approximate dual multipliers from an LP solve, followed by mixed-integer rounding to generate provably valid, although slightly weaker inequalities. We generalize this approach to problem data that is not representable in floating-point arithmetic, add routines for controlling the encoding length of the resulting cutting planes, and show how these cutting planes can be verified according to the VIPR certificate standard. Furthermore, we analyze the performance impact of these cutting planes in the context of an exact MIP framework, showing that we can solve 21.5% more instances and reduce solving times by 26.8% on the MIPLIB 2017 benchmark test set. Y1 - 2023 ER - TY - JOUR A1 - Iravani, Sahar A1 - Conrad, Tim T1 - An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics N2 - Analyzing mass spectrometry-based proteomics data with deep learning (DL) approaches poses several challenges due to the high dimensionality, low sample size, and high level of noise. Additionally, DL-based workflows are often hindered to be integrated into medical settings due to the lack of interpretable explanation. We present DLearnMS, a DL biomarker detection framework, to address these challenges on proteomics instances of liquid chromatography-mass spectrometry (LC-MS) - a well-established tool for quantifying complex protein mixtures. Our DLearnMS framework learns the clinical state of LC-MS data instances using convolutional neural networks. Based on the trained neural networks, we show how biomarkers can be identified using layer-wise relevance propagation. This enables detecting discriminating regions of the data and the design of more robust networks. One of the main advantages over other established methods is that no explicit preprocessing step is needed in our DLearnMS framework. Our evaluation shows that DLearnMS outperforms conventional LC-MS biomarker detection approaches in identifying fewer false positive peaks while maintaining a comparable amount of true positives peaks. Y1 - 2023 U6 - https://doi.org/10.1109/tcbb.2022.3141656 VL - 20 IS - 1 SP - 151 EP - 161 ER - TY - JOUR A1 - Melnyk, Kateryna A1 - Weimann, Kuba A1 - Conrad, Tim T1 - Understanding microbiome dynamics via interpretable graph representation learning JF - Scientific Reports N2 - Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of healthy and ill individuals can be complicated due to the large number of complex interactions among microbes. We propose to model these interactions as a time-evolving graph whose nodes are microbes and edges are interactions among them. Motivated by the need to analyse such complex interactions, we develop a method that learns a low-dimensional representation of the time-evolving graph and maintains the dynamics occurring in the high-dimensional space. Through our experiments, we show that we can extract graph features such as clusters of nodes or edges that have the highest impact on the model to learn the low-dimensional representation. This information can be crucial to identify microbes and interactions among them that are strongly correlated with clinical diseases. We conduct our experiments on both synthetic and real-world microbiome datasets. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-29098-7 VL - 13 SP - 2058 ER - TY - JOUR A1 - Erlekam, Franziska A1 - Zumbansen, Maximilian A1 - Weber, Marcus T1 - Parameter estimation on multivalent ITC data sets JF - Scientific Reports N2 - The Wiseman fitting can be used to extract binding parameters from ITC data sets, such as heat of binding, number of binding sites, and the overall dissociation rate. The classical Wiseman fitting assumes a direct binding process and neglects the possibility of intermediate binding steps. In principle, it only provides thermodynamic information and not the kinetics of the process. In this article we show that a concentration dependent dissociation constant could possibly stem from intermediate binding steps. The mathematical form of this dependency can be exploited with the aid of the Robust Perron Cluster Cluster Analysis method. Our proposed extension of the Wiseman fitting rationalizes the concentration dependency, and can probably also be used to determine the kinetic parameters of intermediate binding steps of a multivalent binding process. The novelty of this paper is to assume that the binding rate varies per titration step due to the change of the ligand concentration and to use this information in the Wiseman fitting. We do not claim to produce the most accurate values of the binding parameters, we rather present a novel method of how to approach multivalent bindings from a different angle. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-17188-x VL - 12 SP - 13402 ER - TY - JOUR A1 - Willie, Bettina M. A1 - Pap, Thomas A1 - Perka, Carsten A1 - Schmidt, Carsten Oliver A1 - Eckstein, Felix A1 - Arampatzis, Adamantios A1 - Hege, Hans-Christian A1 - Madry, Henning A1 - Vortkamp, Andrea A1 - Duda, Georg T1 - OVERLOAD – Rolle der Gelenküberlastung in der primären Arthrose – Die Krankheitsprogression verstehen und vermeiden JF - Zeitschrift für Rheumatologie N2 - Intakte Gelenke sind eine Voraussetzung für das Funktionieren des Skeletts und die Mobilität im Lebensalltag. Ein gesunder Bewegungsapparat ist die Grundlage für die Funktionsfähigkeit des Herz-Kreislauf-Systems wie auch der Immunabwehr. Bewegungs- und Physiotherapie sowie verschiedene Formen der Patientenaktivität stellen essenzielle klinische Ansätze in der Behandlung von neurodegenerativen Erkrankungen, Schlaganfall, Diabetes und Krebs dar. Kommt es zu degenerativen Veränderungen von Gelenken, bedeutet dies eine wesentliche Beeinträchtigung der Mobilität. Nächtliche Schmerzen und Schlafstörungen treten in fortgeschrittenen Stadien auf und sind besonders belastend. Arthrose wird auch als degenerative Gelenkerkrankung bezeichnet. Sie geht mit Veränderungen in der Struktur und Zusammensetzung des Gelenkknorpels wie auch des verkalkten Knorpels, der subchondralen Kortikalis, der subchondralen Spongiosa, des Meniskus, der Gelenkkapsel und der Synovialis einher, was schließlich zur Degeneration dieser Gewebe führt, aus denen sich die Synovialgelenke zusammensetzen. Y1 - 2015 U6 - https://doi.org/10.1007/s00393-014-1561-2 VL - 74 SP - 618 EP - 621 ER - TY - JOUR A1 - Willie, Bettina M. A1 - Pap, Thomas A1 - Perka, Carsten A1 - Schmidt, Carsten Oliver A1 - Eckstein, Felix A1 - Arampatzis, Adamantios A1 - Hege, Hans-Christian A1 - Madry, Henning A1 - Vortkamp, Andrea A1 - Duda, Georg T1 - OVERLOAD of joints and its role in osteoarthritis - Towards understanding and preventing progression of primary osteoarthritis JF - Zeitschrift für Rheumatologie N2 - Intact joints are necessary for skeletal function and mobility in daily life. A healthy musculoskeletal system is the basis for a functional cardiovascular system as well as an intact immune system. Locomotion, physiotherapy, and various forms of patient activity are essential clinical therapies used in the treatment of neurodegeneration, stroke, diabetes, and cancer. Mobility is substantially impaired with degeneration of joints and, in advanced stages, nighttime pain and sleep disturbance are particularly cumbersome. Osteoarthritis (OA) is also known as degenerative joint disease. OA involves structural and compositional changes in the articular cartilage, as well as in the calcified cartilage, subchondral cortical bone, subchondral cancellous bone, meniscus, joint capsular tissue, and synovium; which eventually lead to degeneration of these tissues comprising synovial joints. Y1 - 2015 U6 - https://doi.org/10.1007/s00393-014-1561-2 VL - 76 IS - Suppl. 1 SP - 1 EP - 4 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A Computational Status Update for Exact Rational Mixed Integer Programming JF - Integer Programming and Combinatorial Optimization: 22th International Conference, IPCO 2021 N2 - The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 6.6x over the original framework and 2.8 times as many instances solved within a time limit of two hours. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-73879-2_12 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A computational status update for exact rational mixed integer programming JF - Mathematical Programming N2 - The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 10.7x over the original framework and 2.9 times as many instances solved within a time limit of two hours. Y1 - 2022 U6 - https://doi.org/10.1007/s10107-021-01749-5 PB - Springer ER - TY - JOUR A1 - Weber, Marcus A1 - Fackeldey, Konstantin T1 - Computing the Minimal Rebinding Effect Included in a Given Kinetics JF - Multiscale Model. Simul. N2 - The rebinding effect is a phenomenon which occurs when observing a ligand-receptor binding process. On the macro scale this process comprises the Markov property. This Makovian view is spoiled when switching to the atomistic scale of a binding process. We therefore suggest a model which accurately describes the rebinding effect on the atomistic scale by allowing ''intermediate'' bound states. This allows us to define an indicator for the magnitude of rebinding and to formulate an optimization problem. The results form our examples show good agreement with data form laboratory. Y1 - 2014 U6 - https://doi.org/10.1137/13091124X VL - 12 IS - 1 SP - 318 EP - 334 ER - TY - JOUR A1 - Bujotzek, Alexander A1 - Schütt, Ole A1 - Nielsen, Adam A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling JF - Journal of Mathematical Chemistry Y1 - 2014 U6 - https://doi.org/10.1007/s10910-013-0265-1 VL - 52 IS - 3 SP - 781 EP - 804 ER - TY - JOUR A1 - Gelss, Patrick A1 - Klus, Stefan A1 - Schuster, Ingmar A1 - Schütte, Christof T1 - Feature space approximation for kernel-based supervised learning JF - Knowledge-Based Sytems Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.knosys.2021.106935 VL - 221 PB - Elsevier ER - TY - JOUR A1 - Lie, Han Cheng A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - A Square Root Approximation of Transition Rates for a Markov State Model JF - SIAM. J. Matrix Anal. Appl. Y1 - 2013 U6 - https://doi.org/10.1137/120899959 VL - 34 IS - 2 SP - 738 EP - 756 ER - TY - JOUR A1 - Šofranac, Boro A1 - Gleixner, Ambros A1 - Pokutta, Sebastian T1 - Accelerating domain propagation: An efficient GPU-parallel algorithm over sparse matrices JF - Parallel Computing N2 - • Currently, domain propagation in state-of-the-art MIP solvers is single thread only. • The paper presents a novel, efficient GPU algorithm to perform domain propagation. • Challenges are dynamic algorithmic behavior, dependency structures, sparsity patterns. • The algorithm is capable of running entirely on the GPU with no CPU involvement. • We achieve speed-ups of around 10x to 20x, up to 180x on favorably-large instances. Y1 - 2022 U6 - https://doi.org/10.1016/j.parco.2021.102874 VL - 109 SP - 102874 ER - TY - JOUR A1 - Haack, Fiete A1 - Fackeldey, Konstantin A1 - Röblitz, Susanna A1 - Scharkoi, Olga A1 - Weber, Marcus A1 - Schmidt, Burkhard T1 - Adaptive spectral clustering with application to tripeptide conformation analysis JF - The Journal of Chemical Physics Y1 - 2013 U6 - https://doi.org/10.1063/1.4830409 VL - 139 SP - 110 EP - 194 ER - TY - JOUR A1 - Klus, Stefan A1 - Gelß, Patrick A1 - Peitz, Sebastian A1 - Schütte, Christof T1 - Tensor-based dynamic mode decomposition JF - Nonlinearity Y1 - 2018 U6 - https://doi.org/10.1088/1361-6544/aabc8f VL - 31 IS - 7 PB - IOP Publishing Ltd & London Mathematical Society ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Klimm, Martina A1 - Weber, Marcus T1 - A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules JF - Journal of Mathematical Chemistry Y1 - 2012 VL - 5 IS - 9 SP - 2623 EP - 2635 ER - TY - JOUR A1 - Bonami, Pierre A1 - Gleixner, Ambros A1 - Linderoth, Jeff A1 - Misener, Ruth T1 - Designing and Implementing Algorithms for Mixed-Integer Nonlinear Optimization (Dagstuhl Seminar 18081) JF - Dagstuhl Reports N2 - Mathematical models for optimal decisions often require both nonlinear and discrete components. These mixed-integer nonlinear programs (MINLP) may be used to optimize the energy use of large industrial plants, integrate renewable sources into energy networks, design biological and biomedical systems, and address numerous other applications of societal importance. The first MINLP algorithms and software were designed by application engineers. While these efforts initially proved useful, scientists, engineers, and practitioners have realized that a transformational shift in technology will be required for MINLP to achieve its full potential. MINLP has transitioned to a forefront position in computer science, with researchers actively developing MINLP theory, algorithms, and implementations. Even with their concerted effort, algorithms and available software are often unable to solve practically-sized instances of these important models. Current obstacles include characterizing the computability boundary, effectively exploiting known optimization technologies for specialized classes of MINLP, and effectively using logical formulas holistically throughout algorithms. Y1 - 2018 U6 - https://doi.org/10.4230/DagRep.8.2.64 VL - 8 IS - 2 SP - 64 EP - 87 ER - TY - JOUR A1 - Lang, Annemarie A1 - Helfmeier, Sarah A1 - Stefanowski, Jonathan A1 - Kuppe, Aditi A1 - Sunkara, Vikram A1 - Pfeiffenberger, Moritz A1 - Wolter, Angelique A1 - Damerau, Alexandra A1 - Hemmati-Sadeghi, Shabnam A1 - Ringe, Jochen A1 - Haag, Rainer A1 - Hauser, Anja E. A1 - Löhning, Max A1 - Perka, Carsten A1 - Duda, Georg A1 - Hoff, Paula A1 - Schmidt-Bleek, Katharina A1 - Gaber, Timo A1 - Buttgereit, Frank T1 - HIF-stabilization prevents delayed fracture healing JF - bioarxiv Y1 - 2020 U6 - https://doi.org/10.1101/2020.07.02.182832 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Niknejad, Amir A1 - Weber, Marcus T1 - Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation JF - Special Matrices Y1 - 2017 U6 - https://doi.org/10.1515/spma-2017-0006 IS - 5/1 SP - 73 EP - 81 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - Error Bounds for Discrete-Continuous Free Flight Trajectory Optimization JF - Journal of Optimization Theory and Applications N2 - Flight planning, the computation of optimal routes in view of flight time and fuel consumption under given weather conditions, is traditionally done by finding globally shortest paths in a predefined airway network. Free flight trajectories, not restricted to a network, have the potential to reduce the costs significantly, and can be computed using locally convergent continuous optimal control methods. Hybrid methods that start with a discrete global search and refine with a fast continuous local optimization combine the best properties of both approaches, but rely on a good switchover, which requires error estimates for discrete paths relative to continuous trajectories. Based on vertex density and local complete connectivity, we derive localized and a priori bounds for the flight time of discrete paths relative to the optimal continuous trajectory, and illustrate their properties on a set of benchmark problems. It turns out that localization improves the error bound by four orders of magnitude, but still leaves ample opportunities for tighter bounds using a posteriori error estimators. Y1 - 2023 U6 - https://doi.org/10.1007/s10957-023-02264-7 VL - 198 SP - 830 EP - 856 ER - TY - JOUR A1 - Raharinirina, N. Alexia A1 - Acevedo-Trejos, Esteban A1 - Merico, Agostino T1 - Modelling the acclimation capacity of coral reefs to a warming ocean JF - PLOS COMPUTATIONAL BIOLOGY N2 - The symbiotic relationship between corals and photosynthetic algae is the foundation of coral reef ecosystems. This relationship breaks down, leading to coral death, when sea temperature exceeds the thermal tolerance of the coral-algae complex. While acclimation via phenotypic plasticity at the organismal level is an important mechanism for corals to cope with global warming, community-based shifts in response to acclimating capacities may give valuable indications about the future of corals at a regional scale. Reliable regional-scale predictions, however, are hampered by uncertainties on the speed with which coral communities will be able to acclimate. Here we present a trait-based, acclimation dynamics model, which we use in combination with observational data, to provide a first, crude estimate of the speed of coral acclimation at the community level and to investigate the effects of different global warming scenarios on three iconic reef ecosystems of the tropics: Great Barrier Reef, South East Asia, and Caribbean. The model predicts that coral acclimation may confer some level of protection by delaying the decline of some reefs such as the Great Barrier Reef. However, the current rates of acclimation will not be sufficient to rescue corals from global warming. Based on our estimates of coral acclimation capacities, the model results suggest substantial declines in coral abundances in all three regions, ranging from 12% to 55%, depending on the region and on the climate change scenario considered. Our results highlight the importance and urgency of precise assessments and quantitative estimates, for example through laboratory experiments, of the natural acclimation capacity of corals and of the speed with which corals may be able to acclimate to global warming. Y1 - 2022 U6 - https://doi.org/10.1371/journal.pcbi.1010099 ER - TY - JOUR A1 - Raharinirina, N. Alexia A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Qualitative Euclidean embedding of Disjoint Sets of Points N2 - We consider two disjoint sets of points with a distance metric, or a proximity function, associated with each set. If each set can be separately embedded into separate Euclidean spaces, then we provide sufficient conditions for the two sets to be jointly embedded in one Euclidean space. In this joint Euclidean embedding, the distances between the points are generated by a specific relation-preserving function. Consequently, the mutual distances between two points of the same set are specific qualitative transformations of their mutual distances in their original space; the pairwise distances between the points of different sets can be constructed from an arbitrary proximity function (might require scaling). Y1 - 2022 UR - https://arxiv.org/abs/2212.00058 ER - TY - JOUR A1 - Montefusco, Alberto A1 - Sharma, Upanshu A1 - Tse, Oliver T1 - Fourier-Cattaneo equation: stochastic origin, variational formulation, and asymptotic limits N2 - We introduce a variational structure for the Fourier-Cattaneo (FC) system which is a second-order hyperbolic system. This variational structure is inspired by the large-deviation rate functional for the Kac process which is closely linked to the FC system. Using this variational formulation we introduce appropriate solution concepts for the FC equation and prove an a priori estimate which connects this variational structure to an appropriate Lyapunov function and Fisher information, the so-called FIR inequality. Finally, we use this formulation and estimate to study the diffusive and hyperbolic limits for the FC system. Y1 - 2022 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - Newton's Method for Global Free Flight Trajectory Optimization JF - Operations Research Forum N2 - Globally optimal free flight trajectory optimization can be achieved with a combination of discrete and continuous optimization. A key requirement is that Newton's method for continuous optimization converges in a sufficiently large neighborhood around a minimizer. We show in this paper that, under certain assumptions, this is the case. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-91846 VL - 4 ER - TY - JOUR A1 - Grewe, Carl Martin A1 - Liu, Tuo A1 - Hildebrandt, Andrea A1 - Zachow, Stefan T1 - The Open Virtual Mirror Framework for Enfacement Illusions - Enhancing the Sense of Agency With Avatars That Imitate Facial Expressions JF - Behavior Research Methods Y1 - 2022 U6 - https://doi.org/10.3758/s13428-021-01761-9 PB - Springer ER - TY - JOUR A1 - Raharinirina, Alexia N. A1 - Peppert, Felix A1 - von Kleist, Max A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - Inferring gene regulatory networks from single-cell RNA-seq temporal snapshot data requires higher-order moments JF - Patterns N2 - Single-cell RNA sequencing (scRNA-seq) has become ubiquitous in biology. Recently, there has been a push for using scRNA-seq snapshot data to infer the underlying gene regulatory networks (GRNs) steering cellular function. To date, this aspiration remains unrealized due to technical and computational challenges. In this work we focus on the latter, which is under-represented in the literature. We took a systemic approach by subdividing the GRN inference into three fundamental components: data pre-processing, feature extraction, and inference. We observed that the regulatory signature is captured in the statistical moments of scRNA-seq data and requires computationally intensive minimization solvers to extract it. Furthermore, current data pre-processing might not conserve these statistical moments. Although our moment-based approach is a didactic tool for understanding the different compartments of GRN inference, this line of thinking—finding computationally feasible multi-dimensional statistics of data—is imperative for designing GRN inference methods. Y1 - 2021 U6 - https://doi.org/10.1016/j.patter.2021.100332 VL - 2 IS - 9 ER - TY - JOUR A1 - Montefusco, Alberto A1 - Peletier, Mark A. A1 - Öttinger, Hans Christian T1 - A Framework of Nonequilibrium Statistical Mechanics. II. Coarse-Graining JF - Journal of Non-Equilibrium Thermodynamics N2 - For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a generalization of the classical fluctuation-dissipation theorem (FDT), the structure of a constitutive law is directly related to the distribution of the fluctuations of the state variables. When these fluctuations can be expressed in terms of diffusion processes, one may use Green–Kubo-type coarse-graining schemes to find the constitutive laws. In this paper we propose a coarse-graining method that is valid when the fluctuations are described by means of general Markov processes, which include diffusions as a special case. We prove the success of the method by numerically computing the constitutive law for a simple chemical reaction A⇄B. Furthermore, we show that, for such a system, one cannot find a consistent constitutive law by any Green–Kubo-like scheme. Y1 - 2021 U6 - https://doi.org/10.1515/jnet-2020-0069 VL - 46 IS - 1 SP - 15 EP - 33 PB - De Gruyter ER - TY - JOUR A1 - Mielke, Alexander A1 - Montefusco, Alberto A1 - Peletier, Mark A. T1 - Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence JF - Continuum Mechanics and Thermodynamics N2 - This paper revolves around a subtle distinction between two concepts: passing to the limit in a family of gradient systems, on one hand, and deriving effective kinetic relations on the other. The two concepts are strongly related, and in many examples they even appear to be the same. Our main contributions are to show that they are different, to show that well-known techniques developed for the former may give incorrect results for the latter, and to introduce new tools to remedy this. The approach is based on the Energy-Dissipation Principle that provides a variational formulation to gradient-flow equations that allows one to apply techniques from Γ-convergence of functional on states and functionals on trajectories. Y1 - 2021 U6 - https://doi.org/10.1007/s00161-020-00932-x VL - 33 SP - 611 EP - 637 PB - Springer ER - TY - JOUR A1 - Witzig, Jakob A1 - Berthold, Timo T1 - Conflict Analysis for MINLP JF - INFORMS Journal on Computing N2 - The generalization of MIP techniques to deal with nonlinear, potentially non-convex, constraints have been a fruitful direction of research for computational MINLP in the last decade. In this paper, we follow that path in order to extend another essential subroutine of modern MIP solvers towards the case of nonlinear optimization: the analysis of infeasible subproblems for learning additional valid constraints. To this end, we derive two different strategies, geared towards two different solution approaches. These are using local dual proofs of infeasibility for LP-based branch-and-bound and the creation of nonlinear dual proofs for NLP-based branch-and-bound, respectively. We discuss implementation details of both approaches and present an extensive computational study, showing that both techniques can significantly enhance performance when solving MINLPs to global optimality. Y1 - 2021 U6 - https://doi.org/10.1287/ijoc.2020.1050 VL - 33 IS - 2 SP - 421 EP - 435 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Danecker, Fabian A1 - Weiser, Martin T1 - A Discrete-Continuous Algorithm for Free Flight Planning JF - Algorithms N2 - We propose a hybrid discrete-continuous algorithm for flight planning in free flight airspaces. In a first step, our DisCOptER method discrete-continuous optimization for enhanced resolution) computes a globally optimal approximate flight path on a discretization of the problem using the A* method. This route initializes a Newton method that converges rapidly to the smooth optimum in a second step. The correctness, accuracy, and complexity of the method are goverened by the choice of the crossover point that determines the coarseness of the discretization. We analyze the optimal choice of the crossover point and demonstrate the asymtotic superority of DisCOptER over a purely discrete approach. KW - shortest path KW - flight planning KW - free flight KW - discrete-continuous algorithm KW - optimal control KW - discrete optimization Y1 - 2020 U6 - https://doi.org/10.3390/a14010004 SN - 1438-0064 VL - 14 IS - 1 SP - 4 PB - MDPI ER - TY - JOUR A1 - Grewe, Carl Martin A1 - Liu, Tuo A1 - Kahl, Christoph A1 - Andrea, Hildebrandt A1 - Zachow, Stefan T1 - Statistical Learning of Facial Expressions Improves Realism of Animated Avatar Faces JF - Frontiers in Virtual Reality Y1 - 2021 U6 - https://doi.org/10.3389/frvir.2021.619811 VL - 2 SP - 1 EP - 13 PB - Frontiers ER - TY - JOUR A1 - Witzig, Jakob A1 - Gleixner, Ambros T1 - Conflict-Driven Heuristics for Mixed Integer Programming JF - INFORMS Journal on Computing N2 - Two essential ingredients of modern mixed-integer programming (MIP) solvers are diving heuristics that simulate a partial depth-first search in a branch-and-bound search tree and conflict analysis of infeasible subproblems to learn valid constraints. So far, these techniques have mostly been studied independently: primal heuristics under the aspect of finding high-quality feasible solutions early during the solving process and conflict analysis for fathoming nodes of the search tree and improving the dual bound. Here, we combine both concepts in two different ways. First, we develop a diving heuristic that targets the generation of valid conflict constraints from the Farkas dual. We show that in the primal this is equivalent to the optimistic strategy of diving towards the best bound with respect to the objective function. Secondly, we use information derived from conflict analysis to enhance the search of a diving heuristic akin to classical coefficient diving. The computational performance of both methods is evaluated using an implementation in the source-open MIP solver SCIP. Experiments are carried out on publicly available test sets including Miplib 2010 and Cor@l. Y1 - 2020 U6 - https://doi.org/10.1287/ijoc.2020.0973 VL - 33 IS - 2 SP - 706 EP - 720 ER - TY - JOUR A1 - Öttinger, Hans Christian A1 - Montefusco, Alberto A1 - Peletier, Mark A. T1 - A Framework of Nonequilibrium Statistical Mechanics. I. Role and Types of Fluctuations JF - Journal of Non-Equilibrium Thermodynamics N2 - Understanding the fluctuations by which phenomenological evolution equations with thermodynamic structure can be enhanced is the key to a general framework of nonequilibrium statistical mechanics. These fluctuations provide an idealized representation of microscopic details. We consider fluctuation-enhanced equations associated with Markov processes and elaborate the general recipes for evaluating dynamic material properties, which characterize force-flux constitutive laws, by statistical mechanics. Markov processes with continuous trajectories are conveniently characterized by stochastic differential equations and lead to Green–Kubo-type formulas for dynamic material properties. Markov processes with discontinuous jumps include transitions over energy barriers with the rates calculated by Kramers. We describe a unified approach to Markovian fluctuations and demonstrate how the appropriate type of fluctuations (continuous versus discontinuous) is reflected in the mathematical structure of the phenomenological equations. Y1 - 2021 U6 - https://doi.org/10.1515/jnet-2020-0068 VL - 46 IS - 1 SP - 1 EP - 13 PB - De Gruyter ER - TY - JOUR A1 - Weiss, Selina A1 - Grewe, Carl Martin A1 - Olderbak, Sally A1 - Goecke, Benjamin A1 - Kaltwasser, Laura A1 - Hildebrandt, Andrea T1 - Symmetric or not? A holistic approach to the measurement of fluctuating asymmetry from facial photographs JF - Personality and Individual Differences Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1016/j.paid.2020.110137 VL - 166 SP - 1 EP - 12 ER - TY - JOUR A1 - Weiss, Selina A1 - Grewe, Carl Martin A1 - Olderbak, Sally A1 - Goecke, Benjamin A1 - Kaltwasser, Laura A1 - Hildebrandt, Andrea T1 - Symmetric or not? A holistic approach to the measurement of fluctuating asymmetry from facial photographs JF - PsyArXiv Y1 - 2020 U6 - https://doi.org/10.31234/osf.io/s534t N1 - preprint of https://doi.org/10.1016/j.paid.2020.110137 ER - TY - JOUR A1 - Huynh, Ngoc A1 - Chegini, Fatemeh A1 - Pavarino, Luca A1 - Weiser, Martin A1 - Scacchi, Simone T1 - Convergence analysis of BDDC preconditioners for hybrid DG discretizations of the cardiac cell-by-cell model JF - SIAM Journal on Scientific Computing N2 - A Balancing Domain Decomposition by Constraints (BDDC) preconditioner is constructed and analyzed for the solution of hybrid Discontinuous Galerkin discretizations of reaction-diffusion systems of ordinary and partial differential equations arising in cardiac cell-by-cell models. The latter are different from the classical Bidomain and Monodomain cardiac models based on homogenized descriptions of the cardiac tissue at the macroscopic level, and therefore they allow the representation of individual cardiac cells, cell aggregates, damaged tissues and nonuniform distributions of ion channels on the cell membrane. The resulting discrete cell-by-cell models have discontinuous global solutions across the cell boundaries, hence the proposed BDDC preconditioner is based on appropriate dual and primal spaces with additional constraints which transfer information between cells (subdomains) without influencing the overall discontinuity of the global solution. A scalable convergence rate bound is proved for the resulting BDDC cell-by-cell preconditioned operator, while numerical tests validate this bound and investigate its dependence on the discretization parameters. Y1 - 2023 VL - 45 IS - 6 SP - A2836 EP - A2857 ER - TY - JOUR A1 - Ozel, Mehmet Neset A1 - Kulkarni, Abhishek A1 - Hasan, Amr A1 - Brummer, Josephine A1 - Moldenhauer, Marian A1 - Daumann, Ilsa-Maria A1 - Wolfenberg, Heike A1 - Dercksen, Vincent J. A1 - Kiral, Ferdi Ridvan A1 - Weiser, Martin A1 - Prohaska, Steffen A1 - von Kleist, Max A1 - Hiesinger, Peter Robin T1 - Serial synapse formation through filopodial competition for synaptic seeding factors JF - Developmental Cell N2 - Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses. Y1 - 2019 U6 - https://doi.org/10.1016/j.devcel.2019.06.014 VL - 50 IS - 4 SP - 447 EP - 461 ER - TY - JOUR A1 - Peppert, Felix A1 - von Kleist, Max A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - On the Sufficient Condition for Solving the Gap-Filling Problem Using Deep Convolutional Neural Networks JF - IEEE Transactions on Neural Networks and Learning Systems N2 - Deep convolutional neural networks (DCNNs) are routinely used for image segmentation of biomedical data sets to obtain quantitative measurements of cellular structures like tissues. These cellular structures often contain gaps in their boundaries, leading to poor segmentation performance when using DCNNs like the U-Net. The gaps can usually be corrected by post-hoc computer vision (CV) steps, which are specific to the data set and require a disproportionate amount of work. As DCNNs are Universal Function Approximators, it is conceivable that the corrections should be obsolete by selecting the appropriate architecture for the DCNN. In this article, we present a novel theoretical framework for the gap-filling problem in DCNNs that allows the selection of architecture to circumvent the CV steps. Combining information-theoretic measures of the data set with a fundamental property of DCNNs, the size of their receptive field, allows us to formulate statements about the solvability of the gap-filling problem independent of the specifics of model training. In particular, we obtain mathematical proof showing that the maximum proficiency of filling a gap by a DCNN is achieved if its receptive field is larger than the gap length. We then demonstrate the consequence of this result using numerical experiments on a synthetic and real data set and compare the gap-filling ability of the ubiquitous U-Net architecture with variable depths. Our code is available at https://github.com/ai-biology/dcnn-gap-filling. Y1 - 2022 U6 - https://doi.org/10.1109/TNNLS.2021.3072746 VL - 33 IS - 11 SP - 6194 EP - 6205 ER - TY - JOUR A1 - Anderson, Lovis A1 - Turner, Mark A1 - Koch, Thorsten T1 - Generative deep learning for decision making in gas networks JF - Mathematical Methods of Operations Research N2 - A decision support system relies on frequent re-solving of similar problem instances. While the general structure remains the same in corresponding applications, the input parameters are updated on a regular basis. We propose a generative neural network design for learning integer decision variables of mixed-integer linear programming (MILP) formulations of these problems. We utilise a deep neural network discriminator and a MILP solver as our oracle to train our generative neural network. In this article, we present the results of our design applied to the transient gas optimisation problem. With the trained network we produce a feasible solution in 2.5s, use it as a warm-start solution, and thereby decrease global optimal solution solve time by 60.5%. Y1 - 2022 U6 - https://doi.org/10.1007/s00186-022-00777-x VL - 95 SP - 503 EP - 532 PB - Springer Nature ER - TY - JOUR A1 - Schulze, Kenrick A1 - Peppert, Felix A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - Chimeric U-Net–Modifying the standard U-Net towards Explainability JF - bioRxiv Y1 - 2022 U6 - https://doi.org/10.1101/2022.12.01.518699 ER - TY - JOUR A1 - Dalitz, Wolfgang A1 - Sperber, Wolfram A1 - Chrapary, Hagen T1 - swMATH: A Publication-based Approach to Mathematical Software JF - SIAM Newsletter N2 - The growing importance of mathematical software in everyday life—in applications such as internet communication, traffic, and artificial intelligence—necessitates advances in software documentation services to raise awareness of existing packages and their usage. Such information helps potential software developers and users make informed choices about packages that could advance their work in modeling, simulation, and analysis. At the same time, software presents novel challenges to information services that require the development of new methods and means of processing. swMATH provides users with an overview of a broad range of mathematical software and extends documentation services for publications related to such software. It acts as a counterpart to the established abstracting and reviewing services for mathematical publications and has nearly 30,000 entries, making it one of the most comprehensive documentation services in mathematics. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-80099 VL - Volume 53 IS - Number 06 | July/August 2020 ER - TY - JOUR A1 - Shao, Borong A1 - Bjaanaes, Maria A1 - Helland, Aslaug A1 - Schütte, Christof A1 - Conrad, Tim T1 - EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma JF - PLOS ONE N2 - Various feature selection algorithms have been proposed to identify cancer prognostic biomarkers. In recent years, however, their reproducibility is criticized. The performance of feature selection algorithms is shown to be affected by the datasets, underlying networks and evaluation metrics. One of the causes is the curse of dimensionality, which makes it hard to select the features that generalize well on independent data. Even the integration of biological networks does not mitigate this issue because the networks are large and many of their components are not relevant for the phenotype of interest. With the availability of multi-omics data, integrative approaches are being developed to build more robust predictive models. In this scenario, the higher data dimensions create greater challenges. We proposed a phenotype relevant network-based feature selection (PRNFS) framework and demonstrated its advantages in lung cancer prognosis prediction. We constructed cancer prognosis relevant networks based on epithelial mesenchymal transition (EMT) and integrated them with different types of omics data for feature selection. With less than 2.5% of the total dimensionality, we obtained EMT prognostic signatures that achieved remarkable prediction performance (average AUC values above 0.8), very significant sample stratifications, and meaningful biological interpretations. In addition to finding EMT signatures from different omics data levels, we combined these single-omics signatures into multi-omics signatures, which improved sample stratifications significantly. Both single- and multi-omics EMT signatures were tested on independent multi-omics lung cancer datasets and significant sample stratifications were obtained. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0204186 VL - 14 IS - 1 ER - TY - JOUR A1 - Wulkow, Niklas A1 - Telgmann, Regina A1 - Hungenberg, Klaus-Dieter A1 - Schütte, Christof A1 - Wulkow, Michael T1 - Deterministic and Stochastic Parameter Estimation for Polymer Reaction Kinetics I: Theory and Simple Examples JF - Macromolecular Theory and Simulations N2 - Two different approaches to parameter estimation (PE) in the context of polymerization are introduced, refined, combined, and applied. The first is classical PE where one is interested in finding parameters which minimize the distance between the output of a chemical model and experimental data. The second is Bayesian PE allowing for quantifying parameter uncertainty caused by experimental measurement error and model imperfection. Based on detailed descriptions of motivation, theoretical background, and methodological aspects for both approaches, their relation are outlined. The main aim of this article is to show how the two approaches complement each other and can be used together to generate strong information gain regarding the model and its parameters. Both approaches and their interplay in application to polymerization reaction systems are illustrated. This is the first part in a two-article series on parameter estimation for polymer reaction kinetics with a focus on theory and methodology while in the second part a more complex example will be considered. Y1 - 2021 U6 - https://doi.org/10.1002/mats.202100017 VL - 30 ER - TY - JOUR A1 - Hungenberg, Klaus-Dieter A1 - Schwede, Christian A1 - Wulkow, Michael A1 - Wulkow, Niklas T1 - Determination of reactivity ratios for acrylic acid and its dimer from classical parameter estimation and Bayesian approach JF - Canadian Journal of Chemical Engineering N2 - The reactivity ratios of acrylic acid (AA, M1) and its dimer beta-acroyloxypropionic acid (diAA, M2) are determined from cumulative copolymerization data by two different methods: classical parameter estimation (PE) by minimizing the objective function and a Bayesian analysis. Classical PE gives r1 =0.74 and r2 = 1.23 at the minimum of the residual. From the Bayesian analysis, the probability distribution of the parameter sets is obtained, revealing the existence of parameter sets with rather the same probability. The influence of the number of data and the size of the measurement error are discussed. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1002/cjce.24330 SP - 1 EP - 10 ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - The ice composition close to the surface of comet 67P/Churyumov-Gerasimenko JF - ACS Earth and Space Chemistry N2 - The relation between ice composition in the nucleus of comet 67P/Churyumov-Gerasimenko on the one hand and relative abundances of volatiles in the coma on the other hand is important for the interpretation of density measurements in the environment of the cometary nucleus. For the 2015 apparition, in situ measurements from the two ROSINA (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) sensors COPS (COmet Pressure Sensor) and DFMS (Double Focusing Mass Spectrometer) determined gas densities at the spacecraft position for the 14 gas species H2O, CO2, CO, H2S, O2, C2H6, CH3OH, H2CO, CH4, NH3, HCN, C2H5OH, OCS, and CS2. We derive the spatial distribution of the gas emissions on the complex shape of the nucleus separately for 50 subintervals of the two-year mission time. The most active patches of gas emission are identified on the surface. We retrieve the relation between solar irradiation and observed emissions from these patches. The emission rates are compared to a minimal thermophysical model to infer the surface active fraction of H2O and CO2. We obtain characteristic differences in the ice composition close to the surface between the two hemispheres with a reduced abundance of CO2 ice on the northern hemisphere (locations with positive latitude). We do not see significant differences for the ice composition on the two lobes of 67P/C-G. Y1 - 2022 U6 - https://doi.org/10.1021/acsearthspacechem.1c00378 VL - 6 IS - 5 SP - 1189 EP - 1203 ER - TY - JOUR A1 - Colom, Remi A1 - Mikheeva, Elena A1 - Achouri, Karim A1 - Zuniga-Perez, Jesus A1 - Bonod, Nicolas A1 - Martin, Olivier J. F. A1 - Burger, Sven A1 - Genevet, Patrice T1 - Crossing of the branch cut: the topological origin of a universal 2π-phase retardation in non-Hermitian metasurfaces JF - Laser Photonics Rev. Y1 - 2023 U6 - https://doi.org/10.1002/lpor.202200976 VL - 17 SP - 2200976 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Spreckelsen, Klaus A1 - Gotzes, Uwe A1 - Zittel, Janina A1 - Koch, Thorsten T1 - Beimischung von Wasserstoff zum Erdgas: Eine Kapazitätsstudie des deutschen Gasnetzes T1 - Blending hydrogen into natural gas: An assessment of the capacity of the German gas grid JF - gwf Gas + Energie N2 - Die europaische Gasinfrastruktur wird disruptiv in ein zukunftiges dekarbonisiertes Energiesystem verändert; ein Prozess, der angesichts der jüngsten politischen Situation beschleunigt werden muss. Mit einem wachsenden Wasserstoffmarkt wird der pipelinebasierte Transport unter Nutzung der bestehenden Erdgasinfrastruktur wirtschaftlich sinnvoll, trägt zur Erhöhung der öffentlichen Akzeptanz bei und beschleunigt den Umstellungsprozess. In diesem Beitrag wird die maximal technisch machbare Einspeisung von Wasserstoff in das bestehende deutsche Erdgastransportnetz hinsichtlich regulatorischer Grenzwerte der Gasqualität analysiert. Die Analyse erfolgt auf Basis eines transienten Tracking-Modells, das auf dem allgemeinen Pooling-Problem einschließlich Linepack aufbaut. Es zeigt sich, dass das Gasnetz auch bei strengen Grenzwerten gen ̈ugend Kapazität bietet, um für einen großen Teil der bis 2030 geplanten Erzeugungskapazität für grünen Wasserstoff als garantierter Abnehmer zu dienen. N2 - The European gas infrastructure is being disruptively transformed into a future decarbonised energy system; a process that needs to be accelerated given the recent political situation. With a growing hydrogen market, pipeline-based transport using the existing natural gas infrastructure becomes economically viable, helps to increase public acceptance and accelerates the transition process. In this paper, the maximum technically feasible feed-in of hydrogen into the existing German natural gas transport network is analysed with regard to regulatory limits of gas quality. Analysis is based on a transient tracking model that builds on the general pooling problem including linepack. It is shown that even with strict limits, the gas grid offers sufficient capacity to serve as a guaranteed customer for a large part of the green hydrogen generation capacity planned until 2030. Y1 - 2023 PB - Vulkan Verlag ET - 06/2023 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Spreckelsen, Klaus A1 - Gotzes, Uwe A1 - Zittel, Janina A1 - Koch, Thorsten T1 - Beimischung von Wasserstoff zum Erdgas: Eine Kapazitätsstudie des deutschen Gasnetzes JF - 3R – Fachzeitschrift für Rohrleitungssystem N2 - Die europäische Gasinfrastruktur wird disruptiv in ein zukünftiges dekarbonisiertes Energiesystem verändert; ein Prozess, der angesichts der jüngsten politischen Situation beschleunigt werden muss. Mit einem wachsenden Wasserstoffmarkt wird der pipelinebasierte Transport unter Nutzung der bestehenden Erdgasinfrastruktur wirtschaftlich sinnvoll, trägt zur Erhöhung der öffentlichen Akzeptanz bei und beschleunigt den Umstellungsprozess. In diesem Fachbeitrag wird die maximal technisch machbare Einspeisung von Wasserstoff in das bestehende deutsche Erdgastransportnetz hinsichtlich regulatorischer Grenzwerte der Gasqualität analysiert. Die Analyse erfolgt auf Basis eines transienten Tracking-Modells, das auf dem allgemeinen Pooling-Problem einschließlich Linepack aufbaut. Es zeigt sich, dass das Gasnetz auch bei strengen Grenzwerten genügend Kapazität bietet, um für einen großen Teil der bis 2030 geplanten Erzeugungskapazität für grünen Wasserstoff als garantierter Abnehmer zu dienen. Y1 - 2023 IS - 06/2023 SP - 70 EP - 75 ER - TY - JOUR A1 - Weilandt, Frank A1 - Behling, Robert A1 - Goncalves, Romulo A1 - Madadi, Arash A1 - Richter, Lorenz A1 - Sanona, Tiago A1 - Spengler, Daniel A1 - Welsch, Jona T1 - Early Crop Classification via Multi-Modal Satellite Data Fusion and Temporal Attention JF - Remote Sensing N2 - In this article, we propose a deep learning-based algorithm for the classification of crop types from Sentinel-1 and Sentinel-2 time series data which is based on the celebrated transformer architecture. Crucially, we enable our algorithm to do early classification, i.e., predict crop types at arbitrary time points early in the year with a single trained model (progressive intra-season classification). Such early season predictions are of practical relevance for instance for yield forecasts or the modeling of agricultural water balances, therefore being important for the public as well as the private sector. Furthermore, we improve the mechanism of combining different data sources for the prediction task, allowing for both optical and radar data as inputs (multi-modal data fusion) without the need for temporal interpolation. We can demonstrate the effectiveness of our approach on an extensive data set from three federal states of Germany reaching an average F1 score of 0.92 using data of a complete growing season to predict the eight most important crop types and an F1 score above 0.8 when doing early classification at least one month before harvest time. In carefully chosen experiments, we can show that our model generalizes well in time and space. Y1 - 2023 U6 - https://doi.org/10.3390/rs15030799 VL - 15 IS - 3 SP - 799 ER - TY - JOUR A1 - Nüsken, Nikolas A1 - Richter, Lorenz T1 - Interpolating between BSDEs and PINNs: deep learning for elliptic and parabolic boundary value problems JF - Journal of Machine Learning N2 - Solving high-dimensional partial differential equations is a recurrent challenge in economics, science and engineering. In recent years, a great number of computational approaches have been developed, most of them relying on a combination of Monte Carlo sampling and deep learning based approximation. For elliptic and parabolic problems, existing methods can broadly be classified into those resting on reformulations in terms of backward stochastic differential equations (BSDEs) and those aiming to minimize a regression-type L2-error (physics-informed neural networks, PINNs). In this paper, we review the literature and suggest a methodology based on the novel diffusion loss that interpolates between BSDEs and PINNs. Our contribution opens the door towards a unified understanding of numerical approaches for high-dimensional PDEs, as well as for implementations that combine the strengths of BSDEs and PINNs. The diffusion loss furthermore bears close similarities to (least squares) temporal difference objectives found in reinforcement learning. We also discuss eigenvalue problems and perform extensive numerical studies, including calculations of the ground state for nonlinear Schr ¨odinger operators and committor functions relevant in molecular dynamics. Y1 - 2023 U6 - https://doi.org/0.4208/jml.220416 VL - 2 IS - 1 SP - 31 EP - 64 ER - TY - JOUR A1 - Richter, Lorenz A1 - Berner, Julius A1 - Liu, Guan-Horng T1 - Improved sampling via learned diffusions N2 - Recently, a series of papers proposed deep learning-based approaches to sample from unnormalized target densities using controlled diffusion processes. In this work, we identify these approaches as special cases of the Schrödinger bridge problem, seeking the most likely stochastic evolution between a given prior distribution and the specified target. We further generalize this framework by introducing a variational formulation based on divergences between path space measures of time-reversed diffusion processes. This abstract perspective leads to practical losses that can be optimized by gradient-based algorithms and includes previous objectives as special cases. At the same time, it allows us to consider divergences other than the reverse Kullback-Leibler divergence that is known to suffer from mode collapse. In particular, we propose the so-called log-variance loss, which exhibits favorable numerical properties and leads to significantly improved performance across all considered approaches. Y1 - 2023 ER - TY - JOUR A1 - Conrad, Tim A1 - Genzel, Martin A1 - Cvetkovic, Nada A1 - Wulkow, Niklas A1 - Vybiral, Jan A1 - Kutyniok, Gitta A1 - Schütte, Christof T1 - Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data JF - BMC Bioinformatics N2 - Motivation: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested how MS spectra dier between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust to noise and outliers, and the identied feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA), based on the theory of Compressed Sensing that allows to identify a minimal discriminating set of features from mass spectrometry data-sets. We show how our method performs on artificial and real-world data-sets. Y1 - 2017 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 18 IS - 160 SP - 1 EP - 20 ER - TY - JOUR A1 - Liang, YongTian A1 - Piao, Chengji A1 - Beuschel, Christine B. A1 - Toppe, David A1 - Kollipara, Laxmikanth A1 - Bogdanow, Boris A1 - Maglione, Marta A1 - Lützkendorf, Janine A1 - See, Jason Chun Kit A1 - Huang, Sheng A1 - Conrad, Tim A1 - Kintscher, Ulrich A1 - Madeo, Frank A1 - Liu, Fan A1 - Sickmann, Albert A1 - Sigrist, Stephan J. T1 - eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction JF - Cell Reports Y1 - 2021 U6 - https://doi.org/10.1016/j.celrep.2021.108941 VL - 35 IS - 2 ER - TY - JOUR A1 - Zemann, Berit A1 - Le, Mai-Lee Van A1 - Sherlock, Rob E. A1 - Baum, Daniel A1 - Katija, Kakani A1 - Stach, Thomas T1 - Evolutionary traces of miniaturization in a giant – Comparative anatomy of brain and brain nerves in Bathochordaeus stygius (Tunicata, Appendicularia) JF - Journal of Morphology Y1 - 2023 U6 - https://doi.org/10.1002/jmor.21598 VL - 284 IS - 7 ER - TY - JOUR A1 - Shao, Borong A1 - Cannistraci, Carlo Vittorio A1 - Conrad, Tim T1 - Epithelial Mesenchymal Transition Network-Based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data JF - Genomics and Computational Biology N2 - Epithelial mesenchymal transition (EMT) process has been shown as highly relevant to cancer prognosis. However, although different biological network-based biomarker identification methods have been proposed to predict cancer prognosis, EMT network has not been directly used for this purpose. In this study, we constructed an EMT regulatory network consisting of 87 molecules and tried to select features that are useful for prognosis prediction in Lung Adenocarcinoma (LUAD). To incorporate multiple molecular profiles, we obtained four types of molecular data including mRNA-Seq, copy number alteration (CNA), DNA methylation, and miRNA-Seq data from The Cancer Genome Atlas. The data were mapped to the EMT network in three alternative ways: mRNA-Seq and miRNA-Seq, DNA methylation, and CNA and miRNA-Seq. Each mapping was employed to extract five different sets of features using discretization and network-based biomarker identification methods. Each feature set was then used to predict prognosis with SVM and logistic regression classifiers. We measured the prediction accuracy with AUC and AUPR values using 10 times 10-fold cross validation. For a more comprehensive evaluation, we also measured the prediction accuracies of clinical features, EMT plus clinical features, randomly picked 87 molecules from each data mapping, and using all molecules from each data type. Counter-intuitively, EMT features do not always outperform randomly selected features and the prediction accuracies of the five feature sets are mostly not significantly different. Clinical features are shown to give the highest prediction accuracies. In addition, the prediction accuracies of both EMT features and random features are comparable as using all features (more than 17,000) from each data type. Y1 - 2017 U6 - https://doi.org/10.18547/gcb.2017.vol3.iss3.e57 VL - 3 IS - 3 SP - e57 ER - TY - JOUR A1 - Conrad, Tim A1 - Leichtle, Alexander Benedikt A1 - Nuoffer, Jean-Marc A1 - Ceglarek, Uta A1 - Kase, Julia A1 - Witzigmann, Helmut A1 - Thiery, Joachim A1 - Fiedler, Georg Martin T1 - Serum amino acid profiles and their alterations in colorectal cancer JF - Metabolomics N2 - Mass spectrometry-based serum metabolic profiling is a promising tool to analyse complex cancer associated metabolic alterations, which may broaden our pathophysiological understanding of the disease and may function as a source of new cancer-associated biomarkers. Highly standardized serum samples of patients suffering from colon cancer (n = 59) and controls (n = 58) were collected at the University Hospital Leipzig. We based our investigations on amino acid screening profiles using electrospray tandem-mass spectrometry. Metabolic profiles were evaluated using the Analyst 1.4.2 software. General, comparative and equivalence statistics were performed by R 2.12.2. 11 out of 26 serum amino acid concentrations were significantly different between colorectal cancer patients and healthy controls. We found a model including CEA, glycine, and tyrosine as best discriminating and superior to CEA alone with an AUROC of 0.878 (95\% CI 0.815?0.941). Our serum metabolic profiling in colon cancer revealed multiple significant disease-associated alterations in the amino acid profile with promising diagnostic power. Further large-scale studies are necessary to elucidate the potential of our model also to discriminate between cancer and potential differential diagnoses. In conclusion, serum glycine and tyrosine in combination with CEA are superior to CEA for the discrimination between colorectal cancer patients and controls. Y1 - 2012 U6 - https://doi.org/10.1007/s11306-011-0357-5 ER - TY - JOUR A1 - Conrad, Tim A1 - Karsch, K. A1 - Obermeier, Patrick A1 - Seeber, L. A1 - Chen, X. A1 - Tief, Franziska A1 - Muehlhans, S. A1 - Hoppe, Christian A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Rath, Barbara T1 - Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children JF - The Pediatric Infectious Disease Journal Y1 - 2015 VL - 34 IS - 10 ER - TY - JOUR A1 - Conrad, Tim A1 - Genzel, Martin A1 - Cvetkovic, Nada A1 - Wulkow, Niklas A1 - Leichtle, Alexander Benedikt A1 - Vybiral, Jan A1 - Kytyniok, Gitta A1 - Schütte, Christof T1 - Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data JF - BMC Bioinfomatics N2 - Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust against noise and outliers, while the identified feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA),based on thet heory of compressed sensing that allows us to identify a minimal discriminating set of features from mass spectrometry data-sets. We show (1) how our method performs on artificial and real-world data-sets, (2) that its performance is competitive with standard (and widely used) algorithms for analyzing proteomics data, and (3) that it is robust against random and systematic noise. We further demonstrate the applicability of our algorithm to two previously published clinical data-sets. Y1 - 2017 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 18 IS - 160 ER - TY - JOUR A1 - Vega, Iliusi A1 - Schütte, Christof A1 - Conrad, Tim T1 - Finding metastable states in real-world time series with recurrence networks JF - Physica A: Statistical Mechanics and its Applications N2 - In the framework of time series analysis with recurrence networks, we introduce a self-adaptive method that determines the elusive recurrence threshold and identifies metastable states in complex real-world time series. As initial step, we introduce a way to set the embedding parameters used to reconstruct the state space from the time series. We set them as the ones giving the maximum Shannon entropy of the diagonal line length distribution for the first simultaneous minima of recurrence rate and Shannon entropy. To identify metastable states, as well as the transitions between them, we use a soft partitioning algorithm for module finding which is specifically developed for the case in which a system shows metastability. We illustrate our method with a complex time series example. Finally, we show the robustness of our method for identifying metastable states. Our results suggest that our method is robust for identifying metastable states in complex time series, even when introducing considerable levels of noise and missing data points. Y1 - 2016 U6 - https://doi.org/10.1016/j.physa.2015.10.041 VL - 445 SP - 1 EP - 17 ER - TY - JOUR A1 - Tief, Franziska A1 - Hoppe, Christian A1 - Seeber, L. A1 - Obermeier, Patrick A1 - Chen, X. A1 - Karsch, K. A1 - Muehlhans, S. A1 - Adamou, E. A1 - Conrad, Tim A1 - Schweiger, Brunhilde A1 - Adam, T. A1 - Rath, Barbara T1 - An inception cohort study assessing the role of bacterial co-infections in children with influenza and ILI and a clinical decision model for stringent antibiotic use JF - Antiviral Therapy N2 - BACKGROUND: Influenza-like illness (ILI) is a common reason for paediatric consultations. Viral causes predominate, but antibiotics are used frequently. With regard to influenza, pneumococcal coinfections are considered major contributors to morbidity/mortality. METHODS: In the context of a perennial quality management (QM) programme at the Charit{\'e} Departments of Paediatrics and Microbiology in collaboration with the Robert Koch Institute, children aged 0-18 years presenting with signs and symptoms of ILI were followed from the time of initial presentation until hospital discharge (Charit{\'e} Influenza-Like Disease = ChILD Cohort). An independent QM team performed highly standardized clinical assessments using a disease severity score based on World Health Organization criteria for uncomplicated and complicated/progressive disease. Nasopharyngeal and pharyngeal samples were collected for viral reverse transcription polymerase chain reaction and bacterial culture/sensitivity and MaldiTOF analyses. The term 'detection' was used to denote any evidence of viral or bacterial pathogens in the (naso)pharyngeal cavity. With the ChILD Cohort data collected, a standard operating procedure (SOP) was created as a model system to reduce the inappropriate use of antibiotics in children with ILI. Monte Carlo simulations were performed to assess cost-effectiveness. RESULTS: Among 2,569 ChILD Cohort patients enrolled from 12/2010 to 04/2013 (55\% male, mean age 3.2 years, range 0-18, 19\% {\ensuremath{>}}5 years), 411 patients showed laboratory-confirmed influenza, with bacterial co-detection in 35\%. Influenza and pneumococcus were detected simultaneously in 12/2,569 patients, with disease severity clearly below average. Pneumococcal vaccination rates were close to 90\%. Nonetheless, every fifth patient was already on antibiotics upon presentation; new antibiotic prescriptions were issued in an additional 20\%. Simulation of the model SOP in the same dataset revealed that the proposed decision model could have reduced the inappropriate use of antibiotics significantly (P{\ensuremath{<}}0.01) with an incremental cost-effectiveness ratio of -99.55?. CONCLUSIONS: Physicians should be made aware that in times of pneumococcal vaccination the prevalence and severity of influenza infections complicated by pneumococci may decline. Microbiological testing in combination with standardized disease severity assessments and review of vaccination records could be cost-effective, as well as promoting stringent use of antibiotics and a personalized approach to managing children with ILI. Y1 - 2016 U6 - https://doi.org/10.3851/IMP3034 VL - 21 SP - 413 EP - 424 ER - TY - JOUR A1 - Hoppe, Christian A1 - Obermeier, Patrick A1 - Mehlhans, S. A1 - Alchikh, Maren A1 - Seeber, L. A1 - Tief, Franziska A1 - Karsch, K. A1 - Chen, X. A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Conrad, Tim T1 - Innovative Digital Tools and Surveillance Systems for the Timely Detection of Adverse Events at the Point of Care: A Proof-of-Concept Study JF - Drug Safety N2 - Regulatory authorities often receive poorly structured safety reports requiring considerable effort to investigate potential adverse events post hoc. Automated question-and-answer systems may help to improve the overall quality of safety information transmitted to pharmacovigilance agencies. This paper explores the use of the VACC-Tool (ViVI Automated Case Classification Tool) 2.0, a mobile application enabling physicians to classify clinical cases according to 14 pre-defined case definitions for neuroinflammatory adverse events (NIAE) and in full compliance with data standards issued by the Clinical Data Interchange Standards Consortium. METHODS: The validation of the VACC-Tool 2.0 (beta-version) was conducted in the context of a unique quality management program for children with suspected NIAE in collaboration with the Robert Koch Institute in Berlin, Germany. The VACC-Tool was used for instant case classification and for longitudinal follow-up throughout the course of hospitalization. Results were compared to International Classification of Diseases , Tenth Revision (ICD-10) codes assigned in the emergency department (ED). RESULTS: From 07/2013 to 10/2014, a total of 34,368 patients were seen in the ED, and 5243 patients were hospitalized; 243 of these were admitted for suspected NIAE (mean age: 8.5 years), thus participating in the quality management program. Using the VACC-Tool in the ED, 209 cases were classified successfully, 69 \% of which had been missed or miscoded in the ED reports. Longitudinal follow-up with the VACC-Tool identified additional NIAE. CONCLUSION: Mobile applications are taking data standards to the point of care, enabling clinicians to ascertain potential adverse events in the ED setting and during inpatient follow-up. Compliance with Clinical Data Interchange Standards Consortium (CDISC) data standards facilitates data interoperability according to regulatory requirements. Y1 - 2016 U6 - https://doi.org/10.1007/s40264-016-0437-6 VL - 39 IS - 10 SP - 977 EP - 988 ER - TY - JOUR A1 - Obermeier, Patrick A1 - Muehlhans, S. A1 - Hoppe, Christian A1 - Karsch, K. A1 - Tief, Franziska A1 - Seeber, L. A1 - Chen, X. A1 - Conrad, Tim A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Rath, Barbara T1 - Enabling Precision Medicine With Digital Case Classification at the Point-of-Care JF - EBioMedicine N2 - Infectious and inflammatory diseases of the central nervous system are difficult to identify early. Case definitions for aseptic meningitis, encephalitis, myelitis, and acute disseminated encephalomyelitis (ADEM) are available, but rarely put to use. The VACC-Tool (Vienna Vaccine Safety Initiative Automated Case Classification-Tool) is a mobile application enabling immediate case ascertainment based on consensus criteria at the point-of-care. The VACC-Tool was validated in a quality management program in collaboration with the Robert-Koch-Institute. Results were compared to ICD-10 coding and retrospective analysis of electronic health records using the same case criteria. Of 68,921 patients attending the emergency room in 10/2010-06/2013, 11,575 were hospitalized, with 521 eligible patients (mean age: 7.6 years) entering the quality management program. Using the VACC-Tool at the point-of-care, 180/521 cases were classified successfully and 194/521 ruled out with certainty. Of the 180 confirmed cases, 116 had been missed by ICD-10 coding, 38 misclassified. By retrospective application of the same case criteria, 33 cases were missed. Encephalitis and ADEM cases were most likely missed or misclassified. The VACC-Tool enables physicians to ask the right questions at the right time, thereby classifying cases consistently and accurately, facilitating translational research. Future applications will alert physicians when additional diagnostic procedures are required. Y1 - 2016 U6 - https://doi.org/10.1016/j.ebiom.2016.01.008 VL - 4 SP - 191 EP - 196 ER - TY - JOUR A1 - Conrad, Tim A1 - You, Xintian T1 - Acfs: accurate circRNA identification and quantification from NGS data JF - Nature Scientific Reports N2 - Circular RNAs (circRNAs) are a group of single-stranded RNAs in closed circular form. They are splicing-generated, widely expressed in various tissues and have functional implications in development and diseases. To facilitate genome-wide characterization of circRNAs using RNA-Seq data, we present a freely available software package named acfs. Acfs allows de novo, accurate and fast identification and abundance quantification of circRNAs from single- and paired-ended RNA-Seq data. On simulated datasets, acfs achieved the highest F1 accuracy and lowest false discovery rate among current state-of-the-art tools. On real-world datasets, acfs efficiently identified more bona fide circRNAs. Furthermore, we demonstrated the power of circRNA analysis on two leukemia datasets. We identified a set of circRNAs that are differentially expressed between AML and APL samples, which might shed light on the potential molecular classification of complex diseases using circRNA profiles. Moreover, chromosomal translocation, as manifested in numerous diseases, could produce not only fusion transcripts but also fusion circRNAs of clinical relevance. Featured with high accuracy, low FDR and the ability to identify fusion circRNAs, we believe that acfs is well suited for a wide spectrum of applications in characterizing the landscape of circRNAs from non-model organisms to cancer biology. Y1 - 2016 U6 - https://doi.org/10.1038/srep38820 VL - 6 ER - TY - JOUR A1 - Mireles, Victor A1 - Conrad, Tim T1 - Decomposing biological systems into reusable modules reveals characteristic module size distributions N2 - One of the widely recognized features of biological systems is their modularity. The modules that comprise biological systems are said to be redeployed and combined across several conditions. In this work, we analyze to what extent are these modules indeed reusable as compared to randomized versions of a system. We develop a notion of modular decompositions of systems that allows for modules to overlap while maximizing the number of times a module is reused across several conditions. Different biological systems present modules whose reusability ranges from the condition specific to the constitutive, although their average reusability is not always higher than random equivalents of the system. These decompositions reveal a distinct distribution of module sizes in real biological systems. This distribution stems, in part, from the peculiar usage pattern of the elements of biological systems, and constitutes a new angle to study the evolution of modularity. Y1 - 2016 ER - TY - JOUR A1 - Conrad, Tim A1 - Mireles, Victor T1 - Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrics JF - Procedia Computer Science N2 - Given a set of n binary data points, a widely used technique is to group its features into k clusters. In the case where n {\ensuremath{<}} k, the question of how overlapping are the clusters becomes of interest. In this paper we approach the question through matrix decomposition, and relate the degree of overlap with the sparsity of one of the resulting matrices. We present analytical results regarding bounds on this sparsity, and a heuristic to estimate the minimum amount of overlap that an exact grouping of features into k clusters must have. As shown below, adding new data will not alter this minimum amount of overlap. Y1 - 2015 U6 - https://doi.org/10.1016/j.procs.2015.05.500 VL - 51 SP - 2967 EP - 2971 ER - TY - JOUR A1 - Conrad, Tim A1 - Shao, Borong T1 - Are NoSQL data stores useful for bioinformatics researchers? JF - International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC) Y1 - 2015 U6 - https://doi.org/10.17762/ijritcc2321-8169.1503176 VL - 3 IS - 3 SP - 1704 EP - 1708 ER - TY - JOUR A1 - Conrad, Tim A1 - Lenga, Matthias T1 - Non-convex regularization for supervised learning JF - Technical Report Y1 - 2015 ER - TY - JOUR A1 - Marzban, Forough A1 - Conrad, Tim A1 - Marban, Pouria A1 - Sodoudi, Sahar T1 - Estimation of the Near-Surface Air Temperature during the Day and Nighttime from MODIS in Berlin, Germany JF - International Journal of Advanced Remote Sensing and GIS N2 - Air temperature (Tair or T2m) is an important climatological variable for forest biosphere processes and climate change research. Due to the low density and the uneven distribution of weather stations, traditional ground-based observations cannot accurately capture the spatial distribution of Tair. In this study, Tair in Berlin is estimated during the day and night time over six land cover/land use (LC/LU) types by satellite remote sensing data over a large domain and a relatively long period (7 years). Aqua and Terra MODIS (Moderate Resolution Imaging Spectroradiometer) data and meteorological data for the period from 2007 to 2013 were collected to estimate Tair. Twelve environmental variables (land surface temperature (LST), normalized difference vegetation index (NDVI), Julian day, latitude, longitude, Emissivity31, Emissivity32, altitude, albedo, wind speed, wind direction and air pressure) were selected as predictors. Moreover, a comparison between LST from MODIS Terra and Aqua with daytime and night time air temperatures (Tday, Tnight) was done respectively and in addition, the spatial variability of LST and Tair relationship by applying a varying window size on the MODIS LST grid was examined. An analysis of the relationship between the observed Tair and the spatially averaged remotely sensed LST, indicated that 3 × 3 and 1 × 1 pixel size was the optimal window size for the statistical model estimating Tair from MODIS data during the day and night time, respectively. Three supervised learning methods (Adaptive Neuro Fuzzy Inference system (ANFIS), Artificial Neural Network (ANN) and Support vector machine (SVR)) were used to estimate Tair during the day and night time, and their performances were validated by cross-validation for each LC/LU. Moreover, tuning the hyper parameters of some models like SVR and ANN were investigated. For tuning the hyper parameters of SVR, Simulated Annealing (SA) was applied (SA-SVR model) and a multiple-layer feed-forward (MLF) neural networks with three layers and different nodes in hidden layers are used with Levenber-Marquardt back-propagation (LM-BP), in order to achieve higher accuracy in the estimation of Tair. Results indicated that the ANN model achieved better accuracy (RMSE= 2.16°C, MAE = 1.69°C, R2 = 0.95) than SA_SVR model (RMSE= 2.50°C, MAE = 1.92°C, R2 = 0.91) and ANFIS model (RMSE= 2.88°C, MAE= 2.2°C, R2 = 0.89) over six LC/LU during the day and night time. The Q-Q diagram of SA-SVR, ANFIS and NN show that all three models slightly tended to underestimate and overestimate the extreme and low temperatures for all LC/LU classes during the day and night time. The weak performance in the extreme and low temperatures are a consequence of the small number of data in these temperatures. These satisfactory results indicate that this approach is proper for estimating air temperature and spatial window size is an important factor that should be considered in the estimation of air temperature. KW - ANFIS KW - ANN KW - Cross-validation KW - MODIS KW - Simulated annealing KW - SVR Y1 - 2018 U6 - https://doi.org/10.23953/cloud.ijarsg.337 VL - 7 IS - 1 SP - 2478 EP - 2517 ER - TY - JOUR A1 - Ma, Xiaolin A1 - Conrad, Tim A1 - Alchikh, Maren A1 - Reiche, J. A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review JF - Medical Virology N2 - Studies have shown that the predictive value of “clinical diagnoses” of influenza and other respiratory viral infections is low, especially in children. In routine care, pediatricians often resort to clinical diagnoses, even in the absence of robust evidence‐based criteria. We used a dual approach to identify clinical characteristics that may help to differentiate infections with common pathogens including influenza, respiratory syncytial virus, adenovirus, metapneumovirus, rhinovirus, bocavirus‐1, coronaviruses, or parainfluenza virus: (a) systematic review and meta‐analysis of 47 clinical studies published in Medline (June 1996 to March 2017, PROSPERO registration number: CRD42017059557) comprising 49 858 individuals and (b) data‐driven analysis of an inception cohort of 6073 children with ILI (aged 0‐18 years, 56% male, December 2009 to March 2015) examined at the point of care in addition to blinded PCR testing. We determined pooled odds ratios for the literature analysis and compared these to odds ratios based on the clinical cohort dataset. This combined analysis suggested significant associations between influenza and fever or headache, as well as between respiratory syncytial virus infection and cough, dyspnea, and wheezing. Similarly, literature and cohort data agreed on significant associations between HMPV infection and cough, as well as adenovirus infection and fever. Importantly, none of the abovementioned features were unique to any particular pathogen but were also observed in association with other respiratory viruses. In summary, our “real‐world” dataset confirmed published literature trends, but no individual feature allows any particular type of viral infection to be ruled in or ruled out. For the time being, laboratory confirmation remains essential. More research is needed to develop scientifically validated decision models to inform best practice guidelines and targeted diagnostic algorithms. Y1 - 2018 U6 - https://doi.org/10.1002/rmv.1997 VL - 28 IS - 5 SP - 1 EP - 12 ER - TY - JOUR A1 - Rath, Barbara A1 - Conrad, Tim A1 - Myles, Puja A1 - Alchikh, Maren A1 - Ma, Xiaolin A1 - Hoppe, Christian A1 - Tief, Franziska A1 - Chen, Xi A1 - Obermeier, Patrick A1 - Kisler, Bron A1 - Schweiger, Brunhilde T1 - Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials JF - Expert Review of Anti-infective Therapy N2 - Introduction: Influenza-Like Illness is a leading cause of hospitalization in children. Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Areas covered: We present a composite clinical score allowing individual patient data analyses of disease severity based on systematic literature review and WHO-criteria for uncomplicated and complicated disease. The 22-item ViVI Disease Severity Score showed a normal distribution in a pediatric cohort of 6073 children aged 0–18 years (mean age 3.13; S.D. 3.89; range: 0 to 18.79). Expert commentary: The ViVI Score was correlated with risk of antibiotic use as well as need for hospitalization and intensive care. The ViVI Score was used to track children with influenza, respiratory syncytial virus, human metapneumovirus, human rhinovirus, and adenovirus infections and is fully compliant with regulatory data standards. The ViVI Disease Severity Score mobile application allows physicians to measure disease severity at the point-of care thereby taking clinical trials to the next level. KW - Disease severity KW - influenza-like illness KW - influenza KW - respiratory syncytial virus KW - human metapneumovirus KW - human rhinovirus KW - adenovirus KW - seasonality KW - antivirals KW - clinical trials Y1 - 2017 U6 - https://doi.org/10.1080/14787210.2017.1295847 VL - 15 IS - 6 SP - 545 EP - 568 ER - TY - JOUR A1 - Jayrannejad, Fahrnaz A1 - Conrad, Tim T1 - Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining JF - Springer Lecture Notes in Artificial Intelligence N2 - Recent advances in -omics technology has yielded in large data-sets in many areas of biology, such as mass spectrometry based proteomics. However, analyzing this data is still a challenging task mainly due to the very high dimensionality and high noise content of the data. One of the main objectives of the analysis is the identification of relevant patterns (or features) which can be used for classification of new samples to healthy or diseased. So, a method is required to find easily interpretable models from this data. To gain the above mentioned goal, we have adapted the disjunctive association rule mining algorithm, TitanicOR, to identify emerging patterns from our mass spectrometry proteomics data-sets. Comparison to five state-of-the-art methods shows that our method is advantageous them in terms of identifying the inter-dependency between the features and the TP-rate and precision of the features selected. We further demonstrate the applicability of our algorithm to one previously published clinical data-set. Y1 - 2017 ER - TY - JOUR A1 - Mireles, Victor A1 - Conrad, Tim T1 - Reusable building blocks in biological systems JF - Journal of the Royal Society Interface N2 - One of the most widely recognized features of biological systems is their modularity. The modules that constitute biological systems are said to be redeployed and combined across several conditions, thus acting as building blocks. In this work, we analyse to what extent are these building blocks reusable as compared with those found in randomized versions of a system. We develop a notion of decompositions of systems into phenotypic building blocks, which allows them to overlap while maximizing the number of times a building block is reused across several conditions. Different biological systems present building blocks whose reusability ranges from single use (e.g. condition specific) to constitutive, although their average reusability is not always higher than random equivalents of the system. These decompositions reveal a distinct distribution of building block sizes in real biological systems. This distribution stems, in part, from the peculiar usage pattern of the elements of biological systems, and constitutes a new angle to study the evolution of modularity. Y1 - 2018 U6 - https://doi.org/10.1098/rsif.2018.0595 VL - 15 IS - 149 SP - 1 EP - 10 ER - TY - JOUR A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Hoppe, Christian A1 - Ma, Xiaolin A1 - Broberg, Eeva K. A1 - Penttinen, P. A1 - Reiche, J. A1 - Biere, Barbara A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care. Clinical Microbiology and Infection JF - Clinical Microbiology and Infection Y1 - 2018 U6 - https://doi.org/10.1016/j.cmi.2018.05.023 IS - 06/18 SP - 1 EP - 1 ER - TY - JOUR A1 - Kork, F. A1 - Conrad, Tim A1 - Weiss, B. A1 - Roenneberg, T. A1 - Wernecke, K.-D. A1 - Balzer, Felix T1 - Associations of postoperative mortality with the time of day, week and year JF - Anaesthesia Y1 - 2018 SN - 0959-2962 VL - 73 IS - 6 SP - 711 EP - 718 ER - TY - JOUR A1 - Weimann, K. A1 - Conrad, Tim T1 - Transfer Learning for ECG Classification JF - Scientific Reports N2 - Remote monitoring devices, which can be worn or implanted, have enabled a more effective healthcare for patients with periodic heart arrhythmia due to their ability to constantly monitor heart activity. However, these devices record considerable amounts of electrocardiogram (ECG) data that needs to be interpreted by physicians. Therefore, there is a growing need to develop reliable methods for automatic ECG interpretation to assist the physicians. Here, we use deep convolutional neural networks (CNN) to classify raw ECG recordings. However, training CNNs for ECG classification often requires a large number of annotated samples, which are expensive to acquire. In this work, we tackle this problem by using transfer learning. First, we pretrain CNNs on the largest public data set of continuous raw ECG signals. Next, we finetune the networks on a small data set for classification of Atrial Fibrillation, which is the most common heart arrhythmia. We show that pretraining improves the performance of CNNs on the target task by up to 6.57%, effectively reducing the number of annotations required to achieve the same performance as CNNs that are not pretrained. We investigate both supervised as well as unsupervised pretraining approaches, which we believe will increase in relevance, since they do not rely on the expensive ECG annotations. The code is available on GitHub at https://github.com/kweimann/ecg-transfer-learning. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-84374-8 VL - 11 ER - TY - JOUR A1 - Melnyk, Kateryna A1 - Montavon, Grègoire A1 - Klus, Stefan A1 - Conrad, Tim T1 - Graph Kernel Koopman Embedding for Human Microbiome Analysis JF - Applied Network Science N2 - More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to directly analyze human microbiome and its influence on the health status. Microbial communities are monitored over long periods of time and the associations between their members are explored. These relationships can be described by a time-evolving graph. In order to understand responses of the microbial community members to a distinct range of perturbations such as antibiotics exposure or diseases and general dynamical properties, the time-evolving graph of the human microbial communities has to be analyzed. This becomes especially challenging due to dozens of complex interactions among microbes and metastable dynamics. The key to solving this problem is the representation of the time-evolving graphs as fixed-length feature vectors preserving the original dynamics. We propose a method for learning the embedding of the time-evolving graph that is based on the spectral analysis of transfer operators and graph kernels. We demonstrate that our method can capture temporary changes in the time-evolving graph on both synthetic data and real-world data. Our experiments demonstrate the efficacy of the method. Furthermore, we show that our method can be applied to human microbiome data to study dynamic processes. Y1 - 2020 U6 - https://doi.org/10.1007/s41109-020-00339-2 VL - 5 IS - 96 ER - TY - JOUR A1 - Rams, Mona A1 - Conrad, Tim T1 - Dictionary Learning for transcriptomics data reveals type-specific gene modules in a multi-class setting JF - it - Information Technology Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1515/itit-2019-0048 SN - 2196-7032 VL - 62 IS - 3-4 PB - De Gruyter CY - Oldenbourg ER - TY - JOUR A1 - Rams, Mona A1 - Conrad, Tim T1 - Dictionary learning allows model-free pseudotime estimation of transcriptomics data JF - BMC Genomics Y1 - 2022 U6 - https://doi.org/10.1186/s12864-021-08276-9 VL - 23 PB - BioMed Central ER - TY - JOUR A1 - Le Duc, Huy A1 - Conrad, Tim T1 - A light-weight and highly flexible software system for analyzing large bio-medical datasets JF - Future Generation Computer Systems Y1 - 2020 ER - TY - JOUR A1 - Conrad, Tim A1 - Leichtle, Alexander Benedikt A1 - Ceglarek, Uta A1 - Weinert, P. A1 - Nakas, C.T. A1 - Nuoffer, Jean-Marc A1 - Kase, Julia A1 - Witzigmann, Helmut A1 - Thiery, Joachim A1 - Fiedler, Georg Martin T1 - Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma JF - Metabolomics N2 - Background: Metabolomics as one of the most rapidly growing technologies in the ?-omics?field denotes the comprehensive analysis of low molecular-weight compounds and their pathways. Cancer-specific alterations of the metabolome can be detected by high-throughput massspectrometric metabolite profiling and serve as a considerable source of new markers for the early differentiation of malignant diseases as well as their distinction from benign states. However, a comprehensive framework for the statistical evaluation of marker panels in a multi-class setting has not yet been established. Methods: We collected serum samples of 40 pancreatic carcinoma patients, 40 controls, and 23 pancreatitis patients according to standard protocols and generated amino acid profiles by routine mass-spectrometry. In an intrinsic three-class bioinformatic approach we compared these profiles, evaluated their selectivity and computed multi-marker panels combined with the conventional tumor marker CA 19-9. Additionally, we tested for non-inferiority and superiority to determine the diagnostic surplus value of our multi-metabolite marker panels.  Results: Compared to CA 19-9 alone, the combined amino acid-based metabolite panel had a superior selectivity for the discrimination of healthy controls, pancreatitis, and pancreatic carcinoma patients [Volume under ROC surface (VUS) = 0.891 (95\% CI 0.794 - 0.968)]. Conclusions: We combined highly standardized samples, a three-class study design, a highthroughput mass-spectrometric technique, and a comprehensive bioinformatic framework to identify metabolite panels selective for all three groups in a single approach. Our results suggest that metabolomic profiling necessitates appropriate evaluation strategies and ?despite all its current limitations? can deliver marker panels with high selectivity even in multi-class settings. Y1 - 2013 U6 - https://doi.org/10.1007/s11306-012-0476-7 VL - 9 IS - 3 SP - 677 EP - 687 ER - TY - JOUR A1 - Gupta, Pooja A1 - Conrad, Tim A1 - Spötter, Andreas A1 - Reinsch, Norbert A1 - Bienefeld, Kaspar T1 - Simulating a base population in honey bee for molecular genetic studies JF - Genetics Selection Evolution N2 - Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding values estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has distinct genetic and reproductive biology characteristics. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee.  Results: Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) ?2 statistics for Hardy- Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion: We developed a software program that takes into account the genetic and reproductive biology characteristics specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html Y1 - 2012 U6 - https://doi.org/10.1186/1297-9686-44-14 ER - TY - JOUR A1 - Conrad, Tim T1 - New Appraches for Visualizing and Analyzing Metabolic Pathways JF - Proceedings of the Second Australian Undergraduate Students? Computing Conference N2 - Visualizing of metabolic pathways (or networks) has been done by many differentapproaches. In this work, we implemented and tested existing graph layout algorithms, and present a new approach to lay-out medium size metabolic pathways (500-20,000 vertices) by implementing and combining three well known graph lay-out algorithms (high dimension embedding, spring-embedder preprocessing, spring-embedder), through 3D space density analysis facilitated by the Octree technique. For the analysis of the results of metabolic pathways simulations we present two new techniques: rstly, a powerful technique to visualize pathways simulation data was created to unveil and understand concentration ows through metabolic pathways. This was achieved by mapping the color encoded concentration value of every substance from each time step of the simulation to its graphical representation in the layout. By combining all resulting images (from each time step) and displaying them as a movie, many characteristics such as subnetworks, alternative routes through the network, and differences between a modied pathway and its unmodied version can be revealed. Secondly, a new method to detect co-regulated substances in metabolic pathways and to recognize differences between two versions of a pathway, was established. To do this, we transformed the simulation data into a row-based representation, color-coded these rows, and reordered them with respect to similarity by using a Genetic Algorithm variant. From the arising discrete 2-dimensional matrix consisting of concentration values, a continuous 2-dimensional fourier row function was computed. This function can be used to measure properties, such as similarities in a pathway between time steps, or substances, or to detect and evaluate differences between modied versions of the same pathway. Y1 - 2004 ER - TY - JOUR A1 - Conrad, Tim A1 - Bruckner, Sharon A1 - Kayser, Bastian T1 - Finding Modules in Networks with Non-modular Regions JF - Lecture Notes in Computer Science (Proceedings of SEA 2013) N2 - Most network clustering methods share the assumption that the network can be completely decomposed into modules, that is, every node belongs to (usually exactly one) module. Forcing this constraint can lead to misidentification of modules where none exist, while the true modules are drowned out in the noise, as has been observed e.g. for protein interaction networks. We thus propose a clustering model where networks contain both a modular region consisting of nodes that can be partitioned into modules, and a transition region containing nodes that lie between or outside modules. We propose two scores based on spectral properties to determine how well a network fits this model. We then evaluate three (partially adapted) clustering algorithms from the literature on random networks that fit our model, based on the scores and comparison to the ground truth. This allows to pinpoint the types of networks for which the different algorithms perform well. Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-38527-8_18 VL - 7933 SP - 188 EP - 199 ER - TY - JOUR A1 - Conrad, Tim A1 - Rath, Barbara A1 - Tief, Franziska A1 - Karsch, K. A1 - Muehlhans, S. A1 - Obermeier, Patrick A1 - Adamou, E. A1 - Chen, X. A1 - Seeber, L. A1 - Peiser, Ch. A1 - Hoppe, Christian A1 - von Kleist, Max A1 - Schweiger, Brunhilde T1 - Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir JF - Infectious Disorders - Drug Targets Y1 - 2013 VL - 13 IS - 1 SP - 25 EP - 33 ER - TY - JOUR A1 - Gupta, Pooja A1 - Reinsch, Norbert A1 - Spötter, Andreas A1 - Conrad, Tim A1 - Bienefeld, Kaspar T1 - Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera) JF - BMC Genetics Y1 - 2013 U6 - https://doi.org/10.1186/1471-2156-14-36 VL - 14 IS - 36 ER - TY - JOUR A1 - Conrad, Tim A1 - Wallmeyer, Leonie A1 - Rams, Mona A1 - Börno, Stefan A1 - Timmermann, Bernd A1 - Hedtrich, Sarah T1 - Analyzing the Influence of Filaggrin on Other Skin Associated Genes in a Filaggrin Deficient Skin Model Using the Core Network Approach JF - Technical Report Y1 - 2015 ER - TY - JOUR A1 - Seeber, L. A1 - Conrad, Tim A1 - Hoppe, Christian A1 - Obermeier, Patrick A1 - Chen, X. A1 - Karsch, K. A1 - Muehlhans, S. A1 - Tief, Franziska A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Educating parents about the vaccination status of their children: A user-centered mobile application JF - Preventive Medicine Reports N2 - Parents are often uncertain about the vaccination status of their children. In times of vaccine hesitancy, vaccination programs could benefit from active patient participation. The Vaccination App (VAccApp) was developed by the Vienna Vaccine Safety Initiative, enabling parents to learn about the vaccination status of their children, including 25 different routine, special indication and travel vaccines listed in the WHO Immunization Certificate of Vaccination (WHO-ICV). Between 2012 and 2014, the VAccApp was validated in a hospital-based quality management program in Berlin, Germany, in collaboration with the Robert Koch Institute. Parents of 178 children were asked to transfer the immunization data of their children from the WHO-ICV into the VAccApp. The respective WHO-ICV was photocopied for independent, professional data entry (gold standard). Demonstrating the status quo in vaccine information reporting, a Recall Group of 278 parents underwent structured interviews for verbal immunization histories, without the respective WHO-ICV. Only 9% of the Recall Group were able to provide a complete vaccination status; on average 39% of the questions were answered correctly. Using the WHO-ICV with the help of the VAccApp resulted in 62% of parents providing a complete vaccination status; on average 95% of the questions were answered correctly. After using the VAccApp, parents were more likely to remember key aspects of the vaccination history. User-friendly mobile applications empower parents to take a closer look at the vaccination record, thereby taking an active role in providing accurate vaccination histories. Parents may become motivated to ask informed questions and to keep vaccinations up-to-date. Y1 - 2017 U6 - https://doi.org/10.1016/j.pmedr.2017.01.002 VL - 5 SP - 241 EP - 250 ER - TY - JOUR A1 - Borong, Shao A1 - Cannistraci, Carlo A1 - Conrad, Tim T1 - Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data JF - Genomics and Computational Biology N2 - Epithelial mesenchymal transition (EMT) process has been shown as highly relevant to cancer prognosis. However, although different biological network-based biomarker identification methods have been proposed to predict cancer prognosis, EMT network has not been directly used for this purpose. In this study, we constructed an EMT regulatory network consisting of 87 molecules and tried to select features that are useful for prognosis prediction in Lung Adenocarcinoma (LUAD). To incorporate multiple molecular profiles, we obtained four types of molecular data including mRNA-Seq, copy number alteration (CNA), DNA methylation, and miRNA-Seq data from The Cancer Genome Atlas. The data were mapped to the EMT network in three alternative ways: mRNA-Seq and miRNA-Seq, DNA methylation, and CNA and miRNA-Seq. Each mapping was employed to extract five different sets of features using discretization and network-based biomarker identification methods. Each feature set was then used to predict prognosis with SVM and logistic regression classifiers. We measured the prediction accuracy with AUC and AUPR values using 10 times 10-fold cross validation. For a more comprehensive evaluation, we also measured the prediction accuracies of clinical features, EMT plus clinical features, randomly picked 87 molecules from each data mapping, and using all molecules from each data type. Counter-intuitively, EMT features do not always outperform randomly selected features and the prediction accuracies of the five feature sets are mostly not significantly different. Clinical features are shown to give the highest prediction accuracies. In addition, the prediction accuracies of both EMT features and random features are comparable as using all features (more than 17,000) from each data type. Y1 - 2017 U6 - https://doi.org/http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e57 VL - 3 IS - 3 SP - 1 EP - 13 ER - TY - JOUR A1 - Zhang, Wei A1 - Klus, Stefan A1 - Conrad, Tim A1 - Schütte, Christof T1 - Learning chemical reaction networks from trajectory data JF - SIAM Journal on Applied Dynamical Systems (SIADS) N2 - We develop a data-driven method to learn chemical reaction networks from trajectory data. Modeling the reaction system as a continuous-time Markov chain and assuming the system is fully observed,our method learns the propensity functions of the system with predetermined basis functions by maximizing the likelihood function of the trajectory data under l^1 sparse regularization. We demonstrate our method with numerical examples using synthetic data and carry out an asymptotic analysis of the proposed learning procedure in the infinite-data limit. Y1 - 2019 U6 - https://doi.org/10.1137/19M1265880 VL - 18 IS - 4 SP - 2000 EP - 2046 ER - TY - JOUR A1 - Obermeier, Patrick A1 - Heim, A. A1 - Biere, Barbara A1 - Hage, E. A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Clinical characteristics and disease severity associated with adenovirus infections in infants and children - discovery of a novel adenovirus, HAdV-D80 JF - Clinical Infectious Diseases Y1 - 2018 ER - TY - JOUR A1 - Kork, F. A1 - Spies, Claudia A1 - Conrad, Tim A1 - Weiss, B. A1 - Roenneberg, T. A1 - Wernecke, K.-D. A1 - Balzer, Felix T1 - Associations of postoperative mortality with the time of day, week and year JF - Anaesthesia Y1 - 2018 ER - TY - JOUR A1 - Obermeier, Patrick E A1 - Heim, Albert A1 - Biere, Barbara A1 - Hage, Elias A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Schweiger, Brunhilde A1 - Rath, Barbara A T1 - Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations JF - iScience N2 - To improve the identification and management of viral respiratory infections, we established a clinical and virologic surveillance program for pediatric patients fulfilling pre-defined case criteria of influenza-like illness and viral respiratory infections. The program resulted in a cohort comprising 6,073 patients (56% male, median age 1.6 years, range 0–18.8 years), where every patient was assessed with a validated disease severity score at the point-of-care using the ViVI ScoreApp. We used machine learning and agnostic feature selection to identify characteristic clinical patterns. We tested all patients for human adenoviruses, 571 (9%) were positive. Adenovirus infections were particularly common and mild in children ≥1 month of age but rare and potentially severe in neonates: with lower airway involvement, disseminated disease, and a 50% mortality rate (n = 2/4). In one fatal case, we discovered a novel virus … Y1 - 2022 U6 - https://doi.org/10.1016/j.isci.2022.104276 VL - 25 IS - 5 PB - Cell Press ER - TY - JOUR A1 - Benner, Peter A1 - Burger, Michael A1 - Göddeke, Dominik A1 - Görgen, Christiane A1 - Himpe, Christian A1 - Heiland, Jan A1 - Koprucki, Thomas A1 - Ohlberger, Mario A1 - Rave, Stephan A1 - Reidelbach, Marco A1 - Saak, Jens A1 - Schöbel, Anita A1 - Tabelow, Karsten A1 - Weber, Marcus T1 - Die mathematische Forschungsdateninitiative in der NFDI: MaRDI (Mathematical Research Data Initiative) JF - GAMM Rundbrief Y1 - 2022 IS - 1 SP - 40 EP - 43 ER - TY - JOUR A1 - Cvetkovic, Nada A1 - Conrad, Tim A1 - Lie, Han Cheng T1 - A Convergent Discretisation Method for Transition Path Theory for Diffusion Processes JF - Multiscale Modeling & Simulation Y1 - 2021 U6 - https://doi.org/10.1137/20M1329354 VL - 19 IS - 1 SP - 242 EP - 266 PB - Society for Industrial and Applied Mathematics ER - TY - JOUR A1 - Klenert, Nicolas A1 - Lepper, Verena A1 - Baum, Daniel T1 - A Local Iterative Approach for the Extraction of 2D Manifolds from Strongly Curved and Folded Thin-Layer Structures JF - IEEE Transactions on Visualization and Computer Graphics N2 - Ridge surfaces represent important features for the analysis of 3-dimensional (3D) datasets in diverse applications and are often derived from varying underlying data including flow fields, geological fault data, and point data, but they can also be present in the original scalar images acquired using a plethora of imaging techniques. Our work is motivated by the analysis of image data acquired using micro-computed tomography (μCT) of ancient, rolled and folded thin-layer structures such as papyrus, parchment, and paper as well as silver and lead sheets. From these documents we know that they are 2-dimensional (2D) in nature. Hence, we are particularly interested in reconstructing 2D manifolds that approximate the document’s structure. The image data from which we want to reconstruct the 2D manifolds are often very noisy and represent folded, densely-layered structures with many artifacts, such as ruptures or layer splitting and merging. Previous ridge-surface extraction methods fail to extract the desired 2D manifold for such challenging data. We have therefore developed a novel method to extract 2D manifolds. The proposed method uses a local fast marching scheme in combination with a separation of the region covered by fast marching into two sub-regions. The 2D manifold of interest is then extracted as the surface separating the two sub-regions. The local scheme can be applied for both automatic propagation as well as interactive analysis. We demonstrate the applicability and robustness of our method on both artificial data as well as real-world data including folded silver and papyrus sheets. Y1 - 2023 U6 - https://doi.org/10.1109/TVCG.2023.3327403 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Heitzig, Jobst A1 - Koltai, Péter A1 - Kurths, Jürgen A1 - Schütte, Christof T1 - Statistical analysis of tipping pathways in agent-based models JF - Eur. Phys. J. Spec. Top. N2 - Agent-based models are a natural choice for modeling complex social systems. In such models simple stochastic interaction rules for a large population of individuals on the microscopic scale can lead to emergent dynamics on the macroscopic scale, for instance a sudden shift of majority opinion or behavior. Here we are introducing a methodology for studying noise-induced tipping between relevant subsets of the agent state space representing characteristic configurations. Due to a large number of interacting individuals, agent-based models are high-dimensional, though usually a lower-dimensional structure of the emerging collective behaviour exists. We therefore apply Diffusion Maps, a non-linear dimension reduction technique, to reveal the intrinsic low-dimensional structure. We characterize the tipping behaviour by means of Transition Path Theory, which helps gaining a statistical understanding of the tipping paths such as their distribution, flux and rate. By systematically studying two agent-based models that exhibit a multitude of tipping pathways and cascading effects, we illustrate the practicability of our approach. Y1 - 2021 U6 - https://doi.org/10.1140/epjs/s11734-021-00191-0 VL - 230 SP - 3249 EP - 3271 ER - TY - JOUR A1 - Horenko, Illia A1 - Lorenz, S. A1 - Schütte, Christof A1 - Huisinga, Wilhelm T1 - Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics JF - J. Comp. Chem. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/49/ U6 - https://doi.org/10.1002/jcc.20234 VL - 26 IS - 9 SP - 941 EP - 948 ER - TY - JOUR A1 - Meerbach, E. A1 - Schütte, Christof A1 - Fischer, Alexander T1 - Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains JF - Lin. Alg. Appl. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/54/ U6 - https://doi.org/10.1016/j.laa.2004.10.018 VL - 398 SP - 141 EP - 160 ER - TY - JOUR A1 - Antony, Jens A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes JF - J. Chem. Phys. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/57/ U6 - https://doi.org/10.1063/1.1829057 VL - 122 IS - 1 SP - 014309 ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Schütte, Christof T1 - Reduced Stochastic Models for Complex Molecular Systems JF - Comp. Vis. Sci. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/59/ U6 - https://doi.org/10.1007/s00791-006-0021-1 VL - 9 IS - 2 SP - 89 EP - 102 ER - TY - JOUR A1 - Dellnitz, M. A1 - Neumann, M. A1 - Schütte, Christof T1 - Special Issue on Matrices and Mathematical Biology JF - Lin. Alg. Appl. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/60/ U6 - https://doi.org/10.1016/j.laa.2004.12.006 VL - 398 SP - 1 EP - 245 ER - TY - JOUR A1 - Conrad, Tim A1 - Leichtle, Alexander Benedikt A1 - Hagehülsmann, Andre A1 - Diederichs, Elmar A1 - Baumann, Sven A1 - Thiery, Joachim A1 - Schütte, Christof T1 - Beating the Noise JF - Lecture Notes in Computer Science Y1 - 2006 UR - http://publications.imp.fu-berlin.de/5/ VL - 4216 SP - 119 EP - 128 PB - Springer ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Automated Model Reduction for Complex Systems exhibiting Metastability JF - Mult. Mod. Sim. Y1 - 2006 UR - http://publications.imp.fu-berlin.de/44/ U6 - https://doi.org/10.1137/050623310 VL - 5 IS - 3 SP - 802 EP - 827 ER - TY - JOUR A1 - Metzner, Ph. A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Illustration of Transition Path Theory on a Collection of Simple Examples JF - J. Chem. Phys. Y1 - 2006 UR - http://publications.imp.fu-berlin.de/45/ U6 - https://doi.org/10.1063/1.2335447 VL - 125 IS - 8 SP - 084110 ER - TY - JOUR A1 - Quer, Jannes A1 - Ribera Borrell, Enric T1 - Connecting Stochastic Optimal Control and Reinforcement Learning JF - Journal of Mathematical Physics N2 - In this article we study the connection of stochastic optimal control and reinforcement learning. Our main motivation is an importance sampling application to rare events sampling which can be reformulated as an optimal control problem. By using a parameterized approach the optimal control problem turns into a stochastic optimization problem which still presents some open questions regarding how to tackle the scalability to high-dimensional problems and how to deal with the intrinsic metastability of the system. With the aim to explore new methods we connect the optimal control problem to reinforcement learning since both share the same underlying framework namely a Markov decision process (MDP). We show how the MDP can be formulated for the optimal control problem. Furthermore, we discuss how the stochastic optimal control problem can be interpreted in a reinforcement learning framework. At the end of the article we present the application of two different reinforcement learning algorithms to the optimal control problem and compare the advantages and disadvantages of the two algorithms. Y1 - 2023 ER - TY - JOUR A1 - Ranneberg, Maximilian A1 - Weiser, Martin A1 - Weihrauch, Mirko A1 - Budach, Volker A1 - Gellermann, Johanna A1 - Wust, Peter T1 - Regularized Antenna Profile Adaptation in Online Hyperthermia Treatment JF - Medical Physics Y1 - 2010 U6 - https://doi.org/10.1118/1.3488896 VL - 37 SP - 5382 EP - 5394 ER - TY - JOUR A1 - Rath, Barbara A1 - Yousef, Kaveh A1 - Katzenstein, D. A1 - Shafer, R. A1 - Schütte, Christof A1 - von Kleist, Max A1 - Merigan, T. T1 - HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitor Induced Selective Pressure in vitro JF - PLoS ONE Y1 - 2013 UR - http://publications.imp.fu-berlin.de/1178/ U6 - https://doi.org/10.1371/journal.pone.0061102 VL - 8 IS - 4 PB - Public Library of Science ER - TY - JOUR A1 - Aiche, Stephan A1 - Reinert, Knut A1 - Schütte, Christof A1 - Hildebrand, Diana A1 - Schlüter, Hartmut A1 - Conrad, Tim T1 - Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs JF - PLoS ONE Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1143/ U6 - https://doi.org/10.1371/journal.pone.0040656 VL - 7 IS - 7 SP - e40656 PB - Public Library of Science ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. JF - J. Chem. Theo. Comp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1182/ U6 - https://doi.org/10.1021/ct3003354 VL - 8 IS - 8 SP - 2878 EP - 2887 ER - TY - JOUR A1 - Weiss, Maximilian A1 - Paulus, Florian A1 - Steinhilber, D. A1 - Nikitin, Anatoly A1 - Haag, Rainer A1 - Schütte, Christof T1 - Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures JF - MACROMOLECULAR THEORY and SIMULATIONS Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1142/ U6 - https://doi.org/10.1002/mats.201200003 VL - 21 IS - 7 SP - 470 EP - 481 ER - TY - JOUR A1 - Menz, Stephan A1 - Latorre, J. A1 - Schütte, Christof A1 - Huisinga, Wilhelm T1 - Hybrid Stochastic--Deterministic Solution of the Chemical Master Equation JF - SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS) Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1039/ U6 - https://doi.org/10.1137/110825716 VL - 10 IS - 4 SP - 1232 EP - 1262 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Zhang, P. T1 - Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems JF - Phys. Rev. E Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1125/ U6 - https://doi.org/10.1103/PhysRevE.86.026704 VL - 86 IS - 02 SP - 026704 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Sarich, Marco A1 - Schütte, Christof T1 - Estimating the eigenvalue error of Markov State Models JF - Multiscale Modeling & Simulation Y1 - 2012 UR - http://publications.imp.fu-berlin.de/914/ U6 - https://doi.org/10.1137/100798910 VL - 10 IS - 1 SP - 61 EP - 81 ER - TY - JOUR A1 - Rehfeldt, Daniel A1 - Koch, Thorsten A1 - Shinano, Yuji T1 - Faster exact solution of sparse MaxCut and QUBO problems JF - Mathematical Programming Computation N2 - The maximum-cut problem is one of the fundamental problems in combinatorial optimization. With the advent of quantum computers, both the maximum-cut and the equivalent quadratic unconstrained binary optimization problem have experienced much interest in recent years. This article aims to advance the state of the art in the exact solution of both problems—by using mathematical programming techniques. The main focus lies on sparse problem instances, although also dense ones can be solved. We enhance several algorithmic components such as reduction techniques and cutting-plane separation algorithms, and combine them in an exact branch-and-cut solver. Furthermore, we provide a parallel implementation. The new solver is shown to significantly outperform existing state-of-the-art software for sparse maximum-cut and quadratic unconstrained binary optimization instances. Furthermore, we improve the best known bounds for several instances from the 7th DIMACS Challenge and the QPLIB, and solve some of them (for the first time) to optimality. Y1 - 2023 U6 - https://doi.org/10.1007/s12532-023-00236-6 VL - 15 SP - 445 EP - 470 ER - TY - JOUR A1 - Duwal, Sulav A1 - Schütte, Christof A1 - von Kleist, Max T1 - Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. JF - PLoS One Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1130/ U6 - https://doi.org/10.1371/journal.pone.0040382 VL - 7 IS - 7 SP - e40382 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Bruckner, Stefanie A1 - Conrad, Tim A1 - Schütte, Christof T1 - Random Walks on Complex Modular Networks JF - Journal of Numerical Analysis, Industrial and Applied Mathematics Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1090/ VL - 6 IS - 1-2 SP - 29 EP - 50 PB - European Society of Computational Methods in Sciences and Engineering ER - TY - JOUR A1 - Wang, Han A1 - Zhang, P. A1 - Schütte, Christof T1 - On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems JF - J. Chem. Theo. Comp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1181/ U6 - https://doi.org/10.1021/ct300343y VL - 8 IS - 9 SP - 3243 EP - 3256 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - A pH-dependent coarse-grained model of peptides JF - Soft Matter Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1192/ U6 - https://doi.org/10.1039/C3SM27893J VL - 9 IS - 26 SP - 6118 EP - 6127 ER - TY - JOUR A1 - Marsalek, Ondrej A1 - Frigato, Tomaso A1 - VandeVondele, Joost A1 - Bradforth, Stephen E. A1 - Schmidt, Burkhard A1 - Schütte, Christof A1 - Jungwirth, Pavel T1 - Hydrogen Forms in Water by Proton Transfer to a Distorted Electron JF - J. Phys. Chem. B Y1 - 2010 UR - http://publications.imp.fu-berlin.de/818/ U6 - https://doi.org/10.1021/jp908986z VL - 114 IS - 2 SP - 915 EP - 920 ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. JF - preprint Y1 - 1992 UR - http://publications.imp.fu-berlin.de/109/ ER - TY - JOUR A1 - Fiedler, Georg Martin A1 - Leichtle, Alexander Benedikt A1 - Kase, Julia A1 - Baumann, Sven A1 - Ceglarek, Uta A1 - Felix, Klaus A1 - Conrad, Tim A1 - Witzigmann, Helmut A1 - Weimann, Arved A1 - Schütte, Christof A1 - Hauss, Johann A1 - Büchler, Markus A1 - Thiery, Joachim T1 - Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer JF - Clinical Cancer Research Y1 - 2009 UR - http://publications.imp.fu-berlin.de/155/ U6 - https://doi.org/10.1158/1078-0432.CCR-08-2701 VL - 15 IS - 11 SP - 3812 EP - 3819 PB - American Association for Cancer Research, ER - TY - JOUR A1 - Noé, Frank A1 - Schütte, Christof A1 - Vanden-Eijnden, E. A1 - Reich, L. A1 - Weikl, T. T1 - Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations JF - Proc. Natl. Acad. Sci. USA Y1 - 2009 UR - http://publications.imp.fu-berlin.de/826/ U6 - https://doi.org/10.1073/pnas.0905466106 VL - 106 IS - 45 SP - 19011 EP - 19016 ER - TY - JOUR A1 - Frigato, Tomaso A1 - VandeVondele, Joost A1 - Schmidt, Burkhard A1 - Schütte, Christof A1 - Jungwirth, Pavel T1 - Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion JF - J. Phys. Chem. A Y1 - 2008 UR - http://publications.imp.fu-berlin.de/13/ U6 - https://doi.org/10.1021/jp711545s VL - 112 IS - 27 SP - 6125 EP - 6133 ER - TY - JOUR A1 - Horenko, Illia A1 - Klein, Rupert A1 - Dolaptchiev, S. A1 - Schütte, Christof T1 - Automated Generation of Reduced Stochastic Weather Models I JF - Mult. Mod. Sim. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/15/ U6 - https://doi.org/10.1137/060670535 VL - 6 IS - 4 SP - 1125 EP - 1145 ER - TY - JOUR A1 - Hennings, Felix A1 - Petkovic, Milena A1 - Streubel, Tom T1 - On the Numerical Treatment of Interlaced Target Values - Modeling, Optimization and Simulation of Regulating Valves in Gas Networks JF - Optimization and Engineering N2 - Due to the current and foreseeable shifts towards carbon dioxide neutral energy production, which will likely result in balancing fluctuating renewable energy generation by transforming power-to-gas-to-power as well as building a large-scale hydrogen transport infrastructure, the trading and transport operations of gas will become more dynamic, volatile, and hence also less predictable. Therefore, computer-aided support in terms of rapid simulation and control optimization will further broaden its importance for gas network dispatching. In this paper, we aim to contribute and openly publish two new mathematical models for regulators, also referred to as control valves, which together with compressors make up the most complex and involved types of active elements in gas network infrastructures. They provide direct control over gas networks but are in turn controlled via target values, also known as set-point values, themselves. Our models incorporate up to six dynamical target values to define desired transient states for the elements' local vicinity within the network. That is, each pair of every two target values defines a bounding box for the inlet pressure, outlet pressure as well as the passing mass flow of gas. In the proposed models, those target values are prioritized differently and are constantly in competition with each other, which can only be resolved dynamically at run-time of either a simulation or optimization process. Besides careful derivation, we compare simulation and optimization results with predictions of the widely adopted commercial simulation tool SIMONE, serving as our substitute for actual real-world transport operations. Y1 - 2023 U6 - https://doi.org/10.1007/s11081-023-09812-0 PB - Springer Nature ER - TY - JOUR A1 - Fogalli, Giovani Bressan A1 - Peres Line, Sérgio Roberto A1 - Baum, Daniel T1 - Segmentation of tooth enamel microstructure images using classical image processing and U-Net approaches JF - Frontiers in Imaging N2 - Tooth enamel is the hardest tissue in human organism, formed by prism layers in regularly alternating directions. These prisms form the Hunter-Schreger Bands (HSB) pattern when under side illumination, which is composed of light and dark stripes resembling fingerprints. We have shown in previous works that HSB pattern is highly variable, seems to be unique for each tooth and can be used as a biometric method for human identification. Since this pattern cannot be acquired with sensors, the HSB region in the digital photograph must be identified and correctly segmented from the rest of the tooth and background. Although these areas can be manually removed, this process is not reliable as excluded areas can vary according to the individual‘s subjective impression. Therefore, the aim of this work was to develop an algorithm that automatically selects the region of interest (ROI), thus, making the entire biometric process straightforward. We used two different approaches: a classical image processing method which we called anisotropy-based segmentation (ABS) and a machine learning method known as U-Net, a fully convolutional neural network. Both approaches were applied to a set of extracted tooth images. U-Net with some post processing outperformed ABS in the segmentation task with an Intersection Over Union (IOU) of 0.837 against 0.766. Even with a small dataset, U-Net proved to be a potential candidate for fully automated in-mouth application. However, the ABS technique has several parameters which allow a more flexible segmentation with interactive adjustments specific to image properties. Y1 - 2023 U6 - https://doi.org/10.3389/fimag.2023.1215764 VL - 2 ER - TY - JOUR A1 - Sechi, Renata A1 - Weber, Marcus A1 - Heyne, Karsten T1 - MSM building and projection for the analysis of time-resolved spectra JF - Proceedings in Applied Mathematics and Mechanics N2 - Understanding the kinetics between the components of time-resolved spectra is a crucial step in the study of photo-activatedprocesses. However, modeling the kinetics requires usually some a priori knowledge about the system. In our approach, webuild a Markov State Model (MSM) from the spectral data, and obtain a Koopman transition matrix K(t). With genPCCA,an invariant subspace projection, we project the process into its metastable components. The result of the application of gen-PCCA is a transition matrix Kc(t), from which we can read the transition probability between the metastable components of the reaction. We discuss the application of this analysis method to the transient absorption spectrum of brominated Al-corrole Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?https://onlinelibrary.wiley.com/doi/10.1002/pamm.202100102 IS - 21 SP - e202100102 ER - TY - JOUR A1 - Sechi, Renata A1 - Sikorski, Alexander A1 - Weber, Marcus T1 - Estimation of the Koopman Generator by Newton's Extrapolation JF - Multiscale Modeling and Simulation N2 - This article addresses the problem of estimating the Koopman generator of a Markov process. The direct computation of the infinitesimal generator is not easy because of the discretization of the state space, in particular because of the trade-off inherent in the choice of the best lag time to study the process. Short lag times implies a strong discretization of the state space and a consequent loss of Markovianity. Large lag times bypass events on fast timescales. We propose a method to approximate the generator with the computation of the Newton polynomial extrapolation. This technique is a multistep approach which uses as its input Koopman transfer operators evaluated for a series of lag times. Thus, the estimated infinitesimal generator combines information from different time resolutions and does not bias only fast- or slow-decaying dynamics. We show that the multi-scale Newton method can improve the estimation of the generator in comparison to the computation using finite difference or matrix logarithm methods. Y1 - 2020 U6 - https://doi.org/10.1137/20M1333006 VL - 19 IS - 2 SP - 758 EP - 774 PB - SIAM ER - TY - JOUR A1 - Gräfe, Ch. A1 - Nordmeier, V. A1 - Schütte, Christof T1 - Computerspiel zum Thema Moleküldynamik für Schüler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels JF - Jahrestagung 2008 der GDCP (Gesellschaft für Didaktik der Chemie und Physik) Y1 - 2009 UR - http://publications.imp.fu-berlin.de/163/ VL - 1 SP - 77 EP - 79 PB - LIT VERLAG Dr. W. Hopf ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - A Hybrid Galerkin-Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics JF - Macromol. React. Eng. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/956/ U6 - https://doi.org/10.1002/mren.200900073 VL - 4 IS - 9-10 SP - 562 EP - 577 ER - TY - JOUR A1 - Schütte, Christof A1 - Jahnke, Tobias T1 - Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation JF - Mathematical Modelling and Numerical Analysis (ESAIM) Y1 - 2009 UR - http://publications.imp.fu-berlin.de/26/ U6 - https://doi.org/10.1051/m2an/2009027 VL - 43 IS - 4 SP - 721 EP - 742 PB - EDP Sciences ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - On metastable conformational analysis of non-equilibrium biomolecular time series JF - Multiscale Modeling & Simulation Y1 - 2010 UR - http://publications.imp.fu-berlin.de/146/ U6 - https://doi.org/10.1137/080744347 VL - 8 IS - 2 SP - 701 EP - 716 ER - TY - JOUR A1 - Metzner, Ph. A1 - Noé, Frank A1 - Schütte, Christof T1 - Estimating the Sampling Error JF - Phys. Rev. E Y1 - 2009 UR - http://publications.imp.fu-berlin.de/17/ U6 - https://doi.org/10.1103/PhysRevE.80.021106 VL - 80 IS - 2 SP - 021106 PB - American Physical Society ER - TY - JOUR A1 - Sarich, Marco A1 - Noé, Frank A1 - Schütte, Christof T1 - On the Approximation Quality of Markov State Models JF - Multiscale Model. Simul. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/771/ U6 - https://doi.org/10.1137/090764049 VL - 8 IS - 4 SP - 1154 EP - 1177 ER - TY - JOUR A1 - Arndt, Thomas A1 - Boltze, Julia A1 - Hoffmann, Katrin A1 - Kaden, Ben A1 - Seeliger, Frank T1 - Open Access in Berlin und Brandenburg – Klappe, die zweite JF - b.i.t.online Y1 - 2023 UR - https://www.b-i-t-online.de/heft/2023-01-reportage-arndt.pdf VL - 26 IS - 1 SP - 58 EP - 64 ER - TY - JOUR A1 - Plock, Matthias A1 - Hammerschmidt, Martin A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Schütte, Christof T1 - Impact Study of Numerical Discretization Accuracy on Parameter Reconstructions and Model Parameter Distributions JF - Metrologia N2 - In optical nano metrology numerical models are used widely for parameter reconstructions. Using the Bayesian target vector optimization method we fit a finite element numerical model to a Grazing Incidence x-ray fluorescence data set in order to obtain the geometrical parameters of a nano structured line grating. Gaussian process, stochastic machine learning surrogate models, were trained during the reconstruction and afterwards sampled with a Markov chain Monte Carlo sampler to determine the distribution of the reconstructed model parameters. The numerical discretization parameters of the used finite element model impact the numerical discretization error of the forward model. We investigated the impact of the polynomial order of the finite element ansatz functions on the reconstructed parameters as well as on the model parameter distributions. We showed that such a convergence study allows to determine numerical parameters which allows for efficient and accurate reconstruction results. Y1 - 2023 U6 - https://doi.org/10.1088/1681-7575/ace4cd VL - 60 SP - 054001 ER - TY - JOUR A1 - Faenza, Yuri A1 - Muñoz, Gonzalo A1 - Pokutta, Sebastian T1 - New Limits of Treewidth-based tractability in Optimization JF - Mathematical Programming Y1 - 2020 U6 - https://doi.org/10.1007/s10107-020-01563-5 N1 - URL of the PDF: http://link.springer.com/article/10.1007/s10107-020-01563-5 N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2018/09/22/treewidth-abstract.html VL - 191 SP - 559 EP - 594 ER - TY - JOUR A1 - Schneck, Jakob A1 - Weiser, Martin A1 - Wende, Florian T1 - Impact of mixed precision and storage layout on additive Schwarz smoothers JF - Numerical Linear Algebra with Applications N2 - The growing discrepancy between CPU computing power and memory bandwidth drives more and more numerical algorithms into a bandwidth-bound regime. One example is the overlapping Schwarz smoother, a highly effective building block for iterative multigrid solution of elliptic equations with higher order finite elements. Two options of reducing the required memory bandwidth are sparsity exploiting storage layouts and representing matrix entries with reduced precision in floating point or fixed point format. We investigate the impact of several options on storage demand and contraction rate, both analytically in the context of subspace correction methods and numerically at an example of solid mechanics. Both perspectives agree on the favourite scheme: fixed point representation of Cholesky factors in nested dissection storage. Y1 - 2021 U6 - https://doi.org/10.1002/nla.2366 VL - 28 IS - 4 ER - TY - JOUR A1 - Juds, Carmen A1 - Schmidt, Johannes A1 - Weller, Michael A1 - Lange, Thorid A1 - Conrad, Tim A1 - Boerner, Hans T1 - Combining Phage Display and Next-generation Sequencing for Materials Sciences: A Case Study on Probing Polypropylene Surfaces JF - Journal of the American Chemical Society N2 - Phage display biopanning with Illumina next-generation sequencing (NGS) is applied to reveal insights into peptide-based adhesion domains for polypropylene (PP). One biopanning round followed by NGS selects robust PP-binding peptides that are not evident by Sanger sequencing. NGS provides a significant statistical base that enables motif analysis, statistics on positional residue depletion/enrichment, and data analysis to suppress false-positive sequences from amplification bias. The selected sequences are employed as water-based primers for PP?metal adhesion to condition PP surfaces and increase adhesive strength by 100\% relative to nonprimed PP. Y1 - 2020 U6 - https://doi.org/10.1021/jacs.0c03482 VL - 142 IS - 24 SP - 10624 EP - 10628 ER - TY - JOUR A1 - Kerdreux, Thomas A1 - Roux, Christophe A1 - d'Aspremont, Alexandre A1 - Pokutta, Sebastian T1 - Linear Bandits on Uniformly Convex Sets JF - Journal of Machine Learning Research N2 - Linear bandit algorithms yield O~(n√T) pseudo-regret bounds on compact convex action sets K⊂Rn and two types of structural assumptions lead to better pseudo-regret bounds. When K is the simplex or an ℓp ball with p∈]1,2], there exist bandits algorithms with O~(√n√T) pseudo-regret bounds. Here, we derive bandit algorithms for some strongly convex sets beyond ℓp balls that enjoy pseudo-regret bounds of O~(√n√T), which answers an open question from [BCB12, §5.5.]. Interestingly, when the action set is uniformly convex but not necessarily strongly convex, we obtain pseudo-regret bounds with a dimension dependency smaller than O(√n). However, this comes at the expense of asymptotic rates in T varying between O(√T) and O(T). Y1 - 2021 UR - https://www.jmlr.org/papers/v22/21-0277.html VL - 22 IS - 284 SP - 1 EP - 23 ER - TY - JOUR A1 - Schiela, Anton A1 - Stöcklein, Matthias A1 - Weiser, Martin T1 - A primal dual projection algorithm for efficient constraint preconditioning JF - SIAM Journal on Scientific Computing N2 - We consider a linear iterative solver for large scale linearly constrained quadratic minimization problems that arise, for example, in optimization with PDEs. By a primal-dual projection (PDP) iteration, which can be interpreted and analysed as a gradient method on a quotient space, the given problem can be solved by computing sulutions for a sequence of constrained surrogate problems, projections onto the feasible subspaces, and Lagrange multiplier updates. As a major application we consider a class of optimization problems with PDEs, where PDP can be applied together with a projected cg method using a block triangular constraint preconditioner. Numerical experiments show reliable and competitive performance for an optimal control problem in elasticity. Y1 - 2021 U6 - https://doi.org/10.1137/20M1380739 VL - 43 IS - 6 SP - A4095 EP - A4120 ER - TY - JOUR A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Ma, Xiaolin A1 - Broberg, Eeva K. A1 - Penttinen, P. A1 - Reiche, J. A1 - Biere, Barbara A1 - Schweiger, Brunhilde A1 - Rath, Barbara A1 - Hoppe, Christian T1 - Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care JF - Clinical Microbiology and Infection Y1 - 2019 U6 - https://doi.org/10.1016/j.cmi.2018.05.023 SN - 1469-0691 VL - 25 IS - 3 SP - 380.e9 EP - 380.e16 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Fuerstenau, Daniel A1 - Grabundzija, Ana A1 - Helfmann, Luzie A1 - Park, Martin A1 - Schier, Wolfram A1 - Schütt, Brigitta A1 - Schütte, Christof A1 - Weber, Marcus A1 - Wulkow, Niklas A1 - Zonker, Johannes T1 - Mathematical modeling of the spreading of innovations in the ancient world JF - eTopoi. Journal for Ancient Studies Y1 - 2018 U6 - https://doi.org/10.17171/4-7-1 SN - ISSN 2192-2608 VL - 7 ER - TY - JOUR A1 - Frank, M. A1 - von Kleist, Max A1 - Kunz, A. A1 - Harms, G. A1 - Schütte, Christof A1 - Kloft, Ch. T1 - Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1 JF - Antimicrob. Agents Chemother. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1093/ VL - 55 IS - 12 SP - 5529 EP - 5540 ER - TY - JOUR A1 - von Kleist, Max A1 - Menz, Stephan A1 - Stocker, Hartmut A1 - Arasteh, Keikawus A1 - Huisinga, Wilhelm A1 - Schütte, Christof T1 - HIV Quasispecies Dynamics during Pro-active Treatment Switching JF - Plos One Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1051/ U6 - https://doi.org/10.1371/journal.pone.0018204 VL - 6 IS - 3 SP - e18204 PB - Public Library of Science ER - TY - JOUR A1 - Prinz, J.-H. A1 - Wu, Hao A1 - Sarich, Marco A1 - Keller, B. A1 - Fischbach, M. A1 - Held, M. A1 - Chodera, J. A1 - Schütte, Christof A1 - Noé, Frank T1 - Markov models of molecular kinetics JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/944/ U6 - https://doi.org/10.1063/1.3565032 VL - 134 SP - 174105 ER - TY - JOUR A1 - Schütte, Christof A1 - Noé, Frank A1 - Lu, Jianfeng A1 - Sarich, Marco A1 - Vanden-Eijnden, E. T1 - Markov State Models Based on Milestoning JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1022/ U6 - https://doi.org/10.1063/1.3590108 VL - 134 IS - 20 SP - 204105 ER - TY - JOUR A1 - von Kleist, Max A1 - Metzner, Ph. A1 - Marquet, R. A1 - Schütte, Christof T1 - Polymerase Inhibition by Nucleoside Analogs JF - Plos Computational Biology Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1087/ U6 - https://doi.org/10.1371/journal.pcbi.1002359 VL - 8 IS - 1 SP - e1002359 ER - TY - JOUR A1 - Metzner, Ph. A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Transition Path Theory for Markov Jump Processes JF - Mult. Mod. Sim. Y1 - 2009 UR - http://publications.imp.fu-berlin.de/43/ U6 - https://doi.org/10.1137/070699500 VL - 7 IS - 3 SP - 1192 EP - 1219 ER - TY - JOUR A1 - Meerbach, E. A1 - Latorre, J. A1 - Schütte, Christof T1 - Sequential Change Point Detection in Molecular Dynamics Trajectories JF - Multicale Model. Sim. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1123/ U6 - https://doi.org/10.1137/110850621 VL - 10 IS - 4 SP - 1263 EP - 1291 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation JF - Communications in Mathematical Sciences Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1176/ VL - 12 IS - 859 ER - TY - JOUR A1 - Nettesheim, Peter A1 - Bornemann, Folkmar A. A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics JF - Chem. Phys. Lett. Y1 - 1996 UR - http://publications.imp.fu-berlin.de/101/ U6 - https://doi.org/10.1016/0009-2614(96)00471-X VL - 256 IS - 6 SP - 581 EP - 588 ER - TY - JOUR A1 - Manz, Jörn A1 - Paramonov, G. A1 - Polasek, M. A1 - Schütte, Christof T1 - Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D JF - Isr. J. Chem. Y1 - 1994 UR - http://publications.imp.fu-berlin.de/107/ VL - 34 IS - 1 SP - 115 EP - 125 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Nettesheim, Peter A1 - Schütte, Christof T1 - Quantum-classical molecular dynamics as an approximation to full quantum dynamics JF - J. Chem. Phys. Y1 - 1996 UR - http://publications.imp.fu-berlin.de/103/ U6 - https://doi.org/10.1063/1.471952 VL - 105 IS - 3 SP - 1074 EP - 1083 ER - TY - JOUR A1 - Schütte, Christof T1 - A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation JF - Impact of Computing in Sci. Eng. Y1 - 1993 UR - http://publications.imp.fu-berlin.de/108/ U6 - https://doi.org/10.1006/icse.1993.1008 VL - 5 IS - 3 SP - 176 EP - 200 ER - TY - JOUR A1 - Nettesheim, Peter A1 - Huisinga, Wilhelm A1 - Schütte, Christof T1 - Chebyshev-Approximation for Wavepacket-Dynamics JF - preprint Y1 - 1996 UR - http://publications.imp.fu-berlin.de/102/ ER - TY - JOUR A1 - Schütte, Christof A1 - Zumbusch, Gerhard A1 - Brinkmann, Ralf T1 - Dynamics of Erbium-doped Waveguide Lasers JF - preprint Y1 - 1995 UR - http://publications.imp.fu-berlin.de/104/ ER - TY - JOUR A1 - Schütte, Christof A1 - Dinand, Manfred T1 - Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers JF - J. Lightw. Techn. Y1 - 1995 UR - http://publications.imp.fu-berlin.de/106/ VL - 13 IS - 1 SP - 14 EP - 23 ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble JF - J. Comp. Chem. Y1 - 1998 UR - http://publications.imp.fu-berlin.de/97/ U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - On the Singular Limit of the Quantum-Classical Molecular Dynamics Model JF - J. Appl. Math. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/94/ U6 - https://doi.org/10.1137/S0036139997318834 VL - 59 IS - 4 SP - 1208 EP - 1224 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - A mathematical investigation of the Car-Parrinello Method JF - Num. Math. Y1 - 1998 UR - http://publications.imp.fu-berlin.de/96/ U6 - https://doi.org/10.1007/s002110050316 VL - 78 IS - 3 SP - 359 EP - 376 ER - TY - JOUR A1 - Schütte, Christof A1 - Bornemann, Folkmar A. T1 - Homogenization Approach to Smoothed Molecular Dynamics JF - Nonlinear Analysis Y1 - 1997 UR - http://publications.imp.fu-berlin.de/99/ U6 - https://doi.org/10.1016/S0362-546X(97)00216-2 VL - 30 IS - 3 SP - 1805 EP - 1814 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - Homogenization of Hamiltonian Systems with a Strong Constraining Potential JF - Physica D Y1 - 1997 UR - http://publications.imp.fu-berlin.de/100/ U6 - https://doi.org/10.1016/S0167-2789(96)00245-X VL - 102 IS - 1-2 SP - 57 EP - 77 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/92/ U6 - https://doi.org/10.1002/(SICI)1096-987X(199912)20:16<1760::AID-JCC8>3.0.CO;2-2 VL - 20 IS - 16 SP - 1760 EP - 1774 ER - TY - JOUR A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo JF - J. Comp. Phys Y1 - 1999 UR - http://publications.imp.fu-berlin.de/87/ U6 - https://doi.org/10.1006/jcph.1999.6231 VL - 151 IS - 1 SP - 146 EP - 168 ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with adaptive temperature choice JF - Comp. Phys. Comm. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/93/ U6 - https://doi.org/10.1016/S0010-4655(99)00274-X VL - 121 SP - 37 EP - 39 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - Adaptive Accuracy Control for Car-Parrinello Simulations JF - Num. Math. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/88/ U6 - https://doi.org/10.1007/s002110050445 VL - 83 IS - 2 SP - 179 EP - 186 ER - TY - JOUR A1 - Schütte, Christof T1 - Conformational Dynamics JF - preprint Y1 - 1999 UR - http://publications.imp.fu-berlin.de/89/ ER - TY - JOUR A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains JF - Lin. Alg. Appl. Y1 - 2000 UR - http://publications.imp.fu-berlin.de/84/ U6 - https://doi.org/10.1016/S0024-3795(00)00095-1 VL - 315 IS - 1-3 SP - 39 EP - 59 ER - TY - JOUR A1 - Horenko, Illia A1 - Salzmann, Ch. A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Quantum-Classical Liouville Approach to Molecular Dynamics JF - J. Chem. Phys. Y1 - 2002 UR - http://publications.imp.fu-berlin.de/75/ U6 - https://doi.org/10.1063/1.1522712 VL - 117 IS - 24 SP - 11075 EP - 11088 ER - TY - JOUR A1 - Horenko, Illia A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions JF - J. Chem. Phys. Y1 - 2002 UR - http://publications.imp.fu-berlin.de/73/ U6 - https://doi.org/10.1063/1.1498467 VL - 117 IS - 10 SP - 4643 EP - 4650 ER - TY - JOUR A1 - Horenko, Illia A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - A Theoretical Model for Molecules Interacting with Intense Laser Pulses JF - J. Chem. Phys. Y1 - 2001 UR - http://publications.imp.fu-berlin.de/79/ U6 - https://doi.org/10.1063/1.1398577 VL - 115 IS - 13 SP - 5733 EP - 5743 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Schütte, Christof A1 - Stuart, Andrew T1 - Extracting Macroscopic Stochastic Dynamics JF - Comm. Pure Appl. Math. Y1 - 2003 UR - http://publications.imp.fu-berlin.de/72/ U6 - https://doi.org/10.1002/cpa.10057 VL - 56 IS - 2 SP - 234 EP - 269 ER - TY - JOUR A1 - Horenko, Illia A1 - Weiser, Martin A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Fully Adaptive Propagation of the Quantum-Classical Liouville Equation JF - J. Chem. Phys. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/65/ U6 - https://doi.org/10.1063/1.1691015 VL - 120 IS - 19 SP - 8913 EP - 8923 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Meyn, S. A1 - Schütte, Christof T1 - Phase Transitions and Metastability in Markovian and Molecular Systems JF - Ann. Appl. Prob. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/67/ U6 - https://doi.org/10.1214/aoap/1075828057 VL - 14 IS - 1 SP - 419 EP - 458 ER - TY - JOUR A1 - Preis, R. A1 - Dellnitz, M. A1 - Hessel, M. A1 - Schütte, Christof A1 - Meerbach, E. T1 - Dominant Paths Between Almost Invariant Sets of Dynamical Systems JF - preprint Y1 - 2004 UR - http://publications.imp.fu-berlin.de/64/ ER - TY - JOUR A1 - Walter, J. A1 - Schütte, Christof A1 - Pavliotis, G. A1 - Stuart, Andrew T1 - Averaging of Stochastic Differential Equations JF - preprint Y1 - 2004 UR - http://publications.imp.fu-berlin.de/63/ ER - TY - JOUR A1 - Fischer, Alexander A1 - Waldhausen, S. A1 - Horenko, Illia A1 - Meerbach, E. A1 - Schütte, Christof T1 - Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models JF - J. Comp. Chem. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/38/ U6 - https://doi.org/10.1002/jcc.20692 VL - 28 IS - 15 SP - 2453 EP - 2464 ER - TY - JOUR A1 - Metzner, Ph. A1 - Horenko, Illia A1 - Schütte, Christof T1 - Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time JF - Phys. Rev. E Y1 - 2007 UR - http://publications.imp.fu-berlin.de/36/ U6 - https://doi.org/10.1103/PhysRevE.76.066702 VL - 76 IS - 06 SP - 066702 ER - TY - JOUR A1 - Lorenz, S. A1 - Diederichs, Elmar A1 - Telgmann, R. A1 - Schütte, Christof T1 - Discrimination of Dynamical System Models for Biological and Chemical Processes JF - J. Comp. Chem. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/33/ U6 - https://doi.org/10.1002/jcc.20674 VL - 28 IS - 8 SP - 1384 EP - 1399 ER - TY - JOUR A1 - Metzner, Ph. A1 - Dittmer, E. A1 - Jahnke, Tobias A1 - Schütte, Christof T1 - Generator Estimation of Markov Jump Processes JF - J. Comp. Phys. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/35/ U6 - https://doi.org/10.1016/j.jcp.2007.07.032 VL - 227 IS - 1 SP - 353 EP - 375 ER - TY - JOUR A1 - Noé, Frank A1 - Horenko, Illia A1 - Schütte, Christof A1 - Smith, J. T1 - Hierarchical Analysis of Conformational Dynamics in Biomolecules JF - J. Chem. Phys. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/37/ U6 - https://doi.org/10.1063/1.2714539 VL - 126 IS - 15 SP - 155102 ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Lankas, F. A1 - Maddocks, J. A1 - Metzner, Ph. A1 - Schütte, Christof T1 - Macroscopic Dynamics of Complex Metastable Systems JF - J. Appl. Dyn. Syst. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/56/ U6 - https://doi.org/10.1137/050630064 VL - 7 IS - 2 SP - 532 EP - 560 ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics JF - Mult. Mod. Sim. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/39/ U6 - https://doi.org/10.1137/070687451 VL - 7 IS - 2 SP - 731 EP - 773 ER - TY - JOUR A1 - Noé, Frank A1 - Smith, J. A1 - Schütte, Christof T1 - A network-based approach to biomolecular dynamics JF - From Computational Biophysics to Systems Biology (CBSB07). Editors Y1 - 2007 UR - http://publications.imp.fu-berlin.de/319/ VL - NIC Series 36 PB - John von Neumann Institute for Computing, Jülich ER - TY - JOUR A1 - Diederichs, Elmar A1 - Juditski, A. A1 - Spokoiny, V. A1 - Schütte, Christof T1 - Sparse Non-Gaussian Component Analysis JF - IEEE Transactions on Information Theory, submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/42/ ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications JF - Adv. Data Anal. Class., submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/32/ ER - TY - JOUR A1 - Meerbach, E. A1 - Schütte, Christof T1 - Sequential Change Point Detection in Molecular Dynamics Trajectories JF - Journal of Multivariate Analysis, submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/24/ ER - TY - JOUR A1 - Schiewe, Philine A1 - Goerigk, Marc A1 - Lindner, Niels T1 - Introducing TimPassLib – A Library for Integrated Periodic Timetabling and Passenger Routing JF - Operations Research Forum N2 - Classic models to derive a timetable for public transport often face a chicken-and-egg situation: A good timetable should offer passengers routes with small travel times, but the route choice of passengers depends on the timetable. While models that fix passenger routes were frequently considered in the literature, integrated models that simultaneously optimize timetables and passenger routes have seen increasing attention lately. This creates a growing need for a set of instances that allows to test and compare new algorithmic developments for the integrated problem. Our paper addresses this requirement by presenting TimPassLib, a new benchmark library of instances for integrated periodic timetabling and passenger routing. Y1 - 2023 U6 - https://doi.org/10.1007/s43069-023-00244-1 VL - 4 IS - 3 SP - 64 ER - TY - JOUR A1 - Wagendorf, Oliver A1 - Nahles, Susanne A1 - Vach, Kirstin A1 - Kernen, Florian A1 - Zachow, Stefan A1 - Heiland, Max A1 - Flügge, Tabea T1 - The impact of teeth and dental restorations on gray value distribution in cone-beam computer tomography - a pilot study JF - International Journal of Implant Dentistry N2 - Purpose: To investigate the influence of teeth and dental restorations on the facial skeleton's gray value distributions in cone-beam computed tomography (CBCT). Methods: Gray value selection for the upper and lower jaw segmentation was performed in 40 patients. In total, CBCT data of 20 maxillae and 20 mandibles, ten partial edentulous and ten fully edentulous in each jaw, respectively, were evaluated using two different gray value selection procedures: manual lower threshold selection and automated lower threshold selection. Two sample t tests, linear regression models, linear mixed models, and Pearson's correlation coefficients were computed to evaluate the influence of teeth, dental restorations, and threshold selection procedures on gray value distributions. Results: Manual threshold selection resulted in significantly different gray values in the fully and partially edentulous mandible. (p = 0.015, difference 123). In automated threshold selection, only tendencies to different gray values in fully edentulous compared to partially edentulous jaws were observed (difference: 58–75). Significantly different gray values were evaluated for threshold selection approaches, independent of the dental situation of the analyzed jaw. No significant correlation between the number of teeth and gray values was assessed, but a trend towards higher gray values in patients with more teeth was noted. Conclusions: Standard gray values derived from CT imaging do not apply for threshold-based bone segmentation in CBCT. Teeth influence gray values and segmentation results. Inaccurate bone segmentation may result in ill-fitting surgical guides produced on CBCT data and misinterpreting bone density, which is crucial for selecting surgical protocols. Y1 - 2023 U6 - https://doi.org/10.1186/s40729-023-00493-z VL - 9 IS - 27 ER - TY - JOUR A1 - Lößer, Angar A1 - Witzke, Joel A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis JF - arXiv Y1 - 2022 U6 - https://doi.org/10.48550/arXiv.2209.05358 SP - 1 EP - 20 ER - TY - JOUR A1 - Leser, Ulf A1 - Hilbrich, Marcus A1 - Draxl, Claudia A1 - Eisert, Peter A1 - Grunske, Lars A1 - Hostert, Patrick A1 - Kainmüller, Dagmar A1 - Kao, Odej A1 - Kehr, Birte A1 - Kehrer, Timo A1 - Koch, Christoph A1 - Markl, Volker A1 - Meyerhenke, Henning A1 - Rabl, Tilmann A1 - Reinefeld, Alexander A1 - Reinert, Knut A1 - Ritter, Kerstin A1 - Scheuermann, Björn A1 - Schintke, Florian A1 - Schweikardt, Nicole A1 - Weidlich, Matthias T1 - The Collaborative Research Center FONDA JF - Datenbank-Spektrum Y1 - 2021 U6 - https://doi.org/10.1007/s13222-021-00397-5 VL - 21 IS - 3 SP - 255 EP - 260 ER - TY - JOUR A1 - Salem, Farouk A1 - Schintke, Florian T1 - Large-Scale Performance of the Data-Flow Scheduler (DFS) and FLESnet JF - CBM Progress Report 2021 Y1 - 2022 U6 - https://doi.org/10.15120/GSI-2022-00599 SP - 170 EP - 171 ER - TY - JOUR A1 - Ribera Borrell, Enric A1 - Quer, Jannes A1 - Richter, Lorenz A1 - Schütte, Christof T1 - Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics JF - SIAM Journal on Scientific Computing (SISC) N2 - Sampling rare events in metastable dynamical systems is often a computationally expensive task and one needs to resort to enhanced sampling methods such as importance sampling. Since we can formulate the problem of finding optimal importance sampling controls as a stochastic optimization problem, this then brings additional numerical challenges and the convergence of corresponding algorithms might as well suffer from metastabilty. In this article we address this issue by combining systematic control approaches with the heuristic adaptive metadynamics method. Crucially, we approximate the importance sampling control by a neural network, which makes the algorithm in principle feasible for high dimensional applications. We can numerically demonstrate in relevant metastable problems that our algorithm is more effective than previous attempts and that only the combination of the two approaches leads to a satisfying convergence and therefore to an efficient sampling in certain metastable settings. KW - importance sampling KW - stochastic optimal control KW - rare event simulation KW - metastability KW - neural networks KW - metadynamics Y1 - 2023 U6 - https://doi.org/10.1137/22M1503464 SP - S298 EP - S323 ER - TY - JOUR A1 - Rozsa, Zsofia Borbala A1 - Ragyanszki, Anita A1 - Viskolcz, Bela A1 - Szori, Milan T1 - Chemical space of the singlet C4H8O2 species. A systematic theoretical analysis on their structural and thermochemical properties JF - Computational and Theoretical Chemistry N2 - The goal of this study was to explore and define the thermodynamic properties of one of the subspaces of ‘chemical space’ using a mixture of graph theory and theoretical chemistry tools. Therefore, all possible mo- lecular structures with C4H8O2 stoichiometry were generated, considering constitutional isomers and molecular complexes. The thermodynamic properties of the obtained isomers have been obtained by G3MP2B3 protocol. The classification of the obtained isomers was simplified by using thermodynamic maps, which is an effective method for the comparison of thermodynamic stability for entities of complex molecular systems. Modern computational methods can be used to understand larger systems, which has made it possible to characterize a chemical subspace not only by selecting individual entities, but also as a whole. With this pro- cedure one can catch a glimpse into the diversity of a molecular system and predict further uses of newly discovered molecules or design molecules with predefined properties. Y1 - 2023 U6 - https://doi.org/10.1016/j.comptc.2023.114162 VL - 1225 SP - 114162 ER - TY - JOUR A1 - Mikheeva, Elena A1 - Colom, Rémi A1 - Achouri, Karim A1 - Overvig, Adam A1 - Binkowski, Felix A1 - Duboz, Jean-Yves A1 - Cueff, Sébastien A1 - Fan, Shanhui A1 - Burger, Sven A1 - Alù, Andrea A1 - Genevet, Patrice T1 - Asymmetric phase modulation with light with parity-symmetry broken metasurfaces JF - Optica Y1 - 2023 U6 - https://doi.org/10.1364/OPTICA.495681 VL - 10 SP - 1287 ER - TY - JOUR A1 - Helfmann, Luzie A1 - Ribera Borrell, Enric A1 - Schütte, Christof A1 - Koltai, Peter T1 - Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics JF - Journal of Nonlinear Science Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/s00332-020-09652-7 VL - 30 SP - 3321 EP - 3366 ER - TY - JOUR A1 - Mohammadzadeh, Saeed A1 - H. Nascimento, Vítor A1 - C. de Lamare, Rodrigo A1 - Hajarolasvadi, Noushin T1 - Robust Beamforming Based on Complex-Valued Convolutional Neural Networks for Sensor Arrays JF - IEEE Signal Processing Letters N2 - Robust adaptive beamforming (RAB) plays a vital role in modern communications by ensuring the reception of high-quality signals. This article proposes a deep learning approach to robust adaptive beamforming. In particular, we propose a novel RAB approach where the sample covariance matrix (SCM) is used as the input of a deep 1D Complex-Valued Convolutional Neural Network (CVCNN). The network employs complex convolutional and pooling layers, as well as a Cartesian Scaled Exponential Linear Unit activation function to directly compute the nearly-optimum weight vector through the training process and without prior knowledge about the direction of arrival of the desired signal. This means that reconstruction of the interference plus noise (IPN) covariance matrix is not required. The trained CVCNN accurately computes the nearly-optimum weight vector for data not used during training. The computed weight vector is employed to estimate the signal-to-interference plus noise ratio. Simulations show that the proposed RAB can provide performance close to that of the optimal beamformer. Y1 - 2022 U6 - https://doi.org/10.1109/LSP.2022.3212637 VL - 29 SP - 2018 EP - 2021 ER - TY - JOUR A1 - Hajarolasvadi, Noushin A1 - Sunkara, Vikram A1 - Khavnekar, Sagar A1 - Beck, Florian A1 - Brandt, Robert A1 - Baum, Daniel T1 - Volumetric macromolecule identification in cryo-electron tomograms using capsule networks JF - BMC Bioinformatics N2 - Background: Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data and high structural complexities. To date, the extent of the deep learning methods constructed for this problem is limited to conventional Convolutional Neural Networks (CNNs). Identifying macromolecules of different types and sizes is a tedious and time-consuming task. In this paper, we employ a capsule-based architecture to automate the task of macro- molecule identification, that we refer to as 3D-UCaps. In particular, the architecture is composed of three components: feature extractor, capsule encoder, and CNN decoder. The feature extractor converts voxel intensities of input sub-tomograms to activities of local features. The encoder is a 3D Capsule Network (CapsNet) that takes local features to generate a low-dimensional representation of the input. Then, a 3D CNN decoder reconstructs the sub-tomograms from the given representation by upsampling. Results: We performed binary and multi-class localization and identification tasks on synthetic and experimental data. We observed that the 3D-UNet and the 3D-UCaps had an F1−score mostly above 60% and 70%, respectively, on the test data. In both network architectures, we observed degradation of at least 40% in the F1-score when identifying very small particles (PDB entry 3GL1) compared to a large particle (PDB entry 4D8Q). In the multi-class identification task of experimental data, 3D-UCaps had an F1-score of 91% on the test data in contrast to 64% of the 3D-UNet. The better F1-score of 3D-UCaps compared to 3D-UNet is obtained by a higher precision score. We speculate this to be due to the capsule network employed in the encoder. To study the effect of the CapsNet-based encoder architecture further, we performed an ablation study and perceived that the F1-score is boosted as network depth is increased which is in contrast to the previously reported results for the 3D-UNet. To present a reproducible work, source code, trained models, data as well as visualization results are made publicly available. Conclusion: Quantitative and qualitative results show that 3D-UCaps successfully perform various downstream tasks including identification and localization of macro- molecules and can at least compete with CNN architectures for this task. Given that the capsule layers extract both the existence probability and the orientation of the molecules, this architecture has the potential to lead to representations of the data that are better interpretable than those of 3D-UNet. Y1 - 2022 U6 - https://doi.org/10.1186/s12859-022-04901-w VL - 23 IS - 360 ER - TY - JOUR A1 - Kontou, Eftychia E. A1 - Walter, Axel A1 - Alka, Oliver A1 - Pfeuffer, Julianus A1 - Sachsenberg, Timo A1 - Mohite, Omkar A1 - Nuhamunanda, Matin A1 - Kohlbacher, Oliver A1 - Weber, Tilmann T1 - UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysis JF - Journal of Cheminformatics N2 - Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). Finally, UmetaFlow is also offered as a web-based Graphical User Interface for parameter optimization and processing of smaller-sized datasets. UmetaFlow was validated with in-house LC–MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76% of the molecular formulas and 65% of the structures. As a more generic validation, the publicly available MTBLS733 and MTBLS736 datasets were used for benchmarking, and UmetaFlow detected more than 90% of all ground truth features and performed exceptionally well in quantification and discriminating marker selection. Y1 - 2023 U6 - https://doi.org/10.1186/s13321-023-00724-w VL - 15 ER - TY - JOUR A1 - Masing, Berenike A1 - Lindner, Niels A1 - Ebert, Patricia T1 - Forward and Line-Based Cycle Bases for Periodic Timetabling JF - Operations Research Forum N2 - The optimization of periodic timetables is an indispensable planning task in public transport. Although the periodic event scheduling problem (PESP) provides an elegant mathematical formulation of the periodic timetabling problem that led to many insights for primal heuristics, it is notoriously hard to solve to optimality. One reason is that for the standard mixed-integer linear programming formulations, linear programming relaxations are weak, and the integer variables are of pure technical nature and in general do not correlate with the objective value. While the first problem has been addressed by developing several families of cutting planes, we focus on the second aspect. We discuss integral forward cycle bases as a concept to compute improved dual bounds for PESP instances. To this end, we develop the theory of forward cycle bases on general digraphs. Specifically for the application of timetabling, we devise a generic procedure to construct line-based event-activity networks and give a simple recipe for an integral forward cycle basis on such networks. Finally, we analyze the 16 railway instances of the benchmark library PESPlib, match them to the line-based structure, and use forward cycle bases to compute better dual bounds for 14 out of the 16 instances. Y1 - 2023 U6 - https://doi.org/10.1007/s43069-023-00229-0 VL - 4 IS - 3 SP - 53 ER - TY - JOUR A1 - Bai, Mingze A1 - Deng, Jingwen A1 - Dai, Chengxin A1 - Pfeuffer, Julianus A1 - Sachsenberg, Timo A1 - Perez-Riverol, Yasset T1 - LFQ-Based Peptide and Protein Intensity Differential Expression Analysis JF - J. Proteome Res. N2 - Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform the final tasks of imputation, summarization, normalization, and statistical testing. To evaluate the effects of packages and settings in their substeps on the final list of significant proteins, we studied several packages on three public data sets with known expected protein fold changes. We found that the results between packages and even across different parameters of the same package can vary significantly. In addition to usability aspects and feature/compatibility lists of different packages, this paper highlights sensitivity and specificity trade-offs that come with specific packages and settings. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jproteome.2c00812 VL - 22 IS - 6 SP - 2114 EP - 2123 PB - American Chemical Society ER - TY - JOUR A1 - Subramaniam, Jayant S. A1 - Hubig, Michael A1 - Muggenthaler, Holger A1 - Schenkl, Sebastian A1 - Ullrich, Julia A1 - Pourtier, Grégroire A1 - Weiser, Martin A1 - Mall, Gita T1 - Sensitivity of temperature-based time since death estimation on measurement location JF - International Journal of Legal Medicine N2 - Rectal temperature measurement (RTM) from crime scenes is an important parameter for temperature-based time of death estimation (TDE). Various influential variables exist in TDE methods like the uncertainty in thermal and environmental parameters. Although RTM depends in particular on the location of measurement position, this relationship has never been investigated separately. The presented study fills this gap using Finite Element (FE) simulations of body cooling. A manually meshed coarse human FE model and an FE geometry model developed from the CT scan of a male corpse are used for TDE sensitivity analysis. The coarse model is considered with and without a support structure of moist soil. As there is no clear definition of ideal rectal temperature measurement location for TDE, possible variations in RTM location (RTML) are considered based on anatomy and forensic practice. The maximum variation of TDE caused by RTML changes is investigated via FE simulation. Moreover, the influence of ambient temperature, of FE model change and of the models positioning on a wet soil underground are also discussed. As a general outcome, we notice that maximum TDE deviations of up to ca. 2-3 h due to RTML deviations have to be expected. The direction of maximum influence of RTML change on TDE generally was on the line caudal to cranial. Y1 - 2023 U6 - https://doi.org/10.1007/s00414-023-03040-y VL - 137 SP - 1815 EP - 1837 ER - TY - JOUR A1 - Toulkeridou, Evropi A1 - Gutierrez, Carlos Enrique A1 - Baum, Daniel A1 - Doya, Kenji A1 - Economo, Evan P. T1 - Automated segmentation of insect anatomy from micro-CT images using deep learning JF - Natural Sciences N2 - Three-dimensional (3D) imaging, such as micro-computed tomography (micro-CT), is increasingly being used by organismal biologists for precise and comprehensive anatomical characterization. However, the segmentation of anatomical structures remains a bottleneck in research, often requiring tedious manual work. Here, we propose a pipeline for the fully-automated segmentation of anatomical structures in micro-CT images utilizing state-of-the-art deep learning methods, selecting the ant brain as a test case. We implemented the U-Net architecture for 2D image segmentation for our convolutional neural network (CNN), combined with pixel-island detection. For training and validation of the network, we assembled a dataset of semi-manually segmented brain images of 76 ant species. The trained network predicted the brain area in ant images fast and accurately; its performance tested on validation sets showed good agreement between the prediction and the target, scoring 80% Intersection over Union (IoU) and 90% Dice Coefficient (F1) accuracy. While manual segmentation usually takes many hours for each brain, the trained network takes only a few minutes. Furthermore, our network is generalizable for segmenting the whole neural system in full-body scans, and works in tests on distantly related and morphologically divergent insects (e.g., fruit flies). The latter suggests that methods like the one presented here generally apply across diverse taxa. Our method makes the construction of segmented maps and the morphological quantification of different species more efficient and scalable to large datasets, a step toward a big data approach to organismal anatomy. Y1 - 2023 U6 - https://doi.org/10.1002/ntls.20230010 VL - 3 IS - 4 ER - TY - JOUR A1 - Longren, Luke L. A1 - Eigen, Lennart A1 - Shubitidze, Ani A1 - Lieschnegg, Oliver A1 - Baum, Daniel A1 - Nyakatura, John A. A1 - Hildebrandt, Thomas A1 - Brecht, Michael T1 - Dense Reconstruction of Elephant Trunk Musculature JF - Current Biology N2 - The elephant trunk operates as a muscular hydrostat and is actuated by the most complex musculature known in animals. Because the number of trunk muscles is unclear, we performed dense reconstructions of trunk muscle fascicles, elementary muscle units, from microCT scans of an Asian baby elephant trunk. Muscle architecture changes markedly across the trunk. Trunk tip and finger consist of about 8,000 extraordinarily filigree fascicles. The dexterous finger consists exclusively of microscopic radial fascicles pointing to a role of muscle miniaturization in elephant dexterity. Radial fascicles also predominate (at 82% volume) the remainder of the trunk tip and we wonder if radial muscle fascicles are of particular significance for fine motor control of the dexterous trunk tip. By volume, trunk-shaft muscles comprise one-third of the numerous, small radial muscle fascicles, two-thirds of the three subtypes of large longitudinal fascicles (dorsal longitudinals, ventral outer obliques, and ventral inner obliques), and a small fraction of transversal fascicles. Shaft musculature is laterally, but not radially, symmetric. A predominance of dorsal over ventral radial muscles and of ventral over dorsal longitudinal muscles may result in a larger ability of the shaft to extend dorsally than ventrally and to bend inward rather than outward. There are around 90,000 trunk muscle fascicles. While primate hand control is based on fine control of contraction by the convergence of many motor neurons on a small set of relatively large muscles, evolution of elephant grasping has led to thousands of microscopic fascicles, which probably outnumber facial motor neurons. Y1 - 2023 U6 - https://doi.org/10.1016/j.cub.2023.09.007 VL - 33 SP - 1 EP - 8 ER - TY - JOUR A1 - Masing, Berenike A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Periodic timetabling with integrated track choice for railway construction sites JF - Journal of Rail Transport Planning & Management N2 - We propose a mixed-integer linear programming model to generate and optimize periodic timetables with integrated track choice in the context of railway construction sites. When a section of a railway network becomes unavailable, the nearby areas are typically operated close to their capacity limits, and hence carefully modeling headways and allowing flexible routings becomes vital. We therefore discuss first how to integrate headway constraints into the Periodic Event Scheduling Problem (PESP) that do not only prevent overtaking, but also guarantee conflict-free timetables in general and particularly inside stations. Secondly, we introduce a turn-sensitive event-activity network, which is able to integrate routing alternatives for turnarounds at stations, e.g., turning at a platform vs. at a pocket track for metro-like systems. We propose several model formulations to include track choice, and finally evaluate them on six real construction site scenarios on the S-Bahn Berlin network. Y1 - 2023 U6 - https://doi.org/10.1016/j.jrtpm.2023.100416 VL - 28 SP - 100416 ER - TY - JOUR A1 - Juhasz, Anett A1 - Serra, Uneri Haymana A1 - Lakatos, Csilla A1 - Vadkerti, Bence A1 - Ragyanszki, Anita A1 - Farkas, Odon A1 - Keki, Sandor A1 - Nagy, Lajos T1 - The kinetics of uncatalyzed and catalyzed urethane forming reactions of aliphatic diisocyanates with butan-1-ol JF - New J. Chem. N2 - The kinetics of the urethane forming reactions of hexamethylene diisocyanate (HDI), 4,4′-dicyclohexyl-methane-diisocyanate (HMDI) and isophorone diisocyanate (IPDI) with butan-1-ol were systematically studied by electrospray ionization mass spectrometry (ESI-MS) in the off-line mode. The reactions were performed in toluene solution in the temperature range of 50–80 °C and perdeuterated butan-1-ol was used for quenching the reaction. The butan-1-ol was employed in high excess to diisocyanates to obtain pseudo first-order rate coefficients. For rendering the kinetics, a simple A → B → C consecutive model was applied and found to adequately describe the observed kinetic behaviors. The corresponding rate coefficients were determined and reactivities of the diisocyanates were found to decrease in the order HDI > IPDI > HMDI. Furthermore, it was observed that the second isocyanate group in HDI, due to the ring formation by intramolecular hydrogen bonds, reacted faster with butan-1-ol after the first isocyanate moiety had reacted. The formation of hydrogen bonding rings was also confirmed by DFT calculations. However, the reactivity of the second isocyanate moiety (after the first one has reacted) did not change significantly in the case of HMDI. From the temperature dependences the apparent activation parameters such as the pre-exponential factors and activation energies were determined. In addition, the reactions were also studied at 80 °C in the presence of tin(II)-2-ethylhexanoate at different concentrations and a mechanism was proposed for the catalytic process. Y1 - 2023 U6 - https://doi.org/10.1039/d3nj02747c VL - 47 SP - 16096 EP - 16107 ER - TY - JOUR A1 - Chewle, Surahit A1 - Weber, Marcus A1 - Emmerling, Franziska T1 - Revealing Kinetics of Paracetamol Crystallization Using Time-Resolved Raman Spectroscopy, Orthogonal Time-Lapse Photography, and Non-Negative Matrix Factorization (OSANO) JF - Crystal Growth & Design N2 - Crystallization is a complex phenomenon with far-reaching implications for the production and formulation of active pharmaceutical ingredients. Understanding this process is critical for achieving control over key physicochemical properties that can affect, for example, the bioavailability and stability of a drug. In this study, we were able to reveal intricate and diverse dynamics of the formation of metastable intermediates of paracetamol crystallization varying with the choice of solvent. We demonstrate the efficacy of our novel approach utilizing an objective function-based non-negative matrix factorization technique for the analysis of time-resolved Raman spectroscopy data, in conjunction with time-lapse photography. Furthermore, we emphasize the crucial importance of integrating Raman spectroscopy with supplementary experimental instrumentation for the mathematical analysis of the obtained spectra. Y1 - 2023 U6 - https://doi.org/10.1021/acs.cgd.3c00617 VL - 23 IS - 9 SP - 6737 EP - 6746 PB - American Chemical Society ET - Crystal Growth & Design ER - TY - JOUR A1 - Ji, Hongchen A1 - Ragyanszki, Anita A1 - Fournier, Rene A. T1 - Machine learning estimation of reaction energy barriers JF - Computational and Theoretical Chemistry N2 - We describe a machine learning approach to approximate reaction energy barriers (E), requiring as input only estimates of geometry and energies of reactants and products. Using the dataset of Grambow, Pattanaik, and Green [Sci. Data 7 (1 3 7) (2020)] for reactions involving seven or fewer non-hydrogen atoms, 300 reaction features are computed, and an estimate of E is obtained by fitting a Kernel Ridge Regression (KRR) model with Laplacian kernel to a subset of Density Functional Theory reaction barriers. Our main interest is small energy barriers with the goal of modeling reactions in the interstellar medium and circumstellar envelope. We omitted reactions with E > 40 kcal mol−1 to obtain a subset of 5,276 reactions for 5-fold cross-validation. For this set, the KRR model predicts E with a mean absolute error of 4.13 kcal mol−1 and a root-mean square error of 6.02 kcal mol−1. Y1 - 2023 U6 - https://doi.org/10.1016/j.comptc.2023.114332 VL - 1229 SP - 114332 ER - TY - JOUR A1 - Bleich, Amnon A1 - Linnemann, Antje A1 - Jaidi, Benjamin A1 - Diem, Bjoern H A1 - Conrad, Tim T1 - Enhancing ECG Analysis of Implantable Cardiac Monitor Data: An Efficient Pipeline for Multi-Label Classification JF - Machine Learning and Knowledge Extraction N2 - Implantable Cardiac Monitor (ICM) devices are demonstrating as of today, the fastest-growing market for implantable cardiac devices. As such, they are becoming increasingly common in patients for measuring heart electrical activity. ICMs constantly monitor and record a patient's heart rhythm and when triggered - send it to a secure server where health care professionals (denote HCPs from here on) can review it. These devices employ a relatively simplistic rule-based algorithm (due to energy consumption constraints) to alert for abnormal heart rhythms. This algorithm is usually parameterized to an over-sensitive mode in order to not miss a case (resulting in a relatively high false-positive rate) and this, combined with the device's nature of constantly monitoring the heart rhythm and its growing popularity, results in HCPs having to analyze and diagnose an increasingly growing amount of data. In order to reduce the load on the latter, automated methods for ECG analysis are nowadays becoming a great tool to assist HCPs in their analysis. While state-of-the-art algorithms are data-driven rather than rule-based, training data for ICMs often consist of specific characteristics that make its analysis unique and particularly challenging. This study presents the challenges and solutions in automatically analyzing ICM data and introduces a method for its classification that outperforms existing methods on such data. It does so by combining high-frequency noise detection (which often occurs in ICM data) with a semi-supervised learning pipeline that allows for re-labeling of training episodes, and by using segmentation and dimension reduction techniques that are robust to morphology variations of the sECG signal (which are typical to ICM data). As a result, it performs better than state-of-the-art techniques on such data with e.g. F1 score of 0.51 vs. 0.38 of our baseline state-of-the-art technique in correctly calling Atrial Fibrilation in ICM data. As such, it could be used in numerous ways such as aiding HCPs in the analysis of ECGs originating from ICMs by, e.g., suggesting a rhythm type. Y1 - 2023 U6 - https://doi.org/10.3390/make5040077 VL - 5 IS - 4 PB - MDPI ER - TY - JOUR A1 - Müller, Benjamin A1 - Muñoz, Gonzalo A1 - Gasse, Maxime A1 - Gleixner, Ambros A1 - Lodi, Andrea A1 - Serrano, Felipe T1 - On generalized surrogate duality in mixed-integer nonlinear programming JF - Mathematical Programming N2 - The most important ingredient for solving mixed-integer nonlinear programs (MINLPs) to global ϵ-optimality with spatial branch and bound is a tight, computationally tractable relaxation. Due to both theoretical and practical considerations, relaxations of MINLPs are usually required to be convex. Nonetheless, current optimization solvers can often successfully handle a moderate presence of nonconvexities, which opens the door for the use of potentially tighter nonconvex relaxations. In this work, we exploit this fact and make use of a nonconvex relaxation obtained via aggregation of constraints: a surrogate relaxation. These relaxations were actively studied for linear integer programs in the 70s and 80s, but they have been scarcely considered since. We revisit these relaxations in an MINLP setting and show the computational benefits and challenges they can have. Additionally, we study a generalization of such relaxation that allows for multiple aggregations simultaneously and present the first algorithm that is capable of computing the best set of aggregations. We propose a multitude of computational enhancements for improving its practical performance and evaluate the algorithm’s ability to generate strong dual bounds through extensive computational experiments. Y1 - 2022 U6 - https://doi.org/10.1007/s10107-021-01691-6 VL - 192 IS - 1 SP - 89 EP - 118 ER - TY - JOUR A1 - Gemander, Patrick A1 - Chen, Wei-Kun A1 - Weninger, Dieter A1 - Gottwald, Leona A1 - Gleixner, Ambros T1 - Two-row and two-column mixed-integer presolve using hashing-based pairing methods JF - EURO Journal on Computational Optimization N2 - In state-of-the-art mixed-integer programming solvers, a large array of reduction techniques are applied to simplify the problem and strengthen the model formulation before starting the actual branch-and-cut phase. Despite their mathematical simplicity, these methods can have significant impact on the solvability of a given problem. However, a crucial property for employing presolve techniques successfully is their speed. Hence, most methods inspect constraints or variables individually in order to guarantee linear complexity. In this paper, we present new hashing-based pairing mechanisms that help to overcome known performance limitations of more powerful presolve techniques that consider pairs of rows or columns. Additionally, we develop an enhancement to one of these presolve techniques by exploiting the presence of set-packing structures on binary variables in order to strengthen the resulting reductions without increasing runtime. We analyze the impact of these methods on the MIPLIB 2017 benchmark set based on an implementation in the MIP solver SCIP. Y1 - 2020 U6 - https://doi.org/10.1007/s13675-020-00129-6 VL - 8 IS - 3-4 SP - 205 EP - 240 ER - TY - JOUR A1 - Tuncay, Erhun Giray A1 - Erdur, Rıza Cenk A1 - Conrad, Tim T1 - Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics N2 - The aim of Network Alignment in Protein-Protein Interaction Networks is discovering functionally similar regions between compared organisms. One major compromise for solving a network alignment problem is the trade-off among multiple similarity objectives while applying an alignment strategy. An alignment may lose its biological relevance while favoring certain objectives upon others due to the actual relevance of unfavored objectives. One possible solution for solving this issue may be blending the stronger aspects of various alignment strategies until achieving mature solutions. This study proposes a parallel approach called PERSONA that allows aligners to share their partial solutions continuously while they progress. All these aligners pursue their particular heuristics as part of a particle swarm that searches for multi-objective solutions of the same alignment problem in a reactive actor environment. The actors use the stronger portion of a solution as a subgraph that they receive from leading or other actors and send their own stronger subgraphs back upon evaluation of those partial solutions. Moreover, the individual heuristics of each actor takes randomized parameter values at each cycle of parallel execution so that the problem search space can thoroughly be investigated. The results achieved with PERSONA are remarkably optimized and balanced for both topological and node similarity objectives. Y1 - 2023 U6 - https://doi.org/10.1109/TCBB.2022.3231489 VL - 20 IS - 3 SP - 2064 EP - 2077 ER - TY - JOUR A1 - Kornaropoulos, Evgenios I. A1 - Taylor, William R. A1 - Duda, Georg A1 - Ehrig, Rainald A1 - Matziolis, Georg A1 - Müller, Michael A1 - Wassilew, Georgi A1 - Asbach, Patrick A1 - Perka, Carsten A1 - Heller, Markus O. T1 - Frontal plane alignment: An imageless method to predict the mechanical femoral–tibial angle (mFTA) based on functional determination of joint centres and axes JF - Gait & Posture Y1 - 2010 U6 - https://doi.org/10.1016/j.gaitpost.2009.10.006 VL - 31 IS - 2 SP - 204 EP - 208 ER - TY - JOUR A1 - Kiewisz, Robert A1 - Baum, Daniel A1 - Müller-Reichert, Thomas A1 - Fabig, Gunar T1 - Serial-section electron tomography and quantitative analysis of the microtubule organization in 3D-reconstructed mitotic spindles JF - Bio-protocol Y1 - 2023 U6 - https://doi.org/10.21769/BioProtoc.4849 VL - 13 IS - 20 ER - TY - JOUR A1 - Boeth, Heide A1 - Biesen, Robert A1 - Hollnagel, Jeremias A1 - Herrmann, Sandra A1 - Ehrig, Rainald A1 - Pelli, Lorenzo A1 - Taylor, William R. A1 - Duda, Georg A1 - Buttgereit, Frank T1 - Quantification of morning stiffness to assess disease activity and treatment effects in rheumatoid arthritis JF - Rheumatology N2 - Objectives The clinical parameter “morning stiffness” is widely used to assess the status of rheumatoid arthritis (RA), but its accurate quantitative assessment in a clinical setting has not yet been successful. This lack of individual quantification limits both personalized medication and efficacy evaluation in the treatment of RA. Methods We have developed a novel technology to assess passive resistance of the metacarpophalangeal (MCP) III joint (stiffness) and its Passive Range of Motion (PRoM). Within this pilot study, nineteen female postmenopausal RA patients and nine healthy controls were examined in the evening as well as in the morning of the following day. To verify the specificity of the biomechanical quantification, eleven patients with RA were assessed both prior to and ∼3 h after glucocorticoid therapy. Results While the healthy controls showed only minor changes between afternoon and morning, in RA patients mean±SD PRoM decreased significantly by 18 ± 22% and stiffness increased significantly by 20 ± 18% in the morning compared with the previous afternoon. We found a significant positive correlation between RA activity and biomechanical measures. Glucocorticoids significantly increased mean PRoM by 16 ± 11% and reduced mean stiffness by 23 ± 22%. Conclusion This technology allowed mechanical stiffness to be quantified in MCP joints, and has demonstrated high sensitivity in respect to disease status as well as medication effect in RA patients. Such non-invasive, low risk, and rapid assessment of biomechanical joint stiffness opens a novel avenue for judging therapy efficacy in patients with RA, and potentially also in other non-RA inflammatory joint diseases. Y1 - 2021 U6 - https://doi.org/10.1093/rheumatology/keab323 VL - 60 IS - 11 SP - 5282 EP - 5291 ER - TY - JOUR A1 - Alves, Sónia A1 - Ehrig, Rainald A1 - Raffalt, Peter C. A1 - Bender, Alwina A1 - Duda, Georg A1 - Agres, Alison N. T1 - Quantifying Asymmetry in Gait: A Weighted Universal Symmetry Index to Evaluate 3D Ground Reaction Forces JF - Frontiers in Bioengineering and Biotechnology N2 - Though gait asymmetry is used as a metric of functional recovery in clinical rehabilitation, there is no consensus on an ideal method for its evaluation. Various methods have been proposed but are limited in scope, as they can often use only positive signals or discrete values extracted from time-scale data as input. By defining five symmetry axioms, a framework for benchmarking existing methods was established and a new method was described here for the first time: the weighted universal symmetry index (wUSI), which overcomes limitations of other methods. Both existing methods and the wUSI were mathematically compared to each other and in respect to their ability to fulfill the proposed symmetry axioms. Eligible methods that fulfilled these axioms were then applied using both discrete and continuous approaches to ground reaction force (GRF) data collected from healthy gait, both with and without artificially induced asymmetry using a single instrumented elbow crutch. The wUSI with a continuous approach was the only symmetry method capable of determining GRF asymmetries in different walking conditions in all three planes of motion. When used with a continuous approach, the wUSI method was able to detect asymmetries while avoiding artificial inflation, a common problem reported in other methods. In conclusion, the wUSI is proposed as a universal method to quantify three-dimensional GRF asymmetries, which may also be expanded to other biomechanical signals. Y1 - 2020 ER - TY - JOUR A1 - Boeth, Heide A1 - Duda, Georg A1 - Hinzmann, Daniel A1 - Hermann, Sandra A1 - Taylor, William R. A1 - Ehrig, Rainald A1 - Witaschek, Tom A1 - Buttgereit, Frank T1 - A Novel Approach to Quantify Morning Stiffness in Patients with Rheumatoid Arthritis JF - Annual European Congress of Rheumatology, EULAR 2015, Rome Y1 - 2015 ER - TY - JOUR A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen A1 - Baum, Daniel T1 - Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography JF - Journal of Microscopy N2 - We present a software-assisted workflow for the alignment and matching of filamentous structures across a three-dimensional (3D) stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After the computation of an initial automatic matching, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed in an interdisciplinary collaboration between computer scientists and cell biologists to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite dealing with imperfect data related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time-consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. To the best of our knowledge, it is the only currently available tool which is able to process data of the type and size presented here. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. The final solution presented here is the result of an iterative process with tight feedback loops between the involved computer scientists and cell biologists. Y1 - 2021 U6 - https://doi.org/10.1111/jmi.13039 VL - 284 IS - 1 SP - 25 EP - 44 ER - TY - JOUR A1 - Borndörfer, Ralf A1 - Euler, Ricardo A1 - Karbstein, Marika T1 - Ein Graphen-basiertes Modell zur Beschreibung von Preissystemen im öffentlichen Nahverkehr JF - HEUREKA 21 N2 - In dieser Arbeit wird ein graphenbasiertes Modell zur Einbindung von Preissystemen des öffentlichen Nahverkehrs in Routing-Algorithmen vorgestellt. Jeder Knoten des Graphen repräsentiert einen abstrakten Preiszustand einer Route und ist an einen tatsächlichen Preis gekoppelt. Damit sind sehr einfache und konzise Beschreibungen von Tarifstrukturen möglich, diesich algorithmisch behandeln lassen. Durch das zeitgleiche Tracken eines Pfades im Routinggraphen im Ticketgraphen kann schon während einer Routenberechnung der Preis bestimmt werden. Dies ermöglicht die Berechnung von preisoptimalen Routen. An den Tarifsystemen der Verkehrsverbünde MDV (Mitteldeutscher Verkehrsverbund) und VBB (Verkehrsverbund Berlin-Brandenburg) wird die Konstruktion des Modells detailliert erläutert. Y1 - 2021 UR - https://verlag.fgsv-datenbanken.de/tagungsbaende?kat=HEUREKA&subkat=FGSV+002%2F127+%282021%29&fanr=&va=&titel=&text=&autor=&tagungsband=1256&_titel=Ein+Graphen-basiertes+Modell+zur+Beschreibung+von+Preissystemen+im+%C3%B6ffentlichen+Nahverkehr VL - 002/127 SP - 1 EP - 15 PB - FGSV CY - Stuttgart ER - TY - JOUR A1 - Devriendt, Jo A1 - Gleixner, Ambros A1 - Nordström, Jakob T1 - Learn to Relax: Integrating 0-1 Integer Linear Programming with Pseudo-Boolean Conflict-Driven Search JF - Constraints N2 - Conflict-driven pseudo-Boolean solvers optimize 0-1 integer linear programs by extending the conflict-driven clause learning (CDCL) paradigm from SAT solving. Though pseudo-Boolean solvers have the potential to be exponentially more efficient than CDCL solvers in theory, in practice they can sometimes get hopelessly stuck even when the linear programming (LP) relaxation is infeasible over the reals. Inspired by mixed integer programming (MIP), we address this problem by interleaving incremental LP solving with cut generation within the conflict-driven pseudo-Boolean search. This hybrid approach, which for the first time combines MIP techniques with full-blown conflict analysis operating directly on linear inequalities using the cutting planes method, significantly improves performance on a wide range of benchmarks, approaching a "best-of-both-worlds" scenario between SAT-style conflict-driven search and MIP-style branch-and-cut. Y1 - 2021 U6 - https://doi.org/10.1007/s10601-020-09318-x VL - 26 SP - 26 EP - 55 ER - TY - JOUR A1 - Gelß, Patrick A1 - Klus, Stefan A1 - Knebel, Sebastian A1 - Shakibaei, Zarin A1 - Pokutta, Sebastian T1 - Low-Rank Tensor Decompositions of Quantum Circuits JF - Journal of Computational Physics N2 - Quantum computing is arguably one of the most revolutionary and disruptive technologies of this century. Due to the ever-increasing number of potential applications as well as the continuing rise in complexity, the development, simulation, optimization, and physical realization of quantum circuits is of utmost importance for designing novel algorithms. We show how matrix product states (MPSs) and matrix product operators (MPOs) can be used to express certain quantum states, quantum gates, and entire quantum circuits as low-rank tensors. This enables the analysis and simulation of complex quantum circuits on classical computers and to gain insight into the underlying structure of the system. We present different examples to demonstrate the advantages of MPO formulations and show that they are more efficient than conventional techniques if the bond dimensions of the wave function representation can be kept small throughout the simulation. Y1 - 2022 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Jayaraj, Abhilash A1 - Fackeldey, Konstantin A1 - Arthanari, Haribabu T1 - Emerging frontiers in virtual drug discovery: From quantum mechanical methods to deep learning approaches JF - Current Opinion in Chemical Biology N2 - Virtual screening-based approaches to discover initial hit and lead compounds have the potential to reduce both the cost and time of early drug discovery stages, as well as to find inhibitors for even challenging target sites such as protein–protein interfaces. Here in this review, we provide an overview of the progress that has been made in virtual screening methodology and technology on multiple fronts in recent years. The advent of ultra-large virtual screens, in which hundreds of millions to billions of compounds are screened, has proven to be a powerful approach to discover highly potent hit compounds. However, these developments are just the tip of the iceberg, with new technologies and methods emerging to propel the field forward. Examples include novel machine-learning approaches, which can reduce the computational costs of virtual screening dramatically, while progress in quantum-mechanical approaches can increase the accuracy of predictions of various small molecule properties. Y1 - 2022 U6 - https://doi.org/10.1016/j.cbpa.2022.102156 VL - 69 SP - 102156 EP - 102156-12 ER - TY - JOUR A1 - Nitzke, Isabel A1 - Fackeldey, Konstantin A1 - Vrabec, Jadran T1 - Long range corrections for inhomogeneous fluids containing a droplet or a bubble JF - Molecular Simulation N2 - Long range corrections for molecular simulations of inhomogeneous fluids with a spherical interface are presented. Correction terms for potential energy, force and virial are derived for the monatomic Lennard–Jones fluid. The method is generalised to the Mie potential and arbitrary molecular structures, employing a numerically efficient centre of mass cut-off scheme. The results are validated by a series of droplet simulations for one-centre and two-centre Lennard–Jones fluids with different cut-off radii rc. Systems with rc=8σ provide a check of self-consistence. Further, a system containing a bubble is investigated for the one-centre Lennard–Jones fluid. The equilibrium properties are almost completely independent on the cut-off radius. In comparison with vapour–liquid equilibrium data for systems without a curved interface, all properties show the expected behaviour. Simulation data are used to approximate the surface tension, which is in good agreement with the findings for planar interfaces, thus verifying the present corrections. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1080/08927022.2021.1954639 SP - 1 EP - 14 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Gorgulla, Christoph A1 - Weber, Marcus T1 - Neue Medikamente dank Supercomputern JF - Spektrum der Wissenschaft N2 - Die aktuelle Pandemie verdeutlicht, wie wichtig es ist, rasch geeignete Arzneimittel zu finden. In Computer­simulationen gelingt das erheblich schneller als im Labor. Gegen das Coronavirus ließen sich auf diese Weise bereits Wirkstoffkandidaten identifizieren. Y1 - 2021 IS - 11 SP - 40 EP - 46 ER - TY - JOUR A1 - Riedel, Jerome A1 - Gelß, Patrick A1 - Klein, Rupert A1 - Schmidt, Burkhard T1 - WaveTrain: a Python Package for Numerical Quantum Mechanics of Chain-like Systems Based on Tensor Trains JF - The Journal of Chemical Physics N2 - WaveTrain is an open-source software for numerical simulations of chain-like quantum systems with nearest-neighbor (NN) interactions only. The Python package is centered around tensor train (TT, or matrix product) format representations of Hamiltonian operators and (stationary or time-evolving) state vectors. It builds on the Python tensor train toolbox Scikit_tt, which provides efficient construction methods and storage schemes for the TT format. Its solvers for eigenvalue problems and linear differential equations are used in WaveTrain for the time-independent and time-dependent Schrödinger equations, respectively. Employing efficient decompositions to construct low-rank representations, the tensor-train ranks of state vectors are often found to depend only marginally on the chain length N. This results in the computational effort growing only slightly more than linearly with N, thus mitigating the curse of dimensionality. As a complement to the classes for full quantum mechanics, WaveTrain also contains classes for fully classical and mixed quantum–classical (Ehrenfest or mean field) dynamics of bipartite systems. The graphical capabilities allow visualization of quantum dynamics “on the fly,” with a choice of several different representations based on reduced density matrices. Even though developed for treating quasi-one-dimensional excitonic energy transport in molecular solids or conjugated organic polymers, including coupling to phonons, WaveTrain can be used for any kind of chain-like quantum systems, with or without periodic boundary conditions and with NN interactions only. The present work describes version 1.0 of our WaveTrain software, based on version 1.2 of scikit_tt, both of which are freely available from the GitHub platform where they will also be further developed. Moreover, WaveTrain is mirrored at SourceForge, within the framework of the WavePacket project for numerical quantum dynamics. Worked-out demonstration examples with complete input and output, including animated graphics, are available. Y1 - 2023 U6 - https://doi.org/10.1063/5.0147314 VL - 158 IS - 16 SP - 164801 ER - TY - JOUR A1 - Reuter, Bernhard A1 - Weber, Marcus A1 - Fackeldey, Konstantin A1 - Röblitz, Susanna A1 - Garcia, Martin E. T1 - Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field JF - Journal of Chemical Theory and Computation N2 - Markov state models (MSMs) have received an unabated increase in popularity in recent years, as they are very well suited for the identification and analysis of metastable states and related kinetics. However, the state-of-the-art Markov state modeling methods and tools enforce the fulfillment of a detailed balance condition, restricting their applicability to equilibrium MSMs. To date, they are unsuitable to deal with general dominant data structures including cyclic processes, which are essentially associated with nonequilibrium systems. To overcome this limitation, we developed a generalization of the common robust Perron Cluster Cluster Analysis (PCCA+) method, termed generalized PCCA (G-PCCA). This method handles equilibrium and nonequilibrium simulation data, utilizing Schur vectors instead of eigenvectors. G-PCCA is not limited to the detection of metastable states but enables the identification of dominant structures in a general sense, unraveling cyclic processes. This is exemplified by application of G-PCCA on nonequilibrium molecular dynamics data of the Amyloid β (1−40) peptide, periodically driven by an oscillating electric field. Y1 - 2018 U6 - https://doi.org/10.1021/acs.jctc.8b00079 VL - 14 IS - 7 SP - 3579 EP - 3594 ER - TY - JOUR A1 - Boeth, Heide A1 - Duda, Georg A1 - Heller, Markus O. A1 - Ehrig, Rainald A1 - Doyscher, Ralf A1 - Jung, Tobias A1 - Moewis, Philippe A1 - Scheffler, Sven A1 - Taylor, William R. T1 - Anterior cruciate ligament-deficient patients with passive knee joint laxity have a decreased range of anterior-posterior motion during active movements JF - The American Journal of Sports Medicine Y1 - 2013 U6 - https://doi.org/10.1177/0363546513480465 VL - 41 IS - 5 SP - 1051 EP - 7 ER - TY - JOUR A1 - Ehrig, Rainald A1 - Heller, Markus O. A1 - Kratzenstein, Stefan A1 - Duda, Georg A1 - Trepczynski, Adam A1 - Taylor, William R. T1 - The SCoRE residual: A quality index to assess the accuracy of joint estimations JF - Journal of Biomechanics Y1 - 2011 U6 - https://doi.org/10.1016/j.jbiomech.2010.12.009 VL - 44 IS - 7 SP - 1400 EP - 1404 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Krause, Rolf T1 - Multiscale Coupling in Function Space - Weak Coupling between Molecular Dynamics and Continuum Mechanics JF - International Journal for Numerical Methods in Engineering Y1 - 2009 U6 - https://doi.org/10.1002/nme.2626 VL - 79 IS - 12 SP - 1517 EP - 1535 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Krause, Dorian A1 - Krause, Rolf A1 - Lenzen, Christoph T1 - Coupling Molecular Dynamics and Continua with Weak Constraints JF - SIAM Multiscale Model. Simul. Y1 - 2011 U6 - https://doi.org//10.1137/100782097 N1 - also as MATHEON Preprint VL - 9 SP - 1459 EP - 1494 ER - TY - JOUR A1 - Krause, Dorian A1 - Fackeldey, Konstantin A1 - Krause, Rolf ED - Griebel, Michael T1 - A Parallel Multiscale Simulation Toolbox for Coupling Molecular Dynamics and Finite Elements JF - Singular Phenomena and Scaling in Mathematical Models Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-00786-1_14 SP - 327 EP - 346 PB - Springer International Publishing ER - TY - JOUR A1 - Fackeldey, Konstantin T1 - Coupling Meshbased and Meshfree Methods by a Transfer Operator Approach JF - IJPAM Y1 - 2011 VL - 69 IS - 2 SP - 185 EP - 202 ER - TY - JOUR A1 - Gelß, Patrick A1 - Matera, Sebastian A1 - Schütte, Christof T1 - Solving the master equation without kinetic Monte Carlo: Tensor train approximations for a CO oxidation model JF - Journal of Computational Physics N2 - In multiscale modeling of heterogeneous catalytic processes, one crucial point is the solution of a Markovian master equation describing the stochastic reaction kinetics. Usually, this is too high-dimensional to be solved with standard numerical techniques and one has to rely on sampling approaches based on the kinetic Monte Carlo method. In this study we break the curse of dimensionality for the direct solution of the Markovian master equation by exploiting the Tensor Train Format for this purpose. The performance of the approach is demonstrated on a first principles based, reduced model for the CO oxidation on the RuO2(110) surface. We investigate the complexity for increasing system size and for various reaction conditions. The advantage over the stochastic simulation approach is illustrated by a problem with increased Y1 - 2016 U6 - https://doi.org/10.1016/j.jcp.2016.03.025 VL - 314 SP - 489 EP - 502 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Röblitz, Susanna A1 - Scharkoi, O. A1 - Weber, Marcus T1 - Soft Versus Hard Metastable Conformations in Molecular Simulations JF - Particle Methods II, Fundamentals and Applications, Barcelona, Spain 26-28 Oct. 2011, E. Onate and D.R.J. Owen (eds.) Y1 - 2011 SP - 899 EP - 909 ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - GenPCCA -- Markov State Models for Non-Equilibrium Steady States JF - Big data clustering: Data preprocessing, variable selection, and dimension reduction. WIAS Report No. 29 Y1 - 2017 U6 - https://doi.org/10.20347/WIAS.REPORT.29 SP - 70 EP - 80 ER - TY - JOUR A1 - Dey, Santanu Sabush A1 - Pokutta, Sebastian T1 - Design and verify: a new scheme for generating cutting-planes JF - Mathematical Programming A Y1 - 2014 UR - http://www.optimization-online.org/DB_HTML/2011/04/3002.html N1 - Additional Note: DOI: 10.1007/978-3-642-20807-2_12 VL - 145 SP - 199 EP - 222 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Harth, Philipp A1 - Isoe, Yasuko A1 - Bahl, Armin A1 - Fotowat, Haleh A1 - Engert, Florian A1 - Hege, Hans-Christian A1 - Baum, Daniel T1 - A Visual Interface for Exploring Hypotheses about Neural Circuits JF - IEEE Transactions on Visualization and Computer Graphics N2 - One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa. Y1 - 2023 U6 - https://doi.org/10.1109/TVCG.2023.3243668 ER - TY - JOUR A1 - Tillmann, Peter A1 - Bläsi, Benedikt A1 - Burger, Sven A1 - Hammerschmidt, Martin A1 - Höhn, Oliver A1 - Becker, Christiane A1 - Jäger, Klaus T1 - Optimizing metal grating back reflectors for III-V-on-silicon multijunction solar cells JF - Opt. Express Y1 - 2021 U6 - https://doi.org/10.1364/OE.426761 VL - 29 SP - 22517 ER - TY - JOUR A1 - Jäger, Klaus A1 - Tillmann, Peter A1 - Katz, Eugene A. A1 - Becker, Christiane T1 - Perovskite/silicon tandem solar cells: Effect of luminescent coupling and bifaciality JF - Sol. RRL Y1 - 2021 U6 - https://doi.org/10.1002/solr.202000628 VL - 5 SP - 2000628 ER - TY - JOUR A1 - Kuhn, Alexander A1 - Engelke, Wito A1 - Rössl, Christian A1 - Hadwiger, Markus A1 - Theisel, Holger T1 - Time Line Cell Tracking for the Approximation of Lagrangian Coherent Structures with Subgrid Accuracy JF - Computer Graphics Forum Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43990 SN - 0934-5892 VL - 33 SP - 222 EP - 234 PB - Wiley Blackwell ER - TY - JOUR A1 - Tillmann, Peter A1 - Jäger, Klaus A1 - Becker, Christiane T1 - Minimising levelised cost of electricity of bifacial solar panel arrays using Bayesian optimisation JF - Sustain. Energy Fuels Y1 - 2020 U6 - https://doi.org/10.1039/C9SE00750D VL - 4 SP - 254 ER - TY - JOUR A1 - Jäger, Klaus A1 - Tillmann, Peter A1 - Becker, Christiane T1 - Detailed illumination model for bifacial solar cells JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.383570 VL - 28 SP - 4751 ER - TY - JOUR A1 - Yoo, Danbi A1 - Tillmann, Peter A1 - Krauss, Tobias A1 - Sutter, Johannes A1 - Harter, Angelika A1 - Trofimov, Sergei A1 - Naydenov, Boris A1 - Jäger, Klaus A1 - Hauser, Hubert A1 - Becker, Christiane T1 - Comparative Optical Analysis of Imprinted Nano-, Micro- and Biotextures on Solar Glasses for Increased Energy Yield JF - Solar RRL Y1 - 2023 U6 - https://doi.org/10.1002/solr.202300071 VL - 7 SP - 2300071 ER - TY - JOUR A1 - Tillmann, Peter A1 - Jäger, Klaus A1 - Karsenti, Asher A1 - Kreinin, Lev A1 - Becker, Christiane T1 - Model-Chain Validation for Estimating the Energy Yield of Bifacial Perovskite/Silicon Tandem Solar Cells JF - Sol. RRL Y1 - 2022 U6 - https://doi.org/10.1002/solr.202200079 VL - 6 SP - 2200079 ER - TY - JOUR A1 - Gelß, Patrick A1 - Klein, Rupert A1 - Matera, Sebastian A1 - Schmidt, Burkhard T1 - Solving the time-independent Schrödinger equation for chains of coupled excitons and phonons using tensor trains JF - The Journal of Chemical Physics N2 - We demonstrate how to apply the tensor-train format to solve the time-independent Schrödinger equation for quasi-one-dimensional excitonic chain systems with and without periodic boundary conditions. The coupled excitons and phonons are modeled by Fröhlich–Holstein type Hamiltonians with on-site and nearest-neighbor interactions only. We reduce the memory consumption as well as the computational costs significantly by employing efficient decompositions to construct low-rank tensor-train representations, thus mitigating the curse of dimensionality. In order to compute also higher quantum states, we introduce an approach that directly incorporates the Wielandt deflation technique into the alternating linear scheme for the solution of eigenproblems. Besides systems with coupled excitons and phonons, we also investigate uncoupled problems for which (semi-)analytical results exist. There, we find that in the case of homogeneous systems, the tensor-train ranks of state vectors only marginally depend on the chain length, which results in a linear growth of the storage consumption. However, the central processing unit time increases slightly faster with the chain length than the storage consumption because the alternating linear scheme adopted in our work requires more iterations to achieve convergence for longer chains and a given rank. Finally, we demonstrate that the tensor-train approach to the quantum treatment of coupled excitons and phonons makes it possible to directly tackle the phenomenon of mutual self-trapping. We are able to confirm the main results of the Davydov theory, i.e., the dependence of the wave packet width and the corresponding stabilization energy on the exciton–phonon coupling strength, although only for a certain range of that parameter. In future work, our approach will allow calculations also beyond the validity regime of that theory and/or beyond the restrictions of the Fröhlich–Holstein type Hamiltonians. Y1 - 2022 U6 - https://doi.org/10.1063/5.0074948 VL - 156 IS - 2 SP - 024109 ER - TY - JOUR A1 - Andrae, Karsten A1 - Merkel, Stefan A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Köppen, Robert A1 - Weber, Marcus A1 - Koch, Matthias T1 - Investigation of the Ergopeptide Epimerization Process JF - Computation N2 - Ergopeptides, like ergocornine and a-ergocryptine, exist in an S- and in an R-configuration. Kinetic experiments imply that certain configurations are preferred depending on the solvent. The experimental methods are explained in this article. Furthermore, computational methods are used to understand this configurational preference. Standard quantum chemical methods can predict the favored configurations by using minimum energy calculations on the potential energy landscape. However, the explicit role of the solvent is not revealed by this type of methods. In order to better understand its influence, classical mechanical molecular simulations are applied. It appears from our research that “folding” the ergopeptide molecules into an intermediate state (between the S- and the R-configuration) is mechanically hindered for the preferred configurations. Y1 - 2014 U6 - https://doi.org/10.3390/computation2030102 VL - 2 IS - 3 SP - 102 EP - 111 ER - TY - JOUR A1 - Schweigart, Fleur T1 - KARTHAGO, TUNESIEN Datengesteuerte Modellierung des Romanisierungsprozesses in Nordafrika JF - e-Forschungsberichte des Deutschen Archäologischen Instituts. Berlin: Deutsches Archäologisches Institut, Zentrale. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.34780/d469-84h2 VL - Fasc. 1 ER - TY - JOUR A1 - Andrae, Karsten A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Scharkoi, Olga A1 - Weber, Marcus T1 - Medizin aus dem Computer JF - Der Anaesthesist Y1 - 2013 U6 - https://doi.org/10.1007/s00101-013-2202-x VL - 62 IS - 7 SP - 561 EP - 557 PB - Springer ER - TY - JOUR A1 - Ziesche, Ralf F. A1 - Arlt, Tobias A1 - Finegan, Donal P. A1 - Heenan, Thomas M.M. A1 - Tengattini, Alessandro A1 - Baum, Daniel A1 - Kardjilov, Nikolay A1 - Markötter, Henning A1 - Manke, Ingo A1 - Kockelmann, Winfried A1 - Brett, Dan J.L. A1 - Shearing, Paul R. T1 - 4D imaging of lithium-batteries using correlative neutron and X-ray tomography with a virtual unrolling technique JF - Nature Communications N2 - The temporally and spatially resolved tracking of lithium intercalation and electrode degradation processes are crucial for detecting and understanding performance losses during the operation of lithium-batteries. Here, high-throughput X-ray computed tomography has enabled the identification of mechanical degradation processes in a commercial Li/MnO2 primary battery and the indirect tracking of lithium diffusion; furthermore, complementary neutron computed tomography has identified the direct lithium diffusion process and the electrode wetting by the electrolyte. Virtual electrode unrolling techniques provide a deeper view inside the electrode layers and are used to detect minor fluctuations which are difficult to observe using conventional three dimensional rendering tools. Moreover, the ‘unrolling’ provides a platform for correlating multi-modal image data which is expected to find wider application in battery science and engineering to study diverse effects e.g. electrode degradation or lithium diffusion blocking during battery cycling. Y1 - 2020 U6 - https://doi.org/10.1038/s41467-019-13943-3 VL - 11 SP - 777 ER - TY - JOUR A1 - Gelß, Patrick A1 - Klus, Stefan A1 - Eisert, Jens A1 - Schütte, Christof T1 - Multidimensional Approximation of Nonlinear Dynamical Systems JF - Journal of Computational and Nonlinear Dynamics N2 - A key task in the field of modeling and analyzing nonlinear dynamical systems is the recovery of unknown governing equations from measurement data only. There is a wide range of application areas for this important instance of system identification, ranging from industrial engineering and acoustic signal processing to stock market models. In order to find appropriate representations of underlying dynamical systems, various data-driven methods have been proposed by different communities. However, if the given data sets are high-dimensional, then these methods typically suffer from the curse of dimensionality. To significantly reduce the computational costs and storage consumption, we propose the method multidimensional approximation of nonlinear dynamical systems (MANDy) which combines data-driven methods with tensor network decompositions. The efficiency of the introduced approach will be illustrated with the aid of several high-dimensional nonlinear dynamical systems. Y1 - 2019 U6 - https://doi.org/10.1115/1.4043148 VL - 14 IS - 6 ER - TY - JOUR A1 - Hoerth, Rebecca M. A1 - Baum, Daniel A1 - Knötel, David A1 - Prohaska, Steffen A1 - Willie, Bettina M. A1 - Duda, Georg A1 - Hege, Hans-Christian A1 - Fratzl, Peter A1 - Wagermaier, Wolfgang T1 - Registering 2D and 3D Imaging Data of Bone during Healing JF - Connective Tissue Research Y1 - 2015 U6 - https://doi.org/10.3109/03008207.2015.1005210 VL - 56 IS - 2 SP - 133 EP - 143 PB - Taylor & Francis ER - TY - JOUR A1 - Scharkoi, Olga A1 - Fackeldey, Konstantin A1 - Merkulow, Igor A1 - Andrae, Karsten A1 - Weber, Marcus A1 - Nehls, Irene T1 - Conformational Analysis of Alternariol on the Quantum Level JF - J. Mol. Model. Y1 - 2013 U6 - https://doi.org/10.1007/s00894-013-1803-2 VL - 19 IS - 6 SP - 2567 EP - 2572 ER - TY - JOUR A1 - Schütte, Christof A1 - Klus, Stefan A1 - Hartmann, Carsten T1 - Overcoming the Timescale Barrier in Molecular Dynamics: Transfer Operators, Variational Principles, and Machine Learning JF - Acta Numerica N2 - One of the main challenges in molecular dynamics is overcoming the ‘timescale barrier’: in many realistic molecular systems, biologically important rare transitions occur on timescales that are not accessible to direct numerical simulation, even on the largest or specifically dedicated supercomputers. This article discusses how to circumvent the timescale barrier by a collection of transfer operator-based techniques that have emerged from dynamical systems theory, numerical mathematics and machine learning over the last two decades. We will focus on how transfer operators can be used to approximate the dynamical behaviour on long timescales, review the introduction of this approach into molecular dynamics, and outline the respective theory, as well as the algorithmic development, from the early numerics-based methods, via variational reformulations, to modern data-based techniques utilizing and improving concepts from machine learning. Furthermore, its relation to rare event simulation techniques will be explained, revealing a broad equivalence of variational principles for long-time quantities in molecular dynamics. The article will mainly take a mathematical perspective and will leave the application to real-world molecular systems to the more than 1000 research articles already written on this subject. Y1 - 2023 U6 - https://doi.org/10.1017/S0962492923000016 VL - 32 SP - 517 EP - 673 ER - TY - JOUR A1 - Mikula, Natalia A1 - Dörffel, Tom A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - An Interactive Approach for Identifying Structure Definitions JF - Computer Graphics Forum N2 - Our ability to grasp and understand complex phenomena is essentially based on recognizing structures and relating these to each other. For example, any meteorological description of a weather condition and explanation of its evolution recurs to meteorological structures, such as convection and circulation structures, cloud fields and rain fronts. All of these are spatiotemporal structures, defined by time-dependent patterns in the underlying fields. Typically, such a structure is defined by a verbal description that corresponds to the more or less uniform, often somewhat vague mental images of the experts. However, a precise, formal definition of the structures or, more generally, concepts is often desirable, e.g., to enable automated data analysis or the development of phenomenological models. Here, we present a systematic approach and an interactive tool to obtain formal definitions of spatiotemporal structures. The tool enables experts to evaluate and compare different structure definitions on the basis of data sets with time-dependent fields that contain the respective structure. Since structure definitions are typically parameterized, an essential part is to identify parameter ranges that lead to desired structures in all time steps. In addition, it is important to allow a quantitative assessment of the resulting structures simultaneously. We demonstrate the use of the tool by applying it to two meteorological examples: finding structure definitions for vortex cores and center lines of temporarily evolving tropical cyclones. Ideally, structure definitions should be objective and applicable to as many data sets as possible. However, finding such definitions, e.g., for the common atmospheric structures in meteorology, can only be a long-term goal. The proposed procedure, together with the presented tool, is just a first systematic approach aiming at facilitating this long and arduous way. Y1 - 2022 U6 - https://doi.org/10.1111/cgf.14543 VL - 41 IS - 3 SP - 321 EP - 332 ER - TY - JOUR A1 - Fröhler, Bernhard A1 - Elberfeld, Tim A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Kastner, Johann A1 - Heinzl, Christoph T1 - Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres JF - Nondestructive Testing and Evaluation N2 - We present visual methods for the analysis and comparison of the results of curved fibre reconstruction algorithms, i.e., of algorithms extracting characteristics of curved fibres from X-ray computed tomography scans. In this work, we extend previous methods for the analysis and comparison of results of different fibre reconstruction algorithms or parametrisations to the analysis of curved fibres. We propose fibre dissimilarity measures for such curved fibres and apply these to compare multiple results to a specified reference. We further propose visualisation methods to analyse differences between multiple results quantitatively and qualitatively. In two case studies, we show that the presented methods provide valuable insights for advancing and parametrising fibre reconstruction algorithms, and support in improving their results in characterising curved fibres. Y1 - 2020 U6 - https://doi.org/10.1080/10589759.2020.1774583 VL - 35 IS - 3 SP - 328 EP - 341 ER - TY - JOUR A1 - Latorre, J. A1 - Metzner, Ph. A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Structure-preserving numerical discretization of reversible diffusions JF - Commun. Math. Sci. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/896/ VL - 9 IS - 4 SP - 1051 EP - 1072 ER - TY - JOUR A1 - Zhang, Wei A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Effective dynamics along given reaction coordinates, and reaction rate theory JF - Faraday Discussions Y1 - 2016 U6 - https://doi.org/10.1039/C6FD00147E IS - 195 SP - 365 EP - 394 ER - TY - JOUR A1 - Zhang, Wei A1 - Hartmann, Carsten A1 - von Kleist, Max T1 - Optimal control of Markov jump processes: Asymptotic analysis, algorithms and applications to the modeling of chemical reaction systems JF - Communications in Mathematical Sciences N2 - Markov jump processes are widely used to model natural and engineered processes. In the context of biological or chemical applications one typically refers to the chemical master equation (CME), which models the evolution of the probability mass of any copy-number combination of the interacting particles. When many interacting particles (“species”) are considered, the complexity of the CME quickly increases, making direct numerical simulations impossible. This is even more problematic when one aims at controlling the Markov jump processes defined by the CME. In this work, we study both open loop and feedback optimal control problems of the Markov jump processes in the case that the controls can only be switched at fixed control stages. Based on Kurtz’s limit theorems, we prove the convergence of the respective control value functions of the underlying Markov decision problem as the copy numbers of the species go to infinity. In the case of the optimal control problem on a finite time-horizon, we propose a hybrid control policy algorithm to overcome the difficulties due to the curse of dimensionality when the copy number of the involved species is large. Two numerical examples demonstrate the suitability of both the analysis and the proposed algorithms. Y1 - 2018 U6 - https://doi.org/10.4310/CMS.2018.v16.n2.a1 SP - 293 EP - 331 ER - TY - JOUR A1 - Donati, Luca A1 - Hartmann, Carsten A1 - Keller, Bettina G. T1 - Girsanov reweighting for path ensembles and Markov state models JF - The Journal of Chemical Physics N2 - The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSMs) of the molecular dynamics can be formulated as a combined phase-space and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor “on the fly” during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process and an artificial many-body system to alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics. Y1 - 2017 U6 - https://doi.org/10.1063/1.4989474 VL - 146 IS - 24 SP - 244112 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Zhang, Wei T1 - Jarzynski's equality, fluctuation theorems, and variance reduction: Mathematical analysis and numerical algorithms JF - Journal of Statistical Physics N2 - In this paper, we study Jarzynski's equality and fluctuation theorems for diffusion processes. While some of the results considered in the current work are known in the (mainly physics) literature, we review and generalize these nonequilibrium theorems using mathematical arguments, therefore enabling further investigations in the mathematical community. On the numerical side, variance reduction approaches such as importance sampling method are studied in order to compute free energy differences based on Jarzynski's equality. Y1 - 2018 U6 - https://doi.org/10.1007/s10955-019-02286-4 VL - 175 IS - 6 SP - 1214 EP - 1261 ER - TY - JOUR A1 - Wang, Han A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique JF - Phys. Rev. X Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevX.3.011018 VL - 3 SP - 011018 ER - TY - JOUR A1 - Horenko, Illia A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Noé, Frank T1 - Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes JF - Phys. Rev. E Y1 - 2007 UR - http://publications.imp.fu-berlin.de/31/ U6 - https://doi.org/10.1103/PhysRevE.76.016706 VL - 76 IS - 01 SP - 016706 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Kalibaeva, G. A1 - Pierro, M. A1 - Ciccotti, Giovanni T1 - Fast Simulation of Polymer Chains JF - J. Chem. Phys. Y1 - 2009 UR - http://publications.imp.fu-berlin.de/18/ U6 - https://doi.org/10.1063/1.3110603 VL - 130 SP - 144101 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Efficient rare event simulation by optimal nonequilibrium forcing JF - J. Stat. Mech. Theor. Exp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1153/ U6 - https://doi.org/10.1088/1742-5468/2012/11/P11004 VL - 2012 SP - P11004 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Ciccotti, Giovanni T1 - On the linear response of mechanical systems with constraints JF - J. Chem. Phys. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/794/ U6 - https://doi.org/10.1063/1.3354126 VL - 132 IS - 11 SP - 111103 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Vulcanov, V.-M. A1 - Schütte, Christof T1 - Balanced Truncation of Second Order Systems JF - Multiscale Model. Simul. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/28/ U6 - https://doi.org/10.1137/080732717 VL - 8 IS - 4 SP - 1348 EP - 1367 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Geometric Approach to Constrained Molecular Dynamics and Free Energy JF - Comm. Math. Sci. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/48/ VL - 3 IS - 1 SP - 1 EP - 20 ER - TY - JOUR A1 - Schütte, Christof A1 - Noé, Frank A1 - Meerbach, E. A1 - Metzner, Ph. A1 - Hartmann, Carsten T1 - Conformation Dynamics JF - Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), Y1 - 2009 UR - http://publications.imp.fu-berlin.de/110/ U6 - https://doi.org/10.4171/056-1/15 SP - 297 EP - 335 PB - EMS publishing house ER - TY - JOUR A1 - Schütte, Christof A1 - Walter, J. A1 - Hartmann, Carsten A1 - Huisinga, Wilhelm T1 - An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations JF - Multiscale Model. Simul. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/62/ U6 - https://doi.org/10.1137/030600308 VL - 2 IS - 3 SP - 501 EP - 526 ER - TY - JOUR A1 - Schütte, Christof A1 - Winkelmann, Stefanie A1 - Hartmann, Carsten T1 - Optimal control of molecular dynamics using Markov state models JF - Math. Program. (Series B) Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1107/ U6 - https://doi.org/10.1007/s10107-012-0547-6 VL - 134 IS - 1 SP - 259 EP - 282 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Balancing of partially-observed stochastic differential equations JF - 47th IEEE Conference on Decision and Control Y1 - 2008 UR - http://publications.imp.fu-berlin.de/16/ U6 - https://doi.org/10.1109/CDC.2008.4739161 SP - 4867 EP - 4872 ER - TY - JOUR A1 - Latorre, J. A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Free energy computation by controlled Langevin processes JF - Procedia Computer Science Y1 - 2010 UR - http://publications.imp.fu-berlin.de/801/ U6 - https://doi.org/10.1016/j.procs.2010.04.179 VL - 1 IS - 1 SP - 1591 EP - 1600 ER - TY - JOUR A1 - Schäfer-Bung, B. A1 - Hartmann, Carsten A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Dimension reduction by balanced truncation JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1023/ VL - 135 IS - 1 SP - 014112 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Comment on Two Distinct Notions of Free Energy JF - Physica D Y1 - 2007 UR - http://publications.imp.fu-berlin.de/30/ U6 - https://doi.org/10.1016/j.physd.2007.02.006 VL - 228 IS - 1 SP - 59 EP - 63 ER - TY - JOUR A1 - Udvary, Daniel A1 - Harth, Philipp A1 - Macke, Jakob H. A1 - Hege, Hans-Christian A1 - de Kock, Christiaan P. J. A1 - Sakmann, Bert A1 - Oberlaender, Marcel T1 - The Impact of Neuron Morphology on Cortical Network Architecture JF - Cell Reports N2 - The neurons in the cerebral cortex are not randomly interconnected. This specificity in wiring can result from synapse formation mechanisms that connect neurons depending on their electrical activity and genetically defined identity. Here, we report that the morphological properties of the neurons provide an additional prominent source by which wiring specificity emerges in cortical networks. This morphologically determined wiring specificity reflects similarities between the neurons’ axo-dendritic projections patterns, the packing density and cellular diversity of the neuropil. The higher these three factors are the more recurrent is the topology of the network. Conversely, the lower these factors are the more feedforward is the network’s topology. These principles predict the empirically observed occurrences of clusters of synapses, cell type-specific connectivity patterns, and nonrandom network motifs. Thus, we demonstrate that wiring specificity emerges in the cerebral cortex at subcellular, cellular and network scales from the specific morphological properties of its neuronal constituents. Y1 - 2022 U6 - https://doi.org/10.1016/j.celrep.2022.110677 VL - 39 IS - 2 ER - TY - JOUR A1 - Aboulhassan, Amal A1 - Baum, Daniel A1 - Wodo, Olga A1 - Ganapathysubramanian, Baskar A1 - Amassian, Aram A1 - Hadwiger, Markus T1 - A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials JF - Computer Graphics Forum N2 - The current characterization methods of the Bulk Heterojunction (BHJ) - the main material of the new Organic Photovoltaic solar cells - are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual charac- terization and exploration of local structure-performance correlations. We propose a new formula that correlates the structural features to the performance bottlenecks. Since research into BHJ materials is highly multidisci- plinary, we enable a visual feedback strategy that allows the scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characteri- zations. We furthermore show that our approach could reduce the previous work-flow time from days to minutes. Y1 - 2015 U6 - https://doi.org/10.1111/cgf.12652 VL - 34 IS - 3 SP - 401 EP - 410 PB - Wiley ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables JF - Z. Angew. Math. Mech. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/47/ U6 - https://doi.org/10.1002/zamm.200410218 VL - 85 IS - 10 SP - 700 EP - 710 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Richter, Lorenz T1 - Nonasymptotic bounds for suboptimal importance sampling Y1 - 2021 ER - TY - JOUR A1 - Aboulhassan, Amal A1 - Sicat, Ronell A1 - Baum, Daniel A1 - Wodo, Olga A1 - Hadwiger, Markus T1 - Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies JF - Computer Graphics Forum N2 - The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths. Y1 - 2017 U6 - https://doi.org/10.1111/cgf.13191 VL - 36 IS - 3 SP - 329 EP - 339 PB - Wiley ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Weber, Marcus A1 - Zhang, Wei T1 - Importance sampling in path space for diffusion processes with slow-fast variables JF - Probability Theory and Related Fields N2 - Importance sampling is a widely used technique to reduce the variance of a Monte Carlo estimator by an appropriate change of measure. In this work, we study importance sampling in the framework of diffusion process and consider the change of measure which is realized by adding a control force to the original dynamics. For certain exponential type expectation, the corresponding control force of the optimal change of measure leads to a zero-variance estimator and is related to the solution of a Hamilton–Jacobi–Bellmann equation. We focus on certain diffusions with both slow and fast variables, and the main result is that we obtain an upper bound of the relative error for the importance sampling estimators with control obtained from the limiting dynamics. We demonstrate our approximation strategy with an illustrative numerical example. Y1 - 2017 UR - http://rdcu.be/oA51 U6 - https://doi.org/10.1007/s00440-017-0755-3 N1 - If you are not subscribing to the journal please use the http link below as part of the Springer Nature SharedIt initiative SP - 1 EP - 52 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Zhang, Wei T1 - Model reduction algorithms for optimal control and importance sampling of diffusions JF - Nonlinearity N2 - We propose numerical algorithms for solving optimal control and importance sampling problems based on simplified models. The algorithms combine model reduction techniques for multiscale diffusions and stochastic optimization tools, with the aim of reducing the original, possibly high-dimensional problem to a lower dimensional representation of the dynamics, in which only a few relevant degrees of freedom are controlled or biased. Specifically, we study situations in which either a reaction coordinate onto which the dynamics can be projected is known, or situations in which the dynamics shows strongly localized behavior in the small noise regime. No explicit assumptions about small parameters or scale separation have to be made. We illustrate the approach with simple, but paradigmatic numerical examples. Y1 - 2016 U6 - https://doi.org/10.1088/0951-7715/29/8/2298 VL - 29 IS - 8 SP - 2298 EP - 2326 ER - TY - JOUR A1 - Zhang, Wei A1 - Wang, Han A1 - Hartmann, Carsten A1 - Weber, Marcus A1 - Schütte, Christof T1 - Applications of the cross-entropy method to importance sampling and optimal control of diffusions JF - Siam Journal on Scientific Computing Y1 - 2014 U6 - https://doi.org/10.1137/14096493X VL - 36 IS - 6 SP - A2654 EP - A2672 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Banisch, Ralf A1 - Sarich, Marco A1 - Badowski, Thomas A1 - Schütte, Christof T1 - Characterization of Rare Events in Molecular Dynamics JF - Entropy (Special Issue) Y1 - 2013 U6 - https://doi.org/10.3390/e16010350 VL - 16 IS - 1 SP - 350 EP - 376 ER - TY - JOUR A1 - Wang, Han A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Linear response theory and optimal control for a molecular system under nonequilibrium conditions JF - Molecular Physics Y1 - 2013 UR - http://publications.imp.fu-berlin.de/1297/ U6 - https://doi.org/10.1080/00268976.2013.844370 VL - 111 SP - 3555 EP - 3564 ER - TY - JOUR A1 - Sarich, Marco A1 - Banisch, Ralf A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Markov State Models for Rare Events in Molecular Dynamics JF - Entropy (Special Issue) Y1 - 2013 U6 - https://doi.org/10.3390/e16010258 VL - 16 IS - 1 SP - 258 EP - 286 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Richter, Lorenz A1 - Schütte, Christof A1 - Zhang, Wei T1 - Variational characterization of free energy: theory and algorithms JF - Entropy Y1 - 2017 U6 - https://doi.org/10.3390/e19110626 VL - 19 IS - 11 ER - TY - JOUR A1 - Hanik, Martin A1 - Demirtaş, Mehmet Arif A1 - Gharsallaoui, Mohammed Amine A1 - Rekik, Islem T1 - Predicting cognitive scores with graph neural networks through sample selection learning JF - Brain Imaging and Behavior N2 - Analyzing the relation between intelligence and neural activity is of the utmost importance in understanding the working principles of the human brain in health and disease. In existing literature, functional brain connectomes have been used successfully to predict cognitive measures such as intelligence quotient (IQ) scores in both healthy and disordered cohorts using machine learning models. However, existing methods resort to flattening the brain connectome (i.e., graph) through vectorization which overlooks its topological properties. To address this limitation and inspired from the emerging graph neural networks (GNNs), we design a novel regression GNN model (namely RegGNN) for predicting IQ scores from brain connectivity. On top of that, we introduce a novel, fully modular sample selection method to select the best samples to learn from for our target prediction task. However, since such deep learning architectures are computationally expensive to train, we further propose a \emph{learning-based sample selection} method that learns how to choose the training samples with the highest expected predictive power on unseen samples. For this, we capitalize on the fact that connectomes (i.e., their adjacency matrices) lie in the symmetric positive definite (SPD) matrix cone. Our results on full-scale and verbal IQ prediction outperforms comparison methods in autism spectrum disorder cohorts and achieves a competitive performance for neurotypical subjects using 3-fold cross-validation. Furthermore, we show that our sample selection approach generalizes to other learning-based methods, which shows its usefulness beyond our GNN architecture. Y1 - 2022 U6 - https://doi.org/10.1007/s11682-021-00585-7 VL - 16 SP - 1123 EP - 1138 ER - TY - JOUR A1 - Herter, Felix A1 - Hege, Hans-Christian A1 - Hadwiger, Markus A1 - Lepper, Verena A1 - Baum, Daniel T1 - Thin-Volume Visualization on Curved Domains JF - Computer Graphics Forum N2 - Thin, curved structures occur in many volumetric datasets. Their analysis using classical volume rendering is difficult because parts of such structures can bend away or hide behind occluding elements. This problem cannot be fully compensated by effective navigation alone, because structure-adapted navigation in the volume is cumbersome and only parts of the structure are visible in each view. We solve this problem by rendering a spatially transformed view into the volume so that an unobscured visualization of the entire curved structure is obtained. As a result, simple and intuitive navigation becomes possible. The domain of the spatial transform is defined by a triangle mesh that is topologically equivalent to an open disc and that approximates the structure of interest. The rendering is based on ray-casting in which the rays traverse the original curved sub-volume. In order to carve out volumes of varying thickness, the lengths of the rays as well as the position of the mesh vertices can be easily modified in a view-controlled manner by interactive painting. We describe a prototypical implementation and demonstrate the interactive visual inspection of complex structures from digital humanities, biology, medicine, and materials science. Displaying the structure as a whole enables simple inspection of interesting substructures in their original spatial context. Overall, we show that transformed views utilizing ray-casting-based volume rendering supported by guiding surface meshes and supplemented by local, interactive modifications of ray lengths and vertex positions, represent a simple but versatile approach to effectively visualize thin, curved structures in volumetric data. Y1 - 2021 U6 - https://doi.org/10.1111/cgf.14296 VL - 40 IS - 3 SP - 147 EP - 157 PB - Wiley-Blackwell Publishing Ltd. CY - United Kingdom ER - TY - JOUR A1 - Dell’Amico, M. A1 - Hadjidimitriou, Natalia Selini A1 - Koch, Thorsten A1 - Petkovic, Milena T1 - Forecasting Natural Gas Flows in Large Networks JF - Machine Learning, Optimization, and Big Data. MOD 2017. N2 - Natural gas is the cleanest fossil fuel since it emits the lowest amount of other remains after being burned. Over the years, natural gas usage has increased significantly. Accurate forecasting is crucial for maintaining gas supplies, transportation and network stability. This paper presents two methodologies to identify the optimal configuration o parameters of a Neural Network (NN) to forecast the next 24 h of gas flow for each node of a large gas network. In particular the first one applies a Design Of Experiments (DOE) to obtain a quick initial solution. An orthogonal design, consisting of 18 experiments selected among a total of 4.374 combinations of seven parameters (training algorithm, transfer function, regularization, learning rate, lags, and epochs), is used. The best result is selected as initial solution of an extended experiment for which the Simulated Annealing is run to find the optimal design among 89.100 possible combinations of parameters. The second technique is based on the application of Genetic Algorithm for the selection of the optimal parameters of a recurrent neural network for time series forecast. GA was applied with binary representation of potential solutions, where subsets of bits in the bit string represent different values for several parameters of the recurrent neural network. We tested these methods on three municipal nodes, using one year and half of hourly gas flow to train the network and 60 days for testing. Our results clearly show that the presented methodologies bring promising results in terms of optimal configuration of parameters and forecast error. Y1 - 2018 U6 - https://doi.org/https://doi.org/10.1007/978-3-319-72926-8_14 VL - Lecture Notes in Computer Science IS - vol 10710 SP - 158 EP - 171 ER - TY - JOUR A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - A Hierarchical Geodesic Model for Longitudinal Analysis on Manifolds JF - Journal of Mathematical Imaging and Vision N2 - In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and employ the approach for longitudinal analysis of 2D rat skulls shapes as well as 3D shapes derived from an imaging study on osteoarthritis. Particularly, we perform hypothesis test and estimate the mean trends. Y1 - 2022 U6 - https://doi.org/10.1007/s10851-022-01079-x VL - 64 IS - 4 SP - 395 EP - 407 ER - TY - JOUR A1 - Udvary, Daniel A1 - Harth, Philipp A1 - Macke, Jakob H. A1 - Hege, Hans-Christian A1 - de Kock, Christiaan P. J. A1 - Sakmann, Bert A1 - Oberlaender, Marcel T1 - A Theory for the Emergence of Neocortical Network Architecture JF - BioRxiv Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1101/2020.11.13.381087 ER - TY - JOUR A1 - Hanik, Martin A1 - Ducke, Benjamin A1 - Hege, Hans-Christian A1 - Fless, Friederike A1 - von Tycowicz, Christoph T1 - Intrinsic shape analysis in archaeology: A case study on ancient sundials JF - Journal on Computing and Cultural Heritage N2 - The fact that the physical shapes of man-made objects are subject to overlapping influences—such as technological, economic, geographic, and stylistic progressions—holds great information potential. On the other hand, it is also a major analytical challenge to uncover these overlapping trends and to disentagle them in an unbiased way. This paper explores a novel mathematical approach to extract archaeological insights from ensembles of similar artifact shapes. We show that by considering all shape information in a find collection, it is possible to identify shape patterns that would be difficult to discern by considering the artifacts individually or by classifying shapes into predefined archaeological types and analyzing the associated distinguishing characteristics. Recently, series of high-resolution digital representations of artifacts have become available. Such data sets enable the application of extremely sensitive and flexible methods of shape analysis. We explore this potential on a set of 3D models of ancient Greek and Roman sundials, with the aim of providing alternatives to the traditional archaeological method of “trend extraction by ordination” (typology). In the proposed approach, each 3D shape is represented as a point in a shape space—a high-dimensional, curved, non-Euclidean space. Proper consideration of its mathematical properties reduces bias in data analysis and thus improves analytical power. By performing regression in shape space, we find that for Roman sundials, the bend of the shadow-receiving surface of the sundials changes with the latitude of the location. This suggests that, apart from the inscribed hour lines, also a sundial’s shape was adjusted to the place of installation. As an example of more advanced inference, we use the identified trend to infer the latitude at which a sundial, whose location of installation is unknown, was placed. We also derive a novel method for differentiated morphological trend assertion, building upon and extending the theory of geometric statistics and shape analysis. Specifically, we present a regression-based method for statistical normalization of shapes that serves as a means of disentangling parameter-dependent effects (trends) and unexplained variability. In addition, we show that this approach is robust to noise in the digital reconstructions of the artifact shapes. Y1 - 2023 U6 - https://doi.org/10.1145/3606698 VL - 16 IS - 4 SP - 1 EP - 26 ER - TY - JOUR A1 - Boelts, Jan A1 - Harth, Philipp A1 - Gao, Richard A1 - Udvary, Daniel A1 - Yanez, Felipe A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel A1 - Macke, Jakob H. T1 - Simulation-based inference for efficient identification of generative models in computational connectomics JF - PLOS Computational Biology N2 - Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neuronal networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters, and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a fixed wiring rule to fit the empirical data, SBI considers many parametrizations of a rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rule parameters and relies on machine learning methods to estimate a probability distribution (the 'posterior distribution over parameters conditioned on the data') that characterizes all data-compatible parameters. We demonstrate how to apply SBI in computational connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data. Y1 - 2023 U6 - https://doi.org/10.1371/journal.pcbi.1011406 VL - 19 IS - 9 ER - TY - JOUR A1 - Boelts, Jan A1 - Harth, Philipp A1 - Gao, Richard A1 - Udvary, Daniel A1 - Yanez, Felipe A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel A1 - Macke, Jakob H T1 - Simulation-based inference for efficient identification of generative models in connectomics JF - bioRxiv N2 - Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neural networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a single rule to fit the empirical data, SBI considers many parametrizations of a wiring rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rules and relies on machine learning methods to estimate a probability distribution (the `posterior distribution over rule parameters conditioned on the data') that characterizes all data-compatible rules. We demonstrate how to apply SBI in connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-89890 ER - TY - JOUR A1 - Bienstock, Daniel A1 - Muñoz, Gonzalo A1 - Pokutta, Sebastian T1 - Principled Deep Neural Network Training Through Linear Programming JF - Discrete Optimization N2 - Deep learning has received much attention lately due to the impressive empirical performance achieved by training algorithms. Consequently, a need for a better theoretical understanding of these problems has become more evident and multiple works in recent years have focused on this task. In this work, using a unified framework, we show that there exists a polyhedron that simultaneously encodes, in its facial structure, all possible deep neural network training problems that can arise from a given architecture, activation functions, loss function, and sample size. Notably, the size of the polyhedral representation depends only linearly on the sample size, and a better dependency on several other network parameters is unlikely. Using this general result, we compute the size of the polyhedral encoding for commonly used neural network architectures. Our results provide a new perspective on training problems through the lens of polyhedral theory and reveal strong structure arising from these problems. Y1 - 2023 U6 - https://doi.org/10.1016/j.disopt.2023.100795 VL - 49 ER - TY - JOUR A1 - Le, Thi Thai A1 - Tran, Van Cuc A1 - Phung, Dang Hieu T1 - Numerical simulation of tidal flow in Danang Bay Based on non-hydrostatic shallow water equations JF - Pacific Journal of Mathematics for Industry N2 - This paper presents a numerical simulation of the tidal flow in Danang Bay (Vietnam) based on the non-hydrostatic shallow water equations. First, to test the simulation capability of the non-hydrostatic model, we have made a test simulation comparing it with the experiment by Beji and Battjes 1993. Simulation results for this case are compared with both the experimental data and calculations obtained from the traditional hydrostatic model. It is shown that the non-hydrostatic model is better than the hydrostatic model when the seabed topography variation is complex. The usefulness of the non-hydrostatic model is father shown by successfully simulating the tidal flow of Danang Bay. Y1 - 2016 U6 - https://doi.org/10.1186/s40736-015-0020-6 VL - 8 IS - 1 ER - TY - JOUR A1 - Kevin-Martin, Aigner A1 - Bärmann, Andreas A1 - Braun, Kristin A1 - Liers, Frauke A1 - Pokutta, Sebastian A1 - Schneider, Oskar A1 - Sharma, Kartikey A1 - Tschuppik, Sebastian T1 - Data-driven Distributionally Robust Optimization over Time JF - INFORMS Journal on Optimization N2 - Stochastic optimization (SO) is a classical approach for optimization under uncertainty that typically requires knowledge about the probability distribution of uncertain parameters. Because the latter is often unknown, distributionally robust optimization (DRO) provides a strong alternative that determines the best guaranteed solution over a set of distributions (ambiguity set). In this work, we present an approach for DRO over time that uses online learning and scenario observations arriving as a data stream to learn more about the uncertainty. Our robust solutions adapt over time and reduce the cost of protection with shrinking ambiguity. For various kinds of ambiguity sets, the robust solutions converge to the SO solution. Our algorithm achieves the optimization and learning goals without solving the DRO problem exactly at any step. We also provide a regret bound for the quality of the online strategy that converges at a rate of O(log T/T−−√), where T is the number of iterations. Furthermore, we illustrate the effectiveness of our procedure by numerical experiments on mixed-integer optimization instances from popular benchmark libraries and give practical examples stemming from telecommunications and routing. Our algorithm is able to solve the DRO over time problem significantly faster than standard reformulations. Y1 - 2023 U6 - https://doi.org/10.1287/ijoo.2023.0091 VL - 5 IS - 4 SP - 376 EP - 394 ER - TY - JOUR A1 - Anteghini, Marco A1 - Martins dos Santos, Vitor AP A1 - Saccenti, Edoardo T1 - PortPred: Exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates JF - Journal of Cellular Biochemistry N2 - The physiology of every living cell is regulated at some level by transporter proteins which constitute a relevant portion of membrane-bound proteins and are involved in the movement of ions, small and macromolecules across bio-membranes. The importance of transporter proteins is unquestionable. The prediction and study of previously unknown transporters can lead to the discovery of new biological pathways, drugs and treatments. Here we present PortPred, a tool to accurately identify transporter proteins and their substrate starting from the protein amino acid sequence. PortPred successfully combines pre-trained deep learning-based protein embeddings and machine learning classification approaches and outperforms other state-of-the-art methods. In addition, we present a comparison of the most promising protein sequence embeddings (Unirep, SeqVec, ProteinBERT, ESM-1b) and their performances for this specific task. Y1 - 2023 U6 - https://doi.org/10.1002/jcb.30490 VL - 124 IS - 11 SP - 1665 EP - 1885 ER - TY - JOUR A1 - Boege, Tobias A1 - Fritze, René A1 - Görgen, Christiane A1 - Hanselmann, Jeroen A1 - Iglezakis, Dorothea A1 - Kastner, Lars A1 - Koprucki, Thomas A1 - Krause, Tabea A1 - Lehrenfeld, Christoph A1 - Polla, Silvia A1 - Reidelbach, Marco A1 - Riedel, Christian A1 - Saak, Jens A1 - Schembera, Björn A1 - Tabelow, Karsten A1 - Weber, Marcus T1 - Research-Data Management Planning in the German Mathematical Community JF - Eur. Math. Soc. Mag. N2 - In this paper we discuss the notion of research data for the field of mathematics and report on the status quo of research-data management and planning. A number of decentralized approaches are presented and compared to needs and challenges faced in three use cases from different mathematical subdisciplines. We highlight the importance of tailoring research-data management plans to mathematicians’ research processes and discuss their usage all along the data life cycle. Y1 - 2023 U6 - https://doi.org/10.4171/mag/152 VL - 130 SP - 40 EP - 47 ER - TY - JOUR A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - Ehrenfest dynamics implemented in the all-electron package exciting JF - Electron. Struct. N2 - Ehrenfest dynamics combined with real-time time-dependent density functional theory has proven to be a reliable tool to study non-adiabatic molecular dynamics with a reasonable computational cost. Among other possibilities, it allows for assessing in real time electronic excitations generated by ultra-fast laser pulses, as e.g., in pump–probe spectroscopy, and their coupling to the nuclear vibrations even beyond the linear regime. In this work, we present its implementation in the all-electron full-potential package exciting. Three cases are presented as examples: diamond and cubic boron nitride (BN) relaxed after an initial lattice distortion, and cubic BN exposed to a laser pulse. Comparison with the Octopus code exhibits good agreement. Y1 - 2022 U6 - https://doi.org/10.1088/2516-1075/ac7afc VL - 4 SP - 037001 ER - TY - JOUR A1 - Beron-Vera, Francisco Javier A1 - Olascoaga, Maria Josefina A1 - Helfmann, Luzie A1 - Miron, Philippe T1 - Sampling-Dependent Transition Paths of Iceland-Scotland Overflow Water JF - Journal of Physical Oceanography N2 - In this note, we apply Transition Path Theory (TPT) from Markov chains to shed light on the problem of Iceland-Scotland Overflow Water (ISOW) equatorward export. A recent analysis of observed trajectories of submerged floats demanded revision of the traditional abyssal circulation theory, which postulates that ISOW should steadily flow along a deep boundary current (DBC) around the subpolar North Atlantic prior to exiting it. The TPT analyses carried out here allow to focus the attention on the portions of flow from the origin of ISOW to the region where ISOW exits the subpolar North Atlantic and suggest that insufficient sampling may be biasing the aforementioned demand. The analyses, appropriately adapted to represent a continuous input of ISOW, are carried out on three time-homogeneous Markov chains modeling the ISOW flow. One is constructed using a high number of simulated trajectories homogeneously covering the flow domain. The other two use much fewer trajectories which heterogeneously cover the domain. The trajectories in the latter two chains are observed trajectories or simulated trajectories subsampled at the observed frequency. While the densely sampled chain supports a well-defined DBC, the more heterogeneously sampled chains do not, irrespective of whether observed or simulated trajectories are used. Studying the sampling sensitivity of the Markov chains, we can give recommendations for enlarging the existing float dataset to improve the significance of conclusions about time-asymptotic aspects of the ISOW circulation. Y1 - 2023 U6 - https://doi.org/10.1175/JPO-D-22-0172.1 VL - 53 IS - 4 SP - 1151 EP - 1160 ER - TY - JOUR A1 - Clausecker, Robert A1 - Lemire, Daniel T1 - Transcoding unicode characters with AVX-512 instructions JF - Software: Practice and Experience N2 - Intel includes in its recent processors a powerful set of instructions capable of processing 512-bit registers with a single instruction (AVX-512). Some of these instructions have no equivalent in earlier instruction sets. We leverage these instructions to efficiently transcode strings between the most common formats: UTF-8 and UTF-16. With our novel algorithms, we are often twice as fast as the previous best solutions. For example, we transcode Chinese text from UTF-8 to UTF-16 at more than 5 GiB s−1 using fewer than 2 CPU instructions per character. To ensure reproducibility, we make our software freely available as an open-source library. Our library is part of the popular Node.js JavaScript runtime. Y1 - 2023 U6 - https://doi.org/10.1002/spe.3261 VL - 53 IS - 12 SP - 2430 EP - 2462 PB - John Wiley & Sons Ltd. ER - TY - JOUR A1 - Policht, Veronica R. A1 - Mittenzwey, Henry A1 - Dogadov, Oleg A1 - Katzer, Manuel A1 - Villa, Andrea A1 - Li, Qiuyang A1 - Kaiser, Benjamin A1 - Ross, Aaron M. A1 - Scotognella, Francesco A1 - Zhu, Xiaoyang A1 - Knorr, Andreas A1 - Selig, Malte A1 - Cerullo, Giulio A1 - Dal Conte, Stefano T1 - Time-domain observation of interlayer exciton formation and thermalization in a MoSe2/WSe2 heterostructure JF - Nature Communications N2 - Vertical heterostructures of transition metal dichalcogenides (TMDs) host interlayer excitons with electrons and holes residing in different layers. With respect to their intralayer counterparts, interlayer excitons feature longer lifetimes and diffusion lengths, paving the way for room temperature excitonic optoelectronic devices. The interlayer exciton formation process and its underlying physical mechanisms are largely unexplored. Here we use ultrafast transient absorption spectroscopy with a broadband white-light probe to simultaneously resolve interlayer charge transfer and interlayer exciton formation dynamics in a MoSe2/WSe2 heterostructure. We observe an interlayer exciton formation timescale nearly an order of magnitude (~1 ps) longer than the interlayer charge transfer time (~100 fs). Microscopic calculations attribute this relative delay to an interplay of a phonon-assisted interlayer exciton cascade and thermalization, and excitonic wave-function overlap. Our results may explain the efficient photocurrent generation observed in optoelectronic devices based on TMD heterostructures, as the interlayer excitons are able to dissociate during thermalization. Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-42915-x VL - 14 SP - 1 EP - 9 PB - Springer Nature ER - TY - JOUR A1 - Eifler, Leon A1 - Nicolas-Thouvenin, Jules A1 - Gleixner, Ambros T1 - Combining Precision Boosting with LP Iterative Refinement for Exact Linear Optimization N2 - This article studies a combination of the two state-of-the-art algorithms for the exact solution of linear programs (LPs) over the rational numbers, i.e., without any roundoff errors or numerical tolerances. By integrating the method of precision boosting inside an LP iterative refinement loop, the combined algorithm is able to leverage the strengths of both methods: the speed of LP iterative refinement, in particular in the majority of cases when a double-precision floating-point solver is able to compute approximate solutions with small errors, and the robustness of precision boosting whenever extended levels of precision become necessary. We compare the practical performance of the resulting algorithm with both puremethods on a large set of LPs and mixed-integer programs (MIPs). The results show that the combined algorithm solves more instances than a pure LP iterative refinement approach, while being faster than pure precision boosting. When embedded in an exact branch-and-cut framework for MIPs, the combined algorithm is able to reduce the number of failed calls to the exact LP solver to zero, while maintaining the speed of the pure LP iterative refinement approach. Y1 - 2023 ER - TY - JOUR A1 - Charron, Nicholas A1 - Musil, Félix A1 - Guljas, Andrea A1 - Chen, Yaoyi A1 - Bonneau, Klara A1 - Pasos-Trejo, Aldo A1 - Jacopo, Venturin A1 - Daria, Gusew A1 - Zaporozhets, Iryna A1 - Krämer, Andreas A1 - Templeton, Clark A1 - Atharva, Kelkar A1 - Durumeric, Aleksander A1 - Olsson, Simon A1 - Pérez, Adrià A1 - Majewski, Maciej A1 - Husic, Brooke A1 - Patel, Ankit A1 - De Fabritiis, Gianni A1 - Noé, Frank A1 - Clementi, Cecilia T1 - Navigating protein landscapes with a machine-learned transferable coarse-grained model JF - Arxiv N2 - The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar prediction performance has been a long-standing challenge. By combining recent deep learning methods with a large and diverse training set of all-atom protein simulations, we here develop a bottom-up CG force field with chemical transferability, which can be used for extrapolative molecular dynamics on new sequences not used during model parametrization. We demonstrate that the model successfully predicts folded structures, intermediates, metastable folded and unfolded basins, and the fluctuations of intrinsically disordered proteins while it is several orders of magnitude faster than an all-atom model. This showcases the feasibility of a universal and computationally efficient machine-learned CG model for proteins. Y1 - 2023 U6 - https://doi.org/https://doi.org/10.48550/arXiv.2310.18278 ER - TY - JOUR A1 - Chen, Ying A1 - Koch, Thorsten A1 - Zakiyeva, Nazgul A1 - Liu, Kailiang A1 - Xu, Zhitong A1 - Chen, Chun-houh A1 - Nakano, Junji A1 - Honda, Keisuke T1 - Article's Scientific Prestige: Measuring the Impact of Individual Articles in the Web of Science N2 - We performed a citation analysis on the Web of Science publications consisting of more than 63 million articles and 1.45 billion citations on 254 subjects from 1981 to 2020. We proposed the Article’s Scientific Prestige (ASP) metric and compared this metric to number of citations (#Cit) and journal grade in measuring the scientific impact of individual articles in the large-scale hierarchical and multi-disciplined citation network. In contrast to #Cit, ASP, that is computed based on the eigenvector centrality, considers both direct and indirect citations, and provides steady-state evaluation cross different disciplines. We found that ASP and #Cit are not aligned for most articles, with a growing mismatch amongst the less cited articles. While both metrics are reliable for evaluating the prestige of articles such as Nobel Prize winning articles, ASP tends to provide more persuasive rankings than #Cit when the articles are not highly cited. The journal grade, that is eventually determined by a few highly cited articles, is unable to properly reflect the scientific impact of individual articles. The number of references and coauthors are less relevant to scientific impact, but subjects do make a difference. T3 - ZIB-Report - 22-07 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86380 VL - 17 IS - 1 SP - 101379 ER - TY - JOUR A1 - Tawfik, Christine A1 - Limbourg, Sabine T1 - A Bilevel Model for Network Design and Pricing Based on a Level-of-Service Assessment JF - Transportation Science N2 - Within a wide view to stimulate intermodal transport, this paper is devoted to the examination of the intrinsically related problems of designing freight carrying services and determining their associated prices as observed by the shipper firms. A path-based multicommodity formulation is developed for a medium-term planning horizon, from the perspective of an intermodal operator. In the quest of incorporating nonprice attributes, two approaches are proposed to depict a realistic assessment of the service quality. First, frequency delay constraints are added to the upper level problem. Second, based on a random utility model, behavioural concepts are integrated in the expression of the lower level as a logistics costs minimization problem. Exact tests are invoked on real-world instances, demonstrating the capability of the presented approaches of reaching reasonable results within acceptable computation times and optimality gaps. The broader level-of-service perspective imposes additional costs on the service providers, although to a lesser extent on long-distance freight corridors, as indicated by the computed market share and net profit. Further experiments are conducted to test the impact of certain transport management instruments (e.g. subsidies and service capacities) on the modal split, as well as to assess the intermodality’s future based on a scenario analysis methodology. Y1 - 2019 U6 - https://doi.org/10.1287/trsc.2019.0906 VL - 53 IS - 6 SP - 1609 EP - 1626 PB - Informs CY - Transportation Science ER - TY - JOUR A1 - Tawfik, Christine A1 - Gendron, Bernard A1 - Limbourg, Sabine T1 - An iterative two-stage heuristic algorithm for a bilevel service network design and pricing model JF - European Journal of Operational Research N2 - Building upon earlier research, we revisit a bilevel formulation of service design and pricing for freight networks, with the aim of investigating its algorithmic aspects. The model adds substantial computational challenges to the existing literature, as it deals with general integer network design variables. An iterative heuristic algorithm is introduced, based on the concepts of inverse optimization and neighbourhood search. The procedure alternates between two versions of restricted formulations of the model while inducing promising changes into the service assignments. The approach has proven a high performance for all of the considered real-world instances. Its efficiency rests on its ability to deliver results within a close proximity to those obtained by the exact solver in terms of quality, yet within a significantly smaller amount of time, and to land feasible solutions for the large-sized instances that could not be previously solved. In line with the sustainable transport goals, a deeper observation of the transport management side highlights the strategy of the algorithm favouring freight consolidation and achieving high load factors. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.ejor.2021.07.052 PB - Elsevier CY - European Journal of Operational Research ER - TY - JOUR A1 - Chen, Ying A1 - Zakiyeva, Nazgul A1 - Zhu, Bangzhu A1 - Koch, Thorsten T1 - Modeling and Forecasting the Dynamics of the Natural Gas Transmission Network in Germany with the Demand and Supply Balance Constraint JF - Applied Energy Y1 - 2020 U6 - https://doi.org/10.1016/j.apenergy.2020.115597 N1 - https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3646636 IS - 278 ER - TY - JOUR A1 - Koch, Thorsten A1 - Chen, Ying A1 - Lim, Kian Guan A1 - Xu, Xiaofei A1 - Zakiyeva, Nazgul T1 - A review study of functional autoregressive models with application to energy forecasting JF - WIREs Computational Statistics Y1 - 2020 U6 - https://doi.org/10.1002/wics.1525 N1 - https://ink.library.smu.edu.sg/cgi/viewcontent.cgi?article=7693&context=lkcsb_research ER - TY - JOUR A1 - Ernst, Ariane A1 - Falkenhagen, Undine A1 - Winkelmann, Stefanie T1 - Model reduction for calcium-induced vesicle fusion dynamics JF - Proceedings in Applied Mathematics & Mechanics N2 - In this work, we adapt an established model for the Ca2+-induced fusion dynamics of synaptic vesicles and employ a lumping method to reduce its complexity. In the reduced system, sequential Ca2+-binding steps are merged to a single releasable state, while keeping the important dependence of the reaction rates on the local Ca2+ concentration. We examine the feasibility of this model reduction for a representative stimulus train over the physiologically relevant site-channel distances. Our findings show that the approximation error is generally small and exhibits an interesting nonlinear and non-monotonic behavior where it vanishes for very low distances and is insignificant at intermediary distances. Furthermore, we give expressions for the reduced model’s reaction rates and suggest that our approach may be used to directly compute effective fusion rates for assessing the validity of a fusion model, thereby circumventing expensive simulations. Y1 - 2023 U6 - https://doi.org/10.1002/pamm.202300184 VL - 23 IS - 4 ER - TY - JOUR A1 - Mathieu, Besançon A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - FrankWolfe.jl: a high-performance and flexible toolbox for Frank-Wolfe algorithms and Conditional Gradients JF - INFORMS Journal on Computing N2 - We present FrankWolfe.jl, an open-source implementation of several popular Frank–Wolfe and conditional gradients variants for first-order constrained optimization. The package is designed with flexibility and high performance in mind, allowing for easy extension and relying on few assumptions regarding the user-provided functions. It supports Julia’s unique multiple dispatch feature, and it interfaces smoothly with generic linear optimization formulations using MathOptInterface.jl. Y1 - 2022 U6 - https://doi.org/10.1287/ijoc.2022.1191 VL - 34 IS - 5 SP - 2383 EP - 2865 ER - TY - JOUR A1 - Besançon, Mathieu A1 - Anjos, Miguel F. A1 - Brotcorne, Luce T1 - Complexity of near-optimal robust versions of multilevel optimization problems JF - Optimization Letters N2 - Near-optimality robustness extends multilevel optimization with a limited deviation of a lower level from its optimal solution, anticipated by higher levels. We analyze the complexity of near-optimal robust multilevel problems, where near-optimal robustness is modelled through additional adversarial decision-makers. Near-optimal robust versions of multilevel problems are shown to remain in the same complexity class as the problem without near-optimality robustness under general conditions. Y1 - 2021 U6 - https://doi.org/10.1007/s11590-021-01754-9 VL - 15 IS - 8 SP - 2597 EP - 2610 ER - TY - JOUR A1 - Birk, Ralph A1 - Raharinirina, N. Alexia A1 - Fackeldey, Konstantin A1 - Richter, Tonio Sebastian A1 - Weber, Marcus T1 - Inferring cultural and social processes based on patterns of statistical relationships between Synodal texts N2 - In this paper, we explore the relationship patterns between Ancient Egyptian texts of the corpus ``Synodal decrees'', which are originating between 243 and 185 BCE, during the Ptolemaic period. Particularly, we are interested in analyzing the grammatical features of the different texts. Conventional data analysis methods such as correspondence Analysis are very useful to explore the patterns of statistical interdependence between categories of variables. However, it is based on a PCA-like dimension-reduction method and turned out to be unsuitable for our dataset due to the high dimensionality of our data representations. Additionally, the similarity between pairs of texts and pairs of grammatical features is observed through the distance between their representation, but the degree of association between a particular grammatical feature and a text is not. Here, we applied a qualitative Euclidean embedding method that provides a new Euclidean representation of the categories of variables. This new representation of the categories is constructed in such a way that all the patterns of statistical interdependence, similarity, and association, are seen through the Euclidean distance between them. Nevertheless, the PCA-like dimension-reduction method also performed poorly on our new representation. Therefore, we obtained a two-dimensional visualization using non-linear methods such UMAP or t-SNE. Although these dimension-reduction methods reduced the interpretability of interpoint distances, we were still able to identify important similarity patterns between the Synodal text as well as their association patterns with the grammatical features. Y1 - 2021 ER - TY - JOUR A1 - Ullrich, Julia A1 - Weiser, Martin A1 - Subramaniam, Jayant A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita T1 - The impact of anatomy variation on temperature based time of death estimation JF - International Journal of Legal Medicine N2 - Temperature-based time of death estimation (TTDE) using simulation methods such as the finite element (FE) method promises higher accuracy and broader applicability in nonstandard cooling scenarios than established phenomenological methods. Their accuracy depends crucially on the simulation model to capture the actual situation. The model fidelity in turn hinges on the representation of the corpse’s anatomy in form of computational meshes as well as on the thermodynamic parameters. While inaccuracies in anatomy representation due to coarse mesh resolution are known to have a minor impact on the estimated time of death, the sensitivity with respect to larger differences in the anatomy has so far not been studied. We assess this sensitivity by comparing four independently generated and vastly different anatomical models in terms of the estimated time of death in an identical cooling scenario. In order to isolate the impact of shape variation, the models are scaled to a reference size, and the possible impact of measurement location variation is excluded explicitly, which gives a lower bound on the impact of anatomy on the estimated time of death. Y1 - 2023 U6 - https://doi.org/10.1007/s00414-023-03026-w VL - 137 SP - 1615 EP - 1627 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus T1 - Efficient Estimation of Transition Rates as Functions of pH JF - Proceedings in Applied Mathematics & Mechanics N2 - Extracting the kinetic properties of a system whose dynamics depend on the pH of the environment with which it exchanges energy and atoms requires sampling the Grand Canonical Ensemble. As an alternative, we present a novel strategy that requires simulating only the most recurrent Canonical Ensembles that compose the Grand Canonical Ensemble. The simulations are used to estimate the Gran Canonical distribution for a specific pH value by reweighting and to construct the transition rate matrix by discretizing the Fokker-Planck equation by Square Root Approximation and robust Perron Cluster Cluster Analysis. As an application, we have studied the tripeptide Ala-Asp-Ala. Y1 - 2023 U6 - https://doi.org/10.1002/pamm.202300264 VL - 23 ER - TY - JOUR A1 - Oehme, Stephan A1 - Moewis, Philippe A1 - Boeth, Heide A1 - Bartek, Benjamin A1 - Lippert, Annika A1 - von Tycowicz, Christoph A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Jung, Tobias T1 - PCL insufficient patients with increased translational and rotational passive knee joint laxity have no increased range of anterior–posterior and rotational tibiofemoral motion during level walking JF - Scientific Reports Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-17328-3 VL - 12 IS - 1 SP - 1 EP - 11 ER - TY - JOUR A1 - Lücke, Marvin A1 - Heitzig, Jobst A1 - Koltai, Péter A1 - Molkethin, Nora A1 - Winkelmann, Stefanie T1 - Large population limits of Markov processes on random networks JF - Stochastic Processes and their Applications N2 - We consider time-continuous Markovian discrete-state dynamics on random networks of interacting agents and study the large population limit. The dynamics are projected onto low-dimensional collective variables given by the shares of each discrete state in the system, or in certain subsystems, and general conditions for the convergence of the collective variable dynamics to a mean-field ordinary differential equation are proved. We discuss the convergence to this mean-field limit for a continuous-time noisy version of the so-called "voter model" on Erdős-Rényi random graphs, on the stochastic block model, as well as on random regular graphs. Moreover, a heterogeneous population of agents is studied. For each of these types of interaction networks, we specify the convergence conditions in dependency on the corresponding model parameters. Y1 - 2023 U6 - https://doi.org/10.1016/j.spa.2023.09.007 VL - 166 ER - TY - JOUR A1 - Ernst, Ariane A1 - Unger, Nathalie A1 - Schütte, Christof A1 - Walter, Alexander A1 - Winkelmann, Stefanie T1 - Rate-limiting recovery processes in neurotransmission under sustained stimulation JF - Mathematical Biosciences N2 - At chemical synapses, an arriving electric signal induces the fusion of vesicles with the presynaptic membrane, thereby releasing neurotransmitters into the synaptic cleft. After a fusion event, both the release site and the vesicle undergo a recovery process before becoming available for reuse again. Of central interest is the question which of the two restoration steps acts as the limiting factor during neurotrans-mission under high-frequency sustained stimulation. In order to investigate this question, we introduce a novel non-linear reaction network which involves explicit recovery steps for both the vesicles and the release sites, and includes the induced time-dependent output current. The associated reaction dynamics are formulated by means of ordinary differential equations (ODEs), as well as via the associated stochastic jump process. While the stochastic jump model describes a single release site, the average over many release sites is close to the ODE solution and shares its periodic structure. The reason for this can be traced back to the insight that recovery dynamics of vesicles and release sites are statistically almost independent. A sensitivity analysis on the recovery rates based on the ODE formulation reveals that neither the vesicle nor the release site recovery step can be identified as the essential rate-limiting step but that the rate- limiting feature changes over the course of stimulation. Under sustained stimulation the dynamics given by the ODEs exhibit transient dynamics leading from an initial depression of the postsynaptic response to an asymptotic periodic orbit, while the individual trajectories of the stochastic jump model lack the oscillatory behavior an asymptotic periodicity of the ODE-solution. Y1 - 2023 U6 - https://doi.org/10.1016/j.mbs.2023.109023 VL - 362 ER - TY - JOUR A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Höfling, Felix T1 - Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles JF - The Journal of Physical Chemistry B N2 - This theoretical study concerns a pH oscillator based on the urea-urease reaction confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the phase flow and of the limit cycle, which controls the dynamics for giant vesicles and dominates the pronouncedly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, which are amenable to analytic treatments that are complemented by numerical solutions, and obtain the period and amplitude of the oscillations as well as the parameter domain, where oscillatory behavior persists. We show that the accuracy of these predictions is highly sensitive to the employed reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The faithful modeling of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpcb.2c09092 VL - 127 IS - 13 SP - 2955 EP - 2967 ER - TY - JOUR A1 - Montefusco, Alberto A1 - Schütte, Christof A1 - Winkelmann, Stefanie T1 - A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures JF - SIAM Journal on Applied Mathematics N2 - The reaction-diffusion master equation (RDME) is a lattice-based stochastic model for spatially resolved cellular processes. It is often interpreted as an approximation to spatially continuous reaction-diffusion models, which, in the limit of an infinitely large population, may be described by means of reaction-diffusion partial differential equations. Analyzing and understanding the relation between different mathematical models for reaction-diffusion dynamics is a research topic of steady interest. In this work, we explore a route to the hydrodynamic limit of the RDME which uses gradient structures. Specifically, we elaborate on a method introduced in [J. Maas and A. Mielke, J. Stat. Phys., 181 (2020), pp. 2257–2303] in the context of well-mixed reaction networks by showing that, once it is complemented with an appropriate limit procedure, it can be applied to spatially extended systems with diffusion. Under the assumption of detailed balance, we write down a gradient structure for the RDME and use the method in order to produce a gradient structure for its hydrodynamic limit, namely, for the corresponding RDPDE. Y1 - 2023 U6 - https://doi.org/10.1137/22M1488831 VL - 83 IS - 2 SP - 837 EP - 861 ER - TY - JOUR A1 - Lücke, Marvin A1 - Lu, Jingyi A1 - Quevedo, Daniel E. T1 - Coding for secrecy in remote state estimation with an adversary JF - IEEE Transactions on Automatic Control N2 - We study the problem of remote state estimation in the presence of an eavesdropper. A sensor transmits state information over a packet-dropping link to a legitimate user. This information is randomly overheard by an eavesdropper. To reduce information leakage to the eavesdropper, previous studies have shown that by encoding the estimate with the acknowledgments (Acks), perfect secrecy can be achieved. However, this strategy greatly relies on the accuracy of the Acks and may easily fail if the Acks are compromised by cyberattacks. In this article, we tackle this issue by proposing to switch between sending an encoded state and sending the plain state to stay resilient against fake Acks. Specifically, we assume the Acks to be randomly attacked and derive recursive expressions for the minimum-mean-squared error estimates and error covariance matrices at the legitimate user and at the eavesdropper. Based upon this, we propose a transmission policy that depends on the probability of synchronization. We formulate a partially observable Markov decision process to model the evolution of the synchronization status and derive associated optimal transmission policies. Numerical examples are provided to verify the theoretical results. Y1 - 2022 U6 - https://doi.org/10.1109/TAC.2022.3169839 VL - 67 IS - 9 SP - 4955 EP - 4962 ER - TY - JOUR A1 - Straube, Arthur A1 - Höfling, Felix T1 - Depinning transition of self-propelled particles N2 - A depinning transition is observed in a variety of contexts when a certain threshold force must be applied to drive a system out of an immobile state. A well-studied example is the depinning of colloidal particles from a corrugated landscape, whereas its active-matter analogue has remained unexplored. We discuss how active noise due to self-propulsion impacts the nature of the transition: it causes a change of the critical exponent from 1/2 for quickly reorienting particles to 3/2 for slowly reorienting ones. In between these analytically tractable limits, the drift velocity exhibits a superexponential behavior as is corroborated by high-precision data. Giant diffusion phenomena occur in the two different regimes. Our predictions appear amenable to experimental tests, lay foundations for insight into the depinning of collective variables in active matter, and are relevant for any system with a saddle-node bifurcation in the presence of a bounded noise. Y1 - 2023 ER - TY - JOUR A1 - Ghysbrecht, Simon A1 - Donati, Luca A1 - Keller, Bettina G. T1 - Accuracy of reaction coordinate based rate theories for modelling chemical reactions: insights from the thermal isomerization in retinal JF - Submitted to The Journal of Physical Chemistry A N2 - Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability to studying chemical reactions remains uncertain due to the high and sharp energy barriers and complex reaction coordinates involved. This study focuses on the thermal cis-trans isomerization in retinal, employing molecular simulations and comparing rate constant estimates based on one-dimensional rate theories with those based on sampling transitions and grid-based models for low-dimensional collective variable spaces. Even though each individual method to estimate the rate passes its quality tests, the rate constant estimates exhibit disparities of up to four orders of magnitude. Rate constant estimates based on one-dimensional reaction coordinates prove challenging to converge, even if the reaction coordinate is optimized. However, consistent estimates of the rate constant are achieved by sampling transitions and by multi-dimensional grid-based models. Y1 - 2023 ER - TY - JOUR A1 - Turner, Mark A1 - Berthold, Timo A1 - Besançon, Mathieu A1 - Koch, Thorsten T1 - Branching via Cutting Plane Selection: Improving Hybrid Branching N2 - Cutting planes and branching are two of the most important algorithms for solving mixed-integer linear programs. For both algorithms, disjunctions play an important role, being used both as branching candidates and as the foundation for some cutting planes. We relate branching decisions and cutting planes to each other through the underlying disjunctions that they are based on, with a focus on Gomory mixed-integer cuts and their corresponding split disjunctions. We show that selecting branching decisions based on quality measures of Gomory mixed-integer cuts leads to relatively small branch-and-bound trees, and that the result improves when using cuts that more accurately represent the branching decisions. Finally, we show how the history of previously computed Gomory mixed-integer cuts can be used to improve the performance of the state-of-the-art hybrid branching rule of SCIP. Our results show a $4\%$ decrease in solve time, and an $8\%$ decrease in number of nodes over affected instances of MIPLIB 2017. Y1 - 2023 PB - Springer ER - TY - JOUR A1 - Helfmann, Luzie A1 - Conrad, Natasa Djurdjevac A1 - Lorenz-Spreen, Philipp A1 - Schütte, Christof T1 - Modelling opinion dynamics under the impact of influencer and media strategies JF - Scientific Reports N2 - Digital communication has made the public discourse considerably more complex, and new actors and strategies have emerged as a result of this seismic shift. Aside from the often-studied interactions among individuals during opinion formation, which have been facilitated on a large scale by social media platforms, the changing role of traditional media and the emerging role of "influencers" are not well understood, and the implications of their engagement strategies arising from the incentive structure of the attention economy even less so. Here we propose a novel opinion dynamics model that accounts for these different roles, namely that media and influencers change their own positions on slower time scales than individuals, while influencers dynamically gain and lose followers. Numerical simulations show the importance of their relative influence in creating qualitatively different opinion formation dynamics: with influencers, fragmented but short-lived clusters emerge, which are then counteracted by more stable media positions. Mean-field approximations by partial differential equations reproduce this dynamic. Based on the mean-field model, we study how strategies of influencers to gain more followers can influence the overall opinion distribution. We show that moving towards extreme positions can be a beneficial strategy for influencers to gain followers. Finally, we demonstrate that optimal control strategies allow other influencers or media to counteract such attempts and prevent further fragmentation of the opinion landscape. Our modelling framework contributes to better understanding the different roles and strategies in the increasingly complex information ecosystem and their impact on public opinion formation. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-46187-9 VL - 13 SP - 19375 ER - TY - JOUR A1 - Bartels, Tinko A1 - Fisikopoulos, Vissarion A1 - Weiser, Martin T1 - Fast Floating-Point Filters for Robust Predicates JF - BIT Numerical Mathematics N2 - Geometric predicates are at the core of many algorithms, such as the construction of Delaunay triangulations, mesh processing and spatial relation tests. These algorithms have applications in scientific computing, geographic information systems and computer-aided design. With floating-point arithmetic, these geometric predicates can incur round-off errors that may lead to incorrect results and inconsistencies, causing computations to fail. This issue has been addressed using a combination of exact arithmetic for robustness and floating-point filters to mitigate the computational cost of exact computations. The implementation of exact computations and floating-point filters can be a difficult task, and code generation tools have been proposed to address this. We present a new C++ meta-programming framework for the generation of fast, robust predicates for arbitrary geometric predicates based on polynomial expressions. We combine and extend different approaches to filtering, branch reduction, and overflow avoidance that have previously been proposed. We show examples of how this approach produces correct results for data sets that could lead to incorrect predicate results with naive implementations. Our benchmark results demonstrate that our implementation surpasses state-of-the-art implementations. Y1 - 2023 U6 - https://doi.org/10.1007/s10543-023-00975-x VL - 63 ER - TY - JOUR A1 - Designolle, Sébastien A1 - Besançon, Mathieu A1 - Iommazzo, Gabriele A1 - Knebel, Sebastian A1 - Gelß, Patrick A1 - Pokutta, Sebastian T1 - Improved Local Models and New Bell Inequalities Via Frank-Wolfe Algorithms JF - Physical Review Research N2 - In Bell scenarios with two outcomes per party, we algorithmically consider the two sides of the membership problem for the local polytope: Constructing local models and deriving separating hyperplanes, that is, Bell inequalities. We take advantage of the recent developments in so-called Frank-Wolfe algorithms to significantly increase the convergence rate of existing methods. First, we study the threshold value for the nonlocality of two-qubit Werner states under projective measurements. Here, we improve on both the upper and lower bounds present in the literature. Importantly, our bounds are entirely analytical; moreover, they yield refined bounds on the value of the Grothendieck constant of order three: 1.4367⩽KG(3)⩽1.4546. Second, we demonstrate the efficiency of our approach in multipartite Bell scenarios, and present local models for all projective measurements with visibilities noticeably higher than the entanglement threshold. We make our entire code accessible as a julia library called BellPolytopes.jl. Y1 - 2023 U6 - https://doi.org/10.1103/PhysRevResearch.5.043059 VL - 5 SP - 043059 ER - TY - JOUR A1 - Le, Thi Thai A1 - Petkovic, Milena T1 - Predicting Fluid Interface Instability in Energy Systems for Sustainable Energy Transition JF - Operations Research Proceedings N2 - Due to the coexistence of different gases in underground storage, this work explores the interface stability's impact on energy storage, specifically during the injection and withdrawal of gases such as hydrogen and natural gas. A new approach of combing simulation and time series analysis is used to accurately predict instability modes in energy systems. Our simulation is based on the 2D Euler equations, solved using a second-order finite volume method with a staggered grid. The solution is validated by comparing them to experimental data and analytical solutions, accurately predicting the instability's behavior. We use time series analysis and state-of-the-art regime-switching methods to identify critical features of the interface dynamics, providing crucial insights into system optimization and design. Y1 - 2023 ER - TY - JOUR A1 - Yueksel-Erguen, Inci A1 - Most, Dieter A1 - Wyrwoll, Lothar A1 - Schmitt, Carlo A1 - Zittel, Janina T1 - Modeling the transition of the multimodal pan-European energy system including an integrated analysis of electricity and gas transport JF - Energy Systems N2 - Most recently, the European energy system has undergone a fundamental transformation to meet decarbonization targets without compromising the security of the energy supply. The transition involves several energy-generating and consuming sectors emphasizing sector coupling. The increase in the share of renewable energy sources has revealed the need for flexibility in supporting the electricity grid to cope with the resulting high degree of uncertainty. The new technologies accompanying the energy system transition and the recent political crisis in Europe threatening the security of the energy supply have invalidated the experience from the past by drastically changing the conventional scenarios. Hence, supporting strategic planning tools with detailed operational energy network models with appropriate mathematical precision has become more important than ever to understand the impacts of these disruptive changes. In this paper, we propose a workflow to investigate optimal energy transition pathways considering sector coupling. This workflow involves an integrated operational analysis of the electricity market, its transmission grid, and the gas grid in high spatio-temporal resolution. Thus, the workflow enables decision-makers to evaluate the reliability of high-level models even in case of disruptive events. We demonstrate the capabilities of the proposed workflow using results from a pan-European case study. The case study, spanning 2020-2050, illustrates that feasible potential pathways to carbon neutrality are heavily influenced by political and technological constraints. Through integrated operational analysis, we identify scenarios where strategic decisions become costly or infeasible given the existing electricity and gas networks. Y1 - 2023 U6 - https://doi.org/10.1007/s12667-023-00637-5 ER - TY - JOUR A1 - Kostré, Margarita A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Djurdjevac Conrad, Natasa T1 - Understanding the Romanization Spreading on Historical Interregional Networks in Northern Tunisia JF - Applied Network Science N2 - Spreading processes are important drivers of change in social systems. To understand the mechanisms of spreading it is fundamental to have information about the underlying contact network and the dynamical parameters of the process. However, in many real-wold examples, this information is not known and needs to be inferred from data. State-of-the-art spreading inference methods have mostly been applied to modern social systems, as they rely on availability of very detailed data. In this paper we study the inference challenges for historical spreading processes, for which only very fragmented information is available. To cope with this problem, we extend existing network models by formulating a model on a mesoscale with temporal spreading rate. Furthermore, we formulate the respective parameter inference problem for the extended model. We apply our approach to the romanization process of Northern Tunisia, a scarce dataset, and study properties of the inferred time-evolving interregional networks. As a result, we show that (1) optimal solutions consist of very different network structures and spreading rate functions; and that (2) these diverse solutions produce very similar spreading patterns. Finally, we discuss how inferred dominant interregional connections are related to available archaeological traces. Historical networks resulting from our approach can help understanding complex processes of cultural change in ancient times. KW - mesoscale spreading process KW - network inference KW - time-evolving network KW - romanization spreading KW - scarce data Y1 - 2022 U6 - https://doi.org/10.1007/s41109-022-00492-w VL - 7 PB - Springer Nature ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Köppl, Jonas A1 - Djurdjevac, Ana T1 - Feedback Loops in Opinion Dynamics of Agent-Based Models with Multiplicative Noise JF - Entropy N2 - We introduce an agent-based model for co-evolving opinions and social dynamics, under the influence of multiplicative noise. In this model, every agent is characterized by a position in a social space and a continuous opinion state variable. Agents’ movements are governed by the positions and opinions of other agents and similarly, the opinion dynamics are influenced by agents’ spatial proximity and their opinion similarity. Using numerical simulations and formal analyses, we study this feedback loop between opinion dynamics and the mobility of agents in a social space. We investigate the behaviour of this ABM in different regimes and explore the influence of various factors on the appearance of emerging phenomena such as group formation and opinion consensus. We study the empirical distribution, and, in the limit of infinite number of agents, we derive a corresponding reduced model given by a partial differential equation (PDE). Finally, using numerical examples, we show that a resulting PDE model is a good approximation of the original ABM. Y1 - 2022 U6 - https://doi.org/10.3390/e24101352 VL - 24(10) ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Chemnitz, Robin A1 - Kostre, Margarita A1 - Schweigart, Fleur A1 - Fless, Friederike A1 - Schütte, Christof A1 - Ducke, Benjamin T1 - A Mathematical perspective on Romanisation: Modelling the Roman road activation process in ancient Tunisia Y1 - 2023 ER - TY - JOUR A1 - Gleixner, Ambros A1 - Gottwald, Leona A1 - Hoen, Alexander T1 - PaPILO: A Parallel Presolving Library for Integer and Linear Programming with Multiprecision Support JF - INFORMS Journal on Computing N2 - Presolving has become an essential component of modern mixed integer program (MIP) solvers, both in terms of computational performance and numerical robustness. In this paper, we present PaPILO, a new C++ header-only library that provides a large set of presolving routines for MIP and linear programming problems from the literature. The creation of PaPILO was motivated by the current lack of (a) solver-independent implementations that (b) exploit parallel hardware and (c) support multiprecision arithmetic. Traditionally, presolving is designed to be fast. Whenever necessary, its low computational overhead is usually achieved by strict working limits. PaPILO’s parallelization framework aims at reducing the computational overhead also when presolving is executed more aggressively or is applied to large-scale problems. To rule out conflicts between parallel presolve reductions, PaPILO uses a transaction-based design. This helps to avoid both the memory-intensive allocation of multiple copies of the problem and special synchronization between presolvers. Additionally, the use of Intel’s Threading Building Blocks library aids PaPILO in efficiently exploiting recursive parallelism within expensive presolving routines, such as probing, dominated columns, or constraint sparsification. We provide an overview of PaPILO’s capabilities and insights into important design choices. Y1 - 2023 U6 - https://doi.org/10.1287/ijoc.2022.0171 VL - 35 IS - 6 SP - 1329 EP - 1341 ER - TY - JOUR A1 - Alphonse, Amal A1 - Caetano, Diogo A1 - Djurdjevac, Ana A1 - Elliott, Charles M. T1 - Function spaces, time derivatives and compactness for evolving families of Banach spaces with applications to PDEs JF - Journal of Differential Equations N2 - We develop a functional framework suitable for the treatment of partial differential equations and variational problems posed on evolving families of Banach spaces. We propose a definition for the weak time derivative which does not rely on the availability of an inner product or Hilbertian structure and explore conditions under which the spaces of weakly differentiable functions (with values in an evolving Banach space) relate to the classical Sobolev--Bochner spaces. An Aubin--Lions compactness result in this setting is also proved. We then analyse several concrete examples of function spaces over time-evolving spatial domains and hypersurfaces for which we explicitly provide the definition of the time derivative and verify isomorphism properties with the aforementioned Sobolev--Bochner spaces. We conclude with the formulation and proof of well posedness for a class of nonlinear monotone problems on an abstract evolving space (generalising in particular the evolutionary p-Laplace equation on a moving domain or surface) and identify some additional evolutionary problems that can be appropriately formulated with the abstract setting developed in this work. Y1 - 2023 U6 - https://doi.org/10.1016/j.jde.2022.12.032 VL - 353 SP - 268 EP - 338 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Nigam, AkshatKumar A1 - Koop, Matt A1 - Selim Çınaroğlu, Süleyman A1 - Secker, Christopher A1 - Haddadnia, Mohammad A1 - Kumar, Abhishek A1 - Malets, Yehor A1 - Hasson, Alexander A1 - Li, Minkai A1 - Tang, Ming A1 - Levin-Konigsberg, Roni A1 - Radchenko, Dmitry A1 - Kumar, Aditya A1 - Gehev, Minko A1 - Aquilanti, Pierre-Yves A1 - Gabb, Henry A1 - Alhossary, Amr A1 - Wagner, Gerhard A1 - Aspuru-Guzik, Alán A1 - Moroz, Yurii S. A1 - Fackeldey, Konstantin A1 - Arthanari, Haribabu T1 - VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules JF - bioRxiv KW - preprint Y1 - 2023 U6 - https://doi.org/10.1101/2023.04.25.537981 ER - TY - JOUR A1 - Koyanagi, Gregory K. A1 - Lambo, Ricardo Lewis A1 - Ragyanszki, Anita A1 - Fournier, Rene A. A1 - Horbatsch, Marko W. A1 - Hessels, Eric A. T1 - Accurate calculation of the interaction of a barium monofluoride molecule with an argon atom: A step towards using matrix isolation of BaF for determining the electron electric dipole moment JF - Journal of Molecular Spectroscopy Y1 - 2023 U6 - https://doi.org/10.1016/j.jms.2023.111736 VL - 391 SP - 111736 ER - TY - JOUR A1 - Lambo, Ricardo Lewis A1 - Koyanagi, Gregory K. A1 - Ragyanszki, Anita A1 - Horbatsch, Marko A1 - Fournier, Rene A1 - Hessels, Eric A. T1 - Calculation of the local environment of a barium monofluoride molecule in an argon matrix: a step towards using matrix-isolated BaF for determining the electron electric dipole moment JF - Molecular Physics Y1 - 2023 U6 - https://doi.org/10.1080/00268976.2023.2198044 VL - 121 IS - 6 ER - TY - JOUR A1 - Frank, Anna-Simone A1 - Sikorski, Alexander A1 - Röblitz, Susanna T1 - Spectral clustering of Markov chain transition matrices with complex eigenvalues JF - Journal of Computational and Applied Mathematics N2 - The Robust Perron Cluster Analysis (PCCA+) has become a popular spectral clustering algorithm for coarse-graining transition matrices of nearly decomposable Markov chains with transition states. Originally developed for reversible Markov chains, the algorithm only worked for transition matrices with real eigenvalues. In this paper, we therefore extend the theoretical framework of PCCA+ to Markov chains with a complex eigen-decomposition. We show that by replacing a complex conjugate pair of eigenvectors by their real and imaginary components, a real representation of the same subspace is obtained, which is suitable for the cluster analysis. We show that our approach leads to the same results as the generalized PCCA+ (GPCCA), which replaces the complex eigen-decomposition by a conceptually more difficult real Schur decomposition. We apply the method on non-reversible Markov chains, including circular chains, and demonstrate its efficiency compared to GPCCA. The experiments are performed in the Matlab programming language and codes are provided. Y1 - 2024 U6 - https://doi.org/10.1016/j.cam.2024.115791 VL - 444 SP - 115791 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - Understanding recent deep-learning techniques for identifying collective variables of molecular dynamics BT - Special Issue: 93rd Annual Meeting of the International Association of Applied Mathematics and Mechanics (GAMM) JF - Proceedings in Applied Mathematics and Mechanics N2 - High-dimensional metastable molecular dynamics (MD) can often be characterised by a few features of the system, that is, collective variables (CVs). Thanks to the rapid advance in the area of machine learning and deep learning, various deep learning-based CV identification techniques have been developed in recent years, allowing accurate modelling and efficient simulation of complex molecular systems. In this paper, we look at two different categories of deep learning-based approaches for finding CVs, either by computing leading eigenfunctions of transfer operator associated to the underlying dynamics, or by learning an autoencoder via minimisation of reconstruction error. We present a concise overview of the mathematics behind these two approaches and conduct a comparative numerical study of these two approaches on illustrative examples. Y1 - 2023 U6 - https://doi.org/10.1002/pamm.202300189 VL - 23 IS - 4 ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Chmiela, Antonia A1 - Müller, Benjamin A1 - Serrano, Felipe A1 - Vigerske, Stefan A1 - Wegscheider, Fabian T1 - Global Optimization of Mixed-Integer Nonlinear Programs with SCIP 8.0 JF - Journal of Global Optimization N2 - For over ten years, the constraint integer programming framework SCIP has been extended by capabilities for the solution of convex and nonconvex mixed-integer nonlinear programs (MINLPs). With the recently published version 8.0, these capabilities have been largely reworked and extended. This paper discusses the motivations for recent changes and provides an overview of features that are particular to MINLP solving in SCIP. Further, difficulties in benchmarking global MINLP solvers are discussed and a comparison with several state-of-the-art global MINLP solvers is provided. Y1 - 2023 U6 - https://doi.org/10.1007/s10898-023-01345-1 ER - TY - JOUR A1 - Knoop, Helge A1 - Gronemeier, Tobias A1 - Sühring, Matthias A1 - Steinbach, Peter A1 - Noack, Matthias A1 - Wende, Florian A1 - Steinke, Thomas A1 - Knigge, Christoph A1 - Raasch, Siegfried A1 - Ketelsen, Klaus T1 - Porting the MPI-parallelized LES model PALM to multi-GPU systems and many integrated core processors: an experience report JF - International Journal of Computational Science and Engineering. Special Issue on: Novel Strategies for Programming Accelerators N2 - The computational power and availability of graphics processing units (GPUs), such as the Nvidia Tesla, and Many Integrated Core (MIC) processors, such as the Intel Xeon Phi, on high performance computing (HPC) systems is rapidly evolving. However, HPC applications need to be ported to take advantage of such hardware. This paper is a report on our experience of porting the MPI+OpenMP parallelised large-eddy simulation model (PALM) to multi-GPU as well as to MIC processor environments using the directive-based high level programming paradigm OpenACC and OpenMP, respectively. PALM is a Fortran-based computational fluid dynamics software package, used for the simulation of atmospheric and oceanic boundary layers to answer questions linked to fundamental atmospheric turbulence research, urban modelling, aircraft safety and cloud physics. Development of PALM started in 1997, the project currently entails 140 kLOC and is used on HPC farms of up to 43,200 cores. The main challenges we faced during the porting process are the size and complexity of the PALM code base, its inconsistent modularisation and the complete lack of a unit-test suite. We report the methods used to identify performance issues as well as our experiences with state-of-the-art profiling tools. Moreover, we outline the required porting steps in order to properly execute our code on GPUs and MIC processors, describe the problems and bottlenecks that we encountered during the porting process, and present separate performance tests for both architectures. These performance tests, however, do not provide any benchmark information that compares the performance of the ported code between the two architectures. Y1 - 2017 PB - Inderscience ET - Special Issue on: Novel Strategies for Programming Accelerators ER - TY - JOUR A1 - Quer, Jannes A1 - Lie, Han Cheng T1 - Some connections between importance sampling and enhanced sampling methods in molecular dynamics JF - Journal of Chemical Physics N2 - Enhanced sampling methods play an important role in molecular dynamics, because they enable the collection of better statistics of rare events that are important in many physical phenomena. We show that many enhanced sampling methods can be viewed as methods for performing importance sampling, by identifying important correspondences between the language of molecular dynamics and the language of probability theory. We illustrate these connections by highlighting the similarities between the rare event simulation method of Hartmann and Schütte (J. Stat. Mech. Theor. Exp., 2012), and the enhanced sampling method of Valsson and Parrinello (Phys. Rev. Lett. 113, 090601). We show that the idea of changing a probability measure is fundamental to both enhanced sampling and importance sampling. Y1 - 2017 ER - TY - JOUR A1 - Kruser, Jacqueline M. A1 - Sharma, Kartikey A1 - Holl, Jane L. A1 - Nohadani, Omid T1 - Identifying Patterns of Medical Intervention in Acute Respiratory Failure: A Retrospective Observational Study JF - Critical Care Explorations Y1 - 2023 U6 - https://doi.org/10.1097/CCE.0000000000000984 VL - 5 IS - 10 SP - p e0984 ER - TY - JOUR A1 - Grimm, Boris A1 - Hoogervorst, Rowan A1 - Borndörfer, Ralf T1 - A Comparison of Models for Rolling Stock Scheduling N2 - A major step in the planning process of passenger railway operators is the assignment of rolling stock, i.e., train units, to the trips of the timetable. A wide variety of mathematical optimization models have been proposed to support this task, which we discuss and argue to be justified in order to deal with operational differences between railway operators, and hence different planning requirements, in the best possible way. Our investigation focuses on two commonly used models, the Composition model and the Hypergraph model, that were developed for Netherlands Railways (NS) and DB Fernverkehr AG (DB), respectively. We compare these models in a rolling stock scheduling setting similar to that of NS, which we show to be strongly NP-hard, and propose different variants of the Hypergraph model to tune the model to the NS setting. We prove that, in this setting, the linear programming bounds of both models are equally strong as long as a Hypergraph model variant is chosen that is sufficiently expressive. However, through a numerical evaluation on NS instances, we show that the Composition model is generally more compact in practice and can find optimal solutions in the shortest running time. Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2312.09697 ER - TY - JOUR A1 - Bestuzheva, Ksenia A1 - Besançon, Mathieu A1 - Chen, Wei-Kun A1 - Chmiela, Antonia A1 - Donkiewicz, Tim A1 - Doornmalen, Jasper A1 - Eifler, Leon A1 - Gaul, Oliver A1 - Gamrath, Gerald A1 - Gleixner, Ambros A1 - Gottwald, Leona A1 - Graczyk, Christoph A1 - Halbig, Katrin A1 - Hoen, Alexander A1 - Hojny, Christopher A1 - Hulst, Rolf A1 - Koch, Thorsten A1 - Lübbecke, Marco A1 - Maher, Stephen J. A1 - Matter, Frederic A1 - Mühmer, Erik A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Rehfeldt, Daniel A1 - Schlein, Steffan A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Sofranac, Boro A1 - Turner, Mark A1 - Vigerske, Stefan A1 - Wegscheider, Fabian A1 - Wellner, Philipp A1 - Weninger, Dieter A1 - Witzig, Jakob T1 - Enabling research through the SCIP optimization suite 8.0 JF - ACM Transactions on Mathematical Software N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. The focus of this article is on the role of the SCIP Optimization Suite in supporting research. SCIP’s main design principles are discussed, followed by a presentation of the latest performance improvements and developments in version 8.0, which serve both as examples of SCIP’s application as a research tool and as a platform for further developments. Furthermore, this article gives an overview of interfaces to other programming and modeling languages, new features that expand the possibilities for user interaction with the framework, and the latest developments in several extensions built upon SCIP. Y1 - 2023 U6 - https://doi.org/10.1145/3585516 VL - 49 IS - 2 SP - 1 EP - 21 ER - TY - JOUR A1 - Besançon, Mathieu A1 - Garcia, Joaquim Dias A1 - Legat, Benoît A1 - Sharma, Akshay T1 - Flexible Differentiable Optimization via Model Transformations JF - INFORMS Journal on Computing N2 - We introduce DiffOpt.jl, a Julia library to differentiate through the solution of optimization problems with respect to arbitrary parameters present in the objective and/or constraints. The library builds upon MathOptInterface, thus leveraging the rich ecosystem of solvers and composing well with modeling languages like JuMP. DiffOpt offers both forward and reverse differentiation modes, enabling multiple use cases from hyperparameter optimization to backpropagation and sensitivity analysis, bridging constrained optimization with end-to-end differentiable programming. DiffOpt is built on two known rules for differentiating quadratic programming and conic programming standard forms. However, thanks to its ability to differentiate through model transformations, the user is not limited to these forms and can differentiate with respect to the parameters of any model that can be reformulated into these standard forms. This notably includes programs mixing affine conic constraints and convex quadratic constraints or objective function. Y1 - 2023 U6 - https://doi.org/10.1287/ijoc.2022.0283 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A computational status update for exact rational mixed integer programming JF - Mathematical Programming N2 - The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 10.7x over the original framework and 2.9 times as many instances solved within a time limit of two hours. Y1 - 2023 U6 - https://doi.org/10.1007/s10107-021-01749-5 VL - 197 SP - 793 EP - 812 ER - TY - JOUR A1 - Pokutta, Sebastian T1 - The Frank-Wolfe algorithm: a short introduction JF - Jahresbericht der Deutschen Mathematiker-Vereinigung Y1 - 2023 ER - TY - JOUR A1 - Designolle, Sébastien A1 - Iommazzo, Gabriele A1 - Besançon, Mathieu A1 - Knebel, Sebastian A1 - Gelß, Patrick A1 - Pokutta, Sebastian T1 - Improved local models and new Bell inequalities via Frank-Wolfe algorithms JF - Physical Review Research N2 - In Bell scenarios with two outcomes per party, we algorithmically consider the two sides of the membership problem for the local polytope: Constructing local models and deriving separating hyperplanes, that is, Bell inequalities. We take advantage of the recent developments in so-called Frank-Wolfe algorithms to significantly increase the convergence rate of existing methods. First, we study the threshold value for the nonlocality of two-qubit Werner states under projective measurements. Here, we improve on both the upper and lower bounds present in the literature. Importantly, our bounds are entirely analytical; moreover, they yield refined bounds on the value of the Grothendieck constant of order three: 1.4367⩽KG(3)⩽1.4546. Second, we demonstrate the efficiency of our approach in multipartite Bell scenarios, and present local models for all projective measurements with visibilities noticeably higher than the entanglement threshold. We make our entire code accessible as a julia library called BellPolytopes.jl. Y1 - 2023 U6 - https://doi.org/10.1103/PhysRevResearch.5.043059 VL - 5 SP - 043059 ER - TY - JOUR A1 - Liberti, Leo A1 - Iommazzo, Gabriele A1 - Lavor, Carlile A1 - Maculan, Nelson T1 - Cycle-based formulations in distance geometry JF - Open Journal of Mathematical Optimization N2 - The distance geometry problem asks to find a realization of a given simple edge-weighted graph in a Euclidean space of given dimension , where the edges are realized as straight segments of lengths equal (or as close as possible) to the edge weights. The problem is often modelled as a mathematical programming formulation involving decision variables that determine the position of the vertices in the given Euclidean space. Solution algorithms are generally constructed using local or global nonlinear optimization techniques. We present a new modelling technique for this problem where, instead of deciding vertex positions, the formulations decide the length of the segments representing the edges in each cycle in the graph, projected in every dimension. We propose an exact formulation and a relaxation based on a Eulerian cycle. We then compare computational results from protein conformation instances obtained with stochastic global optimization techniques on the new cycle-based formulation and on the existing edge-based formulation. While edge-based formulations take less time to reach termination, cycle-based formulations are generally better on solution quality measures. Y1 - 2023 U6 - https://doi.org/10.5802/ojmo.18 VL - 4 ER - TY - JOUR A1 - Bolusani, Suresh A1 - Ralphs, Ted K. T1 - a framework for generalized Benders' decomposition and its applications to multilevel optimization JF - Mathematical Programming Y1 - 2022 ER - TY - JOUR A1 - Majewski, Maciej A1 - Pérez, Adrià A1 - Thölke, Philipp A1 - Doerr, Stefan A1 - Charron, Nicholas A1 - Giorgino, Toni A1 - Husic, Brooke A1 - Clementi, Cecilia A1 - Noé, Frank A1 - De Fabritiis, Gianni T1 - Machine learning coarse-grained potentials of protein thermodynamics JF - Nature Communications N2 - A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics. Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-41343-1 VL - 14 ER - TY - JOUR A1 - Durumeric, Aleksander A1 - Charron, Nicholas A1 - Templeton, Clark A1 - Musil, Félix A1 - Bonneau, Klara A1 - Pasos-Trejo, Aldo A1 - Chen, Yaoyi A1 - Kelkar, Atharva A1 - Noé, Frank A1 - Clementi, Cecilia T1 - Machine learned coarse-grained protein force-fields: Are we there yet? JF - Current Opinion in Structural Biology N2 - The successful recent application of machine learning methods to scientific problems includes the learning of flexible and accurate atomic-level force-fields for materials and biomolecules from quantum chemical data. In parallel, the machine learning of force-fields at coarser resolutions is rapidly gaining relevance as an efficient way to represent the higher-body interactions needed in coarse-grained force-fields to compensate for the omitted degrees of freedom. Coarse-grained models are important for the study of systems at time and length scales exceeding those of atomistic simulations. However, the development of transferable coarse-grained models via machine learning still presents significant challenges. Here, we discuss recent developments in this field and current efforts to address the remaining challenges. Y1 - 2023 U6 - https://doi.org/10.1016/j.sbi.2023.102533 VL - 79 ER - TY - JOUR A1 - Krämer, Andreas A1 - Durumeric, Aleksander A1 - Charron, Nicholas A1 - Chen, Yaoyi A1 - Clementi, Cecilia A1 - Noé, Frank T1 - Statistically optimal force aggregation for coarse-graining molecular dynamics JF - The Journal of Physical Chemistry Letters N2 - Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used methodology for learning bottom-up CG force fields maps forces from all-atom molecular dynamics to the CG representation and matches them with a CG force field on average. We show that there is flexibility in how to map all-atom forces to the CG representation and that the most commonly used mapping methods are statistically inefficient and potentially even incorrect in the presence of constraints in the all-atom simulation. We define an optimization statement for force mappings and demonstrate that substantially improved CG force fields can be learned from the same simulation data when using optimized force maps. The method is demonstrated on the miniproteins chignolin and tryptophan cage and published as open-source code. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpclett.3c00444 VL - 14 IS - 17 SP - 3970 EP - 3979 ER - TY - JOUR A1 - Wilken, St. Elmo A1 - Besançon, Mathieu A1 - Kratochvíl, Miroslav A1 - Kuate, Chilperic Armel Foko A1 - Trefois, Christophe A1 - Gu, Wei A1 - Ebenhöh, Oliver T1 - Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models JF - Metabolic Engineering Y1 - 2022 ER - TY - JOUR A1 - Combettes, P. L. A1 - Woodstock, Zev T1 - a variational inequality model for the construction of signals from inconsistent nonlinear equations JF - SIAM Journal on Imaging Sciences Y1 - 2022 ER - TY - JOUR A1 - Ray, Sourav A1 - Sunkara, Vikram A1 - Schütte, Christof A1 - Weber, Marcus T1 - How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs JF - Molecular Simulation N2 - Molecular simulations of ligand–receptor interactions are a computational challenge, especially when their association- (‘on’-rate) and dissociation- (‘off’-rate) mechanisms are working on vastly differing timescales. One way of tackling this multiscale problem is to compute the free-energy landscapes, where molecular dynamics (MD) trajectories are used to only produce certain statistical ensembles. The approach allows for deriving the transition rates between energy states as a function of the height of the activation-energy barriers. In this article, we derive the association rates of the opioids fentanyl and N-(3-fluoro-1-phenethylpiperidin-4-yl)-N-phenyl propionamide (NFEPP) in a μ-opioid receptor by combining the free-energy landscape approach with the square-root-approximation method (SQRA), which is a particularly robust version of Markov modelling. The novelty of this work is that we derive the association rates as a function of the pH level using only an ensemble of MD simulations. We also verify our MD-derived insights by reproducing the in vitro study performed by the Stein Lab. Y1 - 2020 U6 - https://doi.org/10.1080/08927022.2020.1839660 VL - 46 IS - 18 SP - 1443 EP - 1452 PB - Taylor and Francis ER - TY - JOUR A1 - Ray, Sourav A1 - Fackeldey, Konstantin A1 - Stein, Christoph A1 - Weber, Marcus T1 - Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane JF - Biophysica N2 - In our previous studies, a new opioid (NFEPP) was developed to only selectively bind to the 𝜇-opoid receptor (MOR) in inflamed tissue and thus avoid the severe side effects of fentanyl. We know that NFEPP has a reduced binding affinity to MOR in healthy tissue. Inspired by the modelling and simulations performed by Sutcliffe et al., we present our own results of coarse-grained molecular dynamics simulations of fentanyl and NFEPP with regards to their interaction with the 𝜇-opioid receptor embedded within the lipid cell membrane. For technical reasons, we have slightly modified Sutcliffe’s parametrisation of opioids. The pH-dependent opioid simulations are of interest because while fentanyl is protonated at the physiological pH, NFEPP is deprotonated due to its lower pKa value than that of fentanyl. Here, we analyse for the first time whether pH changes have an effect on the dynamical behaviour of NFEPP when it is inside the cell membrane. Besides these changes, our analysis shows a possible alternative interaction of NFEPP at pH 7.4 outside the binding region of the MOR. The interaction potential of NFEPP with MOR is also depicted by analysing the provided statistical molecular dynamics simulations with the aid of an eigenvector analysis of a transition rate matrix. In our modelling, we see differences in the XY-diffusion profiles of NFEPP compared with fentanyl in the cell membrane. Y1 - 2023 U6 - https://doi.org/10.3390/biophysica3020017 VL - 3 IS - 2 SP - 263 EP - 275 ER - TY - JOUR A1 - Rabben, Robert Julian A1 - Ray, Sourav A1 - Weber, Marcus T1 - ISOKANN: Invariant subspaces of Koopman operators learned by a neural network JF - The Journal of Chemical Physics N2 - The problem of determining the rate of rare events in dynamical systems is quite well-known but still difficult to solve. Recent attempts to overcome this problem exploit the fact that dynamic systems can be represented by a linear operator, such as the Koopman operator. Mathematically, the rare event problem comes down to the difficulty in finding invariant subspaces of these Koopman operators K. In this article, we describe a method to learn basis functions of invariant subspaces using an artificial neural Network. Y1 - 2020 U6 - https://doi.org/10.1063/5.0015132 VL - 153 IS - 11 SP - 114109 ER - TY - JOUR A1 - Prasad, Anup K. A1 - Tiwari, Chandni A1 - Ray, Sourav A1 - Holden, Stephanie A1 - Armstrong, David A. A1 - Rosengren, K. Johan A1 - Rodger, Alison A1 - Panwar, Ajay S. A1 - Martin, Lisandra L. T1 - Secondary Structure Transitions for a Family of Amyloidogenic, Antimircobial Uperin 3 Peptides in Contact with Sodium Dodecyl Sulfate JF - ChemPlusChem Y1 - 2022 U6 - https://doi.org/10.1002/cplu.202100408 VL - 87 SP - e202100408 ER - TY - JOUR A1 - Euler, Ricardo A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - Price optimal routing in public transportation JF - EURO Journal on Transportation and Logistics KW - Management Science and Operations Research KW - Transportation KW - Modeling and Simulation Y1 - 2024 U6 - https://doi.org/10.1016/j.ejtl.2024.100128 SN - 2192-4376 VL - 13 SP - 1 EP - 15 PB - Elsevier BV ER - TY - JOUR A1 - Euler, Ricardo A1 - Lindner, Niels A1 - Borndörfer, Ralf T1 - Price Optimal Routing in Public Transportation N2 - We consider the price-optimal earliest arrival problem in public transit (POEAP) in which we aim to calculate the Pareto-front of journeys with respect to ticket price and arrival time in a public transportation network. Public transit fare structures are often a combination of various fare strategies such as, e.g., distance-based fares, zone-based fares or flat fares. The rules that determine the actual ticket price are often very complex. Accordingly, fare structures are notoriously difficult to model as it is in general not sufficient to simply assign costs to arcs in a routing graph. Research into POEAP is scarce and usually either relies on heuristics or only considers restrictive fare models that are too limited to cover the full scope of most real-world applications. We therefore introduce conditional fare networks (CFNs), the first framework for representing a large number of real-world fare structures. We show that by relaxing label domination criteria, CFNs can be used as a building block in label-setting multi-objective shortest path algorithms. By the nature of their extensive modeling capabilities, optimizing over CFNs is NP-hard. However, we demonstrate that adapting the multi-criteria RAPTOR (MCRAP) algorithm for CFNs yields an algorithm capable of solving POEAP to optimality in less than 400 ms on average on a real-world data set. By restricting the size of the Pareto-set, running times are further reduced to below 10 ms. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-86414 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Kraus, Luitgard A1 - Sedeno-Noda, Antonio A1 - Borndörfer, Ralf T1 - Targeted multiobjective Dijkstra Algorithm JF - Networks N2 - We introduce the Targeted Multiobjective Dijkstra Algorithm (T-MDA), a label setting algorithm for the One-to-One Multiobjective Shortest Path (MOSP) Problem. It is based on the recently published Multiobjective Dijkstra Algorithm (MDA) and equips it with A*-like techniques. For any explored subpath, a label setting MOSP algorithm decides whether the subpath can be discarded or must be stored as part of the output. A major design choice is how to store subpaths from the moment they are first explored until the mentioned final decision can be made. The T-MDA combines the polynomially bounded size of the priority queue used in the MDA and alazy management of paths that are not in the queue. The running time bounds from the MDA remain valid. In practice, the T-MDA outperforms known algorithms from the literature and the increased memory consumption is negligible. In this paper, we benchmark the T-MDA against an improved version of the state of the art NAMOA∗drOne-to-One MOSP algorithm from the literature on a standard testbed. Y1 - 2023 U6 - https://doi.org/10.1002/net.22174 VL - 82 IS - 3 SP - 277 EP - 298 ER - TY - JOUR A1 - Hanik, Martin A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph T1 - Bi-invariant Dissimilarity Measures for Sample Distributions in Lie Groups JF - SIAM Journal on Mathematics of Data Science N2 - Data sets sampled in Lie groups are widespread, and as with multivariate data, it is important for many applications to assess the differences between the sets in terms of their distributions. Indices for this task are usually derived by considering the Lie group as a Riemannian manifold. Then, however, compatibility with the group operation is guaranteed only if a bi-invariant metric exists, which is not the case for most non-compact and non-commutative groups. We show here that if one considers an affine connection structure instead, one obtains bi-invariant generalizations of well-known dissimilarity measures: a Hotelling $T^2$ statistic, Bhattacharyya distance and Hellinger distance. Each of the dissimilarity measures matches its multivariate counterpart for Euclidean data and is translation-invariant, so that biases, e.g., through an arbitrary choice of reference, are avoided. We further derive non-parametric two-sample tests that are bi-invariant and consistent. We demonstrate the potential of these dissimilarity measures by performing group tests on data of knee configurations and epidemiological shape data. Significant differences are revealed in both cases. Y1 - 2022 U6 - https://doi.org/10.1137/21M1410373 VL - 4 IS - 4 SP - 1223 EP - 1249 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Sedeño-Noda, Antonio A1 - Borndörfer, Ralf T1 - New Dynamic Programming Algorithm for the Multiobjective Minimum Spanning Tree Problem JF - Arxiv Preprint N2 - The Multiobjective Minimum Spanning Tree (MO-MST) problem is a variant of the Minimum Spanning Tree problem, in which the costs associated with every edge of the input graph are vectors. In this paper, we design a new dynamic programming MO-MST algorithm. Dynamic programming for a MO-MST instance leads to the definition of an instance of the One-to-One Multiobjective Shortest Path (MOSP) problem and both instances have equivalent solution sets. The arising MOSP instance is defined on a so called transition graph. We study the original size of this graph in detail and reduce its size using cost dependent arc pruning criteria. To solve the MOSP instance on the reduced transition graph, we design the Implicit Graph Multiobjective Dijkstra Algorithm (IG-MDA), exploiting recent improvements on MOSP algorithms from the literature. All in all, the new IG-MDA outperforms the current state of the art on a big set of instances from the literature. Our code and results are publicly available. Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2306.16203 ER - TY - JOUR A1 - Maristany de las Casas, Pedro A1 - Sedeño-Noda, Antonio A1 - Borndörfer, Ralf A1 - Huneshagen, Max T1 - K-Shortest Simple Paths Using Biobjective Path Search JF - Arxiv Preprint N2 - In this paper we introduce a new algorithm for the k-Shortest Simple Paths (K-SSP) problem with an asymptotic running time matching the state of the art from the literature. It is based on a black-box algorithm due to Roditty and Zwick (2012) that solves at most 2k instances of the Second Shortest Simple Path (2-SSP) problem without specifying how this is done. We fill this gap using a novel approach: we turn the scalar 2-SSP into instances of the Biobjective Shortest Path problem. Our experiments on grid graphs and on road networks show that the new algorithm is very efficient in practice. Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2309.10377 ER - TY - JOUR A1 - Hunkenschröder, Christoph A1 - Pokutta, Sebastian A1 - Weismantel, Robert T1 - Optimizing a low-dimensional convex function over a high-dimensional cube JF - SIAM Journal on Optimization Y1 - 2022 ER - TY - JOUR A1 - Cereceda-López, Eric A1 - Ostinato, Mattia A1 - Ortiz-Ambriz, Antonio A1 - Straube, Arthur A1 - Palassini, Matteo A1 - Tierno, Pietro T1 - Excluded volume induces buckling in optically driven colloidal rings JF - Phys. Rev. Research N2 - In our combined experimental, theoretical and numerical work, we study the out of equilibrium deformations in a shrinking ring of optically trapped, interacting colloidal particles. Steerable optical tweezers are used to confine dielectric microparticles along a circle of discrete harmonic potential wells, and to reduce the ring radius at a controlled quench speed. We show that excluded-volume interactions are enough to induce particle sliding from their equilibrium positions and nonequilibrium zigzag roughening of the colloidal structure. Our work unveils the underlying mechanism of interfacial deformation in radially driven microscopic discrete rings. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevResearch.6.L012044 VL - 6 SP - L012044 ER - TY - JOUR A1 - Prause, Felix A1 - Hoppmann-Baum, Kai A1 - Defourny, Boris A1 - Koch, Thorsten T1 - The maximum diversity assortment selection problem JF - Mathematical Methods of Operations Research N2 - In this article, we introduce the Maximum Diversity Assortment Selection Problem (MDASP), which is a generalization of the two-dimensional Knapsack Problem (2D-KP). Given a set of rectangles and a rectangular container, the goal of 2D-KP is to determine a subset of rectangles that can be placed in the container without overlapping, i.e., a feasible assortment, such that a maximum area is covered. MDASP is to determine a set of feasible assortments, each of them covering a certain minimum threshold of the container, such that the diversity among them is maximized. Thereby, diversity is defined as the minimum or average normalized Hamming distance of all assortment pairs. MDASP was the topic of the 11th AIMMS-MOPTA Competition in 2019. The methods described in this article and the resulting computational results won the contest. In the following, we give a definition of the problem, introduce a mathematical model and solution approaches, determine upper bounds on the diversity, and conclude with computational experiments conducted on test instances derived from the 2D-KP literature. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1007/s00186-021-00740-2 VL - 93 SP - 521 EP - 554 PB - Mathematical Methods of Operations Research ER - TY - JOUR A1 - Navayazdani, Esfandiar A1 - Ambellan, Felix A1 - Hanik, Martin A1 - von Tycowicz, Christoph T1 - Sasaki Metric for Spline Models of Manifold-Valued Trajectories JF - Computer Aided Geometric Design N2 - We propose a generic spatiotemporal framework to analyze manifold-valued measurements, which allows for employing an intrinsic and computationally efficient Riemannian hierarchical model. Particularly, utilizing regression, we represent discrete trajectories in a Riemannian manifold by composite Bézier splines, propose a natural metric induced by the Sasaki metric to compare the trajectories, and estimate average trajectories as group-wise trends. We evaluate our framework in comparison to state-of-the-art methods within qualitative and quantitative experiments on hurricane tracks. Notably, our results demonstrate the superiority of spline-based approaches for an intensity classification of the tracks. Y1 - 2023 U6 - https://doi.org/10.1016/j.cagd.2023.102220 VL - 104 SP - 102220 ER - TY - JOUR A1 - Breugem, Thomas A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Borndörfer, Ralf T1 - A three-phase heuristic for the Fairness-Oriented Crew Rostering Problem JF - Computers & Operations Research N2 - The Fairness-Oriented Crew Rostering Problem (FCRP) considers the joint optimization of attractiveness and fairness in cyclic crew rostering. Like many problems in scheduling and logistics, the combinatorial complexity of cyclic rostering causes exact methods to fail for large-scale practical instances. In case of the FCRP, this is accentuated by the additionally imposed fairness requirements. Hence, heuristic methods are necessary. We present a three-phase heuristic for the FCRP combining column generation techniques with variable-depth neighborhood search. The heuristic exploits different mathematical formulations to find feasible solutions and to search for improvements. We apply our methodology to practical instances from Netherlands Railways (NS), the main passenger railway operator in the Netherlands Our results show the three-phase heuristic finds good solutions for most instances and outperforms a state-of-the-art commercial solver. Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1016/j.cor.2023.106186 VL - 154 ER - TY - JOUR A1 - Dellnitz, Michael A1 - Hüllermeier, Eyke A1 - Lücke, Marvin A1 - Ober-Blöbaum, Sina A1 - Offen, Christian A1 - Peitz, Sebastian A1 - Pfannschmidt, Karlson T1 - Efficient Time-Stepping for Numerical Integration Using Reinforcement Learning JF - SIAM Journal on Scientific Computing Y1 - 2023 U6 - https://doi.org/10.1137/21M1412682 VL - 45 IS - 2 SP - A579 EP - A595 ER - TY - JOUR A1 - Kreimeier, Timo A1 - Pokutta, Sebastian A1 - Walther, Andrea A1 - Woodstock, Zev T1 - On a Frank-Wolfe approach for abs-smooth functions JF - Optimization Methods and Software Y1 - U6 - https://doi.org/10.1080/10556788.2023.2296985 ER - TY - JOUR A1 - Chmiela, Antonia A1 - Muñoz, Gonzalo A1 - Serrano, Felipe T1 - On the implementation and strengthening of intersection cuts for QCQPs JF - Mathematical Programming B Y1 - 2023 U6 - https://doi.org/10.1007/s10107-022-01808-5 VL - 197 SP - 549 EP - 586 ER - TY - JOUR A1 - Niemann, Jan-Hendrik A1 - Winkelmann, Stefanie A1 - Wolf, Sarah A1 - Schütte, Christof T1 - Agent-based modeling: Population limits and large timescales JF - Chaos: An Interdisciplinary Journal of Nonlinear Science N2 - Modeling, simulation and analysis of interacting agent systems is a broad field of research, with existing approaches reaching from informal descriptions of interaction dynamics to more formal, mathematical models. In this paper, we study agent-based models (ABMs) given as continuous-time stochastic processes and their pathwise approximation by ordinary and stochastic differential equations (ODEs and SDEs, respectively) for medium to large populations. By means of an appropriately adapted transfer operator approach we study the behavior of the ABM process on long time scales. We show that, under certain conditions, the transfer operator approach allows to bridge the gap between the pathwise results for large populations on finite timescales, i.e., the SDE limit model, and approaches built to study dynamical behavior on long time scales like large deviation theory. The latter provides a rigorous analysis of rare events including the associated asymptotic rates on timescales that scale exponentially with the population size. We demonstrate that it is possible to reveal metastable structures and timescales of rare events of the ABM process by finite-length trajectories of the SDE process for large enough populations. This approach has the potential to drastically reduce computational effort for the analysis of ABMs. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77309 SN - 1438-0064 VL - 31 IS - 3 ER - TY - JOUR A1 - Niemann, Jan-Hendrik A1 - Klus, Stefan A1 - Schütte, Christof T1 - Data-driven model reduction of agent-based systems using the Koopman generator JF - PLOS ONE N2 - The dynamical behavior of social systems can be described by agent-based models. Although single agents follow easily explainable rules, complex time-evolving patterns emerge due to their interaction. The simulation and analysis of such agent-based models, however, is often prohibitively time-consuming if the number of agents is large. In this paper, we show how Koopman operator theory can be used to derive reduced models of agent-based systems using only simulation or real-world data. Our goal is to learn coarse-grained models and to represent the reduced dynamics by ordinary or stochastic differential equations. The new variables are, for instance, aggregated state variables of the agent-based model, modeling the collective behavior of larger groups or the entire population. Using benchmark problems with known coarse-grained models, we demonstrate that the obtained reduced systems are in good agreement with the analytical results, provided that the numbers of agents is sufficiently large. Y1 - 2021 U6 - https://doi.org/10.1371/journal.pone.0250970 VL - 16 IS - 5 ER - TY - JOUR A1 - Klus, Stefan A1 - Nüske, Feliks A1 - Peitz, Sebastian A1 - Niemann, Jan-Hendrik A1 - Clementi, Cecilia A1 - Schütte, Christof T1 - Data-driven approximation of the Koopman generator: Model reduction, system identification, and control JF - Physica D: Nonlinear Phenomena Y1 - 2020 U6 - https://doi.org/10.1016/j.physd.2020.132416 VL - 406 ER - TY - JOUR A1 - Schintke, Florian A1 - De Mecquenem, Ninon A1 - Guarino, Vanessa Emanuela A1 - Hilbrich, Marcus A1 - Lehmann, Fabian A1 - Sattler, Rebecca A1 - Sparka, Jan Arne A1 - Speckhard, Daniel A1 - Stolte, Hermann A1 - Vu, Anh Duc A1 - Leser, Ulf T1 - Validity Constraints for Data Analysis Workflows JF - arXiv Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2305.08409 SP - 1 EP - 28 ER - TY - JOUR A1 - Amiranashvili, Tamaz A1 - Lüdke, David A1 - Li, Hongwei Bran A1 - Zachow, Stefan A1 - Menze, Bjoern T1 - Learning continuous shape priors from sparse data with neural implicit functions JF - Medical Image Analysis N2 - Statistical shape models are an essential tool for various tasks in medical image analysis, including shape generation, reconstruction and classification. Shape models are learned from a population of example shapes, which are typically obtained through segmentation of volumetric medical images. In clinical practice, highly anisotropic volumetric scans with large slice distances are prevalent, e.g., to reduce radiation exposure in CT or image acquisition time in MR imaging. For existing shape modeling approaches, the resolution of the emerging model is limited to the resolution of the training shapes. Therefore, any missing information between slices prohibits existing methods from learning a high-resolution shape prior. We propose a novel shape modeling approach that can be trained on sparse, binary segmentation masks with large slice distances. This is achieved through employing continuous shape representations based on neural implicit functions. After training, our model can reconstruct shapes from various sparse inputs at high target resolutions beyond the resolution of individual training examples. We successfully reconstruct high-resolution shapes from as few as three orthogonal slices. Furthermore, our shape model allows us to embed various sparse segmentation masks into a common, low-dimensional latent space — independent of the acquisition direction, resolution, spacing, and field of view. We show that the emerging latent representation discriminates between healthy and pathological shapes, even when provided with sparse segmentation masks. Lastly, we qualitatively demonstrate that the emerging latent space is smooth and captures characteristic modes of shape variation. We evaluate our shape model on two anatomical structures: the lumbar vertebra and the distal femur, both from publicly available datasets. Y1 - 2024 U6 - https://doi.org/10.1016/j.media.2024.103099 VL - 94 SP - 103099 ER - TY - JOUR A1 - Niemann, Jan-Hendrik A1 - Klus, Stefan A1 - Conrad, Natasa Djurdjevac A1 - Schütte, Christof T1 - Koopman-Based Surrogate Models for Multi-Objective Optimization of Agent-Based Systems JF - Physica D: Nonlinear Phenomena N2 - Agent-based models (ABMs) provide an intuitive and powerful framework for studying social dynamics by modeling the interactions of individuals from the perspective of each individual. In addition to simulating and forecasting the dynamics of ABMs, the demand to solve optimization problems to support, for example, decision-making processes naturally arises. Most ABMs, however, are non-deterministic, high-dimensional dynamical systems, so objectives defined in terms of their behavior are computationally expensive. In particular, if the number of agents is large, evaluating the objective functions often becomes prohibitively time-consuming. We consider data-driven reduced models based on the Koopman generator to enable the efficient solution of multi-objective optimization problems involving ABMs. In a first step, we show how to obtain data-driven reduced models of non-deterministic dynamical systems (such as ABMs) that depend on potentially nonlinear control inputs. We then use them in the second step as surrogate models to solve multi-objective optimal control problems. We first illustrate our approach using the example of a voter model, where we compute optimal controls to steer the agents to a predetermined majority, and then using the example of an epidemic ABM, where we compute optimal containment strategies in a prototypical situation. We demonstrate that the surrogate models effectively approximate the Pareto-optimal points of the ABM dynamics by comparing the surrogate-based results with test points, where the objectives are evaluated using the ABM. Our results show that when objectives are defined by the dynamic behavior of ABMs, data-driven surrogate models support or even enable the solution of multi-objective optimization problems. Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1016/j.physd.2024.134052 VL - 460 SP - 134052 ER - TY - JOUR A1 - Niemann, Jan-Hendrik A1 - Uram, Samuel A1 - Wolf, Sarah A1 - Conrad, Natasa Djurdjevac A1 - Weiser, Martin T1 - Multilevel Optimization for Policy Design with Agent-Based Epidemic Models JF - Computational Science N2 - Epidemiological models can not only be used to forecast the course of a pandemic like COVID-19, but also to propose and design non-pharmaceutical interventions such as school and work closing. In general, the design of optimal policies leads to nonlinear optimization problems that can be solved by numerical algorithms. Epidemiological models come in different complexities, ranging from systems of simple ordinary differential equations (ODEs) to complex agent-based models (ABMs). The former allow a fast and straightforward optimization, but are limited in accuracy, detail, and parameterization, while the latter can resolve spreading processes in detail, but are extremely expensive to optimize. We consider policy optimization in a prototypical situation modeled as both ODE and ABM, review numerical optimization approaches, and propose a heterogeneous multilevel approach based on combining a fine-resolution ABM and a coarse ODE model. Numerical experiments, in particular with respect to convergence speed, are given for illustrative examples. Y1 - 2024 U6 - https://doi.org/10.1016/j.jocs.2024.102242 VL - 77 SP - 102242 ER - TY - JOUR A1 - Designolle, Sébastien A1 - Vértesi, Tamás A1 - Pokutta, Sebastian T1 - Symmetric multipartite Bell inequalities via Frank-Wolfe algorithms JF - Physics Review A N2 - In multipartite Bell scenarios, we study the nonlocality robustness of the Greenberger-Horne-Zeilinger (GHZ) state. When each party performs planar measurements forming a regular polygon, we exploit the symmetry of the resulting correlation tensor to drastically accelerate the computation of (i) a Bell inequality via Frank-Wolfe algorithms and (ii) the corresponding local bound. The Bell inequalities obtained are facets of the symmetrized local polytope and they give the best-known upper bounds on the nonlocality robustness of the GHZ state for three to ten parties. Moreover, for four measurements per party, we generalize our facets and hence show, for any number of parties, an improvement on Mermin's inequality in terms of noise robustness. We also compute the detection efficiency of our inequalities and show that some give rise to the activation of nonlocality in star networks, a property that was only shown with an infinite number of measurements. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevA.109.022205 VL - 109 IS - 2 ER - TY - JOUR A1 - Donati, Luca A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Augmented ant colony algorithm for virtual drug discovery JF - Journal of Mathematical Chemistry N2 - Docking is a fundamental problem in computational biology and drug discovery that seeks to predict a ligand’s binding mode and affinity to a target protein. However, the large search space size and the complexity of the underlying physical interactions make docking a challenging task. Here, we review a docking method, based on the ant colony optimization algorithm, that ranks a set of candidate ligands by solving a minimization problem for each ligand individually. In addition, we propose an augmented version that takes into account all energy functions collectively, allowing only one minimization problem to be solved. The results show that our modification outperforms in accuracy and efficiency. Y1 - 2023 U6 - https://doi.org/10.1007/s10910-023-01549-6 VL - 62 SP - 367 EP - 385 ER - TY - JOUR A1 - Deza, Antoine A1 - Pokutta, Sebastian A1 - Pournin, Lionel T1 - The complexity of geometric scaling JF - Operations Research Letters Y1 - 2024 U6 - https://doi.org/10.1016/j.orl.2023.11.010 VL - 52 SP - 107057 ER - TY - JOUR A1 - Mukherjee, Deshabrato A1 - Kertész, Krisztián A1 - Zolnai, Zsolt A1 - Kovács, Zoltán A1 - Deák, András A1 - Pálinkás, András A1 - Osváth, Zoltán A1 - Olasz, Dániel A1 - Romanenko, Alekszej A1 - Fried, Miklós A1 - Burger, Sven A1 - Sáfrán, György A1 - Petrik, Peter T1 - Optimized Sensing on Gold Nanoparticles Created by Graded-Layer Magnetron Sputtering and Annealing Y1 - 2024 U6 - https://doi.org/10.2139/ssrn.4752470 ER - TY - JOUR A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Colom, Remi A1 - Genevet, Patrice A1 - Burger, Sven T1 - Poles and zeros in non-Hermitian systems: Application to photonics JF - Phys. Rev. B Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevB.109.045414 VL - 109 SP - 045414 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Kuen, Lilli A1 - Burger, Sven T1 - Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena JF - SoftwareX Y1 - 2024 U6 - https://doi.org/10.1016/j.softx.2024.101694 VL - 26 SP - 101694 ER - TY - JOUR A1 - Schimunek, Johannes A1 - Seidl, Philipp A1 - Elez, Katarina A1 - Hempel, Tim A1 - Le, Tuan A1 - Noé, Frank A1 - Olsson, Simon A1 - Raich, Lluís A1 - Winter, Robin A1 - Gokcan, Hatice A1 - Gusev, Filipp A1 - Gutkin, Evgeny M. A1 - Isayev, Olexandr A1 - Kurnikova, Maria G. A1 - Narangoda, Chamali H. A1 - Zubatyuk, Roman A1 - Bosko, Ivan P. A1 - Furs, Konstantin V. A1 - Karpenko, Anna D. A1 - Kornoushenko, Yury V. A1 - Shuldau, Mikita A1 - Yushkevich, Artsemi A1 - Benabderrahmane, Mohammed B. A1 - Bousquet-Melou, Patrick A1 - Bureau, Ronan A1 - Charton, Beatrice A1 - Cirou, Bertrand C. A1 - Gil, Gérard A1 - Allen, William J. A1 - Sirimulla, Suman A1 - Watowich, Stanley A1 - Antonopoulos, Nick A1 - Epitropakis, Nikolaos A1 - Krasoulis, Agamemnon A1 - Itsikalis, Vassilis A1 - Theodorakis, Stavros A1 - Kozlovskii, Igor A1 - Maliutin, Anton A1 - Medvedev, Alexander A1 - Popov, Petr A1 - Zaretckii, Mark A1 - Eghbal-Zadeh, Hamid A1 - Halmich, Christina A1 - Hochreiter, Sepp A1 - Mayr, Andreas A1 - Ruch, Peter A1 - Widrich, Michael A1 - Berenger, Francois A1 - Kumar, Ashutosh A1 - Yamanishi, Yoshihiro A1 - Zhang, Kam Y. J. A1 - Bengio, Emmanuel A1 - Bengio, Yoshua A1 - Jain, Moksh J. A1 - Korablyov, Maksym A1 - Liu, Cheng-Hao A1 - Marcou, Gilles A1 - Glaab, Enrico A1 - Barnsley, Kelly A1 - Iyengar, Suhasini M. A1 - Ondrechen, Mary Jo A1 - Haupt, V. Joachim A1 - Kaiser, Florian A1 - Schroeder, Michael A1 - Pugliese, Luisa A1 - Albani, Simone A1 - Athanasiou, Christina A1 - Beccari, Andrea A1 - Carloni, Paolo A1 - D’Arrigo, Giulia A1 - Gianquinto, Eleonora A1 - Goßen, Jonas A1 - Hanke, Anton A1 - Joseph, Benjamin P. A1 - Kokh, Daria B. A1 - Kovachka, Sandra A1 - Manelfi, Candida A1 - Mukherjee, Goutam A1 - Muñiz-Chicharro, Abraham A1 - Musiani, Francesco A1 - Nunes-Alves, Ariane A1 - Paiardi, Giulia A1 - Rossetti, Giulia A1 - Sadiq, S. Kashif A1 - Spyrakis, Francesca A1 - Talarico, Carmine A1 - Tsengenes, Alexandros A1 - Wade, Rebecca C. A1 - Copeland, Conner A1 - Gaiser, Jeremiah A1 - Olson, Daniel R. A1 - Roy, Amitava A1 - Venkatraman, Vishwesh A1 - Wheeler, Travis J. A1 - Arthanari, Haribabu A1 - Blaschitz, Klara A1 - Cespugli, Marco A1 - Durmaz, Vedat A1 - Fackeldey, Konstantin A1 - Fischer, Patrick D. A1 - Gorgulla, Christoph A1 - Gruber, Christian A1 - Gruber, Karl A1 - Hetmann, Michael A1 - Kinney, Jamie E. A1 - Padmanabha Das, Krishna M. A1 - Pandita, Shreya A1 - Singh, Amit A1 - Steinkellner, Georg A1 - Tesseyre, Guilhem A1 - Wagner, Gerhard A1 - Wang, Zi-Fu A1 - Yust, Ryan J. A1 - Druzhilovskiy, Dmitry S. A1 - Filimonov, Dmitry A. A1 - Pogodin, Pavel V. A1 - Poroikov, Vladimir A1 - Rudik, Anastassia V. A1 - Stolbov, Leonid A. A1 - Veselovsky, Alexander V. A1 - De Rosa, Maria A1 - De Simone, Giada A1 - Gulotta, Maria R. A1 - Lombino, Jessica A1 - Mekni, Nedra A1 - Perricone, Ugo A1 - Casini, Arturo A1 - Embree, Amanda A1 - Gordon, D. Benjamin A1 - Lei, David A1 - Pratt, Katelin A1 - Voigt, Christopher A. A1 - Chen, Kuang-Yu A1 - Jacob, Yves A1 - Krischuns, Tim A1 - Lafaye, Pierre A1 - Zettor, Agnès A1 - Rodríguez, M. Luis A1 - White, Kris M. A1 - Fearon, Daren A1 - Von Delft, Frank A1 - Walsh, Martin A. A1 - Horvath, Dragos A1 - Brooks III, Charles L. A1 - Falsafi, Babak A1 - Ford, Bryan A1 - García-Sastre, Adolfo A1 - Yup Lee, Sang A1 - Naffakh, Nadia A1 - Varnek, Alexandre A1 - Klambauer, Günter A1 - Hermans, Thomas M. T1 - A community effort in SARS-CoV-2 drug discovery JF - Molecular Informatics KW - COVID-19 KW - drug discovery KW - machine learning KW - SARS-CoV-2 Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1002/minf.202300262 VL - 43 IS - 1 SP - e202300262 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Niknejad, Amir A1 - Weber, Marcus A1 - Donati, Luca T1 - Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies JF - Journal of Chemical Physics N2 - Estimating the rate of rare conformational changes in molecular systems is one of the goals of molecular dynamics simulations. In the past few decades, a lot of progress has been done in data-based approaches toward this problem. In contrast, model-based methods, such as the Square Root Approximation (SqRA), directly derive these quantities from the potential energy functions. In this article, we demonstrate how the SqRA formalism naturally blends with the tensor structure obtained by coupling multiple systems, resulting in the tensor-based Square Root Approximation (tSqRA). It enables efficient treatment of high-dimensional systems using the SqRA and provides an algebraic expression of the impact of coupling energies between molecular subsystems. Based on the tSqRA, we also develop the projected rate estimation, a hybrid data-model-based algorithm that efficiently estimates the slowest rates for coupled systems. In addition, we investigate the possibility of integrating low-rank approximations within this framework to maximize the potential of the tSqRA. Y1 - 2024 U6 - https://doi.org/10.1063/5.0187792 VL - 160 SP - 104112 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Ribera Borrell, Enric A1 - Weber, Marcus T1 - Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN JF - Journal of Mathematical Physics N2 - The dominant eigenfunctions of the Koopman operator characterize the metastabilities and slow-timescale dynamics of stochastic diffusion processes. In the context of molecular dynamics and Markov state modeling, they allow for a description of the location and frequencies of rare transitions, which are hard to obtain by direct simulation alone. In this article, we reformulate the eigenproblem in terms of the ISOKANN framework, an iterative algorithm that learns the eigenfunctions by alternating between short burst simulations and a mixture of machine learning and classical numerics, which naturally leads to a proof of convergence. We furthermore show how the intermediate iterates can be used to reduce the sampling variance by importance sampling and optimal control (enhanced sampling), as well as to select locations for further training (adaptive sampling). We demonstrate the usage of our proposed method in experiments, increasing the approximation accuracy by several orders of magnitude. Y1 - 2024 U6 - https://doi.org/10.1063/5.0140764 VL - 65 SP - 013502 ER - TY - JOUR A1 - Hanik, Martin A1 - Steidl, Gabriele A1 - von Tycowicz, Christoph T1 - Manifold GCN: Diffusion-based Convolutional Neural Network for Manifold-valued Graphs N2 - We propose two graph neural network layers for graphs with features in a Riemannian manifold. First, based on a manifold-valued graph diffusion equation, we construct a diffusion layer that can be applied to an arbitrary number of nodes and graph connectivity patterns. Second, we model a tangent multilayer perceptron by transferring ideas from the vector neuron framework to our general setting. Both layers are equivariant with respect to node permutations and isometries of the feature manifold. These properties have been shown to lead to a beneficial inductive bias in many deep learning tasks. Numerical examples on synthetic data as well as on triangle meshes of the right hippocampus to classify Alzheimer's disease demonstrate the very good performance of our layers. Y1 - 2024 ER - TY - JOUR A1 - Höfling, Felix A1 - Dietrich, Siegfried T1 - Structure of liquid–vapor interfaces: perspectives from liquid state theory, large-scale simulations, and potential grazing-incidence X-ray diffraction JF - J Chem Phys. N2 - Grazing-incidence X-ray diffraction (GIXRD) is a scattering technique which allows one to characterize the structure of fluid interfaces down to the molecular scale, including the measurement of the surface tension and of the interface roughness. However, the corresponding standard data analysis at non-zero wave numbers has been criticized as to be inconclusive because the scattering intensity is polluted by the unavoidable scattering from the bulk. Here we overcome this ambiguity by proposing a physically consistent model of the bulk contribution which is based on a minimal set of assumptions of experimental relevance. To this end, we derive an explicit integral expression for the background scattering, which can be determined numerically from the static structure factors of the coexisting bulk phases as independent input. Concerning the interpretation of GIXRD data inferred from computer simulations, we account also for the finite sizes of the bulk phases, which are unavoidable in simulations. The corresponding leading-order correction beyond the dominant contribution to the scattered intensity is revealed by asymptotic analysis, which is characterized by the competition between the linear system size and the X-ray penetration depth in the case of simulations. Specifically, we have calculated the expected GIXRD intensity for scattering at the planar liquid--vapor interface of Lennard-Jones fluids with truncated pair interactions via extensive, high-precision simulations. The reported data cover interfacial and bulk properties of fluid states along the whole liquid--vapor coexistence line. A sensitivity analysis demonstrates the robustness of our findings concerning the detailed definition of the mean interface position. We conclude that previous claims of an enhanced surface tension at mesoscopic scales are amenable to unambiguous tests via scattering experiments. Y1 - 2024 U6 - https://doi.org/10.1063/5.0186955 VL - 160 SP - 104107 ER - TY - JOUR A1 - Bürger, Johanna A1 - Hayne, Paul A1 - Gundlach, Bastian A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Blum, Jürgen T1 - A Microphysical Thermal Model for the Lunar Regolith: Investigating the Latitudinal Dependence of Regolith Properties JF - Journal of Geophysical Research: Planets N2 - The microphysical structure of the lunar regolith provides information on the geologic history of the Moon. We used remote sensing measurements of thermal emission and a thermophysical model to determine the microphysical properties of the lunar regolith. We expand upon previous investigations by developing a microphysical thermal model, which more directly simulates regolith properties, such as grain size and volume filling factor. The modeled temperatures are matched with surface temperatures measured by the Diviner Lunar Radiometer Experiment on board the Lunar Reconnaissance Orbiter. The maria and highlands are investigated separately and characterized in the model by a difference in albedo and grain density. We find similar regolith temperatures for both terrains, which can be well described by similar volume filling factor profiles and mean grain sizes obtained from returned Apollo samples. We also investigate a significantly lower thermal conductivity for highlands, which formally also gives a very good solution, but in a parameter range that is well outside the Apollo data. We then study the latitudinal dependence of regolith properties up to ±80° latitude. When assuming constant regolith properties, we find that a variation of the solar incidence-dependent albedo can reduce the initially observed latitudinal gradient between model and Diviner measurements significantly. A better match between measurements and model can be achieved by a variation in intrinsic regolith properties with a decrease in bulk density with increasing latitude. We find that a variation in grain size alone cannot explain the Diviner measurements at higher latitudes. Y1 - 2024 U6 - https://doi.org/10.1029/2023JE008152 VL - 129 IS - 3 ER - TY - JOUR A1 - Schintke, Florian A1 - Belhajjame, Khalid A1 - De Mecquenem, Ninon A1 - Frantz, David A1 - Guarino, Vanessa Emanuela A1 - Hilbrich, Marcus A1 - Lehmann, Fabian A1 - Missier, Paolo A1 - Sattler, Rebecca A1 - Sparka, Jan Arne A1 - Speckhard, Daniel T. A1 - Stolte, Hermann A1 - Vu, Anh Duc A1 - Leser, Ulf T1 - Validity constraints for data analysis workflows JF - Future Generation Computer Systems Y1 - 2024 U6 - https://doi.org/10.1016/j.future.2024.03.037 VL - 157 SP - 82 EP - 97 ER - TY - JOUR A1 - Oehme, Stephan A1 - Moewis, Philippe A1 - Boeth, Heide A1 - Bartek, Benjamin A1 - von Tycowicz, Christoph A1 - Ehrig, Rainald A1 - Duda, Georg A1 - Jung, Tobias T1 - Altered knee kinematics after posterior cruciate single-bundle reconstruction - a comprehensive prospective biomechanical in vivo analysis JF - Frontiers in Bioengineering and Biotechnology Y1 - 2024 U6 - https://doi.org/10.3389/fbioe.2024.1322136 VL - 12 ER - TY - JOUR A1 - Gholami, Masoud A1 - Schintke, Florian T1 - IOSIG: Declarative I/O-Stream Properties Using Pragmas JF - Datenbank-Spektrum Y1 - 2022 U6 - https://doi.org/10.1007/s13222-022-00419-w VL - 22 IS - 2 SP - 109 EP - 119 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Gholami, Masoud A1 - Schintke, Florian T1 - CAWL: A Cache-aware Write Performance Model of Linux Systems JF - arXiv Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2306.05701 SP - 1 EP - 22 ER - TY - JOUR A1 - Erban, Radek A1 - Winkelmann, Stefanie T1 - Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling N2 - The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants, the mgRDME approach improves both accuracy and efficiency of compartment-based reaction-diffusion simulations. The mgRDME framework is examined through its application to morphogen gradient formation in stochastic reaction-diffusion scenarios, using both an analytically tractable first-order reaction network and a model with a second-order reaction. The results obtained by the mgRDME modelling are compared with the standard RDME model and with the (more detailed) particle-based Brownian dynamics simulations. The dependence of error and numerical cost on the compartment sizes is defined and investigated through a multi-objective optimization problem. Y1 - 2024 ER - TY - JOUR A1 - Zakiyeva, Nazgul A1 - Petkovic, Milena T1 - High-dimensional high-frequency time series prediction with a mixed integer optimisation method JF - Operations Research Proceedings N2 - We study a functional autoregressive model for high-frequency time series. We approach the estimation of the proposed model using a Mixed Integer Optimisation method. The proposed model captures serial dependence in the functional time series by including high-dimensional curves. We illustrate our methodology on large-scale natural gas network data. Our model provides more accurate day-ahead hourly out-of-sample forecast of the gas in and out-flows compared to alternative prediction models. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-93068 SN - 1438-0064 ER - TY - JOUR A1 - Anton, Oliver A1 - Henderson, Victoria A. A1 - Da Ros, Elisa A1 - Sekuliĉ, Ivan A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Krutzik, Markus T1 - Review and experimental benchmarking of machine learning algorithms for efficient optimization of cold atom experiments JF - Mach. Learn. Sci. Technol. Y1 - 2024 U6 - https://doi.org/10.1088/2632-2153/ad3cb6 VL - 5 SP - 025022 ER - TY - JOUR A1 - Bopp, Julian M. A1 - Plock, Matthias A1 - Turan, Tim A1 - Pieplow, Gregor A1 - Burger, Sven A1 - Schröder, Tim T1 - Sawfish Photonic Crystal Cavity for Near-Unity Emitter-to-Fiber Interfacing in Quantum Network Applications JF - Adv. Opt. Mater. Y1 - 2024 U6 - https://doi.org/10.1002/adom.202301286 VL - 12 SP - 2301286 ER - TY - JOUR A1 - Müller, Gabriel A1 - Martínez-Lahuerta, V. J. A1 - Sekuliĉ, Ivan A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Gaaloul, Naceur T1 - Bayesian optimization for state engineering of quantum gases JF - arXiv Y1 - 2024 SP - arXiv:2404.18234 ER - TY - JOUR A1 - Binkowski, Felix A1 - Kullig, Julius A1 - Betz, Fridtjof A1 - Zschiedrich, Lin A1 - Walther, Andrea A1 - Wiersig, Jan A1 - Burger, Sven T1 - Computing eigenfrequency sensitivities near exceptional points JF - Phys. Rev. Research Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevResearch.6.023148 VL - 6 SP - 023148 ER - TY - JOUR A1 - Lorenz-Spreen, Philipp A1 - Wolf, Frederik A1 - Braun, Jonas A1 - Ghoshal, Gourab A1 - Djurdjevac Conrad, Natasa A1 - Hövel, Philipp T1 - Tracking online topics over time: understanding dynamic hashtag communities JF - Computational Social Networks N2 - Background: Hashtags are widely used for communication in online media. As a condensed version of information, they characterize topics and discussions. For their analysis, we apply methods from network science and propose novel tools for tracing their dynamics in time-dependent data. The observations are characterized by bursty behaviors in the increases and decreases of hashtag usage. These features can be reproduced with a novel model of dynamic rankings. Hashtag communities in time: We build temporal and weighted co-occurrence networks from hashtags. On static snapshots, we infer the community structure using customized methods. On temporal networks, we solve the bipartite matching problem of detected communities at subsequent timesteps by taking into account higher-order memory. This results in a matching protocol that is robust toward temporal fluctuations and instabilities of the static community detection. The proposed methodology is broadly applicable and its outcomes reveal the temporal behavior of online topics. Modeling topic-dynamics: We consider the size of the communities in time as a proxy for online popularity dynamics. We find that the distributions of gains and losses, as well as the interevent times are fat-tailed indicating occasional, but large and sudden changes in the usage of hashtags. Inspired by typical website designs, we propose a stochastic model that incorporates a ranking with respect to a time-dependent prestige score. This causes occasional cascades of rank shift events and reproduces the observations with good agreement. This offers an explanation for the observed dynamics, based on characteristic elements of online media. Y1 - 2018 U6 - https://doi.org/10.1186/s40649-018-0058-6 VL - 5 IS - 9 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Banisch, Ralf A1 - Schütte, Christof T1 - Modularity of Directed Networks: Cycle Decomposition Approach JF - Journal of Computational Dynamics 2 (2015) pp. 1-24 N2 - The problem of decomposing networks into modules (or clusters) has gained much attention in recent years, as it can account for a coarsegrained description of complex systems, often revealing functional subunits of these systems. A variety of module detection algorithms have been proposed, mostly oriented towards finding hard partitionings of undirected networks. Despite the increasing number of fuzzy clustering methods for directed networks, many of these approaches tend to neglect important directional information. In this paper, we present a novel random walk based approach for finding fuzzy partitions of directed, weighted networks, where edge directions play a crucial role in defining how well nodes in a module are interconnected. We will show that cycle decomposition of a random walk process connects the notion of network modules and information transport in a network, leading to a new, symmetric measure of node communication. Finally, we will use this measure to introduce a communication graph, for which we will show that although being undirected it inherits all necessary information about modular structures from the original network. Y1 - 2015 U6 - https://doi.org/10.3934/jcd.2015.2.1 ER - TY - JOUR A1 - Klus, Stefan A1 - Djurdjevac Conrad, Natasa T1 - Koopman-based spectral clustering of directed and time-evolving graphs JF - Journal of Nonlinear Science N2 - While spectral clustering algorithms for undirected graphs are well established and have been successfully applied to unsupervised machine learning problems ranging from image segmentation and genome sequencing to signal processing and social network analysis, clustering directed graphs remains notoriously difficult. Two of the main challenges are that the eigenvalues and eigenvectors of graph Laplacians associated with directed graphs are in general complex-valued and that there is no universally accepted definition of clusters in directed graphs. We first exploit relationships between the graph Laplacian and transfer operators and in particular between clusters in undirected graphs and metastable sets in stochastic dynamical systems and then use a generalization of the notion of metastability to derive clustering algorithms for directed and time-evolving graphs. The resulting clusters can be interpreted as coherent sets, which play an important role in the analysis of transport and mixing processes in fluid flows. Y1 - 2022 U6 - https://doi.org/10.1007/s00332-022-09863-0 VL - 33 ER - TY - JOUR A1 - Sarich, Marco A1 - Djurdjevac Conrad, Natasa A1 - Bruckner, Sharon A1 - Conrad, Tim A1 - Schütte, Christof T1 - Modularity revisited: A novel dynamics-based concept for decomposing complex networks JF - Journal of Computational Dynamics Y1 - 2014 UR - http://publications.mi.fu-berlin.de/1127/ U6 - https://doi.org/10.3934/jcd.2014.1.191 VL - 1 IS - 1 SP - 191 EP - 212 ER - TY - JOUR A1 - Lorenz, Philipp A1 - Wolf, Frederik A1 - Braun, Jonas A1 - Djurdjevac Conrad, Natasa A1 - Hövel, Philipp T1 - Capturing the Dynamics of Hashtag-Communities JF - International Workshop on Complex Networks and their Applications Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-72150-7_33 SP - 401 EP - 413 ER - TY - JOUR A1 - Zonker, Johannes A1 - Padilla-Iglesias, Cecilia A1 - Djurdjevac Conrad, Natasa T1 - Insights into drivers of mobility and cultural dynamics of African hunter-gatherers over the past 120 000 years JF - Royal Society Open Science N2 - Humans have a unique capacity to innovate, transmit and rely on complex, cumulative culture for survival. While an important body of work has attempted to explore the role of changes in the size and interconnectedness of populations in determining the persistence, diversity and complexity of material culture, results have achieved limited success in explaining the emergence and spatial distribution of cumulative culture over our evolutionary trajectory. Here, we develop a spatio-temporally explicit agent-based model to explore the role of environmentally driven changes in the population dynamics of hunter–gatherer communities in allowing the development, transmission and accumulation of complex culture. By modelling separately demography- and mobility-driven changes in interaction networks, we can assess the extent to which cultural change is driven by different types of population dynamics. We create and validate our model using empirical data from Central Africa spanning 120 000 years. We find that populations would have been able to maintain diverse and elaborate cultural repertoires despite abrupt environmental changes and demographic collapses by preventing isolation through mobility. However, we also reveal that the function of cultural features was also an essential determinant of the effects of environmental or demographic changes on their dynamics. Our work can therefore offer important insights into the role of a foraging lifestyle on the evolution of cumulative culture. Y1 - 2023 U6 - https://doi.org/10.1098/rsos.230495 VL - 10 IS - 11 ER - TY - JOUR A1 - Klus, Stefan A1 - Djurdjevac Conrad, Natasa T1 - Dynamical systems and complex networks: A Koopman operator perspective N2 - The Koopman operator has entered and transformed many research areas over the last years. Although the underlying concept–representing highly nonlinear dynamical systems by infinite-dimensional linear operators–has been known for a long time, the availability of large data sets and efficient machine learning algorithms for estimating the Koopman operator from data make this framework extremely powerful and popular. Koopman operator theory allows us to gain insights into the characteristic global properties of a system without requiring detailed mathematical models. We will show how these methods can also be used to analyze complex networks and highlight relationships between Koopman operators and graph Laplacians. Y1 - 2024 ER - TY - JOUR A1 - Schaible, Jonas A1 - Nouri, Bijan A1 - Höpken, Lars A1 - Kotzab, Tim A1 - Loevenich, Matthias A1 - Blum, Niklas A1 - Hammer, Annette A1 - Stührenberg, Jonas A1 - Jäger, Klaus A1 - Becker, Christiane A1 - Wilbert, Stefan T1 - Application of nowcasting to reduce the impact of irradiance ramps on PV power plants JF - EPJ Photovolt. Y1 - 2024 U6 - https://doi.org/10.1051/epjpv/2024009 VL - 15 SP - 15 ER - TY - JOUR A1 - Schembera, Björn A1 - Wübbeling, Frank A1 - Koprucki, Thomas A1 - Biedinger, Christine A1 - Reidelbach, Marco A1 - Schmidt, Burkhard A1 - Göddeke, Dominik A1 - Fiedler, Jochen T1 - Building Ontologies and Knowledge Graphs for Mathematics and its Applications JF - Proceedings of the Conference on Research Data Infrastructure N2 - Ontologies and knowledge graphs for mathematical algorithms and models are presented, that have been developed by the Mathematical Research Data Initiative. This enables FAIR data handling in mathematics and the applied disciplines. Moreover, challenges of harmonization during the ontology development are discussed. Y1 - 2023 U6 - https://doi.org/10.52825/cordi.v1i.255 SN - 2941-296X VL - 1 PB - TIB Open Publishing ER - TY - JOUR A1 - Reidelbach, Marco A1 - Ferrer, Eloi A1 - Weber, Marcus T1 - MaRDMO Plugin BT - Document and Retrieve Workflows Using the MaRDI Portal JF - Proceedings of the Conference on Research Data Infrastructure N2 - MaRDMO, a plugin for the Research Data Management Organiser, was developed in the Mathematical Research Data Initiative to document interdisciplinary workflows using a standardised scheme. Interdisciplinary workflows recorded this way are published directly on the MaRDI portal. In addition, central information is integrated into the MaRDI knowledge graph. Next to the documentation, MaRDMO offers the possibility to retrieve existing interdisciplinary workflows from the MaRDI Knowledge Graph to allow the reproduction of the initial work and to provide scientists with new researchimpulses. Thus, MaRDMO creates a community-driven knowledge loop that could help to overcome the replication crisis. Y1 - 2023 U6 - https://doi.org/10.52825/cordi.v1i.254 SN - 2941-296X VL - 1 PB - TIB Open Publishing ER - TY - JOUR A1 - Benner, Peter A1 - Danabalan, Renita A1 - Gödekke, Dominik A1 - Kastner, Lars A1 - Krause, Tabea A1 - Mietchen, Daniel A1 - Reidelbach, Marco A1 - Schembera, Björn A1 - Schubotz, Moritz A1 - Sinn, Rainer A1 - Tabelow, Karsten T1 - Research Data Management Planning in Mathematics N2 - Research data are crucial in mathematics and all scientific disciplines, as they form the foundation for empirical evidence, by enabling the validation and reproducibility of scientific findings. Mathematical research data (MathRD) have become vast and complex, and their interdisciplinary potential and abstract nature make them ubiquitous in various scientific fields. The volume of data and the velocity of its creation are rapidly increasing due to advancements in data science and computing power. This complexity extends to other disciplines, resulting in diverse research data and computational models. Thus, proper handling of research data is crucial both within mathematics and for its manifold connections and exchange with other disciplines. The National Research Data Infrastructure (NFDI), funded by the federal and state governments of Germany, consists of discipline-oriented consortia, including the Mathematical Research Data Initiative (MaRDI). MaRDI has been established to develop services, guidelines and outreach measures for all aspects of MathRD, and thus support the mathematical research community. Research data management (RDM) should be an integral component of every scientific project, and is becoming a mandatory component of grants with funding bodies such as the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). At the core of RDM are the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. This document aims to guide mathematicians and researchers from related disciplines who create RDM plans. It highlights the benefits and opportunities of RDM in mathematics and interdisciplinary studies, showcases examples of diverse MathRD, and suggests technical solutions that meet the requirements of funding agencies with specific examples. The document is regularly updated to reflect the latest developments within the mathematical community represented by MaRDI. Y1 - 2023 U6 - https://doi.org/10.5281/zenodo.10018245 ER - TY - JOUR A1 - Diederichs, Katja A1 - Krause, Celia A1 - Lemaire, Marina A1 - Reidelbach, Marco A1 - Windeck, Jürgen T1 - A Vision for Data Management Plans in the NFDI N2 - At present, data management plans (DMPs) are still often perceived as mere documents for funding agencies providing clarity on how research data will be handled during a funded project, but are not usually actively involved in the processes. However, they contain a great deal of information that can be shared automatically to facilitate active research data management (RDM) by providing metadata to research infrastructures and supporting communication between all involved stakeholders. This position paper brings together a number of ideas developed and collected during interdisciplinary workshops of the Data Management Planning Working Group (infra-dmp), which is part of the section Common Infrastructures of the National Research Data Infrastructure (NFDI) in Germany. We present our vision of a possible future role of DMPs, templates, and tools in the upcoming NFDI service architecture. Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10570653 ER - TY - JOUR A1 - Donati, Luca A1 - Schütte, Christof A1 - Weber, Marcus T1 - The Kramers turnover in terms of a macro-state projection on phase space JF - Molecular Physics N2 - We have investigated how Langevin dynamics is affected by the friction coefficient using the novel algorithm ISOKANN, which combines the transfer operator approach with modern machine learning techniques. ISOKANN describes the dynamics in terms of an invariant subspace projection of the Koopman operator defined in the entire state space, avoiding approximations due to dimensionality reduction and discretization. Our results are consistent with the Kramers turnover and show that in the low and moderate friction regimes, metastable macro-states and transition rates are defined in phase space, not only in position space. Y1 - 2024 U6 - https://doi.org/10.1080/00268976.2024.2356748 IS - Ciccotti Special Issue (by invitation only) SP - e2356748 PB - Taylor & Francis ER - TY - JOUR A1 - Schmitt, Kira A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - Polyp-Cavity Segmentation of Cold-Water Corals guided by Ambient Occlusion and Ambient Curvature JF - Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) N2 - The segmentation of cavities in three-dimensional images of arbitrary objects is a difficult problem since the cavities are usually connected to the outside of the object without any difference in image intensity. Hence, the information whether a voxel belongs to a cavity or the outside needs to be derived from the ambient space. If a voxel is enclosed by object material, it is very likely that this voxel belongs to a cavity. However, there are dense structures where a voxel might still belong to the outside even though it is surrounded to a large degree by the object. This is, for example, the case for coral colonies. Therefore, additional information needs to be considered to distinguish between those cases. In this paper, we introduce the notion of ambient curvature, present an efficient way to compute it, and use it to segment coral polyp cavities by integrating it into the ambient occlusion framework. Moreover, we combine the ambient curvature with other ambient information in a Gaussian mixture model, trained from a few user scribbles, resulting in a significantly improved cavity segmentation. We showcase the superiority of our approach using four coral colonies of very different morphological types. While in this paper we restrict ourselves to coral data, we believe that the concept of ambient curvature is also useful for other data. Furthermore, our approach is not restricted to curvature but can be easily extended to exploit any properties given on an object's surface, thereby adjusting it to specific applications. Y1 - 2022 U6 - https://doi.org/10.2312/vcbm.20221189 ER - TY - JOUR A1 - Tateiwa, Nariaki A1 - Shinano, Yuji A1 - Yasuda, Masaya A1 - Kaji, Shizuo A1 - Yamamura, Keiichiro A1 - Fujisawa, Katsuki T1 - Development and analysis of massive parallelization of a lattice basis reduction algorithm JF - Japan Journal of Industrial and Applied Mathematics N2 - The security of lattice-based cryptography relies on the hardness of solving lattice problems. Lattice basis reduction is a strong tool for solving lattice problems, and the block Korkine–Zolotarev (BKZ) reduction algorithm is the de facto standard in cryptanalysis. We propose a parallel algorithm of BKZ-type reduction based on randomization. Randomized copies of an input lattice basis are independently reduced in parallel, while several basis vectors are shared asynchronously among all processes. There is a trade-off between randomization and information sharing; if a substantial amount of information is shared, all processes might work on the same problem, which diminishes the benefit of parallelization. To monitor the balance between randomness and sharing, we propose a new metric to quantify the variety of lattice bases, and we empirically find an optimal parameter of sharing for high-dimensional lattices. We also demonstrate the effectiveness of our parallel algorithm and metric through experiments from multiple perspectives. Y1 - 2023 U6 - https://doi.org/10.1007/s13160-023-00580-z VL - 40 IS - 1 SP - 13 EP - 56 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Heida, Martin T1 - Voronoi Graph - Improved raycasting and integration schemes for high dimensional Voronoi diagrams N2 - The computation of Voronoi Diagrams, or their dual Delauney triangulations is difficult in high dimensions. In a recent publication Polianskii and Pokorny propose an iterative randomized algorithm facilitating the approximation of Voronoi tesselations in high dimensions. In this paper, we provide an improved vertex search method that is not only exact but even faster than the bisection method that was previously recommended. Building on this we also provide a depth-first graph-traversal algorithm which allows us to compute the entire Voronoi diagram. This enables us to compare the outcomes with those of classical algorithms like qHull, which we either match or marginally beat in terms of computation time. We furthermore show how the raycasting algorithm naturally lends to a Monte Carlo approximation for the volume and boundary integrals of the Voronoi cells, both of which are of importance for finite Volume methods. We compare the Monte-Carlo methods to the exact polygonal integration, as well as a hybrid approximation scheme. Y1 - 2024 ER - TY - JOUR A1 - Kuen, Lilli A1 - Löffler, Lorenz A1 - Tsarapkin, Aleksei A1 - Zschiedrich, Lin A1 - Feichtner, Thorsten A1 - Burger, Sven A1 - Höflich, Katja T1 - Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna JF - Appl. Phys. Lett. Y1 - 2024 U6 - https://doi.org/10.1063/5.0201748 VL - 124 SP - 231102 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Weinand, Jann Michael A1 - Syranidou, Chloi A1 - Rehfeldt, Daniel T1 - An efficient solver for large-scale onshore wind farm siting including cable routing JF - European Journal of Operational Research N2 - Existing planning approaches for onshore wind farm siting and grid integration often do not meet minimum cost solutions or social and environmental considerations. In this paper, we develop an exact approach for the integrated layout and cable routing problem of onshore wind farm planning using the Quota Steiner tree problem. Applying a novel transformation on a known directed cut formulation, reduction techniques, and heuristics, we design an exact solver that makes large problem instances solvable and outperforms generic MIP solvers. In selected regions of Germany, the trade-offs between minimizing costs and landscape impact of onshore wind farm siting are investigated. Although our case studies show large trade-offs between the objective criteria of cost and landscape impact, small burdens on one criterion can significantly improve the other criteria. In addition, we demonstrate that contrary to many approaches for exclusive turbine siting, grid integration must be simultaneously optimized to avoid excessive costs or landscape impacts in the course of a wind farm project. Our novel problem formulation and the developed solver can assist planners in decision-making and help optimize wind farms in large regions in the future. Y1 - 2024 U6 - https://doi.org/10.1016/j.ejor.2024.04.026 VL - 317 IS - 2 SP - 616 EP - 630 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Rabben, Robert Julian A1 - Chewle, Surahit A1 - Weber, Marcus T1 - Capturing the Macroscopic Behaviour of Molecular Dynamics with Membership Functions N2 - Markov processes serve as foundational models in many scientific disciplines, such as molecular dynamics, and their simulation forms a common basis for analysis. While simulations produce useful trajectories, obtaining macroscopic information directly from microstate data presents significant challenges. This paper addresses this gap by introducing the concept of membership functions being the macrostates themselves. We derive equations for the holding times of these macrostates and demonstrate their consistency with the classical definition. Furthermore, we discuss the application of the ISOKANN method for learning these quantities from simulation data. In addition, we present a novel method for extracting transition paths based on the ISOKANN results and demonstrate its efficacy by applying it to simulations of the 𝜇-opioid receptor. With this approach we provide a new perspective on analyzing the macroscopic behaviour of Markov systems. Y1 - 2024 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Le, Thi Thai A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Optimal discrete pipe sizing for tree-shaped CO2 networks JF - OR Spectrum N2 - For industries like the cement industry, switching to a carbon-neutral production process is impossible. They must rely on carbon capture, utilization and storage (CCUS) technologies to reduce their production processes’ inevitable carbon dioxide (CO2) emissions. For transporting continuously large amounts of CO2, utilizing a pipeline network is the most effective solution; however, building such a network is expensive. Therefore minimizing the cost of the pipelines to be built is extremely important to make the operation financially feasible. In this context, we investigate the problem of finding optimal pipeline diameters from a discrete set of diameters for a tree-shaped network transporting captured CO2 from multiple sources to a single sink. The general problem of optimizing arc capacities in potential-based fluid networks is already a challenging mixed-integer nonlinear optimization problem. The problem becomes even more complex when adding the highly sensitive nonlinear behavior of CO2 regarding temperature and pressure changes. We propose an iterative algorithm splitting the problem into two parts: a) the pipe-sizing problem under a fixed supply scenario and temperature distribution and b) the thermophysical modeling, including mixing effects, the Joule-Thomson effect, and heat exchange with the surrounding environment. We demonstrate the effectiveness of our approach by applying our algorithm to a real-world network planning problem for a CO2 network in Western Germany. Further, we show the robustness of the algorithm by solving a large artificially created set of network instances. Y1 - 2024 U6 - https://doi.org/10.1007/s00291-024-00773-z ER - TY - JOUR A1 - Thies, Arne A1 - Sunkara, Vikram A1 - Ray, Sourav A1 - Wulkow, Hanna A1 - Celik, M. Özgür A1 - Yergöz, Fatih A1 - Schütte, Christof A1 - Stein, Christoph A1 - Weber, Marcus A1 - Winkelmann, Stefanie T1 - Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design JF - Scientific Reports N2 - We previously reported the successful design, synthesis and testing of the prototype opioid painkiller NFEPP that does not elicit adverse side effects. The design process of NFEPP was based on mathematical modelling of extracellular interactions between G-protein coupled receptors (GPCRs) and ligands, recognizing that GPCRs function differently under pathological versus healthy conditions. We now present an additional and novel stochastic model of GPCR function that includes intracellular dissociation of G-protein subunits and modulation of plasma membrane calcium channels and their dependence on parameters of inflamed and healthy tissue (pH, radicals). The model is validated against in vitro experimental data for the ligands NFEPP and fentanyl at different pH values and radical concentrations. We observe markedly reduced binding affinity and calcium channel inhibition for NFEPP at normal pH compared to lower pH, in contrast to the effect of fentanyl. For increasing radical concentrations, we find enhanced constitutive G-protein activation but reduced ligand binding affinity. Assessing the different effects, the results suggest that, compared to radicals, low pH is a more important determinant of overall GPCR function in an inflamed environment. Future drug design efforts should take this into account. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-27699-w VL - 13 IS - 607 ER - TY - JOUR A1 - del Razo, Mauricio A1 - Winkelmann, Stefanie A1 - Klein, Rupert A1 - Höfling, Felix T1 - Chemical diffusion master equation: formulations of reaction-diffusion processes on the molecular level JF - Journal of Mathematical Physics N2 - The chemical diffusion master equation (CDME) describes the probabilistic dynamics of reaction--diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112:49, 2022]; it can be considered the master equation for reaction--diffusion processes. The CDME consists of an infinite ordered family of Fokker--Planck equations, where each level of the ordered family corresponds to a certain number of particles and each particle represents a molecule. The equations at each level describe the spatial diffusion of the corresponding set of particles, and they are coupled to each other via reaction operators --linear operators representing chemical reactions. These operators change the number of particles in the system, and thus transport probability between different levels in the family. In this work, we present three approaches to formulate the CDME and show the relations between them. We further deduce the non-trivial combinatorial factors contained in the reaction operators, and we elucidate the relation to the original formulation of the CDME, which is based on creation and annihilation operators acting on many-particle probability density functions. Finally we discuss applications to multiscale simulations of biochemical systems among other future prospects. Y1 - 2023 U6 - https://doi.org/10.1063/5.0129620 VL - 64 IS - 1 ER - TY - JOUR A1 - del Razo, Mauricio A1 - Frömberg, Daniela A1 - Straube, Arthur A1 - Schütte, Christof A1 - Höfling, Felix A1 - Winkelmann, Stefanie T1 - A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations JF - Letters in Mathematical Physics Y1 - 2022 U6 - https://doi.org/10.1007/s11005-022-01539-w VL - 112 IS - 49 ER - TY - JOUR A1 - Ernst, Marco A1 - Asselineau, Charles-Alexis A1 - Tillmann, Peter A1 - Jäger, Klaus A1 - Becker, Christiane T1 - Modelling bifacial irradiance – Step-by-step comparison and validation of view factor and ray tracing models JF - Appl. Energy Y1 - 2024 U6 - https://doi.org/10.1016/j.apenergy.2024.123574 SN - 0306-2619 VL - 369 SP - 123574 PB - Elsevier BV ER - TY - JOUR A1 - Montefusco, Alberto A1 - Helfmann, Luzie A1 - Okunola, Toluwani A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - Partial mean-field model for neurotransmission dynamics JF - Mathematical Biosciences N2 - This article addresses reaction networks in which spatial and stochastic effects are of crucial importance. For such systems, particle-based models allow us to describe all microscopic details with high accuracy. However, they suffer from computational inefficiency if particle numbers and density get too large. Alternative coarse-grained-resolution models reduce computational effort tremendously, e.g., by replacing the particle distribution by a continuous concentration field governed by reaction-diffusion PDEs. We demonstrate how models on the different resolution levels can be combined into hybrid models that seamlessly combine the best of both worlds, describing molecular species with large copy numbers by macroscopic equations with spatial resolution while keeping the stochastic-spatial particle-based resolution level for the species with low copy numbers. To this end, we introduce a simple particle-based model for the binding dynamics of ions and vesicles at the heart of the neurotransmission process. Within this framework, we derive a novel hybrid model and present results from numerical experiments which demonstrate that the hybrid model allows for an accurate approximation of the full particle-based model in realistic scenarios. Y1 - 2024 U6 - https://doi.org/10.1016/j.mbs.2024.109143 VL - 369 ER - TY - JOUR A1 - Steudle, Gesine A1 - Winkelmann, Stefanie A1 - Fürst, Steffen A1 - Wolf, Sarah T1 - Understanding Memory Mechanisms in Socio-Technical Systems: the Case of an Agent-based Mobility Model JF - Advances in Complex Systems N2 - This paper explores memory mechanisms in complex socio-technical systems, using a mobility demand model as an example case. We simplified a large-scale agent-based mobility model into a Markov process and discover that the mobility decision process is non-Markovian. This is due to its dependence on the system’s history, including social structure and local infrastructure, which evolve based on prior mobility decisions. To make the process Markovian, we extend the state space by incorporating two history-dependent components. Although our model is a very much reduced version of the original one, it remains too complex for the application of usual analytic methods. Instead, we employ simulations to examine the functionalities of the two history-dependent components. We think that the structure of the analyzed stochastic process is exemplary for many socio-technical, -economic, -ecological systems. Additionally, it exhibits analogies with the framework of extended evolution, which has previously been used to study cultural evolution. Y1 - 2024 U6 - https://doi.org/10.17617/2.3562016 ER - TY - JOUR A1 - Lücke, Marvin A1 - Winkelmann, Stefanie A1 - Heitzig, Jobst A1 - Molkenthin, Nora A1 - Koltai, Péter T1 - Learning interpretable collective variables for spreading processes on networks JF - Physical Review E N2 - Collective variables (CVs) are low-dimensional projections of high-dimensional system states. They are used to gain insights into complex emergent dynamical behaviors of processes on networks. The relation between CVs and network measures is not well understood and its derivation typically requires detailed knowledge of both the dynamical system and the network topology. In this Letter, we present a data-driven method for algorithmically learning and understanding CVs for binary-state spreading processes on networks of arbitrary topology. We demonstrate our method using four example networks: the stochastic block model, a ring-shaped graph, a random regular graph, and a scale-free network generated by the Albert-Barabási model. Our results deliver evidence for the existence of low-dimensional CVs even in cases that are not yet understood theoretically. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevE.109.L022301 VL - 109 IS - 2 SP - L022301 ER - TY - JOUR A1 - Tjusila, Gennesaret A1 - Besançon, Mathieu A1 - Turner, Mark A1 - Koch, Thorsten T1 - How Many Clues To Give? A Bilevel Formulation For The Minimum Sudoku Clue Problem JF - Operations Research Letters N2 - It has been shown that any 9 by 9 Sudoku puzzle must contain at least 17 clues to have a unique solution. This paper investigates the more specific question: given a particular completed Sudoku grid, what is the minimum number of clues in any puzzle whose unique solution is the given grid? We call this problem the Minimum Sudoku Clue Problem (MSCP). We formulate MSCP as a binary bilevel linear program, present a class of globally valid inequalities, and provide a computational study on 50 MSCP instances of 9 by 9 Sudoku grids. Using a general bilevel solver, we solve 95% of instances to optimality, and show that the solution process benefits from the addition of a moderate amount of inequalities. Finally, we extend the proposed model to other combinatorial problems in which uniqueness of the solution is of interest. Y1 - 2024 U6 - https://doi.org/10.1016/j.orl.2024.107105 VL - 54 SP - 107105 ER - TY - JOUR A1 - Weber, Marcus A1 - Weitere Autoren, ED - Reichardt, Christine T1 - DIN SPEC 2343: Übertragung von sprachbasierten Daten zwischen Künstlichen Intelligenzen - Festlegung von Parametern und Formaten JF - Beuth Verlag N2 - Dieses Dokument legt Parameter und Formate für die Übertragung sprachbasierter Daten zwischen verschiedenen KI-Ökosystemen fest. Y1 - 2020 ER - TY - JOUR A1 - Euler, Ricardo A1 - Maristany de las Casas, Pedro T1 - Labeling methods for partially ordered paths JF - European Journal of Operational Research N2 - The landscape of applications and subroutines relying on shortest path computations continues to grow steadily. This growth is driven by the undeniable success of shortest path algorithms in theory and practice. It also introduces new challenges as the models and assessing the optimality of paths become more complicated. Hence, multiple recent publications in the field adapt existing labeling methods in an ad hoc fashion to their specific problem variant without considering the underlying general structure: they always deal with multi-criteria scenarios, and those criteria define different partial orders on the paths. In this paper, we introduce the partial order shortest path problem (POSP), a generalization of the multi-objective shortest path problem (MOSP) and in turn also of the classical shortest path problem. POSP captures the particular structure of many shortest path applications as special cases. In this generality, we study optimality conditions or the lack of them, depending on the objective functions’ properties. Our final contribution is a big lookup table summarizing our findings and providing the reader with an easy way to choose among the most recent multi-criteria shortest path algorithms depending on their problems’ weight structure. Examples range from time-dependent shortest path and bottleneck path problems to the electric vehicle shortest path problem with recharging and complex financial weight functions studied in the public transportation community. Our results hold for general digraphs and, therefore, surpass previous generalizations that were limited to acyclic graphs. Y1 - 2024 U6 - https://doi.org/10.1016/j.ejor.2024.05.002 VL - 318 IS - 1 SP - 19 EP - 30 PB - Elsevier BV ET - 1 ER - TY - JOUR A1 - Takeuchi, Kotaro A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの 設計および運用の階層的関係を考慮した最適化 (多目的最適設計へのモデル縮約の適用) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Application of Model Reduction to Multiobjective Optimal Design) JF - エネルギー・資源学会第36回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - To attain the highest performance of energy supply systems, it is necessary to determine design specifications optimally in consideration of operational strategies corresponding to seasonal and hourly variations in energy demands. Mixed-integer linear programming (MILP) methods have been applied widely to such optimal design problems. A hierarchical MILP method has been proposed to solve the problems very efficiently. In addition, by utilizing features of the hierarchical MILP method, a method of reducing model by clustering periods based on the optimal operational strategies of equipment has been proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, these methods are applied to the multiobjective optimal design of a cogeneration system by considering the annual total cost and primary energy consumption as the objective functions to be minimized. Through a case study, it turns out that the model reduction by the operation-based time-period clustering is effective in terms of the computation efficiency when importance is given to the first objective function, while it is not when importance is given to the second objective function. Y1 - 2020 SP - 724 EP - 729 ER - TY - JOUR A1 - Xu, Xiaofei A1 - Chen, Ying A1 - Zhang, Ge A1 - Koch, Thorsten T1 - Modeling functional time series and mixed-type predictors with partially functional autoregressions* JF - Journal of Business and Economic Statistics N2 - In many business and economics studies, researchers have sought to measure the dynamic dependence of curves with high-dimensional mixed-type predictors. We propose a partially functional autoregressive model (pFAR) where the serial dependence of curves is controlled by coefficient operators that are defined on a two-dimensional surface, and the individual and group effects of mixed-type predictors are estimated with a two-layer regularization. We develop an efficient estimation with the proven asymptotic properties of consistency and sparsity. We show how to choose the sieve and tuning parameters in regularization based on a forward-looking criterion. In addition to the asymptotic properties, numerical validation suggests that the dependence structure is accurately detected. The implementation of the pFAR within a real-world analysis of dependence in German daily natural gas flow curves, with seven lagged curves and 85 scalar predictors, produces superior forecast accuracy and an insightful understanding of the dynamics of natural gas supply and demand for the municipal, industry, and border nodes, respectively. Y1 - 2021 U6 - https://doi.org/10.1080/07350015.2021.2011299 SP - 1 EP - 43 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 時間集約によるエネルギー供給システムの 近似最適設計解の導出および評価 (階層的最適化を援用した設計解の評価) T1 - Derivation and Evaluation of Approximate Optimal Design Solutions of Energy Supply Systems by Time Aggregation (Evaluation of Design Solutions Using Hierarchical Optimization) JF - エネルギー・資源学会第38回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - For the purpose of attaining the highest performance of energy supply systems, it is important to design the systems optimally in consideration of their operational strategies for seasonal and hourly variations in energy demands. An ap- proach to solve such an optimal design problem with a large number of periods efficiently is to derive an approximate optimal design solution by aggregating periods with a clustering method. However, such an approach does not provide any information on the accuracy for the optimal value of the objective function. The purpose of this paper is to provide a time aggregation method for deriving aprroximate optimal design solutions and evaluting their values of the objective function. Especially, a method of evaluating design solutions is presented here using both methods of evaluating the robustness under uncertain energy demands and solving optimal design problems by a hierarchical approach. A case study is conducted for a cogeneration system with a practical configuration, and it turns out that the proposed approach enables one to evaluate effective lower bounds for the optimal value of the objective function as compared with those obtained by a conventional approach. Y1 - 2022 SP - 468 EP - 473 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Hiramatsu, Yuto A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Evaluation of robustness in multiple performance criteria for designing energy supply systems based on a mixed-integer linear model JF - Proceedings of the 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022) N2 - In designing energy supply systems, it is important to consider the uncertainty in energy demands, evaluate the robustness in some performance criteria, and heighten the robustness. A robust optimal design method has been previously proposed to maximize the robustness in a single performance criterion against the uncertainty in energy demands based on a mixed-integer linear model. In this paper, as a preliminary step toward multiobjective robust optimal design, a method of evaluating robustness in multiple performance criteria against the uncertainty in energy demands is proposed based on a mixed-integer linear model. The problems of evaluating the robustness in the performance criteria are formulated as bilevel mixed-integer linear programming (MILP) ones. They are solved by evaluating lower and upper bounds for the maximum regrets in the performance criteria alternately and repeatedly with the aid of a solution method based on reformulation and decomposition. In addition, for the purpose of applying the proposed method to practical problems, a hierarchical MILP method is used to efficiently solve some MILP problems in the solution process. Through a case study on a cogeneration system, the robustness in the annual total cost and primary energy consumption is evaluated and its trade-off relationship is clarified. Y1 - 2022 SP - 1937 EP - 1948 ER - TY - JOUR A1 - Kamada, Hiroki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 階層的最適化手法の援用による エネルギー供給システムのロバスト最適設計 T1 - Robust Optimal Design of Energy Supply Systems With Aid of a Hierarchical Optimization Method JF - エネルギー・資源学会第36回エネルギーシステム・経済・環境コンファレンス講演論文集 N2 - A robust optimal design method of energy supply systems under uncertain energy demands has been proposed using a mixed- integer linear model for constituent equipment. A robust optimal design problem has been formulated as a three-level min-max- min optimization one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret criterion, and considering hierarchical relationships among design variables, uncertain energy demands, and operation variables. Since this problem must be solved by a special algorithm and is too difficult to solve even using a commercial solver, a hierarchical optimization approach has been applied to solve the problem but its application is limited only to small scale toy problems. In this paper, some strategies are introduced into the hierarchical optimization approach to enhance the computation efficiency for the purpose of applying the approach to large scale practical problems. In a case study, the proposed approach is applied to the robust optimal design of a cogeneration system with a complex configuration, and the validity and effectiveness of the method are ascertained. Y1 - 2020 SP - 730 EP - 735 ER - TY - JOUR A1 - Kamada, Hiroki A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 階層的最適化手法を用いた エネルギー供給システムのロバスト性評価 T1 - Evaluating Robustness of Energy Supply Systems Using a Hierarchical Optimization Method JF - 日本機械学会関西支部第95期定時総会講演会講演論文集 N2 - A robust optimal design method of energy supply systems under uncertain energy demands has been proposed using a mixed-integer linear model for constituent equipment. However, this method takes a long computation time, and thus it can be applied only to small-scale problems. In this paper, a hierarchical optimization method is applied to two types of optimization problems for evaluating robustness to solve them efficiently. In a case study, the proposed method is applied to a cogeneration system with a complex configuration, and the validity and effectiveness of the method are ascertained. Y1 - 2020 SP - 1 EP - 4 ER - TY - JOUR A1 - Rehfeldt, Daniel T1 - Faster Algorithms for Steiner Tree and related Problems: From Theory to Practice JF - OR News: Das Magazin der GOR Y1 - 2022 ER - TY - JOUR A1 - Hennings, Felix A1 - Anderson, Lovis A1 - Hoppmann-Baum, Kai A1 - Turner, Mark A1 - Koch, Thorsten T1 - Controlling transient gas flow in real-world pipeline intersection areas JF - Optimization and Engineering N2 - Compressor stations are the heart of every high-pressure gas transport network. Located at intersection areas of the network they are contained in huge complex plants, where they are in combination with valves and regulators responsible for routing and pushing the gas through the network. Due to their complexity and lack of data compressor stations are usually dealt with in the scientific literature in a highly simplified and idealized manner. As part of an ongoing project with one of Germany's largest Transmission System Operators to develop a decision support system for their dispatching center, we investigated how to automatize control of compressor stations. Each station has to be in a particular configuration, leading in combination with the other nearby elements to a discrete set of up to 2000 possible feasible operation modes in the intersection area. Since the desired performance of the station changes over time, the configuration of the station has to adapt. Our goal is to minimize the necessary changes in the overall operation modes and related elements over time, while fulfilling a preset performance envelope or demand scenario. This article describes the chosen model and the implemented mixed integer programming based algorithms to tackle this challenge. By presenting extensive computational results on real world data we demonstrate the performance of our approach. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1007/s11081-020-09559-y VL - 22 SP - 687 EP - 734 PB - Springer Nature ET - 2 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - 時間集約によるエネルギー供給システムの 近似最適設計解の導出および評価 (階層的最適化を援用した近似最適設計) T1 - Derivation and Evaluation of Approximate Optimal Design Solutions of Energy Supply Systems by Time Aggregation (Approximate Optimal Design Using Hierarchical Optimization) JF - 第41回エネルギー・資源学会研究発表会講演論文集 N2 - For the purpose of attaining the highest performance of energy supply systems, it is important to design the systems optimally in consideration of their operational strategies for seasonal and hourly variations in energy demands. An ap- proach to efficiently solve such an optimal design problem with a large number of periods for variations in energy de- mands is to derive an approximate optimal design solution by aggregating periods with a clustering method. However, such an approach does not provide any information on the accuracy for the optimal value of the objective function. The purpose of this paper is to propose a time aggregation approach for deriving suitable aprroximate optimal design solutions and evaluting their values of the objective function accurately. This time aggregation approach is realized by combining a robust optimal design method under uncertain energy demands and a hierarchical approach for solving large scale optimal design problems. A case study is conducted for a cogeneration system with a practical configuration, and it turns out that the proposed approach enables one to evaluate effective upper and lower bounds for the optimal value of the objective function as compared with those obtained by a conventional approach. Y1 - 2022 SP - 144 EP - 148 ER - TY - JOUR A1 - Takeuchi, Kotaro A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の階層的関係を考慮した最適化 (k-メドイド法に基づく期間クラスタリングの適用) T1 - Optimization of Energy Supply Systems in Consideration of Hierachical Relationship Between Design and Operation (Application of Time-Period Clustering Based on k-Medoids Method) JF - 日本機械学会関西支部第95期定時総会講演会講演論文集 N2 - To attain the highest performance of energy supply systems, it is necessary to determine design specifications optimally in consideration of operational strategies corresponding to seasonal and hourly variations in energy demands. A hierarchical mixed-integer linear programming method has been proposed to solve such an optimal design problem efficiently. In this paper, a method of reducing model by clustering periods with the k-medoids method is applied to the relaxed optimal design problem at the upper level. Through a case study, it is clarified how the proposed method is effective to enhance the computation efficiency in a large scale optimal design problem. Y1 - 2020 SP - 1 EP - 4 ER - TY - JOUR A1 - Trepte, Philipp A1 - Secker, Christopher A1 - Kostova, Simona A1 - Maseko, Sibusiso B. A1 - Gang Choi, Soon A1 - Blavier, Jeremy A1 - Minia, Igor A1 - Silva Ramos, Eduardo A1 - Cassonnet, Patricia A1 - Golusik, Sabrina A1 - Zenkner, Martina A1 - Beetz, Stephanie A1 - Liebich, Mara J. A1 - Scharek, Nadine A1 - Schütz, Anja A1 - Sperling, Marcel A1 - Lisurek, Michael A1 - Wang, Yang A1 - Spirohn, Kerstin A1 - Hao, Tong A1 - Calderwood, Michael A. A1 - Hill, David E. A1 - Landthaler, Markus A1 - Olivet, Julien A1 - Twizere, Jean-Claude A1 - Vidal, Marc A1 - Wanker, Erich E. T1 - AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor JF - bioRxiv Y1 - 2023 U6 - https://doi.org/10.1101/2023.06.14.544560 ER - TY - JOUR A1 - Hanik, Martin A1 - Navayazdani, Esfandiar A1 - von Tycowicz, Christoph T1 - De Casteljau's Algorithm in Geometric Data Analysis: Theory and Application JF - Computer Aided Geometric Design N2 - For decades, de Casteljau's algorithm has been used as a fundamental building block in curve and surface design and has found a wide range of applications in fields such as scientific computing, and discrete geometry to name but a few. With increasing interest in nonlinear data science, its constructive approach has been shown to provide a principled way to generalize parametric smooth curves to manifolds. These curves have found remarkable new applications in the analysis of parameter-dependent, geometric data. This article provides a survey of the recent theoretical developments in this exciting area as well as its applications in fields such as geometric morphometrics and longitudinal data analysis in medicine, archaeology, and meteorology. Y1 - 2024 U6 - https://doi.org/10.1016/j.cagd.2024.102288 VL - 110 SP - 102288 ER - TY - JOUR A1 - Winkler, Alexander T1 - Berliner Kulturerbe digital: Ein quantitativer Blick auf die Metadatenqualität JF - EVA BERLIN 2023. Elektronische Medien & Kunst, Kultur und Historie. 27. Berliner Veranstaltung der internationalen EVA-Serie (29. November 2023 – 01. Dezember 2023) N2 - Die Metadatenqualität bestimmt wesentlich den Nutzen und Wert von Kulturerbedaten. ‚Gute‘ Metadaten erhöhen die Auffindbarkeit, Interoperabilität und Nutzbarkeit von Daten signifikant. Mit Blick auf Retrieval bzw. Discovery, Vernetzung im Kontext von Linked Open Data und wissenschaftliches Data Mining hängt die Qualität dabei wesentlich von der Verwendung von maschinenlesbaren kontrollierten Vokabularen ab. Diese wird in der vorliegenden Arbeit quantitativ untersucht. Als Datengrundlage dienen die in der Deutschen Digitalen Bibliothek aggregierten Metadaten aus Berliner Museen (ca. 1,2 Millionen Metadatenobjekte im LIDO-Format) Y1 - 2023 SP - 101 EP - 108 ER - TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Hsiao, Ching-Lien A1 - Hultman, Lars A1 - Birch, Jens A1 - Gueorguiev, Gueorgui Kostov T1 - Electronic and optical properties of core-shell InAlN nanorods: a comparative study via LDA, LDA-1/2, mBJ, HSE06, G0W0 and BSE methods JF - Physical Chemistry Chemical Physics Y1 - 2024 U6 - https://doi.org/10.1039/D3CP05295H VL - 26 SP - 7504 EP - 7514 PB - Royal Society of Chemistry ER - TY - JOUR A1 - Navayazdani, Esfandiar T1 - On Geodesics in the Spaces of Constrained Curves JF - Journal of Differential Geometry and its Applications N2 - In this work, we study the geodesics of the space of certain geometrically and physically motivated subspaces of the space of immersed curves endowed with a first order Sobolev metric. This includes elastic curves and also an extension of some results on planar concentric circles to surfaces. The work focuses on intrinsic and constructive approaches. Y1 - 2024 ER - TY - JOUR A1 - Le, Thi Thai T1 - Effect of water depth on Kelvin - Helmholtz instability in a shallow-water flow JF - Journal of Mathematical Physics N2 - It is well known that the interface between two regions of an incompressible ideal fluid flow moving in a relative motion is necessarily destabilized, regardless of the velocity difference's strength. This phenomenon is the so-called Kelvin-Helmholtz instability (KHI). However, a large number of works demonstrated a surprising result that the instability is suppressed for shallow water flows; the interface is stabilized if the Froude number, defined by the velocity difference's ratio to the gravity wave's speed, is sufficiently large. In a limited way, these authors have been used the shallow-water equations without the higher-order effect of the dispersive terms. Thus, this investigation aims to examine these higher-order dispersive effects to analyze the interface stability problem of tangential-velocity discontinuity in shallow-water flows. In particular, we use the Green-Naghdi equations to introduce the dispersive terms related to the depth and the depth-averaged horizontal velocities of the fluid. We show that the interface stability depends on the Froude number (i.e., the velocity difference's strength) and the water depth. A critical value of the Froude number to stabilize the interface is smaller than the case of no dispersive terms, and the flow in a deeper region is more stable than in a shallower one. We also consider the distribution of kinetic and potential energy to clarify a feature characteristic of a large class of instabilities in shallow water flow. The instability of flows is caused by the decrease in the kinetic energy during the perturbation of waves. This phenomenon is known as negative energy modes and plays a vital role in applying the model to industrial equipment. A conclusion is that the equipartition of energies occurs if and only if the velocity difference is zero and the water depth is shallow enough to ignore the dispersive terms. Y1 - 2021 U6 - https://doi.org/10.1063/1.5145060 VL - 62 IS - 10 PB - AIP Publishing ER - TY - JOUR A1 - Le, Thi Thai A1 - Koch, Thorsten T1 - Instability of a tangential discontinuity surface in a three-dimensional compressible medium JF - Physics of Fluids N2 - Compressible flows appear in many natural and technological processes, for instance, the flow of natural gases in a pipe system. Thus, a detailed study of the stability of tangential velocity discontinuity in compressible media is relevant and necessary. The first early investigation in two-dimensional (2D) media was given more than 70 years ago. In this article, we continue investigating the stability in three-dimensional (3D) media. The idealized statement of this problem in an infinite spatial space was studied by Syrovatskii in 1954. However, the omission of the absolute sign of cos θ with θ being the angle between vectors of velocity and wave number in a certain inequality produced the inaccurate conclusion that the flow is always unstable for entire values of the Mach number M. First, we revisit this case to arrive at the correct conclusion, namely that the discontinuity surface is stabilized for a large Mach number with a given value of the angle θ. Next, we introduce a real finite spatial system such that it is bounded by solid walls along the flow direction. We show that the discontinuity surface is stable if and only if the dispersion relation equation has only real roots, with a large value of the Mach number; otherwise, the surface is always unstable. In particular, we show that a smaller critical value of the Mach number is required to make the flow in a narrow channel stable. Y1 - 2021 U6 - https://doi.org/10.1063/5.0033753 VL - 33 IS - 1 SP - 016106 ER - TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Vona, Cecilia A1 - Lubeck, Sven A1 - Alex, Ben A1 - Gonzalez Oliva, Ignacio A1 - Draxl, Claudia T1 - Critical assessment of G0W0 calculations for 2D materials: the example of monolayer MoS2 JF - npj Comput. Mater. Y1 - 2024 U6 - https://doi.org/10.1038/s41524-024-01253-2 VL - 10 SP - 77 ER - TY - JOUR A1 - Trepte, Philipp A1 - Secker, Christopher A1 - Olivet, Julien A1 - Blavier, Jeremy A1 - Kostova, Simona A1 - Maseko, Sibusiso B A1 - Minia, Igor A1 - Silva Ramos, Eduardo A1 - Cassonnet, Patricia A1 - Golusik, Sabrina A1 - Zenkner, Martina A1 - Beetz, Stephanie A1 - Liebich, Mara J A1 - Scharek, Nadine A1 - Schütz, Anja A1 - Sperling, Marcel A1 - Lisurek, Michael A1 - Wang, Yang A1 - Spirohn, Kerstin A1 - Hao, Tong A1 - Calderwood, Michael A A1 - Hill, David E A1 - Landthaler, Markus A1 - Choi, Soon Gang A1 - Twizere, Jean-Claude A1 - Vidal, Marc A1 - Wanker, Erich E T1 - AI-guided pipeline for protein–protein interaction drug discovery identifies a SARS-CoV-2 inhibitor JF - Molecular Systems Biology N2 - Protein–protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways. KW - Applied Mathematics KW - Computational Theory and Mathematics KW - General Agricultural and Biological Sciences KW - General Immunology and Microbiology KW - General Biochemistry, Genetics and Molecular Biology KW - Information Systems Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1038/s44320-024-00019-8 SN - 1744-4292 VL - 20 IS - 4 SP - 428 EP - 457 PB - Springer Science and Business Media LLC ER - TY - JOUR A1 - Le, Thi Thai A1 - Fukumoto, Yasuhide A1 - Koch, Thorsten T1 - Linear stability of a simple shear layer between two parallel streams in a shallow water flow JF - Physics Letters A N2 - The stability of shear layers in fluid flows is a crucial factor in forming vortices and jets and plays a fundamental role in the development of turbulence. Such shear layer instabilities are ubiquitous in natural phenomena, such as atmospheric and oceanic flows, contributing to the formation of weather systems and predicting tsunamis. This study specifically focuses on the stability of a shear layer sandwiched between two semi-infinite layers within a two-dimensional flow. The velocity profile of the shear layer is assumed to be linearly dependent on the vertical coordinate, while the velocity of the other layers remains uniform with differing strengths. The effect of viscosity and surface tension is ignored to simplify the analysis. The shallow water equations are used to analyze the interface stability of the shear layer, and the resulting dispersion relation between wave frequency and other wave characteristics is obtained. This relation incorporates Whittaker functions and their first derivatives and is used to derive appropriate limits corresponding to various physical conditions. Our study thus contributes to a deeper understanding of the stability of shear layers and their implications for natural phenomena. Y1 - 2024 U6 - https://doi.org/10.1016/j.physleta.2023.129264 VL - 493 PB - Elservier ER - TY - JOUR A1 - Le, Thi Thai A1 - Koch, Thorsten T1 - Viscosity and porosity effects on tangential-discontinuity surface stability in 3D Compressible Media JF - Physics of Fluids N2 - The stability of a flow in porous media relates to the velocity rate of injecting and withdrawing natural gases inside porous storage. We thus aim to analyze the stability of flows in porous media to accelerate the energy transition process. This research examines a flow model of a tangential--velocity discontinuity with porosity and viscosity changes in a three-dimensional (3D) compressible medium because of a co-existence of different gases in a storage. The fluids are assumed to move in a relative motion where the plane y=0 is a tangential-velocity discontinuity surface. We obtain that the critical value of the Mach number to stabilize a tangential discontinuity surface of flows via porous media is smaller than the one of flows in a plane. The critical value of the Mach number M to stabilize a discontinuity surface of the 3D flow is different by a factor |cosθ| compared to the two-dimensional (2D) flow. Here, θ is the angle between velocity and wavenumber vectors. Our results also show that the flow model with viscosity and porosity effects is stable faster than those without these terms. Our analysis is done for both infinite and finite flows. The effect of solid walls along the flow direction could suppress the instability, i.e., the tangential-discontinuity surface is stabilized faster Y1 - 2022 U6 - https://doi.org/10.1063/5.0095970 VL - 34 IS - 7 PB - AIP Publishing ER - TY - JOUR A1 - Le, Thi Thai T1 - Kelvin-Helmholtz instability in a shallow-water flow with a finite width JF - Journal of Mathematical Physics N2 - We examine an effect of side walls on the linear stability of an interface of tangential-velocity discontinuity in shallow-water flow. The flow is pure horizontal in the plane xy, and the fluid is bounded in a finite width 2d in the y− direction. In region 0 < y < d, the fluid is moving with uniform velocity U but is at rest for −d < y < 0. Without side walls, the flow is unstable for a velocity difference U<√8c U < √8 c, with c being the velocity of gravity waves. In this work, we show that if the velocity difference U is smaller than 2c, the interface is always destabilized, also known as the flow is unstable. The unstable region of an infinite width model is shrunken by the effects of side walls in the case of narrow width, while there is no range for the Froude number for stabilization in the case of large width. These results play an important role in predicting the wave propagations and have a wide application in the fields of industry. As a result of the interaction of waves and the mean flow boundary, the flow is unstable, which is caused by a decrease in the kinetic energy of disturbance. Y1 - 2019 U6 - https://doi.org/10.1063/1.5126321 VL - 60 IS - 1 SP - 123101 PB - AIP Publishing ER - TY - JOUR A1 - Le, Thi Thai A1 - Koch, Thorsten T1 - Effect of inertia force on the interface stability of a tangential-velocity discontinuity in porous media JF - International Journal of Multiphase Flow N2 - The present study investigates the stability of a tangential-velocity discontinuity in porous media during the withdrawing and injecting processes of natural gases from and into an underground gas storage. The focus is placed on analyzing the impact of inertia forces on the interface stability using the Forchheimer equations. Other publications have relied primarily on Darcy's law to describe flow stability in porous media. However, Darcy's law only adequately describes flows in which viscous forces dominate over inertia forces. As the flow rate increases, the significance of inertia forces becomes more pronounced, and Darcy's law becomes insufficient for considering such flows. Our findings indicate that even a slight consideration of the inertia effect leads to permanent destabilization of the discontinuity interface, regardless of the fluid viscosity or the Mach number. In contrast, when the inertia effect is neglected, the interface is stabilized across the entire Mach number range if the fluid viscosity is strong enough. Y1 - 2023 U6 - https://doi.org/10.1016/j.ijmultiphaseflow.2023.104612 VL - 169 ER - TY - JOUR A1 - Le, Thi Thai A1 - Koch, Thorsten T1 - Interface stability of compressible fluids in porous media JF - Physics of Fluids N2 - The stability of flows in porous media plays a vital role in transiting energy supply from natural gas to hydrogen, especially for estimating the usability of existing underground gas storage infrastructures. Thus, this research aims to analyze the interface stability of the tangential-velocity discontinuity between two compressible gases by using Darcy's model to include the porosity effect. The results shown in this research will be a basis for considering whether underground gas storages in porous material can be used to store hydrogen. We show the relation between the Mach number M, the viscosity \mu, and the porosity \epsilon on the stability of the interface. This interface stability affects gases' withdrawal and injection processes, thus will help us to determine the velocity which with gas can be extracted and injected into the storage effectively. By imposing solid walls along the flow direction, the critical values of these parameters regarding the stability of the interface are smaller than when considering no walls. The consideration of bounded flows approaches the problem more realistically. In particular, this analysis plays a vital role when considering two-dimensional gas flows in storages and pipes. Y1 - 2021 U6 - https://doi.org/10.1063/5.0059336 VL - 33 IS - 8 SP - 084102 PB - AIP Publishing ER - TY - JOUR A1 - Petkovic, Milena A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Deep learning for spatio-temporal supply anddemand forecasting in natural gas transmission networks JF - Energy Science and Engineering N2 - Germany is the largest market for natural gas in the European Union, with an annual consumption of approx. 95 billion cubic meters. Germany's high-pressure gas pipeline network is roughly 40,000 km long, which enables highly fluctuating quantities of gas to be transported safely over long distances. Considering that similar amounts of gas are also transshipped through Germany to other EU states, it is clear that Germany's gas transport system is essential to the European energy supply. Since the average velocity of gas in a pipeline is only 25km/h, an adequate high-precision, high-frequency forecasting of supply and demand is crucial for efficient control and operation of such a transmission network. We propose a deep learning model based on spatio-temporal convolutional neural networks (DLST) to tackle the problem of gas flow forecasting in a complex high-pressure transmission network. Experiments show that our model effectively captures comprehensive spatio-temporal correlations through modeling gas networks and consistently outperforms state-of-the-art benchmarks on real-world data sets by at least 21%. The results demonstrate that the proposed model can deal with complex nonlinear gas network flow forecasting with high accuracy and effectiveness. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1002/ese3.932 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Kamada, Hiroki A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - A hierarchical optimization approach to robust design of energy supply systems based on a mixed-integer linear model JF - Energy N2 - In designing energy supply systems, designers should heighten the robustness in performance criteria against the uncertainty in energy demands. In this paper, a robust optimal design method using a hierarchical mixed-integer linear programming (MILP) method is proposed to maximize the robustness of energy supply systems under uncertain energy demands based on a mixed-integer linear model. A robust optimal design problem is formulated as a three-level min-max-min MILP one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret criterion, and considering relationships among integer design variables, uncertain energy demands, and integer and continuous operation variables. This problem is solved by evaluating upper and lower bounds for the minimum of the maximum regret of the performance criterion repeatedly outside, and evaluating lower and upper bounds for the maximum regret repeatedly inside. Different types of optimization problems are solved by applying a hierarchical MILP method developed for ordinary optimal design problems without and with its modifications. In a case study, the proposed approach is applied to the robust optimal design of a cogeneration system. Through the study, its validity and effectiveness are ascertained, and some features of the obtained robust designs are clarified. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2021.120343 VL - 229 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Takeuchi, Kotaro A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Effect of model reduction by time aggregation in multiobjective optimal design of energy supply systems by a hierarchical MILP method JF - Energy N2 - The mixed-integer linear programming (MILP) method has been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, a method of reducing model by time aggregation has been proposed to search design candidates accurately and efficiently at the upper level. In this paper, the hierarchical MILP method and model reduction by time aggregation are applied to the multiobjective optimal design. The methods of clustering periods by the order of time series, by the k-medoids method, and based on an operational strategy are applied for the model reduction. As a case study, the multiobjective optimal design of a gas turbine cogeneration system is investigated by adopting the annual total cost and primary energy consumption as the objective functions, and the clustering methods are compared with one another in terms of the computation efficiency. It turns out that the model reduction by any clustering method is effective to enhance the computation efficiency when importance is given to minimizing the first objective function, but that the model reduction only by the k-medoids method is effective very limitedly when importance is given to minimizing the second objective function. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.energy.2021.120505 VL - 228 ER - TY - JOUR A1 - Alzaatreh, Ayman A1 - Aljarrah, Mohammad A1 - Almagambetova, Ayanna A1 - Zakiyeva, Nazgul T1 - On the Regression Model for Generalized Normal Distributions JF - Entropy N2 - The traditional linear regression model that assumes normal residuals is applied extensively in engineering and science. However, the normality assumption of the model residuals is often ineffective. This drawback can be overcome by using a generalized normal regression model that assumes a non-normal response. In this paper, we propose regression models based on generalizations of the normal distribution. The proposed regression models can be used effectively in modeling data with a highly skewed response. Furthermore, we study in some details the structural properties of the proposed generalizations of the normal distribution. The maximum likelihood method is used for estimating the parameters of the proposed method. The performance of the maximum likelihood estimators in estimating the distributional parameters is assessed through a small simulation study. Applications to two real datasets are given to illustrate the flexibility and the usefulness of the proposed distributions and their regression models. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.3390/e23020173 VL - 23 IS - 2 SP - 173 ER - TY - JOUR A1 - Jin, Liangbing A1 - Le, Thi Thai A1 - Fukumoto, Yasuhide T1 - Frictional effect on stability of discontinuity interface in tangential velocity of a shallow-water flow JF - Physics Letters A N2 - We examine a frictional effect on the linear stability of an interface of discontinuity in tangential velocity. The fluid is moving with uniform velocity U in a region but is at rest in the other, and the bottom surface is assumed to exert drag force, quadratic in velocity, on the thin fluid layer. In the absence of the drag, the instability of the Kelvin-Helmholtz type is suppressed for U>√8 c, with c being the propagating speed of the gravity wave. We find by asymptotic analyses for both small and large values of the drag strength that the drag, regardless of its strength, makes the flow unstable for the whole range of the Froude number U/c. Y1 - 2019 U6 - https://doi.org/10.1016/j.physleta.2019.125839 VL - 383 IS - 26 SP - 125839 ER - TY - JOUR A1 - Aigner, Kevin-Martin A1 - Clarner, Jan-Patrick A1 - Liers, Frauke A1 - Martin, Alexander T1 - Robust Approximation of Chance Constrained DC Optimal Power Flow under Decision-Dependent Uncertainty JF - European Journal of Operational Research N2 - We propose a mathematical optimization model and its solution for joint chance constrained DC Optimal Power Flow. In this application, it is particularly important that there is a high probability of transmission limits being satisfied, even in the case of uncertain or fluctuating feed-in from renewable energy sources. In critical network situations where the network risks overload, renewable energy feed-in has to be curtailed by the transmission system operator (TSO). The TSO can reduce the feed-in in discrete steps at each network node. The proposed optimization model minimizes curtailment while ensuring that there is a high probability of transmission limits being maintained. The latter is modeled via (joint) chance constraints that are computationally challenging. Thus, we propose a solution approach based on the robust safe approximation of these constraints. Hereby, probabilistic constraints are replaced by robust constraints with suitably defined uncertainty sets constructed from historical data. The ability to discretely control the power feed-in then leads to a robust optimization problem with decision-dependent uncertainties, i.e. the uncertainty sets depend on decision variables. We propose an equivalent mixed-integer linear reformulation for box uncertainties with the exact linearization of bilinear terms. Finally, we present numerical results for different test cases from the Nesta archive, as well as for a real network. We consider the discrete curtailment of solar feed-in, for which we use real-world weather and network data. The experimental tests demonstrate the effectiveness of this method and run times are very fast. Moreover, on average the calculated robust solutions only lead to a small increase in curtailment, when compared to nominal solutions. Y1 - 2021 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Hiramatsu, Yuto A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Evaluation of robustness in multiple performance criteria for designing energy supply systems based on a mixed-integer linear model JF - The 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022) N2 - In designing energy supply systems, it is important to consider the uncertainty in energy demands, evaluate the robustness in some performance criteria, and heighten the robustness. A robust optimal design method has been previously proposed to maximize the robustness in a single performance criterion against the uncertainty in energy demands based on a mixed-integer linear model. In this paper, as a preliminary step toward multiobjective robust optimal design, a method of evaluating robustness in multiple performance criteria against the uncertainty in energy demands is proposed based on a mixed-integer linear model. The problems of evaluating the robustness in the performance criteria are formulated as bilevel mixed-integer linear programming (MILP) ones. They are solved by evaluating lower and upper bounds for the maximum regrets in the performance criteria alternately and repeatedly with the aid of a solution method based on reformulation and decomposition. In addition, for the purpose of applying the proposed method to practical problems, a hierarchical MILP method is used to efficiently solve some MILP problems in the solution process. Through a case study on a cogeneration system, the robustness in the annual total cost and primary energy consumption is evaluated and its trade-off relationship is clarified. As a result, it turns out how the values of these performance criteria are close to the optimal ones in relation to the uncertainty in energy demands. This work will be an important step toward developing a multiobjective robust optimal design method. Y1 - 2022 SP - 1937 EP - 1948 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Day and time aggregations for optimal design of energy supply systems with storage units by a hierarchical MILP method JF - PROCEEDINGS OF ECOS 2022 - THE 35 TH INTERNATIONAL CONFERENCE ON EFFICIENCY, COST, OPTIMIZATION, SIMULATION AND ENVIRONMENTAL IMPACT OF ENERGY SYSTEMS N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies is extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of reducing model is extended by aggregating both representative days and sampling times separately in consideration of the characteristics of energy storage units. A case study is conducted on the optimal design of a cogeneration system with a thermal storage tank. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solutions in short computation times. It also turns out that the model reduction with day and time aggregations is effective to shorten the computation times furthermore when the number of candidates for equipment capacities is relatively small. Y1 - 2022 SP - 1891 EP - 1902 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - Day and time aggregations for optimal design of energy supply systems with storage units by a hierarchical MILP method JF - The 35th International Conference on Efficiency, Cost, Optimization, Simulation and Environmental Impact of Energy Systems (ECOS 2022) N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies is extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of reducing model is extended by aggregating both representative days and sampling times separately in consideration of the characteristics of energy storage units. A case study is conducted on the optimal design of a cogeneration system with a thermal storage tank. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solutions in short computation times. It also turns out that the model reduction with day and time aggregations is effec- tive to shorten the computation times furthermore when the number of candidates for equipment capacities is relatively small. Y1 - 2022 SP - 1891 EP - 1902 ER - TY - JOUR A1 - Pfeuffer, Julianus A1 - Bielow, Chris A1 - Wein, Samuel A1 - Jeong, Kyowon A1 - Netz, Eugen A1 - Walter, Axel A1 - Alka, Oliver A1 - Nilse, Lars A1 - Colaianni, Pasquale Domenico A1 - McCloskey, Douglas A1 - Kim, Jihyung A1 - Rosenberger, George A1 - Bichmann, Leon A1 - Walzer, Mathias A1 - Veit, Johannes A1 - Boudaud, Bertrand A1 - Bernt, Matthias A1 - Patikas, Nikolaos A1 - Pilz, Matteo A1 - Startek, Michał Piotr A1 - Kutuzova, Svetlana A1 - Heumos, Lukas A1 - Charkow, Joshua A1 - Sing, Justin Cyril A1 - Feroz, Ayesha A1 - Siraj, Arslan A1 - Weisser, Hendrik A1 - Dijkstra, Tjeerd M. H. A1 - Perez-Riverol, Yasset A1 - Röst, Hannes A1 - Kohlbacher, Oliver A1 - Sachsenberg, Timo T1 - OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data JF - Nature Methods Y1 - 2024 U6 - https://doi.org/10.1038/s41592-024-02197-7 SN - 1548-7091 VL - 21 IS - 3 SP - 365 EP - 367 PB - Springer Science and Business Media LLC ER - TY - JOUR A1 - Paltra, Sydney A1 - Conrad, Tim T1 - Clinical Effectiveness of Ritonavir-Boosted Nirmatrelvir—A Literature Review JF - Advances in Respiratory Medicine N2 - Nirmatrelvir/Ritonavir is an oral treatment for mild to moderate COVID-19 cases with a high risk for a severe course of the disease. For this paper, a comprehensive literature review was performed, leading to a summary of currently available data on Nirmatrelvir/Ritonavir’s ability to reduce the risk of progressing to a severe disease state. Herein, the focus lies on publications that include comparisons between patients receiving Nirmatrelvir/Ritonavir and a control group. The findings can be summarized as follows: Data from the time when the Delta-variant was dominant show that Nirmatrelvir/Ritonavir reduced the risk of hospitalization or death by 88.9% for unvaccinated, non-hospitalized high-risk individuals. Data from the time when the Omicron variant was dominant found decreased relative risk reductions for various vaccination statuses: between 26% and 65% for hospitalization. The presented papers that differentiate between unvaccinated and vaccinated individuals agree that unvaccinated patients benefit more from treatment with Nirmatrelvir/Ritonavir. However, when it comes to the dependency of potential on age and comorbidities, further studies are necessary. From the available data, one can conclude that Nirmatrelvir/Ritonavir cannot substitute vaccinations; however, its low manufacturing cost and easy administration make it a valuable tool in fighting COVID-19, especially for countries with low vaccination rates. Y1 - 2024 U6 - https://doi.org/10.3390/arm92010009 VL - 92 IS - 1 ER - TY - JOUR A1 - Müller, Sebastian A1 - Paltra, Sydney A1 - Rehmann, Jakob A1 - Nagel, Kai A1 - Conrad, Tim T1 - Explicit modeling of antibody levels for infectious disease simulations in the context of SARS-CoV-2 JF - iScience N2 - Measurable levels of immunoglobulin G antibodies develop after infections with and vaccinations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These antibody levels are dynamic: due to waning, antibody levels will drop over time. During the COVID-19 pandemic, multiple models predicting infection dynamics were used by policymakers to support the planning of public health policies. Explicitly integrating antibody and waning effects into the models is crucial for reliable calculations of individual infection risk. However, only few approaches have been suggested that explicitly treat these effects. This paper presents a methodology that explicitly models antibody levels and the resulting protection against infection for individuals within an agent-based model. The model was developed in response to the complexity of different immunization sequences and types and is based on neutralization titer studies. This approach allows complex population studies with explicit antibody and waning effects. We demonstrate the usefulness of our model in two use cases. Y1 - 2023 U6 - https://doi.org/10.1016/j.isci.2023.107554 VL - 26 IS - 9 ER - TY - JOUR A1 - Secker, Christopher A1 - Fackeldey, Konstantin A1 - Weber, Marcus A1 - Ray, Sourav A1 - Gorgulla, Christoph A1 - Schütte, Christof T1 - Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists JF - Journal of Cheminformatics N2 - Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the μ-opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives. Here, this multi-objective optimal affinity approach is presented, together with a virtual drug discovery pipeline for its practical implementation. When applied to finding pH-specific drug candidates, it combines protonation state-dependent structure and ligand preparation with high-throughput virtual screening. We employ this pipeline to characterize a set of MOR agonists identifying a morphine-like opioid derivative with higher predicted binding affinities to the MOR at low pH compared to neutral pH. Our results also confirm existing experimental evidence that NFEPP, a previously described fentanyl derivative with reduced side effects, and recently reported β-fluorofentanyls and -morphines show an increased specificity for the MOR at acidic pH when compared to fentanyl and morphine. We further applied our approach to screen a >50K ligand library identifying novel molecules with pH-specific predicted binding affinities to the MOR. The presented differential docking pipeline can be applied to perform multi-objective affinity optimization to identify safer and more specific drug candidates at large scale. Y1 - 2023 U6 - https://doi.org/10.1186/s13321-023-00746-4 VL - 15 ER - TY - JOUR A1 - Wulkow, Hanna A1 - Conrad, Tim A1 - Djurdjevac Conrad, Natasa A1 - Müller, Sebastian A. A1 - Nagel, Kai A1 - Schütte, Christof T1 - Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts JF - PLOS One Y1 - 2021 U6 - https://doi.org/10.1371/journal.pone.0249676 VL - 16 IS - 4 PB - Public Library of Science ER - TY - JOUR A1 - Manley, Phillip A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Jäger, Klaus A1 - Becker, Christiane A1 - Burger, Sven T1 - Modelling luminescent coupling in multi-junction solar cells: perovskite silicon tandem case study JF - Proc. SPIE Y1 - 2024 U6 - https://doi.org/10.1117/12.3023941 VL - 13014 SP - 1301404 ER - TY - JOUR A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Obermeier, Patrick A1 - Ma, Xiaolin A1 - Schweiger, Brunhilde A1 - Opota, Onya A1 - Rath, Barbara T1 - Disease Burden and Inpatient Management of Children with Acute Respiratory Viral Infections during the Pre-COVID Era in Germany: A Cost-of-Illness Study JF - Viruses N2 - Respiratory viral infections (RVIs) are common reasons for healthcare consultations. The inpatient management of RVIs consumes significant resources. From 2009 to 2014, we assessed the costs of RVI management in 4776 hospitalized children aged 0–18 years participating in a quality improvement program, where all ILI patients underwent virologic testing at the National Reference Centre followed by detailed recording of their clinical course. The direct (medical or non-medical) and indirect costs of inpatient management outside the ICU (‘non-ICU’) versus management requiring ICU care (‘ICU’) added up to EUR 2767.14 (non-ICU) vs. EUR 29,941.71 (ICU) for influenza, EUR 2713.14 (non-ICU) vs. EUR 16,951.06 (ICU) for RSV infections, and EUR 2767.33 (non-ICU) vs. EUR 14,394.02 (ICU) for human rhinovirus (hRV) infections, respectively. Non-ICU inpatient costs were similar for all eight RVIs studied: influenza, RSV, hRV, adenovirus (hAdV), metapneumovirus (hMPV), parainfluenza virus (hPIV), bocavirus (hBoV), and seasonal coronavirus (hCoV) infections. ICU costs for influenza, however, exceeded all other RVIs. At the time of the study, influenza was the only RVI with antiviral treatment options available for children, but only 9.8% of influenza patients (non-ICU) and 1.5% of ICU patients with influenza received antivirals; only 2.9% were vaccinated. Future studies should investigate the economic impact of treatment and prevention of influenza, COVID-19, and RSV post vaccine introduction. Y1 - 2024 U6 - https://doi.org/10.3390/v16040507 VL - 16 IS - 4 ER - TY - JOUR A1 - Plock, Matthias A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Schneider, Phillip-Immanuel A1 - Burger, Sven T1 - Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes JF - J. Opt. Soc. Am. B Y1 - 2024 U6 - https://doi.org/10.1364/JOSAB.505767 VL - 41 SP - 850 ER - TY - JOUR A1 - Fürst, Steffen A1 - Conrad, Tim A1 - Jaeger, Carlo A1 - Wolf, Sarah T1 - Vahana.jl - A framework (not only) for large-scale agent-based models JF - Proceedings of Social Simulation Conference 2024 (SSC24) Y1 - 2024 ER - TY - JOUR A1 - Sherratt, Katharine A1 - Srivastava, Ajitesh A1 - Ainslie, Kylie A1 - Singh, David E. A1 - Cublier, Aymar A1 - Marinescu, Maria Cristina A1 - Carretero, Jesus A1 - Garcia, Alberto Cascajo A1 - Franco, Nicolas A1 - Willem, Lander A1 - Abrams, Steven A1 - Faes, Christel A1 - Beutels, Philippe A1 - Hens, Niel A1 - Müller, Sebastian A1 - Charlton, Billy A1 - Ewert, Ricardo A1 - Paltra, Sydney A1 - Rakow, Christian A1 - Rehmann, Jakob A1 - Conrad, Tim A1 - Schütte, Christof A1 - Nagel, Kai A1 - Abbott, Sam A1 - Grah, Rok A1 - Niehus, Rene A1 - Prasse, Bastian A1 - Sandmann, Frank A1 - Funk, Sebastian T1 - Characterising information gains and losses when collecting multiple epidemic model outputs JF - Epidemics N2 - Collaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during epidemic outbreaks. In the process of collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step. We compared this to directly collecting simulated trajectories. We aimed to explore information on key epidemic quantities; ensemble uncertainty; and performance against data, investigating potential to continuously gain information from a single cross-sectional collection of model results. Methods We compared July 2022 projections from the European COVID-19 Scenario Modelling Hub. Five modelling teams projected incidence in Belgium, the Netherlands, and Spain. We compared projections by incidence, peaks, and cumulative totals. We created a probabilistic ensemble drawn from all trajectories, and compared to ensembles from a median across each model’s quantiles, or a linear opinion pool. We measured the predictive accuracy of individual trajectories against observations, using this in a weighted ensemble. We repeated this sequentially against increasing weeks of observed data. We evaluated these ensembles to reflect performance with varying observed data. Results. By collecting modelled trajectories, we showed policy-relevant epidemic characteristics. Trajectories contained a right-skewed distribution well represented by an ensemble of trajectories or a linear opinion pool, but not models’ quantile intervals. Ensembles weighted by performance typically retained the range of plausible incidence over time, and in some cases narrowed this by excluding some epidemic shapes. Conclusions. We observed several information gains from collecting modelled trajectories rather than quantile distributions, including potential for continuously updated information from a single model collection. The value of information gains and losses may vary with each collaborative effort’s aims, depending on the needs of projection users. Understanding the differing information potential of methods to collect model projections can support the accuracy, sustainability, and communication of collaborative infectious disease modelling efforts. Data availability All code and data available on Github: https://github.com/covid19-forecast-hub-europe/aggregation-info-loss KW - Virology KW - Infectious Diseases KW - Public Health, Environmental and Occupational Health KW - Microbiology KW - Parasitology KW - Epidemiology Y1 - 2024 U6 - https://doi.org/10.1016/j.epidem.2024.100765 SN - 1755-4365 VL - 47 PB - Elsevier BV ER - TY - JOUR A1 - Singh, Upkar A1 - Vinayachandran, P. N. A1 - Natarajan, Vijay T1 - Advection-Based Tracking and Analysis of Salinity Movement in the Indian Ocean JF - Computers & Geosciences N2 - The Bay of Bengal (BoB) has maintained its salinity distribution over the years despite a continuous flow of fresh water entering it through rivers on the northern coast, which is capable of diluting the salinity. This can be attributed to the cyclic flow of high salinity water (>= 35 psu), coming from Arabian sea and entering BoB from the south, which moves northward and mixes with this fresh water. The movement of this high salinity water has been studied and analyzed in previous work (Singh et al., 2022). This paper extends the computational methods and analysis of salinity movement. Specifically, we introduce an advection based feature definition that represents the movement of high salinity water, and describe algorithms to track their evolution over time. This method allows us to trace the movement of high salinity water caused due to ocean currents. The method is validated via comparison with established observations on the flow of high salinity water in the BoB, including its entry from the Arabian Sea and its movement near Sri Lanka. Further, the visual analysis and tracking framework enables us to compare it with previous work and analyze the contribution of advection to salinity transport. Y1 - 2024 U6 - https://doi.org/10.1016/j.cageo.2023.105493 VL - 182 IS - 105493 SP - 1 EP - 10 ER - TY - JOUR A1 - Dhar, Amritendu A1 - Natarajan, Vijay A1 - Rathod, Abhishek T1 - Geometric localization of homology cycles JF - CCCG 2024: Proc. 36th Canadian Conference on Computational Geometry N2 - Computing an optimal cycle in a given homology class, also referred to as the homology localization problem, is known to be an NP-hard problem in general. Furthermore, there is currently no known optimality criterion that localizes classes geometrically and admits a stability property under the setting of persistent homology. We present a geometric optimization of the cycles that is computable in polynomial time and is stable in an approximate sense. Tailoring our search criterion to different settings, we obtain various optimization problems like optimal homologous cycle, minimum homology basis, and minimum persistent homology basis. In practice, the (trivial) exact algorithm is computationally expensive despite having a worst case polynomial runtime. Therefore, we design approximation algorithms for the above problems and study their performance experimentally. These algorithms have reasonable runtimes for moderate sized datasets and the cycles computed by these algorithms are consistently of high quality as demonstrated via experiments on multiple datasets. Y1 - 2024 SP - 1 EP - 8 ER - TY - JOUR A1 - Van Bulck, David A1 - Goossens, Dries A1 - Clarner, Jan-Patrick A1 - Dimitsas, Angelos A1 - Fonseca, Georg H. G. A1 - Lamas-Fernandez, Carlos A1 - Lester, Martin Mariusz A1 - Pedersen, Jaap A1 - Phillips, Antony E. A1 - Rosati, Roberto Maria T1 - Which algorithm to select in sports timetabling? JF - European Journal of Operational Research N2 - Any sports competition needs a timetable, specifying when and where teams meet each other. The recent International Timetabling Competition (ITC2021) on sports timetabling showed that, although it is possible to develop general algorithms, the performance of each algorithm varies considerably over the problem instances. This paper provides a problem type analysis for sports timetabling, resulting in powerful insights into the strengths and weaknesses of eight state-of-the-art algorithms. Based on machine learning techniques, we propose an algorithm selection system that predicts which algorithm is likely to perform best based on the type of competition and constraints being used (i.e., the problem type) in a given sports timetabling problem instance. Furthermore, we visualize how the problem type relates to algorithm performance, providing insights and possibilities to further enhance several algorithms. Finally, we assess the empirical hardness of the instances. Our results are based on large computational experiments involving about 50 years of CPU time on more than 500 newly generated problem instances. Y1 - 2024 U6 - https://doi.org/10.1016/j.ejor.2024.06.005 VL - 318 IS - 2 SP - 575 EP - 591 ER - TY - JOUR A1 - Das, Somenath A1 - Sridharamurthy, Raghavendra A1 - Natarajan, Vijay T1 - Time-varying Extremum Graphs JF - Computer Graphics Forum N2 - We introduce time-varying extremum graph (TVEG), a topological structure to support visualization and analysis of a time- varying scalar field. The extremum graph is a substructure of the Morse-Smale complex. It captures the adjacency relationship between cells in the Morse decomposition of a scalar field. We define the TVEG as a time-varying extension of the extremum graph and demonstrate how it captures salient feature tracks within a dynamic scalar field. We formulate the construction of the TVEG as an optimization problem and describe an algorithm for computing the graph. We also demonstrate the capabilities of TVEG towards identification and exploration of topological events such as deletion, generation, split, and merge within a dynamic scalar field via comprehensive case studies including a viscous fingers and a 3D von Kármán vortex street dataset. Y1 - 2024 U6 - https://doi.org/10.1111/cgf.15162 SP - e15162 ER - TY - JOUR A1 - Conrad, Tim A1 - Ferrer, Eloi A1 - Mietchen, Daniel A1 - Pusch, Larissa A1 - Stegmuller, Johannes A1 - Schubotz, Moritz T1 - Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing JF - Scientific Data Y1 - 2024 U6 - https://doi.org/10.1038/s41597-024-03480-0 VL - 11 ER - TY - JOUR A1 - Braun, Gábor A1 - Guzmán, Cristóbal A1 - Pokutta, Sebastian T1 - Corrections to “Lower Bounds on the Oracle Complexity of Nonsmooth Convex Optimization via Information Theory” JF - IEEE Transactions on Information Theory N2 - This note closes a gap in the proof of Theorem VI.3 from the article “Lower Bounds on the Oracle Complexity of Nonsmooth Convex Optimization via Information Theory” (2017). Y1 - 2024 U6 - https://doi.org/10.1109/TIT.2024.3357200 VL - 70 IS - 7 SP - 5408 EP - 5409 ER - TY - JOUR A1 - Rodrigues Pelá, Ronaldo A1 - Draxl, Claudia T1 - Speeding up all-electron real-time TDDFT demonstrated by the exciting package JF - Comput. Phys. Commun. Y1 - 2024 U6 - https://doi.org/10.1016/j.cpc.2024.109292 VL - 304 SP - 109292 ER - TY - JOUR A1 - Raharinirina, Nomenjanahary Alexia A1 - Sunkara, Vikram A1 - von Kleist, Max A1 - Fackeldey, Konstantin A1 - Weber, Marcus T1 - Multi-Input data ASsembly for joint Analysis (MIASA): A framework for the joint analysis of disjoint sets of variables JF - PLOS ONE Y1 - 2024 U6 - https://doi.org/10.1371/journal.pone.0302425 VL - 19 IS - 5 PB - Public Library of Science ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - Safe and verified Gomory mixed integer cuts in a rational MIP framework JF - SIAM Journal on Optimization N2 - This paper is concerned with the exact solution of mixed-integer programs (MIPs) over the rational numbers, i.e., without any roundoff errors and error tolerances. Here, one computational bottleneck that should be avoided whenever possible is to employ large-scale symbolic computations. Instead it is often possible to use safe directed rounding methods, e.g., to generate provably correct dual bounds. In this work, we continue to leverage this paradigm and extend an exact branch-and-bound framework by separation routines for safe cutting planes, based on the approach first introduced by Cook, Dash, Fukasawa, and Goycoolea in 2009 [INFORMS J. Comput., 21 (2009), pp. 641–649]. Constraints are aggregated safely using approximate dual multipliers from an LP solve, followed by mixed-integer rounding to generate provably valid, although slightly weaker inequalities. We generalize this approach to problem data that is not representable in floating-point arithmetic, add routines for controlling the encoding length of the resulting cutting planes, and show how these cutting planes can be verified according to the VIPR certificate standard. Furthermore, we analyze the performance impact of these cutting planes in the context of an exact MIP framework, showing that we can solve 21.5% more instances to exact optimality and reduce solving times by 26.8% on the MIPLIB 2017 benchmark test set. Y1 - 2024 U6 - https://doi.org/10.1137/23M156046X VL - 34 IS - 1 ER - TY - JOUR A1 - Lelièvre, Tony A1 - Pigeon, Thomas A1 - Stoltz, Gabriel A1 - Zhang, Wei T1 - Analyzing multimodal probability measures with autoencoders JF - J. Phys. Chem. B N2 - Finding collective variables to describe some important coarse-grained information on physical systems, in particular metastable states, remains a key issue in molecular dynamics. Recently, machine learning techniques have been intensively used to complement and possibly bypass expert knowledge in order to construct collective variables. Our focus here is on neural network approaches based on autoencoders. We study some relevant mathematical properties of the loss function considered for training autoencoders, and provide physical interpretations based on conditional variances and minimum energy paths. We also consider various extensions in order to better describe physical systems, by incorporating more information on transition states at saddle points, and/or allowing for multiple decoders in order to describe several transition paths. Our results are illustrated on toy two dimensional systems and on alanine dipeptide. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpcb.3c07075 VL - 128 IS - 11 SP - 2607 EP - 2631 ER - TY - JOUR A1 - Prause, Felix A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Tesch, Alexander T1 - Approximating rolling stock rotations with integrated predictive maintenance JF - Journal of Rail Transport Planning & Management N2 - We study the solution of the rolling stock rotation problem with predictive maintenance (RSRP-PdM) by an iterative refinement approach that is based on a state-expanded event-graph. In this graph, the states are parameters of a failure distribution, and paths correspond to vehicle rotations with associated health state approximations. An optimal set of paths including maintenance can be computed by solving an integer linear program. Afterwards, the graph is refined and the procedure repeated. An associated linear program gives rise to a lower bound that can be used to determine the solution quality. Computational results for six instances derived from real-world timetables of a German railway company are presented. The results show the effectiveness of the approach and the quality of the solutions. Y1 - 2024 U6 - https://doi.org/10.1016/j.jrtpm.2024.100434 VL - 30 SP - 100434 ER - TY - JOUR A1 - Krüger, Jan A1 - Manley, Phillip A1 - Bergmann, Detlef A1 - Köning, Rainer A1 - Bodermann, Bernd A1 - Eder, Christian A1 - Heinrich, Andreas A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Manske, Eberhard T1 - Introduction and application of a new approach for model-based optical bidirectional measurements JF - Meas. Sci. Technol. Y1 - 2024 U6 - https://doi.org/10.1088/1361-6501/ad4b53 VL - 35 IS - 8 ER - TY - JOUR A1 - Hennings, Felix A1 - Hoppmann-Baum, Kai A1 - Zittel, Janina T1 - Optimizing transient gas network control for challenging real-world instances using MIP-based heuristics JF - Open Journal of Mathematical Optimization Y1 - 2024 U6 - https://doi.org/10.5802/ojmo.29 VL - 5 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Herrera, Kristian A1 - Tavhelidse-Suck, Tinatini A1 - Knoblich, Simon A1 - Seleit, Ali A1 - Boulanger-Weill, Jonathan A1 - Chambule, Sydney A1 - Aspiras, Ariel A1 - Santoriello, Cristina A1 - Randlett, Owen A1 - Wittbrodt, Joachim A1 - Aulehla, Alexander A1 - Lichtman, Jeff W. A1 - Fishman, Mark A1 - Hege, Hans-Christian A1 - Baum, Daniel A1 - Engert, Florian A1 - Isoe, Yasuko T1 - Multi-species community platform for comparative neuroscience in teleost fish N2 - Studying neural mechanisms in complementary model organisms from different ecological niches in the same animal class can leverage the comparative brain analysis at the cellular level. To advance such a direction, we developed a unified brain atlas platform and specialized tools that allowed us to quantitatively compare neural structures in two teleost larvae, medaka (Oryzias latipes) and zebrafish (Danio rerio). Leveraging this quantitative approach we found that most brain regions are similar but some subpopulations are unique in each species. Specifically, we confirmed the existence of a clear dorsal pallial region in the telencephalon in medaka lacking in zebrafish. Further, our approach allows for extraction of differentially expressed genes in both species, and for quantitative comparison of neural activity at cellular resolution. The web-based and interactive nature of this atlas platform will facilitate the teleost community’s research and its easy extensibility will encourage contributions to its continuous expansion. Y1 - 2024 U6 - https://doi.org/10.1101/2024.02.14.580400 ER - TY - JOUR A1 - Gaskin, Thomas A1 - Conrad, Tim A1 - Pavliotis, Grigorios A. A1 - Schütte, Christof T1 - Neural parameter calibration and uncertainty quantification for epidemic forecasting JF - PLOS ONE N2 - The recent COVID-19 pandemic has thrown the importance of accurately forecasting contagion dynamics and learning infection parameters into sharp focus. At the same time, effective policy-making requires knowledge of the uncertainty on such predictions, in order, for instance, to be able to ready hospitals and intensive care units for a worst-case scenario without needlessly wasting resources. In this work, we apply a novel and powerful computational method to the problem of learning probability densities on contagion parameters and providing uncertainty quantification for pandemic projections. Using a neural network, we calibrate an ODE model to data of the spread of COVID-19 in Berlin in 2020, achieving both a significantly more accurate calibration and prediction than Markov-Chain Monte Carlo (MCMC)-based sampling schemes. The uncertainties on our predictions provide meaningful confidence intervals e.g. on infection figures and hospitalisation rates, while training and running the neural scheme takes minutes where MCMC takes hours. We show convergence of our method to the true posterior on a simplified SIR model of epidemics, and also demonstrate our method's learning capabilities on a reduced dataset, where a complex model is learned from a small number of compartments for which data is available. Y1 - 2024 ER - TY - JOUR A1 - Engel, Maximilian A1 - Olicón-Méndez, Guillermo A1 - Wehlitz, Nathalie A1 - Winkelmann, Stefanie T1 - Synchronization and random attractors in reaction jump processes JF - Journal of Dynamics and Differential Equations N2 - This work explores a synchronization-like phenomenon induced by common noise for continuous-time Markov jump processes given by chemical reaction networks. Based on Gillespie’s stochastic simulation algorithm, a corresponding random dynamical system is formulated in a two-step procedure, at first for the states of the embedded discrete-time Markov chain and then for the augmented Markov chain including random jump times. We uncover a time-shifted synchronization in the sense that—after some initial waiting time—one trajectory exactly replicates another one with a certain time delay. Whether or not such a synchronization behavior occurs depends on the combination of the initial states. We prove this partial time-shifted synchronization for the special setting of a birth-death process by analyzing the corresponding two-point motion of the embedded Markov chain and determine the structure of the associated random attractor. In this context, we also provide general results on existence and form of random attractors for discrete-time, discrete-space random dynamical systems. Y1 - 2024 U6 - https://doi.org/10.1007/s10884-023-10345-4 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Quang Vu, Nhu A1 - Nagel, Soeren T1 - Co-evolving networks for opinion and social dynamics in agent-based models JF - arxiv N2 - The rise of digital social media has strengthened the coevolution of public opinions and social interactions, that shape social structures and collective outcomes in increasingly complex ways. Existing literature often explores this interplay as a one-directional influence, focusing on how opinions determine social ties within adaptive networks. However, this perspective overlooks the intrinsic dynamics driving social interactions, which can significantly influence how opinions form and evolve. In this work, we address this gap, by introducing the co-evolving opinion and social dynamics using stochastic agent-based models. Agents' mobility in a social space is governed by both their social and opinion similarity with others. Similarly, the dynamics of opinion formation is driven by the opinions of agents in their social vicinity. We analyze the underlying social and opinion interaction networks and explore the mechanisms influencing the appearance of emerging phenomena, like echo chambers and opinion consensus. To illustrate the model's potential for real-world analysis, we apply it to General Social Survey data on political identity and public opinion regarding governmental issues. Our findings highlight the model's strength in capturing the coevolution of social connections and individual opinions over time. Y1 - 2024 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - On finding optimal collective variables for complex systems by minimizing the deviation between effective and full dynamics N2 - This paper is concerned with collective variables, or reaction coordinates, that map a discrete-in-time Markov process X_n in R^d to a (much) smaller dimension k≪d. We define the effective dynamics under a given collective variable map ξ as the best Markovian representation of X_n under ξ. The novelty of the paper is that it gives strict criteria for selecting optimal collective variables via the properties of the effective dynamics. In particular, we show that the transition density of the effective dynamics of the optimal collective variable solves a relative entropy minimization problem from certain family of densities to the transition density of X_n. We also show that many transfer operator-based data-driven numerical approaches essentially learn quantities of the effective dynamics. Furthermore, we obtain various error estimates for the effective dynamics in approximating dominant timescales / eigenvalues and transition rates of the original process X_n and how optimal collective variables minimize these errors. Our results contribute to the development of theoretical tools for the understanding of complex dynamical systems, e.g. molecular kinetics, on large timescales. These results shed light on the relations among existing data-driven numerical approaches for identifying good collective variables, and they also motivate the development of new methods. Y1 - 2024 ER - TY - JOUR A1 - Prause, Felix A1 - Borndörfer, Ralf T1 - An Iterative Refinement Approach for the Rolling Stock Rotation Problem with Predictive Maintenance N2 - The rolling stock rotation problem with predictive maintenance (RSRP-PdM) involves the assignment of trips to a fleet of vehicles with integrated maintenance scheduling based on the predicted failure probability of the vehicles. These probabilities are determined by the health states of the vehicles, which are considered to be random variables distributed by a parameterized family of probability distribution functions. During the operation of the trips, the corresponding parameters get updated. In this article, we present a dual solution approach for RSRP-PdM and generalize a linear programming based lower bound for this problem to families of probability distribution functions with more than one parameter. For this purpose, we define a rounding function that allows for a consistent underestimation of the parameters and model the problem by a state-expanded event-graph in which the possible states are restricted to a discrete set. This induces a flow problem that is solved by an integer linear program. We show that the iterative refinement of the underlying discretization leads to solutions that converge from below to an optimal solution of the original instance. Thus, the linear relaxation of the considered integer linear program results in a lower bound for RSRP-PdM. Finally, we report on the results of computational experiments conducted on a library of test instances. Y1 - 2024 ER - TY - JOUR A1 - Meduri, Dhruv A1 - Sharma, Mohit A1 - Natarajan, Vijay T1 - Jacobi Set Simplification for Tracking Topological Features in Time-Varying Scalar Fields JF - Vis Comput N2 - The Jacobi set of a bivariate scalar field is the set of points where the gradients of the two constituent scalar fields align with each other. It captures the regions of topological changes in the bivariate field. The Jacobi set is a bivariate analog of critical points, and may correspond to features of interest. In the specific case of time-varying fields and when one of the scalar fields is time, the Jacobi set corresponds to temporal tracks of critical points, and serves as a feature-tracking graph. The Jacobi set of a bivariate field or a time-varying scalar field is complex, resulting in cluttered visualizations that are difficult to analyze. This paper addresses the problem of Jacobi set simplification. Specifically, we use the time-varying scalar field scenario to introduce a method that computes a reduced Jacobi set. The method is based on a stability measure called robustness that was originally developed for vector fields and helps capture the structural stability of critical points. We also present a mathematical analysis for the method, and describe an implementation for 2D time-varying scalar fields. Applications to both synthetic and real-world datasets demonstrate the effectiveness of the method for tracking features. Y1 - 2024 U6 - https://doi.org/10.1007/s00371-024-03484-2 VL - 40 SP - 4843 EP - 4855 ER - TY - JOUR A1 - Vanaret, Charlie T1 - Interval constraint programming for globally solving catalog-based categorical optimization JF - Journal of Global Optimization N2 - In this article, we propose an interval constraint programming method for globally solving catalog-based categorical optimization problems. It supports catalogs of arbitrary size and properties of arbitrary dimension, and does not require any modeling effort from the user. A novel catalog-based contractor (or filtering operator) guarantees consistency between the categorical properties and the existing catalog items. This results in an intuitive and generic approach that is exact, rigorous (robust to roundoff errors) and can be easily implemented in an off-the-shelf interval-based continuous solver that interleaves branching and constraint propagation. We demonstrate the validity of the approach on a numerical problem in which a categorical variable is described by a two-dimensional property space. A Julia prototype is available as open-source software under the MIT license. Y1 - 2024 U6 - https://doi.org/10.1007/s10898-023-01362-0 VL - 89 SP - 457 EP - 476 ER - TY - JOUR A1 - Kofler, Andreas A1 - Wald, Christian A1 - Kolbitsch, Christoph A1 - von Tycowicz, Christoph A1 - Ambellan, Felix T1 - Joint Reconstruction and Segmentation in Undersampled 3D Knee MRI combining Shape Knowledge and Deep Learning JF - Physics in Medicine and Biology N2 - Task-adapted image reconstruction methods using end-to-end trainable neural networks (NNs) have been proposed to optimize reconstruction for subsequent processing tasks, such as segmentation. However, their training typically requires considerable hardware resources and thus, only relatively simple building blocks, e.g. U-Nets, are typically used, which, albeit powerful, do not integrate model-specific knowledge. In this work, we extend an end-to-end trainable task-adapted image reconstruction method for a clinically realistic reconstruction and segmentation problem of bone and cartilage in 3D knee MRI by incorporating statistical shape models (SSMs). The SSMs model the prior information and help to regularize the segmentation maps as a final post-processing step. We compare the proposed method to a state-of-the-art (SOTA) simultaneous multitask learning approach for image reconstruction and segmentation (MTL) and to a complex SSMs-informed segmentation pipeline (SIS). Our experiments show that the combination of joint end-to-end training and SSMs to further regularize the segmentation maps obtained by MTL highly improves the results, especially in terms of mean and maximal surface errors. In particular, we achieve the segmentation quality of SIS and, at the same time, a substantial model reduction that yields a five-fold decimation in model parameters and a computational speedup of an order of magnitude. Remarkably, even for undersampling factors of up to R=8, the obtained segmentation maps are of comparable quality to those obtained by SIS from ground-truth images. Y1 - 2024 U6 - https://doi.org/10.1088/1361-6560/ad3797 VL - 69 IS - 9 ER - TY - JOUR A1 - Veldhuijzen, Ben A1 - Veltkamp, Remco C. A1 - Ikne, Omar A1 - Allaert, Benjamin A1 - Wannous, Hazem A1 - Emporio, Marco A1 - Giachetti, Andrea A1 - LaViola Jr, Joseph J. A1 - He, Ruiwen A1 - Benhabiles, Halim A1 - Cabani, Adnane A1 - Fleury, Anthony A1 - Hammoudi, Karim A1 - Gavalas, Konstantinos A1 - Vlachos, Christoforos A1 - Papanikolaou, Athanasios A1 - Romanelis, Ioannis A1 - Fotis, Vlassis A1 - Arvanitis, Gerasimos A1 - Moustakas, Konstantinos A1 - Hanik, Martin A1 - Nava-Yazdani, Esfandiar A1 - von Tycowicz, Christoph T1 - SHREC 2024: Recognition Of Dynamic Hand Motions Molding Clay JF - Computers & Graphics N2 - Gesture recognition is a tool to enable novel interactions with different techniques and applications, like Mixed Reality and Virtual Reality environments. With all the recent advancements in gesture recognition from skeletal data, it is still unclear how well state-of- the-art techniques perform in a scenario using precise motions with two hands. This paper presents the results of the SHREC 2024 contest organized to evaluate methods for their recognition of highly similar hand motions using the skeletal spatial coordinate data of both hands. The task is the recognition of 7 motion classes given their spatial coordinates in a frame-by-frame motion. The skeletal data has been captured using a Vicon system and pre-processed into a coordinate system using Blender and Vicon Shogun Post. We created a small, novel dataset with a high variety of durations in frames. This paper shows the results of the contest, showing the techniques created by the 5 research groups on this challenging task and comparing them to our baseline method. Y1 - 2024 ER - TY - JOUR A1 - Zhao, Yue A1 - Zhang, Wei A1 - Li, Tiejun T1 - EPR-Net: Constructing non-equilibrium potential landscape via a variational force projection formulation JF - National Science Review N2 - We present EPR-Net, a novel and effective deep learning approach that tackles a crucial challenge in biophysics: constructing potential landscapes for high-dimensional non-equilibrium steady-state (NESS) systems. EPR-Net leverages a nice mathematical fact that the desired negative potential gradient is simply the orthogonal projection of the driving force of the underlying dynamics in a weighted inner-product space. Remarkably, our loss function has an intimate connection with the steady entropy production rate (EPR), enabling simultaneous landscape construction and EPR estimation. We introduce an enhanced learning strategy for systems with small noise, and extend our framework to include dimensionality reduction and state-dependent diffusion coefficient case in a unified fashion. Comparative evaluations on benchmark problems demonstrate the superior accuracy, effectiveness, and robustness of EPR-Net compared to existing methods. We apply our approach to challenging biophysical problems, such as an 8D limit cycle and a 52D multi-stability problem, which provide accurate solutions and interesting insights on constructed landscapes. With its versatility and power, EPR-Net offers a promising solution for diverse landscape construction problems in biophysics. Y1 - 2024 U6 - https://doi.org/10.1093/nsr/nwae052 VL - 11 IS - 7 ER - TY - JOUR A1 - Nagel, Soeren A1 - Heitzig, Jobst A1 - Schoell, Eckehard T1 - Capital Inequality Induced Business Cycles N2 - In this letter we present a stochastic dynamic model which can explain economic cycles. We show that the macroscopic description yields a complex dynamical landscape consisting of multiple stable fixed points, each corresponding to a split of the population into a large low and a small high income group. The stochastic fluctuations induce switching between the resulting metastable states, and excitation oscillations just below a deterministic bifurcation. The shocks are caused by the decisions of a few agents who have a disproportionate influence over the macroscopic state of the economy due to the unequal distribution of wealth among the population. The fluctuations have a long-term effect on the growth of economic output and lead to business cycle oscillations exhibiting coherence resonance, where the correlation time is controlled by the population size which is inversely proportional to the noise intensity. Y1 - 2023 SP - 1 EP - 6 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Binkowski, Felix T1 - Efficient rational approximation of optical response functions with the AAA algorithm JF - Laser Photonics Rev. Y1 - 2024 ER - TY - JOUR A1 - Semler, Phillip A1 - Weiser, Martin T1 - Adaptive Gaussian Process Regression for Efficient Building of Surrogate Models in Inverse Problems JF - Inverse Problems N2 - In a task where many similar inverse problems must be solved, evaluating costly simulations is impractical. Therefore, replacing the model y with a surrogate model y(s) that can be evaluated quickly leads to a significant speedup. The approximation quality of the surrogate model depends strongly on the number, position, and accuracy of the sample points. With an additional finite computational budget, this leads to a problem of (computer) experimental design. In contrast to the selection of sample points, the trade-off between accuracy and effort has hardly been studied systematically. We therefore propose an adaptive algorithm to find an optimal design in terms of position and accuracy. Pursuing a sequential design by incrementally appending the computational budget leads to a convex and constrained optimization problem. As a surrogate, we construct a Gaussian process regression model. We measure the global approximation error in terms of its impact on the accuracy of the identified parameter and aim for a uniform absolute tolerance, assuming that y(s) is computed by finite element calculations. A priori error estimates and a coarse estimate of computational effort relate the expected improvement of the surrogate model error to computational effort, resulting in the most efficient combination of sample point and evaluation tolerance. We also allow for improving the accuracy of already existing sample points by continuing previously truncated finite element solution procedures. Y1 - 2023 U6 - https://doi.org/10.1088/1361-6420/ad0028 VL - 39 IS - 12 SP - 125003 ER - TY - JOUR A1 - Paltra, Sydney A1 - Bostanci, Inan A1 - Nagel, Kai T1 - The effect of mobility reductions on infection growth is quadratic in many cases JF - Scientific Reports Y1 - 2024 U6 - https://doi.org/10.1038/s41598-024-64230-1 VL - 14 ER - TY - JOUR A1 - Gebhard, Oliver A1 - Hahn-Klimroth, Max A1 - Penschuck, Manuel A1 - Rolvien, Maurice A1 - Scarlett, Jonathan A1 - Tan, Nelvin A1 - Parczyk, Olaf T1 - Near optimal sparsity-constrained group testing: improved bounds JF - IEEE Transactions on Information Theory Y1 - 2022 ER - TY - JOUR A1 - Hahn-Klimroth, Max A1 - Person, Yury A1 - Parczyk, Olaf T1 - Minimum degree conditions for containing an r-regular r-connected subgraph JF - European Journal of Combinatorics Y1 - 2024 ER - TY - JOUR A1 - Mundinger, Konrad A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Zimmer, Max T1 - Extending the Continuum of Six-Colorings JF - Geombinatorics Quarterly Y1 - 2024 ER - TY - JOUR A1 - Parczyk, Olaf A1 - Pokutta, Sebastian A1 - Spiegel, Christoph A1 - Szabó, Tibor T1 - New Ramsey multiplicity bounds and search heuristics JF - Foundations of Computational Mathematics Y1 - 2024 ER - TY - JOUR A1 - Böttcher, Julia A1 - Sgueglia, Amedeo A1 - Skokan, Jozef A1 - Parczyk, Olaf T1 - Triangles in randomly perturbed graphs JF - Combinatorics, Probability and Computing Y1 - 2022 ER - TY - JOUR A1 - Allen, Peter A1 - Pfenninger, Vincent A1 - Parczyk, Olaf T1 - Resilience for tight Hamiltonicity JF - Combinatorial Theory Y1 - 2024 ER - TY - JOUR A1 - Gupta, Pranshu A1 - Hamann, Fabian A1 - Müyesser, Alp A1 - Sgueglia, Amedeo A1 - Parczyk, Olaf T1 - A general approach to transversal versions of Dirac-type theorems JF - Bulletin of the London Mathematical Society Y1 - 2023 ER - TY - JOUR A1 - Prause, Felix A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Tesch, Alexander T1 - Approximating rolling stock rotations with integrated predictive maintenance JF - Journal of Rail Transport Planning & Management Y1 - 2024 ER - TY - JOUR A1 - Barros, Gabriel F. A1 - Cavalar, Bruno P. A1 - Mota, Guilherme O. A1 - Parczyk, Olaf T1 - Anti-Ramsey threshold of cycles for sparse graphs JF - Discrete Applied Mathematics Y1 - 2022 ER - TY - JOUR A1 - Kohayakawa, Yoshiharu A1 - Mota, Guilherme O. A1 - Schnitzer, Jakob A1 - Parczyk, Olaf T1 - Anti-Ramsey threshold of complete graphs for sparse graphs JF - Discrete Mathematics Y1 - 2023 ER - TY - JOUR A1 - Vu-Han, Tu-Lan A1 - Schettino, Rodrigo Bermudez A1 - Weiß, Claudia A1 - Perka, Carsten A1 - Winkler, Tobias A1 - Sunkara, Vikram A1 - Pumberger, Matthias T1 - An interpretable data-driven prediction model to anticipate scoliosis in spinal muscular atrophy in the era of (gene-) therapies JF - Scientific Reports N2 - 5q-spinal muscular atrophy (SMA) is a neuromuscular disorder (NMD) that has become one of the first 5% treatable rare diseases. The efficacy of new SMA therapies is creating a dynamic SMA patient landscape, where disease progression and scoliosis development play a central role, however, remain difficult to anticipate. New approaches to anticipate disease progression and associated sequelae will be needed to continuously provide these patients the best standard of care. Here we developed an interpretable machine learning (ML) model that can function as an assistive tool in the anticipation of SMA-associated scoliosis based on disease progression markers. We collected longitudinal data from 86 genetically confirmed SMA patients. We selected six features routinely assessed over time to train a random forest classifier. The model achieved a mean accuracy of 0.77 (SD 0.2) and an average ROC AUC of 0.85 (SD 0.17). For class 1 ‘scoliosis’ the average precision was 0.84 (SD 0.11), recall 0.89 (SD 0.22), F1-score of 0.85 (SD 0.17), respectively. Our trained model could predict scoliosis using selected disease progression markers and was consistent with the radiological measurements. During post validation, the model could predict scoliosis in patients who were unseen during training. We also demonstrate that rare disease data sets can be wrangled to build predictive ML models. Interpretable ML models can function as assistive tools in a changing disease landscape and have the potential to democratize expertise that is otherwise clustered at specialized centers. Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1038/s41598-024-62720-w VL - 14 IS - 11838 ER - TY - JOUR A1 - Bolusani, Suresh A1 - Besançon, Mathieu A1 - Gleixner, Ambros A1 - Berthold, Timo A1 - D'Ambrosio, Claudia A1 - Muñoz, Gonzalo A1 - Paat, Joseph A1 - Thomopulos, Dimitri T1 - The MIP workshop 2023 computational competition on reoptimization JF - Mathematical Programming Computation N2 - This paper describes the computational challenge developed for a computational competition held in 2023 for the 20th anniversary of the Mixed Integer Programming Workshop. The topic of this competition was reoptimization, also known as warm starting, of mixed integer linear optimization problems after slight changes to the input data for a common formulation. The challenge was to accelerate the proof of optimality of the modified instances by leveraging the information from the solving processes of previously solved instances, all while creating high-quality primal solutions. Specifically, we discuss the competition’s format, the creation of public and hidden datasets, and the evaluation criteria. Our goal is to establish a methodology for the generation of benchmark instances and an evaluation framework, along with benchmark datasets, to foster future research on reoptimization of mixed integer linear optimization problems. Y1 - 2024 U6 - https://doi.org/10.1007/s12532-024-00256-w VL - 16 SP - 255 EP - 266 ER - TY - JOUR A1 - Carderera, Alejandro A1 - Besançon, Mathieu A1 - Pokutta, Sebastian T1 - Scalable Frank-Wolfe on generalized self-concordant functions via simple steps JF - SIAM Journal on Optimization Y1 - 2024 U6 - https://doi.org/10.1137/23M1616789 VL - 34 IS - 3 ER - TY - JOUR A1 - Siqueira Rodrigues, Lucas A1 - Schmidt, Timo Torsten A1 - Israel, Johann Habakuk A1 - Nyakatura, John A1 - Zachow, Stefan A1 - Kosch, Thomas T1 - Comparing the Effects of Visual, Haptic, and Visuohaptic Encoding on Memory Retention of Digital Objects in Virtual Reality N2 - Although Virtual Reality (VR) has undoubtedly improved human interaction with 3D data, users still face difficulties retaining important details of complex digital objects in preparation for physical tasks. To address this issue, we evaluated the potential of visuohaptic integration to improve the memorability of virtual objects in immersive visualizations. In a user study (N=20), participants performed a delayed match-to-sample task where they memorized stimuli of visual, haptic, or visuohaptic encoding conditions. We assessed performance differences between the conditions through error rates and response time. We found that visuohaptic encoding significantly improved memorization accuracy compared to unimodal visual and haptic conditions. Our analysis indicates that integrating haptics into immersive visualizations enhances the memorability of digital objects. We discuss its implications for the optimal encoding design in VR applications that assist professionals who need to memorize and recall virtual objects in their daily work. Y1 - 2024 ER - TY - JOUR A1 - Weimann, Kuba A1 - Tim, Conrad T1 - Federated Learning with Deep Neural Networks: A Privacy-Preserving Approach to Enhanced ECG Classification JF - IEEE Journal of Biomedical and Health Informatics Y1 - 2024 U6 - https://doi.org/10.1109/JBHI.2024.3427787 ER -