@article{MetznerNoeSchuette2009, author = {Metzner, Ph. and No{\´e}, Frank and Sch{\"u}tte, Christof}, title = {Estimating the Sampling Error}, volume = {80}, journal = {Phys. Rev. E}, number = {2}, publisher = {American Physical Society}, doi = {10.1103/PhysRevE.80.021106}, pages = {021106}, year = {2009}, language = {en} } @incollection{GraefeSchuetteNordmeier2009, author = {Gr{\"a}fe, Ch. and Sch{\"u}tte, Christof and Nordmeier, V.}, title = {"Learner as creator" - Sch{\"u}lerInnen generieren eigene Lernspiele}, booktitle = {Didaktik der Physik - Bochum 2009}, publisher = {Lehmanns Media}, address = {Berlin}, year = {2009}, language = {en} } @article{LatorreMetznerHartmannetal.2011, author = {Latorre, J. and Metzner, Ph. and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {A Structure-preserving numerical discretization of reversible diffusions}, volume = {9}, journal = {Commun. Math. Sci.}, number = {4}, pages = {1051 -- 1072}, year = {2011}, language = {en} } @incollection{BernhardZoukraSchuette2010, author = {Bernhard, Stefan and Zoukra, Kristine Al and Sch{\"u}tte, Christof}, title = {From non-invasive hemodynamic measurements towards patient-specific cardiovascular diagnosis}, booktitle = {Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine}, editor = {Daskalaki, A. and Lazakidou, A.}, publisher = {Hershey, PA: Medical Information Science Reference}, year = {2010}, language = {en} } @article{HorenkoSchuette2010, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {On metastable conformational analysis of non-equilibrium biomolecular time series}, volume = {8}, journal = {Multiscale Modeling \& Simulation}, number = {2}, doi = {10.1137/080744347}, pages = {701 -- 716}, year = {2010}, language = {en} } @article{HartmannVulcanovSchuette2010, author = {Hartmann, Carsten and Vulcanov, V.-M. and Sch{\"u}tte, Christof}, title = {Balanced Truncation of Second Order Systems}, volume = {8}, journal = {Multiscale Model. Simul.}, number = {4}, doi = {10.1137/080732717}, pages = {1348 -- 1367}, year = {2010}, language = {en} } @article{LatorreHartmannSchuette2010, author = {Latorre, J. and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Free energy computation by controlled Langevin processes}, volume = {1}, journal = {Procedia Computer Science}, number = {1}, doi = {10.1016/j.procs.2010.04.179}, pages = {1591 -- 1600}, year = {2010}, language = {en} } @article{SchuetteWulkow2010, author = {Sch{\"u}tte, Christof and Wulkow, Michael}, title = {A Hybrid Galerkin-Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics}, volume = {4}, journal = {Macromol. React. Eng.}, number = {9-10}, doi = {10.1002/mren.200900073}, pages = {562 -- 577}, year = {2010}, language = {en} } @article{MarsalekFrigatoVandeVondeleetal.2010, author = {Marsalek, Ondrej and Frigato, Tomaso and VandeVondele, Joost and Bradforth, Stephen E. and Schmidt, Burkhard and Sch{\"u}tte, Christof and Jungwirth, Pavel}, title = {Hydrogen Forms in Water by Proton Transfer to a Distorted Electron}, volume = {114}, journal = {J. Phys. Chem. B}, number = {2}, doi = {10.1021/jp908986z}, pages = {915 -- 920}, year = {2010}, language = {en} } @inproceedings{DjurdjevacConradSarichSchuette2010, author = {Djurdjevac Conrad, Natasa and Sarich, Marco and Sch{\"u}tte, Christof}, title = {On Markov State Models for Metastable Processes}, booktitle = {Proceedings of the International Congress of Mathematics, Hyderabad, India, Section Invited Talks. (ICM) 2010}, year = {2010}, language = {en} } @article{SarichNoeSchuette2010, author = {Sarich, Marco and No{\´e}, Frank and Sch{\"u}tte, Christof}, title = {On the Approximation Quality of Markov State Models}, volume = {8}, journal = {Multiscale Model. Simul.}, number = {4}, doi = {10.1137/090764049}, pages = {1154 -- 1177}, year = {2010}, language = {en} } @article{HartmannSchuetteCiccotti2010, author = {Hartmann, Carsten and Sch{\"u}tte, Christof and Ciccotti, Giovanni}, title = {On the linear response of mechanical systems with constraints}, volume = {132}, journal = {J. Chem. Phys.}, number = {11}, doi = {10.1063/1.3354126}, pages = {111103}, year = {2010}, language = {en} } @article{FrigatoVandeVondeleSchmidtetal.2008, author = {Frigato, Tomaso and VandeVondele, Joost and Schmidt, Burkhard and Sch{\"u}tte, Christof and Jungwirth, Pavel}, title = {Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion}, volume = {112}, journal = {J. Phys. Chem. A}, number = {27}, doi = {10.1021/jp711545s}, pages = {6125 -- 6133}, year = {2008}, language = {en} } @article{HorenkoKleinDolaptchievetal.2008, author = {Horenko, Illia and Klein, Rupert and Dolaptchiev, S. and Sch{\"u}tte, Christof}, title = {Automated Generation of Reduced Stochastic Weather Models I}, volume = {6}, journal = {Mult. Mod. Sim.}, number = {4}, doi = {10.1137/060670535}, pages = {1125 -- 1145}, year = {2008}, language = {en} } @article{HartmannSchuette2008, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Balancing of partially-observed stochastic differential equations}, journal = {47th IEEE Conference on Decision and Control}, doi = {10.1109/CDC.2008.4739161}, pages = {4867 -- 4872}, year = {2008}, language = {en} } @article{HorenkoSchuette2008, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications}, journal = {Adv. Data Anal. Class., submitted}, year = {2008}, language = {en} } @article{HorenkoSchuette2008, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics}, volume = {7}, journal = {Mult. Mod. Sim.}, number = {2}, doi = {10.1137/070687451}, pages = {731 -- 773}, year = {2008}, language = {en} } @article{HorenkoDittmerLankasetal.2008, author = {Horenko, Illia and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Sch{\"u}tte, Christof}, title = {Macroscopic Dynamics of Complex Metastable Systems}, volume = {7}, journal = {J. Appl. Dyn. Syst.}, number = {2}, doi = {10.1137/050630064}, pages = {532 -- 560}, year = {2008}, language = {en} } @article{MeerbachSchuette2008, author = {Meerbach, E. and Sch{\"u}tte, Christof}, title = {Sequential Change Point Detection in Molecular Dynamics Trajectories}, journal = {Journal of Multivariate Analysis, submitted}, year = {2008}, language = {en} } @article{DiederichsJuditskiSpokoinyetal.2008, author = {Diederichs, Elmar and Juditski, A. and Spokoiny, V. and Sch{\"u}tte, Christof}, title = {Sparse Non-Gaussian Component Analysis}, journal = {IEEE Transactions on Information Theory, submitted}, year = {2008}, language = {en} } @incollection{GraefeSchuetteNordmeier2008, author = {Gr{\"a}fe, Ch. and Sch{\"u}tte, Christof and Nordmeier, V.}, title = {Spielend lernen - ein Online-Computerspiel zur Molek{\"u}ldynamik}, booktitle = {Didaktik der Physik ?}, publisher = {Lehmanns Media}, address = {Berlin}, year = {2008}, language = {en} } @article{MetznerHorenkoSchuette2007, author = {Metzner, Ph. and Horenko, Illia and Sch{\"u}tte, Christof}, title = {Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time}, volume = {76}, journal = {Phys. Rev. E}, number = {06}, doi = {10.1103/PhysRevE.76.066702}, pages = {066702}, year = {2007}, language = {en} } @article{BornemannNettesheimSchuette1996, author = {Bornemann, Folkmar A. and Nettesheim, Peter and Sch{\"u}tte, Christof}, title = {Quantum-classical molecular dynamics as an approximation to full quantum dynamics}, volume = {105}, journal = {J. Chem. Phys.}, number = {3}, doi = {10.1063/1.471952}, pages = {1074 -- 1083}, year = {1996}, language = {en} } @article{SchuetteZumbuschBrinkmann1995, author = {Sch{\"u}tte, Christof and Zumbusch, Gerhard and Brinkmann, Ralf}, title = {Dynamics of Erbium-doped Waveguide Lasers}, journal = {preprint}, year = {1995}, language = {en} } @misc{Schuette1995, author = {Sch{\"u}tte, Christof}, title = {Smoothed Molecular Dynamics for Thermally Embedded Systems}, year = {1995}, language = {en} } @article{SchuetteDinand1995, author = {Sch{\"u}tte, Christof and Dinand, Manfred}, title = {Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers}, volume = {13}, journal = {J. Lightw. Techn.}, number = {1}, pages = {14 -- 23}, year = {1995}, language = {en} } @article{ManzParamonovPolaseketal.1994, author = {Manz, J{\"o}rn and Paramonov, G. and Polasek, M. and Sch{\"u}tte, Christof}, title = {Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D}, volume = {34}, journal = {Isr. J. Chem.}, number = {1}, pages = {115 -- 125}, year = {1994}, language = {en} } @article{Schuette1993, author = {Sch{\"u}tte, Christof}, title = {A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation}, volume = {5}, journal = {Impact of Computing in Sci. Eng.}, number = {3}, doi = {10.1006/icse.1993.1008}, pages = {176 -- 200}, year = {1993}, language = {en} } @article{SchuetteWulkow1992, author = {Sch{\"u}tte, Christof and Wulkow, Michael}, title = {Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy.}, journal = {preprint}, year = {1992}, language = {en} } @article{DeuflhardHuisingaFischeretal.2000, author = {Deuflhard, Peter and Huisinga, Wilhelm and Fischer, Alexander and Sch{\"u}tte, Christof}, title = {Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains}, volume = {315}, journal = {Lin. Alg. Appl.}, number = {1-3}, doi = {10.1016/S0024-3795(00)00095-1}, pages = {39 -- 59}, year = {2000}, language = {en} } @inproceedings{SchuetteHuisinga2000, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {On Conformational Dynamics induced by Langevin Processes}, volume = {2}, booktitle = {Equadiff 99}, editor = {Fiedler, B. and Grger, K. and Sprekels, J{\"u}rgen}, publisher = {World Scientific}, doi = {10.1142/9789812792617_0234}, pages = {1247 -- 1262}, year = {2000}, language = {en} } @inproceedings{SchuetteCordes2000, author = {Sch{\"u}tte, Christof and Cordes, Frank}, title = {On Dynamical Transitions between Conformational Ensembles}, booktitle = {Molecular Dynamics on Parallel Computers}, editor = {Esser, R. and Grassberger, P. and Grotendorst, J. and Lewerenz, M.}, publisher = {World Scientific}, doi = {10.1142/9789812793768_0002}, pages = {32 -- 45}, year = {2000}, language = {en} } @article{BornemannSchuette1999, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {Adaptive Accuracy Control for Car-Parrinello Simulations}, volume = {83}, journal = {Num. Math.}, number = {2}, doi = {10.1007/s002110050445}, pages = {179 -- 186}, year = {1999}, language = {en} } @inproceedings{SchuetteBornemann1999, author = {Sch{\"u}tte, Christof and Bornemann, Folkmar A.}, title = {Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model}, volume = {4}, booktitle = {Computational Molecular Dynamics}, editor = {Deuflhard, Peter and Hermans, J. and Leimkuhler, Benedict and Marks, A. and Reich, Sebastian and Skeel, R.}, publisher = {Springer}, pages = {380 -- 395}, year = {1999}, language = {en} } @inproceedings{DeuflhardDellnitzJungeetal.1999, author = {Deuflhard, Peter and Dellnitz, M. and Junge, Oliver and Sch{\"u}tte, Christof}, title = {Computation of Essential Molecular Dynamics by Subdivision Techniques}, volume = {4}, booktitle = {Computational Molecular Dynamics}, editor = {Deuflhard, Peter and Hermans, J. and Leimkuhler, Benedict and Marks, A. and Reich, Sebastian and Skeel, R.}, publisher = {Springer}, pages = {98 -- 115}, year = {1999}, language = {en} } @article{Schuette1999, author = {Sch{\"u}tte, Christof}, title = {Conformational Dynamics}, journal = {preprint}, year = {1999}, language = {en} } @article{SchuetteFischerHuisingaetal.1999, author = {Sch{\"u}tte, Christof and Fischer, Alexander and Huisinga, Wilhelm and Deuflhard, Peter}, title = {A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo}, volume = {151}, journal = {J. Comp. Phys}, number = {1}, doi = {10.1006/jcph.1999.6231}, pages = {146 -- 168}, year = {1999}, language = {en} } @article{HuisingaBestRoitzschetal.1999, author = {Huisinga, Wilhelm and Best, Christoph and Roitzsch, Rainer and Sch{\"u}tte, Christof and Cordes, Frank}, title = {From Simulation Data to Conformational Ensembles}, volume = {20}, journal = {J. Comp. Chem.}, number = {16}, doi = {10.1002/(SICI)1096-987X(199912)20:16<1760::AID-JCC8>3.0.CO;2-2}, pages = {1760 -- 1774}, year = {1999}, language = {en} } @article{FischerCordesSchuette1999, author = {Fischer, Alexander and Cordes, Frank and Sch{\"u}tte, Christof}, title = {Hybrid Monte Carlo with adaptive temperature choice}, volume = {121}, journal = {Comp. Phys. Comm.}, doi = {10.1016/S0010-4655(99)00274-X}, pages = {37 -- 39}, year = {1999}, language = {en} } @article{ConradLeichtleHagehuelsmannetal.2006, author = {Conrad, Tim and Leichtle, Alexander Benedikt and Hageh{\"u}lsmann, Andre and Diederichs, Elmar and Baumann, Sven and Thiery, Joachim and Sch{\"u}tte, Christof}, title = {Beating the Noise}, volume = {4216}, journal = {Lecture Notes in Computer Science}, publisher = {Springer}, pages = {119 -- 128}, year = {2006}, language = {en} } @inproceedings{WalterSchuette2006, author = {Walter, J. and Sch{\"u}tte, Christof}, title = {Conditional Averaging for Diffusive Fast-Slow Systems}, booktitle = {Analysis, Modeling and Simulation of Multiscale Problems}, editor = {Mielke, A.}, publisher = {Springer}, doi = {10.1007/3-540-35657-6_24}, pages = {647 -- 682}, year = {2006}, language = {en} } @inproceedings{DellnitzMoloMetzneretal.2006, author = {Dellnitz, M. and Molo, M. and Metzner, Ph. and Preis, R. and Sch{\"u}tte, Christof}, title = {Graph Algorithms for Dynamical Systems}, booktitle = {Analysis, Modeling and Simulation of Multiscale Problems}, editor = {Mielke, A.}, publisher = {Springer}, doi = {10.1007/3-540-35657-6_23}, pages = {619 -- 645}, year = {2006}, language = {en} } @article{MetznerSchuetteVandenEijnden2006, author = {Metzner, Ph. and Sch{\"u}tte, Christof and Vanden-Eijnden, E.}, title = {Illustration of Transition Path Theory on a Collection of Simple Examples}, volume = {125}, journal = {J. Chem. Phys.}, number = {8}, doi = {10.1063/1.2335447}, pages = {084110}, year = {2006}, language = {en} } @inproceedings{MeerbachDittmerHorenkoetal.2006, author = {Meerbach, E. and Dittmer, E. and Horenko, Illia and Sch{\"u}tte, Christof}, title = {Multiscale Modelling in Molecular Dynamics}, volume = {703}, booktitle = {Computer Simulations in Condensed Matter}, editor = {Ferrario, Mauro and Ciccotti, Giovanni and Binder, Kurt}, publisher = {Springer}, pages = {475 -- 497}, year = {2006}, language = {en} } @inproceedings{HorenkoSchmidtEhrenbergSchuette2006, author = {Horenko, Illia and Schmidt-Ehrenberg, Johannes and Sch{\"u}tte, Christof}, title = {Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models}, volume = {4216}, booktitle = {Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006}, editor = {Berthold, Michael R. and Glen, Robert C. and Fischer, Ingrid}, publisher = {Springer}, doi = {10.1007/11875741_8}, pages = {74 -- 85}, year = {2006}, language = {en} } @article{HorenkoLorenzSchuetteetal.2005, author = {Horenko, Illia and Lorenz, S. and Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics}, volume = {26}, journal = {J. Comp. Chem.}, number = {9}, doi = {10.1002/jcc.20234}, pages = {941 -- 948}, year = {2005}, language = {en} } @article{HartmannSchuette2005, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables}, volume = {85}, journal = {Z. Angew. Math. Mech.}, number = {10}, doi = {10.1002/zamm.200410218}, pages = {700 -- 710}, year = {2005}, language = {en} } @article{MeerbachSchuetteFischer2005, author = {Meerbach, E. and Sch{\"u}tte, Christof and Fischer, Alexander}, title = {Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains}, volume = {398}, journal = {Lin. Alg. Appl.}, doi = {10.1016/j.laa.2004.10.018}, pages = {141 -- 160}, year = {2005}, language = {en} } @article{HartmannSchuette2005, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {A Geometric Approach to Constrained Molecular Dynamics and Free Energy}, volume = {3}, journal = {Comm. Math. Sci.}, number = {1}, pages = {1 -- 20}, year = {2005}, language = {en} } @book{OPUS4-2732, title = {New Algorithms for Macromolecular Simulation}, volume = {49}, journal = {Lecture Notes in Computational Science and Engineering}, editor = {Chipot, C. and Elber, R. and Laaksonen, A. and Leimkuhler, Benedict and Mark, A. and Schlick, T. and Sch{\"u}tte, Christof and Skeel, R.}, publisher = {Springer}, year = {2005}, language = {en} } @article{AntonySchmidtSchuette2005, author = {Antony, Jens and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes}, volume = {122}, journal = {J. Chem. Phys.}, number = {1}, doi = {10.1063/1.1829057}, pages = {014309}, year = {2005}, language = {en} } @article{HorenkoDittmerSchuette2005, author = {Horenko, Illia and Dittmer, E. and Sch{\"u}tte, Christof}, title = {Reduced Stochastic Models for Complex Molecular Systems}, volume = {9}, journal = {Comp. Vis. Sci.}, number = {2}, doi = {10.1007/s00791-006-0021-1}, pages = {89 -- 102}, year = {2005}, language = {en} } @article{DellnitzNeumannSchuette2005, author = {Dellnitz, M. and Neumann, M. and Sch{\"u}tte, Christof}, title = {Special Issue on Matrices and Mathematical Biology}, volume = {398}, journal = {Lin. Alg. Appl.}, doi = {10.1016/j.laa.2004.12.006}, pages = {1 -- 245}, year = {2005}, language = {en} } @inproceedings{SchuetteForsterMeerbachetal.2005, author = {Sch{\"u}tte, Christof and Forster, R. and Meerbach, E. and Fischer, Alexander}, title = {Uncoupling-Coupling Techniques for Metastable Dynamical Systems}, volume = {40}, booktitle = {Domain Decomposition Methods in Science and Engineering}, editor = {Kornhuber, Ralf and Hoppe, Ronald H. W. and P{\~A}\copyrightriaux, J. and Pironneau, O. and Widlund, Olof and Xu, J.}, publisher = {Springer}, pages = {115 -- 129}, year = {2005}, language = {en} } @article{WalterSchuettePavliotisetal.2004, author = {Walter, J. and Sch{\"u}tte, Christof and Pavliotis, G. and Stuart, Andrew}, title = {Averaging of Stochastic Differential Equations}, journal = {preprint}, year = {2004}, language = {en} } @article{SchuetteWalterHartmannetal.2004, author = {Sch{\"u}tte, Christof and Walter, J. and Hartmann, Carsten and Huisinga, Wilhelm}, title = {An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations}, volume = {2}, journal = {Multiscale Model. Simul.}, number = {3}, doi = {10.1137/030600308}, pages = {501 -- 526}, year = {2004}, language = {en} } @article{PreisDellnitzHesseletal.2004, author = {Preis, R. and Dellnitz, M. and Hessel, M. and Sch{\"u}tte, Christof and Meerbach, E.}, title = {Dominant Paths Between Almost Invariant Sets of Dynamical Systems}, journal = {preprint}, year = {2004}, language = {en} } @article{HorenkoWeiserSchmidtetal.2004, author = {Horenko, Illia and Weiser, Martin and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {Fully Adaptive Propagation of the Quantum-Classical Liouville Equation}, volume = {120}, journal = {J. Chem. Phys.}, number = {19}, doi = {10.1063/1.1691015}, pages = {8913 -- 8923}, year = {2004}, language = {en} } @inproceedings{DeuflhardSchuette2004, author = {Deuflhard, Peter and Sch{\"u}tte, Christof}, title = {Molecular Conformation Dynamics and Computational Drug Design}, volume = {116}, booktitle = {Applied Mathematics Entering the 21st Century}, editor = {Hill, James and Moore, Ross}, publisher = {SIAM}, pages = {91 -- 119}, year = {2004}, language = {en} } @article{MetznerDittmerJahnkeetal.2007, author = {Metzner, Ph. and Dittmer, E. and Jahnke, Tobias and Sch{\"u}tte, Christof}, title = {Generator Estimation of Markov Jump Processes}, volume = {227}, journal = {J. Comp. Phys.}, number = {1}, doi = {10.1016/j.jcp.2007.07.032}, pages = {353 -- 375}, year = {2007}, language = {en} } @article{NoeHorenkoSchuetteetal.2007, author = {No{\´e}, Frank and Horenko, Illia and Sch{\"u}tte, Christof and Smith, J.}, title = {Hierarchical Analysis of Conformational Dynamics in Biomolecules}, volume = {126}, journal = {J. Chem. Phys.}, number = {15}, doi = {10.1063/1.2714539}, pages = {155102}, year = {2007}, language = {en} } @article{HartmannSchuette2007, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Comment on Two Distinct Notions of Free Energy}, volume = {228}, journal = {Physica D}, number = {1}, doi = {10.1016/j.physd.2007.02.006}, pages = {59 -- 63}, year = {2007}, language = {en} } @article{LorenzDiederichsTelgmannetal.2007, author = {Lorenz, S. and Diederichs, Elmar and Telgmann, R. and Sch{\"u}tte, Christof}, title = {Discrimination of Dynamical System Models for Biological and Chemical Processes}, volume = {28}, journal = {J. Comp. Chem.}, number = {8}, doi = {10.1002/jcc.20674}, pages = {1384 -- 1399}, year = {2007}, language = {en} } @inproceedings{HeldMeerbachHinderlichetal.2007, author = {Held, M. and Meerbach, E. and Hinderlich, S. and Reutter, W. and Sch{\"u}tte, Christof}, title = {Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity}, volume = {36}, booktitle = {From Computational Biophysics to Systems Biology}, editor = {Hansmann, U. and Meinke, J. and Mohanty, S. and Zimmermann, O.}, publisher = {John von Neumann Institut for Computing}, pages = {145 -- 148}, year = {2007}, language = {en} } @article{HorenkoHartmannSchuetteetal.2007, author = {Horenko, Illia and Hartmann, Carsten and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes}, volume = {76}, journal = {Phys. Rev. E}, number = {01}, doi = {10.1103/PhysRevE.76.016706}, pages = {016706}, year = {2007}, language = {en} } @article{FischerWaldhausenHorenkoetal.2007, author = {Fischer, Alexander and Waldhausen, S. and Horenko, Illia and Meerbach, E. and Sch{\"u}tte, Christof}, title = {Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models}, volume = {28}, journal = {J. Comp. Chem.}, number = {15}, doi = {10.1002/jcc.20692}, pages = {2453 -- 2464}, year = {2007}, language = {en} } @incollection{MeerbachSchuetteHorenkoetal.2007, author = {Meerbach, E. and Sch{\"u}tte, Christof and Horenko, Illia and Schmidt, Burkhard}, title = {Metastable Conformational Structure and Dynamics}, volume = {87}, booktitle = {Analysis and Control of Ultrafast Photoinduced Reactions}, editor = {K{\"u}hn, O. and W{\"o}ste, L.}, publisher = {Springer}, address = {Berlin}, doi = {10.1007/978-3-540-68038-3_9}, pages = {796 -- 806}, year = {2007}, language = {en} } @article{NoeSmithSchuette2007, author = {No{\´e}, Frank and Smith, J. and Sch{\"u}tte, Christof}, title = {A network-based approach to biomolecular dynamics}, volume = {NIC Series 36}, journal = {From Computational Biophysics to Systems Biology (CBSB07). Editors}, publisher = {John von Neumann Institute for Computing, J{\"u}lich}, year = {2007}, language = {en} } @article{HorenkoDittmerFischeretal.2006, author = {Horenko, Illia and Dittmer, E. and Fischer, Alexander and Sch{\"u}tte, Christof}, title = {Automated Model Reduction for Complex Systems exhibiting Metastability}, volume = {5}, journal = {Mult. Mod. Sim.}, number = {3}, doi = {10.1137/050623310}, pages = {802 -- 827}, year = {2006}, language = {en} } @inproceedings{SchuetteNettesheim1999, author = {Sch{\"u}tte, Christof and Nettesheim, Peter}, title = {Nonadiabatic Effects in Quantum-Classical Molecular Dynamics}, booktitle = {Scientific Computing in Chemical Engineering II}, editor = {Keil, F. and Mackens, W. and Voss, H. and Werther, J.}, publisher = {Springer}, pages = {42 -- 56}, year = {1999}, language = {en} } @inproceedings{NettesheimSchuette1999, author = {Nettesheim, Peter and Sch{\"u}tte, Christof}, title = {Numerical Integrators for Quantum-Classical Molecular Dynamics}, volume = {4}, booktitle = {Computational Molecular Dynamics}, editor = {Deuflhard, Peter and Hermans, J. and Leimkuhler, Benedict and Marks, A. and Reich, Sebastian and Skeel, R.}, publisher = {Springer}, pages = {396 -- 411}, year = {1999}, language = {en} } @article{BornemannSchuette1999, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {On the Singular Limit of the Quantum-Classical Molecular Dynamics Model}, volume = {59}, journal = {J. Appl. Math.}, number = {4}, doi = {10.1137/S0036139997318834}, pages = {1208 -- 1224}, year = {1999}, language = {en} } @phdthesis{Schuette1999, author = {Sch{\"u}tte, Christof}, title = {Partial Wigner transforms and the quantum-classical Liouville equation}, year = {1999}, language = {en} } @article{FischerCordesSchuette1998, author = {Fischer, Alexander and Cordes, Frank and Sch{\"u}tte, Christof}, title = {Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble}, volume = {19}, journal = {J. Comp. Chem.}, number = {15}, doi = {10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J}, pages = {1689 -- 1697}, year = {1998}, language = {en} } @article{BornemannSchuette1998, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {A mathematical investigation of the Car-Parrinello Method}, volume = {78}, journal = {Num. Math.}, number = {3}, doi = {10.1007/s002110050316}, pages = {359 -- 376}, year = {1998}, language = {en} } @article{SchuetteBornemann1997, author = {Sch{\"u}tte, Christof and Bornemann, Folkmar A.}, title = {Homogenization Approach to Smoothed Molecular Dynamics}, volume = {30}, journal = {Nonlinear Analysis}, number = {3}, doi = {10.1016/S0362-546X(97)00216-2}, pages = {1805 -- 1814}, year = {1997}, language = {en} } @article{BornemannSchuette1997, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {Homogenization of Hamiltonian Systems with a Strong Constraining Potential}, volume = {102}, journal = {Physica D}, number = {1-2}, doi = {10.1016/S0167-2789(96)00245-X}, pages = {57 -- 77}, year = {1997}, language = {en} } @article{NettesheimHuisingaSchuette1996, author = {Nettesheim, Peter and Huisinga, Wilhelm and Sch{\"u}tte, Christof}, title = {Chebyshev-Approximation for Wavepacket-Dynamics}, journal = {preprint}, year = {1996}, language = {en} } @article{NettesheimBornemannSchmidtetal.1996, author = {Nettesheim, Peter and Bornemann, Folkmar A. and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics}, volume = {256}, journal = {Chem. Phys. Lett.}, number = {6}, doi = {10.1016/0009-2614(96)00471-X}, pages = {581 -- 588}, year = {1996}, language = {en} } @article{HuisingaMeynSchuette2004, author = {Huisinga, Wilhelm and Meyn, S. and Sch{\"u}tte, Christof}, title = {Phase Transitions and Metastability in Markovian and Molecular Systems}, volume = {14}, journal = {Ann. Appl. Prob.}, number = {1}, doi = {10.1214/aoap/1075828057}, pages = {419 -- 458}, year = {2004}, language = {en} } @inproceedings{SchuetteHuisinga2003, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics}, volume = {X}, booktitle = {Special Volume}, editor = {Ciarlet, P. and Le Bris, Claude}, publisher = {Elsevier}, pages = {699 -- 744}, year = {2003}, language = {en} } @article{HuisingaSchuetteStuart2003, author = {Huisinga, Wilhelm and Sch{\"u}tte, Christof and Stuart, Andrew}, title = {Extracting Macroscopic Stochastic Dynamics}, volume = {56}, journal = {Comm. Pure Appl. Math.}, number = {2}, doi = {10.1002/cpa.10057}, pages = {234 -- 269}, year = {2003}, language = {en} } @inproceedings{SchuetteHuisingaMeyn2003, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm and Meyn, S.}, title = {Metastability of Diffusion Processes}, volume = {110}, booktitle = {Nonlinear Stochastic Dynamics}, editor = {Namachchivaya, N. and Lin, Y.}, publisher = {Springer}, pages = {71 -- 81}, year = {2003}, language = {en} } @inproceedings{FischerSchuetteDeuflhardetal.2002, author = {Fischer, Alexander and Sch{\"u}tte, Christof and Deuflhard, Peter and Cordes, Frank}, title = {Hierarchical Uncoupling-Coupling of Metastable Conformations}, volume = {24}, booktitle = {Computational Methods for Macromolecules}, editor = {Schlick, T. and Gan, H.}, publisher = {Springer}, pages = {235 -- 259}, year = {2002}, language = {en} } @article{HorenkoSchmidtSchuette2002, author = {Horenko, Illia and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions}, volume = {117}, journal = {J. Chem. Phys.}, number = {10}, doi = {10.1063/1.1498467}, pages = {4643 -- 4650}, year = {2002}, language = {en} } @article{HorenkoSalzmannSchmidtetal.2002, author = {Horenko, Illia and Salzmann, Ch. and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {Quantum-Classical Liouville Approach to Molecular Dynamics}, volume = {117}, journal = {J. Chem. Phys.}, number = {24}, doi = {10.1063/1.1522712}, pages = {11075 -- 11088}, year = {2002}, language = {en} } @article{HorenkoSchmidtSchuette2001, author = {Horenko, Illia and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {A Theoretical Model for Molecules Interacting with Intense Laser Pulses}, volume = {115}, journal = {J. Chem. Phys.}, number = {13}, doi = {10.1063/1.1398577}, pages = {5733 -- 5743}, year = {2001}, language = {en} } @inproceedings{SchuetteHuisingaDeuflhard2001, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm and Deuflhard, Peter}, title = {Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems}, booktitle = {Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems}, editor = {Fiedler, B.}, publisher = {Springer}, pages = {191 -- 223}, year = {2001}, language = {en} } @inproceedings{SchuetteHuisinga2000, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {Biomolecular Conformations as Metastable Sets of Markov Chains}, booktitle = {Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing, Monticello, Illinoins/USA}, editor = {Sreenivas, R. and Jones, D.}, publisher = {University of Illinois at Urbana-Champaign}, pages = {1106 -- 1115}, year = {2000}, language = {en} } @misc{ZhangHartmannSchuette2016, author = {Zhang, Wei and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Effective Dynamics Along Given Reaction Coordinates, and Reaction Rate Theory}, issn = {1438-0064}, doi = {10.1039/C6FD00147E}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59706}, year = {2016}, abstract = {In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: We first show that if we start with an ergodic diffusion processes whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Zwanzig-Mori, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the "equation-free" approach and the "heterogeneous multiscale method" can be seen as special cases of our approach.}, language = {en} } @misc{CiccottiFerrarioSchuette2018, author = {Ciccotti, Giovanni and Ferrario, Mauro and Sch{\"u}tte, Christof}, title = {Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere?}, volume = {20}, journal = {Special Issue: Understanding Molecular Dynamics via Stochastic Processes, Entropy}, number = {5}, doi = {10.3390/e20050348}, year = {2018}, language = {en} } @article{ZhangSchuette2017, author = {Zhang, Wei and Sch{\"u}tte, Christof}, title = {Reliable approximation of long relaxation timescales in molecular dynamics}, volume = {19}, journal = {Entropy}, number = {7}, doi = {10.3390/e19070367}, year = {2017}, language = {en} } @article{ZhangHartmannSchuette2016, author = {Zhang, Wei and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Effective dynamics along given reaction coordinates, and reaction rate theory}, journal = {Faraday Discussions}, number = {195}, doi = {10.1039/C6FD00147E}, pages = {365 -- 394}, year = {2016}, language = {en} } @article{KlebanovSikorskiSchuetteetal.2021, author = {Klebanov, Ilja and Sikorski, Alexander and Sch{\"u}tte, Christof and R{\"o}blitz, Susanna}, title = {Objective priors in the empirical Bayes framework}, volume = {48}, journal = {Scandinavian Journal of Statistics}, number = {4}, publisher = {Wiley Online Library}, doi = {10.1111/sjos.12485}, pages = {1212 -- 1233}, year = {2021}, abstract = {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.}, language = {en} } @article{HartmannRichterSchuetteetal.2017, author = {Hartmann, Carsten and Richter, Lorenz and Sch{\"u}tte, Christof and Zhang, Wei}, title = {Variational characterization of free energy: theory and algorithms}, volume = {19}, journal = {Entropy}, number = {11}, doi = {10.3390/e19110626}, pages = {626}, year = {2017}, language = {en} } @article{DibakJdelRazoDeSanchoetal.2018, author = {Dibak, Manuel and J. del Razo, Mauricio and De Sancho, David and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations}, volume = {148}, journal = {Journal of Chemical Physics}, number = {214107}, doi = {10.1063/1.5020294}, year = {2018}, abstract = {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.}, language = {en} } @article{DjurdjevacConradHelfmannZonkeretal.2018, author = {Djurdjevac Conrad, Natasa and Helfmann, Luzie and Zonker, Johannes and Winkelmann, Stefanie and Sch{\"u}tte, Christof}, title = {Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach}, volume = {7}, journal = {EPJ Data Science}, number = {1}, edition = {EPJ Data Science}, publisher = {EPJ Data Science}, doi = {10.1140/epjds/s13688-018-0153-9}, pages = {24}, year = {2018}, abstract = {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.}, language = {en} } @article{MoellerIsbilirSungkawornetal.2020, author = {M{\"o}ller, Jan and Isbilir, Ali and Sungkaworn, Titiwat and Osberg, Brenda and Karathanasis, Christos and Sunkara, Vikram and Grushevsky, Eugene O and Bock, Andreas and Annibale, Paolo and Heilemann, Mike and Sch{\"u}tte, Christof and Lohse, Martin J.}, title = {Single molecule mu-opioid receptor membrane-dynamics reveal agonist-specific dimer formation with super-resolved precision}, volume = {16}, journal = {Nature Chemical Biology}, doi = {10.1038/s41589-020-0566-1}, pages = {946 -- 954}, year = {2020}, language = {en} } @article{BittracherSchuette2021, author = {Bittracher, Andreas and Sch{\"u}tte, Christof}, title = {A probabilistic algorithm for aggregating vastly undersampled large Markov chains}, volume = {416}, journal = {Physica D: Nonlinear Phenomena}, doi = {https://doi.org/10.1016/j.physd.2020.132799}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-75874}, year = {2021}, language = {en} } @article{BittracherKlusHamzietal.2021, author = {Bittracher, Andreas and Klus, Stefan and Hamzi, Boumediene and Sch{\"u}tte, Christof}, title = {Dimensionality Reduction of Complex Metastable Systems via Kernel Embeddings of Transition Manifolds}, volume = {31}, journal = {Journal of Nonlinear Science}, doi = {10.1007/s00332-020-09668-z}, year = {2021}, abstract = {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.}, language = {en} } @article{KlusNueskePeitzetal.2020, author = {Klus, Stefan and N{\"u}ske, Feliks and Peitz, Sebastian and Niemann, Jan-Hendrik and Clementi, Cecilia and Sch{\"u}tte, Christof}, title = {Data-driven approximation of the Koopman generator: Model reduction, system identification, and control}, volume = {406}, journal = {Physica D: Nonlinear Phenomena}, doi = {10.1016/j.physd.2020.132416}, year = {2020}, language = {en} }