@article{PloentzkeBergEhrigetal.2022, author = {Pl{\"o}ntzke, Julia and Berg, Mascha and Ehrig, Rainald and Leonhard-Marek, Sabine and M{\"u}ller, Kerstin-Elisabeth and R{\"o}blitz, Susanna}, title = {Model Based Exploration of Hypokalemia in Dairy Cows}, volume = {12, 19781}, journal = {Scientific Reports}, doi = {10.1038/s41598-022-22596-0}, year = {2022}, abstract = {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.}, language = {en} } @misc{SchneckWeiserWende2019, author = {Schneck, Jakob and Weiser, Martin and Wende, Florian}, title = {Impact of mixed precision and storage layout on additive Schwarz smoothers}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-71305}, year = {2019}, abstract = {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.}, language = {en} } @article{BinkowskiZschiedrichBurger2020, author = {Binkowski, Felix and Zschiedrich, Lin and Burger, Sven}, title = {A Riesz-projection-based method for nonlinear eigenvalue problems}, volume = {419}, journal = {J. Comput. Phys.}, arxiv = {http://arxiv.org/abs/1811.11624}, doi = {10.1016/j.jcp.2020.109678}, pages = {109678}, year = {2020}, language = {en} } @misc{OatesCockaynePrangleetal.2020, author = {Oates, Chris and Cockayne, Jon and Prangle, Dennis and Sullivan, T. J. and Girolami, Mark}, title = {Optimality criteria for probabilistic numerical methods}, volume = {27}, journal = {Multivariate Algorithms and Information-Based Complexity}, editor = {Hickernell, F. J. and Kritzer, P.}, publisher = {De Gruyter}, arxiv = {http://arxiv.org/abs/1901.04326}, doi = {10.1515/9783110635461-005}, pages = {65 -- 88}, year = {2020}, abstract = {It is well understood that Bayesian decision theory and average case analysis are essentially identical. However, if one is interested in performing uncertainty quantification for a numerical task, it can be argued that the decision-theoretic framework is neither appropriate nor sufficient. To this end, we consider an alternative optimality criterion from Bayesian experimental design and study its implied optimal information in the numerical context. This information is demonstrated to differ, in general, from the information that would be used in an average-case-optimal numerical method. The explicit connection to Bayesian experimental design suggests several distinct regimes in which optimal probabilistic numerical methods can be developed.}, language = {en} } @article{KerstingSullivanHennig2020, author = {Kersting, Hans and Sullivan, T. J. and Hennig, Philipp}, title = {Convergence rates of Gaussian ODE filters}, volume = {30}, journal = {Statistics and Computing}, publisher = {Springer}, address = {Statistics and Computing}, arxiv = {http://arxiv.org/abs/1807.09737}, doi = {10.1007/s11222-020-09972-4}, pages = {1791 -- 1816}, year = {2020}, language = {en} } @article{StoopStraubeJohansenetal.2020, author = {Stoop, Ralph L. and Straube, Arthur and Johansen, Tom H. and Tierno, Pietro}, title = {Collective directional locking of colloidal monolayers on a periodic substrate}, volume = {124}, journal = {Phys. Rev. Lett.}, doi = {10.1103/PhysRevLett.124.058002}, pages = {058002}, year = {2020}, abstract = {We investigate the directional locking effects that arise when a monolayer of paramagnetic colloidal particles is driven across a triangular lattice of magnetic bubbles. We use an external rotating magnetic field to generate a two-dimensional traveling wave ratchet forcing the transport of particles along a direction that intersects two crystallographic axes of the lattice. We find that, while single particles show no preferred direction, collective effects induce transversal current and directional locking at high density via a spontaneous symmetry breaking. The colloidal current may be polarized via an additional bias field that makes one transport direction energetically preferred.}, language = {en} } @article{LieSullivanTeckentrup2021, author = {Lie, Han Cheng and Sullivan, T. J. and Teckentrup, Aretha}, title = {Error bounds for some approximate posterior measures in Bayesian inference}, journal = {Numerical Mathematics and Advanced Applications ENUMATH 2019}, publisher = {Springer}, arxiv = {http://arxiv.org/abs/1911.05669}, doi = {10.1007/978-3-030-55874-1_26}, pages = {275 -- 283}, year = {2021}, language = {en} } @article{KhorashadBesteiroCorreaDuarteetal.2020, author = {Khorashad, Larousse Khosravi and Besteiro, Lucas V. and Correa-Duarte, Miguel and Burger, Sven and Wang, Zhiming M. and Govorov, Alexander O.}, title = {Hot electrons generated in chiral plasmonic nanocrystals as a mechanism for surface photochemistry and chiral growth}, volume = {142}, journal = {J. Am. Chem. Soc.}, doi = {10.1021/jacs.9b11124}, pages = {4193}, year = {2020}, language = {en} } @article{WerdehausenBurgerStaudeetal.2020, author = {Werdehausen, Daniel and Burger, Sven and Staude, Isabelle and Pertsch, Thomas and Decker, Manuel}, title = {General design formalism for highly efficient flat optics for broadband applications}, volume = {28}, journal = {Opt. Express}, doi = {10.1364/OE.386573}, pages = {6452}, year = {2020}, language = {en} } @article{PfluegerKlineFernandezHerreroetal.2020, author = {Pfl{\"u}ger, Mika and Kline, R. Joseph and Fern{\´a}ndez Herrero, Analia and Hammerschmidt, Martin and Soltwisch, Victor and Krumrey, Michael}, title = {Extracting dimensional parameters of gratings produced with self-aligned multiple patterning using grazing-incidence small-angle x-ray scattering}, volume = {19}, journal = {J. Micro Nanolithogr. MEMS MOEMS}, arxiv = {http://arxiv.org/abs/1910.08532}, doi = {10.1117/1.JMM.19.1.014001}, pages = {014001}, year = {2020}, language = {en} } @article{GutscheSantiagoSchneideretal.2020, author = {Gutsche, Philipp and Santiago, Xavier Garcia and Schneider, Philipp-Immanuel and McPeak, Kevin and Nieto-Vesperinas, Manuel and Burger, Sven}, title = {Role of Geometric Shape in Chiral Optics}, volume = {12}, journal = {Symmetry}, arxiv = {http://arxiv.org/abs/1808.01855}, doi = {10.3390/sym12010158}, pages = {158}, year = {2020}, 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{KlebanovSchusterSullivan2020, author = {Klebanov, Ilja and Schuster, Ingmar and Sullivan, T. J.}, title = {A rigorous theory of conditional mean embeddings}, volume = {2}, journal = {SIAM Journal on Mathematics of Data Science}, number = {3}, arxiv = {http://arxiv.org/abs/1912.00671}, doi = {10.1137/19M1305069}, pages = {583 -- 606}, year = {2020}, language = {en} } @incollection{KantnerHoehneKopruckietal.2020, author = {Kantner, Markus and H{\"o}hne, Theresa and Koprucki, Thomas and Burger, Sven and W{\"u}nsche, Hans-J{\"u}rgen and Schmidt, Frank and Mielke, Alexander and Bandelow, Uwe}, title = {Multi-dimensional modeling and simulation of semiconductor nanophotonic devices}, volume = {194}, booktitle = {Semiconductor Nanophotonics}, editor = {Kneissl, Michael and Knorr, Andreas and Reitzenstein, Stephan and Hoffmann, Axel}, publisher = {Springer}, address = {Cham}, doi = {10.1007/978-3-030-35656-9_7}, pages = {241 -- 283}, year = {2020}, language = {en} } @article{TillmannJaegerBecker2020, author = {Tillmann, Peter and J{\"a}ger, Klaus and Becker, Christiane}, title = {Minimising levelised cost of electricity of bifacial solar panel arrays using Bayesian optimisation}, volume = {4}, journal = {Sustain. Energy Fuels}, doi = {10.1039/C9SE00750D}, pages = {254}, year = {2020}, language = {en} } @article{HammerschmidtDoepkingBurgeretal.2020, author = {Hammerschmidt, Martin and D{\"o}pking, Sandra and Burger, Sven and Matera, Sebastian}, title = {Field Heterogeneities and Their Impact on Photocatalysis: Combining Optical and Kinetic Monte Carlo Simulations on the Nanoscale}, volume = {124}, journal = {J. Phys. Chem. C}, doi = {10.1021/acs.jpcc.9b11469}, pages = {3177}, year = {2020}, 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{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} } @article{ManleyWaldeHagedornetal.2020, author = {Manley, Phillip and Walde, Sebastian and Hagedorn, Sylvia and Hammerschmidt, Martin and Burger, Sven and Becker, Christiane}, title = {Nanopatterned Sapphire Substrates in Deep-UV LEDs: Is there an Optical Benefit?}, volume = {28}, journal = {Opt. Express}, doi = {10.1364/OE.379438}, pages = {3619}, year = {2020}, language = {en} } @book{WinkelmannSchuette2020, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof}, title = {Stochastic Dynamics in Computational Biology}, volume = {8}, journal = {Frontiers in Applied Dynamical Systems: Reviews and Tutorials}, publisher = {Springer International Publishing}, isbn = {978-3-030-62386-9}, doi = {10.1007/978-3-030-62387-6}, year = {2020}, language = {en} } @article{OmariLangePloentzkeetal.2020, author = {Omari, Mohamed and Lange, Alexander and Pl{\"o}ntzke, Julia and R{\"o}blitz, Susanna}, title = {Model-based exploration of the impact of glucose metabolism on the estrous cycle dynamics in dairy cows}, volume = {15}, journal = {Biology Direct}, doi = {10.1186/s13062-019-0256-7}, year = {2020}, language = {en} } @article{BeckerDjurdjevacConradEseretal.2020, author = {Becker, Fabian and Djurdjevac Conrad, Natasa and Eser, Raphael A. and Helfmann, Luzie and Sch{\"u}tt, Brigitta and Sch{\"u}tte, Christof and Zonker, Johannes}, title = {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}, volume = {15}, journal = {PLOS ONE}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0241133}, pages = {1 -- 37}, year = {2020}, language = {en} } @article{GoetschelSchielaWeiser2021, author = {G{\"o}tschel, Sebastian and Schiela, Anton and Weiser, Martin}, title = {Kaskade 7 - a Flexible Finite Element Toolbox}, volume = {81}, journal = {Computers and Mathematics with Applications}, doi = {10.1016/j.camwa.2020.02.011}, pages = {444 -- 458}, year = {2021}, abstract = {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.}, language = {en} } @article{JaegerTillmannBecker2020, author = {J{\"a}ger, Klaus and Tillmann, Peter and Becker, Christiane}, title = {Detailed illumination model for bifacial solar cells}, volume = {28}, journal = {Opt. Express}, doi = {10.1364/OE.383570}, pages = {4751}, year = {2020}, language = {en} } @article{FeisBeutelKoepfleretal.2020, author = {Feis, Joshua and Beutel, Dominik and K{\"o}pfler, Julian and Santiago, Xavier Garcia and Rockstuhl, Carsten and Wegener, Martin and Fernandez-Corbaton, Ivan}, title = {Helicity-Preserving Optical Cavity Modes for Enhanced Sensing of Chiral Molecules}, volume = {124}, journal = {Phys. Rev. Lett.}, doi = {10.1103/PhysRevLett.124.033201}, pages = {033201}, year = {2020}, language = {en} } @article{WerdehausenBurgerStaudeetal.2020, author = {Werdehausen, Daniel and Burger, Sven and Staude, Isabelle and Pertsch, Thomas and Decker, Manuel}, title = {Flat optics in high numerical aperture broadband imaging systems}, volume = {22}, journal = {J. Opt.}, doi = {10.1088/2040-8986/ab8ea2}, pages = {065607}, year = {2020}, language = {en} } @article{FarchminHammerschmidtSchneideretal.2020, author = {Farchmin, Nando and Hammerschmidt, Martin and Schneider, Philipp-Immanuel and Wurm, Matthias and Bodermann, Bernd and B{\"a}r, Markus and Heidenreich, Sebastian}, title = {Efficient Bayesian inversion for shape reconstruction of lithography masks}, volume = {19}, journal = {J. Micro/Nanolith. MEMS MOEMS}, doi = {10.1117/1.JMM.19.2.024001}, pages = {024001}, year = {2020}, language = {en} } @article{BinkowskiBetzColometal.2020, author = {Binkowski, Felix and Betz, Fridtjof and Colom, R{\´e}mi and Hammerschmidt, Martin and Zschiedrich, Lin and Burger, Sven}, title = {Quasinormal mode expansion of optical far-field quantities}, volume = {102}, journal = {Phys. Rev. B}, arxiv = {http://arxiv.org/abs/2003.11305}, doi = {10.1103/PhysRevB.102.035432}, pages = {035432}, year = {2020}, language = {en} } @article{MusiałŻołnaczSrockaetal.2020, author = {Musiał, Anna and Żołnacz, Kinga and Srocka, Nicole and Kravets, Oleh and Große, Jan and Olszewski, Jacek and Poturaj, Krzysztof and Wojcik, Grzegorz and Mergo, Paweł and Kamil, Dybka and Dyrkacz, Mariusz and Dlubek, Michal and Lauritsen, Kristian and B{\"u}lter, Andreas and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Burger, Sven and Rodt, Sven and Urbanczyk, Wacław and Sek, Grzegorz and Reitzenstein, Stephan}, title = {Plug\&play fibre-coupled 73 kHz single-photon source operating in the telecom O-band}, volume = {3}, journal = {Adv. Quantum Technol.}, arxiv = {http://arxiv.org/abs/1912.10351}, doi = {10.1002/qute.202000018}, pages = {2000018}, year = {2020}, language = {en} } @article{ColomStoutBonod2020, author = {Colom, R{\´e}mi and Stout, Brian and Bonod, Nicolas}, title = {Modal Expansion of the Impulse Response Function for Predicting the Time Dynamics of Open Optical Cavities}, journal = {arXiv}, arxiv = {http://arxiv.org/abs/2004.03000}, year = {2020}, language = {en} } @book{Reuter2020, author = {Reuter, Bernhard}, title = {Generalisierte Markov-Modellierung}, publisher = {Springer Spektrum, Wiesbaden}, isbn = {978-3-658-29711-4}, doi = {10.1007/978-3-658-29712-1}, year = {2020}, abstract = {Markov State Models (MSM) sind der Goldstandard zur Modellierung biomolekularer Dynamik, da sie die Identifizierung und Analyse metastabiler Zust{\"a}nde erm{\"o}glichen. Die robuste Perron-Cluster-Cluster-Analyse (PCCA+) ist ein verbreiteter Spectral-Clustering-Algorithmus, der f{\"u}r das Clustering hochdimensionaler MSM verwendet wird. Da die PCCA+ auf reversible Prozesse beschr{\"a}nkt ist, wird sie zur Generalisierten PCCA+ (G-PCCA) verallgemeinert, die geeignet ist, nichtreversible Prozesse aufzukl{\"a}ren. Bernhard Reuter untersucht hier mittels G-PCCA die nichtthermischen Auswirkungen von Mikrowellen auf die Proteindynamik. Dazu f{\"u}hrt er molekulardynamische Nichtgleichgewichtssimulationen des Amyloid-β-(1-40)-Peptids durch und modelliert diese.}, language = {de} } @misc{Wulkow2020, type = {Master Thesis}, author = {Wulkow, Hanna}, title = {Regularization of Elliptic Partial Differential Equations using Neural Networks}, pages = {63}, year = {2020}, abstract = {This thesis presents a method for interpolating data using a neural network. The data is sparse and perturbed and is used as training data for a small neural network. For severely perturbed data, the network does not manage to find a smooth interpolation. But as the data resembles the solution to the one-dimensional and time-independent heat equation, the weak form of this PDE and subsequently its functional can be written down. If the functional is minimized, a solution to the weak form of the heat equation is found. The functional is now added to the traditional loss function of a neural network, the mean squared error between the network prediction and the given data, in order to smooth out fluctuations and interpolate between distanced grid points. This way, the network minimizes both the mean squared error and the functional, resulting in a smoother curve that can be used to predict u(x) for any grid point x.}, language = {en} } @misc{BittracherSchuette2020, author = {Bittracher, Andreas and Sch{\"u}tte, Christof}, title = {A weak characterization of slow variables in stochastic dynamical systems}, volume = {304}, journal = {Advances in Dynamics, Optimization and Computation. Series: Studies in Systems, Decision and Control. A volume dedicated to Michael Dellnitz on the occasion of his 60th birthday}, editor = {Junge, Oliver and Sch{\"u}tze, O. and Froyland, Gary and Ober-Blobaum, S. and Padberg-Gehle, E.}, publisher = {Springer International}, isbn = {978-3-030-51264-4}, doi = {10.1007/978-3-030-51264-4_6}, pages = {132 -- 150}, year = {2020}, language = {en} } @misc{MollenhauerSchusterKlusetal.2020, author = {Mollenhauer, Mattes and Schuster, Ingmar and Klus, Stefan and Sch{\"u}tte, Christof}, title = {Singular Value Decomposition of Operators on Reproducing Kernel Hilbert Spaces}, volume = {304}, journal = {Advances om Dynamics, Optimization and Computation. Series: Studies in Systems, Decision and Control. A volume dedicated to Michael Dellnitz on his 60th birthday}, editor = {Junge, Oliver and Sch{\"u}tze, O. and Froyland, Gary and Ober-Blobaum, S. and Padberg-Gehle, K.}, publisher = {Springer International}, isbn = {978-3-030-51264-4}, doi = {10.1007/978-3-030-51264-4_5}, pages = {109 -- 131}, year = {2020}, language = {en} } @incollection{RodtSchneiderZschiedrichetal.2020, author = {Rodt, Sven and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Heindel, Tobias and Bounouar, Samir and Kantner, Markus and Koprucki, Thomas and Bandelow, Uwe and Burger, Sven and Reitzenstein, Stephan}, title = {Deterministic Quantum Devices for Optical Quantum Communication}, volume = {194}, booktitle = {Semiconductor Nanophotonics}, editor = {Kneissl, Michael and Knorr, Andreas and Reitzenstein, Stephan and Hoffmann, Axel}, publisher = {Springer}, address = {Cham}, doi = {10.1007/978-3-030-35656-9_8}, pages = {285 -- 359}, year = {2020}, language = {en} } @article{GorgullaBoeszoermnyiWangetal.2020, author = {Gorgulla, Christoph and Boeszoermnyi, Andras and Wang, Zi-Fu and Fischer, Patrick D. and Coote, Paul and Das, Krishna M. Padmanabha and Malets, Yehor S. and Radchenko, Dmytro S. and Moroz, Yurii and Scott, David A. and Fackeldey, Konstantin and Hoffmann, Moritz and Iavniuk, Iryna and Wagner, Gerhard and Arthanari, Haribabu}, title = {An open-source drug discovery platform enables ultra-large virtual screens}, volume = {580}, journal = {Nature}, publisher = {Springer Nature}, doi = {https://doi.org/10.1038/s41586-020-2117-z}, pages = {663 -- 668}, year = {2020}, abstract = {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.}, language = {en} } @article{HelfmannRiberaBorrellSchuetteetal.2020, author = {Helfmann, Luzie and Ribera Borrell, Enric and Sch{\"u}tte, Christof and Koltai, Peter}, title = {Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics}, volume = {30}, journal = {Journal of Nonlinear Science}, doi = {https://doi.org/10.1007/s00332-020-09652-7}, pages = {3321 -- 3366}, year = {2020}, language = {en} } @article{NiemannWinkelmannWolfetal.2021, author = {Niemann, Jan-Hendrik and Winkelmann, Stefanie and Wolf, Sarah and Sch{\"u}tte, Christof}, title = {Agent-based modeling: Population limits and large timescales}, volume = {31}, journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}, number = {3}, issn = {1438-0064}, doi = {10.1063/5.0031373}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-77309}, year = {2021}, abstract = {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.}, language = {en} } @misc{Baumann2020, type = {Master Thesis}, author = {Baumann, Felix}, title = {Impact of Contact Surfaces on the Death Estimation}, pages = {69}, year = {2020}, abstract = {The determination of time of death is one of the central tasks in forensic medicine. A standard method of time of death estimation elies on matching temperature measurements of the corpse with a post-mortem cooling model. In addition to widely used empirical post-mortem models, modelling based on a precise mathematical simulation of the cooling process have been gaining popularity. The simulation based cooling models and the resulting time of death estimates dependon a large variety of parameters. These include hermal properties for different body tissue types, environmental conditions such as temperature and air flow, and the presence of clothing and coverings. In this thesis we focus on a specific arameter - the contact between corpse and underground - and investigate its influence on the time of death estimation. Resulting we aim to answer the question whether it is necessary to consider contact mechanics in the underlying mathematical cooling model.}, language = {en} } @article{TempLabuzNegreteetal.2019, author = {Temp, Julia and Labuz, Dominika and Negrete, Roger and Sunkara, Vikram and Machelska, Halina}, title = {Pain and knee damage in male and female mice in the medial meniscal transection-induced osteoarthritis}, journal = {Osteoarthritis and Cartilage}, doi = {10.1016/j.joca.2019.11.003}, year = {2019}, language = {en} } @misc{Semler2020, type = {Master Thesis}, author = {Semler, Phillip}, title = {Mixed finite elements in cloth simulation}, pages = {116}, year = {2020}, abstract = {This master thesis investigates the use and behaviour of a mixed finite element formulation for the simulation of garments. The garment is modelled as an isotropic shell and is related to its mid-surface by energetic degeneration. Based on this, an energy functional is constructed, which contains the deformation and the mid-surface vector as degree of freedom. It is then shown why this problem does not correspond to a saddle point problem, but to a non-convex energy minimization. The implementation of the energy minimization takes place with the ZIB-internal FE framework Kaskade7.4, whereby a geometric linear and different geometric non-linear problems are examined, whereby for a selected, non-linear example a comparison is made with an existing implementation on basis of Morley elements. The further evaluations include the analysis of the quantitative and qualitative results, the used solution method, the behaviour of the system energy as well as the used CPU time.}, language = {en} } @inproceedings{KrauseWeiser2021, author = {Krause, Rolf and Weiser, Martin}, title = {Multilevel augmented Lagrangian solvers for overconstrained contact formulations}, volume = {71}, booktitle = {ESAIM: ProcS}, doi = {10.1051/proc/202171175}, pages = {175 -- 184}, year = {2021}, abstract = {Multigrid methods for two-body contact problems are mostly based on special mortar discretizations, nonlinear Gauss-Seidel solvers, and solution-adapted coarse grid spaces. Their high computational efficiency comes at the cost of a complex implementation and a nonsymmetric master-slave discretization of the nonpenetration condition. Here we investigate an alternative symmetric and overconstrained segment-to-segment contact formulation that allows for a simple implementation based on standard multigrid and a symmetric treatment of contact boundaries, but leads to nonunique multipliers. For the solution of the arising quadratic programs, we propose augmented Lagrangian multigrid with overlapping block Gauss-Seidel smoothers. Approximation and convergence properties are studied numerically at standard test problems.}, language = {en} } @misc{MusiałŻołnaczSrockaetal.2020, author = {Musiał, Anna and Żołnacz, Kinga and Srocka, Nicole and Kravets, Oleh and Große, Jan and Olszewski, Jacek and Poturaj, Krzysztof and Wojcik, Grzegorz and Mergo, Paweł and Dybka, Kamil and Dyrkacz, Mariusz and Dlubek, Michal and Lauritsen, Kristian and B{\"u}lter, Andreas and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Burger, Sven and Rodt, Sven and Urbanczyk, Wacław and Sek, Grzegorz and Reitzenstein, Stephan}, title = {Front Cover: Plug\&Play Fiber-Coupled 73 kHz Single-Photon Source Operating in the Telecom O-Band (Adv. Quantum Technol. 6/2020)}, volume = {3}, journal = {Adv. Quantum Technol.}, doi = {10.1002/qute.202070061}, pages = {2070061}, year = {2020}, language = {en} } @article{MartensBinkowskiNguyenetal.2021, author = {Martens, Kevin and Binkowski, Felix and Nguyen, Linh and Hu, Li and Govorov, Alexander O. and Burger, Sven and Liedl, Tim}, title = {Long- and Short-Ranged Chiral Interactions in DNA Assembled Plasmonic Chains}, volume = {12}, journal = {Nat. Commun.}, arxiv = {http://arxiv.org/abs/2010.12072}, doi = {10.1038/s41467-021-22289-8}, pages = {2025}, year = {2021}, language = {en} } @article{GorgullaFackeldeyWagneretal.2020, author = {Gorgulla, Christoph and Fackeldey, Konstantin and Wagner, Gerhard and Arthanari, Haribabu}, title = {Accounting of Receptor Flexibility in Ultra-Large Virtual Screens with VirtualFlow Using a Grey Wolf Optimization Method}, volume = {7}, journal = {Supercomputing Frontiers and Innovations}, number = {3}, doi = {10.14529/jsfi200301}, pages = {4 -- 12}, year = {2020}, abstract = {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.}, language = {en} } @article{KostreSchuetteNoeetal.2021, author = {Kostre, Margarita and Sch{\"u}tte, Christof and No{\´e}, Frank and del Razo Sarmina, Mauricio}, title = {Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs}, volume = {19}, journal = {Multiscale Modeling \& Simulation}, number = {4}, publisher = {Society for Industrial and Applied Mathematics}, arxiv = {http://arxiv.org/abs/2006.00003}, doi = {10.1137/20M1352739}, pages = {1659 -- 1683}, year = {2021}, abstract = {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.}, language = {en} } @misc{BittracherSchuette2020, author = {Bittracher, Andreas and Sch{\"u}tte, Christof}, title = {A probabilistic algorithm for aggregating vastly undersampled large Markov chains}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-78688}, year = {2020}, abstract = {Model reduction of large Markov chains is an essential step in a wide array of techniques for understanding complex systems and for efficiently learning structures from high-dimensional data. We present a novel aggregation algorithm for compressing such chains that exploits a specific low-rank structure in the transition matrix which, e.g., is present in metastable systems, among others. It enables the recovery of the aggregates from a vastly undersampled transition matrix which in practical applications may gain a speedup of several orders of mag- nitude over methods that require the full transition matrix. Moreover, we show that the new technique is robust under perturbation of the transition matrix. The practical applicability of the new method is demonstrated by identifying a reduced model for the large-scale traffic flow patterns from real-world taxi trip data.}, language = {en} } @article{PakhomovLoechnerZschiedrichetal.2020, author = {Pakhomov, Anton and L{\"o}chner, Franz and Zschiedrich, Lin and Saravi, Sina and Hammerschmidt, Martin and Burger, Sven and Pertsch, Thomas and Setzpfand, Frank}, title = {Far-field polarization signatures of surface optical nonlinearity in noncentrosymmetric semiconductors}, volume = {10}, journal = {Sci. Rep.}, doi = {10.1038/s41598-020-67186-0}, pages = {10545}, year = {2020}, language = {en} } @article{WerdehausenSantiagoBurgeretal.2020, author = {Werdehausen, Daniel and Santiago, Xavier Garcia and Burger, Sven and Staude, Isabelle and Pertsch, Thomas and Rockstuhl, Carsten and Decker, Manuel}, title = {Modeling Optical Materials at the Single Scatterer Level: The Transition from Homogeneous to Heterogeneous Materials}, volume = {3}, journal = {Adv. Theory Simul.}, doi = {10.1002/adts.202000192}, pages = {2000192}, year = {2020}, language = {en} } @article{BoltzSirbuStelzeretal.2021, author = {Boltz, Horst-Holger and Sirbu, Alexei and Stelzer, Nina and Lohse, Martin J. and Sch{\"u}tte, Christof and Annibale, Paolo}, title = {Quantitative spectroscopy of single molecule interaction times}, volume = {46}, journal = {Optic Letters}, number = {7}, doi = {10.1364/OL.413030}, pages = {1538 -- 1541}, year = {2021}, abstract = {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.}, language = {en} } @article{VillatoroZuehlkeRiebeetal.2020, author = {Villatoro, Jos{\´e} and Z{\"u}hlke, Martin and Riebe, Daniel and Beitz, Toralf and Weber, Marcus and L{\"o}hmannsr{\"o}ben, Hans-Gerd}, title = {Sub-ambient pressure IR-MALDI ion mobility spectrometer for the determination of low and high field mobilities}, volume = {412}, journal = {Analytical and Bioanalytical Chemistry}, doi = {10.1007/s00216-020-02735-0}, pages = {5247 -- 5260}, year = {2020}, abstract = {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.}, language = {en} }