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Group by: Date | Item Type Number of items: 199. 2024Gaskin, Thomas and Conrad, T. O. F. and Pavliotis, Grigorios A. and Schütte, Ch. (2024) Neural parameter calibration and uncertainty quantification for epidemic forecasting. PLoS ONE, 19 (10). ISSN 1932-6203 2023Bittracher, Andreas and Mollenhauer, Mattes and Koltai, Péter and Schütte, Ch. (2023) Optimal Reaction Coordinates: Variational Characterization and Sparse Computation. Multiscale Modeling & Simulation, 21 (2). ISSN ISSN (print): 1540-3459 ISSN (online): 1540-3467 2021Helfmann, Luzie and Heitzig, Jobst and Koltai, Péter and Kurths, Jürgen and Schütte, Ch. (2021) Statistical analysis of tipping pathways in agent-based models. The European Physical Journal Special Topics . ISSN 1951-6355 Wulkow, Hanna and Conrad, T. O. F. and Djurdjevac Conrad, Natasa and Mueller, Sebastian Alexander and Nagel, Kai and Schütte, Ch. (2021) Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts. PLoS ONE, 16 (4). ISSN 1932-6203 Helfmann, L. and Djurdjevac Conrad, N. and Djurdjevac, A. and Winkelmann, S. and Schütte, Ch. (2021) From interacting agents to density-based modeling with stochastic PDEs. Commun. Appl. Math. Comput. Sci., 16 (1). pp. 1-32. ISSN Online: 2157-5452; Print: 1559-3940 Wulkow, Niklas and Koltai, Péter and Schütte, Ch. (2021) Memory-Based Reduced Modelling and Data-Based Estimation of Opinion Spreading. Journal of Nonlinear Science, 31 . ISSN 1432-1467 (online) 2019Zhang, W. and Klus, S. and Conrad, T. O. F. and Schütte, Ch. (2019) Learning chemical reaction networks from trajectory data. SIAM Journal on Applied Dynamical Systems, 18 (4). ISSN 1536-0040 Hartmann, C. and Schütte, Ch. and Zhang, W. (2019) Jarzysnki equality, fluctuation theorems and variance reduction: Mathematical analysis and numerical algorithms. J. Stat. Phys., 175 (6). pp. 1214-1261. ISSN 0022-4715; ESSN: 1572-9613 Gupta, P. and Peter, S. and Jung, M. and Lewin, A. and Hemmrich-Stanisak, G. and Franke, A. and von Kleist, M. and Schütte, Ch. and Einspanier, R. and Sharbati, S. and zur Bruegge, J. (2019) Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Sci. Rep., 9 (1571). ISSN 2045-2322 Shao, Borong and Bjaanæs, Maria and Helland, Åslaug and Schütte, Ch. and Conrad, T. O. F. (2019) EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma. PLoS ONE, 14 (1). ISSN 1932-6203 2018Djurdjevac, N. and Helfmann, L. and Zonker, J. and Winkelmann, S. and Schütte, Ch. (2018) Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach. EPJ Data Science, 7 (1). p. 24. Ciccotti, G. and Ferrario, M. and Schütte, Ch. (2018) Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere? Entropy (Special Issue), 20 (5). p. 348. ISSN 1099-4300 Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2018) Tensor-based dynamic mode decomposition. Nonlinearity, 31 (7). pp. 3359-3380. ISSN 0951-7715 Dibak, M. and del Razo, M.J. and De Sancho, D. and Schütte, Ch. and Noé, F. (2018) MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations. Journal of Chemical Physics, 148 (214107). ISSN 0021-9606 Bittracher, A. and Koltai, P. and Klus, S. and Banisch, R. and Dellnitz, M. and Schütte, Ch. (2018) Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics. Journal of Nonlinear Science, 28 (2). pp. 471-512. ISSN 1432-1467 (online) Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W. (2018) Importance sampling in path space for diffusion processes with slow-fast variables. Probab. Theory Rel. Fields, 170 (1-2). pp. 177-228. ISSN 0178-8051 (print) 1432-2064 (online) Koltai, P. and Wu, H. and Noé, F. and Schütte, Ch. (2018) Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics. Computation, 6(1) (22). ISSN 2079-3197 (online) von Kleist, M. and Schütte, Ch. and Zhang, W. (2018) Statistical Analysis of the First Passage Path Ensemble of Jump Processes. Journal of Statistical Physics, 170 (4). pp. 809-843. Klus, S. and Nüske, F. and Koltai, P. and Wu, H. and Kevrekidis, I. and Schütte, Ch. and Noé, F. (2018) Data-driven model reduction and transfer operator approximation. Journal of Nonlinear Science, 28 (1). pp. 1-26. Djurdjevac, N. and Fuerstenau, D. and Grabundzija, A. and Helfmann, L. and Park, M. and Schier, W. and Schütt, B. and Schütte, Ch. and Weber, M. and Wulkow, N. and Zonker, J. (2018) Mathematical Modeling of the Spreading of Innovations in the Ancient World. eTopoi. Journal for Ancient Studies, 7 . ISSN 2192-2608 Koltai, P. and Schütte, Ch. (2018) A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 16 (4). pp. 1455-1485. ISSN 1540-3459 2017Hartmann, C. and Richter, L. and Schütte, Ch. and Zhang, W. (2017) Variational characterization of free energy: theory and algorithms. Entropy (Special Issue), 19 (11). pp. 1-27. ISSN 1099-4300 Bittracher, A. and Koltai, P. and Klus, S. and Banisch, R. and Dellnitz, M. and Schütte, Ch. (2017) Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Koltai, P. and Schütte, Ch. (2017) A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics. ZIB-Report . ISSN 1438-0064 Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18. Gelß, P. and Klus, S. and Matera, S. and Schütte, Ch. (2017) Nearest-neighbor interaction systems in the tensor-train format. Journal of Computational Physics, 341 . pp. 140-162. ISSN 0021-9991 Conrad, T. O. F. and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Vybiral, Jan and Kutyniok, Gitta and Schütte, Ch. (2017) Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. BMC Bioinformatics, 18 (160). ISSN 1471-2105 Weber, M. and Fackeldey, K. and Schütte, Ch. (2017) Set-free Markov state model building. Journal of Chemical Physics, 146 (12). p. 124133. Huttary, R. and Goubergrits, L. and Schütte, Ch. and Bernhard, S. (2017) Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling. Computers in Biology and Medicine . ISSN 0010-4825 (In Press) Gupta, Pooja and Gramatke, A and Einspanier, R and Schütte, Ch. and von Kleist, M. and Sharbati, J (2017) In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements. Toxicology in Vitro, 41 . pp. 179-188. ISSN 08872333 Zhang, W. and Schütte, Ch. (2017) Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics. Entropy, 19 (7). p. 367. Benn, A. and Hiepen, C. and Osterland, M. and Schütte, Ch. and Zwijsen, A. and Knaus, P. (2017) Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence. FASEB Journal, 31 (11). pp. 4720-4733. Rüdrich, S. and Sarich, M. and Schütte, Ch. (2017) Utilizing hitting times for finding metastable sets in non-reversible Markov chains. Journal of Comp. Dynamics . (In Press) 2016Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107. Koltai, P. and Ciccotti, G. and Schütte, Ch. (2016) On metastability and Markov state models for non-stationary molecular dynamics. Journal of Chemical Physics, 145 (17). p. 174103. Klus, S. and Schütte, Ch. (2016) Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics . ISSN 2158-2491 Djurdjevac, N. and Weber, M. and Schütte, Ch. (2016) Finding dominant structures of nonreversible Markov processes. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 14 (4). pp. 1319-1340. ISSN 1540-3459 Hartmann, C. and Schütte, Ch. and Zhang, W. (2016) Model reduction algorithms for optimal control and importance sampling of diffusions. Nonlinearity, 29 (8). pp. 2298-2326. ISSN 0951-7715 Zhang, W. and Hartmann, C. and Schütte, Ch. (2016) Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday discussions, 195 . pp. 365-394. ISSN 1359-6640 Gelß, P. and Matera, S. and Schütte, Ch. (2016) Solving the master equation without kinetic Monte Carlo: tensor train approximations for a CO oxidation model. Journal of Computational Physics, 314 . pp. 489-502. ISSN 0021-9991 Klus, S. and Koltai, P. and Schütte, Ch. (2016) On the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics, 3 (1). pp. 51-79. ISSN 2158-2491 Vega del Valle, I. and Schütte, Ch. and Conrad, T. O. F. (2016) Finding metastable states in real-world time series with recurrence networks. Physica A, 445 . Djurdjevac, N. and Weber, M. and Schütte, Ch. (2016) Finding dominant structures of nonreversible Markov processes. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 14 (4). pp. 1319-1340. ISSN 1540-3459 Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2016) Tensor-based dynamic mode decomposition. SIAM Journal on Scientific Computing . ISSN ISSN 1064-8275 (print); 1095-7197 (electronic) (Submitted) 2015Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606 Kryven, I. and Röblitz, S. and Schütte, Ch. (2015) Solution of the chemical master equation by radial basis functions approximation with interface tracking. BMC Systems Biology, 9 (67). ISSN 1752-0509 Banisch, Ralf and Djurdjevac, N. and Schütte, Ch. (2015) Reactive flows and unproductive cycles in irreversible Markov chains. The European Physical Journal Special Topics, 224 (12). pp. 2369-2387. ISSN 1951-6355 Schütte, Ch. and Sarich, M. (2015) A critical appraisal of Markov state models. The European Physical Journal Special Topics, 224 (12). pp. 2445-2462. ISSN 1951-6355 Djurdjevac, N. and Banisch, Ralf and Schütte, Ch. (2015) Modularity of Directed Networks: Cycle Decomposition Approach. Journal of Computational Dynamics, 2 (1). pp. 1-24. ISSN 2158-2491 Duwal, S. and Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2015) Optimal treatment strategies in the context of 'treatment for prevention' against HIV-1 in resource-poor settings. PLOS Computational Biology, 11 . e1004200. Schütte, Ch. and Wang, H. (2015) Building Markov State Models for Periodically Driven Non-Equilibrium Systems. Journal of Chemical Theory and Computation, 11 (4). pp. 1819-1831. ISSN 1549-9618 Schütte, Ch. and Sarich, M. (2015) A Critical Appraisal of Markov State Models. SFB 1114 Preprint, 15-18 . ISSN 1438-0064 Schütte, Ch. and Nielsen, A. and Weber, M. (2015) Markov state models and molecular alchemy. Molecular Physics, 113 (1). pp. 69-78. ISSN 0026-8976 Yousef, K. P. and Streck, A. and Schütte, Ch. and Siebert, H. and Hengge, R. and von Kleist, M. (2015) Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. BMC Systems Biology, 9 . p. 39. ISSN 1752-0509 2014Hartmann, C. and Banisch, Ralf and Sarich, M. and Badowski, T. and Schütte, Ch. (2014) Characterization of Rare Events in Molecular Dynamics. In: Molecular Dynamics Simulation. MDPI AG, Basel, pp. 222-249. ISBN 978-3-906980-65-2 Sarich, M. and Banisch, Ralf and Hartmann, C. and Schütte, Ch. (2014) Markov State Models for Rare Events in Molecular Dynamics. In: Molecular Dynamics Simulation. MDPI AG, Basel, pp. 250-279. ISBN 978-3-906980-65-2 Ciccotti, G. and Ferrario, M. and Schütte, Ch. (2014) Molecular Dynamics Simulation. MDPI AG, Basel. ISBN 978-3-906980-65-2 Sarich, M. and Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2014) Modularity revisited: A novel dynamics-based concept for decomposing complex networks. Journal of Computational Dynamics, 1 (1). pp. 191-212. ISSN 2158-2491 Bockmayr, A. and Siebert, H. and Röblitz, S. and Schütte, Ch. and Deuflhard, P. (2014) Advanced mathematical modeling in systems biology. In: MATHEON : mathematics for key technologies. EMS series in industrial and applied mathematics, 1 . EMS Publishing House, Zürich, pp. 22-44. ISBN 978-3-03719-137-8 Schütte, Ch. and Deuflhard, P. and Noé, F. and Weber, M. (2014) Design of functional molecules. In: MATHEON : mathematics for key technologies. EMS series in industrial and applied mathematics, 1 . EMS Publishing House, Zürich, pp. 49-65. ISBN 978-3-03719-137-8 Schütte, Ch. and Deuflhard, P. (2014) Life sciences. In: MATHEON : mathematics for key technologies. EMS series in industrial and applied mathematics, 1 . EMS Publishing House, Zürich, pp. 1-6. ISBN 978-3-03719-137-8 Deuflhard, P. and Grötschel, M. and Hömberg, D. and Horst, U. and Kramer, J. and Mehrmann, V. and Polthier, K. and Schmidt, F. and Schütte, Ch. and Skutella, M. and Sprekels, J., eds. (2014) MATHEON: mathematics for key technologies. EMS Series in Industrial and Applied Mathematics, 1 . EMS Publishing House, Zürich. ISBN 978-3-03719-137-8 Schütte, Ch. and Conrad, T. O. F. (2014) Showcase 3: Information-based medicine. In: MATHEON : mathematics for key technologies. EMS Series in Industrial and Applied Mathematics, 1 . EMS Publishing House, Zürich, pp. 66-67. ISBN 978-3-03719-137-8 Wang, H. and Schütte, Ch. and Ciccotti, G. and Delle Site, L. (2014) Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation. Journal of Chemical Theory and Computation, 10 (4). pp. 1376-1386. ISSN 1549-9618 Zhang, W. and Wang, H. and Hartmann, C. and Weber, M. and Schütte, Ch. (2014) Applications of the cross-entropy method to importance sampling and optimal control of diffusions. SIAM J. Sci. Comput., 36 (6). A2654-A2672. ISSN 1064-8275 Agarwal, A. and Wang, H. and Schütte, Ch. and Delle Site, L. (2014) Chemical potential of liquids and mixtures via Adaptive Resolution Simulation. Journal of Chemical Physics, 141 (3). ISSN 0021-9606 Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2014) Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1. Communications in Mathematical Sciences, 12 (5). pp. 859-877. ISSN 1539-6746 Sarich, M. and Prinz, J.-H. and Schütte, Ch. (2014) Markov Model Theory. In: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology, 797 (797). Springer, Dordrecht, Heidelberg, New York, London, pp. 23-44. ISBN 978-94-007-7605-0 Lie, Han Cheng and Schütte, Ch. and Hartmann, C. (2014) Martingale-based gradient descent algorithm for estimating free energy values of diffusions. SIAM J. Sci. Comput. . ISSN 1064-8275 (Submitted) 2013Hartmann, C. and Banisch, Ralf and Sarich, M. and Badowski, T. and Schütte, Ch. (2013) Characterization of Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 350-376. ISSN 1099-4300 Schütte, Ch. and Sarich, M. (2013) Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches. Courant Lecture Notes, 24 . American Mathematical Society. ISBN 0821843591 Paulus, F. and Weiss, M. E. R. and Steinhilber, D. and Nikitin, A. and Schütte, Ch. and Haag, R. (2013) Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights. Macromolecules, 46 (21). pp. 8458-8466. ISSN 0024-9297 Wang, H. and Hartmann, C. and Schütte, Ch. (2013) Linear response theory and optimal control for a molecular system under nonequilibrium conditions. Molecular Physics, 111 . pp. 3555-3564. ISSN 0026-8976 Nikitin, A. and Wulkow, M. and Schütte, Ch. (2013) Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique. Macromolecular Theory and Simulation, 22 (9). pp. 475-489. Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study. Molecular Physics, 111 (22-23). pp. 3363-3371. ISSN 0026-8976 Rath, B. A. and Yousef, K. P. and Katzenstein, D. K. and Shafer, R. W. and Schütte, Ch. and von Kleist, M. and Merigan, T. C. (2013) In vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PLoS ONE, 8 (4). e61102. ISSN 1932-6203 Sarich, M. and Banisch, Ralf and Hartmann, C. and Schütte, Ch. (2013) Markov State Models for Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 258-286. ISSN 1099-4300 Wang, H. and Hartmann, C. and Schütte, Ch. and Delle Site, L. (2013) Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique. Phys. Rev. X, 3 . 011018. Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2013) Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. International Journal of Biomathematics and Biostatistics, 2 (1). ISSN 0973-7340 Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent coarse-grained model of peptides. Soft Matter, 9 (26). pp. 6118-6127. 2012Hartmann, C. and Schütte, Ch. (2012) Efficient rare event simulation by optimal nonequilibrium forcing. J. Stat. Mech. Theor. Exp., 2012 . P11004. Sarich, M. and Schütte, Ch. (2012) Approximating Selected Non-dominant Timescales by Markov State Models. Comm. Math. Sci., 10 (3). pp. 1001-1013. Wang, H. and Schütte, Ch. and Zhang, P. (2012) Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems. Phys. Rev. E, 86 (02). 026704. Schütte, Ch. and Winkelmann, S. and Hartmann, C. (2012) Optimal control of molecular dynamics using Markov state models. Math. Program. (Series B), 134 (1). pp. 259-282. Wang, H. and Zhang, P. and Schütte, Ch. (2012) On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems. J. Chem. Theo. Comp., 8 (9). pp. 3243-3256. Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203 Weiss, M. E. R. and Paulus, F. and Steinhilber, D. and Nikitin, A. and Haag, R. and Schütte, Ch. (2012) Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures. MACROMOLECULAR THEORY and SIMULATIONS, 21 (7). pp. 470-481. Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2012) Random Walks on Complex Modular Networks. Journal of Numerical Analysis, Industrial and Applied Mathematics, 6 (1-2). pp. 29-50. ISSN 1790–8140 Wang, H. and Schütte, Ch. and Delle Site, L. (2012) Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. J. Chem. Theo. Comp., 8 (8). pp. 2878-2887. Senne, M. and Trendelkamp-Schroer, B. and Mey, A.S.J.S. and Schütte, Ch. and Noé, F. (2012) EMMA - A software package for Markov model building and analysis. Journal of Chemical Theory and Computation, 8 . pp. 2223-2238. Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2012) Estimating the eigenvalue error of Markov State Models. Multiscale Modeling & Simulation, 10 (1). pp. 61-81. Menz, S. and Latorre, J.C. and Schütte, Ch. and Huisinga, W. (2012) Hybrid Stochastic–Deterministic Solution of the Chemical Master Equation. SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS), 10 (4). pp. 1232-1262. Duwal, S. and Schütte, Ch. and von Kleist, M. (2012) Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. PLoS One, 7 (7). e40382. von Kleist, M. and Metzner, Ph. and Marquet, R. and Schütte, Ch. (2012) Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection. Plos Computational Biology, 8 (1). e1002359. Meerbach, E. and Latorre, J.C. and Schütte, Ch. (2012) Sequential Change Point Detection in Molecular Dynamics Trajectories. Multicale Model. Sim., 10 (4). pp. 1263-1291. 2011Schäfer-Bung, B. and Hartmann, C. and Schmidt, B. and Schütte, Ch. (2011) Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems. J. Chem. Phys., 135 (1). 014112. Schütte, Ch. and Noé, F. and Lu, Jianfeng and Sarich, M. and Vanden-Eijnden, E. (2011) Markov State Models Based on Milestoning. J. Chem. Phys., 134 (20). p. 204105. Prinz, J.-H. and Wu, H. and Sarich, M. and Keller, B. and Senne, M. and Held, M. and Chodera, J. D. and Schütte, Ch. and Noé, F. (2011) Markov models of molecular kinetics: Generation and Validation. J. Chem. Phys., 134 . p. 174105. von Kleist, M. and Menz, S. and Stocker, H. and Arasteh, K. and Huisinga, W. and Schütte, Ch. (2011) HIV Quasispecies Dynamics during Pro-active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs. Plos One, 6 (3). e18204. Frank, M. and von Kleist, M. and Kunz, A. and Harms, G. and Schütte, Ch. and Kloft, Ch. (2011) Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1: A combined pharmacokinetic, pharmaco- and viral dynamic analysis to predict clinical outcomes. Antimicrob. Agents Chemother., 55 (12). pp. 5529-5540. Bernhard, S. and Al Zoukra, K. and Schütte, Ch. (2011) Statistical parameter estimation and signal classification in cardiovascular diagnosis. In: Modelling in Medicine and Biology. WIT Transactions on Biomedicine and Health, IX (15). WIT Press, Southampton & Boston. ISBN 978-1-84564-546-5 Latorre, J.C. and Metzner, Ph. and Hartmann, C. and Schütte, Ch. (2011) A Structure-preserving numerical discretization of reversible diffusions. Commun. Math. Sci., 9 (4). pp. 1051-1072. 2010Metzner, Ph. and Weber, M. and Schütte, Ch. (2010) Observation Uncertainty in Reversible Markov Chains. Phys. Rev. E, 82 (3). 031114. Bernhard, S. and Al Zoukra, K. and Schütte, Ch. (2010) From non-invasive hemodynamic measurements towards patient-specific cardiovascular diagnosis. In: Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine. Hershey, PA: Medical Information Science Reference. (Submitted) Diederichs, E. and Juditski, A. and Spokoiny, V. and Schütte, Ch. (2010) Sparse Non-Gaussian Component Analysis. IEEE Transactions on Information Theory, 56 (6). pp. 3033-3047. ISSN 0018-9448 Horenko, I. and Schütte, Ch. (2010) On metastable conformational analysis of non-equilibrium biomolecular time series. Multiscale Modeling & Simulation, 8 (2). pp. 701-716. ISSN 15403467 Hartmann, C. and Vulcanov, V.-M. and Schütte, Ch. (2010) Balanced Truncation of Second Order Systems: a Hamiltonian approach. Multiscale Model. Simul., 8 (4). pp. 1348-1367. Latorre, J.C. and Hartmann, C. and Schütte, Ch. (2010) Free energy computation by controlled Langevin processes. Procedia Computer Science, 1 (1). pp. 1591-1600. Schütte, Ch. and Wulkow, M. (2010) A Hybrid Galerkin–Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics. Macromol. React. Eng., 4 (9-10). pp. 562-577. Marsalek, O. and Frigato, T. and VandeVondele, J. and Bradforth, P. E. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2010) Hydrogen Forms in Water by Proton Transfer to a Distorted Electron. J. Phys. Chem. B, 114 (2). pp. 915-920. Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2010) On Markov State Models for Metastable Processes. In: ICM 2010. Sarich, M. and Noé, F. and Schütte, Ch. (2010) On the Approximation Quality of Markov State Models. Multiscale Model. Simul., 8 (4). pp. 1154-1177. Hartmann, C. and Schütte, Ch. and Ciccotti, G. (2010) On the linear response of mechanical systems with constraints. J. Chem. Phys., 132 (11). p. 111103. Sarich, M. and Schütte, Ch. and Vanden-Eijnden, E. (2010) Optimal Fuzzy Aggregation of Networks. Multiscale Modeling and Simulation, 8 (4). pp. 1535-1561. 2009Noé, F. and Schütte, Ch. and Vanden-Eijnden, E. and Reich, L. and Weikl, T. (2009) Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106 (45). pp. 19011-19016. Schütte, Ch. and Jahnke, T. (2009) Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation. Mathematical Modelling and Numerical Analysis (ESAIM), 43 (4). pp. 721-742. Schütte, Ch. and Noé, F. and Meerbach, E. and Metzner, Ph. and Hartmann, C. (2009) Conformation Dynamics. Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), . pp. 297-335. Fiedler, G. M. and Leichtle, A. and Kase, J. and Baumann, S. and Ceglarek, U. and Felix, K. and Conrad, T. O. F. and Witzigmann, H. and Weimann, A. and Schütte, Ch. and Hauss, J. and Büchler, M. and Thiery, J. (2009) Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer. Clinical Cancer Research, 15 (11). pp. 3812-3819. ISSN 1078-0432 Hartmann, C. and Schütte, Ch. and Kalibaeva, G. and Di Pierro, M. and Ciccotti, G. (2009) Fast Simulation of Polymer Chains. J. Chem. Phys., 130 . p. 144101. Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2009) Transition Path Theory for Markov Jump Processes. Mult. Mod. Sim., 7 (3). pp. 1192-1219. Gräfe, Ch. and Nordmeier, V. and Schütte, Ch. (2009) Computerspiel zum Thema Moleküldynamik für Schüler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels. Jahrestagung 2008 der GDCP (Gesellschaft für Didaktik der Chemie und Physik), 1 . pp. 77-79. ISSN 978-3-643-10010-8 Metzner, Ph. and Noé, F. and Schütte, Ch. (2009) Estimating the Sampling Error: Distribution of Transition Matrices and Functions of Transition Matrices for Given Trajectory Data. Phys. Rev. E, 80 (2). 021106. Gräfe, Ch. and Schütte, Ch. and Nordmeier, V. (2009) "Learner as creator" - SchülerInnen generieren eigene Lernspiele. In: Didaktik der Physik - Bochum 2009. Lehmanns Media, Berlin. ISBN 978-3-86541-371-0 2008Frigato, T. and VandeVondele, J. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2008) Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion: From an Interior to a Surface Located Excess Electron via a Delocalized State. J. Phys. Chem. A, 112 (27). pp. 6125-6133. Horenko, I. and Klein, R. and Dolaptchiev, S. and Schütte, Ch. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model reduction for Time Series Analysis. Mult. Mod. Sim., 6 (4). pp. 1125-1145. Hartmann, C. and Schütte, Ch. (2008) Balancing of partially-observed stochastic differential equations. 47th IEEE Conference on Decision and Control . pp. 4867-4872. Horenko, I. and Schütte, Ch. (2008) Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications. Adv. Data Anal. Class., submitted . (Submitted) Horenko, I. and Schütte, Ch. (2008) Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics. Mult. Mod. Sim., 7 (2). pp. 731-773. Horenko, I. and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Schütte, Ch. (2008) Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA. J. Appl. Dyn. Syst., 7 (2). pp. 532-560. Meerbach, E. and Schütte, Ch. (2008) Sequential Change Point Detection in Molecular Dynamics Trajectories. Journal of Multivariate Analysis, submitted . Gräfe, Ch. and Schütte, Ch. and Nordmeier, V. (2008) Spielend lernen - ein Online-Computerspiel zur Moleküldynamik. In: Didaktik der Physik – Berlin 2008. Lehmanns Media, Berlin. 2007Metzner, Ph. and Horenko, I. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time. Phys. Rev. E, 76 (06). 066702. Metzner, Ph. and Dittmer, E. and Jahnke, T. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes. J. Comp. Phys., 227 (1). pp. 353-375. Noé, F. and Horenko, I. and Schütte, Ch. and Smith, J. C. (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J. Chem. Phys., 126 (15). p. 155102. Hartmann, C. and Schütte, Ch. (2007) Comment on Two Distinct Notions of Free Energy. Physica D, 228 (1). pp. 59-63. Lorenz, S. and Diederichs, E. and Telgmann, R. and Schütte, Ch. (2007) Discrimination of Dynamical System Models for Biological and Chemical Processes. J. Comp. Chem., 28 (8). pp. 1384-1399. Held, M. and Meerbach, E. and Hinderlich, S. and Reutter, W. and Schütte, Ch. (2007) Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity. In: From Computational Biophysics to Systems Biology. Horenko, I. and Hartmann, C. and Schütte, Ch. and Noé, F. (2007) Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes. Phys. Rev. E, 76 (01). 016706. Fischer, A. and Waldhausen, S. and Horenko, I. and Meerbach, E. and Schütte, Ch. (2007) Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models. J. Comp. Chem., 28 (15). pp. 2453-2464. Meerbach, E. and Schütte, Ch. and Horenko, I. and Schmidt, B. (2007) Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution. In: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics, 87 . Springer, Berlin, pp. 796-806. Noé, F. and Smith, J. C. and Schütte, Ch. (2007) A network-based approach to biomolecular dynamics. From Computational Biophysics to Systems Biology (CBSB07). Editors: U. H. E. Hansmann, J. Meinke, S. Mohanty and O. Zimmermann, NIC Se . 2006Horenko, I. and Dittmer, E. and Fischer, A. and Schütte, Ch. (2006) Automated Model Reduction for Complex Systems exhibiting Metastability. Mult. Mod. Sim., 5 (3). pp. 802-827. Conrad, T. O. F. and Leichtle, A. and Hagehülsmann, A. and Diederichs, E. and Baumann, S. and Thiery, J. and Schütte, Ch. (2006) Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level. Lecture Notes in Computer Science, 4216 . pp. 119-128. Walter, J. and Schütte, Ch. (2006) Conditional Averaging for Diffusive Fast-Slow Systems: A Sketch for Derivation. In: Analysis, Modeling and Simulation of Multiscale Problems. Dellnitz, M. and Molo, M. and Metzner, Ph. and Preis, R. and Schütte, Ch. (2006) Graph Algorithms for Dynamical Systems. In: Analysis, Modeling and Simulation of Multiscale Problems. Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2006) Illustration of Transition Path Theory on a Collection of Simple Examples. J. Chem. Phys., 125 (8). 084110. Meerbach, E. and Dittmer, E. and Horenko, I. and Schütte, Ch. (2006) Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States. In: Computer Simulations in Condensed Matter: Systems: From Materials to Chemical Biology. Volume I. Horenko, I. and Schmidt-Ehrenberg, J. and Schütte, Ch. (2006) Set-Oriented Dimension Reduction: Localizing Principal Component Analysis via Hidden Markov Models. In: Computational Life Sciences II. 2005Horenko, I. and Lorenz, S. and Schütte, Ch. and Huisinga, W. (2005) Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics. J. Comp. Chem., 26 (9). pp. 941-948. Hartmann, C. and Schütte, Ch. (2005) A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables. Z. Angew. Math. Mech., 85 (10). pp. 700-710. Meerbach, E. and Schütte, Ch. and Fischer, A. (2005) Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 398 . pp. 141-160. Hartmann, C. and Schütte, Ch. (2005) A Geometric Approach to Constrained Molecular Dynamics and Free Energy. Comm. Math. Sci., 3 (1). pp. 1-20. Chipot, C. and Elber, R. and Laaksonen, A. and Leimkuhler, B. and Mark, A. and Schlick, T. and Schütte, Ch. and Skeel, R., eds. (2005) New Algorithms for Macromolecular Simulation. Lecture Notes in Computational Science and Engineering, 49 . Springer. Antony, J. and Schmidt, B. and Schütte, Ch. (2005) Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes. J. Chem. Phys., 122 (1). 014309. Horenko, I. and Dittmer, E. and Schütte, Ch. (2005) Reduced Stochastic Models for Complex Molecular Systems. Comp. Vis. Sci., 9 (2). pp. 89-102. Dellnitz, M. and Neumann, M. and Schütte, Ch. (2005) Special Issue on Matrices and Mathematical Biology. Lin. Alg. Appl., 398 . pp. 1-245. Schütte, Ch. and Forster, R. and Meerbach, E. and Fischer, A. (2005) Uncoupling-Coupling Techniques for Metastable Dynamical Systems. In: Domain Decomposition Methods in Science and Engineering. 2004Schütte, Ch. and Walter, J. and Hartmann, C. and Huisinga, W. (2004) An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations. Multiscale Model. Simul., 2 (3). pp. 501-526. Walter, J. and Schütte, Ch. and Pavliotis, G. A. and Stuart, A. (2004) Averaging of Stochastic Differential Equations: Kurtz's Theorem Revisited. preprint . Preis, R. and Dellnitz, M. and Hessel, M. and Schütte, Ch. and Meerbach, E. (2004) Dominant Paths Between Almost Invariant Sets of Dynamical Systems. preprint . Horenko, I. and Weiser, M. and Schmidt, B. and Schütte, Ch. (2004) Fully Adaptive Propagation of the Quantum-Classical Liouville Equation. J. Chem. Phys., 120 (19). pp. 8913-8923. Deuflhard, P. and Schütte, Ch. (2004) Molecular Conformation Dynamics and Computational Drug Design. In: Applied Mathematics Entering the 21st Century. Huisinga, W. and Meyn, S. and Schütte, Ch. (2004) Phase Transitions and Metastability in Markovian and Molecular Systems. Ann. Appl. Prob., 14 (1). pp. 419-458. 2003Schütte, Ch. and Huisinga, W. (2003) Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics. In: Special Volume: Computational Chemistry. Huisinga, W. and Schütte, Ch. and Stuart, A. M. (2003) Extracting Macroscopic Stochastic Dynamics: Model Problems. Comm. Pure Appl. Math., 56 (2). pp. 234-269. Schütte, Ch. and Huisinga, W. and Meyn, S. (2003) Metastability of Diffusion Processes. In: Nonlinear Stochastic Dynamics. 2002Fischer, A. and Schütte, Ch. and Deuflhard, P. and Cordes, F. (2002) Hierarchical Uncoupling-Coupling of Metastable Conformations. In: Computational Methods for Macromolecules: Challenges and Applications. Horenko, I. and Schmidt, B. and Schütte, Ch. (2002) Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions. J. Chem. Phys., 117 (10). pp. 4643-4650. Horenko, I. and Salzmann, Ch. and Schmidt, B. and Schütte, Ch. (2002) Quantum-Classical Liouville Approach to Molecular Dynamics: Surface Hopping Gaussian Phase-Space Packets. J. Chem. Phys., 117 (24). pp. 11075-11088. 2001Horenko, I. and Schmidt, B. and Schütte, Ch. (2001) A Theoretical Model for Molecules Interacting with Intense Laser Pulses: The Floquet-based Quantum-Classical Liouville Equation. J. Chem. Phys., 115 (13). pp. 5733-5743. Schütte, Ch. and Huisinga, W. and Deuflhard, P. (2001) Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems. In: Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems. 2000Schütte, Ch. and Huisinga, W. (2000) Biomolecular Conformations as Metastable Sets of Markov Chains. In: Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing, Monticello, Illinoins/USA. Deuflhard, P. and Huisinga, W. and Fischer, A. and Schütte, Ch. (2000) Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 315 (1-3). pp. 39-59. Schütte, Ch. and Huisinga, W. (2000) On Conformational Dynamics induced by Langevin Processes. In: Equadiff 99. Schütte, Ch. and Cordes, F. (2000) On Dynamical Transitions between Conformational Ensembles. In: Molecular Dynamics on Parallel Computers. 1999Bornemann, F. A. and Schütte, Ch. (1999) Adaptive Accuracy Control for Car-Parrinello Simulations. Num. Math., 83 (2). pp. 179-186. Schütte, Ch. and Bornemann, F. A. (1999) Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model. In: Computational Molecular Dynamics: Challenges, Methods, Ideas. Deuflhard, P. and Dellnitz, M. and Junge, O. and Schütte, Ch. (1999) Computation of Essential Molecular Dynamics by Subdivision Techniques. In: Computational Molecular Dynamics: Challenges, Methods, Ideas. Schütte, Ch. (1999) Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules. preprint . Schütte, Ch. and Fischer, A. and Huisinga, W. and Deuflhard, P. (1999) A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo. J. Comp. Phys, 151 (1). pp. 146-168. Huisinga, W. and Best, Ch. and Roitzsch, R. and Schütte, Ch. and Cordes, F. (1999) From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods. J. Comp. Chem., 20 (16). pp. 1760-1774. Fischer, A. and Cordes, F. and Schütte, Ch. (1999) Hybrid Monte Carlo with adaptive temperature choice: Efficient conformational analysis of RNA. Comp. Phys. Comm., 121 . pp. 37-39. Schütte, Ch. and Nettesheim, P. (1999) Nonadiabatic Effects in Quantum-Classical Molecular Dynamics. In: Scientific Computing in Chemical Engineering II. Nettesheim, P. and Schütte, Ch. (1999) Numerical Integrators for Quantum-Classical Molecular Dynamics. In: Computational Molecular Dynamics: Challenges, Methods, Ideas. Bornemann, F. A. and Schütte, Ch. (1999) On the Singular Limit of the Quantum-Classical Molecular Dynamics Model. J. Appl. Math., 59 (4). pp. 1208-1224. Schütte, Ch. (1999) Partial Wigner transforms and the quantum-classical Liouville equation. Other thesis, UNSPECIFIED. 1998Fischer, A. and Cordes, F. and Schütte, Ch. (1998) Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA. J. Comp. Chem., 19 (15). pp. 1689-1697. Bornemann, F. A. and Schütte, Ch. (1998) A mathematical investigation of the Car-Parrinello Method. Num. Math., 78 (3). pp. 359-376. 1997Schütte, Ch. and Bornemann, F. A. (1997) Homogenization Approach to Smoothed Molecular Dynamics. Nonlinear Analysis, 30 (3). pp. 1805-1814. Bornemann, F. A. and Schütte, Ch. (1997) Homogenization of Hamiltonian Systems with a Strong Constraining Potential. Physica D, 102 (1-2). pp. 57-77. 1996Nettesheim, P. and Huisinga, W. and Schütte, Ch. (1996) Chebyshev-Approximation for Wavepacket-Dynamics: better than expected. preprint . Nettesheim, P. and Bornemann, F. A. and Schmidt, B. and Schütte, Ch. (1996) An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics. Chem. Phys. Lett., 256 (6). pp. 581-588. Bornemann, F. A. and Nettesheim, P. and Schütte, Ch. (1996) Quantum-classical molecular dynamics as an approximation to full quantum dynamics. J. Chem. Phys., 105 (3). pp. 1074-1083. 1995Schütte, Ch. and Zumbusch, M. D. G and Brinkmann, R. (1995) Dynamics of Erbium-doped Waveguide Lasers: Modelling, Reliable Simulation, and Comparison with Experiments. preprint . Schütte, Ch. (1995) Smoothed Molecular Dynamics for Thermally Embedded Systems. preprint . (Unpublished) Schütte, Ch. and Dinand, M. (1995) Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers. J. Lightw. Techn., 13 (1). pp. 14-23. 1994Manz, J. and Paramonov, G. K. and Polasek, M. and Schütte, Ch. (1994) Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D. Isr. J. Chem., 34 (1). pp. 115-125. 1993Schütte, Ch. (1993) A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation. Impact of Computing in Sci. Eng., 5 (3). pp. 176-200. 1992Schütte, Ch. and Wulkow, M. (1992) Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. preprint . |
