TY - GEN A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Empirical Bayes Methods, Reference Priors, Cross Entropy and the EM Algorithm N2 - When estimating a probability density within the empirical Bayes framework, the non-parametric maximum likelihood estimate (NPMLE) usually tends to overfit the data. This issue is usually taken care of by regularization - a penalization term is subtracted from the marginal log-likelihood before the maximization step, so that the estimate favors smooth solutions, resulting in the so-called maximum penalized likelihood estimation (MPLE). The majority of penalizations currently in use are rather arbitrary brute-force solutions, which lack invariance under transformation of the parameters(reparametrization) and measurements. This contradicts the principle that, if the underlying model has several equivalent formulations, the methods of inductive inference should lead to consistent results. Motivated by this principle and using an information-theoretic point of view, we suggest an entropy-based penalization term that guarantees this kind of invariance. The resulting density estimate can be seen as a generalization of reference priors. Using the reference prior as a hyperprior, on the other hand, is argued to be a poor choice for regularization. We also present an insightful connection between the NPMLE, the cross entropy and the principle of minimum discrimination information suggesting another method of inference that contains the doubly-smoothed maximum likelihood estimation as a special case. T3 - ZIB-Report - 16-56 KW - parameter estimation KW - Bayesian inference KW - Bayesian hierarchical modeling KW - hyperparameter KW - hyperprior KW - EM algorithm KW - NPMLE KW - MPLE KW - DS-MLE KW - principle of maximum entropy KW - cross entropy KW - minimum discrimination information KW - reference prior KW - Jeffreys prior Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61230 SN - 1438-0064 ER - TY - GEN A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Empirical Bayes Methods for Prior Estimation in Systems Medicine N2 - One of the main goals of mathematical modelling in systems medicine related to medical applications is to obtain patient-specific parameterizations and model predictions. In clinical practice, however, the number of available measurements for single patients is usually limited due to time and cost restrictions. This hampers the process of making patient-specific predictions about the outcome of a treatment. On the other hand, data are often available for many patients, in particular if extensive clinical studies have been performed. Therefore, before applying Bayes’ rule separately to the data of each patient (which is typically performed using a non-informative prior), it is meaningful to use empirical Bayes methods in order to construct an informative prior from all available data. We compare the performance of four priors - a non-informative prior and priors chosen by nonparametric maximum likelihood estimation (NPMLE), by maximum penalized lilelihood estimation (MPLE) and by doubly-smoothed maximum likelihood estimation (DS-MLE) - by applying them to a low-dimensional parameter estimation problem in a toy model as well as to a high-dimensional ODE model of the human menstrual cycle, which represents a typical example from systems biology modelling. T3 - ZIB-Report - 16-57 KW - Parameter estimation KW - Bayesian inference KW - Bayesian hierarchical modelling KW - NPMLE KW - MPLE KW - DS-MLE KW - EM algorithm KW - Jeffreys prior KW - reference prior KW - hyperparameter KW - hyperprior KW - principle of maximum entropy Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61307 SN - 1438-0064 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Weber, Marcus A1 - Zhang, Wei T1 - Importance sampling in path space for diffusion processes with slow-fast variables JF - Probability Theory and Related Fields N2 - Importance sampling is a widely used technique to reduce the variance of a Monte Carlo estimator by an appropriate change of measure. In this work, we study importance sampling in the framework of diffusion process and consider the change of measure which is realized by adding a control force to the original dynamics. For certain exponential type expectation, the corresponding control force of the optimal change of measure leads to a zero-variance estimator and is related to the solution of a Hamilton–Jacobi–Bellmann equation. We focus on certain diffusions with both slow and fast variables, and the main result is that we obtain an upper bound of the relative error for the importance sampling estimators with control obtained from the limiting dynamics. We demonstrate our approximation strategy with an illustrative numerical example. Y1 - 2017 UR - http://rdcu.be/oA51 U6 - https://doi.org/10.1007/s00440-017-0755-3 N1 - If you are not subscribing to the journal please use the http link below as part of the Springer Nature SharedIt initiative SP - 1 EP - 52 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof T1 - The Spatiotemporal Master Equation: Approximation of Reaction-Diffusion Dynamics via Markov State Modeling JF - Journal of Chemical Physics N2 - Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest.We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method. We present the theory of Markov state models (MSM) as a theoretical foundation of this intuitive approach. By means of Markov state modeling, both the number and shape of compartments and the transition rates between them can be determined. We consider the ST-CME for two reaction-diffusion systems and compare it to more detailed models. Moreover, a rigorous formal justification of the ST-CME by Galerkin projection methods is presented. Y1 - 2016 U6 - https://doi.org/10.1063/1.4971163 VL - 145 IS - 21 ER - TY - JOUR A1 - Duwal, Sulav A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV/1 in Resource-Poor Settings JF - PloS Computational Biology N2 - An estimated 2.7 million new HIV-1 infections occurred in 2010. `Treatment-for-prevention’ may strongly prevent HIV-1 transmission. The basic idea is that immediate treatment initiation rapidly decreases virus burden, which reduces the number of transmittable viruses and thereby the probability of infection. However, HIV inevitably develops drug resistance, which leads to virus rebound and nullifies the effect of `treatment-for-prevention’ for the time it remains unrecognized. While timely conducted treatment changes may avert periods of viral rebound, necessary treatment options and diagnostics may be lacking in resource-constrained settings. Within this work, we provide a mathematical platform for comparing different treatment paradigms that can be applied to many medical phenomena. We use this platform to optimize two distinct approaches for the treatment of HIV-1: (i) a diagnostic-guided treatment strategy, based on infrequent and patient-specific diagnostic schedules and (ii) a pro-active strategy that allows treatment adaptation prior to diagnostic ascertainment. Both strategies are compared to current clinical protocols (standard of care and the HPTN052 protocol) in terms of patient health, economic means and reduction in HIV-1 onward transmission exemplarily for South Africa. All therapeutic strategies are assessed using a coarse-grained stochastic model of within-host HIV dynamics and pseudo-codes for solving the respective optimal control problems are provided. Our mathematical model suggests that both optimal strategies (i)-(ii) perform better than the current clinical protocols and no treatment in terms of economic means, life prolongation and reduction of HIV-transmission. The optimal diagnostic-guided strategy suggests rare diagnostics and performs similar to the optimal pro-active strategy. Our results suggest that ‘treatment-for-prevention’ may be further improved using either of the two analyzed treatment paradigms. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pcbi.1004200 VL - 11 IS - 4 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 VL - 20 IS - 16 SP - 1760 EP - 1774 ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with Adaptive Temperature in Mixed–Canonical Ensemble: Efficient conformational analysis of RNA JF - J. Comp. Chem. Y1 - 1998 U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - CHAP A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://www.zib.de/PaperWeb/abstracts/ZR-01-03 IS - 24 SP - 235 EP - 259 PB - Springer ER - TY - JOUR A1 - Metzner, Ph. A1 - Weber, Marcus A1 - Schütte, Christof T1 - Observation uncertainty in reversible Markov chains JF - Phys. Rev. E Y1 - 2010 U6 - https://doi.org/10.1103/PhysRevE.82.031114 VL - 82 IS - 3 SP - 031114 PB - American Physical Society ER - TY - JOUR A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo JF - J. Comput. Phys. Y1 - 1999 UR - http://www.zib.de/PaperWeb/abstracts/SC-98-45 VL - 151 SP - 146 EP - 168 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter ED - Fiedler, Bernold T1 - Transfer operator approach to conformational dynamics in biomolecular systems T2 - Ergodic theory, analysis, and efficient simulation of dynamical systems Y1 - 2001 SP - 191 EP - 223 PB - Berlin: Springer ER - TY - JOUR A1 - Wang, Han A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique JF - Phys. Rev. X Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevX.3.011018 VL - 3 SP - 011018 ER - TY - JOUR A1 - Sarich, Marco A1 - Djurdjevac Conrad, Natasa A1 - Bruckner, Sharon A1 - Conrad, Tim A1 - Schütte, Christof T1 - Modularity revisited: A novel dynamics-based concept for decomposing complex networks JF - Journal of Computational Dynamics Y1 - 2014 UR - http://publications.mi.fu-berlin.de/1127/ U6 - https://doi.org/10.3934/jcd.2014.1.191 VL - 1 IS - 1 SP - 191 EP - 212 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Efficient rare event simulation by optimal nonequilibrium forcing JF - J. Stat. Mech. Theor. Exp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1153/ U6 - https://doi.org/10.1088/1742-5468/2012/11/P11004 VL - 2012 SP - P11004 ER - TY - JOUR A1 - Sarich, Marco A1 - Schütte, Christof T1 - Approximating Selected Non-dominant Timescales by Markov State Models JF - Comm. Math. Sci. Y1 - 2012 U6 - https://doi.org/10.4310/CMS.2012.v10.n3.a14 VL - 10 IS - 3 SP - 1001 EP - 1013 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Zhang, P. T1 - Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems JF - Phys. Rev. E Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1125/ U6 - https://doi.org/10.1103/PhysRevE.86.026704 VL - 86 IS - 02 SP - 026704 ER - TY - JOUR A1 - Schütte, Christof A1 - Winkelmann, Stefanie A1 - Hartmann, Carsten T1 - Optimal control of molecular dynamics using Markov state models JF - Math. Program. (Series B) Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1107/ U6 - https://doi.org/10.1007/s10107-012-0547-6 VL - 134 IS - 1 SP - 259 EP - 282 ER - TY - JOUR A1 - Wang, Han A1 - Zhang, P. A1 - Schütte, Christof T1 - On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems JF - J. Chem. Theo. Comp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1181/ U6 - https://doi.org/10.1021/ct300343y VL - 8 IS - 9 SP - 3243 EP - 3256 ER - TY - JOUR A1 - Enciso, Marta A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - A pH-dependent coarse-grained model of peptides JF - Soft Matter Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1192/ U6 - https://doi.org/10.1039/C3SM27893J VL - 9 IS - 26 SP - 6118 EP - 6127 ER - TY - JOUR A1 - Duwal, Sulav A1 - Schütte, Christof A1 - von Kleist, Max T1 - Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. JF - PLoS One Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1130/ U6 - https://doi.org/10.1371/journal.pone.0040382 VL - 7 IS - 7 SP - e40382 ER - TY - JOUR A1 - von Kleist, Max A1 - Metzner, Ph. A1 - Marquet, R. A1 - Schütte, Christof T1 - Polymerase Inhibition by Nucleoside Analogs JF - Plos Computational Biology Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1087/ U6 - https://doi.org/10.1371/journal.pcbi.1002359 VL - 8 IS - 1 SP - e1002359 ER - TY - JOUR A1 - Meerbach, E. A1 - Latorre, J. A1 - Schütte, Christof T1 - Sequential Change Point Detection in Molecular Dynamics Trajectories JF - Multicale Model. Sim. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1123/ U6 - https://doi.org/10.1137/110850621 VL - 10 IS - 4 SP - 1263 EP - 1291 ER - TY - JOUR A1 - Schäfer-Bung, B. A1 - Hartmann, Carsten A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Dimension reduction by balanced truncation JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1023/ VL - 135 IS - 1 SP - 014112 ER - TY - JOUR A1 - Schütte, Christof A1 - Noé, Frank A1 - Lu, Jianfeng A1 - Sarich, Marco A1 - Vanden-Eijnden, E. T1 - Markov State Models Based on Milestoning JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1022/ U6 - https://doi.org/10.1063/1.3590108 VL - 134 IS - 20 SP - 204105 ER - TY - JOUR A1 - Prinz, J.-H. A1 - Wu, Hao A1 - Sarich, Marco A1 - Keller, B. A1 - Fischbach, M. A1 - Held, M. A1 - Chodera, J. A1 - Schütte, Christof A1 - Noé, Frank T1 - Markov models of molecular kinetics JF - J. Chem. Phys. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/944/ U6 - https://doi.org/10.1063/1.3565032 VL - 134 SP - 174105 ER - TY - JOUR A1 - von Kleist, Max A1 - Menz, Stephan A1 - Stocker, Hartmut A1 - Arasteh, Keikawus A1 - Huisinga, Wilhelm A1 - Schütte, Christof T1 - HIV Quasispecies Dynamics during Pro-active Treatment Switching JF - Plos One Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1051/ U6 - https://doi.org/10.1371/journal.pone.0018204 VL - 6 IS - 3 SP - e18204 PB - Public Library of Science ER - TY - JOUR A1 - Frank, M. A1 - von Kleist, Max A1 - Kunz, A. A1 - Harms, G. A1 - Schütte, Christof A1 - Kloft, Ch. T1 - Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1 JF - Antimicrob. Agents Chemother. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1093/ VL - 55 IS - 12 SP - 5529 EP - 5540 ER - TY - CHAP A1 - Bernhard, Stefan A1 - Zoukra, Kristine Al A1 - Schütte, Christof ED - Knets, I. ED - Brebbia, C. ED - Miftahof, R. ED - Kasyanov, V. ED - Popov, V. T1 - Statistical parameter estimation and signal classification in cardiovascular diagnosis T2 - Modelling in Medicine and Biology Y1 - 2011 UR - http://publications.imp.fu-berlin.de/1070/ VL - IX IS - 15 PB - WIT Press CY - Southampton & Boston ER - TY - JOUR A1 - Aiche, Stephan A1 - Reinert, Knut A1 - Schütte, Christof A1 - Hildebrand, Diana A1 - Schlüter, Hartmut A1 - Conrad, Tim T1 - Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs JF - PLoS ONE Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1143/ U6 - https://doi.org/10.1371/journal.pone.0040656 VL - 7 IS - 7 SP - e40656 PB - Public Library of Science ER - TY - JOUR A1 - Weiss, Maximilian A1 - Paulus, Florian A1 - Steinhilber, D. A1 - Nikitin, Anatoly A1 - Haag, Rainer A1 - Schütte, Christof T1 - Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures JF - MACROMOLECULAR THEORY and SIMULATIONS Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1142/ U6 - https://doi.org/10.1002/mats.201200003 VL - 21 IS - 7 SP - 470 EP - 481 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Bruckner, Stefanie A1 - Conrad, Tim A1 - Schütte, Christof T1 - Random Walks on Complex Modular Networks JF - Journal of Numerical Analysis, Industrial and Applied Mathematics Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1090/ VL - 6 IS - 1-2 SP - 29 EP - 50 PB - European Society of Computational Methods in Sciences and Engineering ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Site, Luigi Delle T1 - Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. JF - J. Chem. Theo. Comp. Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1182/ U6 - https://doi.org/10.1021/ct3003354 VL - 8 IS - 8 SP - 2878 EP - 2887 ER - TY - JOUR A1 - Senne, M. A1 - Trendelkamp-Schroer, B. A1 - Mey, A. A1 - Schütte, Christof A1 - Noé, Frank T1 - EMMA - A software package for Markov model building and analysis JF - Journal of Chemical Theory and Computation Y1 - 2012 U6 - https://doi.org/10.1021/ct300274u VL - 8 SP - 2223 EP - 2238 ER - TY - JOUR A1 - Djurdjevac Conrad, Natasa A1 - Sarich, Marco A1 - Schütte, Christof T1 - Estimating the eigenvalue error of Markov State Models JF - Multiscale Modeling & Simulation Y1 - 2012 UR - http://publications.imp.fu-berlin.de/914/ U6 - https://doi.org/10.1137/100798910 VL - 10 IS - 1 SP - 61 EP - 81 ER - TY - JOUR A1 - Rath, Barbara A1 - Yousef, Kaveh A1 - Katzenstein, D. A1 - Shafer, R. A1 - Schütte, Christof A1 - von Kleist, Max A1 - Merigan, T. T1 - HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitor Induced Selective Pressure in vitro JF - PLoS ONE Y1 - 2013 UR - http://publications.imp.fu-berlin.de/1178/ U6 - https://doi.org/10.1371/journal.pone.0061102 VL - 8 IS - 4 PB - Public Library of Science ER - TY - JOUR A1 - Menz, Stephan A1 - Latorre, J. A1 - Schütte, Christof A1 - Huisinga, Wilhelm T1 - Hybrid Stochastic--Deterministic Solution of the Chemical Master Equation JF - SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS) Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1039/ U6 - https://doi.org/10.1137/110825716 VL - 10 IS - 4 SP - 1232 EP - 1262 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control Processes with Rare State Observation JF - Communications in Mathematical Sciences Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1176/ VL - 12 IS - 859 ER - TY - JOUR A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - von Kleist, Max T1 - Markov Control with Rare State Observation JF - International Journal of Biomathematics and Biostatistics Y1 - 2012 UR - http://publications.mi.fu-berlin.de/1177/ ER - TY - JOUR A1 - Sarich, Marco A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Optimal Fuzzy Aggregation of Networks JF - Multiscale Modeling and Simulation Y1 - 2010 U6 - https://doi.org/10.1137/090758519 VL - 8 IS - 4 SP - 1535 EP - 1561 ER - TY - JOUR A1 - Noé, Frank A1 - Schütte, Christof A1 - Vanden-Eijnden, E. A1 - Reich, L. A1 - Weikl, T. T1 - Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations JF - Proc. Natl. Acad. Sci. USA Y1 - 2009 UR - http://publications.imp.fu-berlin.de/826/ U6 - https://doi.org/10.1073/pnas.0905466106 VL - 106 IS - 45 SP - 19011 EP - 19016 ER - TY - JOUR A1 - Schütte, Christof A1 - Jahnke, Tobias T1 - Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation JF - Mathematical Modelling and Numerical Analysis (ESAIM) Y1 - 2009 UR - http://publications.imp.fu-berlin.de/26/ U6 - https://doi.org/10.1051/m2an/2009027 VL - 43 IS - 4 SP - 721 EP - 742 PB - EDP Sciences ER - TY - JOUR A1 - Schütte, Christof A1 - Noé, Frank A1 - Meerbach, E. A1 - Metzner, Ph. A1 - Hartmann, Carsten T1 - Conformation Dynamics JF - Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), Y1 - 2009 UR - http://publications.imp.fu-berlin.de/110/ U6 - https://doi.org/10.4171/056-1/15 SP - 297 EP - 335 PB - EMS publishing house ER - TY - JOUR A1 - Fiedler, Georg Martin A1 - Leichtle, Alexander Benedikt A1 - Kase, Julia A1 - Baumann, Sven A1 - Ceglarek, Uta A1 - Felix, Klaus A1 - Conrad, Tim A1 - Witzigmann, Helmut A1 - Weimann, Arved A1 - Schütte, Christof A1 - Hauss, Johann A1 - Büchler, Markus A1 - Thiery, Joachim T1 - Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer JF - Clinical Cancer Research Y1 - 2009 UR - http://publications.imp.fu-berlin.de/155/ U6 - https://doi.org/10.1158/1078-0432.CCR-08-2701 VL - 15 IS - 11 SP - 3812 EP - 3819 PB - American Association for Cancer Research, ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Kalibaeva, G. A1 - Pierro, M. A1 - Ciccotti, Giovanni T1 - Fast Simulation of Polymer Chains JF - J. Chem. Phys. Y1 - 2009 UR - http://publications.imp.fu-berlin.de/18/ U6 - https://doi.org/10.1063/1.3110603 VL - 130 SP - 144101 ER - TY - JOUR A1 - Metzner, Ph. A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Transition Path Theory for Markov Jump Processes JF - Mult. Mod. Sim. Y1 - 2009 UR - http://publications.imp.fu-berlin.de/43/ U6 - https://doi.org/10.1137/070699500 VL - 7 IS - 3 SP - 1192 EP - 1219 ER - TY - JOUR A1 - Gräfe, Ch. A1 - Nordmeier, V. A1 - Schütte, Christof T1 - Computerspiel zum Thema Moleküldynamik für Schüler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels JF - Jahrestagung 2008 der GDCP (Gesellschaft für Didaktik der Chemie und Physik) Y1 - 2009 UR - http://publications.imp.fu-berlin.de/163/ VL - 1 SP - 77 EP - 79 PB - LIT VERLAG Dr. W. Hopf ER - TY - JOUR A1 - Metzner, Ph. A1 - Noé, Frank A1 - Schütte, Christof T1 - Estimating the Sampling Error JF - Phys. Rev. E Y1 - 2009 UR - http://publications.imp.fu-berlin.de/17/ U6 - https://doi.org/10.1103/PhysRevE.80.021106 VL - 80 IS - 2 SP - 021106 PB - American Physical Society ER - TY - CHAP A1 - Gräfe, Ch. A1 - Schütte, Christof A1 - Nordmeier, V. T1 - "Learner as creator" - SchülerInnen generieren eigene Lernspiele T2 - Didaktik der Physik - Bochum 2009 Y1 - 2009 UR - http://publications.imp.fu-berlin.de/806/ PB - Lehmanns Media CY - Berlin ER - TY - JOUR A1 - Latorre, J. A1 - Metzner, Ph. A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Structure-preserving numerical discretization of reversible diffusions JF - Commun. Math. Sci. Y1 - 2011 UR - http://publications.imp.fu-berlin.de/896/ VL - 9 IS - 4 SP - 1051 EP - 1072 ER - TY - CHAP A1 - Bernhard, Stefan A1 - Zoukra, Kristine Al A1 - Schütte, Christof ED - Daskalaki, A. ED - Lazakidou, A. T1 - From non-invasive hemodynamic measurements towards patient-specific cardiovascular diagnosis T2 - Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine Y1 - 2010 UR - http://publications.imp.fu-berlin.de/945/ PB - Hershey, PA: Medical Information Science Reference ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - On metastable conformational analysis of non-equilibrium biomolecular time series JF - Multiscale Modeling & Simulation Y1 - 2010 UR - http://publications.imp.fu-berlin.de/146/ U6 - https://doi.org/10.1137/080744347 VL - 8 IS - 2 SP - 701 EP - 716 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Vulcanov, V.-M. A1 - Schütte, Christof T1 - Balanced Truncation of Second Order Systems JF - Multiscale Model. Simul. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/28/ U6 - https://doi.org/10.1137/080732717 VL - 8 IS - 4 SP - 1348 EP - 1367 ER - TY - JOUR A1 - Latorre, J. A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Free energy computation by controlled Langevin processes JF - Procedia Computer Science Y1 - 2010 UR - http://publications.imp.fu-berlin.de/801/ U6 - https://doi.org/10.1016/j.procs.2010.04.179 VL - 1 IS - 1 SP - 1591 EP - 1600 ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - A Hybrid Galerkin-Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics JF - Macromol. React. Eng. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/956/ U6 - https://doi.org/10.1002/mren.200900073 VL - 4 IS - 9-10 SP - 562 EP - 577 ER - TY - JOUR A1 - Marsalek, Ondrej A1 - Frigato, Tomaso A1 - VandeVondele, Joost A1 - Bradforth, Stephen E. A1 - Schmidt, Burkhard A1 - Schütte, Christof A1 - Jungwirth, Pavel T1 - Hydrogen Forms in Water by Proton Transfer to a Distorted Electron JF - J. Phys. Chem. B Y1 - 2010 UR - http://publications.imp.fu-berlin.de/818/ U6 - https://doi.org/10.1021/jp908986z VL - 114 IS - 2 SP - 915 EP - 920 ER - TY - CHAP A1 - Djurdjevac Conrad, Natasa A1 - Sarich, Marco A1 - Schütte, Christof T1 - On Markov State Models for Metastable Processes T2 - Proceedings of the International Congress of Mathematics, Hyderabad, India, Section Invited Talks. (ICM) 2010 Y1 - 2010 UR - http://publications.imp.fu-berlin.de/991/ ER - TY - JOUR A1 - Sarich, Marco A1 - Noé, Frank A1 - Schütte, Christof T1 - On the Approximation Quality of Markov State Models JF - Multiscale Model. Simul. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/771/ U6 - https://doi.org/10.1137/090764049 VL - 8 IS - 4 SP - 1154 EP - 1177 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Ciccotti, Giovanni T1 - On the linear response of mechanical systems with constraints JF - J. Chem. Phys. Y1 - 2010 UR - http://publications.imp.fu-berlin.de/794/ U6 - https://doi.org/10.1063/1.3354126 VL - 132 IS - 11 SP - 111103 ER - TY - JOUR A1 - Frigato, Tomaso A1 - VandeVondele, Joost A1 - Schmidt, Burkhard A1 - Schütte, Christof A1 - Jungwirth, Pavel T1 - Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion JF - J. Phys. Chem. A Y1 - 2008 UR - http://publications.imp.fu-berlin.de/13/ U6 - https://doi.org/10.1021/jp711545s VL - 112 IS - 27 SP - 6125 EP - 6133 ER - TY - JOUR A1 - Horenko, Illia A1 - Klein, Rupert A1 - Dolaptchiev, S. A1 - Schütte, Christof T1 - Automated Generation of Reduced Stochastic Weather Models I JF - Mult. Mod. Sim. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/15/ U6 - https://doi.org/10.1137/060670535 VL - 6 IS - 4 SP - 1125 EP - 1145 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Balancing of partially-observed stochastic differential equations JF - 47th IEEE Conference on Decision and Control Y1 - 2008 UR - http://publications.imp.fu-berlin.de/16/ U6 - https://doi.org/10.1109/CDC.2008.4739161 SP - 4867 EP - 4872 ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications JF - Adv. Data Anal. Class., submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/32/ ER - TY - JOUR A1 - Horenko, Illia A1 - Schütte, Christof T1 - Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics JF - Mult. Mod. Sim. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/39/ U6 - https://doi.org/10.1137/070687451 VL - 7 IS - 2 SP - 731 EP - 773 ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Lankas, F. A1 - Maddocks, J. A1 - Metzner, Ph. A1 - Schütte, Christof T1 - Macroscopic Dynamics of Complex Metastable Systems JF - J. Appl. Dyn. Syst. Y1 - 2008 UR - http://publications.imp.fu-berlin.de/56/ U6 - https://doi.org/10.1137/050630064 VL - 7 IS - 2 SP - 532 EP - 560 ER - TY - JOUR A1 - Meerbach, E. A1 - Schütte, Christof T1 - Sequential Change Point Detection in Molecular Dynamics Trajectories JF - Journal of Multivariate Analysis, submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/24/ ER - TY - JOUR A1 - Diederichs, Elmar A1 - Juditski, A. A1 - Spokoiny, V. A1 - Schütte, Christof T1 - Sparse Non-Gaussian Component Analysis JF - IEEE Transactions on Information Theory, submitted Y1 - 2008 UR - http://publications.imp.fu-berlin.de/42/ ER - TY - CHAP A1 - Gräfe, Ch. A1 - Schütte, Christof A1 - Nordmeier, V. T1 - Spielend lernen - ein Online-Computerspiel zur Moleküldynamik T2 - Didaktik der Physik ? Y1 - 2008 UR - http://publications.imp.fu-berlin.de/811/ PB - Lehmanns Media CY - Berlin ER - TY - JOUR A1 - Metzner, Ph. A1 - Horenko, Illia A1 - Schütte, Christof T1 - Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time JF - Phys. Rev. E Y1 - 2007 UR - http://publications.imp.fu-berlin.de/36/ U6 - https://doi.org/10.1103/PhysRevE.76.066702 VL - 76 IS - 06 SP - 066702 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Nettesheim, Peter A1 - Schütte, Christof T1 - Quantum-classical molecular dynamics as an approximation to full quantum dynamics JF - J. Chem. Phys. Y1 - 1996 UR - http://publications.imp.fu-berlin.de/103/ U6 - https://doi.org/10.1063/1.471952 VL - 105 IS - 3 SP - 1074 EP - 1083 ER - TY - JOUR A1 - Schütte, Christof A1 - Zumbusch, Gerhard A1 - Brinkmann, Ralf T1 - Dynamics of Erbium-doped Waveguide Lasers JF - preprint Y1 - 1995 UR - http://publications.imp.fu-berlin.de/104/ ER - TY - GEN A1 - Schütte, Christof T1 - Smoothed Molecular Dynamics for Thermally Embedded Systems Y1 - 1995 UR - http://publications.imp.fu-berlin.de/105/ ER - TY - JOUR A1 - Schütte, Christof A1 - Dinand, Manfred T1 - Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers JF - J. Lightw. Techn. Y1 - 1995 UR - http://publications.imp.fu-berlin.de/106/ VL - 13 IS - 1 SP - 14 EP - 23 ER - TY - JOUR A1 - Manz, Jörn A1 - Paramonov, G. A1 - Polasek, M. A1 - Schütte, Christof T1 - Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D JF - Isr. J. Chem. Y1 - 1994 UR - http://publications.imp.fu-berlin.de/107/ VL - 34 IS - 1 SP - 115 EP - 125 ER - TY - JOUR A1 - Schütte, Christof T1 - A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation JF - Impact of Computing in Sci. Eng. Y1 - 1993 UR - http://publications.imp.fu-berlin.de/108/ U6 - https://doi.org/10.1006/icse.1993.1008 VL - 5 IS - 3 SP - 176 EP - 200 ER - TY - JOUR A1 - Schütte, Christof A1 - Wulkow, Michael T1 - Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. JF - preprint Y1 - 1992 UR - http://publications.imp.fu-berlin.de/109/ ER - TY - JOUR A1 - Deuflhard, Peter A1 - Huisinga, Wilhelm A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains JF - Lin. Alg. Appl. Y1 - 2000 UR - http://publications.imp.fu-berlin.de/84/ U6 - https://doi.org/10.1016/S0024-3795(00)00095-1 VL - 315 IS - 1-3 SP - 39 EP - 59 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm ED - Fiedler, B. ED - Grger, K. ED - Sprekels, Jürgen T1 - On Conformational Dynamics induced by Langevin Processes T2 - Equadiff 99 Y1 - 2000 UR - http://publications.imp.fu-berlin.de/131/ U6 - https://doi.org/10.1142/9789812792617_0234 VL - 2 SP - 1247 EP - 1262 PB - World Scientific ER - TY - CHAP A1 - Schütte, Christof A1 - Cordes, Frank ED - Esser, R. ED - Grassberger, P. ED - Grotendorst, J. ED - Lewerenz, M. T1 - On Dynamical Transitions between Conformational Ensembles T2 - Molecular Dynamics on Parallel Computers Y1 - 2000 UR - http://publications.imp.fu-berlin.de/132/ U6 - https://doi.org/10.1142/9789812793768_0002 SP - 32 EP - 45 PB - World Scientific ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - Adaptive Accuracy Control for Car-Parrinello Simulations JF - Num. Math. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/88/ U6 - https://doi.org/10.1007/s002110050445 VL - 83 IS - 2 SP - 179 EP - 186 ER - TY - CHAP A1 - Schütte, Christof A1 - Bornemann, Folkmar A. ED - Deuflhard, Peter ED - Hermans, J. ED - Leimkuhler, Benedict ED - Marks, A. ED - Reich, Sebastian ED - Skeel, R. T1 - Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model T2 - Computational Molecular Dynamics Y1 - 1999 UR - http://publications.imp.fu-berlin.de/134/ VL - 4 SP - 380 EP - 395 PB - Springer ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dellnitz, M. A1 - Junge, Oliver A1 - Schütte, Christof ED - Deuflhard, Peter ED - Hermans, J. ED - Leimkuhler, Benedict ED - Marks, A. ED - Reich, Sebastian ED - Skeel, R. T1 - Computation of Essential Molecular Dynamics by Subdivision Techniques T2 - Computational Molecular Dynamics Y1 - 1999 UR - http://publications.mi.fu-berlin.de/135/ VL - 4 SP - 98 EP - 115 PB - Springer ER - TY - JOUR A1 - Schütte, Christof T1 - Conformational Dynamics JF - preprint Y1 - 1999 UR - http://publications.imp.fu-berlin.de/89/ ER - TY - JOUR A1 - Schütte, Christof A1 - Fischer, Alexander A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter T1 - A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo JF - J. Comp. Phys Y1 - 1999 UR - http://publications.imp.fu-berlin.de/87/ U6 - https://doi.org/10.1006/jcph.1999.6231 VL - 151 IS - 1 SP - 146 EP - 168 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/92/ U6 - https://doi.org/10.1002/(SICI)1096-987X(199912)20:16<1760::AID-JCC8>3.0.CO;2-2 VL - 20 IS - 16 SP - 1760 EP - 1774 ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with adaptive temperature choice JF - Comp. Phys. Comm. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/93/ U6 - https://doi.org/10.1016/S0010-4655(99)00274-X VL - 121 SP - 37 EP - 39 ER - TY - JOUR A1 - Conrad, Tim A1 - Leichtle, Alexander Benedikt A1 - Hagehülsmann, Andre A1 - Diederichs, Elmar A1 - Baumann, Sven A1 - Thiery, Joachim A1 - Schütte, Christof T1 - Beating the Noise JF - Lecture Notes in Computer Science Y1 - 2006 UR - http://publications.imp.fu-berlin.de/5/ VL - 4216 SP - 119 EP - 128 PB - Springer ER - TY - CHAP A1 - Walter, J. A1 - Schütte, Christof ED - Mielke, A. T1 - Conditional Averaging for Diffusive Fast-Slow Systems T2 - Analysis, Modeling and Simulation of Multiscale Problems Y1 - 2006 UR - http://publications.imp.fu-berlin.de/117/ U6 - https://doi.org/10.1007/3-540-35657-6_24 SP - 647 EP - 682 PB - Springer ER - TY - CHAP A1 - Dellnitz, M. A1 - Molo, M. A1 - Metzner, Ph. A1 - Preis, R. A1 - Schütte, Christof ED - Mielke, A. T1 - Graph Algorithms for Dynamical Systems T2 - Analysis, Modeling and Simulation of Multiscale Problems Y1 - 2006 UR - http://publications.imp.fu-berlin.de/118/ U6 - https://doi.org/10.1007/3-540-35657-6_23 SP - 619 EP - 645 PB - Springer ER - TY - JOUR A1 - Metzner, Ph. A1 - Schütte, Christof A1 - Vanden-Eijnden, E. T1 - Illustration of Transition Path Theory on a Collection of Simple Examples JF - J. Chem. Phys. Y1 - 2006 UR - http://publications.imp.fu-berlin.de/45/ U6 - https://doi.org/10.1063/1.2335447 VL - 125 IS - 8 SP - 084110 ER - TY - CHAP A1 - Meerbach, E. A1 - Dittmer, E. A1 - Horenko, Illia A1 - Schütte, Christof ED - Ferrario, Mauro ED - Ciccotti, Giovanni ED - Binder, Kurt T1 - Multiscale Modelling in Molecular Dynamics T2 - Computer Simulations in Condensed Matter Y1 - 2006 UR - http://publications.imp.fu-berlin.de/119/ VL - 703 SP - 475 EP - 497 PB - Springer ER - TY - CHAP A1 - Horenko, Illia A1 - Schmidt-Ehrenberg, Johannes A1 - Schütte, Christof ED - Berthold, Michael R. ED - Glen, Robert C. ED - Fischer, Ingrid T1 - Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models T2 - Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006 Y1 - 2006 UR - http://publications.imp.fu-berlin.de/121/ U6 - https://doi.org/10.1007/11875741_8 VL - 4216 SP - 74 EP - 85 PB - Springer ER - TY - JOUR A1 - Horenko, Illia A1 - Lorenz, S. A1 - Schütte, Christof A1 - Huisinga, Wilhelm T1 - Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics JF - J. Comp. Chem. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/49/ U6 - https://doi.org/10.1002/jcc.20234 VL - 26 IS - 9 SP - 941 EP - 948 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables JF - Z. Angew. Math. Mech. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/47/ U6 - https://doi.org/10.1002/zamm.200410218 VL - 85 IS - 10 SP - 700 EP - 710 ER - TY - JOUR A1 - Meerbach, E. A1 - Schütte, Christof A1 - Fischer, Alexander T1 - Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains JF - Lin. Alg. Appl. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/54/ U6 - https://doi.org/10.1016/j.laa.2004.10.018 VL - 398 SP - 141 EP - 160 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - A Geometric Approach to Constrained Molecular Dynamics and Free Energy JF - Comm. Math. Sci. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/48/ VL - 3 IS - 1 SP - 1 EP - 20 ER - TY - JOUR A1 - Antony, Jens A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes JF - J. Chem. Phys. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/57/ U6 - https://doi.org/10.1063/1.1829057 VL - 122 IS - 1 SP - 014309 ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Schütte, Christof T1 - Reduced Stochastic Models for Complex Molecular Systems JF - Comp. Vis. Sci. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/59/ U6 - https://doi.org/10.1007/s00791-006-0021-1 VL - 9 IS - 2 SP - 89 EP - 102 ER - TY - JOUR A1 - Dellnitz, M. A1 - Neumann, M. A1 - Schütte, Christof T1 - Special Issue on Matrices and Mathematical Biology JF - Lin. Alg. Appl. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/60/ U6 - https://doi.org/10.1016/j.laa.2004.12.006 VL - 398 SP - 1 EP - 245 ER - TY - CHAP A1 - Schütte, Christof A1 - Forster, R. A1 - Meerbach, E. A1 - Fischer, Alexander ED - Kornhuber, Ralf ED - Hoppe, Ronald H. W. ED - PÃ\copyrightriaux, J. ED - Pironneau, O. ED - Widlund, Olof ED - Xu, J. T1 - Uncoupling-Coupling Techniques for Metastable Dynamical Systems T2 - Domain Decomposition Methods in Science and Engineering Y1 - 2005 UR - http://publications.imp.fu-berlin.de/124/ VL - 40 SP - 115 EP - 129 PB - Springer ER - TY - JOUR A1 - Walter, J. A1 - Schütte, Christof A1 - Pavliotis, G. A1 - Stuart, Andrew T1 - Averaging of Stochastic Differential Equations JF - preprint Y1 - 2004 UR - http://publications.imp.fu-berlin.de/63/ ER - TY - JOUR A1 - Schütte, Christof A1 - Walter, J. A1 - Hartmann, Carsten A1 - Huisinga, Wilhelm T1 - An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations JF - Multiscale Model. Simul. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/62/ U6 - https://doi.org/10.1137/030600308 VL - 2 IS - 3 SP - 501 EP - 526 ER -