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 - TY - JOUR A1 - Preis, R. A1 - Dellnitz, M. A1 - Hessel, M. A1 - Schütte, Christof A1 - Meerbach, E. T1 - Dominant Paths Between Almost Invariant Sets of Dynamical Systems JF - preprint Y1 - 2004 UR - http://publications.imp.fu-berlin.de/64/ ER - TY - JOUR A1 - Horenko, Illia A1 - Weiser, Martin A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Fully Adaptive Propagation of the Quantum-Classical Liouville Equation JF - J. Chem. Phys. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/65/ U6 - https://doi.org/10.1063/1.1691015 VL - 120 IS - 19 SP - 8913 EP - 8923 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Schütte, Christof ED - Hill, James ED - Moore, Ross T1 - Molecular Conformation Dynamics and Computational Drug Design T2 - Applied Mathematics Entering the 21st Century Y1 - 2004 UR - http://publications.imp.fu-berlin.de/125/ VL - 116 SP - 91 EP - 119 PB - SIAM ER - TY - JOUR A1 - Metzner, Ph. A1 - Dittmer, E. A1 - Jahnke, Tobias A1 - Schütte, Christof T1 - Generator Estimation of Markov Jump Processes JF - J. Comp. Phys. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/35/ U6 - https://doi.org/10.1016/j.jcp.2007.07.032 VL - 227 IS - 1 SP - 353 EP - 375 ER - TY - JOUR A1 - Noé, Frank A1 - Horenko, Illia A1 - Schütte, Christof A1 - Smith, J. T1 - Hierarchical Analysis of Conformational Dynamics in Biomolecules JF - J. Chem. Phys. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/37/ U6 - https://doi.org/10.1063/1.2714539 VL - 126 IS - 15 SP - 155102 ER - TY - JOUR A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Comment on Two Distinct Notions of Free Energy JF - Physica D Y1 - 2007 UR - http://publications.imp.fu-berlin.de/30/ U6 - https://doi.org/10.1016/j.physd.2007.02.006 VL - 228 IS - 1 SP - 59 EP - 63 ER - TY - JOUR A1 - Lorenz, S. A1 - Diederichs, Elmar A1 - Telgmann, R. A1 - Schütte, Christof T1 - Discrimination of Dynamical System Models for Biological and Chemical Processes JF - J. Comp. Chem. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/33/ U6 - https://doi.org/10.1002/jcc.20674 VL - 28 IS - 8 SP - 1384 EP - 1399 ER - TY - CHAP A1 - Held, M. A1 - Meerbach, E. A1 - Hinderlich, S. A1 - Reutter, W. A1 - Schütte, Christof ED - Hansmann, U. ED - Meinke, J. ED - Mohanty, S. ED - Zimmermann, O. T1 - Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity T2 - From Computational Biophysics to Systems Biology Y1 - 2007 UR - http://publications.imp.fu-berlin.de/113/ VL - 36 SP - 145 EP - 148 PB - John von Neumann Institut for Computing ER - TY - JOUR A1 - Horenko, Illia A1 - Hartmann, Carsten A1 - Schütte, Christof A1 - Noé, Frank T1 - Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes JF - Phys. Rev. E Y1 - 2007 UR - http://publications.imp.fu-berlin.de/31/ U6 - https://doi.org/10.1103/PhysRevE.76.016706 VL - 76 IS - 01 SP - 016706 ER - TY - JOUR A1 - Fischer, Alexander A1 - Waldhausen, S. A1 - Horenko, Illia A1 - Meerbach, E. A1 - Schütte, Christof T1 - Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models JF - J. Comp. Chem. Y1 - 2007 UR - http://publications.imp.fu-berlin.de/38/ U6 - https://doi.org/10.1002/jcc.20692 VL - 28 IS - 15 SP - 2453 EP - 2464 ER - TY - CHAP A1 - Meerbach, E. A1 - Schütte, Christof A1 - Horenko, Illia A1 - Schmidt, Burkhard ED - Kühn, O. ED - Wöste, L. T1 - Metastable Conformational Structure and Dynamics T2 - Analysis and Control of Ultrafast Photoinduced Reactions Y1 - 2007 UR - http://publications.imp.fu-berlin.de/114/ U6 - https://doi.org/10.1007/978-3-540-68038-3_9 VL - 87 SP - 796 EP - 806 PB - Springer CY - Berlin ER - TY - JOUR A1 - Noé, Frank A1 - Smith, J. A1 - Schütte, Christof T1 - A network-based approach to biomolecular dynamics JF - From Computational Biophysics to Systems Biology (CBSB07). Editors Y1 - 2007 UR - http://publications.imp.fu-berlin.de/319/ VL - NIC Series 36 PB - John von Neumann Institute for Computing, Jülich ER - TY - JOUR A1 - Horenko, Illia A1 - Dittmer, E. A1 - Fischer, Alexander A1 - Schütte, Christof T1 - Automated Model Reduction for Complex Systems exhibiting Metastability JF - Mult. Mod. Sim. Y1 - 2006 UR - http://publications.imp.fu-berlin.de/44/ U6 - https://doi.org/10.1137/050623310 VL - 5 IS - 3 SP - 802 EP - 827 ER - TY - CHAP A1 - Schütte, Christof A1 - Nettesheim, Peter ED - Keil, F. ED - Mackens, W. ED - Voss, H. ED - Werther, J. T1 - Nonadiabatic Effects in Quantum-Classical Molecular Dynamics T2 - Scientific Computing in Chemical Engineering II Y1 - 1999 UR - http://publications.imp.fu-berlin.de/136/ SP - 42 EP - 56 PB - Springer ER - TY - CHAP A1 - Nettesheim, Peter A1 - Schütte, Christof ED - Deuflhard, Peter ED - Hermans, J. ED - Leimkuhler, Benedict ED - Marks, A. ED - Reich, Sebastian ED - Skeel, R. T1 - Numerical Integrators for Quantum-Classical Molecular Dynamics T2 - Computational Molecular Dynamics Y1 - 1999 UR - http://publications.imp.fu-berlin.de/137/ VL - 4 SP - 396 EP - 411 PB - Springer ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - On the Singular Limit of the Quantum-Classical Molecular Dynamics Model JF - J. Appl. Math. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/94/ U6 - https://doi.org/10.1137/S0036139997318834 VL - 59 IS - 4 SP - 1208 EP - 1224 ER - TY - THES A1 - Schütte, Christof T1 - Partial Wigner transforms and the quantum-classical Liouville equation Y1 - 1999 UR - http://publications.imp.fu-berlin.de/95/ ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble JF - J. Comp. Chem. Y1 - 1998 UR - http://publications.imp.fu-berlin.de/97/ U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - A mathematical investigation of the Car-Parrinello Method JF - Num. Math. Y1 - 1998 UR - http://publications.imp.fu-berlin.de/96/ U6 - https://doi.org/10.1007/s002110050316 VL - 78 IS - 3 SP - 359 EP - 376 ER - TY - JOUR A1 - Schütte, Christof A1 - Bornemann, Folkmar A. T1 - Homogenization Approach to Smoothed Molecular Dynamics JF - Nonlinear Analysis Y1 - 1997 UR - http://publications.imp.fu-berlin.de/99/ U6 - https://doi.org/10.1016/S0362-546X(97)00216-2 VL - 30 IS - 3 SP - 1805 EP - 1814 ER - TY - JOUR A1 - Bornemann, Folkmar A. A1 - Schütte, Christof T1 - Homogenization of Hamiltonian Systems with a Strong Constraining Potential JF - Physica D Y1 - 1997 UR - http://publications.imp.fu-berlin.de/100/ U6 - https://doi.org/10.1016/S0167-2789(96)00245-X VL - 102 IS - 1-2 SP - 57 EP - 77 ER - TY - JOUR A1 - Nettesheim, Peter A1 - Huisinga, Wilhelm A1 - Schütte, Christof T1 - Chebyshev-Approximation for Wavepacket-Dynamics JF - preprint Y1 - 1996 UR - http://publications.imp.fu-berlin.de/102/ ER - TY - JOUR A1 - Nettesheim, Peter A1 - Bornemann, Folkmar A. A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics JF - Chem. Phys. Lett. Y1 - 1996 UR - http://publications.imp.fu-berlin.de/101/ U6 - https://doi.org/10.1016/0009-2614(96)00471-X VL - 256 IS - 6 SP - 581 EP - 588 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Meyn, S. A1 - Schütte, Christof T1 - Phase Transitions and Metastability in Markovian and Molecular Systems JF - Ann. Appl. Prob. Y1 - 2004 UR - http://publications.imp.fu-berlin.de/67/ U6 - https://doi.org/10.1214/aoap/1075828057 VL - 14 IS - 1 SP - 419 EP - 458 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm ED - Ciarlet, P. ED - Le Bris, Claude T1 - Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics T2 - Special Volume Y1 - 2003 UR - http://publications.imp.fu-berlin.de/126/ VL - X SP - 699 EP - 744 PB - Elsevier ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Schütte, Christof A1 - Stuart, Andrew T1 - Extracting Macroscopic Stochastic Dynamics JF - Comm. Pure Appl. Math. Y1 - 2003 UR - http://publications.imp.fu-berlin.de/72/ U6 - https://doi.org/10.1002/cpa.10057 VL - 56 IS - 2 SP - 234 EP - 269 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Meyn, S. ED - Namachchivaya, N. ED - Lin, Y. T1 - Metastability of Diffusion Processes T2 - Nonlinear Stochastic Dynamics Y1 - 2003 UR - http://publications.imp.fu-berlin.de/127/ VL - 110 SP - 71 EP - 81 PB - Springer 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://publications.imp.fu-berlin.de/128/ VL - 24 SP - 235 EP - 259 PB - Springer ER - TY - JOUR A1 - Horenko, Illia A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions JF - J. Chem. Phys. Y1 - 2002 UR - http://publications.imp.fu-berlin.de/73/ U6 - https://doi.org/10.1063/1.1498467 VL - 117 IS - 10 SP - 4643 EP - 4650 ER - TY - JOUR A1 - Horenko, Illia A1 - Salzmann, Ch. A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Quantum-Classical Liouville Approach to Molecular Dynamics JF - J. Chem. Phys. Y1 - 2002 UR - http://publications.imp.fu-berlin.de/75/ U6 - https://doi.org/10.1063/1.1522712 VL - 117 IS - 24 SP - 11075 EP - 11088 ER - TY - JOUR A1 - Horenko, Illia A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - A Theoretical Model for Molecules Interacting with Intense Laser Pulses JF - J. Chem. Phys. Y1 - 2001 UR - http://publications.imp.fu-berlin.de/79/ U6 - https://doi.org/10.1063/1.1398577 VL - 115 IS - 13 SP - 5733 EP - 5743 ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm A1 - Deuflhard, Peter ED - Fiedler, B. T1 - Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems T2 - Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems Y1 - 2001 UR - http://publications.imp.fu-berlin.de/129/ SP - 191 EP - 223 PB - Springer ER - TY - CHAP A1 - Schütte, Christof A1 - Huisinga, Wilhelm ED - Sreenivas, R. ED - Jones, D. T1 - Biomolecular Conformations as Metastable Sets of Markov Chains T2 - Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing, Monticello, Illinoins/USA Y1 - 2000 UR - http://publications.imp.fu-berlin.de/130/ SP - 1106 EP - 1115 PB - University of Illinois at Urbana-Champaign ER - TY - GEN A1 - Zhang, Wei A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Effective Dynamics Along Given Reaction Coordinates, and Reaction Rate Theory N2 - In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: We first show that if we start with an ergodic diffusion processes whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Zwanzig-Mori, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the ”equation-free” approach and the ”heterogeneous multiscale method” can be seen as special cases of our approach. T3 - ZIB-Report - 16-35 KW - Ergodic diffusion KW - reaction coordinate KW - effective dynamics KW - model reduction KW - equation-free KW - heterogeneous multiscale method Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59706 SN - 1438-0064 ER - TY - GEN A1 - Ciccotti, Giovanni A1 - Ferrario, Mauro A1 - Schütte, Christof T1 - Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere? T2 - Special Issue: Understanding Molecular Dynamics via Stochastic Processes, Entropy Y1 - 2018 U6 - https://doi.org/10.3390/e20050348 VL - 20 IS - 5 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - Reliable approximation of long relaxation timescales in molecular dynamics JF - Entropy Y1 - 2017 U6 - https://doi.org/10.3390/e19070367 VL - 19 IS - 7 ER - TY - JOUR A1 - Zhang, Wei A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Effective dynamics along given reaction coordinates, and reaction rate theory JF - Faraday Discussions Y1 - 2016 U6 - https://doi.org/10.1039/C6FD00147E IS - 195 SP - 365 EP - 394 ER - TY - JOUR A1 - Klebanov, Ilja A1 - Sikorski, Alexander A1 - Schütte, Christof A1 - Röblitz, Susanna T1 - Objective priors in the empirical Bayes framework JF - Scandinavian Journal of Statistics N2 - When dealing with Bayesian inference the choice of the prior often remains a debatable question. Empirical Bayes methods offer a data-driven solution to this problem by estimating the prior itself from an ensemble of data. In the nonparametric case, the maximum likelihood estimate is known to overfit the data, an issue that is commonly tackled by regularization. However, the majority of regularizations are ad hoc choices which lack invariance under reparametrization of the model and result in inconsistent estimates for equivalent models. We introduce a nonparametric, transformation-invariant estimator for the prior distribution. Being defined in terms of the missing information similar to the reference prior, it can be seen as an extension of the latter to the data-driven setting. This implies a natural interpretation as a trade-off between choosing the least informative prior and incorporating the information provided by the data, a symbiosis between the objective and empirical Bayes methodologies. Y1 - 2021 U6 - https://doi.org/10.1111/sjos.12485 VL - 48 IS - 4 SP - 1212 EP - 1233 PB - Wiley Online Library ER - TY - JOUR A1 - Hartmann, Carsten A1 - Richter, Lorenz A1 - Schütte, Christof A1 - Zhang, Wei T1 - Variational characterization of free energy: theory and algorithms JF - Entropy Y1 - 2017 U6 - https://doi.org/10.3390/e19110626 VL - 19 IS - 11 ER - TY - JOUR A1 - Dibak, Manuel A1 - J. del Razo, Mauricio A1 - De Sancho, David A1 - Schütte, Christof A1 - Noé, Frank T1 - MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations JF - Journal of Chemical Physics N2 - Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long-timescale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large lengthscales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time- and lengthscales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step towards MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B <--> C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported. Y1 - 2018 U6 - https://doi.org/10.1063/1.5020294 VL - 148 IS - 214107 ER -