@incollection{BernhardZoukraSchuette2011, author = {Bernhard, Stefan and Zoukra, Kristine Al and Sch{\"u}tte, Christof}, title = {Statistical parameter estimation and signal classification in cardiovascular diagnosis}, volume = {IX}, booktitle = {Modelling in Medicine and Biology}, number = {15}, editor = {Knets, I. and Brebbia, C. and Miftahof, R. and Kasyanov, V. and Popov, V.}, publisher = {WIT Press}, address = {Southampton \& Boston}, year = {2011}, language = {en} } @article{AicheReinertSchuetteetal.2012, author = {Aiche, Stephan and Reinert, Knut and Sch{\"u}tte, Christof and Hildebrand, Diana and Schl{\"u}ter, Hartmut and Conrad, Tim}, title = {Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs}, volume = {7}, journal = {PLoS ONE}, number = {7}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0040656}, pages = {e40656}, year = {2012}, language = {en} } @article{WeissPaulusSteinhilberetal.2012, author = {Weiss, Maximilian and Paulus, Florian and Steinhilber, D. and Nikitin, Anatoly and Haag, Rainer and Sch{\"u}tte, Christof}, title = {Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures}, volume = {21}, journal = {MACROMOLECULAR THEORY and SIMULATIONS}, number = {7}, doi = {10.1002/mats.201200003}, pages = {470 -- 481}, year = {2012}, language = {en} } @article{DjurdjevacConradBrucknerConradetal.2012, author = {Djurdjevac Conrad, Natasa and Bruckner, Stefanie and Conrad, Tim and Sch{\"u}tte, Christof}, title = {Random Walks on Complex Modular Networks}, volume = {6}, journal = {Journal of Numerical Analysis, Industrial and Applied Mathematics}, number = {1-2}, publisher = {European Society of Computational Methods in Sciences and Engineering}, pages = {29 -- 50}, year = {2012}, language = {en} } @article{WangSchuetteSite2012, author = {Wang, Han and Sch{\"u}tte, Christof and Site, Luigi Delle}, title = {Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion.}, volume = {8}, journal = {J. Chem. Theo. Comp.}, number = {8}, doi = {10.1021/ct3003354}, pages = {2878 -- 2887}, year = {2012}, language = {en} } @article{SenneTrendelkampSchroerMeyetal.2012, author = {Senne, M. and Trendelkamp-Schroer, B. and Mey, A. and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {EMMA - A software package for Markov model building and analysis}, volume = {8}, journal = {Journal of Chemical Theory and Computation}, doi = {10.1021/ct300274u}, pages = {2223 -- 2238}, year = {2012}, language = {en} } @article{DjurdjevacConradSarichSchuette2012, author = {Djurdjevac Conrad, Natasa and Sarich, Marco and Sch{\"u}tte, Christof}, title = {Estimating the eigenvalue error of Markov State Models}, volume = {10}, journal = {Multiscale Modeling \& Simulation}, number = {1}, doi = {10.1137/100798910}, pages = {61 -- 81}, year = {2012}, language = {en} } @article{RathYousefKatzensteinetal.2013, author = {Rath, Barbara and Yousef, Kaveh and Katzenstein, D. and Shafer, R. and Sch{\"u}tte, Christof and von Kleist, Max and Merigan, T.}, title = {HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitor Induced Selective Pressure in vitro}, volume = {8}, journal = {PLoS ONE}, number = {4}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0061102}, pages = {e61102}, year = {2013}, language = {en} } @article{MenzLatorreSchuetteetal.2012, author = {Menz, Stephan and Latorre, J. and Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {Hybrid Stochastic--Deterministic Solution of the Chemical Master Equation}, volume = {10}, journal = {SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS)}, number = {4}, doi = {10.1137/110825716}, pages = {1232 -- 1262}, year = {2012}, language = {en} } @article{WinkelmannSchuettevonKleist2012, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Markov Control Processes with Rare State Observation}, volume = {12}, journal = {Communications in Mathematical Sciences}, number = {859}, year = {2012}, language = {en} } @article{WinkelmannSchuettevonKleist2012, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Markov Control with Rare State Observation}, journal = {International Journal of Biomathematics and Biostatistics}, year = {2012}, language = {en} } @article{SarichSchuetteVandenEijnden2010, author = {Sarich, Marco and Sch{\"u}tte, Christof and Vanden-Eijnden, E.}, title = {Optimal Fuzzy Aggregation of Networks}, volume = {8}, journal = {Multiscale Modeling and Simulation}, number = {4}, doi = {10.1137/090758519}, pages = {1535 -- 1561}, year = {2010}, language = {en} } @article{NoeSchuetteVandenEijndenetal.2009, author = {No{\´e}, Frank and Sch{\"u}tte, Christof and Vanden-Eijnden, E. and Reich, L. and Weikl, T.}, title = {Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations}, volume = {106}, journal = {Proc. Natl. Acad. Sci. USA}, number = {45}, doi = {10.1073/pnas.0905466106}, pages = {19011 -- 19016}, year = {2009}, language = {en} } @article{SchuetteJahnke2009, author = {Sch{\"u}tte, Christof and Jahnke, Tobias}, title = {Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation}, volume = {43}, journal = {Mathematical Modelling and Numerical Analysis (ESAIM)}, number = {4}, publisher = {EDP Sciences}, doi = {10.1051/m2an/2009027}, pages = {721 -- 742}, year = {2009}, language = {en} } @article{SchuetteNoeMeerbachetal.2009, author = {Sch{\"u}tte, Christof and No{\´e}, Frank and Meerbach, E. and Metzner, Ph. and Hartmann, Carsten}, title = {Conformation Dynamics}, journal = {Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.),}, publisher = {EMS publishing house}, doi = {10.4171/056-1/15}, pages = {297 -- 335}, year = {2009}, language = {en} } @article{FiedlerLeichtleKaseetal.2009, author = {Fiedler, Georg Martin and Leichtle, Alexander Benedikt and Kase, Julia and Baumann, Sven and Ceglarek, Uta and Felix, Klaus and Conrad, Tim and Witzigmann, Helmut and Weimann, Arved and Sch{\"u}tte, Christof and Hauss, Johann and B{\"u}chler, Markus and Thiery, Joachim}, title = {Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer}, volume = {15}, journal = {Clinical Cancer Research}, number = {11}, publisher = {American Association for Cancer Research,}, doi = {10.1158/1078-0432.CCR-08-2701}, pages = {3812 -- 3819}, year = {2009}, language = {en} } @article{HartmannSchuetteKalibaevaetal.2009, author = {Hartmann, Carsten and Sch{\"u}tte, Christof and Kalibaeva, G. and Pierro, M. and Ciccotti, Giovanni}, title = {Fast Simulation of Polymer Chains}, volume = {130}, journal = {J. Chem. Phys.}, doi = {10.1063/1.3110603}, pages = {144101}, year = {2009}, language = {en} } @article{MetznerSchuetteVandenEijnden2009, author = {Metzner, Ph. and Sch{\"u}tte, Christof and Vanden-Eijnden, E.}, title = {Transition Path Theory for Markov Jump Processes}, volume = {7}, journal = {Mult. Mod. Sim.}, number = {3}, doi = {10.1137/070699500}, pages = {1192 -- 1219}, year = {2009}, language = {en} } @article{GraefeNordmeierSchuette2009, author = {Gr{\"a}fe, Ch. and Nordmeier, V. and Sch{\"u}tte, Christof}, title = {Computerspiel zum Thema Molek{\"u}ldynamik f{\"u}r Sch{\"u}ler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels}, volume = {1}, journal = {Jahrestagung 2008 der GDCP (Gesellschaft f{\"u}r Didaktik der Chemie und Physik)}, publisher = {LIT VERLAG Dr. W. Hopf}, pages = {77 -- 79}, year = {2009}, language = {en} } @article{MetznerNoeSchuette2009, author = {Metzner, Ph. and No{\´e}, Frank and Sch{\"u}tte, Christof}, title = {Estimating the Sampling Error}, volume = {80}, journal = {Phys. Rev. E}, number = {2}, publisher = {American Physical Society}, doi = {10.1103/PhysRevE.80.021106}, pages = {021106}, year = {2009}, language = {en} } @incollection{GraefeSchuetteNordmeier2009, author = {Gr{\"a}fe, Ch. and Sch{\"u}tte, Christof and Nordmeier, V.}, title = {"Learner as creator" - Sch{\"u}lerInnen generieren eigene Lernspiele}, booktitle = {Didaktik der Physik - Bochum 2009}, publisher = {Lehmanns Media}, address = {Berlin}, year = {2009}, language = {en} } @article{LatorreMetznerHartmannetal.2011, author = {Latorre, J. and Metzner, Ph. and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {A Structure-preserving numerical discretization of reversible diffusions}, volume = {9}, journal = {Commun. Math. Sci.}, number = {4}, pages = {1051 -- 1072}, year = {2011}, language = {en} } @incollection{BernhardZoukraSchuette2010, author = {Bernhard, Stefan and Zoukra, Kristine Al and Sch{\"u}tte, Christof}, title = {From non-invasive hemodynamic measurements towards patient-specific cardiovascular diagnosis}, booktitle = {Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine}, editor = {Daskalaki, A. and Lazakidou, A.}, publisher = {Hershey, PA: Medical Information Science Reference}, year = {2010}, language = {en} } @article{HorenkoSchuette2010, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {On metastable conformational analysis of non-equilibrium biomolecular time series}, volume = {8}, journal = {Multiscale Modeling \& Simulation}, number = {2}, doi = {10.1137/080744347}, pages = {701 -- 716}, year = {2010}, language = {en} } @article{HartmannVulcanovSchuette2010, author = {Hartmann, Carsten and Vulcanov, V.-M. and Sch{\"u}tte, Christof}, title = {Balanced Truncation of Second Order Systems}, volume = {8}, journal = {Multiscale Model. Simul.}, number = {4}, doi = {10.1137/080732717}, pages = {1348 -- 1367}, year = {2010}, language = {en} } @article{LatorreHartmannSchuette2010, author = {Latorre, J. and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Free energy computation by controlled Langevin processes}, volume = {1}, journal = {Procedia Computer Science}, number = {1}, doi = {10.1016/j.procs.2010.04.179}, pages = {1591 -- 1600}, year = {2010}, language = {en} } @article{SchuetteWulkow2010, author = {Sch{\"u}tte, Christof and Wulkow, Michael}, title = {A Hybrid Galerkin-Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics}, volume = {4}, journal = {Macromol. React. Eng.}, number = {9-10}, doi = {10.1002/mren.200900073}, pages = {562 -- 577}, year = {2010}, language = {en} } @article{MarsalekFrigatoVandeVondeleetal.2010, author = {Marsalek, Ondrej and Frigato, Tomaso and VandeVondele, Joost and Bradforth, Stephen E. and Schmidt, Burkhard and Sch{\"u}tte, Christof and Jungwirth, Pavel}, title = {Hydrogen Forms in Water by Proton Transfer to a Distorted Electron}, volume = {114}, journal = {J. Phys. Chem. B}, number = {2}, doi = {10.1021/jp908986z}, pages = {915 -- 920}, year = {2010}, language = {en} } @inproceedings{DjurdjevacConradSarichSchuette2010, author = {Djurdjevac Conrad, Natasa and Sarich, Marco and Sch{\"u}tte, Christof}, title = {On Markov State Models for Metastable Processes}, booktitle = {Proceedings of the International Congress of Mathematics, Hyderabad, India, Section Invited Talks. (ICM) 2010}, year = {2010}, language = {en} } @article{SarichNoeSchuette2010, author = {Sarich, Marco and No{\´e}, Frank and Sch{\"u}tte, Christof}, title = {On the Approximation Quality of Markov State Models}, volume = {8}, journal = {Multiscale Model. Simul.}, number = {4}, doi = {10.1137/090764049}, pages = {1154 -- 1177}, year = {2010}, language = {en} } @article{HartmannSchuetteCiccotti2010, author = {Hartmann, Carsten and Sch{\"u}tte, Christof and Ciccotti, Giovanni}, title = {On the linear response of mechanical systems with constraints}, volume = {132}, journal = {J. Chem. Phys.}, number = {11}, doi = {10.1063/1.3354126}, pages = {111103}, year = {2010}, language = {en} } @article{FrigatoVandeVondeleSchmidtetal.2008, author = {Frigato, Tomaso and VandeVondele, Joost and Schmidt, Burkhard and Sch{\"u}tte, Christof and Jungwirth, Pavel}, title = {Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion}, volume = {112}, journal = {J. Phys. Chem. A}, number = {27}, doi = {10.1021/jp711545s}, pages = {6125 -- 6133}, year = {2008}, language = {en} } @article{HorenkoKleinDolaptchievetal.2008, author = {Horenko, Illia and Klein, Rupert and Dolaptchiev, S. and Sch{\"u}tte, Christof}, title = {Automated Generation of Reduced Stochastic Weather Models I}, volume = {6}, journal = {Mult. Mod. Sim.}, number = {4}, doi = {10.1137/060670535}, pages = {1125 -- 1145}, year = {2008}, language = {en} } @article{HartmannSchuette2008, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Balancing of partially-observed stochastic differential equations}, journal = {47th IEEE Conference on Decision and Control}, doi = {10.1109/CDC.2008.4739161}, pages = {4867 -- 4872}, year = {2008}, language = {en} } @article{HorenkoSchuette2008, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications}, journal = {Adv. Data Anal. Class., submitted}, year = {2008}, language = {en} } @article{HorenkoSchuette2008, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics}, volume = {7}, journal = {Mult. Mod. Sim.}, number = {2}, doi = {10.1137/070687451}, pages = {731 -- 773}, year = {2008}, language = {en} } @article{HorenkoDittmerLankasetal.2008, author = {Horenko, Illia and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Sch{\"u}tte, Christof}, title = {Macroscopic Dynamics of Complex Metastable Systems}, volume = {7}, journal = {J. Appl. Dyn. Syst.}, number = {2}, doi = {10.1137/050630064}, pages = {532 -- 560}, year = {2008}, language = {en} } @article{MeerbachSchuette2008, author = {Meerbach, E. and Sch{\"u}tte, Christof}, title = {Sequential Change Point Detection in Molecular Dynamics Trajectories}, journal = {Journal of Multivariate Analysis, submitted}, year = {2008}, language = {en} } @article{DiederichsJuditskiSpokoinyetal.2008, author = {Diederichs, Elmar and Juditski, A. and Spokoiny, V. and Sch{\"u}tte, Christof}, title = {Sparse Non-Gaussian Component Analysis}, journal = {IEEE Transactions on Information Theory, submitted}, year = {2008}, language = {en} } @incollection{GraefeSchuetteNordmeier2008, author = {Gr{\"a}fe, Ch. and Sch{\"u}tte, Christof and Nordmeier, V.}, title = {Spielend lernen - ein Online-Computerspiel zur Molek{\"u}ldynamik}, booktitle = {Didaktik der Physik ?}, publisher = {Lehmanns Media}, address = {Berlin}, year = {2008}, language = {en} } @article{MetznerHorenkoSchuette2007, author = {Metzner, Ph. and Horenko, Illia and Sch{\"u}tte, Christof}, title = {Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time}, volume = {76}, journal = {Phys. Rev. E}, number = {06}, doi = {10.1103/PhysRevE.76.066702}, pages = {066702}, year = {2007}, language = {en} } @article{BornemannNettesheimSchuette1996, author = {Bornemann, Folkmar A. and Nettesheim, Peter and Sch{\"u}tte, Christof}, title = {Quantum-classical molecular dynamics as an approximation to full quantum dynamics}, volume = {105}, journal = {J. Chem. Phys.}, number = {3}, doi = {10.1063/1.471952}, pages = {1074 -- 1083}, year = {1996}, language = {en} } @article{SchuetteZumbuschBrinkmann1995, author = {Sch{\"u}tte, Christof and Zumbusch, Gerhard and Brinkmann, Ralf}, title = {Dynamics of Erbium-doped Waveguide Lasers}, journal = {preprint}, year = {1995}, language = {en} } @misc{Schuette1995, author = {Sch{\"u}tte, Christof}, title = {Smoothed Molecular Dynamics for Thermally Embedded Systems}, year = {1995}, language = {en} } @article{SchuetteDinand1995, author = {Sch{\"u}tte, Christof and Dinand, Manfred}, title = {Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers}, volume = {13}, journal = {J. Lightw. Techn.}, number = {1}, pages = {14 -- 23}, year = {1995}, language = {en} } @article{ManzParamonovPolaseketal.1994, author = {Manz, J{\"o}rn and Paramonov, G. and Polasek, M. and Sch{\"u}tte, Christof}, title = {Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D}, volume = {34}, journal = {Isr. J. Chem.}, number = {1}, pages = {115 -- 125}, year = {1994}, language = {en} } @article{Schuette1993, author = {Sch{\"u}tte, Christof}, title = {A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation}, volume = {5}, journal = {Impact of Computing in Sci. Eng.}, number = {3}, doi = {10.1006/icse.1993.1008}, pages = {176 -- 200}, year = {1993}, language = {en} } @article{SchuetteWulkow1992, author = {Sch{\"u}tte, Christof and Wulkow, Michael}, title = {Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy.}, journal = {preprint}, year = {1992}, language = {en} } @article{DeuflhardHuisingaFischeretal.2000, author = {Deuflhard, Peter and Huisinga, Wilhelm and Fischer, Alexander and Sch{\"u}tte, Christof}, title = {Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains}, volume = {315}, journal = {Lin. Alg. Appl.}, number = {1-3}, doi = {10.1016/S0024-3795(00)00095-1}, pages = {39 -- 59}, year = {2000}, language = {en} } @inproceedings{SchuetteHuisinga2000, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {On Conformational Dynamics induced by Langevin Processes}, volume = {2}, booktitle = {Equadiff 99}, editor = {Fiedler, B. and Grger, K. and Sprekels, J{\"u}rgen}, publisher = {World Scientific}, doi = {10.1142/9789812792617_0234}, pages = {1247 -- 1262}, year = {2000}, language = {en} } @inproceedings{SchuetteCordes2000, author = {Sch{\"u}tte, Christof and Cordes, Frank}, title = {On Dynamical Transitions between Conformational Ensembles}, booktitle = {Molecular Dynamics on Parallel Computers}, editor = {Esser, R. and Grassberger, P. and Grotendorst, J. and Lewerenz, M.}, publisher = {World Scientific}, doi = {10.1142/9789812793768_0002}, pages = {32 -- 45}, year = {2000}, language = {en} } @article{BornemannSchuette1999, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {Adaptive Accuracy Control for Car-Parrinello Simulations}, volume = {83}, journal = {Num. Math.}, number = {2}, doi = {10.1007/s002110050445}, pages = {179 -- 186}, year = {1999}, language = {en} } @inproceedings{SchuetteBornemann1999, author = {Sch{\"u}tte, Christof and Bornemann, Folkmar A.}, title = {Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model}, volume = {4}, booktitle = {Computational Molecular Dynamics}, editor = {Deuflhard, Peter and Hermans, J. and Leimkuhler, Benedict and Marks, A. and Reich, Sebastian and Skeel, R.}, publisher = {Springer}, pages = {380 -- 395}, year = {1999}, language = {en} } @inproceedings{DeuflhardDellnitzJungeetal.1999, author = {Deuflhard, Peter and Dellnitz, M. and Junge, Oliver and Sch{\"u}tte, Christof}, title = {Computation of Essential Molecular Dynamics by Subdivision Techniques}, volume = {4}, booktitle = {Computational Molecular Dynamics}, editor = {Deuflhard, Peter and Hermans, J. and Leimkuhler, Benedict and Marks, A. and Reich, Sebastian and Skeel, R.}, publisher = {Springer}, pages = {98 -- 115}, year = {1999}, language = {en} } @article{Schuette1999, author = {Sch{\"u}tte, Christof}, title = {Conformational Dynamics}, journal = {preprint}, year = {1999}, language = {en} } @article{SchuetteFischerHuisingaetal.1999, author = {Sch{\"u}tte, Christof and Fischer, Alexander and Huisinga, Wilhelm and Deuflhard, Peter}, title = {A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo}, volume = {151}, journal = {J. Comp. Phys}, number = {1}, doi = {10.1006/jcph.1999.6231}, pages = {146 -- 168}, year = {1999}, language = {en} } @article{HuisingaBestRoitzschetal.1999, author = {Huisinga, Wilhelm and Best, Christoph and Roitzsch, Rainer and Sch{\"u}tte, Christof and Cordes, Frank}, title = {From Simulation Data to Conformational Ensembles}, volume = {20}, journal = {J. Comp. Chem.}, number = {16}, doi = {10.1002/(SICI)1096-987X(199912)20:16<1760::AID-JCC8>3.0.CO;2-2}, pages = {1760 -- 1774}, year = {1999}, language = {en} } @article{FischerCordesSchuette1999, author = {Fischer, Alexander and Cordes, Frank and Sch{\"u}tte, Christof}, title = {Hybrid Monte Carlo with adaptive temperature choice}, volume = {121}, journal = {Comp. Phys. Comm.}, doi = {10.1016/S0010-4655(99)00274-X}, pages = {37 -- 39}, year = {1999}, language = {en} } @article{ConradLeichtleHagehuelsmannetal.2006, author = {Conrad, Tim and Leichtle, Alexander Benedikt and Hageh{\"u}lsmann, Andre and Diederichs, Elmar and Baumann, Sven and Thiery, Joachim and Sch{\"u}tte, Christof}, title = {Beating the Noise}, volume = {4216}, journal = {Lecture Notes in Computer Science}, publisher = {Springer}, pages = {119 -- 128}, year = {2006}, language = {en} } @inproceedings{WalterSchuette2006, author = {Walter, J. and Sch{\"u}tte, Christof}, title = {Conditional Averaging for Diffusive Fast-Slow Systems}, booktitle = {Analysis, Modeling and Simulation of Multiscale Problems}, editor = {Mielke, A.}, publisher = {Springer}, doi = {10.1007/3-540-35657-6_24}, pages = {647 -- 682}, year = {2006}, language = {en} } @inproceedings{DellnitzMoloMetzneretal.2006, author = {Dellnitz, M. and Molo, M. and Metzner, Ph. and Preis, R. and Sch{\"u}tte, Christof}, title = {Graph Algorithms for Dynamical Systems}, booktitle = {Analysis, Modeling and Simulation of Multiscale Problems}, editor = {Mielke, A.}, publisher = {Springer}, doi = {10.1007/3-540-35657-6_23}, pages = {619 -- 645}, year = {2006}, language = {en} } @article{MetznerSchuetteVandenEijnden2006, author = {Metzner, Ph. and Sch{\"u}tte, Christof and Vanden-Eijnden, E.}, title = {Illustration of Transition Path Theory on a Collection of Simple Examples}, volume = {125}, journal = {J. Chem. Phys.}, number = {8}, doi = {10.1063/1.2335447}, pages = {084110}, year = {2006}, language = {en} } @inproceedings{MeerbachDittmerHorenkoetal.2006, author = {Meerbach, E. and Dittmer, E. and Horenko, Illia and Sch{\"u}tte, Christof}, title = {Multiscale Modelling in Molecular Dynamics}, volume = {703}, booktitle = {Computer Simulations in Condensed Matter}, editor = {Ferrario, Mauro and Ciccotti, Giovanni and Binder, Kurt}, publisher = {Springer}, pages = {475 -- 497}, year = {2006}, language = {en} } @inproceedings{HorenkoSchmidtEhrenbergSchuette2006, author = {Horenko, Illia and Schmidt-Ehrenberg, Johannes and Sch{\"u}tte, Christof}, title = {Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models}, volume = {4216}, booktitle = {Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006}, editor = {Berthold, Michael R. and Glen, Robert C. and Fischer, Ingrid}, publisher = {Springer}, doi = {10.1007/11875741_8}, pages = {74 -- 85}, year = {2006}, language = {en} } @article{HorenkoLorenzSchuetteetal.2005, author = {Horenko, Illia and Lorenz, S. and Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics}, volume = {26}, journal = {J. Comp. Chem.}, number = {9}, doi = {10.1002/jcc.20234}, pages = {941 -- 948}, year = {2005}, language = {en} } @article{HartmannSchuette2005, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables}, volume = {85}, journal = {Z. Angew. Math. Mech.}, number = {10}, doi = {10.1002/zamm.200410218}, pages = {700 -- 710}, year = {2005}, language = {en} } @article{MeerbachSchuetteFischer2005, author = {Meerbach, E. and Sch{\"u}tte, Christof and Fischer, Alexander}, title = {Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains}, volume = {398}, journal = {Lin. Alg. Appl.}, doi = {10.1016/j.laa.2004.10.018}, pages = {141 -- 160}, year = {2005}, language = {en} } @article{HartmannSchuette2005, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {A Geometric Approach to Constrained Molecular Dynamics and Free Energy}, volume = {3}, journal = {Comm. Math. Sci.}, number = {1}, pages = {1 -- 20}, year = {2005}, language = {en} } @book{OPUS4-2732, title = {New Algorithms for Macromolecular Simulation}, volume = {49}, journal = {Lecture Notes in Computational Science and Engineering}, editor = {Chipot, C. and Elber, R. and Laaksonen, A. and Leimkuhler, Benedict and Mark, A. and Schlick, T. and Sch{\"u}tte, Christof and Skeel, R.}, publisher = {Springer}, year = {2005}, language = {en} } @article{AntonySchmidtSchuette2005, author = {Antony, Jens and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes}, volume = {122}, journal = {J. Chem. Phys.}, number = {1}, doi = {10.1063/1.1829057}, pages = {014309}, year = {2005}, language = {en} } @article{HorenkoDittmerSchuette2005, author = {Horenko, Illia and Dittmer, E. and Sch{\"u}tte, Christof}, title = {Reduced Stochastic Models for Complex Molecular Systems}, volume = {9}, journal = {Comp. Vis. Sci.}, number = {2}, doi = {10.1007/s00791-006-0021-1}, pages = {89 -- 102}, year = {2005}, language = {en} } @article{DellnitzNeumannSchuette2005, author = {Dellnitz, M. and Neumann, M. and Sch{\"u}tte, Christof}, title = {Special Issue on Matrices and Mathematical Biology}, volume = {398}, journal = {Lin. Alg. Appl.}, doi = {10.1016/j.laa.2004.12.006}, pages = {1 -- 245}, year = {2005}, language = {en} } @inproceedings{SchuetteForsterMeerbachetal.2005, author = {Sch{\"u}tte, Christof and Forster, R. and Meerbach, E. and Fischer, Alexander}, title = {Uncoupling-Coupling Techniques for Metastable Dynamical Systems}, volume = {40}, booktitle = {Domain Decomposition Methods in Science and Engineering}, editor = {Kornhuber, Ralf and Hoppe, Ronald H. W. and P{\~A}\copyrightriaux, J. and Pironneau, O. and Widlund, Olof and Xu, J.}, publisher = {Springer}, pages = {115 -- 129}, year = {2005}, language = {en} } @article{WalterSchuettePavliotisetal.2004, author = {Walter, J. and Sch{\"u}tte, Christof and Pavliotis, G. and Stuart, Andrew}, title = {Averaging of Stochastic Differential Equations}, journal = {preprint}, year = {2004}, language = {en} } @article{SchuetteWalterHartmannetal.2004, author = {Sch{\"u}tte, Christof and Walter, J. and Hartmann, Carsten and Huisinga, Wilhelm}, title = {An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations}, volume = {2}, journal = {Multiscale Model. Simul.}, number = {3}, doi = {10.1137/030600308}, pages = {501 -- 526}, year = {2004}, language = {en} } @article{PreisDellnitzHesseletal.2004, author = {Preis, R. and Dellnitz, M. and Hessel, M. and Sch{\"u}tte, Christof and Meerbach, E.}, title = {Dominant Paths Between Almost Invariant Sets of Dynamical Systems}, journal = {preprint}, year = {2004}, language = {en} } @article{HorenkoWeiserSchmidtetal.2004, author = {Horenko, Illia and Weiser, Martin and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {Fully Adaptive Propagation of the Quantum-Classical Liouville Equation}, volume = {120}, journal = {J. Chem. Phys.}, number = {19}, doi = {10.1063/1.1691015}, pages = {8913 -- 8923}, year = {2004}, language = {en} } @inproceedings{DeuflhardSchuette2004, author = {Deuflhard, Peter and Sch{\"u}tte, Christof}, title = {Molecular Conformation Dynamics and Computational Drug Design}, volume = {116}, booktitle = {Applied Mathematics Entering the 21st Century}, editor = {Hill, James and Moore, Ross}, publisher = {SIAM}, pages = {91 -- 119}, year = {2004}, language = {en} } @article{MetznerDittmerJahnkeetal.2007, author = {Metzner, Ph. and Dittmer, E. and Jahnke, Tobias and Sch{\"u}tte, Christof}, title = {Generator Estimation of Markov Jump Processes}, volume = {227}, journal = {J. Comp. Phys.}, number = {1}, doi = {10.1016/j.jcp.2007.07.032}, pages = {353 -- 375}, year = {2007}, language = {en} } @article{NoeHorenkoSchuetteetal.2007, author = {No{\´e}, Frank and Horenko, Illia and Sch{\"u}tte, Christof and Smith, J.}, title = {Hierarchical Analysis of Conformational Dynamics in Biomolecules}, volume = {126}, journal = {J. Chem. Phys.}, number = {15}, doi = {10.1063/1.2714539}, pages = {155102}, year = {2007}, language = {en} } @article{HartmannSchuette2007, author = {Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Comment on Two Distinct Notions of Free Energy}, volume = {228}, journal = {Physica D}, number = {1}, doi = {10.1016/j.physd.2007.02.006}, pages = {59 -- 63}, year = {2007}, language = {en} } @article{LorenzDiederichsTelgmannetal.2007, author = {Lorenz, S. and Diederichs, Elmar and Telgmann, R. and Sch{\"u}tte, Christof}, title = {Discrimination of Dynamical System Models for Biological and Chemical Processes}, volume = {28}, journal = {J. Comp. Chem.}, number = {8}, doi = {10.1002/jcc.20674}, pages = {1384 -- 1399}, year = {2007}, language = {en} } @inproceedings{HeldMeerbachHinderlichetal.2007, author = {Held, M. and Meerbach, E. and Hinderlich, S. and Reutter, W. and Sch{\"u}tte, Christof}, title = {Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity}, volume = {36}, booktitle = {From Computational Biophysics to Systems Biology}, editor = {Hansmann, U. and Meinke, J. and Mohanty, S. and Zimmermann, O.}, publisher = {John von Neumann Institut for Computing}, pages = {145 -- 148}, year = {2007}, language = {en} } @article{HorenkoHartmannSchuetteetal.2007, author = {Horenko, Illia and Hartmann, Carsten and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes}, volume = {76}, journal = {Phys. Rev. E}, number = {01}, doi = {10.1103/PhysRevE.76.016706}, pages = {016706}, year = {2007}, language = {en} } @article{FischerWaldhausenHorenkoetal.2007, author = {Fischer, Alexander and Waldhausen, S. and Horenko, Illia and Meerbach, E. and Sch{\"u}tte, Christof}, title = {Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models}, volume = {28}, journal = {J. Comp. Chem.}, number = {15}, doi = {10.1002/jcc.20692}, pages = {2453 -- 2464}, year = {2007}, language = {en} } @incollection{MeerbachSchuetteHorenkoetal.2007, author = {Meerbach, E. and Sch{\"u}tte, Christof and Horenko, Illia and Schmidt, Burkhard}, title = {Metastable Conformational Structure and Dynamics}, volume = {87}, booktitle = {Analysis and Control of Ultrafast Photoinduced Reactions}, editor = {K{\"u}hn, O. and W{\"o}ste, L.}, publisher = {Springer}, address = {Berlin}, doi = {10.1007/978-3-540-68038-3_9}, pages = {796 -- 806}, year = {2007}, language = {en} } @article{NoeSmithSchuette2007, author = {No{\´e}, Frank and Smith, J. and Sch{\"u}tte, Christof}, title = {A network-based approach to biomolecular dynamics}, volume = {NIC Series 36}, journal = {From Computational Biophysics to Systems Biology (CBSB07). Editors}, publisher = {John von Neumann Institute for Computing, J{\"u}lich}, year = {2007}, language = {en} } @article{HorenkoDittmerFischeretal.2006, author = {Horenko, Illia and Dittmer, E. and Fischer, Alexander and Sch{\"u}tte, Christof}, title = {Automated Model Reduction for Complex Systems exhibiting Metastability}, volume = {5}, journal = {Mult. Mod. Sim.}, number = {3}, doi = {10.1137/050623310}, pages = {802 -- 827}, year = {2006}, language = {en} } @inproceedings{SchuetteNettesheim1999, author = {Sch{\"u}tte, Christof and Nettesheim, Peter}, title = {Nonadiabatic Effects in Quantum-Classical Molecular Dynamics}, booktitle = {Scientific Computing in Chemical Engineering II}, editor = {Keil, F. and Mackens, W. and Voss, H. and Werther, J.}, publisher = {Springer}, pages = {42 -- 56}, year = {1999}, language = {en} } @inproceedings{NettesheimSchuette1999, author = {Nettesheim, Peter and Sch{\"u}tte, Christof}, title = {Numerical Integrators for Quantum-Classical Molecular Dynamics}, volume = {4}, booktitle = {Computational Molecular Dynamics}, editor = {Deuflhard, Peter and Hermans, J. and Leimkuhler, Benedict and Marks, A. and Reich, Sebastian and Skeel, R.}, publisher = {Springer}, pages = {396 -- 411}, year = {1999}, language = {en} } @article{BornemannSchuette1999, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {On the Singular Limit of the Quantum-Classical Molecular Dynamics Model}, volume = {59}, journal = {J. Appl. Math.}, number = {4}, doi = {10.1137/S0036139997318834}, pages = {1208 -- 1224}, year = {1999}, language = {en} } @phdthesis{Schuette1999, author = {Sch{\"u}tte, Christof}, title = {Partial Wigner transforms and the quantum-classical Liouville equation}, year = {1999}, language = {en} } @article{FischerCordesSchuette1998, author = {Fischer, Alexander and Cordes, Frank and Sch{\"u}tte, Christof}, title = {Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble}, volume = {19}, journal = {J. Comp. Chem.}, number = {15}, doi = {10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J}, pages = {1689 -- 1697}, year = {1998}, language = {en} } @article{BornemannSchuette1998, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {A mathematical investigation of the Car-Parrinello Method}, volume = {78}, journal = {Num. Math.}, number = {3}, doi = {10.1007/s002110050316}, pages = {359 -- 376}, year = {1998}, language = {en} } @article{SchuetteBornemann1997, author = {Sch{\"u}tte, Christof and Bornemann, Folkmar A.}, title = {Homogenization Approach to Smoothed Molecular Dynamics}, volume = {30}, journal = {Nonlinear Analysis}, number = {3}, doi = {10.1016/S0362-546X(97)00216-2}, pages = {1805 -- 1814}, year = {1997}, language = {en} } @article{BornemannSchuette1997, author = {Bornemann, Folkmar A. and Sch{\"u}tte, Christof}, title = {Homogenization of Hamiltonian Systems with a Strong Constraining Potential}, volume = {102}, journal = {Physica D}, number = {1-2}, doi = {10.1016/S0167-2789(96)00245-X}, pages = {57 -- 77}, year = {1997}, language = {en} } @article{NettesheimHuisingaSchuette1996, author = {Nettesheim, Peter and Huisinga, Wilhelm and Sch{\"u}tte, Christof}, title = {Chebyshev-Approximation for Wavepacket-Dynamics}, journal = {preprint}, year = {1996}, language = {en} } @article{NettesheimBornemannSchmidtetal.1996, author = {Nettesheim, Peter and Bornemann, Folkmar A. and Schmidt, Burkhard and Sch{\"u}tte, Christof}, title = {An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics}, volume = {256}, journal = {Chem. Phys. Lett.}, number = {6}, doi = {10.1016/0009-2614(96)00471-X}, pages = {581 -- 588}, year = {1996}, language = {en} } @article{HuisingaMeynSchuette2004, author = {Huisinga, Wilhelm and Meyn, S. and Sch{\"u}tte, Christof}, title = {Phase Transitions and Metastability in Markovian and Molecular Systems}, volume = {14}, journal = {Ann. Appl. Prob.}, number = {1}, doi = {10.1214/aoap/1075828057}, pages = {419 -- 458}, year = {2004}, language = {en} } @inproceedings{SchuetteHuisinga2003, author = {Sch{\"u}tte, Christof and Huisinga, Wilhelm}, title = {Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics}, volume = {X}, booktitle = {Special Volume}, editor = {Ciarlet, P. and Le Bris, Claude}, publisher = {Elsevier}, pages = {699 -- 744}, year = {2003}, language = {en} }