BA Rath et al. (2013) In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors and in silico phenotypic analysis. PLoS One, 8 (4): e61102
H Wang, C Schütte, P Zhang (2012) Error estimate of short-range force calculation in inhomogeneous molecular systems. Phys Rev E Stat Nonlin Soft Matter Phys., 86 (2-2): 026704
S Aiche, K Reinert, C Schütte, D Hildebrand, H Schlüter, TO Conrad (2012) Inferring proteolytic processes from mass spectrometry time series data using degradation graphs. PLoS One, 7 (7): e40656
S Duwal, C Schütte, M von Kleist (2012) Pharmacokinetics and pharmacodynamics of the reverse transcriptase inhibitor tenofovir and prophylactic efficacy against HIV-1 infection. PLoS One, 7 (7): e40382
M von Kleist, P Metzner, R Marquet, C Schütte (2012) HIV-1 polymerase inhibition by nucleoside analogs: cellular- and kinetic parameters of efficacy, susceptibility and resistance selection. PLoS Comput Biol., 8 (1): e1002359
M Frank, M von Kleist, A Kunz, G Harms, C Schütte, C Kloft (2011) Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1: A combined pharmacokinetic, pharmaco- and viral dynamic analysis to predict clinical outcomes. Antimicrob Agents Chemother., 55 (12): 5529-40
B Schäfer-Bung, C Hartmann, B Schmidt, C Schütte (2011) Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems. J Chem Phys., 135 (1): 014112
C Schütte, F Noé, J Lu, M Sarich, E Vanden-Eijnden (2011) Markov state models based on milestoning. J Chem Phys., 134 (20): 204105
JH Prinz, H Wu, M Sarich, B Keller, M Senne, M Held, JD Chodera, C Schütte, F Noé (2011) Markov models of molecular kinetics: Generation and validation. J Chem Phys., 134 (17): 174105
M von Kleist, S Menz, H Stocker, K Arasteh, C Schütte, W Huisinga (2011) HIV quasispecies dynamics during pro-active treatment switching: impact on multi-drug resistance and resistance archiving in latent reservoirs. PLoS One, 6 (3): e18204
P Metzner, M Weber and C Schütte (2010) Observation uncertainty in reversible Markov chains. Phys. Rev. E82(3 Pt 1):031114
I Horenko and Ch Schütte (2010) On metastable conformational analysis of non-equilibrium biomolecular time series. Mult. Mod. Sim.8(2):701-16
C Hartmann, VM Vulcanov and Ch Schütte (2010) Balanced truncation of second order systems: a Hamiltonian approach. Mult. Mod. Sim.8(4):1348-67
M Sarich, F Noé, Ch. Schütte (2010) On the approximation quality of Markov state models. Mult. Mod. Sim.8(4):1154-77
M Sarich, Ch Schütte and E Vanden-Eijnden (2010) Optimal fuzzy aggregation of networks. Mult. Mod. Sim.8(4):1535-61
JC Latorre, C Hartmann and Ch Schütte (2010) Free energy computation by controlled Langevin processes. Procedia Computer Science1(1):1591-1600
Ch Schütte and M Wulkow (2010) A hybrid Galerkin-Monte-Carlo approach to higher-dimensional population balances in polymerization kinetics. Macromol. React. Eng.4(9-10):562-77
O Marsalek et al. (2010) Hydrogen forms in water by proton transfer to a distorted electron. J. Phys. Chem. B114(2):915-20
C Hartmann, Ch Schütte and G Ciccotti (2010) On the linear response of mechanical systems with constraints. J. Chem. Phys. 132(11):111103
S Bernhard, K Al Zoukra and Ch Schütte (2010) From non-invasive hemodynamic measurements towards patient-specific cardiovascular diagnosis. In: Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine, Hershey, PA Medical Information Science Reference (Submitted)
JC Latorre, Ph Metzner, C Hartmann and Ch Schütte (2011) A structure-preserving numerical discretization of reversible diffusions. Commun. Math. Sci, 9 (4): 1051-72
N Djurdjevac, M Sarich and Ch Schütte (2010) Estimating the eigenvalue error of Markov state models. Mult. Mod. Sim. Submitted
F Noé, Ch Schütte, E Vanden-Eijnden, L Reich and T Weikl (2009) Constructing the full ensemble of folding pathways from short off-equilibrium simulations. Proc. Natl. Acad. Sci USA106(45):19011-6
GM Fiedler et al. (2009) Serum peptidome profiling revealed platelet factor 4 as a potential discriminating peptide associated with pancreatic cancer. Clinical Cancer Research15(11):3812-9
C Hartmann, Ch Schütte, G Kalibaeva, M Di Pierro and G Ciccotti (2009) Fast simulation of polymer chains. J. Chem. Phys.130:144101
Ph Metzner, Ch Schütte and E Vanden-Eijnden (2009) Transition path theory for Markov jump processes. Mult. Mod. Sim.7(3):1192-1219
Ph Metzner, F Noé and Ch Schütte (2009) Estimating the sampling error: distribution of transition matrices and functions of transition matrices for given trajectory data. Phys. Rev. E80, 021106
Ch Gräfe, Ch Schütte and V Nordmeier (2009) Learner as creator - SchülerInnen generieren eigene Lernspiele. In: Didaktik der Physik, Lehmanns Media, Berlin.
Ch Schütte, T Jahnke (2009) Towards effective dynamics in complex systems by Markov kernel approximation. Mathematical Modelling and Numerical Analysis (ESAIM)
T Frigato, J VandeVondele, B Schmidt, Ch Schütte and P Jungwirth (2008) Ab initio molecular dynamics simulation of a medium-sized water cluster anion: from an interior to a surface located exces electron via a delocalized state. J. Phys. Chem. A112(27):6125-33
C Hartmann and Ch Schütte (2008) Balancing of partially-observed stochastic differential equations. 47th IEEE Conference on Decision and Control, pp. 4867-72
I Horenko, E Dittmer, F Lankas, J Maddocks, Ph Metzner and Ch Schütte (2008) Macroscopic dynamics of complex metastable systems: theory and application to B-DNA. J Appl. Dyn. Syst.7(2):632-60
E Meerbach and Ch Schütte (2008) Sequential change point detection in molecular dynamics trajectories. Journal of Multivariate Analysis submitted
E Diederichs, A Juditski, V Spokoiny and Ch Schütte (2008) Sparse non-Gaussian component analysis. IEEE Transactions on Information Theory submitted
Ch Gräfe, Ch Schütte and V Nordmeier (2008) Spielend lernen - ein Online-Computerspiel zur Moleküldynamik. In: Didaktik der Physik, Lehmanns Media, Berlin.
I Horenko and Ch Schütte (2008) Likelihood-based estimation of multidimensional Langevin Models and its Application to Biomolecular Dynamics. Mult. Mod. Sim.7(2):731-73
Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model reduction for Time Series Analysis I. Horenko, R. Klein, S. Dolaptchiev, and Ch. Schütte Mult. Mod. Sim. 6 (4):1125-45 (2008)
M Held, E Meerbach, S Hinderlich, W Reutter, Ch Schütte (2007) Conformational studies of UDP-GlcNAc in environments of increasing complexity. From Computational Biophysics to Systems Biology (CBSB07) Editors: Hansmann, Meinke, Mohanty and Zimmermann NIC Series 36
F Noé, JC Smith and Ch Schütte (2007) A network-based approach to biomolecular dynamics. From Computational Biophysics to Systems Biology (CBSB07). Editors: Hansmann, Meinke, Mohanty and Zimmermann NIC Series 36
I Horenko, C Hartmann, Ch Schütte and F Noé (2007) Data-based parameter estimation of generalized multidimensional Langevin processes. Phys. Rev. E76, 016706
S Lorenz, E Diederichs, R Telgmann and Ch Schütte (2007) Discrimination of dynamical system models for biological and chemical processes. J. Comp. Chem.28(8):1384-99
Ph Metzner, E Dittmer, T Jahnke and Ch Schütte (2007) Generator estimation of Markov jump processes. J. Comp. Phys.227(1):353-75
Ph Metzner, I Horenko and Ch Schütte (2007) Generator estimation of Markov jump processes based on incomplete observations nonequidistant in time. Phys. Rev. E76, 066702
A Fischer, S Waldhausen, I Horenko, E Meerbach and Ch Schütte (2007). Identification of biomolecular conformations from incomplete torsion angle observations by Hidden Markov Models. J. Comp. Chem.28(15):2453-2464
Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution E. Meerbach, Ch. Schütte, I. Horenko, and B. Schmidt In 'Analysis and Control of Ultrafast Photoinduced Reactions' Eds.: O. Kühn and L. Wüste Series in Chemical Physics 87, pp. 796-806, Springer (2007)
Comment on Two Distinct Notions of Free Energy C. Hartmann and Ch. Schütte Physica D, 228 (1):59-63 (2007)
F Noe, I Horenko, Ch Schütte and JC Smith (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J Chem Phys126(15):155102
Automated Model Reduction for Complex Systems exhibiting Metastability I. Horenko, E. Dittmer, A. Fischer, and Ch. Schütte Mult. Mod. Sim. 5 (3), pp. 802-827 (2006)
Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra below Noise Level T. O. F. Conrad, A. Leichtle, A. Hagehülsmann, E. Diederichs, S. Baumann, J. Thiery, and Ch. Schütte In 'Computational Life Sciences II' Eds.: M. R. Berthold, R. Glen, and I. Fischer Lecture Notes in Computer Science 4216, pp. 119-128, Springer (2006)
Conditional Averaging for Diffusive Fast-Slow Systems: A Sketch for Derivation J. Walter and Ch. Schütte In 'Analysis, Modeling and Simulation of Multiscale Problems' Eds.: A. Mielke pp. 647-682, Springer (2006)
Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications I. Horenko and Ch. Schütte Submitted to Adv. Data Anal. Class.
Graph Algorithms for Dynamical Systems M. Dellnitz, M. Hessel-von Molo, Ph. Metzner, R. Preis, and Ch. Schütte In 'Analysis, Modeling and Simulation of Multiscale Problems' Eds.: A. Mielke pp. 619-645, Springer (2006)
Illustration of Transition Path Theory on a Collection of Simple Examples P.Metzner, Ch. Schütte, E. Vanden-Eijnden J. Chem. Phys. 125 (8), pp. 084110 (2006)
Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States E. Meerbach, E. Dittmer, I. Horenko, and Ch. Schütte In 'Computer Simulations in Condensed Matter: Systems: From Materials to Chemical Biology. Volume I' Eds.: M. Ferrario, G. Ciccotti, and K. Binder Lecture Notes in Physics 703, pp. 475-497, Springer (2006)
Set-Oriented Dimension Reduction: Localizing Principal Component Analysis via Hidden Markov Models I. Horenko, J. Schmidt-Ehrenberg, and Ch. Schütte In 'Computational Life Sciences II ' Eds.: M.R. Berthold, R. Glen, and I. Fischer Lecture Notes in Computer Science 4216, pp. 74-85, Springer (2006)
A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables C. Hartmann and Ch. Schütte Z. Angew. Math. Mech. 85 (10), pp. 700-710 (2005)
A Geometric Approach to Constrained Molecular Dynamics and Free Energy C. Hartmann and Ch. Schütte Comm. Math. Sci. 3 (1), pp. 1-20 (2005)
Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics I. Horenko, S. Lorenz, Ch. Schütte, and W. Huisinga J. Comp. Chem. 26 (9), pp. 941-948 (2005)
Discrimination of Dynamical System Models for Biological and Chemical Processes S. Lorenz, E. Diederichs, R. Telgmann, and Ch. Schütte Submitted to J. Comp. Chem. (2005)
Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains E. Meerbach, Ch. Schütte, and A. Fischer Lin. Alg. Appl. 398, pp. 141-160 (2005)
Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models A. Fischer, S. Waldhausen, I. Horenko, E. Meerbach, and Ch. Schütte Submitted to J. Comp. Chem. (2005)
Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA I. Horenko, E. Dittmer, F. Lankas, J. Maddocks, Ph. Metzner, and Ch. Schütte Submitted to J. Appl. Dyn. Syst. (2005)
Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes J. Antony, B. Schmidt, and Ch. Schütte J. Chem. Phys. 122 (1), pp. 014309 (2005)
Reduced Stochastic Models for Complex Molecular Systems I. Horenko, E. Dittmer, and Ch. Schütte Comp. Vis. Sci. 9 (2), pp. 89-102 (2005)
Special Issue on Matrices and Mathematical Biology Eds.: M. Dellnitz, S. Kirkland, M. Neumann, and C. Schütte Lin. Alg. Appl. 398, pp. 1-245 (2005)
Uncoupling-Coupling Techniques for Metastable Dynamical Systems Ch. Schütte, R. Forster, E. Meerbach, and A. Fischer In 'Domain Decomposition Methods in Science and Engineering' Eds.: R. Kornhuber, R. Hoppe, J. Püriaux, O. Pironneau, O. Widlund, J. Xu Lecture Notes in Computational Science and Engineering 40, pp. 115-129, Springer (2005)
An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations Ch. Schütte, J. Walter, C. Hartmann, and W. Huisinga Mult. Mod. Sim. 2 (3), pp. 501-526 (2004)
Averaging of Stochastic Differential Equations: Kurtz's Theorem Revisited J. Walter, Ch. Schütte, G. A. Pavliotis, and A. Stuart Preprint (2004)
Dominant Paths Between Almost Invariant Sets of Dynamical Systems R. Preis, M. Dellnitz, M. Hessel, Ch. Schütte, and E. Meerbach Preprint (2004)
Fully Adaptive Propagation of the Quantum-Classical Liouville Equation I. Horenko, M. Weiser, B. Schmidt, and Ch. Schütte J. Chem. Phys. 120 (19), pp. 8913-8923 (2004)
Molecular Conformation Dynamics and Computational Drug Design P. Deuflhard and Ch. Schütte In 'Applied Mathematics Entering the 21st Century' Eds.: J. M. Hill and R. Moore Proceedings in Applied Mathematics 116, pp. 91-119, SIAM (2004)
Phase Transitions and Metastability in Markovian and Molecular Systems W. Huisinga, S. Meyn, and Ch. Schütte Ann. Appl. Prob. 14 (1), pp. 419-458 (2004)
Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics Ch. Schütte and W. Huisinga In 'Special Volume: Computational Chemistry' Eds.: P. G. Ciarlet and C. Le Bris Handbook of Numerical Analysis X, pp. 699-744, Elsevier (2003)
Extracting Macroscopic Stochastic Dynamics: Model Problems W. Huisinga, Ch. Schütte, and A. M. Stuart Comm. Pure Appl. Math. 56 (2), pp. 234-269 (2003)
Metastability of Diffusion Processes Ch. Schütte, W. Huisinga, and S. Meyn In 'Nonlinear Stochastic Dynamics' Eds.: N. Sri Namachchivaya and Y. K. Lin Solid Mechanics and Its Applications 110, pp. 71-81, Springer (2003)
Hierarchical Uncoupling-Coupling of Metastable Conformations A. Fischer, Ch. Schütte, P. Deuflhard, and F. Cordes In 'Computational Methods for Macromolecules: Challenges and Applications' Eds.: T. Schlick and H. H. Gan Lecture Notes in Computational Science and Engineering 24, pp. 235-259, Springer (2002)
Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions I. Horenko, B. Schmidt, and Ch. Schütte J. Chem. Phys. 117 (10), pp. 4643-4650 (2002)
Quantum-Classical Liouville Approach to Molecular Dynamics: Surface Hopping Gaussian Phase-Space Packets I. Horenko, Ch. Salzmann, B. Schmidt, and Ch. Schütte J. Chem. Phys. 117 (24), pp. 11075-11088 (2002)
A Theoretical Model for Molecules Interacting with Intense Laser Pulses: The Floquet-based Quantum-Classical Liouville Equation I. Horenko, B. Schmidt, and Ch. Schütte J. Chem. Phys. 115 (13), pp. 5733-5743 (2001)
Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems Ch. Schütte, W. Huisinga, and P. Deuflhard In 'Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems' Eds.: B. Fiedler pp. 191-223, Springer (2001)
Biomolecular Conformations as Metastable Sets of Markov Chains Ch. Schütte and W. Huisinga In 'Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing, Monticello, Illinoins/USA' Eds.: R. S. Sreenivas and D. L. Jones pp. 1106-1115, University of Illinois at Urbana-Champaign (2000)
Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains P. Deuflhard, W. Huisinga, A. Fischer, and Ch. Schütte Lin. Alg. Appl. 315 (1-3), pp. 39-59 (2000)
On Conformational Dynamics induced by Langevin Processes Ch. Schütte and W. Huisinga In 'Equadiff 99' Eds.: B. Fiedler, K. Grüger and J. Sprekels Proceedings of the International Conference on Differential Equations 2, pp. 1247-1262, World Scientific (2000)
On Dynamical Transitions between Conformational Ensembles Ch. Schütte and F. Cordes In 'Molecular Dynamics on Parallel Computers' Eds.: R. Esser, P. Grassberger, J. Grotendorst, M. Lewerenz pp. 32-45, World Scientific (2000)
A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo Ch. Schütte, A. Fischer, W. Huisinga, and P. Deuflhard J. Comp. Phys 151 (1), pp. 146-168 (1999)
Adaptive Accuracy Control for Car-Parrinello Simulations F. A. Bornemann and Ch. Schütte Num. Math. 83 (2), pp. 179-186 (1999)
Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model Ch. Schütte and F. A. Bornemann In 'Computational Molecular Dynamics: Challenges, Methods, Ideas' Eds.: P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Marks, S. Reich, R. D. Skeel Lecture Notes in Computational Science and Engineering 4, pp. 380-395, Springer (1999)
Computation of Essential Molecular Dynamics by Subdivision Techniques P. Deuflhard, M. Dellnitz, O. Junge, and Ch. Schütte In 'Computational Molecular Dynamics: Challenges, Methods, Ideas' Eds.: P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Marks, S. Reich, R. D. Skeel Lecture Notes in Computational Science and Engineering 4, pp. 98-115, Springer (1999)
Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules Ch. Schütte Preprint (1999)
From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods W. Huisinga, Ch. Best, R. Roitzsch, Ch. Schütte, and F. Cordes J. Comp. Chem. 20 (16), pp. 1760-1774 (1999)
Hybrid Monte Carlo with adaptive temperature choice: Efficient conformational analysis of RNA A. Fischer, F. Cordes, and Ch. Schütte Comp. Phys. Comm. 121, pp. 37-39 (1999)
Nonadiabatic Effects in Quantum-Classical Molecular Dynamics Ch. Schütte and P. Nettesheim In 'Scientific Computing in Chemical Engineering II' Eds.: F. Keil, W. Mackens, H. Voss and J. Werther pp. 42-56, Springer (1999)
Numerical Integrators for Quantum-Classical Molecular Dynamics P. Nettesheim and Ch. Schütte In 'Computational Molecular Dynamics: Challenges, Methods, Ideas' Eds.: P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Marks, S. Reich, R. D. Skeel Lecture Notes in Computational Science and Engineering 4, pp. 396-411, Springer (1999)
On the Singular Limit of the Quantum-Classical Molecular Dynamics Model F. Bornemann and Ch. Schütte J. Appl. Math. 59 (4), pp. 1208-1224 (1999)
Partial Wigner transforms and the quantum-classical Liouville equation Ch. Schütte Preprint (1999)
A mathematical investigation of the Car-Parrinello Method F. A. Bornemann and Ch. Schütte Num. Math. 78 (3), pp. 359-376 (1998)
Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA A. Fischer, F. Cordes, and Ch. Schütte J. Comp. Chem. 19 (15), pp. 1689-1697 (1998)
Homogenization Approach to Smoothed Molecular Dynamics Ch. Schütte and F. A. Bornemann Nonlinear Analysis 30 (3), pp. 1805-1814 (1997)
Homogenization of Hamiltonian Systems with a Strong Constraining Potential F. A. Bornemann and Ch. Schütte Physica D 102 (1-2), pp. 57-77 (1997)
An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics P. Nettesheim, F. A. Bornemann, B. Schmidt, and Ch. Schütte Chem. Phys. Lett. 256 (6), pp. 581-588 (1996)
Chebyshev-Approximation for Wavepacket-Dynamics: better than expected P. Nettesheim, W. Huisinga, and Ch. Schütte Preprint (1996)
Quantum-classical molecular dynamics as an approximation to full quantum dynamics F. A. Bornemann, P. Nettesheim, and Ch. Schütte J. Chem. Phys. 105 (3), pp. 1074-1083 (1996)
Dynamics of Erbium-doped Waveguide Lasers: Modelling, Reliable Simulation, and Comparison with Experiments Ch. Schütte, M. Dinand, G. Zumbusch, and R. Brinkmann Preprint (1995)
Smoothed Molecular Dynamics for Thermally Embedded Systems Ch. Schütte Preprint (1995)
Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers M. Dinand and Ch. Schütte J. Lightw. Techn. 13 (1), pp. 14-23 (1995)
Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D J. Manz, G. K. Paramonov, M. Polasek, and Ch. Schütte Isr. J. Chem. 34 (1), pp. 115-125 (1994)
A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation Ch. Schütte Impact of Computing in Sci. Eng. 5 (3), pp. 176-200 (1993)
Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. Ch. Schütte and M. Wulkow Preprint (1992)