Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems
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1 publications Listing in reversed chronological order. Scientific Journals and Refereed Proceedings: A. Alfonsi, E. Cances, G. Turinici, B. Di Ventura and W. Huisinga Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems ESAIM: Proc. 14 (2005), pp Journal ( PDF-Preprint ( W. Liebermeister, U. Baur and E. Klipp Complexity reduction of biochemical network models based on balanced truncation FEBS Journal 272 (2005), pp Journal ( W. Huisinga and B. Schmidt Metastability and Dominant Eigenvalues of Transfer Operators In 'Advances in Algorithms for Macromolecular Simulation', Lecture Notes in Computational Science and Engineering, Springer (2005). PDF-Preprint ( I. Horenko, S. Lorenz, C. Schütte and W. Huisinga Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics J. Comp. Chem. 26 (2005), pp Journal ( PDF-Preprint ( K. Abraham, H. Mielke, W. Huisinga and U. Gundert-Remy Elevated Internal Exposure of Children in Simulated Acute Inhalation of Volatile Organic Compounds: Dependency on Properties of the Chemical, Seite 1
2 Basic & Clinical Pharmacology & Toxicology (2005), pp PDF-Preprint ( K. Abraham, H. Mielke, W. Huisinga and U. Gundert-Remy Elevated Internal Exposure of Children in Simulated Acute Inhalation of Volatile Organic Compounds: Effects of Concentration and Duration Arch Toxicol 79 (2005) pp Journal ( ( ) Ch. Schütte, J. Walter, C. Hartmann and W. Huisinga An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations SIAM Multiscale Modeling and Simulation 2 (2004) pp Journal ( PDF-Preprint ( W. Huisinga, S. Meyn and Ch. Schütte Phase Transitions & Metastability in Markovian and Molecular Systems Ann. Appl. Probab. 14 (2004), Journal ( ( Ch. Schütte, W. Huisinga and S. Meyn Metastability of Diffusion Processes Proceeding of the IUTAM Symposium on Nonlinear Stochastic Dynamics (August 26 - August 30, 2002, Illinois/USA), 2003 Book ( PDF-Preprint ( W. Huisinga, Ch. Schütte and A. M. Stuart Extracting Macroscopic Stochastic Dynamics: Model Problems Comm. Pure Appl. Math. 56 (2003), Journal ( PDF-Peprint Seite 2
3 ( Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics in Handbook of Numerical Analysis edited by P. G. Ciarlet, Special Volume: Computational Chemistry (Vol X), guest editor C. Le Bris (2003) Book ( ( Ch. Schütte, W. Huisinga and P. Deuflhard Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems in "Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems" edited by B. Fiedler (2001) pp Book ( PDF-Preprint ( Biomolecular Conformations as Metastable Sets of Markov Chains Proceedings of the 38th. Annual Allerton Conference on Communication, Control, and Computing, Oct. 4-6, Allerton House, Monticello, Illinoins/USA (2000) pp Journal ( PDF-Preprint ( T. Galliat, Wilhelm Huisinga and P. Deuflhard Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification in "Neural Computation" edited by H. Bothe and R. Rojas, ICSC Academic Press (2000) pp PDF-Preprint ( On Conformational Dynamics induced by Langevin Processes in "International Conference on Differential Equations (EquaDiff 99)", edited by B. Fiedler K. Gröger and J. Sprekels, Vol.2 (2000) pp Seite 3
4 Book ( ( P. Deuflhard, W. Huisinga, A. Fischer and Ch. Schütte Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains Lin. Alg. Appl. 315 (2000) pp Journal ( PDF-Preprint ( W. Huisinga, Ch. Best, R. Roitzsch, Ch. Schütte and F. Cordes From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods J. Comp. Chem., Vol.20 (1999) pp Journal ( PDF-Preprint ( Ch. Schütte, A. Fischer, W. Huisinga and P. Deuflhard A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo J. Comp. Phys. 151 (1999) pp Journal ( ( W. Huisinga, L. Pesce, R. Kosloff and P. Saalfrank Faber and Newton Polynomial Integrators for Open-System Density Matrix Propagation J. Chem. Phys., Vol.110 (1999) pp Journal ( PDF-Preprint ( Preprints and Submitted Articles: W. Huisinga; 2000 Seite 4
5 The Esssential Spectral Radius and Asymptotic Properties of Transfer Operators PDF-Preprint ( Ch. Schütte, A. Fischer, W. Huisinga and P. Deuflhard Hybrid Monte Carlo Method for Essential Molecular Dynamics ZIB Preprint, P. Nettesheim, W. Huisinga and Ch. Schütte Chebyshev Approximation for Wavepacket Dynamics: better than expected ZIB preprint, 1996 PDF-Preprint ( Theses: W. Huisinga Metastability of Markovian systems: A transfer operator approach in application to molecular dynamics PhD thesis in mathematics, Freie Universität Berlin, 2001 PDF Preprint ( W. Huisinga Faber-, Newton- und Krylov-Approximation zur Integration grosser Differentialgleichungssysteme aus der Quantenmechanik Diploma thesis in mathematics at Free University Berlin, 1997 Awarded by the Deutsche Mathematiker Vereinigung (1998). PDF-Link ( (c) 2005 JRG Computational Physiology Seite 5
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References [1] A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen. Essential dynamics of proteins. Proteins, 17:412 425, 1993. [2] H. Andersen. Molecular dynamics simulations at constant pressure and/or
[2] M.P. Allen and D.J. Tildesley. Computer Simulations of Liquids. Clarendon Press, Oxford, 1990.
![[2] M.P. Allen and D.J. Tildesley. Computer Simulations of Liquids. Clarendon Press, Oxford, 1990.](/thumbs/95/125844166.jpg "[2] M.P. Allen and D.J. Tildesley. Computer Simulations of Liquids. Clarendon Press, Oxford, 1990.")
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