@misc{HorenkoWeiser, author = {Horenko, Illia and Weiser, Martin}, title = {Adaptive Integration of Multidimensional Molecular Dynamics with Quantum Initial Conditions}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6967}, number = {02-29}, abstract = {The paper presents a particle method framework for resolving molecular dynamics. Error estimators for both the temporal and spatial discretization are advocated and facilitate a fully adaptive propagation. For time integration, the implicit trapezoidal rule is employed, where an explicit predictor enables large time steps. The framework is developed and exemplified in the context of the classical Liouville equation, where Gaussian phase-space packets are used as particles. Simplified variants are discussed shortly, which should prove to be easily implementable in common molecular dynamics codes. A concept is illustrated by numerical examples for one-dimensional dynamics in double well potential.}, language = {en} } @misc{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}, series = {Computational Life Sciences II}, volume = {4216}, journal = {Computational Life Sciences II}, publisher = {Springer}, pages = {98 -- 115}, 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}, series = {J. Comp. Chem.}, volume = {26}, journal = {J. Comp. Chem.}, number = {9}, doi = {10.1002/jcc.20234}, pages = {941 -- 948}, 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}, series = {Comp. Vis. Sci.}, volume = {9}, journal = {Comp. Vis. Sci.}, number = {2}, doi = {10.1007/s00791-006-0021-1}, pages = {89 -- 102}, year = {2005}, 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}, series = {Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006}, 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} } @incollection{MeerbachSchuetteHorenkoetal.2007, author = {Meerbach, E. and Sch{\"u}tte, Christof and Horenko, Illia and Schmidt, Burkhard}, title = {Metastable Conformational Structure and Dynamics}, series = {Analysis and Control of Ultrafast Photoinduced Reactions}, 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} } @inproceedings{MeerbachDittmerHorenkoetal.2006, author = {Meerbach, E. and Dittmer, E. and Horenko, Illia and Sch{\"u}tte, Christof}, title = {Multiscale Modelling in Molecular Dynamics}, series = {Computer Simulations in Condensed Matter}, 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} } @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}, series = {Mult. Mod. Sim.}, volume = {5}, journal = {Mult. Mod. Sim.}, number = {3}, doi = {10.1137/050623310}, pages = {802 -- 827}, year = {2006}, 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}, series = {Mult. Mod. Sim.}, volume = {6}, journal = {Mult. Mod. Sim.}, number = {4}, doi = {10.1137/060670535}, pages = {1125 -- 1145}, year = {2008}, language = {en} } @article{HorenkoSchuette2010, author = {Horenko, Illia and Sch{\"u}tte, Christof}, title = {On metastable conformational analysis of non-equilibrium biomolecular time series}, series = {Multiscale Modeling \& Simulation}, volume = {8}, journal = {Multiscale Modeling \& Simulation}, number = {2}, doi = {10.1137/080744347}, pages = {701 -- 716}, year = {2010}, language = {en} }