TY - GEN A1 - Koltai, Peter A1 - Ciccotti, Giovanni A1 - Schütte, Christof T1 - On metastability and Markov state models for non-stationary molecular dynamics BT - 2016 Editor's Choice of The Journal of Chemical Physics T2 - The Journal of Chemical Physics N2 - We utilize the theory of coherent sets to build Markov state models for non- equilibrium molecular dynamical systems. Unlike for systems in equilibrium, “meta- stable” sets in the non-equilibrium case may move as time evolves. We formalize this concept by relying on the theory of coherent sets, based on this we derive finite-time non-stationary Markov state models, and illustrate the concept and its main differences to equilibrium Markov state modeling on simple, one-dimensional examples. T3 - ZIB-Report - 16-11 KW - coherent set, KW - Markov state model KW - non-equilibrium molecular dynamics KW - metastability Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57869 SN - 1438-0064 VL - 174103 ET - 145 ER - TY - JOUR A1 - Koltai, Peter A1 - Ciccotti, Giovanni A1 - Schütte, Christof T1 - On Markov state models for non-equilibrium molecular dynamics JF - The Journal of Chemical Physics Y1 - 2016 U6 - https://doi.org/10.1063/1.4966157 N1 - 2016 Editor's Choice of The Journal of Chemical Physics VL - 145 IS - 174103 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Ciccotti, Giovanni A1 - Delle Site, Luigi T1 - Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation JF - Journal of Chemical Theory and Computation Y1 - 2014 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 10 IS - 4 SP - 1376 EP - 1386 ER - TY - JOUR A1 - Wang, Han A1 - Schütte, Christof A1 - Ciccotti, Giovanni A1 - von Kleist, Max T1 - Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation JF - Journal of Chemical Theory and Computation N2 - In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context, we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and nontrivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes. Y1 - 2014 U6 - https://doi.org/10.1021/ct400993e VL - 10 IS - 4 SP - 1376 EP - 1386 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 - 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 - 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 -