TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with Adaptive Temperature in Mixed–Canonical Ensemble: Efficient conformational analysis of RNA JF - J. Comp. Chem. Y1 - 1998 U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - CHAP A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://www.zib.de/PaperWeb/abstracts/ZR-01-03 IS - 24 SP - 235 EP - 259 PB - Springer ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with adaptive temperature choice JF - Comp. Phys. Comm. Y1 - 1999 UR - http://publications.imp.fu-berlin.de/93/ U6 - https://doi.org/10.1016/S0010-4655(99)00274-X VL - 121 SP - 37 EP - 39 ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble JF - J. Comp. Chem. Y1 - 1998 UR - http://publications.imp.fu-berlin.de/97/ U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - CHAP A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://publications.imp.fu-berlin.de/128/ VL - 24 SP - 235 EP - 259 PB - Springer ER - TY - GEN A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with Adaptive Temperature in a Mixed-Canonical Ensemble: Efficient Conformational Analysis of RNA N2 - A hybrid Monte Carlo method with adaptive temperature choice is presented, which exactly generates the distribution of a mixed-canonical ensemble composed of two canonical ensembles at low and high temperature. The analysis of resulting Markov chains with the reweighting technique shows an efficient sampling of the canonical distribution at low temperature, whereas the high temperature component facilitates conformational transitions, which allows shorter simulation times. \\The algorithm was tested by comparing analytical and numerical results for the small n-butane molecule before simulations were performed for a triribonucleotide. Sampling the complex multi-minima energy landscape of these small RNA segments, we observed enforced crossing of energy barriers. T3 - ZIB-Report - SC-97-67 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3364 ER - TY - GEN A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations N2 - Uncoupling-coupling Monte Carlo (UCMC) combines uncoupling techniques for finite Markov chains with Markov chain Monte Carlo methodology. UCMC aims at avoiding the typical metastable or trapping behavior of Monte Carlo techniques. From the viewpoint of Monte Carlo, a slowly converging long-time Markov chain is replaced by a limited number of rapidly mixing short-time ones. Therefore, the state space of the chain has to be hierarchically decomposed into its metastable conformations. This is done by means of combining the technique of conformation analysis as recently introduced by the authors, and appropriate annealing strategies. We present a detailed examination of the uncoupling-coupling procedure which uncovers its theoretical background, and illustrates the hierarchical algorithmic approach. Furthermore, application of the UCMC algorithm to the $n$-pentane molecule allows us to discuss the effect of its crucial steps in a typical molecular scenario. T3 - ZIB-Report - 01-03 KW - almost invariant sets KW - bridge sampling KW - metastability KW - hierarchical annealing KW - hybrid Monte Carlo KW - $n$-pentane molecule KW - ratio of normalizing co Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6296 ER -