%0 Journal Article %1 ISI:000261141300001 %A Gruenwald, Michael %A Dellago, Christoph %A Geissler, Phillip L. %C CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA %D 2008 %I AMER INST PHYSICS %J JOURNAL OF CHEMICAL PHYSICS %K Carlo Monte energy free isomerisation kinetics methods processes random reaction theory %N 19 %R 10.1063/1.2978000 %T Precision shooting: Sampling long transition pathways %V 129 %X The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest simulated trajectories that exemplify such processes is typically made difficult by a very low acceptance rate for newly generated trajectories. We address this problem by introducing a new generation algorithm based on the linear short time behavior of small disturbances in phase space. Using this ``precision shooting'' technique, arbitrarily small disturbances can be propagated in time, and any desired acceptance ratio of shooting moves can be obtained. We demonstrate the method for a simple but computationally problematic isomerization process in a dense liquid of soft spheres. We also discuss its applicability to barrier-crossing events involving metastable intermediate states.

@article{ISI:000261141300001, abstract = {{The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest simulated trajectories that exemplify such processes is typically made difficult by a very low acceptance rate for newly generated trajectories. We address this problem by introducing a new generation algorithm based on the linear short time behavior of small disturbances in phase space. Using this ``precision shooting{''} technique, arbitrarily small disturbances can be propagated in time, and any desired acceptance ratio of shooting moves can be obtained. We demonstrate the method for a simple but computationally problematic isomerization process in a dense liquid of soft spheres. We also discuss its applicability to barrier-crossing events involving metastable intermediate states.}}, added-at = {2009-01-11T03:04:50.000+0100}, address = {{CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}}, affiliation = {{Grunwald, M (Reprint Author), Univ Vienna, Fac Phys, Boltzmanngasse 5, A-1090 Vienna, Austria. {[}Gruenwald, Michael; Dellago, Christoph] Univ Vienna, Fac Phys, A-1090 Vienna, Austria. {[}Gruenwald, Michael; Dellago, Christoph] Univ Vienna, Ctr Computat Mat Sci, A-1090 Vienna, Austria. {[}Geissler, Phillip L.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. {[}Geissler, Phillip L.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Chem Sci, Berkeley, CA 94720 USA.}}, article-number = {{194101}}, author = {Gruenwald, Michael and Dellago, Christoph and Geissler, Phillip L.}, author-email = {{christoph.dellago@univie.ac.at}}, biburl = {https://www.bibsonomy.org/bibtex/26e39bb1e76c7372e8cd254ef8a33b093/huiyangsfsu}, cited-references = {{ALLEN RJ, 2005, PHYS REV LETT, V94, P8104. ANDERSEN HC, 1980, J CHEM PHYS, V72, P2384. BOLHUIS PG, 2003, J PHYS-CONDENS MAT, V15, S113. DELLAGO C, ADV POLYM S IN PRESS. DELLAGO C, 1996, PHYS REV E, V53, P1485. DELLAGO C, 1998, J CHEM PHYS, V108, P1964. DELLAGO C, 2002, ADV CHEM PHYS, V123, P1. DELLAGO C, 2002, PHYS REV E 2, V65, ARTN 056216. DELLAGO C, 2006, COMPUTER SIMULATIONS, V1. FRENKEL D, 2002, UNDERSTANDING MOLECU. GEISSLER PL, 2001, SCIENCE, V291, P2121. GRUNWALD M, 2007, J CHEM PHYS, V127, ARTN 154718. JURASZEK J, 2006, P NATL ACAD SCI USA, V103, P15859, DOI 10.1073/pnas.0606692103. POSCH HA, 1989, PHYS REV A, V39, P2175. WEEKS JD, 1971, J CHEM PHYS, V54, P5237.}}, doc-delivery-number = {{375VG}}, doi = {{10.1063/1.2978000}}, interhash = {1fe91b194ed47a26e43877894188c413}, intrahash = {6e39bb1e76c7372e8cd254ef8a33b093}, issn = {{0021-9606}}, journal = {{JOURNAL OF CHEMICAL PHYSICS}}, journal-iso = {{J. Chem. Phys.}}, keywords = {Carlo Monte energy free isomerisation kinetics methods processes random reaction theory}, keywords-plus = {{EQUILIBRIUM}}, language = {{English}}, month = {{NOV 21}}, number = {{19}}, number-of-cited-references = {{15}}, publisher = {{AMER INST PHYSICS}}, subject-category = {{Physics, Atomic, Molecular \& Chemical}}, times-cited = {{0}}, timestamp = {2009-01-11T03:04:50.000+0100}, title = {{Precision shooting: Sampling long transition pathways}}, type = {{Article}}, unique-id = {{ISI:000261141300001}}, volume = {{129}}, year = {{2008}} }