From thermodynamics to kinetics: enhanced sampling of rare events

Accounts of Chemical Research
Lijiang YangYi Qin Gao

Abstract

Despite great advances in molecular dynamics simulations, there remain large gaps between the simulations and experimental observations in terms of the time and length scales that can be approached. Developing fast and accurate algorithms and methods is of ultimate importance to bridge these gaps. In this Account, we briefly summarize recent efforts in such directions. In particular, we focus on integrated tempering sampling. The efficiency of this sampling method has been demonstrated by applications to a range of chemical and biological problems: protein folding, molecular cluster structure searches, and chemical reactions. The combination of integrated tempering sampling and a trajectory sampling method allows the calculation of rate constants and reaction pathways without predefined collective coordinates.

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Citations

Oct 21, 2015·The Journal of Physical Chemistry. B·Jun ZhangYi Qin Gao
Jan 16, 2017·The Journal of Chemical Physics·Liangxu XieMingjun Yang
Jun 28, 2018·Physical Chemistry Chemical Physics : PCCP·Qiang Shao, Weiliang Zhu
Apr 2, 2019·Physical Chemistry Chemical Physics : PCCP·Qiang Shao, Weiliang Zhu
May 28, 2019·Physical Chemistry Chemical Physics : PCCP·Qiang Shao, Weiliang Zhu
Aug 24, 2019·The Journal of Chemical Physics·Yi Isaac YangYi Qin Gao
Jan 9, 2017·The Journal of Chemical Physics·Christopher D FuJim Pfaendtner
Sep 5, 2020·International Journal of Molecular Sciences·Raudah LazimSun Choi
Feb 27, 2018·Physical Chemistry Chemical Physics : PCCP·Qiang Shao, Weiliang Zhu
Jun 3, 2021·International Journal of Molecular Sciences·Xiaoyong Cao, Pu Tian
Nov 5, 2019·Accounts of Chemical Research·Haohao FuChristophe Chipot
Jun 28, 2019·The Journal of Physical Chemistry Letters·Tuan A HoJeffery A Greathouse
Dec 1, 2018·Journal of Chemical Information and Modeling·Doris A SchuetzAndrea Cavalli
Nov 10, 2017·Journal of Chemical Theory and Computation·Qiang Shao, Weiliang Zhu
Sep 17, 2019·The Journal of Physical Chemistry Letters·Jun ZhangFrank Noé
Oct 26, 2018·The Journal of Physical Chemistry Letters·Yi Isaac YangMichele Parrinello
Feb 3, 2018·Journal of Chemical Theory and Computation·Xiangda PengGuohui Li
May 2, 2018·Journal of Chemical Theory and Computation·Yi Isaac Yang, Michele Parrinello

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