TY - JOUR
T1 - Recent advances in transition path sampling
T2 - Accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics
AU - Peters, Baron
N1 - Funding Information:
We thank Peter Bolhuis, Eric Vanden-Eijnden, Giovanni Ciccotti, Aaron Dinner, David Chandler, Berend Smit and Ravi Radhakrishnan for years of stimulating interactions. We thank Graeme Henkelman for discussions about variational TST. We also thank Gregg Beckham, Bernhardt Trout, Mike Doherty and Brandon Knott for central contributions to the ideas and examples in this work. We acknowledge the support of The American Chemical Society Petroleum Research Fund.
Copyright:
Copyright 2011 Elsevier B.V., All rights reserved.
PY - 2010/12
Y1 - 2010/12
N2 - Because transition states are too rare and transient to observe in experiments, simulations are among the best sources of molecular-level insight on transition states and reaction mechanisms. A first step in many rare-event simulations is to identify a reaction coordinate. For reactions that break and make strong bonds, the reaction coordinate is the unstable eigenmode at a saddle point on the potential energy surface. However, processes such as nucleation and protein folding may disrupt and reorganise thousands of interactions, so identifying a reaction coordinate is a major challenge. An accurate reaction coordinate should result in a free energy profile that is consistent with the projected dynamics. Ten years ago, this intuitive requirement led to committor analysis, a trial-and-error procedure for testing putative reaction coordinates. Since then, our ability to identify accurate reaction coordinates has dramatically improved. First, new versions of committor analysis are quantitative and more efficient. Second, likelihood maximisation can systematically and efficiently identify accurate reaction coordinates from thousands of candidates using only the shooting point data from a path sampling simulation. Finally, the new aimless shooting version of transition path sampling retains a high sampling efficiency even for systems with highly diffusive barrier-crossing dynamics.
AB - Because transition states are too rare and transient to observe in experiments, simulations are among the best sources of molecular-level insight on transition states and reaction mechanisms. A first step in many rare-event simulations is to identify a reaction coordinate. For reactions that break and make strong bonds, the reaction coordinate is the unstable eigenmode at a saddle point on the potential energy surface. However, processes such as nucleation and protein folding may disrupt and reorganise thousands of interactions, so identifying a reaction coordinate is a major challenge. An accurate reaction coordinate should result in a free energy profile that is consistent with the projected dynamics. Ten years ago, this intuitive requirement led to committor analysis, a trial-and-error procedure for testing putative reaction coordinates. Since then, our ability to identify accurate reaction coordinates has dramatically improved. First, new versions of committor analysis are quantitative and more efficient. Second, likelihood maximisation can systematically and efficiently identify accurate reaction coordinates from thousands of candidates using only the shooting point data from a path sampling simulation. Finally, the new aimless shooting version of transition path sampling retains a high sampling efficiency even for systems with highly diffusive barrier-crossing dynamics.
KW - diffusive dynamics
KW - likelihood maximisation
KW - rare events
KW - reaction coordinates
KW - transition path sampling
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U2 - 10.1080/08927020903536382
DO - 10.1080/08927020903536382
M3 - Article
AN - SCOPUS:78650372031
VL - 36
SP - 1265
EP - 1281
JO - Molecular Simulation
JF - Molecular Simulation
SN - 0892-7022
IS - 15
ER -