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J Chem Phys. 2006 Aug 7;125(5):054108.

Obtaining reaction coordinates by likelihood maximization.

Author information

1
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Abstract

We present a new approach for calculating reaction coordinates in complex systems. The new method is based on transition path sampling and likelihood maximization. It requires fewer trajectories than a single iteration of existing procedures, and it applies to both low and high friction dynamics. The new method screens a set of candidate collective variables for a good reaction coordinate that depends on a few relevant variables. The Bayesian information criterion determines whether additional variables significantly improve the reaction coordinate. Additionally, we present an advantageous transition path sampling algorithm and an algorithm to generate the most likely transition path in the space of collective variables. The method is demonstrated on two systems: a bistable model potential energy surface and nucleation in the Ising model. For the Ising model of nucleation, we quantify for the first time the role of nuclei surface area in the nucleation reaction coordinate. Surprisingly, increased surface area increases the stability of nuclei in two dimensions but decreases nuclei stability in three dimensions.

PMID:
16942204
DOI:
10.1063/1.2234477

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