Literature DB >> 25338883

A fast tomographic method for searching the minimum free energy path.

Changjun Chen1, Yanzhao Huang1, Xuewei Jiang2, Yi Xiao1.   

Abstract

Minimum Free Energy Path (MFEP) provides a lot of important information about the chemical reactions, like the free energy barrier, the location of the transition state, and the relative stability between reactant and product. With MFEP, one can study the mechanisms of the reaction in an efficient way. Due to a large number of degrees of freedom, searching the MFEP is a very time-consuming process. Here, we present a fast tomographic method to perform the search. Our approach first calculates the free energy surfaces in a sequence of hyperplanes perpendicular to a transition path. Based on an objective function and the free energy gradient, the transition path is optimized in the collective variable space iteratively. Applications of the present method to model systems show that our method is practical. It can be an alternative approach for finding the state-to-state MFEP.

Year:  2014        PMID: 25338883     DOI: 10.1063/1.4897983

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  3 in total

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Authors:  Stefan Vogt-Geisse
Journal:  J Mol Model       Date:  2016-04-23       Impact factor: 1.810

2.  Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA.

Authors:  Dhiman Ray; Ioan Andricioaei
Journal:  Biophys J       Date:  2020-09-02       Impact factor: 4.033

3.  Fast exploration of an optimal path on the multidimensional free energy surface.

Authors:  Changjun Chen
Journal:  PLoS One       Date:  2017-05-18       Impact factor: 3.240

  3 in total

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