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Finding multiple reaction pathways via global optimization of action.

ABSTRACT: Global searching for reaction pathways is a long-standing challenge in computational chemistry and biology. Most existing approaches perform only local searches due to computational complexity. Here we present a computational approach, Action-CSA, to find multiple diverse reaction pathways connecting fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing (CSA) method. Action-CSA successfully overcomes large energy barriers via crossovers and mutations of pathways and finds all possible pathways of small systems without initial guesses on pathways. The rank order and the transition time distribution of multiple pathways are in good agreement with those of long Langevin dynamics simulations. The lowest action folding pathway of FSD-1 is consistent with recent experiments. The results show that Action-CSA is an efficient and robust computational approach to study the multiple pathways of complex reactions and large-scale conformational changes.

SUBMITTER: Lee J

PROVIDER: S-EPMC5458546 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Finding multiple reaction pathways via global optimization of action.

Lee Juyong J Lee In-Ho IH Joung InSuk I Lee Jooyoung J Brooks Bernard R BR

Nature communications 20170526

Global searching for reaction pathways is a long-standing challenge in computational chemistry and biology. Most existing approaches perform only local searches due to computational complexity. Here we present a computational approach, Action-CSA, to find multiple diverse reaction pathways connecting fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing (CSA) method. Action-CSA successfully overcomes large energy barrier ...[more]

PMID: 28548089

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Finding multiple reaction pathways via global optimization of action.

Publications

Finding multiple reaction pathways via global optimization of action.

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