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Revisiting Shooting Point Monte Carlo Methods for Transition Path Sampling

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arxiv 2408.03054 v3 pith:7MWJSLL4 submitted 2024-08-06 physics.comp-ph cond-mat.stat-mech

classification physics.comp-phcond-mat.stat-mech
keywords shootingpathsamplingpointtransitionalgorithmsmethodsacceptance
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Rare event sampling algorithms are essential for understanding processes that occur infrequently on the molecular scale, yet they are important for the long-time dynamics of complex molecular systems. One of these algorithms, transition path sampling (TPS), has become a standard technique to study such rare processes since no prior knowledge on the transition region is required. Most TPS methods generate new trajectories from old trajectories by selecting a point along the old trajectory, modifying its momentum in some way, and then ``shooting'' a new trajectory by integrating forward and backward in time. In some procedures, the shooting point is selected independently for each trial move, but in others, the shooting point evolves from one path to the next so that successive shooting points are related to each other. To account for this memory effect, we introduce a theoretical framework based on an extended ensemble that includes both paths and shooting indices. We derive appropriate acceptance rules for various path sampling algorithms in this extended formalism, ensuring the correct sampling of the transition path ensemble. Our framework reveals the need for amended acceptance criteria in the flexible-length aimless shooting and spring shooting methods.

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  1. The bcc coating of Lennard-Jones crystal nuclei vanishes with a change of local structure detection algorithm

    cond-mat.soft 2024-12 conditional novelty 6.0 of 10

    Using multiple local structure detection algorithms on transition path sampling data, the paper shows that the bcc coating on Lennard-Jones crystal nuclei nearly vanishes with strict outlier-detection-based methods.

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