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PreprintCited by 0Advanced Physical and Chemical Molecular InteractionsAdvanced Thermodynamics and Statistical Mechanicsstochastic dynamics and bifurcation

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Potential Energy Weighted Reactive Flux and Total Rate of Change of Potential Energy: Theory and Illustrative Applications

Open access
Li, Wenjin·2022·The Journal of Physical Chemistry A
DOI 10.1101/2022.07.08.499260

Preprint — published as 10.1021/acs.jpca.2c04886

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Abstract

Reactive flux can be largely non-zero in a nonequilibrium ensemble of trajectories and provide insightful information for reactive transitions from the reactant state to the product state. Based on the reactive flux, a theoretical framework is proposed here for two quantities, the potential energy weighted reactive flux and the total rate of change of potential energy, which are useful for the identification of mechanism from a nonequilibrium ensemble. From such quantities, two multidimensional free energy analogues can be derived in the subspace of collective variables and they are equivalent in the regions where the reactive flux is divergence-free. These free energy analogues are assumed to be closely related to the free energy in the subspace of collective variables and they are reduced in the one-dimensional case to be the ensemble average of the potential energy weighted with reactive flux intensity, which was proposed recently and could be decomposed into energy components at the per-coordinate level. In the subspace of collective variables, the decomposition of the multidimensional free energy analogues at the per-coordinate level is theoretically possible and is numerically difficult to be calculated. Interestingly, the total rate of change of potential energy is able to identify the location of the transition state ensemble or the stochastic separatrix, in addition to the locations of the reactant and product states. The total rate of change of potential energy can be decomposed at the per-coordinate level and its components can quantify the contribution of a coordinate to the reactive transition in the subspace of collective variables. We then illustrated the main insights and objects that can be provided by the approach in the application to the alanine peptide in vacuum in various nonequilibrium ensembles of short trajectories and the results from these ensembles were found to be consistent.

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Metadata

Authors
Li, W.
Affiliations
Shenzhen University (CN)
Corresponding author
Li, Wenjin
ORCID
Li, Wenjin
Venue
The Journal of Physical Chemistry A
Publisher
openRxiv
Published
2022-07-10
Volume
126
Issue
42
Pages
7774-7786
ISSN
1089-5639 (ISSN-L)
DOI
10.1101/2022.07.08.499260
OpenAlex
W4306410250
Cited by
0
References
1
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • The Journal of Physical Chemistry A (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
  • Natural Science Foundation of Guangdong Province (2020A1515010984, 860-000002110384)
  • Shenzhen University (860-000002110384)
Topics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Physical Sciences › Physics and Astronomy › Statistical and Nonlinear Physics › Advanced Thermodynamics and Statistical Mechanics
  • Physical Sciences › Physics and Astronomy › Statistical and Nonlinear Physics › stochastic dynamics and bifurcation
Keywords
reactive flux, collective variables, transition state ensemble, diffusion anisotropy, alanine peptides
MeSH terms
Alanine

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