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Cited by 417Advanced Physical and Chemical Molecular InteractionsTheoretical and Computational PhysicsStochastic processes and statistical mechanics

The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.

Obtaining reaction coordinates by likelihood maximization

Peters, Baron, Trout, Bernhardt L.·2006·The Journal of Chemical Physics
DOI 10.1063/1.2234477
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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.

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Research works printed but not linked: 3

  1. 2004, J. Phys.: Condens. Matter, 1, 0408331
  2. 1978, Ann. Stat., 6, 461
  3. 1996, Metastable Liquids

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Metadata

Authors
Peters, B., & Trout, B. L.
Affiliations
Massachusetts Institute of Technology (US)
ORCID
Venue
The Journal of Chemical Physics
Publisher
AIP Publishing
Published
2006-08-04
Volume
125
Issue
5
Pages
054108-054108
ISSN
  • 0021-9606 (ISSN-L)
  • 1089-7690
DOI
10.1063/1.2234477
OpenAlex
W2011242225
Cited by
417
References
45
Citations by year
2026: 15 · 2025: 20 · 2024: 22 · 2023: 41 · 2022: 22 · 2021: 23 · 2020: 26 · 2019: 21 · 2018: 19 · 2017: 50 · 2016: 27 · 2015: 23 · 2014: 14 · 2013: 13 · 2012: 15
FWCI
6.61
Type
journal article
Language
en
Open access
closed
Locations
  • The Journal of Chemical Physics (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Physical Sciences › Physics and Astronomy › Condensed Matter Physics › Theoretical and Computational Physics
  • Physical Sciences › Mathematics › Mathematical Physics › Stochastic processes and statistical mechanics
Keywords
reaction coordinate, transition path sampling, likelihood maximization, collective variables, Bayesian information criterion, nucleation, Ising model, surface area effect

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