Obtaining reaction coordinates by likelihood maximization
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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It is possible to automate the parameter optimization, so as to maximise the similarity with the committor.
“It is then possible to automate the parameter optimization, so as to maximise the similarity with the committor 100-102 .”
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Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies
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An Experimental and Computational Investigation of Spontaneous Lasso Formation in Microcin J25
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Rogal, J., Lechner, W., Juraszek, J., Ensing, B., & Bolhuis, P. G. (2010) · The Journal of Chemical Physics · doi:10.1063/1.3491817 · Cited by 69 · see citing works
Beckham, G. T., & Peters, B. (2011) · The Journal of Physical Chemistry Letters · doi:10.1021/jz2002887 · Cited by 69 · see citing works
Self-citationPeters, B. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3271024 · Cited by 65 · see citing works
Self-citationFoundations and latest advances in replica exchange transition interface sampling
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Ravindra, P., Smith, Z., & Tiwary, P. (2019) · Molecular Systems Design & Engineering · doi:10.1039/c9me00115h · Cited by 67 · see citing works
Limit of validity of Ostwald's rule of stages in a statistical mechanical model of crystallization
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Trajectory‐Based Rare Event Simulations
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Allen, R. J., Valeriani, C., Tănase‐Nicola, S., ten Wolde, P. R., & Frenkel, D. (2008) · The Journal of Chemical Physics · doi:10.1063/1.2981052 · Cited by 65 · see citing works
Quantitative comparison of adaptive sampling methods for protein dynamics
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Nucleation in a Potts lattice gas model of crystallization from solution
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The potential for machine learning in hybrid QM/MM calculations
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On Reaction Coordinate Optimality
Krivov, S. V. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct3008292 · Cited by 61 · see citing works
Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide
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Mehdi, S., Wang, D., Pant, S., & Tiwary, P. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00058 · Cited by 60 · see citing works
Recent advances in molecular simulation: A chemical engineering perspective
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Pathways to self-organization: Crystallization via nucleation and growth
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Molecular Understanding of Homogeneous Nucleation of CO2 Hydrates Using Transition Path Sampling
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Inertial likelihood maximization for reaction coordinates with high transmission coefficients
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Self-citationEvidence for a Size Dependent Nucleation Mechanism in Solid State Polymorph Transformations
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Self-citationCalculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning
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- Authors
- Peters, B., & Trout, B. L.
- Affiliations
- Massachusetts Institute of Technology (US)
- 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
- 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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