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Building Markov state models using optimal transport theory
Open accessPublished version of a preprint
Abstract
Markov State Models (MSMs) describe the rates and routes in conformational dynamics of biomolecules. Computational estimation of MSMs can be expensive because molecular simulations are slow to find and sample the rare transient events. We describe here an efficient approximate way to determine MSM rate matrices by combining maximum caliber (maximizing path entropies) with optimal transport theory (minimizing some path cost function, as when routing trucks on transportation networks) to patch together transient dynamical information from multiple non-equilibrium simulations. We give toy examples.
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Cites
Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163
Self-citationMarkov state models of biomolecular conformational dynamics
Chodera, J. D., & Noé, F. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.04.002 · Cited by 776
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Metadata
- Authors
- Dixit, P. D., & Dill, K. A.
- Affiliations
- Columbia University (US)
- Stony Brook University (US)
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2019-02-06
- Volume
- 150
- Issue
- 5
- Pages
- 054105-054105
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2913155865
- Cited by
- 9
- References
- 2
- Citations by year
- 2024: 1 · 2023: 1 · 2022: 1 · 2021: 1 · 2020: 3 · 2019: 2
- FWCI
- 0.58
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- The Journal of Chemical Physics (publishedVersion)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Royal College of Surgeons in Ireland (submittedVersion, cc-by-nc-nd)
- Funders
- NSF (PHY1205881)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- 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
- Keywords
- Markov state models, optimal transport, maximum caliber, path entropy, conformational dynamics, biomolecules, rate matrix, non-equilibrium simulation, path cost minimization
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