Journal article
Transition-Path Theory Calculations on Non-Uniform Meshes in Two and Three Dimensions using Finite Elements
Computer physics communications, v 184(10), pp 2310-2315
Oct 2013
PMID: 24014889
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Rare events between states in complex systems are fundamental in many scientific fields and can be studied by building reaction pathways. A theoretical framework to analyze reaction pathways is provided by transition-path theory (TPT). The central object in TPT is the committor function, which is found by solution of the backward-Kolmogorov equation on a given potential. Once determined, the committor can be used to calculate reactive fluxes and rates, among other important quantities. We demonstrate here that the committor can be calculated using the method of finite elements on non-uniform meshes. We show that this approach makes it feasible to perform TPT calculations on 3D potentials because it requires many fewer degrees of freedom than a regular-mesh finite-difference approach. In various illustrative 2D and 3D problems, we calculate the committor function and reaction rates at different temperatures, and we discuss effects of temperatures and simple entropic barriers on the structure of the committor and the reaction rate constants.
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Details
- Title
- Transition-Path Theory Calculations on Non-Uniform Meshes in Two and Three Dimensions using Finite Elements
- Creators
- Mauro Lapelosa - Department of Chemical and Biological Engineering, Drexel University, 3141 Chestnut St., Philadelphia, Pennsylvania 19104Cameron F Abrams - Department of Chemical and Biological Engineering, Drexel University, 3141 Chestnut St., Philadelphia, Pennsylvania 19104
- Publication Details
- Computer physics communications, v 184(10), pp 2310-2315
- Publisher
- Elsevier
- Grant note
- R01 GM100472 || GM / National Institute of General Medical Sciences : NIGMS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000324604200008
- Scopus ID
- 2-s2.0-84883150079
- Other Identifier
- 991014878453804721
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InCites Highlights
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- Web of Science research areas
- Computer Science, Interdisciplinary Applications
- Physics, Mathematical