期刊
JOURNAL OF CHEMICAL PHYSICS
卷 132, 期 13, 页码 -出版社
AMER INST PHYSICS
DOI: 10.1063/1.3372802
关键词
bifurcation; biochemistry; molecular biophysics; potential energy surfaces; reaction kinetics theory
资金
- Research and Development of the Next-Generation Integrated Simulation of Living Matter
- Ministry of Education, Culture, Sports, Science and Technology (MEXT)
For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system, a path in Cartesian space is transformed into that in Fourier space, and an overdamped Langevin equation is derived for the Fourier components to achieve a canonical ensemble of the path at a finite temperature. To avoid path trapping around an initially guessed path, the path sampling method is further combined with a powerful sampling technique, the replica exchange method. The principle and algorithm of our method is numerically demonstrated for a model two-dimensional system with a bifurcated potential landscape. The results are compared with those of conventional transition path sampling and the equilibrium theory, and the error due to path discretization is also discussed.
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