期刊
JOURNAL OF CHEMICAL PHYSICS
卷 135, 期 5, 页码 -出版社
AMER INST PHYSICS
DOI: 10.1063/1.3613678
关键词
biochemistry; biomechanics; Brownian motion; chemical relaxation; elastic constants; hydrodynamics; molecular biophysics; molecular configurations; proteins
资金
- Robert A. Welch Foundation [F-1514]
- National Science Foundation [CHE 0848571]
- Department of Energy (U.S.) Department of Energy (DOE) [06-14-11 DE-FG02-05ER25701]
- Grand Challenge Faculty Fellowship
Reduced-dimensionality, coarse-grained models are commonly employed to describe the structure and dynamics of large molecular systems. In those models, the dynamics is often described by Langevin equations of motion with phenomenological parameters. This paper presents a rigorous coarse-graining method for the dynamics of linear systems. In this method, as usual, the conformational space of the original atomistic system is divided into master and slave degrees of freedom. Under the assumption that the characteristic timescales of the masters are slower than those of the slaves, the method results in Langevin-type equations of motion governed by an effective potential of mean force. In addition, coarse-graining introduces hydrodynamic-like coupling among the masters as well as non-trivial inertial effects. Application of our method to the long-timescale part of the relaxation spectra of proteins shows that such dynamic coupling is essential for reproducing their relaxation rates and modes. (C) 2011 American Institute of Physics. [doi:10.1063/1.3613678]
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