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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Zheng, Weihua Andrec, Michael Gallicchio, Emilio Levy, Ronald M. |
| Description | Author Affiliation: Zheng W ( Department of Physics and Astronomy, Rutgers, The State University of New Jersey, 136 Frelinghuysen Road, Piscataway, New Jersey 08854, USA.) |
| Abstract | We present an approach to recover kinetics from a simplified protein folding model at different temperatures using the combined power of replica exchange (RE), a kinetic network, and effective stochastic dynamics. While RE simulations generate a large set of discrete states with the correct thermodynamics, kinetic information is lost due to the random exchange of temperatures. We show how we can recover the kinetics of a 2D continuous potential with an entropic barrier by using RE-generated discrete states as nodes of a kinetic network. By choosing the neighbors and the microscopic rates between the neighbors appropriately, the correct kinetics of the system can be recovered by running a kinetic simulation on the network. We fine-tune the parameters of the network by comparison with the effective drift velocities and diffusion coefficients of the system determined from short-time stochastic trajectories. One of the advantages of the kinetic network model is that the network can be built on a high-dimensional discretized state space, which can consist of multiple paths not consistent with a single reaction coordinate. |
| ISSN | 15206106 |
| e-ISSN | 15205207 |
| Journal | The Journal of Physical Chemistry B |
| Issue Number | 34 |
| Volume Number | 113 |
| Language | English |
| Publisher | American Chemical Society (United States) |
| Publisher Date | 2009-08-27 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Computer Simulation Models, Chemical Proteins Chemistry Thermodynamics Kinetics Protein Folding Research Support, N.I.H., Extramural Physical chemistry |
| Content Type | Text |
| Resource Type | Article |
| Subject | Surfaces, Coatings and Films Materials Chemistry Medicine Physical and Theoretical Chemistry |
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