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- W2016938198 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." @default.
- W2016938198 created "2016-06-24" @default.
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- W2016938198 date "2009-08-05" @default.
- W2016938198 modified "2023-09-25" @default.
- W2016938198 title "Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics" @default.
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- W2016938198 doi "https://doi.org/10.1021/jp900445t" @default.
- W2016938198 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2975981" @default.
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