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Fractional Brownian dynamics in proteins
The Journal of Chemical Physics, 2004Correlation functions describing relaxation processes in proteins and other complex molecular systems are known to exhibit a nonexponential decay. The simulation study presented here shows that fractional Brownian dynamics is a good model for the internal dynamics of a lysozyme molecule in solution.
Kneller, Gerald, Hinsen, Konrad
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Interfacing Brownian dynamics simulations
The Journal of Chemical Physics, 2004Starting from the flux of particles in a Brownian dynamics simulation we derive boundary conditions, which allow us (i) to couple a Brownian dynamics calculation to a reservoir of particles of a given density, i.e., setting up constant density boundary conditions, and (ii) to build an interface between Brownian dynamics and a diffusional treatment of ...
T, Geyer, C, Gorba, V, Helms
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Dynamics of a polymer in a Brownian ratchet
Physical Review E, 2010We have used Brownian dynamics simulations to study the dynamics of a bead-and-spring polymer subject to a flashing ratchet potential. To elucidate the role of hydrodynamic (HD) interactions, simulations were carried out for the cases where HD interactions are present and when they are absent.
James M, Polson +4 more
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Bayesian inference for Brownian dynamics
Physical Review E, 2010We present a Bayesian method for inferring the potential energy experienced by a particle subject to Brownian dynamics. Assuming polynomial potentials, the best polynomial order can be determined by analytical computation of a series of Bayes factors. The coefficients can be estimated from marginal posterior distributions.
Daniel L, Ensign, Vijay S, Pande
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Algorithms for brownian dynamics
Molecular Physics, 1982Two recently proposed algorithms for brownian dynamics, one based on the Verlet method of molecular dynamics and the other on Beeman's version of this same method, are shown to be numerically equivalent. The Beemanbased algorithm is slightly more economical on computer storage, since it does not require the transfer of stochastic information from one ...
van Gunsteren, W. F. +1 more
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2014
This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum ...
Tongye, Shen, Chung F, Wong
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This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum ...
Tongye, Shen, Chung F, Wong
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Brownian dynamics with constraints
Molecular Physics, 2001Systems possessing degrees of freedom operating on widely separated timescales, where the effects of those operating on the smaller timescales are relatively unimportant, may be modelled by the use of the Langevin equation. In order to study such systems containing complex polyatomic particles, holonomic constraints may be used. Though there is no lack
Toby O. White +2 more
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