ON ALGORITHMS FOR BROWNIAN DYNAMICS COMPUTER SIMULATIONS

On Algorithms for Brownian Dynamics Computer Simulations

Several Brownian Dynamics numerical schemes for treating stochastic differential equations at the position Langevin level are analyzed from the point of view of their algorithmic efficiency. The algorithms are tested using model colloidal fluid of particles interacting via the Yukawa potential. Limitations in the conventional Brownian Dynamics algorithm are shown and it is demonstrated that muc...

Algorithms for Molecular Dynamics Simulations

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Predicting Protein Interactions by Brownian Dynamics Simulations

We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation ef...

Profile of RNA Helices: Brownian Dynamics Simulations

Bends in nucleic acid helices can be quantified in a transient electric birefringence (TEB) experiment from the ratio of the terminal decay times of the bent molecule and its fully duplex counterpart (T-ratio method). The apparent bend angles can be extracted from the experimental T-ratios through the application of static (equilibrium-ensemble) hydrodynamic models; however, such models do not ...

Brownian Dynamics Simulations on Hard-Sphere Colloidal Suspensions