Dresden 2011 – wissenschaftliches Programm

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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 29: Biopolymers and Biomaterials III (jointly with BP)

CPP 29.4: Vortrag

Mittwoch, 16. März 2011, 15:45–16:00, ZEU 260

Coarse Grained Simulations of Biopolymers: Effects of Finite Damping and Hydrodynamic Interactions — Uwe Winter and •Tihamer Geyer — Center for Bioinformatics, Saarland University, Saarbrücken

In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong that the particles’ velocities are damped much faster than the duration of an integration timestep. Here we show that this conceptual limit can be dropped with an analytic integration of the equations of damped motion. In the resulting Langevin integration scheme our recently proposed approximate form of the hydrodynamic interactions between the particles [1] can be incorparated conveniently, leading to a fast multi-particle propagation scheme, which captures more of the short-time and short-range solvent effects than standard BD. Comparing the dynamics of a bead-spring model of a short peptide, we recommend to run simulations of biological molecules and polymers with the Langevin type finite damping and to include the hydrodynamic interactions [2].

[1] Geyer, Winter, J. Chem. Phys. 130 (2009) 114905

[2] Winter, Geyer, J. Chem. Phys. 131 (2009) 104102