Algorithm for rigid-body Brownian dynamics.
We present an algorithm for performing rigid-body Brownian dynamics that can take into account the hydrodynamic properties (translational and rotational friction tensors and the coupling between them) of each rigid body. In the zero temperature limit, the error term scales as Delta;{4} for time step Delta , while at nonzero temperatures the error scaling is Delta;{5/2} . We test the algorithm by applying it to a molecule of four-aminopyridine in water. We intend to use the algorithm to model the interaction between biological ion channels and other channel blocker molecules, but it may also have applicability to modeling other small particles such as colloids or nanoparticles.
Gordon
Dan
D
Computational Biophysics Group, Research School of Biology, The Australian National University, Acton, ACT, Australia. dan.gordon@anu.edu.au
Hoyles
Matthew
M
Chung
Shin-Ho
SH
D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D003102:Colloids / Q000737:chemistry; D004058:Diffusion; D007473:Ion Channels / Q000737:chemistry*; D007477:Ions; D015233:Models, Statistical; D053758:Nanoparticles / Q000737:chemistry; D013696:Temperature; D013997:Time Factors
D003102:Colloids; D007473:Ion Channels; D007477:Ions