TABLE I.
Description of simulation algorithms for crowded macromolecular solutions.
Algorithm | Description | Methodology |
---|---|---|
SD: Stokesian dynamics | Includes both many-body far-field HI and the near-field lubrication forces at low Reynolds number.54 | Original SD algorithm requires an O(N3) matrix inversion and Cholesky factorization of dense matrices. |
BD: Brownian dynamics | Includes HI at the level of Oseen62 or RPY tensors.63 | Algorithm developed by Ermak and McCammon.51 |
FD: Free draining | BD without HI; the diffusion matrix is diagonal and constant. | Limiting case of BD.51 |
FLD: Far field version of SD | Far-field hydrodynamic matrix is approximated by a diagonal matrix, but lubrication forces are explicitly considered. | Developed in Ref. 7. The algorithm scales O(N). |