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. 2016 Sep 8;145(10):100901. doi: 10.1063/1.4962258

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).