Evaluating changes of writhe in computer simulations of supercoiled DNA.
We compute changes in the writhe of a polygonal space curve when one of the vertices is displaced. The resulting expressions can be used in simulations of supercoiled DNA. For Brownian dynamics simulations, the expressions can be used to eliminate the explicit twisting degree of freedom. For Monte Carlo simulations, they can be used in fast local moves. Preliminary Monte Carlo simulations using only such fast local moves show that these can be used to efficiently simulate small DNA supercoils.
de Vries
Renko
R
Laboratory of Physical Chemistry and Colloid Science, Wageningen University, P.O. Box 8038, 6700 EK Wageningen, The Netherlands.
D000465:Algorithms; D003198:Computer Simulation; D004278:DNA, Superhelical / Q000737:chemistry*; D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation
D004278:DNA, Superhelical