A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes

Biophysical Journal
K KleninJ Langowski

Abstract

For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation of such DNAs, we have developed an efficient and easy way to set up a program based on a second-order explicit Brownian dynamics algorithm. The DNA is modeled by a chain of rigid segments interacting through harmonic spring potentials for bending, torsion, and stretching. The electrostatics are handled using precalculated energy tables for the interactions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prager tensor. While maintaining acceptable precision, the simulation can be accelerated by recalculating this tensor only once in a certain number of steps.

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Citations

Aug 10, 2000·Biopolymers·K Klenin, J Langowski
Jul 19, 2002·Biophysical Journal·Svetlana S ZakharovaJohan R C van der Maarel
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