Monte Carlo simulation of a supercoiled double-stranded DNA model

Abstract

An efficient Monte Carlo Metropolis simulation [Monte Carlo et al, 1953] wasconducted on the double stranded DNA model proposed by [Zhang et al, 2000]. Themodel was mathematically discussed in detail and the calculation time for the energycomponents were improved. The mathematical characteristic of the writhe calculationwas also examined and a fast algorithm which reduces the writhe calculation by 45-55% was presented. The method was verified with the conventional algorithm and thecalculated writhe was found to be accurate within usable limits. The force versusextension and supercoiling degree versus extension relationships of the model werealso investigated and verified with the experimental results published by [Strick et al,1998]. The results obtained from the simulation coincide reasonably with theexperimental measurements.