RT Journal Article
SR Electronic
T1 A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 069310
DO 10.1101/069310
A1 Y. A. G. Fosado
A1 D. Michieletto
A1 Jim Allan
A1 Chris Brackley
A1 O. Henrich
A1 D. Marenduzzo
YR 2016
UL http://biorxiv.org/content/early/2016/08/12/069310.abstract
AB The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules — up to a million base pairs — for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. We compare the behaviour of our model with single molecule experiments where dsDNA is manipulated by external forces or torques. We also present some results on the kinetics of denaturation of linear DNA.