TY - JOUR T1 - A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA JF - bioRxiv DO - 10.1101/069310 SP - 069310 AU - Y. A. G. Fosado AU - D. Michieletto AU - Jim Allan AU - Chris Brackley AU - O. Henrich AU - D. Marenduzzo Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/08/12/069310.abstract N2 - 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. ER -