We recently developed a new powerful method to reproduce in silico single-molecule manipulation experiments1. As a proof of principle, we demonstrate that flexible polymers like DNA can be simulated at nanometer resolution using physics engines thanks to an original implementation of Langevin Dynamics in the open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We retrieve force-extension as well as rotation-extension diagrams of reference experimental studies. We also obtain plectoneme diffusion along the DNA molecule and multiplectoneme conformations sporadically, in agreement with quite recent experiments [van Loenhout MTJ, de Grunt MV, Dekker C (2012) Dynamics of dna supercoils. Science 338: 94-97] and theoretical predictions [Emanuel M, Lanzani G, Schiessel H (2013) Multiplectoneme phase of double-stranded dna under tension. Phys Rev E 88: 022706].
We are also currently implementing this methodology to simulate the self assembly of individual nano-objects. Preliminary results on “tangram assemblies” will be presented.
1. P. Carrivain, M. Barbi, J-M. Victor (2014) In silico single-molecule manipulation of DNA with rigid body dynamics, PloS Computational Biology, doi: 10.1371/journal.pcbi.1003456, in press.