Copyright 2016. Massachusetts Institute of Technology. Rights Reserved. M.I.T. hereby makes following copyrightable material available to the public under GNU General Public License, version 2 (GPL-2.0). A copy of this license is available at https://opensource.org/licenses/GPL-2.0
Programmed DNA assemblies of high molecular weight (reaching millions of Daltons for M13-scaffolded DNA origami) fluctuate thermally at room temperature on large length-scales and long time-scales that render conventional all-atom molecular dynamics simulations computationally infeasible. Brownian Dynamics is an alternative, coarse-grained computational approach  that enables the computationally efficient simulation of the over-damped conformational dynamics of DNA nanostructures in a viscous solvent environment. To enable the long time-scale simulation of the over-damped conformational dynamics of DNA nanostructures about a single equilibrium ground-state conformation, we have developed a theoretical Brownian Dynamics framework that is implemented in MATLAB. The MATLAB script with accompanying documentation and an example is available here.
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