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 [14] 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.

Users of this tool are kindly requested to cite the following reference:

  • RS Sedeh, K Pan, MR Adendorff, O Hallatschek, KJ Bathe, M Bathe. Computing nonequilibrium conformational dynamics of structured nucleic acid assemblies. Journal of Chemical Theory and Computation, 12: 261-273 (2016). [ Pubmed Article ]