isDNA: A Tool for Real-Time Visualization of Plasmid DNA Monte-Carlo Simulations in 3D

摘要

Computational simulation of plasmid DNA (pDNA) molecules, owning a closed-circular shape, has been a subject of study for many years. Monte-Carlo methods are the most popular family of methods that have been used in pDNA simulations. However, though there are many software tools for assembling and visualizing DNA molecules, none of them allows the user to visualize the course of the simulation in 3D. As far as we know, we present here the first software (called isDNA) allowing the user to visualize 3D MC simulations of pDNA in real-time. This is sustained on an adaptive DNA assembly algorithm that uses Gaussian molecular surfaces of the nucleotides as building blocks, and an efficient deformation algorithm for pDNA's MC simulations.