A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA

Abstract

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.

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Cited by in corpus (7)

• Coarse-Grained Simulation of DNA using LAMMPS
• Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
• Length scale dependent elasticity in DNA from coarse-grained and all-atom models
• Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance
• Overtwisting induces polygonal shapes in bent DNA
• Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting
• Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+