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arXiv · 1607.08062

Varying the resolution of the Rouse model on temporal and spatial scales: application to multiscale modelling of DNA dynamics

Edward Rolls·Yuichi Togashi·Radek Erban
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Abstract

A multi-resolution bead-spring model for polymer dynamics is developed as a generalization of the Rouse model. A polymer chain is described using beads of variable sizes connected by springs with variable spring constants. A numerical scheme which can use different timesteps to advance the positions of different beads is presented and analyzed. The position of a particular bead is only updated at integer multiples of the timesteps associated with its connecting springs. This approach extends the Rouse model to a multiscale model on both spatial and temporal scales, allowing simulations of localized regions of a polymer chain with high spatial and temporal resolution, while using a coarser modelling approach to describe the rest of the polymer chain. A method for changing the model resolution on-the-fly is developed using the Metropolis-Hastings algorithm. It is shown that this approach maintains key statistics of the end-to-end distance and diffusion of the polymer filament and makes computational savings when applied to a model for the binding of a protein to the DNA filament.

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Edward Rolls, Yuichi Togashi, Radek Erban. 2016-07-27. Varying the resolution of the Rouse model on temporal and spatial scales: application to multiscale modelling of DNA dynamics. https://arxiv.org/abs/1607.08062

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