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

Journal article

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.

Authors: Rolls, E; Togashi, Y; Erban, R

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Society for Industrial and Applied Mathematics
• Journal: Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal
• Volume: 15
• Issue: 4
• Pages: 1672–1693
• Publication date: 2017-11-16
• Acceptance date: 2017-05-22
• DOI: 10.1137/16M108700X
• EISSN: 1540-3467
• ISSN: 1540-3459
• Keywords: physics.comp-ph; physics.bio-ph