期刊
MULTISCALE MODELING & SIMULATION
卷 15, 期 4, 页码 1672-1693出版社
SIAM PUBLICATIONS
DOI: 10.1137/16M108700X
关键词
polymer dynamics; DNA; Rouse model; Brownian dynamics; multiscale modeling
资金
- EPSRC [EP/K032208/1, EP/G03706X/1]
- Simons Foundation
- Royal Society
- MEXT/JSPS KAKENHI [JP23115007, JP16H01408]
- Platform for Dynamic Approaches to Living System, AMED, Japan
- Engineering and Physical Sciences Research Council [1511074, EP/K032208/1] Funding Source: researchfish
- EPSRC [EP/K032208/1] Funding Source: UKRI
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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