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

DOI10.1137/16M108700XzbMATH Open1386.60205arXiv1607.08062OpenAlexW2963644712MaRDI QIDQ4601609FDOQ4601609

Authors: Edward Rolls, Yuichi Togashi, Radek Erban 

Publication date: 17 January 2018

Published in: Multiscale Modeling & Simulation (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1607.08062

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zbMATH Keywords

DNABrownian dynamicsmultiscale modelingpolymer dynamicsRouse model

Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Protein sequences, DNA sequences (92D20) Stochastic ordinary differential equations (aspects of stochastic analysis) (60H10) Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31) Statistical mechanics of polymers (82D60)

Cites Work

• Slice sampling. (With discussions and rejoinder)
• Title not available (Why is that?)
• Covariance control theory
• Stability Analysis of Numerical Schemes for Stochastic Differential Equations
• Title not available (Why is that?)
• Brownian dynamics simulations of bead-rod and bead-spring chains: Numerical algorithms and coarse-graining issues.
• From molecular dynamics to Brownian dynamics
• Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

Cited In (3)

• Multiscale Method for Simulating Protein-DNA Complexes
• Multiscale Coupling of Molecular Dynamics and Hydrodynamics: Application to DNA Translocation through a Nanopore
• Inferring parameters for an elementary step model of DNA structure kinetics with locally context-dependent Arrhenius rates

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