Dynamics Of Dna Squeezed Inside A Nanochannel Via A Sliding Gasket

Keywords

Brownian dynamics; Coarse-grained model; DNA; Nanochannel; Nonlinear diffusion equation; Polymer physics; Statistical mechanics

Abstract

We use Brownian dynamics (BD) simulation of a coarse-grained (CG) bead-spring model of DNA to study the nonequilibrim dynamics of a single DNA molecule confined inside a rectangular nanochannel being squeezed with a sliding gasket piston or "nanodozer". From our simulations we extract the nonequilibrim density profile c(x, t) of the squeezed molecule along the channel axis (x-coordinate) and then analyze the non-equilibrium profile using a recently introduced phenomenological Nonlinear Partial Differential Equation (NPDE) model. Since the NPDE approach also fits the experimental results well and is numerically efficient to implement, the combined BD + NPDE methods can be a powerful approach to analyze details of the confined molecular dynamics. In particular, the overall excellent agreement between the two complementary sets of data provides a strategy for carrying out large scale simulation on semi-flexible biopolymers in confinement at biologically relevant length scales.

Publication Date

9-29-2016

Publication Title

Polymers

Volume

8

Issue

10

Document Type

Article

Personal Identifier

scopus

DOI Link

https://doi.org/10.3390/polym8100352

Socpus ID

84994810312 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/84994810312

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