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Polymers 2016, 8(10), 352; doi:10.3390/polym8100352

Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket

1
University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA
2
McGill University, 845 Rue Sherbrooke O, Montréal, QC H3A 0G4, Canada
*
Author to whom correspondence should be addressed.
Academic Editor: Martin Kröger
Received: 29 June 2016 / Revised: 8 September 2016 / Accepted: 9 September 2016 / Published: 29 September 2016
(This article belongs to the Special Issue Semiflexible Polymers)
View Full-Text   |   Download PDF [1763 KB, uploaded 29 September 2016]   |  

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. View Full-Text
Keywords: DNA; nanochannel; coarse-grained model; polymer physics; Brownian dynamics; nonlinear diffusion equation; statistical mechanics DNA; nanochannel; coarse-grained model; polymer physics; Brownian dynamics; nonlinear diffusion equation; statistical mechanics
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Huang, A.; Reisner, W.; Bhattacharya, A. Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket. Polymers 2016, 8, 352.

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