Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket

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 nonequilib...

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Main Authors: Aiqun Huang, Walter Reisner, Aniket Bhattacharya
Format: Article
Language:English
Published: MDPI AG 2016-09-01
Series:Polymers
Subjects:
DNA
Online Access:http://www.mdpi.com/2073-4360/8/10/352
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spelling doaj-f32e1804a3d44dba995e4c2c62c87aea2020-11-24T20:58:47ZengMDPI AGPolymers2073-43602016-09-0181035210.3390/polym8100352polym8100352Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding GasketAiqun Huang0Walter Reisner1Aniket Bhattacharya2University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USAMcGill University, 845 Rue Sherbrooke O, Montréal, QC H3A 0G4, CanadaUniversity of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USAWe 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.http://www.mdpi.com/2073-4360/8/10/352DNAnanochannelcoarse-grained modelpolymer physicsBrownian dynamicsnonlinear diffusion equationstatistical mechanics
collection DOAJ
language English
format Article
sources DOAJ
author Aiqun Huang
Walter Reisner
Aniket Bhattacharya
spellingShingle Aiqun Huang
Walter Reisner
Aniket Bhattacharya
Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket
Polymers
DNA
nanochannel
coarse-grained model
polymer physics
Brownian dynamics
nonlinear diffusion equation
statistical mechanics
author_facet Aiqun Huang
Walter Reisner
Aniket Bhattacharya
author_sort Aiqun Huang
title Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket
title_short Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket
title_full Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket
title_fullStr Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket
title_full_unstemmed Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket
title_sort dynamics of dna squeezed inside a nanochannel via a sliding gasket
publisher MDPI AG
series Polymers
issn 2073-4360
publishDate 2016-09-01
description 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.
topic DNA
nanochannel
coarse-grained model
polymer physics
Brownian dynamics
nonlinear diffusion equation
statistical mechanics
url http://www.mdpi.com/2073-4360/8/10/352
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