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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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 |
work_keys_str_mv |
AT aiqunhuang dynamicsofdnasqueezedinsideananochannelviaaslidinggasket AT walterreisner dynamicsofdnasqueezedinsideananochannelviaaslidinggasket AT aniketbhattacharya dynamicsofdnasqueezedinsideananochannelviaaslidinggasket |
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1716784531957088256 |