Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket
University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA
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
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
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.
This is an open access article distributed under the Creative Commons Attribution License
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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MDPI and ACS Style
Huang, A.; Reisner, W.; Bhattacharya, A. Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket. Polymers 2016, 8, 352.
Huang A, Reisner W, Bhattacharya A. Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket. Polymers. 2016; 8(10):352.
Huang, Aiqun; Reisner, Walter; Bhattacharya, Aniket. 2016. "Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket." Polymers 8, no. 10: 352.
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