Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket a

作者：Huang Aiqun; Reisner Walter; Bhattacharya Aniket^*

来源：Polymers, 2016, 8(10): 352.

DOI：10.3390/polym8100352

• DNA
• nanochannel
• coarse-grained model
• polymer physics
• Brownian dynamics
• nonlinear diffusion equation
• statistical mechanics

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.

• 出版日期2016-10
• 单位McGill