DNA dynamics squeezed inside a nano-channel with a sliding gasket

We study transients and steady states of a DNA inside a rectangular nano-channel squeezed by a sliding gasket$^{1,2,3}$. We carry out Brownian dynamics (BD) simulation for a DNA modeled as a semi-flexible polymer characterized by its contour length $L$ and the persistence length $\ell_p$. Specifically we study the evolution of one dimensional concentration profile $c(x,t)$ and the chain extension $R$ along the channel axis ($x$-axis) during both the contracting as well as the retracting phases as a function of the velocity of the nano-dozer, both in steady states and in transients as a function of the dimensionless parameter $\ell_p/D$, where $D$ is the channel diameter. Consistent with the equilibrium conformations in the form of de Gennes blobs ($\ell_p/D \sim 1$) and Odijk deflection lengths ($\ell_p/D \gg 1$), our systematic studies of the non-equilibrium dynamics of the squeezed DNA reveal interesting features which could be rationalized with their corresponding equilibrium conformations. \\ $^1$ A. Khorshid et al., Phys. Rev. Lett, {\bf 113}, 268104 (2014)).\\ $^2$ A. Khorshid, S. Amin, Z. Zhang, T. Sakaue, and W. Reisner, Macromolecules {\bf 49}, 1933 (2016).\\ $^3$ A. Huang, W. Reisner,and A. Bhattacharya, Polymers {\bf 8}, 352 (2016).