Sharif Digital Repository

Deformation of single stranded DNA in a translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the electric field inside and outside a narrow pore is obtained. With an analysis based on the "electrohydrodynamic equivalence" we determine the possibility of the extension of a charged polymer due to the presence of an electric field gradient in the vicinity of the pore entrance. With a multi-scale hybrid simulation (LB-MD), it is shown that an effective deformation before reaching the pore occurs, which facilitates the process of finding the entrance for... 

Combining the advection-diffusion equation approach with Monte Carlo simulations we study chaperone driven polymer translocation of a stiff polymer through a nanopore. We demonstrate that the probability density function of first passage times across the pore depends solely on the Péclet number, a dimensionless parameter comparing drift strength and diffusivity. Moreover it is shown that the characteristic exponent in the power-law dependence of the translocation time on the chain length, a function of the chaperone-polymer binding energy, the chaperone concentration, and the chain length, is also effectively determined by the Péclet number. We investigate the effect of the chaperone size on...