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First passage time distribution of chaperone driven polymer translocation through a nanopore: Homopolymer and heteropolymer cases

Abdolvahab, R. H ; Sharif University of Technology | 2011

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  1. Type of Document: Article
  2. DOI: 10.1063/1.3669427
  3. Publisher: 2011
  4. Abstract:
  5. 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 the translocation process. In particular, for large chaperone size, the translocation progress and the mean waiting time as function of the reaction coordinate exhibit pronounced sawtooth-shapes. The effects of a heterogeneous polymer sequence on the translocation dynamics is studied in terms of the translocation velocity, the probability distribution for the translocation progress, and the monomer waiting times
  6. Keywords:
  7. Advection diffusion equation ; Characteristic exponents ; Dimensionless parameters ; First passage time ; First passage time distributions ; Heterogeneous polymers ; Mean waiting time ; Monte Carlo Simulation ; Polymer translocation ; Power-law dependences ; Reaction coordinates ; Stiff polymers ; Translocation dynamics ; Translocation process ; Waiting time ; Advection ; Binding energy ; Chain length ; Electron transitions ; Monte Carlo methods ; Nanopores ; Partial differential equations ; Polymers ; Probability distributions ; Probability density function ; Polymer ; Chemical model ; Chemistry ; Nanopore ; Computer Simulation ; Diffusion ; Models, Chemical ; Monte Carlo Method
  8. Source: Journal of Chemical Physics ; Volume 135, Issue 24 , 2011 ; 00219606 (ISSN)
  9. URL: http://scitation.aip.org/content/aip/journal/jcp/135/24/10.1063/1.3669427