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Chain deformation in translocation phenomena

Farahpour, F ; Sharif University of Technology | 2013

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  1. Type of Document: Article
  2. DOI: 10.1039/c2sm27416g
  3. Publisher: 2013
  4. Abstract:
  5. 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 the end monomers. We also highlight the role of long range hydrodynamic interactions via comparison of the LB-MD results with those obtained using a Langevin thermostat instead of the LB solver
  6. Keywords:
  7. Approximate solution ; Co-ordinate system ; Effective deformations ; Electric field gradients ; Hydrodynamic interaction ; Multi-scale hybrid simulations ; Single-stranded DNA ; Translocation process ; Electric fields ; Electrohydrodynamics ; Laplace equation ; Deformation
  8. Source: Soft Matter ; Volume 9, Issue 9 , 2013 , Pages 2750-2759 ; 1744683X (ISSN)
  9. URL: http://pubs.rsc.org/en/Content/ArticleLanding/2013/SM/c2sm27416g#!divAbstract