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Study on Dynamics of Charged Study on Dynamics of Charged Polyelectrolytes in Inhomogeneous Electric Fields and Its Application in Translocation Phenomenon

Farahpour, Farnoush | 2013

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  1. Type of Document: Ph.D. Dissertation
  2. Language: Farsi
  3. Document No: 45389 (04)
  4. University: Sharif University of Technology
  5. Department: Physics
  6. Advisor(s): Ejtehadi, Mohammad Reza
  7. Abstract:
  8. Polymers not just because of their increasing applications in industry but according to their fundamental role in biological mechanisms, has been a topic of interest among different scientific groups. Chemical structure, acroscopic properties and dynamical behavior of these macromolecules are studied in different ways. An important sub-group of polymers are those which according to their chemical properties, after dissolving, release some ions in water and become charged and called polyelectrolytes. A polyelectrolyte with vital importance in our life is DNA which encodes the genetic instructions used in the development and functioning of all known living organisms. One of the main goals in last decades of genetic is to find fast and cheap methods for DNA sequencing.Two effective methods are extensively used to obtain microscopic information of polyelectrolytes:Electrophoresis and Translocation. In electrophoresis, charged polyelectrolytes under the action of an electric field move in a gel or a constrained nanometer environment and regarding to the length dependence of their mobility, separation and analysis of their structure is possible. In translocation, an applied force due to an electric field or pressure difference, forces a polyelectrolyte to translocate through a pore embedded in a membrane.
    During the translocation one can access the chemical details of the chain. In both methods if the motive factor is an inhomogeneous electric field, the charged chain would experience a deformation induced by the gradient of the field.In the first part of this study, deformation of a single stranded DNA in 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 of a narrow pore is obtained. With an analysis based on “electrohydrodynamic equivalence” we determine the possibility of 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.In the second part, to obtain a general understanding about the dynamics of polyelectrolytes in inhomogeneous fields, by considering some different constrained environment in which there is a gradient of electric field, role of different factors like strength and gradient of the electric field, hydrodynamic interaction and the presence of explicit free ions in the system is investigated. By simulation and comparison of the result of different situation it is shown that in the absence of explicit ions the electric field gradient is the only factor that can generate an effective deformation. Neglecting hydrodynamic interaction only yields an artificial increase in extension and has no major role in overall behavior
  9. Keywords:
  10. Polyelectrolyte ; Deformation ; Nanopore ; Electrophoretic ; Translocation Phenomena

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