24-10-2012, 11:27 AM
Using Molecular Simulations to Understand Complex Nanoscale Dynamic Phenomena in Polymer Solutions
ABSTRACT
The first half of the project concentrated on molecular simulation studies of the translocation of model molecules for
single-stranded DNA through a nanosized pore. This has resulted in the publication, Translocation of a polymer chain across
a nanopore: A Brownian dynamics simulation study, by Pu Tian and Grant D. Smith, JOURNAL of CHEMICAL PHYSICS
VOLUME 119, NUMBER 21 1 DECEMBER 2003, which is attached to this report. In this work we carried out Brownian
dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an
applied field (chemical potential gradient) designed to mimic an electrostatic field. The translocation process can be either
dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical
gradient). We focused on the latter case in our studies. Calculation of radius of gyration of the translocating chain at the two
opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this
fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the
dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent
viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our
simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tube-like pore geometry, more
than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both
repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied. Attraction
facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of
polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing
field strength, and decreasing pore diameter.
ABSTRACT
The first half of the project concentrated on molecular simulation studies of the translocation of model molecules for
single-stranded DNA through a nanosized pore. This has resulted in the publication, Translocation of a polymer chain across
a nanopore: A Brownian dynamics simulation study, by Pu Tian and Grant D. Smith, JOURNAL of CHEMICAL PHYSICS
VOLUME 119, NUMBER 21 1 DECEMBER 2003, which is attached to this report. In this work we carried out Brownian
dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an
applied field (chemical potential gradient) designed to mimic an electrostatic field. The translocation process can be either
dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical
gradient). We focused on the latter case in our studies. Calculation of radius of gyration of the translocating chain at the two
opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this
fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the
dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent
viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our
simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tube-like pore geometry, more
than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both
repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied. Attraction
facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of
polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing
field strength, and decreasing pore diameter.