Condensed Matter Theory

Abstract:

Multivalent ions can induce condensation of like-charged polyelectrolytes into compact states, a process that requires different ion valence for different polyelectrolyte species. We have examined the trivalent ion-induced condensation behavior in binary anionic polyelectrolyte mixtures consisting of DNA coils and F-actin rods, and observe a micro-phase separation between the two polyelectrolytes into coexisting finite-sized F-actin bundles and DNA toroids. Further, by increasing the DNA volume fraction in the mixture, condensed F-actin bundles can be completely destabilized, leading to only DNA condensation within the mixture. We examine a number of possible causes and propose a model based on polyelectrolyte competition for ions. © EDP Sciences.

Abstract:

We investigate the behavior of a tethered polymer in Poiseuille flow using a multiscale algorithm. The polymer, treated using molecular dynamics, is coupled to a solvent modeled by the stochastic rotation algorithm, a particle-based Navier-Stokes integrator. The expected series of morphological transitions of the polymer: sphere to distorted sphere to trumpet to stem and flower to rod are recovered, and we discuss how the polymer extension depends on the flow velocity. Backflow effects cause an effective increase in viscosity, which appears to be primarily due to the fluctuations of the free end of the polymer. © 2005 American Institute of Physics.

Abstract:

We investigate the behavior of a tethered polymer in Poiseuille flow using a multiscale algorithm. The polymer, treated using molecular dynamics, is coupled to a solvent modeled by the stochastic rotation algorithm, a particle-based Navier-Stokes integrator. The expected series of morphological transitions of the polymer: sphere to distorted sphere to trumpet to stem and flower to rod are recovered, and we discuss how the polymer extension depends on the flow velocity. Backflow effects cause an effective increase in viscosity, which appears to be primarily due to the fluctuations of the free end of the polymer.

Abstract:

We use a kinetic theory approach to derive the continuum Navier-Stokes and heat conduction equations for stochastic rotation dynamics, a particle based algorithm for simulating a fluid. Hence we obtain expressions for the viscosity and thermal conductivity in two and three dimensions. The predictions are tested numerically and good agreement is found.