Julia Yeomans OBE FRS

Abstract:

We investigate numerically the dynamical behavior of a polymer chain collapsing in a dilute solution. The rate of collapse is measured with and without the presence of hydrodynamic interactions. We find that hydrodynamic interactions accelerate polymer collapse. We present a scaling theory describing the physical process responsible for the collapse kinetics. Predicted collapse times in a hydrodynamic (tauH approximately N(4/3)) and a Brownian heat bath (tauB approximately N2) agree well with the numerical results (tauH approximately N(1.40+/-0.08) and tauB approximately N(1.89+/-0.09)) where N denotes chain length. The folding kinetics of Go models of proteins is also examined. We show that for these systems, where many free energy minima compete, hydrodynamics has little effect on the kinetics.

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.