Condensed Matter Theory

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.

Abstract:

We study the propulsion of two model swimmers at low Reynolds number. Inspired by Purcell's model, we propose a very simple one-dimensional swimmer consisting of three spheres that are connected by two arms whose lengths can change between two values. The proposed swimmer can swim with a special type of motion, which breaks the time-reversal symmetry. We also show that an ellipsoidal membrane with tangential travelling wave on it can also propel itself in the direction preferred by the travelling wave. This system resembles the realistic biological animals like Paramecium. © 2005 IOP Publishing Ltd.

Abstract:

The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities. It is shown that due to the helical structure of DNA, the anisotropy in the bending rigidities can lead to the formation of kinks and modulations in the curvature, depending on the values of the elastic constants. The typical wavelength for the modulations, or the distance between the neighbouring kinks, is found to be set by half of the DNA pitch. © 2005 IOP Publishing Ltd.