“KMC-TDGL”—a coarse-grained methodology for simulating interfacial dynamics in complex fluids: application to protein-mediated membrane processes

Abstract

In this article, we describe a new multiscale simulation algorithm (which we term the ‘KMC-TDGL’ method) applicable for the description of equilibrium and dynamic processes associated with a particular class of complex fluids with nanoscale inclusions, namely, biological membranes mediated by membrane-associating and membrane-bound proteins. We adopt a novel strategy of integrating two different phenomenological approaches, namely, a field theoretic (continuum) description for the membrane dynamics given by the time-dependent Ginzburg–Landau equation and a random walk on a discretized lattice description for protein diffusion dynamics. We illustrate that this integrated approach results in a unified description of protein-mediated membrane dynamics.

Acknowledgements

This work constituted J. Weinstein's Senior Undergraduate Project in the Department of Physics at The University of Pennsylvania. We thank Dr Mark Goulian for numerous discussions on this subject and for pointing us towards many references in the literature. We thank Dr Charlie Epstein for discussions on the numerical stability of the finite difference scheme. Funding for this work was partially available by a grant from the Whitaker Foundation.

Notes

†Current Address: Department of Bioengineering, Stanford University, USA.

Additional information

Notes on contributors

R. Radhakrishnan

†Current Address: Department of Bioengineering, Stanford University, USA.