TCB Publications - Abstract

Ivan Teo and Klaus Schulten. A computational kinetic model of diffusion for molecular systems. Journal of Chemical Physics, 139:121929, 2013. (15 pages). (PMC: 3795746)

TEO2013 Regulation of biomolecular transport in cells involves intra-protein steps like gating and passage through channels, but these steps are preceded by extra-protein steps, namely, diffusive approach and admittance of solutes. The extra-protein steps develop over a 10 - 100 nm length scale typically in a highly particular environment, for example near a membrane surface. In order to account for solute energetics and diffusion space geometries at a relevant resolution, we propose a particle-based kinetic model of diffusion based on a Markov State Model (MSM) framework. Prerequisite input data consist of diffusion coefficient and potential of mean force (PMF) maps of the simulated systems. The systems are represented by a discrete set of states specified by the positions, volumes, and surface elements of Voronoi grid cell centers distributed according to a density function reflecting the often intricate cellular diffusion space. Validation tests show that the model and the associated Brownian motion algorithm are viable over a large range of parameter values such as time step, diffusion coefficient, and grid density. A concrete application of the method is demonstrated for ion diffusion around and through the bacterial (Eschericia coli ) mechanosensitive channel of small conductance (ecMscS).

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