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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