Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution.
A computational framework is presented for the continuum modeling of cellular biomolecular diffusion influenced by electrostatic driving forces. This framework is developed from a combination of state-of-the-art numerical methods, geometric meshing, and computer visualization tools. In particular, a hybrid of (adaptive) finite element and boundary element methods is adopted to solve the Smoluchowski equation (SE), the Poisson equation (PE), and the Poisson-Nernst-Planck equation (PNPE) in order to describe electrodiffusion processes. The finite element method is used because of its flexibility in modeling irregular geometries and complex boundary conditions. The boundary element method is used due to the convenience of treating the singularities in the source charge distribution and its accurate solution to electrostatic problems on molecular boundaries. Nonsteady-state diffusion can be studied using this framework, with the electric field computed using the densities of charged small molecules and mobile ions in the solvent. A solution for mesh generation for biomolecular systems is supplied, which is an essential component for the finite element and boundary element computations. The uncoupled Smoluchowski equation and Poisson-Boltzmann equation are considered as special cases of the PNPE in the numerical algorithm, and therefore can be solved in this framework as well. Two types of computations are reported in the results: stationary PNPE and time-dependent SE or Nernst-Planck equations solutions. A biological application of the first type is the ionic density distribution around a fragment of DNA determined by the equilibrium PNPE. The stationary PNPE with nonzero flux is also studied for a simple model system, and leads to an observation that the interference on electrostatic field of the substrate charges strongly affects the reaction rate coefficient. The second is a time-dependent diffusion process: the consumption of the neurotransmitter acetylcholine by acetylcholinesterase, determined by the SE and a single uncoupled solution of the Poisson-Boltzmann equation. The electrostatic effects, counterion compensation, spatiotemporal distribution, and diffusion-controlled reaction kinetics are analyzed and different methods are compared.
Lu
Benzhuo
B
Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093-0365, USA. blu@mccammon.ucsd.edu
Zhou
Y C
YC
Huber
Gary A
GA
Bond
Stephen D
SD
Holst
Michael J
MJ
McCammon
J Andrew
JA
D001704:Biopolymers / Q000737:chemistry* / Q000528:radiation effects*; D002462:Cell Membrane / Q000737:chemistry* / Q000528:radiation effects*; D003198:Computer Simulation; D004058:Diffusion / Q000528:radiation effects; D004574:Electromagnetic Fields; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular
D001704:Biopolymers