Molecular meshing and continuum modeling

Benzhuo Lu (April 27, 2011)

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Abstract

Continuum modeling can be a proper choice to overcome the limitations on time and length scales of all-atom biomolecular simulations. The main concerns in this area are the model's accuracy and the numerical techniques/implementation. Besides, the molecular surface/volume meshing is also an unavoidable issue in many cases. I'll talk about our works on calculations of the Poisson-Boltzmann electrostatics, electro-diffusion-reaction simulations described by the Poisson-Nernst-Planck equations, and a general size-modified PNP/PB model. The latter method is applied to both equilibrium electrostatic calculation and rate prediction for diffusion-controlled enzyme-substrate reaction, and the particle (either ions or substrate molecule) size-effects to their concentrations and the reaction rate will be reported. Finally, I'll talk about our recently developed method and software TMSmesh for molecular surface meshing, which seems to be a useful tool to enable future macromolecular simulation using boundary element, finite element, or some other numerical methods.