Computations of electrostatic potentials and energies of dynamic biomolecules
Kim, Jerry Chil
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We present ongoing research into the simulation of biomolecules in a solvent. We first describe the various models used to model molecular electrostatics including the methods that attempt to modify the Poisson-Boltzmann equation due to its limitations. We then modify the boundary element solver MolEnergy, which solves the linearized Poisson-Boltzmann equation to determine the polarization energies of biomolecules. With our modifications it can now rely on an automated process, utilize a low-discrepancy pseudo-random number generator to yield different molecular configurations, and implement parallel computing to determine the potentials and energies of those configurations in parallel. Our modifications increase the accuracy and speed of MolEnergy.