Computational Methods for Molecular Analysis and Design

The text presents a set of numerical techniques that§extend and improve computational modeling§approaches for biomolecule analysis and design. The§presented research focuses on surface§formulations of modeling problems related to the§estimation of the energetic cost to transfer a§biomolecule from the gas phase to aqueous solution.§Four contributions to modeling biomolecular§interactions are presented. The first section§describes an approach to allow accurate§discretization of the most prevalent definitions of§the biomolecule solvent interface, and numerical§methods for numerically integrating possibly singular§functions over these discretizations. The second§section presents a fast multiscale numerical§algorithm, FFTSVD, that efficiently solves large§problems in biomolecule electrostatics. The third§part describes an integral-equation formulation and§boundary-element method implementation for§biomolecule electrostatic analysis. The final§section details an efficient numerical method for§calculating a biomolecular charge distribution that§minimizes the free energy of binding to another§molecule. This approach represents a novel§PDE-constrained optimization technique.