Computational Methods for Molecular Analysis and Design

ISBN-13: 9783639142617 / Angielski / Miękka / 2009 / 196 str.

Jaydeep Bardhan

Opis

The text presents a set of numerical techniques thatextend and improve computational modelingapproaches for biomolecule analysis and design. Thepresented research focuses on surfaceformulations of modeling problems related to theestimation of the energetic cost to transfer abiomolecule from the gas phase to aqueous solution.Four contributions to modeling biomolecularinteractions are presented. The first sectiondescribes an approach to allow accuratediscretization of the most prevalent definitions ofthe biomolecule-solvent interface, and numericalmethods for numerically integrating possibly singularfunctions over these discretizations. The secondsection presents a fast multiscale numericalalgorithm, FFTSVD, that efficiently solves largeproblems in biomolecule electrostatics. The thirdpart describes an integral-equation formulation andboundary-element method implementation forbiomolecule electrostatic analysis. The finalsection details an efficient numerical method forcalculating a biomolecular charge distribution thatminimizes the free energy of binding to anothermolecule. This approach represents a novelPDE-constrained optimization technique.

O autorze

Jaydeep received his S.B., M.Eng., and Ph.D. degrees from the
department of Electrical Engineering and Computer Science at the
Massachusetts Institute of Technology. His research focuses on
computational methods for molecular analysis and design.