2026-09-19T15:00:13Zhttps://dspace.mit.edu/server/oai/requestoai:dspace.mit.edu:1721.1/378972022-01-13T07:54:29Zcom_1721.1_7582com_1721.1_7581col_1721.1_131022
Jacob K. White and Bruce Tidor.
Bardhan, Jaydeep Porter, 1978-
Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
2007-07-18T13:06:06Z
2007-07-18T13:06:06Z
2006
2006
http://hdl.handle.net/1721.1/37897
132692710
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.
Includes bibliographical references (p. 179-183).
This thesis 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. The thesis discusses four contributions to modeling biomolecular interactions. First, the thesis presents an approach to allow accurate discretization of the most prevalent mathematical definitions of the biomolecule-solvent interface; also presented are a number of accurate techniques for numerically integrating possibly singular functions over the discretized surfaces. Such techniques are essential for solving surface formulations numerically. The second part of the thesis presents a fast multiscale numerical algorithm, FFTSVD, that efficiently solves large boundary-element method problems in biomolecule electrostatics. The algorithm synthesizes elements of other popular fast algorithms to achieve excellent efficiency and flexibility. The third thesis component describes an integral-equation formulation and boundary-element method implementation for biomolecule electrostatic analysis.
(cont.) The formulation and implementation allow the solution of complicated molecular topologies and physical models. Furthermore, by applying the methods developed in the first half of the thesis, the implementation can deliver superior accuracy for competitive performance. Finally, the thesis describes a highly efficient numerical method for calculating a biomolecular charge distribution that minimizes the free energy' change of binding to another molecule. The approach, which represents a novel PDE-constrained methodology, builds on well-developed physical theory. Computational results illustrate not only the method's improved performance but also its application to realistic biomolecule problems.
by Jaydeep Porter Bardhan.
Ph.D.
193 p.
eng
Massachusetts Institute of Technology
M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.
http://dspace.mit.edu/handle/1721.1/7582
Electrical Engineering and Computer Science.
Efficient numerical algorithms for surface formulations of mathematical models for biomolecule analysis and design
Thesis
application/pdf
Publication
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<Abstract>This thesis 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. The thesis discusses four contributions to modeling biomolecular interactions. First, the thesis presents an approach to allow accurate discretization of the most prevalent mathematical definitions of the biomolecule-solvent interface; also presented are a number of accurate techniques for numerically integrating possibly singular functions over the discretized surfaces. Such techniques are essential for solving surface formulations numerically. The second part of the thesis presents a fast multiscale numerical algorithm, FFTSVD, that efficiently solves large boundary-element method problems in biomolecule electrostatics. The algorithm synthesizes elements of other popular fast algorithms to achieve excellent efficiency and flexibility. The third thesis component describes an integral-equation formulation and boundary-element method implementation for biomolecule electrostatic analysis.</Abstract>
<Abstract>(cont.) The formulation and implementation allow the solution of complicated molecular topologies and physical models. Furthermore, by applying the methods developed in the first half of the thesis, the implementation can deliver superior accuracy for competitive performance. Finally, the thesis describes a highly efficient numerical method for calculating a biomolecular charge distribution that minimizes the free energy' change of binding to another molecule. The approach, which represents a novel PDE-constrained methodology, builds on well-developed physical theory. Computational results illustrate not only the method's improved performance but also its application to realistic biomolecule problems.</Abstract>
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