Numerical Methods for Computing the Free Energy of Coarse-Grained Molecular Systems
Cyr, Eric C.
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Permalink
https://hdl.handle.net/2142/81845
Description
Title
Numerical Methods for Computing the Free Energy of Coarse-Grained Molecular Systems
Author(s)
Cyr, Eric C.
Issue Date
2008
Doctoral Committee Chair(s)
Stephen D. Bond
Department of Study
Computer Science
Discipline
Computer Science
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Computer Science
Language
eng
Abstract
The second coarse-grained system reduces a fully explicit solvent-solute system to an explicit solute in an implicitly represented solvent environment. The critical step in this reduction is to solve a partial differential equation known as the Poisson-Boltzmann equation. We develop algorithms that accurately compute the solvation free energy by using goal-oriented mesh refinement. Results indicating the benefits of goal-oriented refinement are presented.
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