Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)



Degree Granting Department


Major Professor

Sagar A. Pandit, Ph.D.

Committee Member

Ananth Y. Grama, Ph.D.

Committee Member

Martin Muschol, Ph.D.

Committee Member

Jianjun Pan, Ph.D.

Committee Member

Lilia M. Woods, Ph.D.


Molecular Modeling, Optimization, Simulation


Molecular models allow computer simulations to predict the microscopic properties of macroscopic systems. Molecular modeling can also provide a fully understood test system for the application of theoretical methods. The power of a model lies in the accuracy of the parameter values which govern its mathematical behavior. In this work, a new software, called ParOpt, for general high dimensional non-linear optimization will be presented. The software provides a very general framework for the optimization of a wide variety of parameter sets. The software is especially powerful when applied to the difficult task of molecular model parameter optimization. Three applications of the ParOpt software, and the Nelder-Mead algorithm implemented within it, are presented: a coarse-grained (CG) water--ion model, a model for the determination of lipid bilayer structure via the interpretation of scattering data, and a reactive molecular dynamics (ReaxFF) model for oxygen and hydrogen. Each problem presents specific difficulties. The power and generality of the ParOpt software is illustrated by the successful optimization of such a diverse set of problems.

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