Type of Document	Dissertation
Author	Silalahi, Alexander R. J.
Author's Email Address	as05h@fsu.edu
URN	etd-04092011-190041
Title	A Novel Stochastic Poisson-Boltzmann Solver and Incorporation of Finite Ion Sizes
Degree	Doctor of Philosophy
Department	Physics, Department of
Advisory Committee	Advisor Name Title Jorge Piekarewicz Committee Co-Chair Marcia O. Fenley Committee Co-Chair David Van Winkle Committee Member Nicholas Bonesteel Committee Member Volker Crede Committee Member Michael Mascagni University Representative
Keywords	Modified Poisson Boltzmann Electrostatics Ion Size Effects Salt Effects Generalized Born
Date of Defense	2011-03-03
Availability	unrestricted
Abstract Electrostatic interactions play an important role in many aspects of the structural and functional properties of biomolecules because of their long-range behavior. The nonlinear Poisson-Boltzmann equation (NLPBE) theory has long been used as a standard tool for modeling non-specific electrostatic interactions of biomolecules in aqueous salt solution. In the NLPBE framework, ions are treated as point-like charged particles and their size effects are neglected. A major contribution in this dissertation is the incorporation of the ion sizes effect into the NLPBE framework. In this dissertation we developed a non-uniform ion size modified Poisson-Boltzmann equation (SMPBE) to study the distribution of ions around an A-form ribonucleic acid (RNA) duplex and compare it with predictions obtained with molecular dynamics (MD) simulations. We showed that the ion distribution profiles of a 25-mer RNA duplex in aqueous 1:1 salt solution computed with the two approaches agree quite well with each other. However, the predictions of ionic profiles for a 25-mer RNA duplex obtained with MD simulations and the non-uniform ion SMPBE approach developed in as part of this thesis differ when multivalent ions are present in the aqueous ionic solution, potentially due to site bound ions and/or ion-ion correlations. We also modified a stochastic-based numerical method to solve the linear Poisson-Boltzmann equation (LPBE) simultaenoulsy at multiple salt concentrations using a single Monte Carlo (MC) Poisson-Boltzmann run. We showed that by using this method, the salt dependence of the electrostatic solvation free energy and the electrostatic potential can be computed to arbitrary accuracy. We then used this stochastic approach to compute Born radii of a biomolecule.
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