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The dielectric constant or relative static permittivity of a material represents the capacitance of the material relative to a vacuum and is important in many industrial applications. Nevertheless, accurate experimental values are often unavailable and current prediction methods lack accuracy and are often unreliable. A new QSPR (quantitative structure-property relation) correlation of dielectric constant for pure organic chemicals is developed and tested. The average absolute percent error is expected to be less than 3% when applied to hydrocarbons and non-polar compounds and less than 18% when applied to polar compounds with dielectric constant values ranging from 1.0 to 50.0. A local composition model is developed for mixture dielectric constants based on the Nonrandom-Two-Liquid (NRTL) model commonly used for correlating activity coefficients in vapor-liquid equilibrium data regression. It is predictive in that no mixture dielectric constant data are used and there are no adjustable parameters. Predictions made on 16 binary and six ternary systems at various compositions and temperatures compare favorably to extant correlations data that require experimental values to fit an adjustable parameter in the mixing rule and are significantly improved over values predicted by Oster's equation that also has no adjustable parameters. In addition, molecular dynamics (MD) simulations provide an alternative to analytic relations. Results suggest that MD simulations require very accurate force field models, particularly with respect to the charge distribution within the molecules, to yield accurate pure chemical values of dielectric constant, but with the development of more accurate pure chemical force fields, it appears that mixture simulations of any number of components are likely possible. Using MD simulations, the impact of different portions of the force field on the calculated dielectric constant were examined. The results obtained suggest that rotational polarization arising from the permanent dipole moments makes the dominant contribution to dielectric constant. Changes in the dipole moment due to angle bending and bond stretching (distortion polarization) have less impact on dielectric constant than rotational polarization due to permanent dipole alignment, with angle bending being more significant than bond stretching.

This dissertation describes the development and testing of modified embedded atom method (MEAM) interatomic potentials for Al, Si, Mg, Cu, Fe, and their alloys, with primary concentration on Mg-Al system. We performed the density functional theory (DFT) based ab initio calculations to determine the structural and elastic properties of element pairs that are impractical to obtain from experimental measurements. Specifically, we estimated the cohesive energy, equilibrium atomic volume, bulk modulus, and elastic moduli of every element pair in the NaCl reference structure. Based on the results of DFT calculations, MEAM parameters for each element pair were constructed. We extensively tested the new MEAM potential for Mg-Al alloy system. The new Mg-Al MEAM potential was compared with DFT calculations, previously published semi-empirical interatomic potentials, and experiments. Applicability of the new MEAM potential to atomistic modeling was demonstrated by calculating stress-strain responses from molecular dynamics (MD) simulations of Mg and Al systems in a variety of configurations. The effects of alloying, porosity, and strain rate conditions on the stress-strain response were quantified. The underlying mechanisms for tension-compression asymmetry observed in the macroscale experiments of Mg alloys were investigated at the nanoscale. This work presents a contribution to the task of bridging quantum-mechanical and classical atomistic scale simulations. Information from ab initio electronic structure calculations was used to construct parameters of semi-empirical MEAM potentials for large-scale atomistic simulations of alloys. The results of the new MEAM models compare extremely well to those from other published interatomic potentials. The applicability of the new MEAM potential to investigate nanoscale mechanisms of the deformation and fracture for Al, Mg and Mg-Al alloys was demonstrated. It has been shown that the MEAM provides a single universal formalism for classical atomistic simulations of a wide range of elements and their alloys.

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Analysis of genome sequences is enabling identification of numerous novel characteristics that provide valuable means for genetic and biochemical studies. Of these characteristics, Conserved Signature Indels (CSIs) in proteins which are specific for a given group of organisms have proven particularly useful for evolutionary and biochemical studies. My research work focused on using comparative genomics techniques to identify a large number of CSIs which are distinctive characteristics of fungi and other important groups of organisms. These CSIs were utilized to understand the evolutionary relationships among different proteins (species), and also regarding their structural features and functional significance. Based on multiple CSIs that I have identified for the PIP4K/PIP5K family of proteins, different isozymes of these proteins and also their subfamilies can now be reliably distinguished in molecular terms. Further, the species distribution of CSIs in the PIP4K/PIP5K proteins and phylogenetic analyses of these protein sequences, my work provides important insights into the evolutionary history of this protein family. The functional significance of one of the CSI in the PIP5K proteins, specific for the Saccharomycetaceae family of fungi, was also investigated. The results from structural analysis and molecular dynamics (MD) simulation studies show that this 8 aa CSI plays an important role in facilitating the binding of fungal PIP5K protein to the membrane surface. In other work, we identified multiple highly-specific CSIs in the phosphoketolase (PK) proteins, which clearly distinguish the bifunctional form of PK found in bifidobacteria from its homologs (monofunctional) found in other organisms. Structural analyses and docking studies with these proteins indicate that the CSIs in bifidobacterial PK, which are located on the subunit interface, play a role in the formation/stabilization of the protein dimer. We have also identified 2 large CSIs in SecA proteins that are uniquely found in thermophilic species from two different phyla of bacteria. Detailed bioinformatics analyses on one of these CSIs show that a number of residues from this CSI, through their interaction with a conserved network of water molecules, play a role in stabilizing the binding of ADP/ATP to the SecA protein at high temperature. My work also involved developing an integrated software pipeline for homology modeling of proteins and analyzing the location of CSIs in protein structures. Overall, my thesis work establishes the usefulness of CSIs in protein sequences as valuable means for genetic, biochemical, structural and evolutionary studies. / Dissertation / Doctor of Philosophy (PhD)

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Adsorption is a ubiquitous phenomenon that plays key roles in numerous applications including molecule separation, energy storage, catalysis, and lubrications. Since adsorption is sensitive to molecular details of adsorbate molecule and adsorbent materials, it is often difficult to describe theoretically. Molecular modeling capable of resolving physical processes at atomistic scales is an effective method for studying adsorption. In this dissertation, the adsorption of small molecules in three emerging materials systems: porous liquids, room-temperature ionic liquids, and atomically sharp electrodes immersed in aqueous electrolytes, are investigated to understand the physics of adsorption as well as to help design and optimize these materials systems. Thermodynamics and kinetics of gas storage in the recently synthesized porous liquids (crown-ether-substituted cage molecules dispersed in an organic solvent) were studied. Gas molecules were found to store differently in cage molecules with gas storage capacity per cage in the following order: CO2>CH4>N2. The cage molecules show selectivity of CO2 over CH4/N2 and demonstrate capability in gas separation. These studies suggest that porous liquids can be useful for CO2 capture from power plants and CH4 separation from shale gas. The effect of adsorbed water on the three-dimensional structure of ionic liquids [BMIM][Tf2N] near mica surfaces was investigated. It was shown that water, as a dielectric solvent and a molecular liquid, can alter layering and ordering of ions near mica surfaces. A three-way coupling between the self-organization of ions, the adsorption of interfacial water, and the electrification of the solid surfaces was suggested to govern the structure of ionic liquid near solid surfaces. The effects of electrode charge and surface curvature on adsorption of N2 molecules near electrodes immersed in water were studied. N2 molecules are enriched near neutral electrodes. Their enrichment is enhanced as the electrode becomes moderately charged but is reduced when the electrode becomes highly charged. Near highly charged electrodes, the amount of N2 molecules available for electrochemical reduction is an order of magnitude higher near spherical electrodes with radius ~1nm than near planar electrodes. The underlying molecular mechanisms are elucidated and their implications for development of electrodes for electrochemical reduction of N2 are discussed. / Doctor of Philosophy / Adsorption is a ubiquitous phenomenon that plays key roles in numerous applications including molecule separation, energy storage, catalysis, and lubrications. Since adsorption is sensitive to molecular details of adsorbate molecule and adsorbent materials, it is often difficult to describe theoretically. Molecular modeling capable of resolving physical processes at atomistic scales is an effective method for studying adsorption. In this dissertation, the adsorption of small molecules in three emerging materials systems: porous liquids, room-temperature ionic liquids, and atomically sharp electrodes immersed in aqueous electrolytes, are investigated to understand the physics of adsorption as well as to help design and optimize these materials systems. Thermodynamics and kinetics of gas storage in the recently synthesized porous liquids (crown-ether-substituted cage molecules dispersed in an organic solvent) were studied. Gas molecules were found to store differently in cage molecules with gas storage capacity per cage in the following order: CO2>CH4>N2. The cage molecules show selectivity of CO2 over CH4/N2 and demonstrate capability in gas separation. These studies suggest that porous liquids can be useful for CO2 capture from power plants and CH4 separation from shale gas. The effect of adsorbed water on the three-dimensional structure of ionic liquids [BMIM][Tf2N] near mica surfaces was investigated. It was shown that water, as a dielectric solvent and a molecular liquid, can alter layering and ordering of ions near mica surfaces. vi A three-way coupling between the self-organization of ions, the adsorption of interfacial water, and the electrification of the solid surfaces was suggested to govern the structure of ionic liquid near solid surfaces. The effects of electrode charge and surface curvature on adsorption of N2 molecules near electrodes immersed in water were studied. N2 molecules are enriched near neutral electrodes. Their enrichment is enhanced as the electrode becomes moderately charged but is reduced when the electrode becomes highly charged. Near highly charged electrodes, the amount of N2 molecules available for electrochemical reduction is an order of magnitude higher near spherical electrodes with radius ~1nm than near planar electrodes. The underlying molecular mechanisms are elucidated and their implications for development of electrodes for electrochemical reduction of N2 are discussed.