A new method for molecular calculations was applied to the hydrogen molecule ion. Energies were calculated at different internuclear separations and simple energy differences were found. The method used was an approximate one which included two basic approximations: the use of Gaussian wave functions and the one-center method. The one-center method gives a good approximation for the electronic energies but does not give near-atomic electron densities. The title "Floating Potential Curves" comes from the fact that the Gaussian wave functions give good potential curves over a restricted region, but these curves are not oriented correctly with respect to the minimum energy. This is an indication that calculated energy differences would be more accurate than calculated energies. This was seen to be true in a prior calculation.

Metallic alloys are important structural and cladding materials for current and future reactors. Understanding radiation-induced damage on metallic alloys is important for maintaining the safety of nuclear reactors. This dissertation mainly focuses on radiation-induced primary damage in iron-based metallic. Systematic molecular dynamics simulations were conducted to study the alloying element effects on the primary damage in Fe-based alloys, including defect production and dislocation loop transformations, and their connections with defect thermodynamics. First, effects of alloying elements on the primary damage in three Fe-based ferritic alloy systems were studied, with a particular focus on the production behaviors of solute interstitials. The production behaviors of solute interstitials include over-production or under-production, compared with their solute concentration in the Fe matrix. The three alloy systems are: (1) a Fe-Cr alloy system; (2) a Fe-Cu alloy system; and (3) an ideal but artificial Fe-Cr alloy system, which is used as a reference system. It is found that the number ratio of solute interstitials to the total interstitials is distinct in these alloys. The solute interstitials are over-produced in the Fe-Cr systems but under-produced in the Fe-Cu system, compared with solute composition in the alloys. The defect formation energies in both dilute and concentrated alloys, interstitial-solute binding energies, liquid diffusivities of Fe and solute atoms, and heat of mixing have been calculated for both Fe-Cr and Fe-Cu alloys. Among these factors, our analysis shows that the relative thermodynamic stability between Fe self-interstitials and solute interstitials plays the most important role on the production behaviors of solute interstitials. Next, to obtain a correlation that can quantitatively estimate the solute interstitial fraction in the Fe-based alloys, molecular dynamics simulations were conducted to simulate the cascade damage in a series of "artificial" Fe-Cr alloys with tunable binding energies between a substitutional solute (Cr) atom and a Fe self-interstitial atom (SIA). To achieve this, the Fe-Cr cross pair interaction in the interatomic potential was modified by multiplying a scaling factor so that the solute-SIA binding energy varies linearly from positive to negative values. It is found that the solute interstitial fraction has a strong correlation with the solute-SIA binding energy, and the correlation can be approximately described by a Fermi-Dirac-Distribution-like equation. The independent defect production results reported in literature are found to align well with this correlation. The correlation may be used to estimate the solute interstitial fraction in a wide range of Fe-based alloys simply based on the solute-SIA binding energy, without conducting laborious cascade simulations. Furthermore, primary damage was further investigated in Fe-tungsten (W) alloys to investigate the atomic size effect. The large difference in atomic size between Fe and W can introduce both global volume expansion and local lattice distortion in the Fe matrix. In order to understand how oversized W influences the defect production behaviors in Fe-based alloys, molecular dynamics simulations were conducted to study the primary damage in three systems at 300 K: (a) unstrained pure Fe, (b) Fe-5at.%W alloy, and (c) strained pure Fe with the same volume expansion as the Fe-5%W. The investigation of defect production behaviors include the production of Frenkel pairs, and cluster formation preference. Based on the total number of Frenkel pairs, it indicates that the global volume expansion introduced by oversized W and external strain can lead to enhanced defect production. Meanwhile, the defect cluster analysis in all three systems indicates that the local lattice distortion induced by oversized W can significantly influence the morphologies and size distributions of defect structures. Defect formation energies were calculated to interpret the different defect production behaviors in these systems. Finally, radiation can produce not only point defects but also both <100> and ½<111> type dislocation loops in pure Fe and Fe-Cr alloys. However, contradictory experimental results have been reported on how the Cr concentration affects the ratio of <100> to ½<111> dislocation loops. In this section, molecular dynamics simulations were conducted to study how Cr concentration affects the formation probability of <100> dislocation loops from overlapping cascades on a pre-existing ½<111> dislocation loop in a series of Fe-Cr alloys with 0 – 15%Cr at 300 K. Our atomistic modeling directly demonstrates that the ratio of <100> to ½<111> dislocation loops decreases with the increasing Cr concentration, which is consistent with many experimental observations. Next, independent molecular statics calculations show that the formation energies of both <100> and ½<111> dislocation loops increase with the increasing of Cr content. However, the former has a much faster increase rate than the latter, indicating that the formation of <100> loops becomes energetically more and more unfavorable than ½<111> loops as the Cr content increases. The results provide a thermodynamics-based explanation for why Cr suppresses the formation of <100> dislocation loops in Fe-Cr alloys, which can be applied to all <100> loop formation mechanisms proposed in literature. The possible effects of other alloying elements on the formation probability of <100> loops in Fe-based alloys are also discussed. / Doctor of Philosophy / Metallic alloys are important structural and cladding materials for current and future nuclear reactors. The understanding of radiation-induced damage in metallic alloys is important for the safe operation of nuclear reactors. This dissertation mainly focuses on radiation-induced primary damage in iron-based ferritic alloys. Systematic molecular dynamics simulations were conducted to study how different alloying elements influence the primary damage behaviors in iron-based alloys, including defect production behaviors and dislocation loop transformations. The relations between defect production and defect thermodynamics are also studied. First, molecular dynamics simulations were conducted to study the effects of alloying elements on the primary damage behavior in three Fe-based ferritic alloy systems (Fe-Cr, Fe-Cu, and ideal Fe-Cr), with a particular focus on the production behaviors of solute interstitials. It is found that the number ratio of solute interstitials to the total interstitials has distinct behavior in these alloys. In the Fe-Cr alloys, the ratio of Cr interstitials is much higher than the Cr concentration in the Fe-Cr alloys. By contrast, in the Fe-Cu alloys Cu interstitials are barely produced. In the ideal alloy system, the fraction of solute interstitials is close to the solute concentration in the alloys. Among all the factors we have investigated, it is found the relative thermodynamic stability between Fe self-interstitials and solute interstitials plays the most important role on affecting the production behaviors of solute interstitials. Next, to obtain a quantitative correlation that can predict the solute interstitial fraction in the Fe-based alloys, molecular dynamics simulations were conducted to simulate the cascade damage in a series of "artificial" Fe-Cr alloys with tunable binding energies between a substitutional solute (Cr) atom and a Fe self-interstitial atom (SIA). It is found that the solute interstitial fraction has a strong correlation with the solute-SIA binding energy, and the correlation can be approximately described by an analytical equation. The correlation may be used to estimate the solute interstitial fraction in a wide range of Fe-based alloys simply based on the solute-SIA binding energy, without conducting laborious cascade simulations. Furthermore, primary damage was further investigated in iron-tungsten (Fe-W) alloys. W is about 10.5% larger in atomic radius or 34.8% larger in atomic volume than Fe. The oversize W can introduce both global volume expansion and local lattice distortion in the Fe matrix. Through molecular dynamics simulations in a series of model systems for comparison, it is found that oversized W can lead to enhanced defect production. In addition, it is found that oversized W can significantly influence the morphologies and size distributions of defect clusters. Finally, molecular dynamics simulations were conducted to study how Cr concentration affects the formation probability of <100> and ½<111> dislocation loops in a series of Fe-Cr alloys. Our results demonstrate that the ratio of <100> to ½<111> dislocation loops decreases with the increasing Cr concentration, which is consistent with many experimental observations. The formation energies of both <100> and ½<111> dislocation loops indicate that the formation of <100> loops becomes energetically more and more unfavorable than ½<111> loops as the Cr content increases. The results provide a thermodynamics-based explanation for why Cr suppresses the formation of <100> dislocation loops in Fe-Cr alloys.

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Transport phenomena at the nanoscale can differ from that at the continuum because the large surface area to volume ratio significantly influences material properties. While the modeling of many such transport processes have been reported in the literature, a few examples exist that integrate molecular approaches into the more typical macroscale perspective. This thesis extends the understanding of nanoscale transport governed by charge, mass and energy transfer, comparing these phenomena with the corresponding continuum behavior where applicable. For instance, molecular simulations enable us to predict the solvation structure around ions and describe the diffusion of water in salt solutions. In another case, we find that in the absence of interfacial effects, the stagnation flow produced by two opposing nanojets can be suitably described using continuum relations. We also examine heat conduction within solids of nanometer dimensions due to both the ballistic propagation of lattice vibrations in small confined dimensions and a diffusive behavior that is observed at larger length scales. Our simulations determine the length dependence of thermal conductivity for these cases as well as effects of isotope substitution in a material. We find that a temperature discontinuity at interfaces between dissimilar materials arises due to interfacial thermal resistance. We successfully incorporate these interfacial nanoscale effects into a continuum model through a modified heat conduction approach and also by a multiscale computational scheme. Finally, our efforts at integrating research with education are described through our initiative for developing and implementing a nanotechnology module for freshmen, which forms the first step of a spiral curriculum. / Ph. D.

Molecular dynamics simulations were performed to study the interactions of bioactive catechins and theaflavins commonly found in tea with lipid bilayers, as a model for cell membranes. Previously, multiple experimental studies rationalized the anticarcinogenic, antibacterial, and other beneficial effects of these compounds in terms of physicochemical molecular interactions with cell membranes. To contribute toward understanding the molecular role of tea polyphenols on the structure of cell membranes, simulation results are presented for seven catechins and three theaflavins in lipid bilayer systems which are both pure (POPC) and representative of HepG2 cancer cells (POPC and POPE). Our simulations show that the catechins and theaflavins evaluated have a strong affinity for the lipid bilayer \textit{via} hydrogen bonding to the bilayer surface, with many of the catechins able to penetrate beneath the surface. Epigallocatechin-gallate (EGCG) and Theaflavin-3,3'-digallate showed the strongest interaction with the lipid bilayers based on the number of hydrogen bonds formed with lipid headgroups. The simulations also provide insight into the functional characteristics of the tea compounds that distinguish them as effective compounds to potentially alter the lipid bilayer properties. The results on the hydrogen-bonding effects may contribute to a better understanding of proposed multiple molecular mechanisms of the action of catechins and theaflavins in microorganisms, cancer cells, and tissues. / Ph. D.

Molecular dynamics (MD) simulations are routinely used to study the structure and function of biological molecules. However the accuracy and duration of these simulations are constrained by their computational costs, thus limiting the ability to accurately simulate systems of realistic sizes over biologically relevant time periods. The two most computationally demanding steps in these simulations are (1) determining the charge state of ionizable sites in biomolecules, which is a key input to the simulation, and (2) calculating long range electrostatic interactions during the simulation. Presented here are two novel methods, the <i>direct interaction approximation (DIA)</i> and the <i>hierarchical charge partitioning (HCP) approximation</i>, for speeding up each of these two computations. The average charge state of ionizable sites in biomolecules can be calculated as the statistical average over all possible (2^N) microstates for a molecule, where N is the number of ionizable sites. In general this computation scales exponentially as O(N² 2^N). The DIA is an O(²) approximation for calculating the average charge state of ionizable sites. For each site, the DIA treats direct interactions (interactions involving the site of interest) <i>exactly</i>, while using an <i>average</i> value for indirect interactions (interactions not involving the site of interest). The DIA was tested on two problems. The computation of thermal average properties for the 2-D Ising model of ferromagnetism, and the average charge state of ionizable residues in biomolecules. Compared to the commonly used non-deterministic Monte Carlo method, for the same computational cost, the deterministic DIA was found to be at least as accurate, as measured by RMS error relative to the exact computation. Thus, the DIA may be a practical alternative to the Monte Carlo method for some problems. In atomistic MD simulations, the computation of long range electrostatic interactions, scale as O(<i>n</i>²), where <i>n</i> is the number of atoms. For most biologically relevant timescales the simulations involve 10^12–16 simulation steps. Thus, the computational cost of long range interactions become the limiting factor in the size and duration of MD simulations. The HCP is an O(<i>n</i> log <i>n</i>) approximation for computing long range electrostatic interactions. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of components. For components that are far from the point of interest, the charge distribution for each component is approximated by a much smaller number of charges. For nearby components, the HCP uses the full set of atomic charges. For large structures the HCP can be several orders of magnitude faster than the exact pairwise O(<i>n</i>²) all-atom computation. For a representative set of structures, the accuracy of the HCP is comparable to the industry standard explicit solvent particle mesh Ewald (PME), and is in general more accurate than the spherical cutoff method. And, unlike the PME, the DIA can be easily extended to implicit solvent GB models. 50 ns implicit solvent simulations for a representative set of four biomolecules suggests that the HCP could be a practical alternative for implicit solvent simulations, and preferable to the cutoff based method. The HCP is available for general use in the open source MD software, NAB within AmberTools. / Ph. D.

Raman and/or infrared (IR) bandshape analysis to probe molecular dynamics in liquids has become a rapidly expanding field of study in recent years. Determination of spinning and tumbling diffusion constants, Dι and D⊥, which characterize the reorientation of symmetric-top moleclues has been successfully studied in a number of D6H and D3H molecules. For molecules of CV3 symmetry, however, previous attempts to extract spinning diffusion constants from Raman doubly degenerate vibrations (E mode) have proved unsuccessful. Presented here is a new methodology which resolves the problems encountered by former researchers through calculation of Dι utilizing the narrower Lorentzian component of E vibrations.

Yes / We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base−graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene−aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine−graphene interactions.