Molecular dynamics (MD) simulations were used in order to investigate structure and mechanical properties of zirconium and zirconium hydride. Calculation of temperature dependent failure of zirconium, diffusion of hydrogen in zirconium, properties of interfaces in zirconium and zirconium hydride and effect of hydrogen on crack nucleation and propagation were in good agreement with available experimental data. These are the first computer simulations where large-scale atomic/molecular massively parallel simulator (LAMMPS) code was used with the Embedded Atom Method (EAM) and Modified Embedded Atom Method (MEAM) to study structure and mechanical properties of zirconium hydrogen system (Zr-H) and zirconium hydride (ZrH2). Verification of methods was done in order to establish the best potential for zirconium and zirconium hydride. EAM and MEAM potentials successfully predicted lattice parameters, mechanical properties and variation of lattice parameters with temperature for α-Zr. MEAM potential was used to predict correctly the face centered structure for ZrH2 and also its mechanical properties. Temperature dependent stress-strain curves were calculated in order to predict yielding point for α-Zr. Results indicate early yielding and failure with increase of temperature in zirconium on application of tensile and compressive strains. Anisotropic stress variation with temperature in α-Zr was calculated. Hydrogen ingress through diffusion of hydrogen in zirconium is a mechanism responsible for formation of hydrides. Temperature-dependent hydrogen diffusion and activation energy for diffusion was calculated and the agreement with experiments was satisfactory. Anisotropy of diffusion of hydrogen is observed for Zr crystal. Hydrogen diffusion was also modeled under tensile and compressive strain and a possible formation of hydrides in the direction perpendicular to applied strain was observed. The effect of strain on orientation of hydride was investigated. Hydride {111} oriented crystal was strained along [1 1 ̅ 0] and [111] direction. Energy as a function of strain is calculated along both directions [111] and [1 1 ̅ 0] and it was found that energy of the system increase with increase in strain along [1 1 ̅ 0] and decrease with increase of strain along [111] direction. Calculated stress and strain curves indicate lower stresses along [111] direction and this causing the hydride to reorient in a direction perpendicular to applied strain. Structure of the interface (0 0 0 1) α-Zr // {1 1 1} δ-ZrH2 is modeled in order to investigate the crack initiation at this interface. Interfacial cracking of hydride under stress is observed. This observation is in good agreement with available experimental studies. Cracks are seen to nucleate earlier at higher temperature. Cracks and voids are common defects in zirconium fuel cladding. A crack is modeled along (0 0 0 1) plane of zirconium with hydrogen. In the presence of hydrogen cracks nucleate in zirconium causing fracture. This observation is in good agreement with previous experimental studies. Bonds surrounding atoms and stress concentration analysis were performed using OVITO and VMD software’s respectively. Weaker bonds and higher stress concentrations are observed in the presence of hydrogen in zirconium. The presented results clearly demonstrate that MD simulation can be used to predict structure and processes that are important for understanding failure in Zr based nuclear materials.

Ion irradiation has been known to be an effective tool for structure modification with micro/nano-scale precision. Recently, demonstrations have been made for nano-machining, such as the cutting and welding of carbon nanotubes. Understanding the fundamental effects of ion irradiation on carbon nanotubes is critical for advancing this technique as well as for scientific curiosity. Molecular dynamics modeling was performed to study irradiation stability, structural changes, and corresponding thermal properties. In our study, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) was used to perform atomic scale simulation. In order to understand size and geometry effects on carbon damage creation, the threshold energy of displacement was calculated as a function of recoiling angles for both single-walled and multi-walled nanotubes. A strong directional dependence was found to exist in different shells of multi-walled carbon nanotubes. We found that carbon atoms on the innermost tube were more susceptible to be displaced toward the center of axis. The calculation matrix was further extended to nanotubes having different diameters for a full-scale understanding of the creation of defects. Besides studies on defects creation, thermal properties of carbon nanotubes were studied via a simplified model of the carbon nanotube network. Thermal conductivity, were found to be increased nearly one order of magnitude in carbon nanotube networks after irradiation and subsequent annealing. All the modeling results were compared with experimental observations either obtained from this project as a parallel study or from previous works, for the purpose of verification and validation. For experimental works, atomic scale characterization was performed by using transmission electron microscopy and the thermal conductivity measurement was characterized by using laser flash technique. Through a combination of modeling and experimentation, we proved that ion beam techniques can be used to enhance thermal conductivity in carbon nanotube bundles by inter-tube defects mediated phonon transport.

Chirality can be induced in achiral solvent molecules located near a chiral molecule or surface, but there have been very few systematic studies in this field either experimentally or theoretically. The focus of this thesis is to study the chirality transfer from chiral molecules to achiral solvents. To capture the chirality transfer in solvent molecules, a solvent model that is sensitive to the changes in the environment is needed. We developed new polarizable and flexible models based on an extensive series of ab initio calculations and molecular dynamics simulations. The models include electric field dependence in both the atomic charges and the intramolecular degrees of freedom. Modified equations of motion are required and we have implemented a multiple time step algorithm to solve these equations. Our methodology is general and has been applied to ethanol as a test. For other solvents in our simulations, such as 2-propanol, limited models are used. The chirality transfer from chiral solutes to achiral solvents and its dependence on the solute and solvent characteristics are then explored using the new polarizable models in molecular dynamics simulations. The chirality induced in the solvent is assessed based on a series of related chirality indexes originally proposed by Osipov[Osipov et al., Mol. Phys.84, 1193(1995)]. Two solvents are considered: Ethanol and benzyl alcohol. The solvation of three chiral solutes is examined: Styrene oxide, acenaphthenol, and n-(1-(4-bromophenyl)ethyl)pivalamide (PAMD). All three solutes have the possibility of hydrogen-bonding with the solvent, the last two may also form π-π interactions, and the last has multiple hydrogen bonding sites. The chirality transfer from chiral surfaces to achiral solvents is also explored. Emphasis is placed on the extent of this chirality transfer and its dependence on the surface and solvent characteristics is explored. Three surfaces employed in chiral chromatography are examined: The Whelk-O1 interface; a phenylglycine-derived chiral stationary phase (CSP); and a leucine-derived CSP. The solvents consist of ethanol, a binary n-hexane/ethanol solvent, 2-propanol, and a binary n-hexane/2-propanol solvent. Molecular dynamics simulations of the solvated chiral interfaces form the basis of the analysis and position dependent chirality indexes are analyzed in detail. / Thesis (Ph.D, Chemistry) -- Queen's University, 2009-09-24 00:25:15.174

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Molecular Dynamics (MD) simulations were used in conjunction with the Kirkwood-Buff (KB) theory to compute partial molar volume (PMV) for solutes of various chemical natures. Simulations performed with only the Lennard-Jones (LJ) potential yield PMV for solutes which coincide with the cavity volumes derived from calculations with scaled particle theory (SPT). Whereas, simulations carried out with only the repulsive LJ term produced PMV of solutes closer to their excluded volumes. We also determined the thermal volume, VT, which represents the volume of the effective void created around solutes of varying cavity sizes and applied the spherical approximation of solute geometry to evaluate the thickness of the thermal volume, . Our results reveal an increase in the thickness of thermal volume, , with an increase in the size of the solute. Our theoretical results are in good agreement with the reported empirical schemes for parsing PMV data on small solutes.

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The electron density of an ion is strongly influenced by its environment in a condensed phase. When the environment changes, for example due to thermal motion, non-trivial changes in the electron density, and hence the interionic interactions occur. These interactions give rise to many-body effects in the potential. In order to represent this phenomenon in molecular dynamics (MD) simulations a method has been developed in which the environmentally-induced changes in the ionic properties are represented by extra dynamical variables. These extra variables are handled in an extended Lagrangian formalism by techniques analogous to those used in Car and Parrinello's ab initio MD method. At its simplest level (the polarizable-ion model or PIM) induced dipoles are represented. With the PIM it has proven possible to quantitatively account for numerous properties of divalent metal halides, which had previously been attributed to unspecific "covalent" effects. In the solid-state the prevalence of layered crystal structures is explained. Analogous non-coulombic features in liquid structures, in particular network formation in "strong" liquids like ZnCl₂ , have been studied as has network disruption by "modifiers" like RbCl. This work leads to an understanding of the relationship between the microscopic structure and anomalous peaks ("prepeaks") seen in diffraction data of such materials. The PIM was extended to include induced quadrupoles and their effect studied in simulations of AgCl. In the solid-state it is found that the both are crucial in improving the phonon dispersion curves with respect to experiment. In the liquidstate polarization effects lower the melting point markedly. For oxides the short-range energy has been further partitioned into overlap and rearrangement energies and electronic structure calculations are used to parameterize a model in which the radius of the anion is included as an additional degree of freedom. The Bl → B2 phase transition is studied in MgO and CaO and the differences between the new model and a rigid-ion model are analysed.

In this thesis, Molecular Dynamics simulations of shocked single crystals of Copper and Iron are studied using simulated X-ray diffraction. Strains and volumetric compression in modeled Copper crystals shock-compressed on picosecond time-scales are found. By comparing the shifts in the second and fourth diffraction orders, the density of dislocations is calculated. In Iron, simulated X-ray diffraction is used to verify the modelling of the α-ε phase transition induced by shock-compression on picosecond time-scales. No plastic deformation of Iron is found in the studied pressure range of ~ 15-53 GPa. The results are then compared with data from in situ X-ray diffraction experiments of laser-shocked single crystals. Near-hydrostatic compression of shock-compressed Copper on nanosecond time-scales is confirmed using a new wide-angle film diagnostic capturing diffraction from multiple crystal planes. Also, the first in situ X-ray diffraction evidence of the onset of the α-ε phase transition in laser-shocked single crystal Iron is shown. No plastic yield of the crystal lattice is found, which is in agreement with the simulation results. Results from both the Molecular Dynamics simulations and experiments are used to suggest enhancements in computer modelling of shocked crystals, as well as future experimental studies. In particular, the need for a measurement of dislocation densities during the shock wave passage through a crystal is highlighted, and a method enabling such a measurement is proposed.