Computational chemistry offers one the ability to develop a better understanding of the complex physical and chemical interactions that are fundamental to macro- and mesoscopic processes that are seen in laboratory experiments, industrial processes, and ordinary, everyday life. For many systems, the physics of interest occur at the molecular or atomistic levels, and in these cases, computational modeling and two well refined simulation techniques become invaluable: Monte Carlo (MC) and molecular dynamics (MD). In this work, two well established problems were tackled. First, models and potentials for various gas molecules were produced and refined from first principles. These models, although based on work done previously by Belof et al., are novel due to the inclusion of many-body van der Waals interactions, advanced r-12 repulsion combining rules for treating unlike intra- and intermolecular interactions, and highly-efficient treatment of induction interactions. Second, a multitude of models were developed and countless MD simulations were performed in order to describe and understand the giant frictional anisotropy of d-AlCoNi, first observed by Park et al. in 2005.

In a 2005 article in Science [45], Park et al. measured in vacuum the friction between a coated atomic-force-microscope tip and the clean two-fold surface of an AlNiCo quasicrystal. Because the two-fold surface is periodic in one direction and aperiodic (with a quasiperiodicity related to the Fibonacci sequence) in the perpendicular direction, frictional anisotropy is not unexpected; however, the magnitude of that anisotropy in the Park experiment, a factor of eight, is unprecedented. By eliminating chemistry as a variable, the experiment also demonstrated that the low friction of quasicrystals must be tied in some way to their quasiperiodicity. Through various models, we investigate generic geometric mechanisms that might give rise to this anisotropy.

In this thesis, we use first-principles calculations to study the structural, electronic, and thermal properties of several complex hydrides. We investigate structural and electronic properties of Na-Li alanates. Although Na alanate can reversibly store H with Ti catalyst, its weight capacity needs to be improved. This can be accomplished by partial replacement of Na with lighter elements. We explore the structures of possible Na-Li alloy alanates, and study their phase stability. We also study the structural and thermal properties of Li/Mg/Li-Mg Amides/Imides. Current experimental results give a disordered model about the structure of Li-Mg Imide, in which the positions of Li and Mg are not specified. In addition the model gives a controversial composition stoichiometry. We try to resolve this controversy by searching for low-energy ordered phases. In the last part, we study the structural, energetic, and electronic properties of the La-Mg-Pd-H system. This quaternary system is another example of hydrogenation-induced metal-nonmetal transition without major reconstruction of metal host structure, and it is also with partial reversible H capacity. Experiment gives partially disordered H occupancy on two Wyckoff positions. Our calculation explains the structural and bonding characteristics observed in experiment.

In this thesis, we focus on theoretical study of adsorbates on metal and oxide surfaces that are important for surface chemistry and catalysis. Based on first principles calculations, the adsorption ofCO, NO, NO2, C4H6S2, C22H27SH and other molecules or radicals on nobel metal surfaces (gold and silver) are investigated. Also, NO oxidation on oxygen pre-covered Au(111)surface and CO oxidation on water-oxygen covered Au(111)surface aretheoretically studied. A new mechanism of water-enhanced COoxidation is proposed. As for oxide surfaces, we first investigatethe geometric, electronic and magnetic structures of FeO ultrathin film on Pt(111) surface. The experimentally observed scanning tunneling microscopy images are well reproduced for the first timewith our model. The adsorption and dissociation of water on rutileTiO2(110) surface are investigated by quantum molecular dynamics.By theoretical X-ray photoemission spectroscopy (XPS) calculations,the surface species are properly assigned. The same strategy has applied to the study of the phase transition of water covered reconstructed anatase TiO2(001) surface, from which two different phases are theoretically identified. The structure of graphene oxideis also studied by comparing experimental and theoretical XPS spectra. Based on the novel structures identified, a new cutmechanism of graphene oxide is proposed. / QC 20100819

This thesis presents work done on the calculation of the effects of anharmonic nuclear motion on the properties of solid materials from first principles. Such anharmonic effects can be significant in many cases. A vibrational self-consistent field (VSCF) method is used as the basis for these calculations, which is then improved and applied to a variety of solid state systems. Firstly, work done to improve the efficiency of the VSCF method is presented. The standard VSCF method involves using density functional theory (DFT) to map the Born-Oppenheimer (BO) energy surface that the nuclei move in, a computationally expensive process. It is shown that the accurate forces available in plane-wave basis DFT can be used to help map the BO surface more accurately and reduce the computational cost. This improved VSCF+f method is tested on molecular and solid hydrogen, as well as lithium and zirconium, and is found to give a speed-up of up to 40%. The VSCF method is then applied to two different systems of physical interest. It is first applied to the case of the neutral vacancy in diamond, in order to resolve a known discrepancy between harmonic ab initio calculations and experiment -- the former predict a static Jahn-Teller distortion, whilst the latter leads to a dynamic Jahn-Teller effect. By including anharmonic corrections to the energy and nuclear wavefunction, we show that the inclusion of these effects results in agreement between first-principles calculations and experiment for the first time. Lastly, the VSCF method is applied to barium titanate, a prototypical ferroelectric material which undergoes a series of phase transitions from around 400 K downwards. The nature of these phase transitions is still unclear, and understanding them is an active area of research. We describe the physics of the phase transitions of barium titanate, including both anharmonicity and the effect of polarisation caused by long wavelength vibrations, to help understand the important physics from first principles.

abstract: In recent years, there has been increased interest in the Indium Gallium Nitride (InGaN) material system for photovoltaic (PV) applications. The InGaN alloy system has demonstrated high performance for high frequency power devices, as well as for optical light emitters. This material system is also promising for photovoltaic applications due to broad range of bandgaps of InxGa1-xN alloys from 0.65 eV (InN) to 3.42 eV (GaN), which covers most of the electromagnetic spectrum from ultraviolet to infrared wavelengths. InGaN’s high absorption coefficient, radiation resistance and thermal stability (operating with temperature > 450 ℃) makes it a suitable PV candidate for hybrid concentrating solar thermal systems as well as other high temperature applications. This work proposed a high efficiency InGaN-based 2J tandem cell for high temperature (450 ℃) and concentration (200 X) hybrid concentrated solar thermal (CSP) application via numerical simulation. In order to address the polarization and band-offset issues for GaN/InGaN hetero-solar cells, band-engineering techniques are adopted and a simple interlayer is proposed at the hetero-interface rather than an Indium composition grading layer which is not practical in fabrication. The base absorber thickness and doping has been optimized for 1J cell performance and current matching has been achieved for 2J tandem cell design. The simulations also suggest that the issue of crystalline quality (i.e. short SRH lifetime) of the nitride material system to date is a crucial factor limiting the performance of the designed 2J cell at high temperature. Three pathways to achieve ~25% efficiency have been proposed under 450 ℃ and 200 X. An anti-reflection coating (ARC) for the InGaN solar cell optical management has been designed. Finally, effective mobility model for quantum well solar cells has been developed for efficient quasi-bulk simulation. / Dissertation/Thesis / Doctoral Dissertation Physics 2017

abstract: Amorphous materials can be uniformly deposited over a large area at lower cost compared to crystalline semiconductors (Silicon or Germanium). This property along with its high resistivity and wide band-gap found many applications in devices like rectifiers, xerography, xero-radiography, ultrahigh sensitivity optical cameras, digital radiography, and mammography (2D and 3D tomosynthesis). Amorphous selenium is the only amorphous material that undergoes impact ionization where only holes avalanche at high electric fields. This leads to a small excess noise factor which is a very important performance comparison matrix for avalanche photodetectors. Thus, there is a need to model high field avalanche process in amorphous selenium. At high fields, the transport in amorphous selenium changes from low values of activated trap-limited drift mobility to higher values of band transport mobility, via extended states. When the transport shifts from activated mobility with a high degree of localization to extended state band transport, the wavefunction of the amorphous material resembles that of its crystalline counterpart. To that effect, crystalline monoclinic selenium which has the closest resemblance to vapor deposited amorphous selenium has been studied. Modelling a crystalline semiconductor makes calculations simpler. The transport phenomena in crystalline monoclinic selenium is studied by using a bulk Monte Carlo technique to solve the semi-classical Boltzman Transport equation and thus calculate vital electrical parameters like mobility, critical field and mobility variations against temperatures. The band structure and the density of states function for monoclinic selenium was obtained by using an atomistic simulation tool, the Atomistic Toolkit in the Virtual Nano Lab, Quantum Wise, Copenhagen, Denmark. Moreover, the velocity and energy against time characteristics have been simulated for a wide range of electric fields (1-1000 $\frac{kV}{cm}$), which is further used to find the hole drift mobility. The low field mobility is obtained from the slope of the velocity vs. electric field plot. The low field hole mobility was calculated to be 5.51 $\frac{cm^{2}}{Vs}$ at room temperature. The experimental value for low field hole mobility is 7.29 $\frac{cm^{2}}{Vs}$. The energy versus electric field simulation at high fields is used to match the experimental onset of avalanche (754 $\frac{kV}{cm}$) for an ionization threshold energy of 2.1 eV. The Arrhenius plot for mobility against temperature is simulated and compared with published experimental data. The experimental and simulation results show a close match, thus validating the study. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2017

abstract: This thesis focuses on studying the interaction between floating objects and an air-water flow system driven by gravity. The system consists of an inclined channel in which a gravity driven two phase flow carries a series of floating solid objects downstream. Numerical simulations of such a system requires the solution of not only the basic Navier-Stokes equation but also dynamic interaction between the solid body and the two-phase flow. In particular, this requires embedding of dynamic mesh within the two-phase flow. A computational fluid dynamics solver, ANSYS fluent, is used to solve this problem. Also, the individual components for these simulations are already available in the solver, few examples exist in which all are combined. A series of simulations are performed by varying the key parameters, including density of floating objects and mass flow rate at the inlet. The motion of the floating objects in those simulations are analyzed to determine the stability of the coupled flow-solid system. The simulations are successfully performed over a broad range of parametric values. The numerical framework developed in this study can potentially be used in applications, especially in assisting the design of similar gravity driven systems for transportation in manufacturing processes. In a small number of the simulations, two kinds of numerically instability are observed. One is characterized by a sudden vertical acceleration of the floating object due to a strong imbalance of the force acting on the body, which occurs when the mass flow of water is weak. The other is characterized by a sudden vertical movement of air-water interface, which occurs when two floating objects become too close together. These new types of numerical instability deserve future studies and clarifications. This study is performed only for a 2-D system. Extension of the numerical framework to a full 3-D setting is recommended as future work. / Dissertation/Thesis / Masters Thesis Mechanical Engineering 2018

abstract: With the maturity of advanced composites as feasible structural materials for various applications there is a critical need to solve the challenge of designing these material systems for optimal performance. However, determining superior design methods requires a deep understanding of the material-structure properties at various length scales. Due to the length-scale dependent behavior of advanced composites, multiscale modeling techniques may be used to describe the dominant mechanisms of damage and failure in these material systems. With polymer matrix fiber composites and nanocomposites it becomes essential to include even the atomic length scale, where the resin-hardener-nanofiller molecules interact, in the multiscale modeling framework. Additionally, sources of variability are also critical to be included in these models due to the important role of uncertainty in advance composite behavior. Such a methodology should be able to describe length scale dependent mechanisms in a computationally efficient manner for the analysis of practical composite structures. In the research presented in this dissertation, a comprehensive nano to macro multiscale framework is developed for the mechanical and multifunctional analysis of advanced composite materials and structures. An atomistically informed statistical multiscale model is developed for linear problems, to estimate and scale elastic properties of carbon fiber reinforced polymer composites (CFRPs) and carbon nanotube (CNT) enhanced CFRPs using information from molecular dynamics simulation of the resin-hardener-nanofiller nanoscale system. For modeling inelastic processes, an atomistically informed coupled damage-plasticity model is developed using the framework of continuum damage mechanics, where fundamental nanoscale covalent bond disassociation information is scaled up as a continuum scale damage identifying parameter. This damage model is coupled with a nanocomposite microstructure generation algorithm to study the sub-microscale damage mechanisms in CNT/CFRP microstructures. It is further integrated in a generalized method of cells (GMC) micromechanics model to create a low-fidelity computationally efficient nonlinear multiscale method with imperfect interfaces between the fiber and matrix, where the interface behavior is adopted from nanoscale MD simulations. This algorithm is used to understand damage mechanisms in adhesively bonded composite joints as a case study for the comprehensive nano to macroscale structural analysis of practical composites structures. At each length scale sources of variability are identified, characterized, and included in the multiscale modeling framework. / Dissertation/Thesis / Doctoral Dissertation Aerospace Engineering 2018

abstract: The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, however many of the essential features of life are system level properties which only manifest in the collective behavior of many components. In order to make progress towards solving the origin of life new modeling techniques are needed. In this dissertation I review historical approaches to modeling the origin of life. I proceed to elaborate on new approaches to understanding biology that are derived from statistical physics and prioritize the collective properties of living systems rather than the component parts. In order to study these collective properties of living systems, I develop computational models of chemical systems. Using these computational models I characterize several system level processes which have important implications for understanding the origin of life on Earth. First, I investigate a model of molecular replicators and demonstrate the existence of a phase transition which occurs dynamically in replicating systems. I characterize the properties of the phase transition and argue that living systems can be understood as a non-equilibrium state of matter with unique dynamical properties. Then I develop a model of molecular assembly based on a ribonucleic acid (RNA) system, which has been characterized in laboratory experiments. Using this model I demonstrate how the energetic properties of hydrogen bonding dictate the population level dynamics of that RNA system. Finally I return to a model of replication in which replicators are strongly coupled to their environment. I demonstrate that this dynamic coupling results in qualitatively different evolutionary dynamics than those expected in static environments. A key difference is that when environmental coupling is included, evolutionary processes do not select a single replicating species but rather a dynamically stable community which consists of many species. Finally, I conclude with a discussion of how these computational models can inform future research on the origins of life. / Dissertation/Thesis / Doctoral Dissertation Physics 2018