<div>Global warming is considered to result from excessive emission of CO₂ caused by human activity. The security of long term CO₂ capture and sequestration on the subsurface depends on the integrity of caprocks. Natural and engineered subsurface activities can generate fractures in caprocks that can lead to CO₂ leakage. Reactive fluids that flow through a fracture may seal a fracture through mineral precipitation or open a fracture through dissolution. It is extremely useful to CO₂ storage to understand the behavior of reactive fluids that generates mineral precipitation that can seal a fracture. Experiments on non-reactive and reactive fluid mixing were performed to explore gravity-driven chemical dynamics that control the mixing and spatial distribution of mineral precipitates. Fracture inclination, fracture apertures, fluid pumping rates, and density contrasts between fluids were studied for their effects on fluid mixing. From non-reactive fluid mixing experiments, a less dense fluid was found to be confined to a narrow path (runlet) by the denser fluid under the influence of gravity. Fracture inclination angle affected the shape of the less dense fluid runlet. As the angle of inclination decreased, the area of the less dense runlet increased. Improved mixing and a potentially larger area of precipitation formation will occur during reactive fluid mixing when the fracture plane is perpendicular to gravity. Fracture aperture affected the time evolution of the mixing of the fluids, while pumping rate affected fluid mixing by controlling the relative velocities between the two fluids. The fact that the spatial distribution of the two fluids, instead of the fracture roughness, dominated the fluid mixing sheds light on the potential behaviors of reactive fluids mixing in fractures. The location for the majority of precipitation formation and the transport of precipitates can be accordingly predicted from knowledge of the properties of the two reactive fluids and the orientation of the fracture.</div><div>From a small study on wave propagation across fractures with precipitates, simulation results showed that the impedance difference between the matrix material and the precipitate affects the transmitted signal amplitude. Both the aperture and fraction of aperture filled with precipitates affect signal amplitude.</div><div><br></div>

<p>Proton beam therapy has shown great promise for cancer treatment due to its high precision in irradiating tumor volumes. However, due to the massive size and expense of the cyclotrons/synchrotrons needed to accelerate the protons, the widespread use of proton therapy is limited. Laser plasma accelerated (LPA) proton beams may be a potential alternative to conventional proton beams: by shooting an ultraintense, ultrashort pulsed laser at a thin target, a plasma sheath electric field may be formed with the capability of accelerating protons to potentially therapeutic energies in very short distances. In addition to accessibility, there is significant uncertainty in proton range in heterogeneous tissues. Thermoacoustic computed tomographic (TACT) imaging has the potential to provide <em>in vivo</em> dose imaging and range verification to address these uncertainties. TACT measures thermoacoustic waves generated from the absorbed dose and implements a 3D filtered backprojection to reconstruct volumetric images of the dose. The purpose of this thesis is to determine the feasibility of integrating LPA proton beams with thermoacoustic imaging into a novel image-guided small animal therapy platform as an early step towards clinical  translation to address the issues of accessibility and dosimetric spatial uncertainty. A Monte Carlo (MC) method is used to simulate an LPA proton beam with characteristics based on literature, thermoacoustic waves are simulated on a voxel-wise basis of the MC dose, and 3D filtered backprojection is used to reconstruct a volumetric image of the dose. In Specific Aim 1, the dependence of image accuracy on transducer array angular coverage is investigated; in Specific Aim 2, an iterative reconstruction algorithm is implemented to improve image accuracy through increased sampling of projection space when transducer array angular coverage is insufficient; and in Specific Aim 3, the detector sensitivity to dose is determined for several therapeutic endpoints. The work presented in this thesis not only demonstrates the feasibility of integrating LPA and thermoacoustic technologies but necessary design changes to realize a functional small animal platform.</p>

<p>The capability of manipulation of the flow of mechanical energy in the form of mechanical waves (including acoustic and elastic waves) has always been a challenge and a critical part in various areas of engineering. The recent advances in topological acoustic/elastic metamaterials certainly open a new pathway to the manipulation of mechanical waves, especially for the novel scattering-immune wave-guiding capability, even in the presence of defects, disorders or sharp bends along the waveguide. In this Dissertation, the theoretical background and experimental evidence of various types of elastic-wave topological metamaterials including analogues to 2D quantum valley Hall effect (QVHE) materials, 2D quantum spin Hall effect (QSHE) topological insulators are presented. First, the formulation the elastic-wave analogue to QVHE materials in a general continuous elastic phononic structure (not limited to local resonant lattices, filling the gap in the literature) is proposed, and a strategy using pressurized cells to actively control the phononic lattice is presented. By finite prestrain and geometric nonlinear effect, the space inversion symmetry of the original hexagonal lattice is broken, resulting in distinct QVHE phases (characterized by valley Chern numbers) in lattice domains with opposite pressurization. With such mechanism, the edge-state path, i.e., the domain wall connecting lattices with distinct QVHE phases, can be real-time configured. Further more, edge states with tunable frequency-wavenumber dispersion can be created at the external boundaries of the lattice by appropriate pressurization of the outermost cells. An aluminum reticular sheet built with water-jet cutting is machined in the pre-deformed pattern with a Z-shape domain wall at the center, which spatially divides the sheet into two domains with opposite QVHE phases. Using piezoelectric transducers and laser Doppler vibrometry, the measured harmonic and transient responses confirm the back-scattering-immunity of the topological edge states, and the frequency-wavenumber dispersion matches the numerical prediction. A strategy is proposed for unidirectionally generating edge states along the domain wall using two off-phase transducers, which is also experimentally demonstrated. For elastic-wave analogue to QSHE topological insulators, we focus on the ``zone-folding'' method and propose a honeycomb 2D elastic beam network with periodically altered thickness with a generalized Kekule distortion pattern. Such framework provides a parametric space with exhaustive control in the topological phase diagram of waves in the lattice compared to earlier works in the literature. The effective Hamiltonian as well as the characterized topological phase are gauge dependent, particularly they change with different reference frames. This lead to ambiguity in the topological phase of such phononic crystal. Based on this argument, it is predicted that edge states could exist at a dislocation interface connecting two piece of phononic structures of the same pattern with relative displacement. Following the same idea, but considering the available fabrication options, a phononic plate with honeycomb groove pattern engraved on both sides is built, which the depth varied according to the Kekule pattern. With proper tuning of the parameters, it realizes an analogue to the QSHE topological insulator. With <em>ab initio</em> calculation of the Berry curvature (without involving any approximations such as the perturbative approach), a new topological invariant <em>local topological charge</em> is defined and evaluated as the counterpart of the Z₂ invariant in the classical-wave-zone-folding analogue. The local topological charge has intrinsic ambiguity and its value depends on the selected reference frame. However, its <em>change </em>according to changes in the parameters, under a consistent reference frame, is well-defined. Given the fact that shifting the reference frame by certain fractions of a lattice constant was equivalent to changing one of the parameters by a certain amount, it also lead to a well-defined change in the local topological charge, which indicates topological phase transition, and one can predict the existence of edge states at the displacement-dislocation interface between two neighboring lattices having the same pattern up to a rigid-body shifting. The phononic plate is machined by a CNC mill, and the experiment is carried out using piezoelectric transducers and laser Doppler vibrometry, which confirms the existence and robustness of the topological edge states at such dislocation interface connecting identical pattern, which was unprecedented in both quantum and classical systems. The final part of this Dissertation focuses on creating classical mechanical analogues to the 1D Kitaev superconducting model and Majorana-like bound states aimed at future acoustic-wave based computation.</p>

Finite amplitude perturbations in compressible media are ubiquitous in scientific and engineering applications such as gas-turbine engines, rocket propulsion systems, combustion instabilities, inhomogeneous solids, and traffic flow prediction models, to name a few. Small amplitude waves in compressible fluids propagate as sound and are very well described by linear theory. On the other hand, the theory of nonlinear acoustics, concerning high-amplitude wave propagation (Mach<2) is relatively underdeveloped. Most of the theoretical development in nonlinear acoustics has focused on wave steepening and has been centered around the Burgers' equation, which can be extended to nonlinear acoustics only for purely one-way traveling waves. In this dissertation, theoretical and computational developments are discussed with the objective of advancing the multi-fidelity modeling of nonlinear acoustics, ranging from quasi one-dimensional high-amplitude waves to combustion-induced detonation waves. <br> <br> We begin with the theoretical study of spectral energy cascade due to the propagation of high amplitude sound in the absence of thermal sources. To this end, a first-principles-based system of governing equations, correct up to second order in perturbation variables is derived. The exact energy corollary of such second-order system of equations is then formulated and used to elucidate the spectral energy dynamics of nonlinear acoustic waves. We then extend this analysis to thermoacoustically unstable waves -- i.e. amplified as a result of thermoacoustic instability. We drive such instability up until the generation of shock waves. We further study the nonlinear wave propagation in geometrically complex case of waves induced by the spark plasma between the electrodes. This case adds the geometrical complexity of a curved, three-dimensional shock, yielding vorticity production due to baroclinic torque. Finally, detonation waves are simulated by using a low-order approach, in a periodic setup subjected to high pressure inlet and exhaust of combustible gaseous mixture. An order adaptive fully compressible and unstructured Navier Stokes solver is currently under development to enable higher fidelity studies of both the spark plasma and detonation wave problem in the future. <br>

Multisymplectic integration is a relatively new addition to the field of geometric integration, which is a modern approach to the numerical integration of systems of differential equations. Multisymplectic integration is carried out by numerical integrators known as multisymplectic integrators, which preserve a discrete analogue of a multisymplectic conservation law. In recent years, it has been shown that various discretisations of a multi-Hamiltonian PDE satisfy a discrete analogue of a multisymplectic conservation law. In particular, discretisation in time and space by the popular symplectic Runge–Kutta methods has been shown to be multisymplectic. However, a multisymplectic integrator not only needs to satisfy a discrete multisymplectic conservation law, but it must also form a well-defined numerical method. One of the main questions considered in this thesis is that of when a multi-Hamiltonian PDE discretised by Runge–Kutta or partitioned Runge–Kutta methods gives rise to a well-defined multisymplectic integrator. In particular, multisymplectic integrators that are explicit are sought, since an integrator that is explicit will, in general, be well defined. The first class of discretisation methods that I consider are the popular symplectic Runge–Kutta methods. These have previously been shown to satisfy a discrete analogue of the multisymplectic conservation law. However, these previous studies typically fail to consider whether or not the system of equations resulting from such a discretisation is well defined. By considering the semi-discretisation and the full discretisation of a multi-Hamiltonian PDE by such methods, I show the following: • For Runge–Kutta (and for partitioned Runge–Kutta methods), the active variables in the spatial discretisation are the stage variables of the method, not the node variables (as is typical in the time integration of ODEs). • The equations resulting from a semi-discretisation with periodic boundary conditions are only well defined when both the number of stages in the Runge–Kutta method and the number of cells in the spatial discretisation are odd. For other types of boundary conditions, these equations are not well defined in general. • For a full discretisation, the numerical method appears to be well defined at first, but for some boundary conditions, the numerical method fails to accurately represent the PDE, while for other boundary conditions, the numerical method is highly implicit, ill-conditioned and impractical for all but the simplest of applications. An exception to this is the Preissman box scheme, whose simplicity avoids the difficulties of higher order methods. • For a multisymplectic integrator, boundary conditions are treated differently in time and in space. This breaks the symmetry between time and space that is inherent in multisymplectic geometry. The second class of discretisation methods that I consider are partitioned Runge– Kutta methods. Discretisation of a multi-Hamiltonian PDE by such methods has lead to the following two major results: 1. There is a simple set of conditions on the coefficients of a general partitioned Runge– Kutta method (which includes Runge–Kutta methods) such that a general multi- Hamiltonian PDE, discretised (either fully or partially) by such methods, satisfies a natural discrete analogue of the multisymplectic conservation law associated with that multi-Hamiltonian PDE. 2. I have defined a class of multi-Hamiltonian PDEs that, when discretised in space by a member of the Lobatto IIIA–IIIB class of partitioned Runge–Kutta methods, give rise to a system of explicit ODEs in time by means of a construction algorithm. These ODEs are well defined (since they are explicit), local, high order, multisymplectic and handle boundary conditions in a simple manner without the need for any extra requirements. Furthermore, by analysing the dispersion relation for these explicit ODEs, it is found that such spatial discretisations are stable. From these explicit ODEs in time, well-defined multisymplectic integrators can be constructed by applying an explicit discretisation in time that satisfies a fully discrete analogue of the semi-discrete multisymplectic conservation law satisfied by the ODEs. Three examples of explicit multisymplectic integrators are given for the nonlinear Schr¨odinger equation, whereby the explicit ODEs in time are discretised by the 2-stage Lobatto IIIA– IIIB, linear–nonlinear splitting and real–imaginary–nonlinear splitting methods. These are all shown to satisfy discrete analogues of the multisymplectic conservation law, however, only the discrete multisymplectic conservation laws satisfied by the first and third multisymplectic integrators are local. Since it is the stage variables that are active in a Runge–Kutta or partitioned Runge– Kutta discretisation in space of a multi-Hamiltonian PDE, the order of such a spatial discretisation is limited by the order of the stage variables. Moreover, the spatial discretisation contains an approximation of the spatial derivatives, and thus, the order of the spatial discretisation may be further limited by the order of this approximation. For the explicit ODEs resulting from an r-stage Lobatto IIIA–IIIB discretisation in space of an appropriate multi-Hamiltonian PDE, the order of this spatial discretisation is r - 1 for r = 10; this is conjectured to hold for higher values of r. For r = 3, I show that a modification to the initial conditions improves the order of this spatial discretisation. It is expected that a similar modification to the initial conditions will improve the order of such spatial discretisations for higher values of r.

<p dir="ltr">The onset of smart manufacturing signifies a crucial shift in the industrial landscape, underscoring the pressing need for systems capable of adapting to and managing the complex dynamics of modern production environments. In this context, the importance of smart monitoring becomes increasingly apparent, serving as a vital tool for ensuring operational efficiency and reliability. Inspired by the critical role of auditory perception in human decision-making, this study investigated the application of machine sound recognition for practical use in manufacturing environments. Addressing the challenge of utilizing machine sounds in the loud noises of factories, the study employed an Internal Sound Sensor (ISS).</p><p dir="ltr">The study examined how sound propagates through structures and further explored acoustic characteristics of the ISS, aiming to apply these findings in machine monitoring. To leverage the ISS effectively and achieve a higher level of monitoring, a smart sound monitoring framework was proposed to integrate sound monitoring with machine data and human-machine interface. Designed for applicability and cost effectiveness, this system employs real-time edge computing, making it adaptable for use in various industrial settings.</p><p dir="ltr">The proposed framework and ISS deployed across a diverse range of production environments, showcasing a leap forward in the integration of smart technologies in manufacturing. Their application extends beyond continuous manufacturing to include discrete manufacturing systems, demonstrating adaptability. By analyzing sound signals from various production equipment, this study delves into developing machine sound recognition models that predict operational states and productivity, aiming to enhance manufacturing efficiency and oversight on real factory floors. This comprehensive and practical approach underlines the framework's potential to revolutionize operational management and manufacturing productivity. The study progressed to integrating manufacturing context with sound data, advancing towards high-level monitoring for diagnostic predictions and digital twin. This approach confirmed sound recognition's role in manufacturing diagnostics, laying a foundation for future smart monitoring improvements.</p>

The theory of radiative transfer is applied to the problem of multiple wave scattering in a one-dimensional multilayer. A new mathematical model of a multilayer is presented in which both the refractive index and width of each layer are randomized. The layer widths are generated by a new probability distribution which allows for strong layer width disorder. An expression for the transport mean free path of the multilayer is derived based on its single-scattering properties. It will be shown that interference between the field reflected from adjacent layer interfaces remains significant even in the presence of strong layer width disorder. It will be proven that even when the scattering is weak, the field in a random multilayer localizes at certain frequencies. The effect of increasing layer width randomization on this form of localization is quantified. The radiative transfer model of time-harmonic scattering in multilayers is extended to narrow-band pulse propagation in weakly scattering media. The tendency of pulses to broaden in this medium is discussed. A radiative transport model of the system is developed and compared to numerical solutions of the wave equation. It is observed that pulse broadening is not described by simple transfer theory. The radiative transfer model is extended by the addition of a Laplacian term in an attempt to model the effect of ensemble average pulse broadening. Numerical simulation results in support of this proposal are given, and applications for the theory suggested. Finally, the problem of acoustic wave scattering by planar screens is considered. The study was motivated by the idea that multiple scattering experiments may prove possible in a medium composed of such scatterers. Successful multiple scattering in a medium of planar scatterers will depend on the scattering cross-section at angles away from normal incidence. The scattering cross-section is calculated for a circular disc using a new technique for solving the acoustic wave equation on planar surfaces. The method is validated by comparison with available analytic solutions and the geometric theory of diffraction.

The theory of radiative transfer is applied to the problem of multiple wave scattering in a one-dimensional multilayer. A new mathematical model of a multilayer is presented in which both the refractive index and width of each layer are randomized. The layer widths are generated by a new probability distribution which allows for strong layer width disorder. An expression for the transport mean free path of the multilayer is derived based on its single-scattering properties. It will be shown that interference between the field reflected from adjacent layer interfaces remains significant even in the presence of strong layer width disorder. It will be proven that even when the scattering is weak, the field in a random multilayer localizes at certain frequencies. The effect of increasing layer width randomization on this form of localization is quantified. The radiative transfer model of time-harmonic scattering in multilayers is extended to narrow-band pulse propagation in weakly scattering media. The tendency of pulses to broaden in this medium is discussed. A radiative transport model of the system is developed and compared to numerical solutions of the wave equation. It is observed that pulse broadening is not described by simple transfer theory. The radiative transfer model is extended by the addition of a Laplacian term in an attempt to model the effect of ensemble average pulse broadening. Numerical simulation results in support of this proposal are given, and applications for the theory suggested. Finally, the problem of acoustic wave scattering by planar screens is considered. The study was motivated by the idea that multiple scattering experiments may prove possible in a medium composed of such scatterers. Successful multiple scattering in a medium of planar scatterers will depend on the scattering cross-section at angles away from normal incidence. The scattering cross-section is calculated for a circular disc using a new technique for solving the acoustic wave equation on planar surfaces. The method is validated by comparison with available analytic solutions and the geometric theory of diffraction.

The theory of radiative transfer is applied to the problem of multiple wave scattering in a one-dimensional multilayer. A new mathematical model of a multilayer is presented in which both the refractive index and width of each layer are randomized. The layer widths are generated by a new probability distribution which allows for strong layer width disorder. An expression for the transport mean free path of the multilayer is derived based on its single-scattering properties. It will be shown that interference between the field reflected from adjacent layer interfaces remains significant even in the presence of strong layer width disorder. It will be proven that even when the scattering is weak, the field in a random multilayer localizes at certain frequencies. The effect of increasing layer width randomization on this form of localization is quantified. The radiative transfer model of time-harmonic scattering in multilayers is extended to narrow-band pulse propagation in weakly scattering media. The tendency of pulses to broaden in this medium is discussed. A radiative transport model of the system is developed and compared to numerical solutions of the wave equation. It is observed that pulse broadening is not described by simple transfer theory. The radiative transfer model is extended by the addition of a Laplacian term in an attempt to model the effect of ensemble average pulse broadening. Numerical simulation results in support of this proposal are given, and applications for the theory suggested. Finally, the problem of acoustic wave scattering by planar screens is considered. The study was motivated by the idea that multiple scattering experiments may prove possible in a medium composed of such scatterers. Successful multiple scattering in a medium of planar scatterers will depend on the scattering cross-section at angles away from normal incidence. The scattering cross-section is calculated for a circular disc using a new technique for solving the acoustic wave equation on planar surfaces. The method is validated by comparison with available analytic solutions and the geometric theory of diffraction.

The theory of radiative transfer is applied to the problem of multiple wave scattering in a one-dimensional multilayer. A new mathematical model of a multilayer is presented in which both the refractive index and width of each layer are randomized. The layer widths are generated by a new probability distribution which allows for strong layer width disorder. An expression for the transport mean free path of the multilayer is derived based on its single-scattering properties. It will be shown that interference between the field reflected from adjacent layer interfaces remains significant even in the presence of strong layer width disorder. It will be proven that even when the scattering is weak, the field in a random multilayer localizes at certain frequencies. The effect of increasing layer width randomization on this form of localization is quantified. The radiative transfer model of time-harmonic scattering in multilayers is extended to narrow-band pulse propagation in weakly scattering media. The tendency of pulses to broaden in this medium is discussed. A radiative transport model of the system is developed and compared to numerical solutions of the wave equation. It is observed that pulse broadening is not described by simple transfer theory. The radiative transfer model is extended by the addition of a Laplacian term in an attempt to model the effect of ensemble average pulse broadening. Numerical simulation results in support of this proposal are given, and applications for the theory suggested. Finally, the problem of acoustic wave scattering by planar screens is considered. The study was motivated by the idea that multiple scattering experiments may prove possible in a medium composed of such scatterers. Successful multiple scattering in a medium of planar scatterers will depend on the scattering cross-section at angles away from normal incidence. The scattering cross-section is calculated for a circular disc using a new technique for solving the acoustic wave equation on planar surfaces. The method is validated by comparison with available analytic solutions and the geometric theory of diffraction.