Nitride semiconductor materials have been used in a variety of applications, such as LEDs, lasers, photovoltaic cells and medical applications. If incandescent bulbs could be replaced by white GaN LEDs, they would not only provide compactness and longer lifetime, but this would also result in huge energy savings. A renewed interest in InGaN emerged recently after it was discovered that the band gap for InN is 0.7eV, instead of the previously published value of 1.9eV. Thus InGaN solid solutions cover almost the whole visible spectrum, from a band gap of 3.34eV for GaN and 0.7eV for InN. Hence, InGaN can have excellent applications for photovoltaic cells. The objective of this work was to investigate and search for new ways of synthesis of nitrides. We studied the thermodynamics and evaluated chemical compatibilities for the growth of AlN, GaN, InN and their solid solutions from metallic solvents. The compatibility between potential substrate, crucible and solvent materials and various growth atmospheres was evaluated from Gibbs free energy calculations. Most of the nitride synthesis experiments performed by other groups were at higher temperatures (around 2,000C) and pressures up to 1GPa using different growth methods. Therefore, their results could not be extrapolated to our growth system, as their growth conditions were significantly different from ours Moreover, to the best of our knowledge; no-one has ever evaluated such compatibilities by thermodynamic calculations. We used those calculations to design our experiments for further studies on nitrides. Experimentally, we encountered fewer issues such as corrosion problems than others observed with their growth procedures, because near-atmospheric pressures and temperatures not exceeding 1,000C could be used. Preliminary experiments were performed to confirm the thermodynamic computations and test the behavior of the chosen system. A suitable configuration was found that allowed to nucleate films of InGaN on the templates. Nitride templates or 'Buffer layers' were used to saturate the solution and grow the films. A relatively simpler configuration, to create a temperature gradient in the solution was used. Two templates were placed in the crucible, one at the top and the other one at the bottom. The temperature was raised to 950C and they were soaked there for 15-20hrs. After the growth the surface morphology was analyzed using an optical microscope and it was found to be entirely different for both the templates. The atoms from the top template dissolved and attached at the bottom template. This can be explained by the thermal gradient between the two templates: one at the bottom was at lower temperature than the top template, so there was diffusion from the top substrate towards the bottom one. AFM studies were carried out on the film to study the surface morphology of the top and the bottom templates. Growth hillocks having step height typically between 15 and 50 nm were observed. Such hillocks were not present on the templates before the experiment.

This thesis describes the modifications made to the Cal Poly Thermal Science Laboratory’s steam turbine experiment. While the use of superheating or reheating is commonly used to increase efficiency in a Rankine cycle the methods prove unfeasible in a small scale project. For this reason, a mathematical model and proof of concept design using hydrostatic head generated by elevation and venturi ejection for use by the condenser is developed along with the equations needed to predict the changes to the system. These equations were used to create software to predict efficiency as well as lay down the foundation for future improvements of the system.

Problem Statement: The use of pulsed electric fields (PEFs) as a tumor treatment modality is receiving increased traction. A typical clinical procedure involves insertion of a pair of electrodes into the tumor and administration of PEFs (amplitude: ~1 kV/cm; pulse-width: 100 μs). This leaves a zone of complete cell death and a sub-lethal zone where a fraction of the cells survive. There is substantial evidence of an anti-tumor systemic immune profile in animal patients treated with PEFs. However, the mechanism behind such immune profile alterations remains unknown, and the effect of PEFs on cell signaling within sub-lethal zones remains largely unexplored. Moreover, different values of a PEF pulse parameter, for e.g. the pulse-widths of 100 μs and 100 ns, may have different effects on cell signaling. Thus, the challenge of answering the mechanistic questions is compounded by the large PEF parameter space consisting of different combinations of pulse-widths, amplitudes, and exposure times. Intellectual merit: This Ph.D. research provides proof that sub-lethal PEFs can enhance anti-tumor signaling in triple negative breast cancer cells by abrogating thymic stromal lymphopoietin signaling and enhancing stimulatory proteins such as the tumor necrosis factor. Furthermore, experimental evidence produced during this Ph.D. research demonstrates that PEFs may not directly impact the intracellular mitochondrial membrane at clinically relevant field amplitudes. As demonstrated in this work, PEFs may influence the mitochondria via an indirect route such as disruption of the actin cytoskeleton and/or alteration of ionic environment in the cytoplasm due to cell membrane permeabilization. Thus, a reductionist approach to understanding the influence of PEFs on cell signaling is proposed by limiting the study to membrane dynamics. To overcome the problem of investigating the entire PEF parameter space, this Ph.D. research proposes a first-principle thermodynamic approach of scaling the PEF parameter space such that an understanding developed in one regime of PEF pulse parameter values can be used to understand other regimes of the parameter space. Demonstration of the validity of this scaling model is provided by coupling Monte-Carlo methods for density-of-states with the steepest-entropy-ascent quantum thermodynamic framework for the non-equilibrium prediction of the lipid membrane dynamics. / Ph. D. / A complete cure for cancer is still far from being realized despite very promising developments on the front of molecular drug therapy. One promising conceptual approach would be to achieve the ability to re-tune the cancerous signals that drive disease progression. To overcome current challenges in tuning cancerous signaling a paradigm change in cancer treatment is necessary. For example, a treatment strategy to alter cell signaling which leverages both the physical and chemical properties that accompany malignancy may be required. Electric fields, be it in the form of low-amplitude steady state fields or high-amplitude pulsed electric fields (PEFs), can induce distinct physical and chemical effects on cells. Hence, the use of electric fields as a clinical tumor treatment modality is receiving increased traction. However, the effect of these electric fields on cell signaling and cell behavior remains largely unexplored. This Ph.D. work provides experimental evidence that PEFs can directly impact cancerous cell signaling towards a less inflammatory and possibly less cancerous state. Although a noteworthy finding, the data poses another challenging question, i.e., how does the electric field impact cell behavior? Answering this mechanistic question is essential for FDA approval and a broader clinical use of the electric field modalities. An impediment to answering this question is the vast parameter space of electric fields (e.g., amplitude, pulse width, and number of pulses), which makes performing experimental mechanistic studies untenable. It is argued via experimental evidence gathered during this work that applying scaling laws applicable to lipid membranes may provide a solution to reducing the candidate PEF parameters to a manageable number. A non-equilibrium thermodynamic model is proposed that allows studying the behavior of lipid species using scaled electric field parameters. Thus, the v understanding gained via the proposed model can direct the next level of extensive biological assays and animal studies and eventually lead to effective cancer treatments.

Phase change material (PCM)-based ocean thermal energy harvesting is a relatively new method, which extracts the thermal energy from the temperature gradient in the ocean thermocline. Its basic idea is to utilize the temperature variation along the ocean water depth to cyclically freeze and melt a specific kind of PCM. The volume expansion, which happens in the melting process, is used to do useful work (e.g., drive a turbine generator), thereby converting a fraction of the absorbed thermal energy into mechanical energy or electrical energy. Compared to other ocean energy technologies (e.g., wave energy converters, tidal current turbines, and ocean thermal energy conversion), the proposed PCM-based approach can be easily implemented at a small scale with a relatively simple structural system, which makes it a promising method to extend the range and service life of battery-powered devices, e.g, autonomous underwater vehicles (AUVs). This dissertation presents a combined theoretical and experimental study of the PCM-based ocean thermal energy harvesting approach, which aims at demonstrating the feasibility of the proposed approach and investigating possible methods to improve the overall performance of prototypical systems. First, a solid/liquid phase change thermodynamic model is developed, based on which a specific upperbound of the thermal efficiency is derived for the PCM-based approach. Next, a prototypical PCM-based ocean thermal energy harvesting system is designed, fabricated, and tested. To predict the performance of specific systems, a thermo-mechanical model, which couples the thermodynamic behaviors of the fluid materials and the elastic behavior of the structural system, is developed and validated based on the comparison with the experimental measurement. For the purpose of design optimization, the validated thermo-mechanical model is employed to conduct a parametric study. Based on the results of the parametric study, a new scalable and portable PCM-based ocean thermal energy harvesting system is developed and tested. In addition, the thermo-mechanical model is modified to account for the design changes. However, a combined analysis of the results from both the prototypical system and the model reveals that achieving a good performance requires maintaining a high internal pressure, which will complicate the structural design. To mitigate this issue, the idea of using a hydraulic accumulator to regulate the internal pressure is proposed, and experimentally and theoretically examined. Finally, a spatial-varying Robin transmission condition for fluid-structure coupled problems with strong added-mass effect is proposed and investigated using fluid structure interaction (FSI) model problems. This can be a potential method for the future research on the fluid-structure coupled numerical analysis of AUVs, which are integrated with and powered by the PCM-based thermal energy harvesting devices. / Doctor of Philosophy / The global ocean, which covers about 71% of the Earth’s surface, absorbs a great amount of heat from the sunshine everyday, making it a reliable and renewable source of thermal energy. Also, the temperature of the ocean water varies with depth, which provides a necessary condition (i.e, a temperature gradient) to extract the thermal energy. If harvested and converted into electrical energy using small scale portable devices, the ocean thermal energy can be a potential energy resource to provide power for autonomous underwater vehicles (AUVs), which are conventionally powered by on-board rechargeable batteries. To this end, this dissertation presents a study of using solid/liquid phase change materials (PCMs) to extract thermal energy from the temperature gradient in the ocean. The basic idea is to use the warm surface water and deep cold water to melt and freeze the PCM cyclically. In the meantime, the volume of PCM will expand and contract accordingly. Therefore, a turbine generator can be driven by the volume expansion in the melting process, thereby converting a fraction of the absorbed thermal energy into electrical energy. This study includes four key aspects. First, to evaluate the theoretical full potential of the PCM-based approach, a solid/liquid phase change thermodynamic model – which represents an idealized energy harvester – is developed. Based on the thermodynamic model, an upperbound of the thermal efficiency is derived. Secondly, two prototypical systems, as well as a thermo-mechanical model which can predict the performance of specific designs, are developed. Third, for the purposes of performance improvement and pressure regulation, the latter of which is associated with the structural safety, a hydraulic accumulator is added to the existing system and its effects are examined using both experimental and theoretical methods. Finally, a computational method is proposed and demonstrated, which can be a potential tool for the design of PCM-based ocean thermal energy harvesting systems when they are integrated with exiting AUVs.

Proteins and nanoparticles (NPs) provide a promising platform for supramolecular interaction. We are currently exploring both fundamental and applied aspects of this interaction. On the fundamental side, we have fabricated a series of water-soluble anionic and cationic NPs to interact with cationic and anionic proteins respectively. A Varity of studies such as, activity assay, fluorescence titration, isothermal titration calorimetry etc. were carried out to quantify the binding properties of these functional NPs with those proteins. Those studies reveal the prospect of tuning the affinity between the nanoparticles and proteins by the surface modification. On the application side, we have used this protein-nanoparticle interaction in protein refolding where we successfully refolded the thermally denatured proteins toward its native structure. We have also applied this particle-protein recognition to create a biocompatible protein sensor using a protein-NP conjugate. Green fluorescent protein and a series of cationic NPs were used for a protein sensor for the identification of protein analytes through displacement process. We have extended this application even in sensing the proteins in human serum.

In this thesis I present a derivation of statistical mechanics starting from a closed, isolated quantum many body system. I first establish under what conditions we expect static equilibrium to emerge. It is found that the purity of the diagonal ensemble is a sufficient criteria for equilibration to occur and avoid short time recurrences. I next derive the usual ensembles of statistical mechanics using the principle of maximum entropy. These ensembles are then connected to the diagonal ensemble through the strong and the weak eigenstate thermalization hypothesis (ETH). Counter examples to ETH are discussed along with the process of scrambling. The thesis contains three contributed articles relevant to this introductory chapter studying early time relaxation, recurrences and scrambling. / Thesis / Doctor of Philosophy (PhD)

In recent years, there has been significant progress in the development of integrated photonic circuits (PICs). Matured fabrication and simulation techniques have enabled the development of novel devices and system architectures. Ideally, these newly developed technologies are put to test in the lab, both to verify that they perform as simulated and to demonstrate the viability of the technology. Testing the increasingly complex optical circuits brings various challenges. One of these challenges is the sensitivity to temperature changes of many optical circuits, especially micro ring and micro disk resonators (MRRs and MDRs). Due to the nature of these resonators, slight deviations in the material properties have a large impact on their resonant frequency. Despite this, their small footprint and wavelength selectivity makes them promising components for many future technologies, especially Dense Wavelength Division Multiplexed (DWDM) communication links. Multiple resonators cascaded on a single bus waveguide can operate on multiple wavelengths simultaneously with relatively few components and in a small combined area. Since every extra connection to a PIC has a footprint similar to that of a micro resonator, a packaging optimized thermal control scheme is needed to fully leverage all advantages of micro resonators. This work will focus on the thermal stabilization of cascaded micro resonators and how thermal control can be optimized to simplify the packaging of PIC prototypes. This simplification enables the demonstration of complex systems and more realistic scenarios for thermal control of both resonators and other circuits. It will first show how a number of PICs and their respective packages were built, keeping subsequent testing in mind. Then, it demonstrates automatic initialization of cascaded MRR and how stable operation, while undergoing large temperature swings, can be achieved using a minimum number of connections to the PIC. Next, it shows stable operation of an eight-wavelength receiver, operating uncooled at 16 Gb/s/?, over a record 75 °C. Finally, it presents how all the learned lessons are brought together to built a 2.5D integrated SiPh transceiver that is capable of transmitting 512 Gb/s bidirectionally. This transceiver can be plugged into Field Programmable Gate Arrays (FPGAs), which can then be used to implement accelerators for real computing problems, used as a PCIe bridge to a standard compute server, or both. The transceiver is also designed to work with many types of optical switches, allowing demonstrations of novel switching algorithms and network architectures. The contributions discussed in this thesis can assist in enabling future high bandwidth optical interfaces by optimizing the thermal control strategy and may be used at all stages of PIC design and packaging to facilitate the development of new technologies.

The traditional paradigm declares tetravalent uranium to be immobile under reducing conditions – an assumption widely employed for nuclear waste management strategies. In contrast, experiments presented here demonstrate this assumption, although valid for low temperatures, can be erroneous for high temperature natural systems. This project focuses on the ability of sulfate-bearing solutions to transport uranium at reduced conditions and elevated temperatures, identifies the new species U(OH)2SO4, derives thermodynamic constants necessary for modeling, and expands the quantifiable range of U4+ mobility to more neutral pH conditions. The data obtained enable more accurate assessment of uranium mobility by updating the existing uranium thermodynamic databases and is applicable to uranium fluid transport in oreorming systems and nuclear waste repositories.

Log K values, valid at zero ionic strength are reported for the interaction in aqueous solution of CN- with Ni2+ and Hg2+ at 10°, 25° and 40°C, and with Pd2+ at 25°C. ∆H° and ∆S° values valid at zero ionic strength and 25°C are also reported for the interaction of CN- with Hg2+ and for the reaction Pd(CN)42- + CN- = Pd(CN)53-. In connection with the study of Pd2+ - CN- interaction, log K values for the hydrolysis of Pd2+ to give PqOH+ and Pd(OH)2 and an E° value for the reaction Pd(s) = Pd2+ + 2e- are reported. A least squares computational method is developed for the calculation of the equilibrium constants, enthalpy changes and entropy changes for metal-ligand interactions from a single thermometric titration curve (Entropy Titration). This method has been tested by determining log K, ∆H° and ∆S° values for the interaction of Ag+ and Cu2+ with pyridine, Hg(CN)2 with CN- and HgCl2 with Cl-. The results indicate that both the computational method and entropy titration technique are applicable to the determination of the thermodynamics of interaction of metal-ligand systems. Log K, ∆H° and ∆S° values have been determined for the interaction of SO42+ with H+ and thirty +1, +2 and +3 metal ions. The results are compared to electrostatic predictions and deviations from electrostatic predictions are attributed to specific solvent interactions. Log K, ∆H° and ∆S° values are reported for the interaction of Hg(CN)2 with thiourea in water-ethanol solvent mixtures. The results indicate that there is a significant change in the solvolysis of the species in solution at approximately 20 mole per-cent ethanol.

The object of the work presented in this thesis was to obtain quantitative values of the thermodynamic changes in water upon adsorption by silica. Two methods were used. The first was a determination of the differential entropy and heat of adsorption independent of any theory of adsorption. The second method included a new interpretation of the "c" constant of the Brunauer, Emmett, and Teller Theory in which c was expressed in terms of the standard free energy of adsorption. The experimental data gave satisfactory results in determining the differential heat and entropy of adsorption. The results obtained in determining the standard entropy and heat of adsoption of use of the B.E.T. equation were questionable. The standard entropy of adsorption as determined by the B.E.T. equation was less negative than the corresponding entropy of condensation. It is unlikely that water molecules adsorbed on silica would have more freedom than water molecules in the liquid state. The adsorption of water on silica appears to be a van der Waals type of adsorption, the heats of adsoption being only 1-4 k. cal. greater than the heat of condensation of water.