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Cellular lineages underlie several important biological phenomena, from embyrogenesis to tumor development. Traditional approaches for studying for these lineages have been limited in their throughput or resolution, and have thus have been largely incapable of profiling lineage dynamics in complex organisms. Recently, advances in microfluidic devices, sequencing technologies, and molecular biology have facilitated a genomics revolution enabling researchers to profile molecular species at single-cell resolution. Simultaneously, progress in precise genome editing with CRISPR/Cas9 technologies have been coupled with the revolution in single-cell genomics to provide single-cell-resolution lineage tracing technologies.In this thesis, I first describe computational methodology for inferring models of cell lineages, or phylogenies, from the CRISPR/Cas9-based lineage tracing technology. Using both simulated and real data, I demonstrate that our methodology is both scalable and accurate in comparison to other algorithms. I additionally detail the functionality of our end-to-end software suite, Cassiopeia, and speculate on lineage tracing data analysis best practices.Next, I describe a series of applications of a CRISPR/Cas9-based lineage tracing technology and our computational tools to in vivo cancer models. In one application, I describe the first report of using such technologies to investigate the transcriptional drivers of metastatic dynamics in a xenograft model of non-small-cell lung cancer. Next, I describe work in a genetically engineered mouse model of non-small-cell lung cancer in which we characterize the phylodynamics and evolutionary trajectories that govern a primary tumor as it evolves from a single, transformed cell to a complex, metastatic tumor.Finally, I conclude by contextualizing how the work presented in this thesis fits into the larger picture of lineage tracing technologies and in vivo tumor studies and by speculating on how this informs future work.

Infertility is a broad disorder with numerous causes including physical, genetic and environmental. While techniques are currently in use to address certain causes of infertility, such as in vitro fertilization and hormonal therapies, there is currently no treatment option for those who are either unable to make or no longer possess viable gametes. Recently, advances have been made in the development of in vitro gametogenesis which, if perfected, promises an option for gametes to be derived from a patient’s own tissue. In order to bring this technique to fruition, further research is needed into the mechanics directing the specification and epigenetic reprogramming of the earliest stage of the germline, the primordial germ cells (PGCs).Mammalian PGCs are specified early in embryonic development and give rise to the entire adult germline. Following specification, PGCs undergo epigenetic reprogramming in order to establish a permissive epigenetic landscape for proper gametogenesis prior to differentiation into either oocyte or spermatogonial progenitors. Any errors in either of these processes can result in the complete loss of the germline and infertility. In order to better understand the mechanisms underlying PGC development, we utilized the in vitro PGC-like cell (PGCLC) differentiation to study human PGC specification and PGC-specific conditional knockout mice to assess epigenetic remodeling. In our studies into specification, we further characterized the differences between mouse and human PGC specification mechanisms. Using CRISPR/Cas9 gene editing we identified that EOMES directs human PGCLC specification, whereas in the mouse this role is accomplished by T. Our exploration into epigenetic reprogramming utilized a Cre/lox driven PGC-specific conditional knockout mouse to assess the role of epigenetic regulatory proteins during PGC differentiation. We used two knockouts, the first being UHRF1 which interacts with DNMT1 to promote DNA methylation maintenance and the second being EED, a key component of PRC2 which adds the repressive H3K27me3. Through this we identified that while UHRF1 appears to play no role in regulating the PGC stage of germline development, it is necessary for the viability of the spermatogonial stem cell population within the adult testes. In the case of EED, we identified that PRC2 is essential for regulating the timing of sex-specific differentiation in PGCs as well as a novel role for H3K27me3 in X chromosome decompensation within the embryonic testis. Finally, we identified a dual enrichment of H3K27me3 and DNA methylation within the promoters of gametogenesis genes at the time of PGC specification from the mouse epiblast. This provides an exciting glimpse into the complex interactions between the epigenetic regulatory networks that direct PGC differentiation. Further work will need to be conducted to identify the extent of these epigenetic regulator interactions in human PGCs and to apply these findings into developing better methods to more accurately recapitulate human PGC differentiation in vitro.

Organic electronics are an exciting alternative to traditional inorganic electronics. Compared to inorganic materials, organic electronics are lightweight, flexible, solution-processable, and inexpensive, and are made with non-toxic earth-abundant elements. Semiconducting polymers, discovered in the 1970s, are promising materials for use in organic electronics; the materials are easily tunable through organic synthesis, and their promise allowed researchers to earn the Nobel Prize for their discovery in 2000. Semiconducting polymers have potential applications in LEDs, solar cells, electrochromics, and thermoelectrics. Like the case with inorganic semiconductors, doping of organic semiconductors produces a charge (usually a positive charge) on the polymer. If the charge is mobile, the material’s electrical conductivity is enhanced. The belief in the literature is that initially, at low dopant concentrations, trapped polarons (singly charged cation radicals) form, which can be Coulombically-bound to the dopant counterion. As the concentration increases, the Coulomb wells of the dopants overlap and create mobile free polarons. As the dopant concentration increases further, polarons become too crowded on the polymer chains and can pair up to form doubly-charged bipolarons instead. My thesis work investigates polarons and bipolarons in conjugated polymers to better understand the nature and formation of these charge carriers.The work presented in this thesis is the first use of ultrafast spectroscopy to understand and identify the electronic structure of the doped species on conjugated polymers. The first chapter in my thesis introduces semiconducting polymers and their applications, as well as the techniques I used to study them. The second chapter in my thesis demonstrates that ultrafast transient absorption spectroscopy can be used to distinguish the roles of free carriers and carriers that are Coulomb bound to the dopant counterions. The work presented in Chapter 2 also refutes one model of polaron energy levels, the band-bending model, based upon the transitions observed in the ultrafast transient absorption experiments. The final chapter of my thesis applies the ultrafast spectroscopy techniques developed in Chapter 2 to rule out the formation of polarons in a novel doped polymer system and to show that in this novel polymer, doping produces solely bipolarons instead of single polarons. We argue based on quantum chemistry calculations that it is the particular chemical structure of the polymer that produces this unusual behavior. Overall, my thesis work has made great strides in identifying and understanding the charge carrier(s) present in doped polymer systems.

The Galactic Center (GC) is an extremely energetic region, host to a variety of powerful astronomical sources and rare astrophysical processes that emit a large flux of non-thermal radiation. The inner 375x600 pc region, called the Central Molecular Zone (CMZ), is home to the supermassive black hole Sgr A*, massive cloud complexes, supernova remnants, and likely the peak concentration of dark matter in the Galaxy. It has been studied across an extremely wide range of wavelengths by many instruments. In this dissertation, I present the results of my analysis of the very high-energy (VHE) (E > 100 GeV) gamma-ray emission from the GC using data from about 155 hours of quality observations taken with the VERITAS imaging atmospheric Cherenkov telescope. This emission includes a strong central point source VER J1745-290, coincident with the position of Sgr A*, and diffuse emission that extends along the Galactic ridge. VER J1745-290 is detected at a significance of 38 sigma, and I reconstruct its spectrum and lightcurve. Its spectrum is best fit by a power law with an index of -2.16 +/- 0.18 and flux normalization of (11.76 +/- 2.03)e-12 TeV/cm2/s at 1 TeV, and an exponential cutoff at 10.8 +/- 3.0 TeV. The exponential cutoff in its spectral shape, along with its apparent lack of variability in the very-high-energy gamma ray range favor electron models of its emission, such as the plerion model of emission from the pulsar wind nebula G359.95--0.04.I also present the results of my analysis on the morphology and, for the first time with VERITAS, the spectrum of diffuse emission in the GC.I find an approximately 52\% correlation of the gamma signal to molecular gas as traced by CS(1-0) line emission. I report an energy spectrum that is best fit by a pure power law with a hard index of -2.26 +/- 0.13, showing no evidence of a cutoff over 40 TeV. This strengthens the evidence of a potential accelerator of PeV cosmic rays being present in the GC. Using these results, I discuss the impact on current models of diffuse emission and possible connections to the central source. I also provide detections and spectra of other sources within the field of view of VERITAS.

Submission note: This thesis is submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy to the La Trobe Sport and Exercise Medicine Research Centre, Department of Physiotherapy, Podiatry, Prosthetics and Orthotics, School of Allied Health, Human Services, and Sport, College of Science, Health, and Engineering, La Trobe University, Victoria, Australia.Hip-related pain is common in football players, with persistent pain associated with poor quality of life and restricted participation. Hip-related pain is a movement-related disorder; however, information on how people with hip-related pain move is scarce. A greater understanding of the movement limitations associated with hip-related pain is needed to develop interventions and preventative strategies to improve long-term outcomes. A systematic review established that people with more severe presentations of hip-related pain walk with a lower peak hip extension angle and were unable to squat as deep as asymptomatic controls. The review found no information on people with hip-related pain still participating in sport and physical activities. This thesis aimed to extend our knowledge of the movement limitations in this condition by evaluating the biomechanics of football players with hip-related pain. The lower limb biomechanics of 88 football players (median age: 26 years, 23 women) with hip-related pain and 30 (median age: 27 years, 13 women) asymptomatic players were compared during walking and the single leg drop jump. This thesis demonstrated that: 1)Men and women with hip-related pain move differently. Future studies should consider if the relationship between hip-related pain and biomechanics is sex-dependent.2)The relationship between hip-related pain and biomechanics is modified by sex. Male football players with hip-related pain demonstrated biomechanical impairments at the hip and pelvis in the transverse plane and women demonstrated impairments at the knee.3)Differences observed between football players with and without hip-related pain were few in number, small in magnitude, and rarely at the hip. In conclusion, biomechanical impairments were not common among football players with hip-related pain. It is unknown whether the biomechanical impairments observed affect disease progression or long-term outcomes. Longitudinal evaluations of biomechanics in people with hip-related pain will assist in further contextualising the thesis findings.

Objectives To compare displacement between the cuneiforms and metatarsals for a typical Lisfranc screw and a transmetatarsal base screw under biomechanical loading. Methods Eight pairs of cadaveric feet (16 total) were evaluated. The Lisfranc ligamentous structures were transected in all specimens. All feet were repaired with screws traversing the first and second tarsometatarsal joints. A Lisfranc screw was placed from the first cuneiform to the second metatarsal in 8 specimens. A transmetatarsal base screw from the first metatarsal to the second metatarsal was placed in the remaining 8 corresponding feet. The repairs were randomized by side. Markers were placed on the dorsum of the midfoot for optical tracking. The feet were mounted into a load frame and loaded on the plantar forefoot to 100, 400, 800, and 1100 N. Displacement was measured and recorded using 3D camera tracking. Results Displacement between the first cuneiform and second metatarsal base was found to be significantly less (P = 0.02) with the transmetatarsal screw than the Lisfranc screw. There were no significant differences between displacements at any other articulations. Conclusions This study demonstrates biomechanical superiority using a modified transmetatarsal base screw compared with the highly used Lisfranc screw for fixation of ligamentous Lisfranc injuries.

Purpose The treatment of distal femur fractures with extensive metaphyseal comminution is frequently complicated by high rates of nonunion and varus collapse. Dual plating with lateral and medial locking plates for these types of fractures has shown promising results in the recent literature. We hypothesize that dual plating of comminuted distal femur fractures leads to higher union rates and lower revision rates compared to an isolated lateral locking plate. Methods A retrospective medical chart review between January 2015 and December 2017 was conducted. Inclusion criteria included patients 18 years of age and older who sustained a complex distal femur fracture (AO/OTA 33-C2/33-C3 or periprosthetic fracture with significant metaphyseal comminution) and at least 6 months of follow up. Patients with simple fracture patterns, alternative fixation methods, and inadequate follow up were excluded. All patients in the single plating group were treated with a lateral distal femoral locking plate using a lateral approach. In the patients treated with dual plating, an extensile parapatellar approach was utilized for fracture reduction and placement of an adjunctive medial plate. Demographic information, fracture types, injury severity score (ISS), medical comorbidities, type of surgical fixation, union rates, complications, knee range of motion, time to follow up, and need for revision surgery were extrapolated from the medical charts for analysis. Results Twenty-one patients were included in the study. Thirteen patients underwent single plate fixation and 8 underwent dual plate fixation. There were no significant differences in demographics, number of co-morbidities, fracture classification, or ISS between single and dual plate groups (p > 0.05 for all). There was a statistically significant difference in union rates between the single plate group (6 nonunions, 4 unions, and 3 delayed unions) and the dual plate group, with no nonunions or delayed unions (p = 0.0049). Although not statistically significant, 4 patients treated with single plating underwent revision ORIF, compared to none in the dual plating group (p = 0.13). There were no significant differences in time to follow up, time to full weight bearing, or infection rates (p > 0.1 for all). Conclusion Based on these results, the medial and lateral locked plating technique demonstrates a higher union rate, with possible lower rates of revision surgery, compared to a single lateral plate in highly comminuted distal femur fractures. Level of evidence Level 3. Retrospective Cohort Study.

Lung cancer is one of the top five deadliest cancers, and Black Americans have a higher mortality rate when compared to White Americans. Lung adenocarcinoma (LUAD) is the most common histological lung cancer subtype in all population groups including Blacks. Unfortunately, there are no in vitro model systems to study lung cancer and its treatments for Black subjects. Herein we aim to utilize three-dimensional (3D) printing to develop an in vitro three-dimensional (3D) alveolar model using a lung adenocarcinoma cell line from a Black patient (NCI-H23). The developed model is further utilized to study the therapeutic effects of potential LUAD therapeutic agents, polyisoprenylated cysteinyl amide inhibitors (PCAIs), which target and disrupt the RAS-mediated signaling pathway. KRAS is the most commonly mutated oncogene in LUAD in Blacks, and is mutated in NCI-H23 cells. For comparison, hAEC-FT-C7 cells, which are immortalized human alveolar epithelial cells and do not carry the KRAS mutation, will also be used separately to print the alveolar models and test the effects of PCAIs. The experimental results will be further compared to those using two-dimensional (2D) models to better understand the therapeutic effects of PCAIs on Black LUAD. The resulting knowledge will help design better treatments for ethnically/racially diverse patients in whom the RAS signaling pathway is frequently altered. Citation Format: Nadine L. Belony, Bing Ren, Phuc Pham, Matthew Gregory, Pablo E. Puente, Nazarius S. Lamango, Ite A. Offringa, Yong Huang. Study of therapeutic effects of polyisoprenylated cysteinyl amide inhibitors on lung cancer cells of Black American patients using 3D-printed alveolar models [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C024.

Lung cancer is a source of racial disparity among Black Americans, especially men. Despite lower tobacco exposure among Black men than White men, Black men are 37% more likely to develop lung cancer. Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer in all ethnic/racial groups, including Blacks. KRASis the most frequently mutated driver gene in Black LUAD (~30%), and NRAS mutations are also seen (1-2%). A given oncogenic mutation could have different effects on a patient based on their racial/ethnic genetic background. Thus, studying the appropriate driver mutations in the correct model and genetic background is essential. Unfortunately, to our knowledge, there is only one LUAD cell line from a Black subject. Therefore, we are deriving immortalized human alveolar epithelial cell (hAEC) lines from Black Americans to develop models to study lung adenocarcinoma in Blacks. The Offringa lab has recently developed a rapid method to generate hAEC lines. We have generated three distinct hAEC lines from de-identified remnant transplant lungs from White Americans. Here, we will use the same method to establish new hAEC lines from de-identified human remnant transplant lungs from Black American subjects. hAECs grow well in 2-dimensional (2D) cultures as epithelial monolayers are capable of forming alveolar-like organoids in 3-dimensional (3D) cultures with fibroblasts and Matrigel. We will introduce the KRAS driver mutation alone or in combination with other oncogenes into the hAECs using CRISPR/Cas9 editing. The cell lines will be used to test KRAS-targeting therapeutics, including polyisoprenylated cysteinyl amide inhibitors (PCAIs). These agents have been shown to disrupt RAS-mediated signaling in ethnically/racially diverse cell lines. Our approach yields new cell lines that provide a valuable system to study LUAD in Black Americans. Through our research, we intend to address one facet of the prominent lack of representation of Black Americans in LUAD studies. Citation Format: Pablo E. Puente, Chunli Yan, Matthew Gregory, Nadine Belony, Nazarius Lamango, Yong Huang, Ite A. Offringa. Developing immortalized human alveolar epithelial cell models to study lung adenocarcinoma in Black Americans [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A087.

For several decades oncologists have been faced with the obstacle of properly classifying tumors for effective patient treatment. Traditionally, this was accomplished by documenting changes in cancer cells, and through observation of canonical changes to the extracellular matrix (ECM). However, even when I began my graduate studies in 2010, it was still unclear if cancer cells were driven to metastasize by changes to the ECM, or if changes to the ECM were a result of malignant progression. Over the past 5 years I have worked in Dr. Valerie Weaver’s laboratory at UCSF to answer how cancer cells interpret extracellular mechanical cues in 3D and how these cues can be translated into oncogenic signals at the cell-ECM interface. In order to study molecular interactions of oncogenic proteins in invasive cancer cells, I participated in the development of a new super-resolution microscopy technique, Scanning Angle Interference Microscopy (SAIM). I then employed this technology to determine how ECM stiffness and composition can drive vinculin mediated PI3-kinase signaling to enhance cell invasion, and studied how paxillin mediated mechano-sensing of the ECM could drive metastasis in difficult to treat triple negative breast cancer patients.

The recent approval of aducanumab for Alzheimer's disease has heightened the interest in therapies targeting the amyloid hypothesis. Our research has focused on identification of novel compounds to improve amyloid processing by modulating gamma secretase activity, thereby addressing a significant biological deficit known to plague the familial form of the disease. Herein, we describe the design, synthesis, and optimization of new gamma secretase modulators (GSMs) based on previously reported oxadiazine 1. Potency improvements with a focus on predicted and measured properties afforded high-quality compounds further differentiated via robust Aβ42 reductions in both rodents and nonhuman primates. Extensive preclinical profiling, efficacy studies, and safety studies resulted in the nomination of FRM-024, (+)-cis-5-(4-chlorophenyl)-6-cyclopropyl-3-(6-methoxy-5-(4-methyl-1H-imidazole-1-yl)pyridin-2-yl)-5,6-dihydro-4H-1,2,4-oxadiazine, as a GSM preclinical candidate for familial Alzheimer's disease.

Laser absorption spectroscopy has enabled fast and precise diagnostics for measuring gas conditions in a wide variety of applications. This thesis presents a high-speed mid-IR LAS diagnostic for CO and demonstrates its capabilities by taking measurements inside the annulus of a rotation detonation rocket engine. This scanned direct absorption diagnostic utilizes a quantum cascade laser to interrogate CO absorption lines near 2008.5 cm-1 to measure temperature, pressure, and CO at 750 kHz. This diagnostic reports precise measurements (95% CI of < 10%) even at elevated temperatures (2500 K) and pressures (6 atm). The presented diagnostic is the first of its kind to permit mid-infrared measurement of CO inside an RDRE annulus at repetition rates > 100 kHz.

Lung cancer is one of the top five deadliest cancers, and black Americans have a higher mortality rate when compared to white Americans even though they smoke relatively fewer cigarettes. Lung adenocarcinoma (LUAD) is the most common histological lung cancer subtype in all population groups including blacks. There are no in vitro model systems to study lung cancer in black subjects, and there is only one lung adenocarcinoma cell line from a black patient (NCI-H23). Here we aim to address the lack of in vitro models to study black LUAD. Using three-dimensional (3D) biofabrication technologies, we’ve developed a thick vascularized tissue model to recapitulate physiologically relevant heterogeneous human alveoli. Specifically, the blood-air barrier of the alveolar model is simulated with two perfusable channels embedded in a thick vascularized tissue construct: a helical blood channel and a straight air channel. Spatially, the air channel is in the center and is surrounded by the blood channel. Human endothelial cells are seeded onto the inner surface of the blood channel and NCI-H23 cells (which carry a KRAS mutation) or untransformed alveolar epithelial cells derived from black subjects, are seeded on the inner surface of the air channel. The blood and air channels are perfused using cell medium and oxygenated air, respectively. The model is used for the study of potential LUAD therapeutic agents such as polyisoprenylated cysteinyl amide inhibitors (PCAIs), which target and disrupt the RAS-mediated signaling pathway. KRAS is the most commonly mutated oncogene in LUAD in blacks, and our experiments are aimed at ensuring that PCAIs are effective in black LUAD and may offer better treatment outcomes for ethnically/racially diverse patients in whom the RAS signaling pathway is frequently altered and for whom pharmaceutical therapy is necessitated by the late diagnoses. Citation Format: Nadine Belony, Bing Ren, Phuc Pham, Matthew Gregory, Pablo E. Puente, Nazarius S. Lamango, Ite A. Offringa, Yong Huang. Study of therapeutic effects of polyisoprenylated cysteinyl amide inhibitors on lung cancer cells of black patients using 3D-Printed alveolar model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4038.

Lung cancer is a source of cancer health disparity among black Americans, especially men. Lung cancer incidence rates and mortality rates are higher in black Americans than in white Americans despite lower tobacco exposure among black men than white men. Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer in all ethnic/racial groups, including blacks. Genetic driver mutations differ among racial/ethnic groups. In addition, the same mutation could have different effects based on the genetic background arising from different racial/ethnic groups. Therefore, it is important to study appropriate driver mutations in the correct genetic background. Protooncogenes from the RAS family, KRAS, NRAS, and HRAS, play a crucial role in cell growth regulation, cell proliferation, and survival. KRAS is the most frequently mutated driver gene in black LUAD (~14%). NRAS mutations are also seen (1-2%). It is therefore important to study LUAD cell lines carrying different RAS mutations in black Americans’ genetic backgrounds. Unfortunately, to our knowledge, there is only one LUAD cell line from a black subject. The NCI-H23 cell line contains a heterozygous KRAS mutation at codon 12. We are generating a collection of isogenic cell lines derived from NCI-H23, tailored to study RAS gene activation in black Americans. We will correct the KRAS mutation to wildtype through CRISPR/Cas9 deletion with co-transfection of the wild-type sequence. However, we expect that the NCI-H23 cells may not tolerate the removal of the KRAS without simultaneous replacement with another driver mutation. Therefore, we will replace the KRAS mutation with either mutated NRAS, HRAS, or EGFR. EGFR functions as a receptor tyrosine kinase in the RAS-RAF-MEK-ERK pathway to control the activation of RAS oncogenes and is also frequently mutated in black LUAD (~8%). We have identified a heterozygous single nucleotide polymorphism, rs11047919, 839 nucleotides downstream from the KRAS mutation which we are using to differentiate between the wild-type and mutated KRAS alleles following CRISPR editing. We will use the new cell lines to test the efficacy of polyisoprenylated cysteinyl amide inhibitors (PCAIs). These agents have been shown to disrupt RAS-mediated signaling in ethnically/racially diverse cell lines. In the future, we will develop immortalized alveolar epithelial cell lines from black subjects to further address the lack of lung cancer models representing black Americans. Through our research, we intend to address one facet of the prominent lack of representation of black Americans in LUAD studies. Citation Format: Pablo E. Puente, Chunli Yan, Matthew Gregory, Nadine L. Belony, Nazarius Lamango, Yong Huang, Ite A. Offringa. Generating a collection of isogenic lung adenocarcinoma cell lines to study RAS gene activation in black Americans [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2213.

A low mass and reliable thermal protection system for Martian atmospheric entry requires an accurate prediction of the aerothermal environment encountered by the spacecraft. In order to move forward with predictive models for larger vehicles needed for manned and sample return missions, anomalous data needs to be resolved. This work aims to address two critical problems relevant for Mars missions. I) We investigate significant discrepancies between experimental and simulated blunt body bow shock standoff distance in ground test facilities. Experiments using high-speed and high-resolution schlieren imaging are conducted in the T5 reflected shock tunnel and the Hypervelocity Expansion Tube (HET) to examine facility independence of the measurements. A recently-developed model for sphere and sphere-cone behavior is in good agreement with experiments, and with predictions from Navier-Stokes simulations with thermal and chemical nonequilibrium. The need to account for the divergence of the streamlines in conical nozzles is highlighted. The contributions of vibrational and chemical nonequilibrium to the stagnation-line density profile are quantified using the simulation results in order to compare different reaction rate models. II) We measure and characterize carbon dioxide mid-wave infrared radiation in hypervelocity flow. Initially assumed negligible in the design of the Mars Science Laboratory (MSL) mission heat shield, this mechanism of heating must be considered for accurate predictions of the heating environment. Specifically, carbon dioxide radiation can be a dominant source of heating in the afterbody, particularly later in the trajectory at lower velocities. Presented are spectral measurements of the 4.3 μm fundamental band of carbon dioxide radiation measured using fiber optics embedded on the surface of an MSL scaled heat shield model. When comparing experiments and simulations, good agreement is found when running the HET in shock tube mode where the shock layer is optically thick, while discrepancies are observed in expansion tube mode where the shock layer is optically thin. A thorough analysis of flow features in the line-of-sight including freestream uncertainties is performed to explore possible reasons for this discrepancy. After developing the spectroscopic calibration technique and obtaining forebody measurements in the expansion tube, an experimental campaign is completed in the T5 Reflected Shock Tunnel to measure spectral radiation in the forebody and afterbody. The accompanying T5 simulations needed for radiation predictions are being carried out by NASA Ames.

The possibility of building a computer that takes advantage of the most subtle nature of quantum physics has been driving a lot of research in atomic and solid state physics for some time. It is still not clear what physical system or systems can be used for this purpose. One possibility that has been attracting significant attention from researchers is to use the spin state of an electron confined in a semiconductor quantum dot. The electron spin is magnetic in nature, so it naturally is well isolated from electrical fluctuations that can a loss of quantum coherence. It can also be manipulated electrically, by taking advantage of the exchange interaction. In this work we describe several experiments we have done to study the electron spin properties of lateral quantum dots. We have developed lateral quantum dot devices based on the silicon metal-oxide-semiconductor transistor, and studied the physics of electrons confined in these quantum dots. We measured the electron spin excited state lifetime, which was found to be as long as 30 ms at the lowest magnetic fields that we could measure. We fabricated and characterized a silicon double quantum dot. Using this double quantum dot design, we fabricated devices which combined a silicon double quantum dot with a superconducting microwave resonator. The microwave resonator was found to be sensitive to two-dimensional electrons in the transistor channel, which we measured and characterized. We developed a new method for extracting information from random telegraph signals, which are produced when we observe thermal fluctuations of electrons in quantum dots. The new statistical method, based on the hidden Markov model, allows us to detect spin-dependent effects in such fluctuations even though we are not able to directly observe the electron spin. We use this analysis technique on data from two experiments involving gallium arsenide quantum dots and use it to measure spin-dependent tunneling rates. Our results advance the understanding of electron spin physics in lateral quantum dots, in silicon and in gallium arsenide.

The Silurian climate was volatile and punctuated by multiple short-lived climate events, each associated with biotic crisis and perturbations to the global carbon cycle. In total, seven positive carbon isotopic excursions are globally recognized in the Silurian with the large excursions of the Wenlock-Ludlow interval in the Baltic succession garnering the most research; these excursions are recorded in association with cyclic facies changes and the enigmatic resurgence of microbial carbonates. Climate models, hypothesizing cycles of alternating humid and arid climate states, have been developed to explain these paired lithologic-isotopic fluctuations; however, little work has been done to test these models on lower Silurian strata. To test for the presence of δ13Ccarb excursions and the stratigraphic motif of proposed climate events, we developed a high-resolution integrated stratigraphic framework for the upper Hirnantian to mid-Telychian (Upper Ordovician to Llandovery) carbonate-dominated succession of Anticosti Island, by examining ~450 m of strata from a recent drill core, supplemented by ~120 m of outcrop. Four facies assemblages and three time-specific facies are identified and organized into three orders of superimposed transgressive-regressive cycles. High-resolution isotopic curves reveal the presence of four global positive carbon isotope excursions all sequentially recorded in the study interval; the HICE (peak of +5‰), Early Aeronian (peak of +2‰), Late Aeronian (peak of +6‰), and Valgu (peak of +3.5‰) excursions. Common cyclic stratigraphic trends are recognized with these δ13Ccarb excursions, where each excursion is associated with a shift from shale-rich to shale-poor facies, an intermediate-order transgression, and a minor δ18O excursion. These repetitive lithologic-isotopic patterns in the Llandovery succession of Anticosti Island are linked to cyclic fluctuations between low-latitude humid and arid climate states. In addition to these patterns, microbial-rich carbonates are associated with the Late Aeronian and Valgu δ13Ccarb excursions on Anticosti Island; this suggests a genetic link between the elevated δ13C values and the proliferation of calcified cyanobacteria and associated microfossils. This integrated stratigraphic model linking carbon excursions with climate and carbonate factory shifts provides an excellent framework for future studies, using a wide variety of geochemical systems, to better understand the processes that drove environmental and biodiversity changes through the Llandovery.