Gamma-ray glows are long duration emission coming from thunderclouds. They are one example of high-energy atmospheric physics, a relatively new field studying high-energy phenomena from thunderstorms and lightning. Glows arise from sustained relativistic runaway electron avalanches (RREA). Gamma-ray instruments on the ground, balloons and airplanes have detected glows. The Airborne Detector for Energetic Lightning Emissions (ADELE) is an array of gamma-ray detectors, built at the University of California, Santa Cruz. ADELE detected 12 gamma-ray glows during its summer 2009 campaign.

ADELE was designed to study another type of high-energy atmospheric physics, terrestrial gamma-ray flashes (TGFs). TGFs are incredibly bright, sub-millisecond bursts of gamma-rays coming from thunderstorms. ADELE was installed on NCAR's Gulfstream V for the summer of 2009. While many glows were detected, only one TGF was observed. In this thesis I present a detailed explanation of the 2009 version of ADELE along with the results of the 2009 campaign.

ADELE was modified to become a smaller, autonomous instrument to fly on the NASA drone, a Global Hawk. This was a piggyback to NASA's Hurricane and Severe Storm Sentinel mission. These flights took place during the summer of 2013. The following summer, ADELE flew on an Orion P3 as a piggyback of NOAA's Hurricane Hunters. This newer, modified instrument is discussed in detail in this thesis.

The 12 gamma-ray glows from the 2009 campaign are presented, with information about nearby lightning activity. I show that lightning activity is suppressed after a glow. This could be from the glow causing the cloud to discharge and therefore reduce the lightning activity. It is also possible that glows can only occur once lightning activity has diminished. Lightning is also used to find a distance to the glow. Using this distance, it is found that the brightness of glow cannot be explained as a function of distance while the duration of the glow is related to the distance.

The glow measured on August 21, 2009 was 20 times brighter than any other glow. This glow was modeled most extensively and it was found that ADELE was in the end of a downward facing avalanche, implying that is was lying between the upper positive and negative screening layer of the thunderstorm. The brightness of this glow also showed that the avalanche was approaching the levels necessary for relativistic feedback. I also show that this glow provides a significant discharge current and for a short while is discharging the cloud as much as nearby lightning.

The solar corona is an extremely hot, dynamic region of the solar atmosphere. Hard X-ray (HXR) observations of the corona have revealed the temporal and spatial properties of solar flares that release energy between ~10^25 and ~10^33 ergs in active regions. Flare-like events with energies <10^26 ergs have been seen in the quiet Sun by extreme ultraviolet (EUV) and soft X-ray (SXR) instruments. However, non-flaring active regions and quiet coronal regions cannot be imaged by the Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI), the current solar-dedicated HXR observatory, due to a lack of sensitivity and dynamic range.

Even in the absence of heating and particle acceleration from solar flares, the corona maintains an average peak temperature 1--4~MK. This is several hundred times hotter than the photosphere; this discrepancy is known as the coronal heating problem. While the precise physical mechanisms that heat the corona are still unknown, observations at multiple wavelengths can constrain the properties of unresolved impulsive heating events (``nanoflares'') in active regions and the quiet Sun. Until recently, only EUV and SXR data were available to investigate the nature of these events.

Focusing optics that directly image HXRs have recently been used to observe the Sun. The Nuclear Spectroscopic Telescope Array (NuSTAR) satellite is an astrophysics mission that was launched in 2013 and has pointed at the Sun on nine occasions to date. The Focusing Optics X-ray Solar Imager (FOXSI) sounding rocket was designed for solar observing and has flown two times (2012 and 2014). Both NuSTAR and FOXSI have observed non-flaring active regions and quiet Sun regions. In this text two analysis projects will be described in detail: NuSTAR observations of a quiet Sun region and the resulting limits on transient flare-like events, and constraints on the physical properties of nanoflares in active regions observed by NuSTAR and FOXSI.

NuSTAR first observed quiet Sun regions on 2014 November 1, although out-of-view active regions contributed a notable amount of background in the form of single-bounce (unfocused) X-rays. These data are used to search for quiet Sun transient brightenings on time scales of 30, 60, and 100 s and set upper limits on emission in two energy bands. 2.5--4 keV limits are expressed as the temperature T and emission measure EM of a thermal plasma, and 10--20 keV limits as model-independent photon fluxes. The limits in both bands are well below previous HXR microflare detections, though not low enough to detect events of equivalent T and EM as quiet Sun brightenings seen in previous soft X-ray observations. Future observations during solar minimum will increase the NuSTAR sensitivity by over two orders of magnitude due to higher instrument livetime and reduced background.

Active region spectra from the FOXSI-2 sounding rocket and the NuSTAR satellite are used to constrain the physical properties of nanoflares simulated with the EBTEL field-line-averaged hydrodynamics code. X-ray spectra are modeled for various nanoflare heating amplitudes, durations, delay times, and filling factors. Additional constraints on the nanoflare parameter space are determined from energy flux limits and EUV/SXR data. For trains of homogeneous nanoflares, theFOXSI-observed region is well fit by nanoflares with large heating amplitudes >0.02 erg cm^-3 s^-1 and a wide range of delay times and durations. The best fits for this region occur when the delay time is longer than ~1700 s. The NuSTAR-observed regions are not fit as well by the homogeneous nanoflare model, and the good-fit regions of parameter space are fairly different. Three of the NuSTAR-observed regions are fit by smaller heating amplitudes <0.02-0.04 erg cm^-3 s^-1 and shorter delay times, and the other two regions are not well-fit at all. Additional studies of active regions observed by HXR instruments are needed to determine if similar nanoflare distributions can provide good fits to a range of ARs.

Terrestrial Gamma-ray Flashes (TGFs) are extremely bright, short bursts of gamma radiation associated with lightning flashes. The story of their discovery spans nearly a century and involves contributions from researchers in many different subdisciplines of physics - lightning physicists, astrophysicists, and meteorologists to name a few. This work summarizes those contributions and the evolving theories on how thunderstorms are able to generate the enormous ”avalanches” of relativistic electrons responsible for the gamma rays.This work also summarizes 3 important contributions from the Santa Cruz High Energy At- mospheric Physics group over the past 5 years: 1. Development of a new ground based detector array with μs absolute timing accuracy, large dynamic range, high resolution data during triggered events, and EMI noise sealing. 2. Quantification of the expected flux from the reverse positron beam of a TGF under the so- called ”feedback model”, and the detectability of such an event from various altitudes on the ground. 3. Observation of two TGFs detected from an unprecedented angle of more than 70◦ off the vertical axis, and Monte Carlo simulations of deviations in source parameters that could lead to the observable beam of gamma-rays reaching farther than existing theory says it should.

Terrestrial gamma-ray Flashes (TGFs) are intense, sub-millisecond bursts of gamma-rays routinely observed by satellites with energy spectra and timing characteristics consistent with bremsstrahlung from electron avalanches produced in thunderstorm electric fields. Since their discovery in 1994, the overwhelming majority of TGF observations have been from satellites. The goal of this work was to see how well TGFs could be observed from instruments on the ground or in the air, and whether there exist TGFs too dim to be seen from space, or TGF related phenomena impossible to observe from satellite.

Using portable instruments consisting of scintillation radiation detectors, we report on the ground observation of a 100 ms duration neutron flash from a lightning strike to a wind turbine in Japan, and evidence of positrons associated with lightning from observations aboard an airplane inside the eyewall of Hurricane Patricia. We discuss methods for deriving TGF brightness by comparing our observations to Monte Carlo simulations. Both the neutron flash seen in Japan, and the evidence for a downward beam of positrons produced in the eyewall of Hurricane Patricia are consistent with production from TGFs with brightnesses typical of TGFs so far observed from space.

Many X-ray sources are now understood to be ``black hole X-ray binaries'' in which a stellar remnant black hole either tidally ``squeezes'' gas off a companion star, or pulls in some fraction the companion's wind. This gas can drain inward through a dense, thin disk characterized by thermalized radiation, or a sparse and radiatively-inefficient flow, or some combination of the two. Observations at other energies often provide crucial information, but our primary tools to study accretion, especially closest to the black hole, are X-ray spectra and their time evolution. This evolution includes numerous behaviors spanning orders of magnitude in timescale and luminosity, and also hints at spatial structure since draining is generally faster at smaller radii. This includes variability at time-scales of weeks to months which remains difficult to explain despite an abundance of possible variability mechanisms since direct simulations covering the full spatial and temporal range remain impractical.

After reviewing general aspects of accretion, I present both more and less familiar forms of longterm variability. Based on these, I argue the problem involves finding a physical process (or combination) that can generate repeatable yet adjustable cycles in luminosity and evolution of low and high energy spectral components, while letting the ionization instability dominate conventional outbursts. Specific models examined include: disks embedded in, and interacting with, hot, sparse flows, and another instability that quenches viscous-draining of the disk at more fundamental level. Testing these theories, alone and in combination, motivates building a very general and simplified numerical model presented here. I find that two-phase flow models still predict excessive recondensation in LMC X-3 among other problems, while the viscosity-quenching instability may account for rapid drops and slow recoveries in disk accretion rate but also likely requires diffusivity orders of magnitude above the Spitzer value.

I also present complementary work on how total mass supply can vary (on day-week timescales) when the companion is irradiated by accretion-generated X-rays as the model is built with the intention (and features) to be used with more detailed disk models.

X-ray and gamma-ray emissions from storm clouds and lightning are routinely emitted over timescales from microsecond bursts of x-rays associated with lightning leaders and sub-millisecond bursts of gamma-rays called terrestrial gamma-ray flashes (TGFs) to seconds long 'glows' of gamma radiation. The focus of this dissertation will be on the physics and analysis of TGFs. To begin, I will review the physics of thundercloud charging, lightning initiation and the propagation of lightning leader channels. Understanding the varied electric field environments of these thunderstorm processes is important context to understanding the TGF mechanism and the prevailing theories of TGF production. I will give an overview of the current understanding of TGF physics detailing those competing theories and the prevailing questions for future research. From the experimental perspective I will discuss TGF distribution trends using observations by orbiting spacecraft as well as give a summary of the use of low frequency lightning radio sferics; how they are used to provide location data for TGF analysis and more recently the importance of multi-wavelength measurements of the TGFs current moment to increase our understanding of the TGF-lightning leader relationship.

This introduction will be followed by two soon to be published papers on TGF observations and coincident radio sferic data. The first paper will focus on an observation of a possible reverse beamed TGF by the Gamma-Ray Burst Monitor aboard the Fermi spacecraft. This is a follow up paper on Pu et al. (2020), who published the coincident radio sferic data along with the Fermi gamma-ray observation proposing the possibility the observation was the reverse beam component of a downward TGF associated with a -CG lightning event initiating at 6km. I investigate this possibility with an in depth analysis of the gamma-ray data using Monte Carlo simulations, meteorological analysis of the storms charge structure and updated analysis of the radio data in cooperation with the original authors.

The second paper is the publication of three new TGF observations made by a gamma-ray instrument deployed by my research group to the summit of Mt. S\"antis in Switzerland. Three TGFs were observed during the 2021 summer storm season. Each TGF was coincident with a unique radio sferic, two of which have been associated with orbital TGF observations in the past. I conclude this dissertation with a summary of my instrumentation work, my current hardware projects and how my future research plans and goals are coming into focus.

Antiretroviral therapy (ART) improves the quality of life for individuals with HIV by suppressing HIV replication but fails to eliminate HIV reservoirs. Consequently, HIV persists in deep tissue reservoirs throughout the body, leading to various comorbidities including cardiovascular, respiratory, and hepatic diseases despite ART regimens.17-20 To better understand where HIV hides within the body, we established the ‘Last Gift’ Cohort (http://lastgift.ucsd.edu). This cohort includes altruistic individuals who generously donate their bodies to research after death, enabling exploration of deep tissue reservoirs and the potential impact of the dying process on reservoir characteristics such as size and activity.1-13,30,31 We collected clinical data, pre-mortem, and post-mortem specimens through rapid autopsy from each participant. By doing so, our goal was to determine whether specific EOL (end of life) biomarkers and deep tissue reservoirs are influenced by the dying process and whether these observations can be extrapolated to healthy PWH. We then developed an innovative method to identify an association between biomarker trajectories measured in blood prior to death and HIV reservoir size. Ultimately, our research is vital in advancing our knowledge of HIV persistence and its implications for individuals with HIV receiving ART, contributing to the development of more effective treatment strategies.

Research on human immunodeficiency virus type I (HIV-1) has led to the development and use of different antiretroviral therapies (ART) to effectively inhibit viral replication and to decrease the transmission rates. However, poor adherence or interruption of therapy may select for drug resistance which leads to a decrease in the overall effectiveness of ART. Even though there is research performed to understand drug resistance mutations through blood sampling, there is a need to understand HIV drug resistance in tissues outside of blood in people living with HIV. For this study, various tissues of two participants with HIV in the Last Gift cohort were examined. HIV drug-resistance mutations and viral populations were obtained through single-genome amplification of the full-length HIV pol gene. The results obtained showed that there were many sequences found within and across various tissues that had nearly identical sequences, which might be due to viral migration. The lymph nodes and spleen exhibited high levels of DRMs to more than one class of ART. We also observed that drugs taken early after HIV diagnosis possibly selected for DRMs that were archived in HIV reservoirs. Also, PBMCs from whole blood did not have certain DRMs that were present in other tissues of the corresponding participants. Overall, the study suggests blood may not be fully capable of characterizing viral reservoirs in other anatomical locations. These findings, in hopes, can provide aid in improving current ART regimens for people living with HIV worldwide.

Abstract

The MINIS Balloon Campaign:

Duskside Relativistic Electron Precipitation

by

John Glen Sample

Doctor of Philosophy in Physics

University of California, Berkeley

Professor Frances Hellman, Chair

The Earth's radiation belts are a dynamic population of highly-energetic (> MeV) electrons and ions trapped in the dipole geometry of the Earth's magnetic field . These particles can strongly influence atmospheric chemistry, satellite operations, human explorers, long distance communications and even the electrical grid. The belts are also the most accessible laboratory for study of the particle acceleration that we see taking place throughout the universe. This dissertation presents the results from the MINIS balloon campaign, a January 2005 effort to observe the loss of relativistic electrons from the belts through relativistic electron precipitation (REP). MINIS launched 6 balloon payloads equipped with X-ray spectrometers into high-altitude, high-latitude, long-duration flights. These flights took place during a dramatic series of solar activity that set off a -99 Dst geomagnetic storm. During the storm sudden commencement phase, three payloads measured bremsstrahlung X-rays from electrons hitting the top of the atmosphere, making MINIS the first multi-point measurement of relativistic electron precipitation. The observations took place at dusk local times, consistent with other high energy precipitation observations from single point balloons. Measuring the scale size and motions of the precipitation region as well as its energy and intensity allow improved measurement of the average loss rate as well as more tightly constraining the instantaneous loss rate from the belts. Scale sizes and motions can also be better tied to the physical structures in the belts which lead to these particle losses. During the MINIS observed precipitation, the scale size was at least 0.6 L (a unit of Earth radii when mapped to the magnetic equator) by 1 hour of magnetic local time, and expansion rates of the precipitation were well faster than the drift rate for ~MeV electrons. The MINIS balloons also served as a proof of concept for a much larger balloon campaign that began in January 2013 and will continue at least until February 2014. That campaign, BARREL, and estimates of what it will observe as well as a possible satellite mission to observe REP are also detailed here.