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Cavity Ring-Down and Multi-Pass Spectroscopies for Methane Source Attribution and Chemical Kinetics Studies
Get PDFMethane is the most abundant hydrocarbon in the Earth atmosphere, is also an important greenhouse gas, energy source, and microbial metabolic energy source and product. With the rapid increase of atmospheric methane concentration, it has become very important to quantify methane emissions from different sources. This thesis describes the applications of cavity ring-down applications on atmospheric ethane measurements and measurements of doubly substituted methane for methane source attributions. We also present our work on chemical kinetics studies of an alkene ozonolysis intermediate, Criegee intermediate, using a multi-pass absorption technique.
In Chapter 2, we demonstrated the performance of a continuous-wave (cw) interband cascade laser (ICL) based mid-infrared cavity ring-down spectroscopy (CRDS) sensor for atmospheric ethane (C2H6) detection. A 3.36 µm cw ICL with an was used to target two ethane absorption bands at 2976.788 cm-1 and 2983.383 cm-1. This technique utilizes the long effective pathlength (~ 4.5 km) of CRDS to increase sensitivity of atmospheric ethane detection. Our spectrometer can measure atmospheric ethane concentration as low as 200 pptv at standard temperature and pressure. We have used this instrument to measure the atmospheric ethane composition in ambient air collected in Pasadena, California. We have utilized this instrument to aid in the study of soil microbial response post the Porter Ranch gas leak. Results were shown in Chapter 3.
In Chapter 4, we demonstrate high sensitivity measurements of both 13CH3D and 12CH2D2 isotopologues using a high precision and high resolution spectroscopy technique, frequency stabilized cavity ring-down spectroscopy (FS-CRDS). Measurements of the abundances of doubly-substituted methane isotopologues (13CH3D and 12CH2D2) are important in methane source attributions. Currently, methods developed for 13CH3D and 12CH2D2 measurements have been mostly focused on the use of isotope ratio mass spectrometry (IRMS), which faces the challenges of mass resolutions. In this work, we focus on measuring these low abundant methane isotopologues optically, taking advantage of the distinct absorption features of them. This technique can be used as a potential complement to IRMS measurements for its ability to measure abundances of rare methane isotopologues with a short time average (~1 hour average per isotope ratio measurement).
In Chapter 5, we utilized our IR kinetic spectroscopy (IRKS) apparatus to study the formation of HCO radicals from the smallest Criegee Intermediate (CH2OO), which is an important intermediate from oznolysis of the smallest alkene.</p
Virology By The Numbers: A Quantitative Exploration of Viral Energetics, Genomics, and Ecology
Get PDFOver the past couple of decades, technological advancements in sequencing and imaging have unequivocally proven that the world of viruses is far bigger and more consequential than previously imagined. There are 1031 viruses estimated to inhabit our planet, outnumbering even bacteria. Despite their astronomical numbers and staggering sequence diversity, environmental viruses are poorly characterized. In this thesis we will demonstrate our three-pronged exploration of viruses through the lenses of energetics (Chapters 2 and 3), genomics (Chapter 4) and ecology (Chapter 5). We will first focus on one of the defining features of viruses, namely their reliance on their host for energy, and demonstrate the energetic cost of building a virus and mounting an infection. In our second study, we present one of the largest surveys of complete viral genomes, providing a comprehensive and quantitative snapshot of viral genomic trends for thousands of viruses. In our third study, we shift our focus towards ecological questions surrounding the large number of commensal phages inhabiting the human body. We discovered that phage community composition could serve as a fingerprint, or a "phageprint" – highly personal and stable over time. To our knowledge, this study is one of the largest studies of human phages and the first to demonstrate the feasibility of human identification based on phage sequences.</p
Colonization of the Intestinal Surface by Indigenous Microbiota
Get PDFThe mammalian gut evolved to foster the development and maintenance of a community of specific bacterial symbionts that persist for years. Bacteroides fragilis is one of a number of species that are able to colonize the mucus of the large intestine in mice and humans. This thesis explores the mechanisms and functions of mucosal colonization, most notably by using reductionist approaches with gnotobiotic mice. Harnessing genetics on both the host and microbial side allowed the dissection of a pathway by which immunoglobulin A enhances mucosal colonization by B. fragilis. Novel colonization assays were developed to explore the importance of mucosal colonization to bacterial fitness. Finally, an enrichment method for host-associated bacterial transcriptomics was used to define the behavior of this symbiont within the mucus layer.</p
On the Origin of Scales and Scaling Laws in Star Formation
Get PDFStars are the fundamental objects of astrophysics and their formation is a key process that influences the evolution of galaxies and planets, and the development of life. Understanding how stars form is crucial even for seemingly unconnected fields of astronomy, as the interpretation of observed starlight from galaxies (even as a background) and other unresolved sources relies on our understanding of star formation. There is no comprehensive theory of star formation, despite intense effort on both the theoretical and observational sides, due to the complicated, non-linear physics involved (e.g., magnetohydrodynamics, gravity, radiation) and the enormous dynamic range of the problem. My goal has been to identify the role different physical processes (e.g., turbulence, feedback) play in star formation.
Using the semi-analytical framework that I developed, I found that a large number of star formation models are inherently sensitive to the initial conditions of the progenitor clouds (e.g., temperature). This led to another study where I predicted the expected variation of the initial mass function (IMF) of stars in a Milky-Way-like galaxy for different star formation models. I showed that IMF models where the peak is either set by turbulent properties or cooling physics (using an effective equation of state) are unable to reproduce the universal IMF of the Milky Way. I also utilized my semi-analytical tools to predict higher-order statistics of star formation: stellar correlation, multiplicity and the companion mass distribution for binaries. I showed that due to observational biases all explored models could roughly reproduce the observed multiplicity and companion mass distributions. This means that observations are currently unable to differentiate between most models.
While working on these projects I found that several scaling relations (e.g., the slopes of IMF, stellar correlation function and gas column density distribution) are insensitive to our choice of physical model; they are universal. Inspired by this I developed an analytic model that I used to show that scale-free structure formation inherently leads to these scaling relations. This provides a deep physical reason why the mass functions and correlation functions of very different systems (e.g., stars, protostellar cores, star clusters, Dark matter halos) follow roughly the same power-law relations.
My previous findings with my semi-analytical models indicated that isothermal collapse would lead to an infinite fragmentation cascade, i.e. there is no inherent low-mass cut-off. Part of the literature supports these findings and claims that additional physics is needed to imprint a mass scale into the problem, but there are theoretical models and simulations that claim that such a cut-off exists. Using GIZMO, a fully adaptive, meshless MHD code, I have carried out a convergence study and have shown that the isothermal fragmentation cascade continues to ever smaller scales without limit.</p
Partially Mixed Selectivity and Parietal Cortex
Get PDFBrain-machine interfaces (BMIs) decode intention signals and other variables from the brain in order to control a computer, tablet, or prosthetic limb. In order to improve the technology, a better understanding of the representational mechanisms within the brain is necessary. Here we study how the anterior intraparietal area (AIP) of human posterior parietal cortex is able to represent many variables within a small patch of cortex. We record single unit activity using a 4 x 4 mm microelectrode array implanted in AIP of a human tetraplegic volunteer. Testing movements of different cognitive strategies, body parts, and body sides, we find that the neural population represents information in a high-dimensional way, termed "mixed selectivity", with individual units coding for idiosyncratic combinations of variables. Furthermore, we find that the variables are not randomly mixed but exhibited "partially mixed selectivity" with certain variables more randomly mixed than others. Representations were "functionally segregated", with representations of the hand and shoulder largely orthogonal despite the high degree of anatomical overlap; representations of body side and strategy were organized by body part. We also examine how the representations changed between BMI training and online BMI control. We find that the structure of the movement representations was preserved, with the different representations found during calibration maintained during online control. Finally, we study the sensory mirror system, a system that processes observed sensations similarly to experienced sensations. We once again find partially mixed selectivity and functional segregation by body parts, showing that this method of encoding information exists not just in the action intention domain but also in the sensory domain. Our results propose partially mixed selectivity as a general mechanism for encoding high dimensional in formation in a small neural population, while also advancing the possibility of limited electrode-array BMIs decoding movements of a large extent of the body.</p
Quantum Steampunk: Quantum Information, Thermodynamics, Their Intersection, and Applications Thereof Across Physics
Get PDFCombining quantum information theory (QIT) with thermodynamics unites 21st-century technology with 19th-century principles. The union elucidates the spread of information, the flow of time, and the leveraging of energy. This thesis contributes to the theory of quantum thermodynamics, particularly to QIT thermodynamics. The thesis also contains applications of the theory, wielded as a toolkit, across physics. Fields touched on include atomic, molecular, and optical physics; nonequilibrium statistical mechanics; condensed matter; high-energy physics; and chemistry. I propose the name quantum steampunk for this program. The term derives from the steampunk genre of literature, art, and cinema that juxtaposes futuristic technologies with 19th-century settings.</p
Observations of Failure Phenomena in Periodic Media
Get PDFNew manufacturing techniques, such as 3D printing, allow for greater control over material properties and can be used to create custom heterogeneous materials. Heterogeneities can be leveraged to increase fracture toughness by redistributing the stresses, such as due to an elastic heterogeneity, or by impeding crack propagation, such as the renucleation at a material interface or edge of a void. The goal of this research is to study the mechanisms by which heterogeneities work to make composite materials more resistant to fracture than either of the individual base materials.
The influence of heterogeneities on the deformation and fracture of 3D printed fracture specimens is investigated. Brick-like heterogeneities are studied in compact tension and plate specimens with soft, stiff, and void heterogeneities. Horizontally layered heterogeneities are studied in compact tension specimens. The specimens are manufactured using a printer capable of printing multiple materials. The specimens are loaded until failure, and full-field displacement and strain data are collected using digital image correlation. The evolution of resistance to fracture is quantified by the energy release rate and fracture toughness values calculated using load, load-point displacement measurements, and crack extension data determined from images of the specimen. Both in soft specimens with stiff heterogeneities and in stiff specimens with soft heterogeneities, stresses are observed to be higher in the stiffer material. Fracture toughness is observed to increase in the presence of stiff inclusions and voids, although in the case of voids this is due to the crack terminating at the edge of the void and renucleating at the other edge.
The effects of interfaces on crack propagation in periodic media are experimentally studied. Comparative experiments on two proposed heterogeneity architectures aim to separate the effects of elastic deformation caused by heterogeneous inclusions in a composite from the effects of passing through an interface during crack propagation. The first, 'stripe' specimens, alternate equal width stripes perpendicular to the plane of the crack. The second, 'cross' specimens, have the same stripe pattern but with a narrow strip of one of the constituent materials in the plane of crack propagation. The 'cross' is wide enough to contain the crack to an area without material interfaces but thin enough that its overall effect on elastic deformation is minimal. Specimens are manufactured from two polymers using polyjet 3D printing. Energy release rate for fracture is calculated from load and displacement measurements. Digital image correlation is used to study strain and stress fields during crack propagation. While the stress fields during crack propagation appear similar, the fracture toughness in the 'stripe' specimens was found to be higher than that of the 'cross' specimens, indicating that fracture toughness is enhanced by renucleation at the interfaces. Additionally, the amount of enhancement was observed to depend on the width of the heterogeneous layers.
The interaction between the cohesive zone and elastic stiffness heterogeneity in the peeling of an adhesive tape from a rigid substrate is examined experimentally and with finite element simulations. It is understood that elastic stiffness heterogeneities can greatly enhance the adhesion of a tape without changing the properties of the interface. However, in peeling experiments performed on pressure sensitive adhesive tapes with both an elastic stiffness heterogeneity and a substantial cohesive zone, muted adhesion enhancement was observed. It is proposed that the cohesive zone acts to smooth out the effect of the discontinuity at the edge of the elastic stiffness heterogeneities, suppressing their effect on peel force enhancement. The results of numerical simulations show that the peel force enhancement depends on the strength of the adhesive and the size of the cohesive zone.</p
Charge Transport Analysis Using the Seebeck Coefficient-Conductivity Relation
Get PDFCharge transport properties like electrical conductivity or the Seebeck coefficient are defined phenomenologically from near-equilibrium thermodynamics, while the analysis or modeling of them often involves a physical model based on mechanistic principles. In other words, physical models connect microscopic and physical parameters to phenomenological and experimental properties. One of the challenges is that the complexity of solid state requires many physical parameters, whereas the measurable properties which help to determine those parameters are limited. The interrelations of measured properties are very important to overcome this challenge, but this aspect is not well recognized in conventional analysis themes. In this thesis, the concept of using a phenomenological transport function is devised to help combine a collection of measurements into an intermediate level of phenomenology, relevant for Fermion transport but not dependent on a particular physical model. This phenomenological transport function can be determined by examining the electrical conductivity, the Seebeck coefficient, and potentially the Lorenz number. Because the phenomenological transport function combines information from a set of multiple measurable properties, a direct comparison to the transport function of a physical model serves as a strong test for the model.
Particular usefulness comes from extracting transport functions from the Seebeck coefficient-conductivity relation, especially in doped semiconductors. This approach is applied to contrast CeO2-x and n-type SrTiO3 as narrow and dispersive transport function materials, each consistent with polaron and band conduction, respectively. In band conductors such as SrTiO3 and Mg3Sb2, the approach is used to test and refute previous claims about the scattering mechanism and find consistency with deformation potential scattering in both cases. In conducting polymers, which do not resemble any other type of conventional conductors, the Seebeck-conductivity relation reveals a qualitative disagreement with the commonly cited Mott's models. For the case of Cu2Se, a peculiar band conductor which shows anomalies in the Hall measurement of the high temperature phase and also in other transport properties at the phase transition, the transport function approach is applied as a workaround for modeling. On the practical side, for thermoelectric applications, the transport function approach is used to characterize material quality factors for both majority carrier conduction and bipolar conduction. Finally, experimental efforts for improving the accuracy and applicability of Seebeck measurements is discussed.</p
Astrophysical Applications of Quantum Mechanics
Get PDFFrom an outside point of view, astrophysics and quantum mechanics as subclasses of the physical sciences could not be further from each other. Yet these two sides of nature are deeply intertwined. The influence of quantum mechanics on astrophysics and astrophysics on quantum mechanics has been profound: spectral lines as diagnostics, radiative transport, the interiors of celestial bodies, neutrino oscillations, constraints on neutrino mass and graviton mass. In this work, I discuss several applications of quantum mechanics in astrophysics: (1) I examine the use of submm recombination lines of H, He and He+ to probe the extreme ultraviolet luminosity of starbursts and Active Galactic Nuclei. (2) I use the hydrogen recombination line H30α to study the accretion zone of the Milky Way's Galactic Center black hole. I discuss detection of an accretion disk of radius <0.008 pc, consisting of ~104 K gas the disk properties, and its importance in the context of accretion on the black hole. (3) I carry out an extensive study and comparison of M1 closure schemes for neutrino radiation transport, using the protoneutron star interior as a background. (4) I study first-order hydrodynamics of a chiral fluid on a vortex background, and in an external magnetic field, as the precursor for a study of neutron star interiors. I show that there are two previously undiscovered modes describing heat waves propagating along the vortex and magnetic field
Development, Implementation, and Improvements on an Effective Electrochemical Wastewater Treatment and Recycling Unit as a Sustainable Sanitation Solution for the Developing World
Get PDFIn this thesis, I present my work on the development of a self-contained toilet wastewater treatment and recycling system, the “Caltech Solar Toilet”. The Caltech Solar Toilet technology is based on electrolysis of toilet wastewater with TiO2-coated semiconductor anodes and stainless steel cathodes. This is a potentially viable onsite sanitation solution in parts of the world that lack the needed infrastructure for centralized wastewater treatment.
Prototypes of Caltech Solar Toilets were designed to fit in shipping containers in order to provide toilets and onsite wastewater treatment with clean water recycling. Units were designed to handle the waste of 25 users per day (or 130 L of toilet wastewater). The various prototypes were able to provide for the disinfection of pathogens, reduction of chemical oxygen demand (COD), [NH3], and color at an average energy consumption of 35 Wh L-1. The treated wastewater was recycled for use as toilet flushing water.
The addition of a microbial fuel cell system for urine pre-treatment was investigated to lower the overall energy consumption of the Solar Toilets. The microbial fuel cell system used consisted of two stacks of 32 cells connected in parallel. An average power density of 23 mW m‑2 was produced at an effective current density of 65 mA m‑2 for more than 120 days. [NH3], total inorganic carbon, COD, and total organic carbon levels were monitored frequently to understand the chemical energy conversion to electricity as well as to determine the best electrical configuration of the stacks. Archaeal and bacterial population on selected anode felts and in the anolyte of both stacks were investigated as well.
In addition to treating toilet wastewater, pilot-scale and bench-scale experiments demonstrated that electrolysis can remove phosphate by cathodic precipitation as hydroxyapatite at no additional energy cost. Phosphate removal could be predicted based on initial phosphate and calcium concentrations, and up to 80% total phosphate removal was achieved. While calcium was critical for phosphate removal, magnesium and bicarbonate had only minor impacts on phosphate removal rates at concentrations typical of toilet wastewater.</p