Black holes in the early universe, in compact binaries, and as energy sources inside solar-type stars

This thesis consists of three separate studies of roles that black holes might play in our universe.

In the first part we formulate a statistical method for inferring the cosmological parameters of our universe from LIGO/VIRGO measurements of the gravitational waves produced by coalescing black-hole/neutron-star binaries. This method is based on the cosmological distance-redshift relation, with "luminosity distances" determined directly, and redshifts indirectly, from the gravitational waveforms. Using the current estimates of binary coalescence rates and projected "advanced" LIGO noise spectra, we conclude that by our method the Hubble constant should be measurable to within an error of a few percent. The errors for the mean density of the universe and the cosmological constant will depend strongly on the size of the universe, varying from about 10% for a "small" universe up to and beyond 100% for a "large" universe. We further study the effects of random gravitational lensing and find that it may strongly impair the determination of the cosmological constant.

In the second part of this thesis we disprove a conjecture that black holes cannot form in an early, inflationary era of our universe, because of a quantum-field-theory induced instability of the black-hole horizon. This instability was supposed to arise from the difference in temperatures of any black-hole horizon and the inflationary cosmological horizon; it was thought that this temperature difference would make every quantum state that is regular at the cosmological horizon be singular at the black-hole horizon. We disprove this conjecture by explicitly constructing a quantum vacuum state that is everywhere regular for a massless scalar field. We further show that this quantum state has all the nice thermal properties that one has come to expect of "good" vacuum states, both at the black-hole horizon and at the cosmological horizon.

In the third part of the thesis we study the evolution and implications of a hypothetical primordial black hole that might have found its way into the center of the Sun or any other solar-type star. As a foundation for our analysis, we generalize the mixing-length theory of convection to an optically thick, spherically symmetric accretion flow (and find in passing that the radial stretching of the inflowing fluid elements leads to a modification of the standard Schwarzschild criterion for convection). When the accretion is that of solar matter onto the primordial hole, the rotation of the Sun causes centrifugal hangup of the inflow near the hole, resulting in an "accretion torus" which produces an enhanced outflow of heat. We find, however, that the turbulent viscosity, which accompanies the convective transport of this heat, extracts angular momentum from the inflowing gas, thereby buffering the torus into a lower luminosity than one might have expected. As a result, the solar surface will not be influenced noticeably by the torus's luminosity until at most three days before the Sun is finally devoured by the black hole. As a simple consequence, accretion onto a black hole inside the Sun cannot be an answer to the solar neutrino puzzle.

Single cell proteomics microchip to profile immune function, with applications in stem cell biology, translational disease mechanism study and clinical therapeutics monitoring

In response to infection or tissue dysfunction, immune cells develop into highly heterogeneous repertoires with diverse functions. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. However, currently only 3-5 functional proteins can be measured from single cells. We developed a single cell functional proteomics approach that integrates a microchip platform with multiplex cell purification. This approach can quantitate 20 proteins from >5,000 phenotypically pure single cells simultaneously. With a 1-million fold miniaturization, the system can detect down to ~100 molecules and requires only ~104 cells. Single cell functional proteomic analysis finds broad applications in basic, translational and clinical studies. In the three studies conducted, it yielded critical insights for understanding clinical cancer immunotherapy, inflammatory bowel disease (IBD) mechanism and hematopoietic stem cell (HSC) biology.

To study phenotypically defined cell populations, single cell barcode microchips were coupled with upstream multiplex cell purification based on up to 11 parameters. Statistical algorithms were developed to process and model the high dimensional readouts. This analysis evaluates rare cells and is versatile for various cells and proteins. (1) We conducted an immune monitoring study of a phase 2 cancer cellular immunotherapy clinical trial that used T-cell receptor (TCR) transgenic T cells as major therapeutics to treat metastatic melanoma. We evaluated the functional proteome of 4 antigen-specific, phenotypically defined T cell populations from peripheral blood of 3 patients across 8 time points. (2) Natural killer (NK) cells can play a protective role in chronic inflammation and their surface receptor – killer immunoglobulin-like receptor (KIR) – has been identified as a risk factor of IBD. We compared the functional behavior of NK cells that had differential KIR expressions. These NK cells were retrieved from the blood of 12 patients with different genetic backgrounds. (3) HSCs are the progenitors of immune cells and are thought to have no immediate functional capacity against pathogen. However, recent studies identified expression of Toll-like receptors (TLRs) on HSCs. We studied the functional capacity of HSCs upon TLR activation. The comparison of HSCs from wild-type mice against those from genetics knock-out mouse models elucidates the responding signaling pathway.

In all three cases, we observed profound functional heterogeneity within phenotypically defined cells. Polyfunctional cells that conduct multiple functions also produce those proteins in large amounts. They dominate the immune response. In the cancer immunotherapy, the strong cytotoxic and antitumor functions from transgenic TCR T cells contributed to a ~30% tumor reduction immediately after the therapy. However, this infused immune response disappeared within 2-3 weeks. Later on, some patients gained a second antitumor response, consisted of the emergence of endogenous antitumor cytotoxic T cells and their production of multiple antitumor functions. These patients showed more effective long-term tumor control. In the IBD mechanism study, we noticed that, compared with others, NK cells expressing KIR2DL3 receptor secreted a large array of effector proteins, such as TNF-α, CCLs and CXCLs. The functions from these cells regulated disease-contributing cells and protected host tissues. Their existence correlated with IBD disease susceptibility. In the HSC study, the HSCs exhibited functional capacity by producing TNF-α, IL-6 and GM-CSF. TLR stimulation activated the NF-κB signaling in HSCs. Single cell functional proteome contains rich information that is independent from the genome and transcriptome. In all three cases, functional proteomic evaluation uncovered critical biological insights that would not be resolved otherwise. The integrated single cell functional proteomic analysis constructed a detail kinetic picture of the immune response that took place during the clinical cancer immunotherapy. It revealed concrete functional evidence that connected genetics to IBD disease susceptibility. Further, it provided predictors that correlated with clinical responses and pathogenic outcomes.

Determination of source finiteness and depth of large earthquakes

In this thesis, a method to retrieve the source finiteness, depth of faulting, and the mechanisms of large earthquakes from long-period surface waves is developed and applied to several recent large events.

In Chapter 1, source finiteness parameters of eleven large earthquakes were determined from long-period Rayleigh waves recorded at IDA and GDSN stations. The basic data set is the seismic spectra of periods from 150 to 300 sec. Two simple models of source finiteness are studied. The first model is a point source with finite duration. In the determination of the duration or source-process times, we used Furumoto's phase method and a linear inversion method, in which we simultaneously inverted the spectra and determined the source-process time that minimizes the error in the inversion. These two methods yielded consistent results. The second model is the finite fault model. Source finiteness of large shallow earthquakes with rupture on a fault plane with a large aspect ratio was modeled with the source-finiteness function introduced by Ben-Menahem. The spectra were inverted to find the extent and direction of the rupture of the earthquake that minimize the error in the inversion. This method is applied to the 1977 Sumbawa, Indonesia, 1979 Colombia-Ecuador, 1983 Akita-Oki, Japan, 1985 Valparaiso, Chile, and 1985 Michoacan, Mexico earthquakes. The method yielded results consistent with the rupture extent inferred from the aftershock area of these earthquakes.

In Chapter 2, the depths and source mechanisms of nine large shallow earthquakes were determined. We inverted the data set of complex source spectra for a moment tensor (linear) or a double couple (nonlinear). By solving a least-squares problem, we obtained the centroid depth or the extent of the distributed source for each earthquake. The depths and source mechanisms of large shallow earthquakes determined from long-period Rayleigh waves depend on the models of source finiteness, wave propagation, and the excitation. We tested various models of the source finiteness, Q, the group velocity, and the excitation in the determination of earthquake depths.

The depth estimates obtained using the Q model of Dziewonski and Steim (1982) and the excitation functions computed for the average ocean model of Regan and Anderson (1984) are considered most reasonable. Dziewonski and Steim's Q model represents a good global average of Q determined over a period range of the Rayleigh waves used in this study. Since most of the earthquakes studied here occurred in subduction zones Regan and Anderson's average ocean model is considered most appropriate.

Our depth estimates are in general consistent with the Harvard CMT solutions. The centroid depths and their 90 % confidence intervals (numbers in the parentheses) determined by the Student's t test are: Colombia-Ecuador earthquake (12 December 1979), d = 11 km, (9, 24) km; Santa Cruz Is. earthquake (17 July 1980), d = 36 km, (18, 46) km; Samoa earthquake (1 September 1981), d = 15 km, (9, 26) km; Playa Azul, Mexico earthquake (25 October 1981), d = 41 km, (28, 49) km; El Salvador earthquake (19 June 1982), d = 49 km, (41, 55) km; New Ireland earthquake (18 March 1983), d = 75 km, (72, 79) km; Chagos Bank earthquake (30 November 1983), d = 31 km, (16, 41) km; Valparaiso, Chile earthquake (3 March 1985), d = 44 km, (15, 54) km; Michoacan, Mexico earthquake (19 September 1985), d = 24 km, (12, 34) km.

In Chapter 3, the vertical extent of faulting of the 1983 Akita-Oki, and 1977 Sumbawa, Indonesia earthquakes are determined from fundamental and overtone Rayleigh waves. Using fundamental Rayleigh waves, the depths are determined from the moment tensor inversion and fault inversion. The observed overtone Rayleigh waves are compared to the synthetic overtone seismograms to estimate the depth of faulting of these earthquakes. The depths obtained from overtone Rayleigh waves are consistent with the depths determined from fundamental Rayleigh waves for the two earthquakes. Appendix B gives the observed seismograms of fundamental and overtone Rayleigh waves for eleven large earthquakes.

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Study of the origins of toughness in amorphous metals

Amorphous metals that form fully glassy parts over a few millimeters in thickness are still relatively new materials. Their glassy structure gives them particularly high strengths, high yield strains, high hardness values, high resilience, and low damping losses, but this can also result in an extremely low tolerance to the presence of flaws in the material. Since this glassy structure lacks the ordered crystal structure, it also lacks the crystalline defect (dislocations) that provides the micromechanism of toughening and flaw insensitivity in conventional metals. Without a sufficient and reliable toughness that results in a large tolerance of damage in the material, metallic glasses will struggle to be adopted commercially. Here, we identify the origin of toughness in metallic glass as the competition between the intrinsic toughening mechanism of shear banding ahead of a crack and crack propagation by the cavitation of the liquid inside the shear bands. We present a detailed study over the first three chapters mainly focusing on the process of shear banding; its crucial role in giving rise to one of the most damage-tolerant materials known, its extreme sensitivity to the configurational state of a glass with moderate toughness, and how the configurational state can be changed with the addition of minor elements. The last chapter is a novel investigation into the cavitation barrier in glass-forming liquids, the competing process to shear banding. The combination of our results represents an increased understanding of the major influences on the fracture toughness of metallic glasses and thus provides a path for the improvement and development of tougher metallic glasses.

Mathematical study of complex networks : brain, internet, and power grid

The dissertation is concerned with the mathematical study of various network problems. First, three real-world networks are considered: (i) the human brain network (ii) communication networks, (iii) electric power networks. Although these networks perform very different tasks, they share similar mathematical foundations. The high-level goal is to analyze and/or synthesis each of these systems from a “control and optimization” point of view. After studying these three real-world networks, two abstract network problems are also explored, which are motivated by power systems. The first one is “flow optimization over a flow network” and the second one is “nonlinear optimization over a generalized weighted graph”. The results derived in this dissertation are summarized below.

Brain Networks: Neuroimaging data reveals the coordinated activity of spatially distinct brain regions, which may be represented mathematically as a network of nodes (brain regions) and links (interdependencies). To obtain the brain connectivity network, the graphs associated with the correlation matrix and the inverse covariance matrix—describing marginal and conditional dependencies between brain regions—have been proposed in the literature. A question arises as to whether any of these graphs provides useful information about the brain connectivity. Due to the electrical properties of the brain, this problem will be investigated in the context of electrical circuits. First, we consider an electric circuit model and show that the inverse covariance matrix of the node voltages reveals the topology of the circuit. Second, we study the problem of finding the topology of the circuit based on only measurement. In this case, by assuming that the circuit is hidden inside a black box and only the nodal signals are available for measurement, the aim is to find the topology of the circuit when a limited number of samples are available. For this purpose, we deploy the graphical lasso technique to estimate a sparse inverse covariance matrix. It is shown that the graphical lasso may find most of the circuit topology if the exact covariance matrix is well-conditioned. However, it may fail to work well when this matrix is ill-conditioned. To deal with ill-conditioned matrices, we propose a small modification to the graphical lasso algorithm and demonstrate its performance. Finally, the technique developed in this work will be applied to the resting-state fMRI data of a number of healthy subjects.

Communication Networks: Congestion control techniques aim to adjust the transmission rates of competing users in the Internet in such a way that the network resources are shared efficiently. Despite the progress in the analysis and synthesis of the Internet congestion control, almost all existing fluid models of congestion control assume that every link in the path of a flow observes the original source rate. To address this issue, a more accurate model is derived in this work for the behavior of the network under an arbitrary congestion controller, which takes into account of the effect of buffering (queueing) on data flows. Using this model, it is proved that the well-known Internet congestion control algorithms may no longer be stable for the common pricing schemes, unless a sufficient condition is satisfied. It is also shown that these algorithms are guaranteed to be stable if a new pricing mechanism is used.

Electrical Power Networks: Optimal power flow (OPF) has been one of the most studied problems for power systems since its introduction by Carpentier in 1962. This problem is concerned with finding an optimal operating point of a power network minimizing the total power generation cost subject to network and physical constraints. It is well known that OPF is computationally hard to solve due to the nonlinear interrelation among the optimization variables. The objective is to identify a large class of networks over which every OPF problem can be solved in polynomial time. To this end, a convex relaxation is proposed, which solves the OPF problem exactly for every radial network and every meshed network with a sufficient number of phase shifters, provided power over-delivery is allowed. The concept of “power over-delivery” is equivalent to relaxing the power balance equations to inequality constraints.

Flow Networks: In this part of the dissertation, the minimum-cost flow problem over an arbitrary flow network is considered. In this problem, each node is associated with some possibly unknown injection, each line has two unknown flows at its ends related to each other via a nonlinear function, and all injections and flows need to satisfy certain box constraints. This problem, named generalized network flow (GNF), is highly non-convex due to its nonlinear equality constraints. Under the assumption of monotonicity and convexity of the flow and cost functions, a convex relaxation is proposed, which always finds the optimal injections. A primary application of this work is in the OPF problem. The results of this work on GNF prove that the relaxation on power balance equations (i.e., load over-delivery) is not needed in practice under a very mild angle assumption.

Generalized Weighted Graphs: Motivated by power optimizations, this part aims to find a global optimization technique for a nonlinear optimization defined over a generalized weighted graph. Every edge of this type of graph is associated with a weight set corresponding to the known parameters of the optimization (e.g., the coefficients). The motivation behind this problem is to investigate how the (hidden) structure of a given real/complex valued optimization makes the problem easy to solve, and indeed the generalized weighted graph is introduced to capture the structure of an optimization. Various sufficient conditions are derived, which relate the polynomial-time solvability of different classes of optimization problems to weak properties of the generalized weighted graph such as its topology and the sign definiteness of its weight sets. As an application, it is proved that a broad class of real and complex optimizations over power networks are polynomial-time solvable due to the passivity of transmission lines and transformers.

I. A seismotectonic study of the Middle America Subduction Zone. II. Lithosphere and upper mantle structure of the Canadian Shield and Eastern North America

This thesis consists of two separate parts. Part I (Chapter 1) is concerned with seismotectonics of the Middle America subduction zone. In this chapter, stress distribution and Benioff zone geometry are investigated along almost 2000 km of this subduction zone, from the Rivera Fracture Zone in the north to Guatemala in the south. Particular emphasis is placed on the effects on stress distribution of two aseismic ridges, the Tehuantepec Ridge and the Orozco Fracture Zone, which subduct at seismic gaps. Stress distribution is determined by studying seismicity distribution, and by analysis of 190 focal mechanisms, both new and previously published, which are collected here. In addition, two recent large earthquakes that have occurred near the Tehuantepec Ridge and the Orozco Fracture Zone are discussed in more detail. A consistent stress release pattern is found along most of the Middle America subduction zone: thrust events at shallow depths, followed down-dip by an area of low seismic activity, followed by a zone of normal events at over 175 km from the trench and 60 km depth. The zone of low activity is interpreted as showing decoupling of the plates, and the zone of normal activity as showing the breakup of the descending plate. The portion of subducted lithosphere containing the Orozco Fracture Zone does not differ significantly, in Benioff zone geometry or in stress distribution, from adjoining segments. The Playa Azul earthquake of October 25, 1981, M_s=7.3, occurred in this area. Body and surface wave analysis of this event shows a simple source with a shallow thrust mechanism and gives M_o=1.3x10²⁷ dyne-cm. A stress drop of about 45 bars is calculated; this is slightly higher than that of other thrust events in this subduction zone. In the Tehuantepec Ridge area, only minor differences in stress distribution are seen relative to adjoining segments. For both ridges, the only major difference from adjoining areas is the infrequency or lack of occurrence of large interplate thrust events.

Part II involves upper mantle P wave structure studies, for the Canadian shield and eastern North America. In Chapter 2, the P wave structure of the Canadian shield is determined through forward waveform modeling of the phases P_nl, P, and PP. Effects of lateral heterogeneity are kept to a minimum by using earthquakes just outside the shield as sources, with propagation paths largely within the shield. Previous mantle structure studies have used recordings of P waves in the upper mantle triplication range of 15-30°; however, the lack of large earthquakes in the shield region makes compilation of a complete P wave dataset difficult. By using the phase PP, which undergoes triplications at 30-60°, much more information becomes available. The WKBJ technique is used to calculate synthetic seismograms for PP, and these records are modeled almost as well as the P. A new velocity model, designated S25, is proposed for the Canadian shield. This model contains a thick, high-Q, high-velocity lid to 165 km and a deep low-velocity zone. These features combine to produce seismograms that are markedly different from those generated by other shield structure models. The upper mantle discontinuities in S25 are placed at 405 and 660 km, with a simple linear gradient in velocity between them. Details of the shape of the discontinuities are not well constrained. Below 405 km, this model is not very different from many proposed P wave models for both shield and tectonic regions.

Chapter 3 looks in more detail at recordings of P_nl in eastern North America. First, seismograms from four eastern North American earthquakes are analyzed, and seismic moments for the events are calculated. These earthquakes are important in that they are among the largest to have occurred in eastern North America in the last thirty years, yet in some cases were not large enough to produce many good long-period teleseismic records. A simple layer-over-a-halfspace model is used for the initial modeling, and is found to provide an excellent fit for many features of the observed waveforms. The effects on P_nl of varying lid structure are then investigated. A thick lid with a positive gradient in velocity, such as that proposed for the Canadian shield in Chapter 2, will have a pronounced effect on the waveforms, beginning at distances of 800 or 900 km. P_nl records from the same eastern North American events are recalculated for several lid structure models, to survey what kinds of variations might be seen. For several records it is possible to see likely effects of lid structure in the data. However, the dataset is too sparse to make any general observations about variations in lid structure. This type of modeling is expected to be important in the future, as the analysis is extended to more recent eastern North American events, and as broadband instruments make more high-quality regional recordings available.

A Cerenkov-ΔΕ-Cerenkov detector for high energy cosmic ray isotopes and an accelerator study of ^(40)Ar & ^(56)Fe fragmentation

This thesis has two major parts. The first part of the thesis will describe a high energy cosmic ray detector -- the High Energy Isotope Spectrometer Telescope (HEIST). HEIST is a large area (0.25 m²sr) balloon-borne isotope spectrometer designed to make high-resolution measurements of isotopes in the element range from neon to nickel (10 ≤ Z ≤ 28) at energies of about 2 GeV/nucleon. The instrument consists of a stack of 12 NaI(Tl) scintilla tors, two Cerenkov counters, and two plastic scintillators. Each of the 2-cm thick NaI disks is viewed by six 1.5-inch photomultipliers whose combined outputs measure the energy deposition in that layer. In addition, the six outputs from each disk are compared to determine the position at which incident nuclei traverse each layer to an accuracy of ~2 mm. The Cerenkov counters, which measure particle velocity, are each viewed by twelve 5-inch photomultipliers using light integration boxes.

HEIST-2 determines the mass of individual nuclei by measuring both the change in the Lorentz factor (Δγ) that results from traversing the NaI stack, and the energy loss (ΔΕ) in the stack. Since the total energy of an isotope is given by Ε = γM, the mass M can be determined by M = ΔΕ/Δγ. The instrument is designed to achieve a typical mass resolution of 0.2 amu.

The second part of this thesis presents an experimental measurement of the isotopic composition of the fragments from the breakup of high energy ⁴⁰Ar and ⁵⁶Fe nuclei. Cosmic ray composition studies rely heavily on semi-empirical estimates of the cross-sections for the nuclear fragmentation reactions which alter the composition during propagation through the interstellar medium. Experimentally measured yields of isotopes from the fragmentation of ⁴⁰Ar and ⁵⁶Fe are compared with calculated yields based on semi-empirical cross-section formulae. There are two sets of measurements. The first set of measurements, made at the Lawrence Berkeley Laboratory Bevalac using a beam of 287 MeV/nucleon ⁴⁰Ar incident on a CH₂ target, achieves excellent mass resolution (σ_m ≤ 0.2 amu) for isotopes of Mg through K using a Si(Li) detector telescope. The second set of measurements, also made at the Lawrence Berkeley Laboratory Bevalac, using a beam of 583 MeV/nucleon ⁵⁶FeFe incident on a CH₂ target, resolved Cr, Mn, and Fe fragments with a typical mass resolution of ~ 0.25 amu, through the use of the Heavy Isotope Spectrometer Telescope (HIST) which was later carried into space on ISEE-3 in 1978. The general agreement between calculation and experiment is good, but some significant differences are reported here.

Structural and Biophysical Characterization of Variants of the Mechanosensitive Channel of Large Conductance (MSCL)

The ability to sense mechanical force is vital to all organisms to interact with and respond to stimuli in their environment. Mechanosensation is critical to many physiological functions such as the senses of hearing and touch in animals, gravitropism in plants and osmoregulation in bacteria. Of these processes, the best understood at the molecular level involve bacterial mechanosensitive channels. Under hypo-osmotic stress, bacteria are able to alleviate turgor pressure through mechanosensitive channels that gate directly in response to tension in the membrane lipid bilayer. A key participant in this response is the mechanosensitive channel of large conductance (MscL), a non-selective channel with a high conductance of ~3 nS that gates at tensions close to the membrane lytic tension.

It has been appreciated since the original discovery by C. Kung that the small subunit size (~130 to 160 residues) and the high conductance necessitate that MscL forms a homo-oligomeric channel. Over the past 20 years of study, the proposed oligomeric state of MscL has ranged from monomer to hexamer. Oligomeric state has been shown to vary between MscL homologues and is influenced by lipid/detergent environment. In this thesis, we report the creation of a chimera library to systematically survey the correlation between MscL sequence and oligomeric state to identify the sequence determinants of oligomeric state. Our results demonstrate that although there is no combination of sequences uniquely associated with a given oligomeric state (or mixture of oligomeric states), there are significant correlations. In the quest to characterize the oligomeric state of MscL, an exciting discovery was made about the dynamic nature of the MscL complex. We found that in detergent solution, under mild heating conditions (37 °C – 60 °C), subunits of MscL can exchange between complexes, and the dynamics of this process are sensitive to the protein sequence.

Extensive efforts were made to produce high diffraction quality crystals of MscL for the determination of a high resolution X-ray crystal structure of a full length channel. The surface entropy reduction strategy was applied to the design of S. aureus MscL variants and while the strategy appears to have improved the crystallizability of S. aureus MscL, unfortunately the diffraction qualities of these crystals were not significantly improved. MscL chimeras were also screened for crystallization in various solubilization detergents, but also failed to yield high quality crystals.

MscL is a fascinating protein and continues to serve as a model system for the study of the structural and functional properties of mechanosensitive channels. Further characterization of the MscL chimera library will offer more insight into the characteristics of the channel. Of particular interest are the functional characterization of the chimeras and the exploration of the physiological relevance of intercomplex subunit exchange.

Complexity of rupture propagation in large earthquakes in relation to tectonic environment

Complexity in the earthquake rupture process can result from many factors. This study investigates the origin of such complexity by examining several recent, large earthquakes in detail. In each case the local tectonic environment plays an important role in understanding the source of the complexity.

Several large shallow earthquakes (M_s > 7.0) along the Middle American Trench have similarities and differences between them that may lead to a better understanding of fracture and subduction processes. They are predominantly thrust events consistent with the known subduction of the Cocos plate beneath N. America. Two events occurring along this subduction zone close to triple junctions show considerable complexity. This may be attributable to a more heterogeneous stress environment in these regions and as such has implications for other subduction zone boundaries.

An event which looks complex but is actually rather simple is the 1978 Bermuda earthquake (M_s ~ 6). It is located predominantly in the mantle. Its mechanism is one of pure thrust faulting with a strike N 20°W and dip 42°NE. Its apparent complexity is caused by local crustal structure. This is an important event in terms of understanding and estimating seismic hazard on the eastern seaboard of N. America.

A study of several large strike-slip continental earthquakes identifies characteristics which are common to them and may be useful in determining what to expect from the next great earthquake on the San Andreas fault. The events are the 1976 Guatemala earthquake on the Motagua fault and two events on the Anatolian fault in Turkey (the 1967, Mudurnu Valley and 1976, E. Turkey events). An attempt to model the complex P-waveforms of these events results in good synthetic fits for the Guatemala and Mudurnu Valley events. However, the E. Turkey event proves to be too complex as it may have associated thrust or normal faulting. Several individual sources occurring at intervals of between 5 and 20 seconds characterize the Guatemala and Mudurnu Valley events. The maximum size of an individual source appears to be bounded at about 5 x 10²⁶ dyne-cm. A detailed source study including directivity is performed on the Guatemala event. The source time history of the Mudurnu Valley event illustrates its significance in modeling strong ground motion in the near field. The complex source time series of the 1967 event produces amplitudes greater by a factor of 2.5 than a uniform model scaled to the same size for a station 20 km from the fault.

Three large and important earthquakes demonstrate an important type of complexity --- multiple-fault complexity. The first, the 1976 Philippine earthquake, an oblique thrust event, represents the first seismological evidence for a northeast dipping subduction zone beneath the island of Mindanao. A large event, following the mainshock by 12 hours, occurred outside the aftershock area and apparently resulted from motion on a subsidiary fault since the event had a strike-slip mechanism.

An aftershock of the great 1960 Chilean earthquake on June 6, 1960, proved to be an interesting discovery. It appears to be a large strike-slip event at the main rupture's southern boundary. It most likely occurred on the landward extension of the Chile Rise transform fault, in the subducting plate. The results for this event suggest that a small event triggered a series of slow events; the duration of the whole sequence being longer than 1 hour. This is indeed a "slow earthquake".

Perhaps one of the most complex of events is the recent Tangshan, China event. It began as a large strike-slip event. Within several seconds of the mainshock it may have triggered thrust faulting to the south of the epicenter. There is no doubt, however, that it triggered a large oblique normal event to the northeast, 15 hours after the mainshock. This event certainly contributed to the great loss of life-sustained as a result of the Tangshan earthquake sequence.

What has been learned from these studies has been applied to predict what one might expect from the next great earthquake on the San Andreas. The expectation from this study is that such an event would be a large complex event, not unlike, but perhaps larger than, the Guatemala or Mudurnu Valley events. That is to say, it will most likely consist of a series of individual events in sequence. It is also quite possible that the event could trigger associated faulting on neighboring fault systems such as those occurring in the Transverse Ranges. This has important bearing on the earthquake hazard estimation for the region.

Development and Application of Embedding Methods for the Simulation of Large Chemical Systems

The high computational cost of correlated wavefunction theory (WFT) calculations has motivated the development of numerous methods to partition the description of large chemical systems into smaller subsystem calculations. For example, WFT-in-DFT embedding methods facilitate the partitioning of a system into two subsystems: a subsystem A that is treated using an accurate WFT method, and a subsystem B that is treated using a more efficient Kohn-Sham density functional theory (KS-DFT) method. Representation of the interactions between subsystems is non-trivial, and often requires the use of approximate kinetic energy functionals or computationally challenging optimized effective potential calculations; however, it has recently been shown that these challenges can be eliminated through the use of a projection operator. This dissertation describes the development and application of embedding methods that enable accurate and efficient calculation of the properties of large chemical systems.

Chapter 1 introduces a method for efficiently performing projection-based WFT-in-DFT embedding calculations on large systems. This is accomplished by using a truncated basis set representation of the subsystem A wavefunction. We show that naive truncation of the basis set associated with subsystem A can lead to large numerical artifacts, and present an approach for systematically controlling these artifacts.

Chapter 2 describes the application of the projection-based embedding method to investigate the oxidative stability of lithium-ion batteries. We study the oxidation potentials of mixtures of ethylene carbonate (EC) and dimethyl carbonate (DMC) by using the projection-based embedding method to calculate the vertical ionization energy (IE) of individual molecules at the CCSD(T) level of theory, while explicitly accounting for the solvent using DFT. Interestingly, we reveal that large contributions to the solvation properties of DMC originate from quadrupolar interactions, resulting in a much larger solvent reorganization energy than that predicted using simple dielectric continuum models. Demonstration that the solvation properties of EC and DMC are governed by fundamentally different intermolecular interactions provides insight into key aspects of lithium-ion batteries, with relevance to electrolyte decomposition processes, solid-electrolyte interphase formation, and the local solvation environment of lithium cations.

A study of the proposed Diamond Creek Reservoir

Politically the Colorado river is an interstate as well as an international stream. Physically the basin divides itself distinctly into three sections. The upper section from head waters to the mouth of San Juan comprises about 40 percent of the total of the basin and affords about 87 percent of the total runoff, or an average of about 15 000 000 acre feet per annum. High mountains and cold weather are found in this section. The middle section from the mouth of San Juan to the mouth of the Williams comprises about 35 percent of the total area of the basin and supplies about 7 percent of the annual runoff. Narrow canyons and mild weather prevail in this section. The lower third of the basin is composed of mainly hot arid plains of low altitude. It comprises some 25 percent of the total area of the basin and furnishes about 6 percent of the average annual runoff.

The proposed Diamond Creek reservoir is located in the middle section and is wholly within the boundary of Arizona. The site is at the mouth of Diamond Creek and is only 16 m. from Beach Spring, a station on the Santa Fe railroad. It is solely a power project with a limited storage capacity. The dam which creats the reservoir is of the gravity type to be constructed across the river. The walls and foundation are of granite. For a dam of 290 feet in height, the back water will be about 25 m. up the river.

The power house will be placed right below the dam perpendicular to the axis of the river. It is entirely a concrete structure. The power installation would consist of eighteen 37 500 H.P. vertical, variable head turbines, directly connected to 28 000 kwa. 110 000 v. 3 phase, 60 cycle generators with necessary switching and auxiliary apparatus. Each unit is to be fed by a separate penstock wholly embedded into the masonry.

Concerning the power market, the main electric transmission lines would extend to Prescott, Phoenix, Mesa, Florence etc. The mining regions of the mountains of Arizona would be the most adequate market. The demand of power in the above named places might not be large at present. It will, from the observation of the writer, rapidly increase with the wonderful advancement of all kinds of industrial development.

All these things being comparatively feasible, there is one difficult problem: that is the silt. At the Diamond Creek dam site the average annual silt discharge is about 82 650 acre feet. The geographical conditions, however, will not permit silt deposites right in the reservoir. So this design will be made under the assumption given in Section 4.

The silt condition and the change of lower course of the Colorado are much like those of the Yellow River in China. But one thing is different. On the Colorado most of the canyon walls are of granite, while those on the Yellow are of alluvial loess: so it is very hard, if not impossible, to get a favorable dam site on the lower part. As a visitor to this country, I should like to see the full development of the Colorado: but how about THE YELLOW!

A molecular dynamics study of the microscopic properties of simple dense fluids

The microscopic properties of a two-dimensional model dense fluid of Lennard-Jones disks have been studied using the so-called "molecular dynamics" method. Analyses of the computer-generated simulation data in terms of "conventional" thermodynamic and distribution functions verify the physical validity of the model and the simulation technique.

The radial distribution functions g(r) computed from the simulation data exhibit several subsidiary features rather similar to those appearing in some of the g(r) functions obtained by X-ray and thermal neutron diffraction measurements on real simple liquids. In the case of the model fluid, these "anomalous" features are thought to reflect the existence of two or more alternative configurations for local ordering.

Graphical display techniques have been used extensively to provide some intuitive insight into the various microscopic phenomena occurring in the model. For example, "snapshots" of the instantaneous system configurations for different times show that the "excess" area allotted to the fluid is collected into relatively large, irregular, and surprisingly persistent "holes". Plots of the particle trajectories over intervals of 2.0 to 6.0 x 10^-12 sec indicate that the mechanism for diffusion in the dense model fluid is "cooperative" in nature, and that extensive diffusive migration is generally restricted to groups of particles in the vicinity of a hole.

A quantitative analysis of diffusion in the model fluid shows that the cooperative mechanism is not inconsistent with the statistical predictions of existing theories of singlet, or self-diffusion in liquids. The relative diffusion of proximate particles is, however, found to be retarded by short-range dynamic correlations associated with the cooperative mechanism--a result of some importance from the standpoint of bimolecular reaction kinetics in solution.

A new, semi-empirical treatment for relative diffusion in liquids is developed, and is shown to reproduce the relative diffusion phenomena observed in the model fluid quite accurately. When incorporated into the standard Smoluchowski theory of diffusion-controlled reaction kinetics, the more exact treatment of relative diffusion is found to lower the predicted rate of reaction appreciably.

Finally, an entirely new approach to an understanding of the liquid state is suggested. Our experience in dealing with the simulation data--and especially, graphical displays of the simulation data--has led us to conclude that many of the more frustrating scientific problems involving the liquid state would be simplified considerably, were it possible to describe the microscopic structures characteristic of liquids in a concise and precise manner. To this end, we propose that the development of a formal language of partially-ordered structures be investigated.

A Multiwavelength Study of the Intracluster Medium and the Characterization of the Multiwavelength Sub/millimeter Inductance Camera

The first part of this thesis combines Bolocam observations of the thermal Sunyaev-Zel’dovich (SZ) effect at 140 GHz with X-ray observations from Chandra, strong lensing data from the Hubble Space Telescope (HST), and weak lensing data from HST and Subaru to constrain parametric models for the distribution of dark and baryonic matter in a sample of six massive, dynamically relaxed galaxy clusters. For five of the six clusters, the full multiwavelength dataset is well described by a relatively simple model that assumes spherical symmetry, hydrostatic equilibrium, and entirely thermal pressure support. The multiwavelength analysis yields considerably better constraints on the total mass and concentration compared to analysis of any one dataset individually. The subsample of five galaxy clusters is used to place an upper limit on the fraction of pressure support in the intracluster medium (ICM) due to nonthermal processes, such as turbulent and bulk flow of the gas. We constrain the nonthermal pressure fraction at r500c to be less than 0.11 at 95% confidence, where r500c refers to radius at which the average enclosed density is 500 times the critical density of the Universe. This is in tension with state-of-the-art hydrodynamical simulations, which predict a nonthermal pressure fraction of approximately 0.25 at r500c for the clusters in this sample.

The second part of this thesis focuses on the characterization of the Multiwavelength Sub/millimeter Inductance Camera (MUSIC), a photometric imaging camera that was commissioned at the Caltech Submillimeter Observatory (CSO) in 2012. MUSIC is designed to have a 14 arcminute, diffraction-limited field of view populated with 576 spatial pixels that are simultaneously sensitive to four bands at 150, 220, 290, and 350 GHz. It is well-suited for studies of dusty star forming galaxies, galaxy clusters via the SZ Effect, and galactic star formation. MUSIC employs a number of novel detector technologies: broadband phased-arrays of slot dipole antennas for beam formation, on-chip lumped element filters for band definition, and Microwave Kinetic Inductance Detectors (MKIDs) for transduction of incoming light to electric signal. MKIDs are superconducting micro-resonators coupled to a feedline. Incoming light breaks apart Cooper pairs in the superconductor, causing a change in the quality factor and frequency of the resonator. This is read out as amplitude and phase modulation of a microwave probe signal centered on the resonant frequency. By tuning each resonator to a slightly different frequency and sending out a superposition of probe signals, hundreds of detectors can be read out on a single feedline. This natural capability for large scale, frequency domain multiplexing combined with relatively simple fabrication makes MKIDs a promising low temperature detector for future kilopixel sub/millimeter instruments. There is also considerable interest in using MKIDs for optical through near-infrared spectrophotometry due to their fast microsecond response time and modest energy resolution. In order to optimize the MKID design to obtain suitable performance for any particular application, it is critical to have a well-understood physical model for the detectors and the sources of noise to which they are susceptible. MUSIC has collected many hours of on-sky data with over 1000 MKIDs. This work studies the performance of the detectors in the context of one such physical model. Chapter 2 describes the theoretical model for the responsivity and noise of MKIDs. Chapter 3 outlines the set of measurements used to calibrate this model for the MUSIC detectors. Chapter 4 presents the resulting estimates of the spectral response, optical efficiency, and on-sky loading. The measured detector response to Uranus is compared to the calibrated model prediction in order to determine how well the model describes the propagation of signal through the full instrument. Chapter 5 examines the noise present in the detector timestreams during recent science observations. Noise due to fluctuations in atmospheric emission dominate at long timescales (less than 0.5 Hz). Fluctuations in the amplitude and phase of the microwave probe signal due to the readout electronics contribute significant 1/f and drift-type noise at shorter timescales. The atmospheric noise is removed by creating a template for the fluctuations in atmospheric emission from weighted averages of the detector timestreams. The electronics noise is removed by using probe signals centered off-resonance to construct templates for the amplitude and phase fluctuations. The algorithms that perform the atmospheric and electronic noise removal are described. After removal, we find good agreement between the observed residual noise and our expectation for intrinsic detector noise over a significant fraction of the signal bandwidth.

Part I: Total yield measurements for the ^(21)Ne(α,n)^)(24)Mg reaction. Part II: A study of the ^(12)C(He,p)^(14)N reaction

PART I

The total cross-section for the reaction ²¹Ne(α, n)²⁴Mg has been measured in the energy range 1.49 Mev ≤ E_cm ≤ 2.6 Mev. The cross-section factor, S(O), for this reaction has been determined, by means of an optical model calculation, to be in the range 1.52 x 10¹² mb-Mev to 2.67 x 10¹² mb-Mev, for interaction radii in the range 5.0 fm to 6.6 fm. With S(O) ≈ 2 x 10¹² mb-Mev, the reaction ²¹Ne(α, n)²⁴Mg can produce a large enough neutron flux to be a significant astrophysical source of neutrons.

PART II

The reaction¹²C(³He, p)¹⁴N has been studied over the energy range 12 Mev ≤ E_lab ≤ 18 Mev. Angular distributions of the proton groups leading to the lowest seven levels in ¹⁴N were obtained.

Distorted wave calculations, based on two-nucleon transfer theory, were performed, and were found to be reliable for obtaining the value of the orbital angular momentum transferred. The present work shows that such calculations do not yield unambiguous values for the spectroscopic factors.