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Fifty Years of Dividing Lines: From Selma and Montgomery, 1965 to Ferguson, 2015
No full text"Just as local politics was essential to the creation of southern segregation, so local politics was the crucial factor in creating the circumstances that ended it." Though segregation is no longer the battle du jour, this sentiment is just as true for today’s conflict over police brutality. The same factors come into play: the idea, if less outspoken, of white supremacy; an establishment dedicated to preserving itself by suppressing dissent; the notion that change is possible; and a cocktail of continued oppression, retaliation, and escalation guaranteed to explode
Light Dependent Regulation of Sleep/Wake States by Prokineticin 2 in Larval Zebrafish
Get PDFSleep is an evolutionarily conserved behavior and essential to survival. The classic two process model of sleep regulation proposes that sleep results from the interaction between circadian and homeostatic processes, but the details remain elusive. Most sleep research is performed using nocturnal rodents, and diurnal vertebrates are under-represented. It is unclear whether circadian regulatory mechanisms of sleep in nocturnal animals can be directly translated into diurnal animals. In this thesis, I first briefly describe sleep behavior and the two process model of sleep regulation, focusing on the circadian process, and then discuss the advantages of using larval zebrafish as a model to study sleep behavior in diurnal vertebrates. In Chapter 2, I characterize the role of Prokineticin 2, a proposed circadian output factor in nocturnal animals, in sleep/wake regulation in larval zebrafish. I show that, similar to nocturnal rodents, Prok2 is both necessary for daytime sleep/wake behavior and sufficient to modulate sleep/wake states in a light dependent manner. However, unlike nocturnal rodents and similar to humans, Prok2 is not required for maintaining circadian rhythmicity in larval zebrafish after removing external light cue. This result demonstrates the potential functional difference of circadian output factors in different chronotypes, and establishes larval zebrafish as an alternative model for studying circadian regulation of sleep and possibly other behaviors in humans. In Chapter 3, I describe the adaptation and development of TRP channels to manipulate neuronal activity in larval zebrafish, in an effort to expand the existing repertoire of genetic tools for studying behavior in zebrafish. I show that three TRP channels, TRPV1, TRPM8 and TRPA1, can inducibly activate specific populations of neurons in larval zebrafish by using their appropriate agonists. At high agonist concentrations, TRPV1, can rapidly induce cell ablation. Adaptation of TRP channels for use in larval zebrafish expands the variety of behavioral experiments and combinatorial manipulation of neuronal activity that can be performed in zebrafish. In summary, this work deepens our understanding of sleep regulation, establishes larval zebrafish as an appropriate model for studying circadian regulation of sleep in diurnal vertebrates, and presents novel genetic tools for studying behavior in larval zebrafish
Thermoelectric Skutterudites: Why and How High zT Can Be Achieved
Get PDFThermoelectric materials have been widely studied over the past few decades due to their ability to convert waste heat into useful electricity. Among various thermoelectric materials, skutterudite distinguishes itself in both space and terrestrial applications with its excellent thermoelectric performance, robust mechanical properties, and thermal stability. The thermoelectric excellence of skutterudites is mostly attributed to the low thermal conductivity due to the addition of filler atoms (R) into the void (one per primitive cell Co4Sb12). Essential though this is to high zT, the importance of the intrinsic electronic structure in skutterudites is often understated or ignored completely. In this thesis, by combining experimental and computational studies, the electronic origin of high thermoelectric performance of CoSb3-based skutterudites is investigated. The high zT was shown to be a direct result of the high valley degeneracy inherent to CoSb3, which is further enhanced by band convergence at high temperatures. This successfully explains why the optimum doping carrier concentration in n-CoSb3 skutterudites is independent on the type of fillers. With the electronic origin of high thermoelectric performance clarified, the thesis moves on to elaborate how to achieve high zT in skutterudite with the aid of phase diagram study. By mapping out the phase regions near the skutterudite phase on the isothermal section of the R-Co-Sb ternary phase diagram, the solubility region of the CoSb3 skutterudite phase can be determined along with the solubility limit of R, both of which are often determined in stable compositions resulting in a synthesis window. The temperature dependence of the filler solubility is also demonstrated experimentally. This overturns the general understanding that the filler solubility is a single value only dependent on the filler type. The temperature dependence of stable compositions enables easy carrier concentration tuning which allows the optimization of thermoelectric performance. High zT values are achieved in single In, Yb, Ce-CoSb3 skutterudites. The methodology applied here are not confined to n-CoSb3, but can be generalized to any other ternary systems
Gas Phase Spectroscopy and Kinetics of Atmospheric Radicals
Get PDFAn important goal for atmospheric and combustion chemists is continued improvement in our understanding of the gas phase reactivity of free radical intermediates formed during hydrocarbon oxidation. The primary focus of this thesis was to measure gas phase kinetics of prototypical free radicals relevant to atmospheric and combustion chemistry, a goal that requires spectroscopy, quantitative product detection, and computational chemistry in order to address these complex chemical systems.
Near-infrared cavity ringdown spectroscopy was used to study the peroxy radicals (RO2) formed from chlorine-initiated oxidation of isoprene and other unsaturated hydrocarbons. Isoprene is one of the most important hydrocarbons in the atmosphere; detection of RO2 formed directly from isoprene oxidation will aid in understanding the initial steps of its fate in the atmosphere. As expected, the near-infrared chloro-isoprenyl peroxy radical spectrum has many features; each spectral feature corresponds to a different isomer and conformer, indicating that several RO2 structures are formed. In small RO2, it was possible to identify the molecular structure of the absorber by comparing the experimental spectrum with the vibrationally-resolved electronic spectrum generated by computational chemistry. Identification of each feature then enabled preliminary isomer-specific kinetics measurements.
Photoionization mass spectrometry is another useful method for selective detection of radicals, with the added bonus of detecting many of the other species of interest, leading to a comprehensive understanding of the reaction mechanism. The yields of radical chain-propagating product channels of prototypical RO2 reactions (self- and cross-reactions) are important in understanding radical chemistry in gas phase hydrocarbon oxidation. We obtained branching ratio information for reactions of acetyl peroxy radicals with HO2, with particular focus on OH-regenerating reactions. Along the way, we observed unexpected product formation from low-pressure reactions of acetyl radicals and oxygen. Using the same techniques, we also looked at the self-reaction of ethyl peroxy radicals, confirming past measurements of the radical-propagating channel for this reaction, and investigated interesting product formation, like what may be the dialkyl peroxide. These studies were supported by measurements of VUV photoionization cross sections for several radical species. The utility of this instrumentation was also extended by the development of a low-temperature (200–300 K) flow reactor.
Finally, using time-resolved broadband cavity-enhanced absorption spectroscopy, we measured the rate coefficient of reactions of the smallest Criegee intermediate, CH2OO with ozone. We observed that this reaction is rather fast, which could have significant implications for experimental ozonolysis studies that are carried out under high initial reactant concentrations. </p
Bio-Inspired Homometallic and Heterometallic Clusters Relevant to the Oxygen-Evolving Complex of Photosystem II
Get PDFThe following two chapters delineate several endeavors to isolate and characterize functional models of the oxygen-evolving complex (OEC) of photosystem II. Understanding the electronic structure and the precise mechanism of the O–O bond coupling step in the Kok cycle affords insight into this fundamental process and will guide the design of new earth-abundant catalysts to perform water oxidation under environmentally benign conditions. Nature performs this transformation by a heterometallic CaMn4O5 cluster arranged a tetra-metallic cubane bridged to a dangling manganese ion. Although a myriad of synthetic inorganic complexes are capable of water oxidation, these structures significantly underperform the OEC in terms of turnover number and turnover frequency. The objectives of this thesis are (i) to construct multimetallic clusters using the OEC as inspiration, (ii) to explore the reactivity of these clusters with oxygen-atom transfer reagents, and (iii) to identify intermediates responsible for oxygen-based chemistry.
In Chapter 1, a series of pseudo-C3 symmetric tetra-manganese clusters with an interstitial µ4-oxygen was synthesized and characterized in several oxidation states. These clusters (of the general formula [LMn3(PhPz)3OMn][OTx]x; x = 1, 2) are supported by pyridine and alkoxide donors connected by a 1,3,5-triarylbenzene spacer. A µ4-oxygen coordinates all four metal centers that are also bridged by phenyl pyrazolate (PhPz) ligands. This arrangement furnishes a vacant coordination site at a site-differentiated (apical) metal center. Exposure of these clusters to oxygen-atom transfer reagents (OAT’s) results in the intramolecular oxygenation of a C(sp2)–H bond of the bridging phenyl pyrazolate. Similarly, using 2,6-difluorophenyl pyrazolate (F2ArPz) as the bridging ligand results in the oxygenation of the C–F bond with concurrent F-atom transfer. This reactivity represents an unprecedented C–F activation for molecular manganese complexes. All hydroxylated and fluorinated clusters were independently prepared to confirm the observed reactivity upon exposure to OAT’s. The pathways responsible for arene activation – postulated to proceed through an iodosobenzene adduct and subsequent formation of a transient high-valent manganese-oxo motif – are discussed.
In Chapter 2, a series of pseudo-C3 symmetric heterometallic Fe3Mn clusters of the general formula [LMn3(PhPz)3OMn][OTf]x (x = 1–3) was synthesized and characterized. Similar to their homometallic tetra-manganese and tetra-iron analogs (Chapter 1), these clusters contain four metal centers with a central bridging interstitial µ4-oxygen atom and bridging phenyl pyrazolate ligands. These clusters are further supported by pyridine and alkoxide donors, linked through a 1,3,5-triarylbenzene spacer. All complexes were characterized by zero-field 57Fe Mössbauer spectroscopy to confirm the presence of a manganese metal center in the apical position, illustrating that these clusters are stable with respect to metal scrambling and/or decomposition. Treatment of these clusters with 1-(tert-butylsulfonyl)-2-iodosylbenzene (sPhIO) resulted in the oxygenation of the C(sp2)–H bond of the proximal phenyl pyrazolate motif to afford [LMn3(PhPz)2(OArPz)OMn][OTf]x (x = 2, 3). During these studies, an unusual iodosobenzene adduct of [FeIII3MnII]3+ was isolated prior to C–H activation. This adduct has been characterized both by single-crystal XRD and 1H-NMR spectroscopy. In order to gain insight into the C–H bond oxygenation by this iodosobenzene adduct, preliminary computational studies are presented to discuss the viability of a transient manganese-oxo species responsible for arene hydroxylation.</p
Simulations and Mechanisms of Subtropical Low-cloud Response to Climate Change
Get PDFThis thesis focuses on improving the simulation skills and the theoretical understanding of the subtropical low cloud response to climate change.
First, an energetically consistent forcing framework is designed and implemented for the large eddy simulation (LES) of the low-cloud response to climate change. The three representative current-day subtropical low cloud regimes of cumulus (Cu), cumulus-over-stratocumulus, and stratocumulus (Sc) are all well simulated with this framework, and results are comparable to the conventional fixed-SST approach. However, the cumulus response to climate warming subject to energetic constraints differs significantly from the conventional approach with fixed SST. Under the energetic constraint, the subtropics warm less than the tropics, since longwave (LW) cooling is more efficient with the drier subtropical free troposphere. The surface latent heat flux (LHF) also increases only weakly subject to the surface energetic constraint. Both factors contribute to an increased estimated inversion strength (EIS), and decreased inversion height. The decreased Cu-depth contributes to a decrease of liquid water path (LWP) and weak positive cloud feedback. The conventional fixed-SST approach instead simulates a strong increase in LHF and deepening of the Cu layer, leading to a weakly negative cloud feedback. This illustrates the importance of energetic constraints to the simulation and understanding of the sign and magnitude of low-cloud feedback.
Second, an extended eddy-diffusivity mass-flux (EDMF) closure for the unified representation of sub-grid scale (SGS) turbulence and convection processes in general circulation models (GCM) is presented. The inclusion of prognostic terms and the elimination of the infinitesimal updraft fraction assumption makes it more flexible for implementation in models across different scales. This framework can be consistently extended to formulate multiple updrafts and downdrafts, as well as variances and covariances. It has been verified with LES in different boundary layer regimes in the current climate, and further development and implementation of this closure may help to improve our simulation skills and understanding of low-cloud feedback through GCMs.</p
A Multiwavelength Study of the Intracluster Medium and the Characterization of the Multiwavelength Sub/millimeter Inductance Camera
Get PDFThe 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.</p
Firing Patterns of Cerebellar Purkinje Cells During Locomotion and Sleep
Get PDFThe cerebellum is a major supraspinal center involved in the coordination of movement. The principal neurons of the cerebellar cortex, Purkinje cells, receive excitatory synaptic input from two sources: the parallel and climbing fibers. These pathways have markedly different effects: the parallel fibers control the rate of simple sodium spikes, while the climbing fibers induce characteristic complex spike bursts, which are accompanied by dendritic calcium transients and play a key role in regulating synaptic plasticity. While many studies using a variety of species, behaviors, and cerebellar regions have documented modulation in Purkinje cell activity during movement, few have attempted to record from these neurons in unrestrained rodents. In this dissertation, we use chronic, multi-tetrode recording in freely-behaving rats to study simple and complex spike firing patterns during locomotion and sleep. Purkinje cells discharge rhythmically during stepping, but this activity is highly variable across steps. We show that behavioral variables systematically influence the step-locked firing rate in a step-phase-dependent way, revealing a functional clustering of Purkinje cells. Furthermore, we find a pronounced disassociation between patterns of variability driven by the parallel and climbing fibers, as well as functional differences between cerebellar lobules. These results suggest that Purkinje cell activity not only represents step phase within each cycle, but is also shaped by behavior across steps, facilitating control of movement under dynamic conditions. During sleep, we observe an attenuation of both simple and complex spiking, relative to awake behavior. Although firing rates during slow wave sleep (SWS) and rapid eye movement sleep (REM) are similar, simple spike activity is highly regular in SWS, while REM is characterized by phasic increases and pauses in simple spiking. This phasic activity in REM is associated with pontine waves, which propagate into the cerebellar cortex and modulate both simple and complex spiking. Such a temporal coincidence between parallel and climbing fiber activity is known to drive plasticity at parallel fiber synapses; consequently, pontocerebellar waves may provide a mechanism for tuning synaptic weights in the cerebellum during active sleep
Synthetic Circuits for Feedback and Detection in Bacteria
Get PDFSynthetic biology, by co-opting molecular machinery from existing organisms, can be used as a tool for building new genetic systems from scratch, for understanding natural networks through perturbation, or for hybrid circuits that piggy-back on existing cellular infrastructure. Although the toolbox for genetic circuits has greatly expanded in recent years, it is still difficult to separate the circuit function from its specific molecular implementation. In this thesis, we discuss the function-driven design of two synthetic circuit modules, and use mathematical models to understand the fundamental limits of circuit topology versus operating regimes as determined by the specific molecular implementation. First, we describe a protein concentration tracker circuit that sets the concentration of an output protein relative to the concentration of a reference protein. The functionality of this circuit relies on a single negative feedback loop that is implemented via small programmable protein scaffold domains. We build a mass-action model to understand the relevant timescales of the tracking behavior and how the input/output ratios and circuit gain might be tuned with circuit components. Second, we design an event detector circuit with permanent genetic memory that can record order and timing between two chemical events. This circuit was implemented using bacteriophage integrases that recombine specific segments of DNA in response to chemical inputs. We simulate expected population-level outcomes using a stochastic Markov-chain model, and investigate how inferences on past events can be made from differences between single-cell and population-level responses. Additionally, we present some preliminary investigations on spatial patterning using the event detector circuit as well as the design of stationary phase promoters for growth-phase dependent activation. These results advance our understanding of synthetic gene circuits, and contribute towards the use of circuit modules as building blocks for larger and more complex synthetic networks
Mixing, Chemical Reactions, and Combustion in Supersonic Flows
Get PDFExperiments were conducted at the GALCIT supersonic shear-layer facility to investigate
aspects of reacting transverse jets in supersonic crossflow using chemiluminescence and schlieren
image-correlation velocimetry. In particular, experiments were designed to examine mixing-delay
length dependencies on jet-fluid molar mass, jet diameter, and jet inclination.
The experimental results show that mixing-delay length depends on jet Reynolds number, when
appropriately normalized, up to a jet Reynolds number of 500,000. Jet inclination increases the
mixing-delay length, but causes less disturbance to the crossflow when compared to normal jet
injection. This can be explained, in part, in terms of a control-volume analysis that relates jet
inclination to flow conditions downstream of injection.
In the second part of this thesis, a combustion-modeling framework is proposed and developed
that is tailored to large-eddy simulations of turbulent combustion in high-speed flows. Scaling arguments place supersonic hydrocarbon combustion in a regime of autoignition-dominated distributed
reaction zones (DRZ). The proposed evolution-variable manifold (EVM) framework incorporates an
ignition-delay data-driven induction model with a post-ignition manifold that uses a Lagrangian
convected 'balloon' reactor model for chemistry tabulation. A large-eddy simulation incorporating
the EVM framework captures several important reacting-flow features of a transverse hydrogen jet
in heated-air crossflow experiment.</p