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Fundamental Physics in the Era of Gravitational-Wave Astronomy: The Direct Measurement of Gravitational-Wave Polarizations and Other Topics
Get PDFIn this thesis, I explore several avenues for learning about fundamental physics from gravitational-wave (GW) observations. In particular, I focus on the phenomenological study of basic properties of GWs in ways that require minimal assumptions about the underlying nature of gravity. I place a special emphasis on GW polarizations, but also consider their speed and possible dispersion. To constrain possible modifications to general relativity, I develop data-analysis frameworks to measure these properties with both transient and persistent signals detected by ground-based detectors. This includes, among other results, the analysis of two LIGO and Virgo compact-binary detections, GW170814 and GW170817, to produce the first direct observational statements about the local geometry of GW polarizations. I also present constraints on the potential amplitude of nontensorial monochromatic signals from 200 known pulsars in the Milky Way and describe in detail the methods used to obtain them. Because stochastic signals will be a great resource for studying GW properties, I also carefully review the assumptions that go into standard stochastic analyses and explore their applicability beyond general relativity, concluding that those measurements will have to be interpreted carefully to make meaningful statements about corrections to Einstein’s theory. Besides the properties of the waves themselves, I also study the prospect for using GWs as a means to uncover signatures of new ultralight bosons—an exciting possibility that could bring particle physics into the reach of GW astronomy. I explore the potential of current and future detectors to detect these conjectured particles, concluding that third-generation instruments are certain to place theoretically interesting constraints. Because little can be done in the absence of signals, I also propose data-analysis methods to improve LIGO and Virgo’s chances of detecting both transient and continuous signals. The latter have now been used to diagnose real detection candidates on several occasions.</p
Numerical Investigation of Spinal Neuron Facilitation with Multi-electrode Epidural Stimulation
Get PDFApproximately 1,275,000 people in the US have a spinal cord injury severe enough to cause some paralysis of the arms and/or legs. Epidural stimulation using implanted multi-electrode stimulating arrays over the lumbosacral spinal cord has recently shown promise in assisting individuals with severe spinal cord injuries to stand, walk, and even facilitate voluntary movement. Both animal model and human studies have shown that sub-threshold facilitation of motor recovery gives the best results. The underlying neural mechanisms by which sub-threshold epidural stimulation leads to motor recovery are incompletely known.
This thesis uses computational methods to study the facilitation effect. A neuron is facilitated if a sub-threshold synaptic input can cause a neuronal output under the influence of a stimulating electric field. The analysis in this thesis is based on a computational model of the epidural spinal stimulation process in the rat spinal cord. This model includes a time-domain finite element simulation (using COMSOL®) of the various tissues in the spinal cord with the appropriate anisotropic and frequency-dependent complex relative permittivities. The voltages obtained from the finite element simulations were used as the extracellular voltage in NEURON simulations.
A population of neurons were simulated under a wide variety of conditions. These simulations highlight the effect of neuron orientation, location, and synaptic timing as key parameters which influence facilitation.
This study indicates that regions of the spinal cord that have previously been ignored may be actively involved in motor recovery. These results may also enable the design of specialized epidural electrode arrays and the design of new stimulation protocols.</p
The Genomics of Stress-Induced Life Cycle Decisions in Nematodes
Get PDFOrganisms including bacteria, insects, and mammals make decisions to alter aspects of their development based on signals from the environment. The roundworm Caenorhabditis elegans can escape environmental collapse by halting reproductive growth and entering the stress-resistant dauer larval stage. Dauer larvae are spore-like and have specialized behaviors for finding and stowing onto carrier animals for dispersal. The decision to enter dauer is an anticipatory decision that is based on the inputs of food, pheromone, and temperature.
Here, I show that touch is an overlooked input into the dauer entry decision. Using quantitative dauer entry assays on CRISPR knock-ins and existing mutants in mechanosensation, I demonstrate that gentle, harsh, and piezo touch promote dauer entry. By measuring pheromone sensation and signal tranmission in mechnanosensation-defective mutants, I show that mechanosensation likely inputs into the decision in parallel with pheromone. Further confirmation that touch promotes dauer entry is provided using direct mechanical stimulation of C. elegans, and I provide a plausible role for touch in sensing dauer-promoting weather and crowding conditions.
Using RNA-seq, I also show that 8,042 genes are differentially expressed between dauer and reproductive development. Within this dataset, we observed the striking up-regulation of 64 neuropeptide genes (encoding 215 peptides) during dauer. By comparison, the entire human genome contains 97 neuropeptide genes (encoding 270 peptides). In particular, we observed coordinated up-regulation of the FMRFamide-like neuropeptides (FLPs). Using sbt-1 mutants to knock down neuropeptide processing, we demonstrate that peptidergic signaling promotes the dauer entry decision, promotes vigorous waving during the dauer-specific nictation behavior (carrier animal-hitchhiking), and is necessary for switching from repulsion to CO2 (a carrier animal cue) in non-dauers to CO2 attraction in dauers. By testing individual neuropeptides using CRISPR knockouts and existing strains, we show that 7 FLPs promote dauer entry while 4 FLPs inhibit. I therefore propose plausible roles for these FLPs in acting downstream of and/or modulating the sensation of food, pheromone, temperature, and touch inputs. We also demonstrate that FLP-10/FLP-17, which are expressed in the CO2-sensing BAG neuron, promote CO2 chemotaxis and nictation in dauers. These findings reveal that neuropeptides can alter decision-making and behavior during C. elegans dauer entry. Through a meta-analysis, we discovered similar up-regulation of FLPs in the dauer-like infective juveniles of diverse parasitic nematodes, suggesting that this may be an ancient mechanism for expanding the behavioral repertoire of nematodes.
Further utilizing our RNA-seq dataset, I identified several markers for conveniently tracking and manipulating the dauer entry decision. These include col-183 (which tracks dauer fate in the hypodermis), ets-10 (neurons and intestine), nhr-246 (intestine and muscle), and led-1 (reproductive fate in hypodermis). Using condition shift experiments, we demonstrate that the dauer markers label animals during dauer-commitment. We show that these markers can be used to manipulate the entry decision by driving the reproduction-promoting gene daf-9/Cytochrome P450 under the control of the dauer-commitment markers. We further demonstrate that the markers can be used to track tissue coordination and its breakdown in partial dauer mutants, and propose strategies for using the markers to identify the intercellular signals that coordinate the dauer entry decision.
I have discovered that the C. elegans dauer entry decision is more complex than previously realized, I have shown that C. elegans dauers obtain new behaviors through FLP signaling, and I have engineered tools for conveniently tracking and manipulating the dauer entry decision. My findings may illuminate how animals make robust decisions in uncertain environments, and have implications for how densely information and behaviors can be packed into a nervous system.</p
Addressing Thermodynamic Inefficiencies of Hydrogen Storage in Transition Metal Hydrides
Get PDFTransition metal hydrides (MH) are an attractive class of materials for several energy technologies. Primary benefits include their large volumetric storage capacity (often exceeding that of liquid hydrogen) and capability to absorb and desorb hydrogen for hundreds of cycles. In this thesis, we set out to understand two of the thermodynamic inefficiencies of MH: the pressure hysteresis associated with hydrogen absorption and desorption and the corrosion and dissolution of high capacity MH alloys in high pH electrolyte environments.
The volume change associated with hydriding transitions can exceed 10%, and a macroscopic nucleation barrier resulting from coherency strains has been proposed as the origin of the pressure hysteresis. We investigated this hypothesis for the palladium-hydrogen system. The hysteresis and phase transformation characteristics of bulk and nanocrystalline PdH were characterized with coupled in situ X-ray diffraction and pressure composition isotherm measurements. Size effects are observed in the total hydrogen uptake and hydrogen solubility in the hydride phases. Experimentally determined hysteresis energies were found to be comparable to the misfit strain between the Pd and PdH phases and much larger than the energy for dislocation formation. Theoretical predictions of pressure hysteresis overestimate the experimentally measured hysteresis, and we suggest methods of accommodation which could explain the discrepancy. Finally, we propose that an effect of the nucleation barrier is to split the coherent spinodal phase diagram and introduce directionally dependent phase boundaries.
We report a successful development of Ti29V62-xNi9Crx (x = 0, 6, 12) body-centered cubic (BCC) MH electrodes for MH batteries by addressing vanadium corrosion and dissolution in potassium hydroxide electrolytes. The effectiveness of a limited oxygen environment and vanadate ion addition against corrosion are compared to the effects of Cr substitution. By identifying oxygen as the primary source of corrosion and eliminating oxygen with an Ar-purged cell, the Cr-free alloy electrode achieved a maximum capacity of 594 mAh/g, double the capacity of commercial AB5 MH electrodes. With modified coin cells suppressing oxygen evolution, the cycle stability of the Ti29V62Ni9 alloy electrode was greatly improved with either vanadate ion additions to the electrolyte or Cr-substitution in the alloy. Both approaches lead to reversible capacity of 500 mAh/g for 200 cycles.</p
How Polymers Shape the Physicochemical Environment of the Gut
Get PDFThe gut is where food is digested and nutrients are absorbed, therapeutics are often delivered, and many infections take hold. The gut microbiota is in symbiosis with its host, and can influence host health and behavior. Though the gut holds these central roles, little is understood about the physics of how soft materials interact with and shape the physicochemical environment of the gut. Soft materials abound in the gut in the form of particulates (e.g., microbes, viruses, therapeutic particles, food granules) and polymers (e.g., dietary fibers, therapeutics, food additives). This thesis explores the soft matter physics of the gut and how physicochemical interactions can influence gut structure and function. This is studied through a combination of mouse experiments and numerical calculations. In the first part of this thesis, we investigate how particulates interact with polymers in the small intestine. We find that polymers from dietary fiber can aggregate particulates by a mechanism that is qualitatively consistent with depletion interactions. This mechanism is distinct from agglutination via specific chemical interactions. In the second part of this thesis, we investigate how polymers interact with the colonic mucus hydrogel. Colonic mucus is the nexus of host-microbe interactions. It is a barrier which protects against microbial infiltration, and alterations to its physical structure have been linked to changes in host health. Here, we find that polymers compress the colonic mucus hydrogel. For uncharged polymers, this mechanism can be described by a simple, mean-field model based on Flory-Huggins solution theory. Further, we find that microbes can modulate the extent of mucus compression by degrading polymers in the gut. In the last part of this thesis, we find that charged polymers (polyelectrolytes) compress mucus by a Donnan mechanism.</p
Stellar Feedback, AGN Feedback and Fluid Microphysics in Galaxy Evolution
Get PDFUnderstanding how the baryonic physics affects the formation and evolution of galaxies is one of the most critical questions in modern astronomy. Significant progress in understanding stellar feedback and modeling them explicitly in simulations have made it possible to reproduce a wide range of observed galaxy properties. However, there are still various pieces of missing physics and uncertainties in galaxies of different mass range.
In this thesis, I will explore these missing pieces in baryonic physics on top of the Feedback in Realistic Environments (FIRE) stellar feedback in the cosmological hydrodynamic zoom-in simulations (FIRE-2 suite) and isolated galaxy simulations. These high-resolution simulations with FIRE physics capture multi-phase realistic interstellar medium (ISM) with gas cooling down to 10K, and star formations in dense clumps in giant molecular clouds. They are, therefore, an ideal tool for investigating the missing pieces in baryonic physics.
In the first part of the thesis, Chapter 2, I will focus on the discrete effects of stellar feedback like individual supernovae, hypernovae, and initial mass function (IMF) sampling in dwarfs (109-1010 M⊙). These discrete processes of stellar feedback can have maximum effects on the small galaxies without being averaged out. I will show that the discretization of supernovae (SNe) is absolutely necessary, while the effects from IMF sampling and hypernovae (HNe) is not apparent, due to the strong clustering nature of star formation.
In the second part of the thesis, Chapter 3-4, I will focus on fluid microphysics, exploring their effects on galaxy properties and their interplay with stellar feedback in sub-L* galaxies. I will demonstrate that, once the stellar feedback is explicitly implemented as FIRE stellar feedback model, fluid microphysics such as magnetic fields, conduction, and viscosity only have minor effects on the galaxy properties like star formation rate (SFR), phase structure, or outflows. Stellar feedback also strongly alters the amplifications and morphology of the magnetic fields, resulting in much more randomly-oriented field lines. However, despite the stellar feedback, the amplification of magnetic fields in ISM gas is primarily dominated by flux-freezing compression.
In the final part of my thesis, I focus on the massive cluster ellipticals of 1012-1014 M⊙, where the physical mechanisms that regulate the observation-inferred cooling flows are highly uncertain -- the classic "cooling flow problem". I showed that solutions in the literature not associated with an active galactic nucleus (AGN), including stellar feedback, the cosmic ray from stellar feedback, magnetic fields, conduction, and morphological quenching, cannot possibly quench the galaxies, mostly because of the insufficient energy and the limited size of the affected region. After ruling out the non-AGN feedback solutions to the cooling flow problem, I will go into the most accessible, and perhaps promising solution: "AGN feedback", exploring the generic classes of AGN feedback models proposed in the literature. I am going to show that enhancing turbulence and injecting cosmic ray are probably the most important aspects of AGN feedback in galaxy quenching. Since they provide non-thermal pressure support that stably suppresses the core density, they can stably reduce the cooling flows without overheating the galactic cores.</p
Understanding How People Make Trait Attributions from Faces
Get PDFThis thesis is motivated by the fascinating question of how people make inferences about others from their faces. How do we infer somebody’s intent or personality merely from looking at them? I studied this question by investigating how people make trait attributions in two specific contexts -- political election (Chapter 2) and political corruption (Chapter 3) -- as well as how people make a large variety of trait attributions from faces in general (Chapter 4). I employed novel methods to representatively sample the words used to rate faces, and to select the facial stimuli themselves (e.g., using artificial neural networks), to test the reproducibility and generalizability of my results (e.g., pre-registration, generalization across participants from different cultures), and to elucidate the underlying mechanisms (e.g., mediation modeling, digital manipulation of facial stimuli). The results demonstrated that trait attributions from politician’s faces were associated with real election outcomes in different cultures, and that culture shaped trait attributions relevant to a given context (Chapter 2); trait attributions from politician’s faces were also associated with real corruption/violation records of the politicians, and perceived corruptibility was associated with the width of the face (Chapter 3). Trait attributions from faces in general (Chapter 4) were well-described by four novel dimensions that I discovered: critical/condescending, leadership/competence, female-stereotype, and youth-stereotype. Taken together, the findings provide a new psychological framework for trait attributions, demonstrate cross- cultural generalizability, and link trait attributions to real-world behaviors.</p
Surviving Quantum Chaos: Weak Thermalization, Prethermalization and Quantum Many-Body Scar States
Get PDFQuantum chaos and the eigenstate thermalization hypothesis are based on the assumption of the validity of random matrix theory description on the spectrum and eigenstates. They provide the foundation and descriptions for the typical dynamics and thermalization in generic closed quantum systems. In this thesis, we investigate situations where the systems show atypical dynamics or anomalous thermalization, conflicting with the usual expectations from quantum chaos and eigenstate thermalization hypothesis.
We first examine weak thermalization in a nonintegrable spin chain. The system shows long-lived strong oscillations and relaxes to the thermal equilibrium weakly. We identify the dynamics describable by quasiparticles and recognize the oscillation frequency to be the quasiparticle mass gap. We also estimate the damping time for the oscillations.
Next, we study prethermalization, a phenomenon where a system relaxes to an intermediate almost-equilibrium stage before reaching the true thermal equilibrium. We study a nonintegrable spin chain in the strong coupling limit, where an almost-conserved quantity emerges and gives rise to the prethermalization.
We also study a newly proposed diagnostic for quantum chaos: out-of-time-ordered correlators. Contrasting to the chaotic systems, we inspect their behaviors in various noninteracting integrable models.
Finally, we dig into the quantum many-body scar states in the PXP model which describes a Rydberg atom chain. These special states do not satisfy the random matrix theory description nor the eigenstate thermalization hypothesis, therefore defying quantum chaos
Oceanic Bottom Boundary Layers and Abyssal Overturning Circulation
Get PDFThe vast amount of carbon and heat exchange between the abyssal and upper ocean and subsequently the atmosphere is paced by the abyssal overturning circulation. A key component of the abyssal overturning circulation is the formation and consumption of the densest water mass on Earth, Antarctic Bottom Water (AABW), namely the conversion of North Atlantic Deep Water (NADW) to AABW and the consumption of AABW via small-scale diapycnal mixing. Yet, this pathway of AABW spanning thousands of kilometers has not been successfully reproduced in large-scale general circulation models (GCM). What is missing is essentially the understanding and resolution of small-scale physics involved in converting deep and bottom waters from one density class to another, the water mass transformation (WMT). In this thesis, we focus on small-scale (both in the horizontal and vertical directions) dynamics near the BBL, where enhanced shear, mixing and turbulence exist to facilitate effective WMT above the seafloor.
From high-resolution ocean glider observations around Antarctica, we find that a portion of Lower Circumpolar Deep Water, a branch of NADW, becomes lighter via mixing with light shelf water over the continental slope and shelf, instead of being converted into dense AABW under sea ice. This mixing is likely induced by submesoscale symmetric instability coming from a strong boundary current interacting with the sloping topography in the BBL. We then consider how to sustain the consumption of AABW in the global mid-ocean ridge system. Using numerical models, we show that submesoscale baroclinic eddies are crucial to maintaining strong stratification over the flanks of the mid-ocean ridges and thus permitting effective WMT. Lastly, we consider the interaction between external mean flows and stratified BBL over sloping topography. With the large-scale turbulence resolved in a large-eddy simulation model, we propose a new theoretical framework to describe the evolution of the BBL and the Eulerian advection of its associated stratification when external barotropic flows are present. This new framework can be used to parameterize bottom friction, important for closing the kinetic energy budget of the global ocean. We further extend this interaction to a horizontally-sheared and temporally-oscillating external mean flow and explore the response of the BBL and the BBL-interior mass exchange with simple turbulent parameterizations.
Using a combination of different approaches, we confirm that the long-overlooked oceanic BBL is the key location for closing the abyssal overturning circulation. More importantly, without appropriate techniques to tackle the currently unresolved small-scale processes, they will likely remain a narrow bottleneck in understanding the abyssal overturning circulation.</p
Taming the Molecular Dance: Harnessing Statistical Mechanics to Quantitatively Characterize Allosteric Systems
Get PDFThe pace of biological research continues to grow at a staggering pace as high-throughput experimental techniques rapidly increase our ability to sequence DNA, quantify cell behavior, and image molecules of all types within the cellular milieu. Given this surge in experimental prowess, the time is ripe to examine how well our conceptual cartoons of biological phenomena can not only recapitulate the data but also successfully predict the outcomes of future experiments.
One of the fundamental challenges in biology is that the space of possible molecules is overwhelmingly large. The number of variants of a moderately-sized protein (20^300) is larger than the number of atoms in the universe, as is the space of possible bacterial genomes, protein interaction networks, and effector functions; progress in any of these fronts requires a theory-experiment dialogue that can extrapolate our small drop of data to explain large swaths of parameter space.
My thesis strives towards this goal by analyzing a number of central molecular players in biology including enzymes (biological catalysts that accelerate chemical reactions), transcription factors (proteins that bind to DNA and regulate its expression), and ion channels (signaling proteins that regulate ion transport). I develop a quantitative description in each context by harnessing the statistical mechanical Monod-Wyman-Changeux model of allostery which coarse-grains the behavior of a multi-state system into two effective states, demonstrating that these seemingly diverse molecules are all governed by the same fundamental equation.
Writ large, there are two overarching goals encompassed by these projects. The first is to translate our biological knowledge into concrete physical models, enabling us to quantitatively describe how the key molecular components in each system interact to carry out their function. The second goal is to analyze how mutations can be mapped into the fundamental biophysical parameters governing each system. In my opinion, predicting the effects of mutations remains one of the great unsolved problems in biology, and it has been incredibly exciting to make progress on this front.
Looking back at my amazing graduate school experience, one of the most surprising aspects of my PhD was how closely each of my projects revolved around experiments. I entered graduate school as a theoretical physicist expecting to work on esoteric mathematical models, yet the direct connection with data provided a window into the exhilarating world of biology. While I have never physically manipulated these biological systems in the lab, my models allow me to push and prod and examine their behavior from the most mundane to the utterly extreme limits. Through modeling, I test our assumptions of how these systems work and tease out insights into their underlying biophysical mechanism. Most importantly, these models enable me to harness the incredible wealth of hard-won data to weave a few more threads of understanding into our tapestry of how these incredible living systems operate.</p