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Determining How Biophysical Cues Regulate the Myofibroblast Differentiation of Corneal Keratocytes
No full textFollowing traumatic injury or refractive surgery, corneal wound healing can initiate a fibrotic
response which can lead to a decrease in ocular function. This fibrosis is due to, in part, the
differentiation of quiescent corneal keratocytes into mechanically active myofibroblasts. Signaling
downstream of transforming growth factor beta 1 (TGF-β1) has been shown to be a key regulator
of this transformation. Myofibroblast differentiation is characterized by an increase is contractility
and secretion of unorganized extracellular matrix (ECM) proteins, which can disrupt the
organization of the stroma’s highly-aligned ECM structure and lead to corneal hazing. Past works
have shown that ECM stiffness can modulate keratocyte behaviors; however, the biophysical cues
that guide these changes are still unclear. Here, to better understand how ECM stiffness can
modulate keratocyte behavior in response to TGF- β1, we fabricated soft (1 kPa) or stiff (10 kPa)
polyacrylamide gels, functionalized with unpolymerized collagen I, to mimic normal or fibrotic
corneal tissue. Harvested rabbit corneal keratocytes (NRKs) were then plated on these substrata or
collagen-coated glass coverslips in the presence or absence of exogenous TGF-β1 with or without
pharmacological inhibitors for either contractility (blebbistatin) or focal adhesion assembly (PF-
573228). After 5 days of culture, cells were fixed and stained for molecular markers of
myofibroblast differentiation (α-SMA), contractility (pMLC), focal adhesion formation (vinculin),
or TGF-β1 signaling (pSmad3). In other experiments, polystyrene microspheres were embedded
within the gels to preform traction force microscopy (TFM). Results from these in vitro
experiments show that when cultured in serum-free media regardless of substratum stiffness or the
addition of inhibitors, NRKs exhibited morphologies characteristic of quiescent keratocytes,
exerted low contractile forces with negligible levels myofibroblast differentiation, and focal
adhesions were observed to be small, few and localized at the tips of cellular extensions. When
NRKs were cultured in the presence of TGF-β1 without inhibitors, NRKs on stiff PA gels or
collagen-coated glass coverslips displayed phenotypes typical of a myofibroblast differentiation:
broad morphologies, increased numbers α-SMA-positive cells, increased contractility
corresponding with large, abundant focal adhesions. On softer substrata, cells exhibited a more
quiescent phenotype displaying long dendritic processes, less myofibroblast differentiation,
decreased contractility and small focal adhesions localized at the tips of cellular extensions. The
use of pharmacological inhibitors targeted the phosphorylation of non-muscle myosin light chain
or focal adhesion kinase (FAK) significantly reduced stiffness-dependent differences in
contractility and morphology. Treatment with FAK inhibitor also resulted in a significant decrease
in myofibroblast differentiation and striking changes in subcellular patterning and size of focal
adhesions. In other experiments, lamellar constructs were made by sandwiching FBS- or TGF-β1-
treated NRKs between functionalized soft or stiff PA gels. In lamellar constructs of varying
stiffness, FBS-induced fibroblasts remained viable and exerted relatively equal peak contractile
stresses on both top and bottom substrates of varying stiffness. pSMAD3 nuclearization was
observed in nearly all TGF-β1-treated NRKs cultured in the lamellar constructs regardless of ECM
stiffness. Together, these data provide insight into the potential role of ECM stiffness on the
myofibroblast differentiation of corneal keratocytes in response to TGF-β1 during wound healing
Micro-earthquake Source Characterization With Full-wavefield Imaging, Uncertainty Analysis, and Deep-learning
No full textMicroseismic events are very weak earthquakes that occur at very small spatial scales, either natural or induced by man-made changes to the in-situ stress conditions of the earth’s
interior. This induced seismicity or induced earthquakes can be used to monitor fluid and
pressure fronts, characterize reservoirs (oil and gas, geothermal resource, CO2 storage, etc.),
and help optimize production. However, if the increasing fluid pressure pushes a fault or
fracture closer to failure, it can trigger larger and sometimes felt earthquakes. In this sense,
correctly locating micro-earthquakes events in or near the reservoir help improve reservoir
characterization and production recovery, and locating events near faults, especially in basement rocks, can help avoid triggering large felt earthquakes which may cause damage to
infrastructure or people.
In practice, observed arrival times of P and S wave phases are often used to locate the micro-
earthquake sources and estimate the relative source origin times. For low signal-to-noise ratio
microseismic data, or complex wave phenomena, phase picking can be inaccurate and ray-
based methods may fail to focus seismic energy at the correct source location. In terms of
source location uncertainty and resolution, how to reduce the uncertainty and enhance the
resolution based on a certain kind of earthquake source location method and incorporating
as much information as we can in the recorded waveforms is still an important research topic.
In addition, extracting useful information from the continuously-recorded microseismic data
and using these micro-earthquake events to characterize the subsurface fracture growth helps
us to understand the mechanisms of induced seismicity.
In this study, instead of using acoustic data or direct P wave arrivals only, I use elastic
multicomponent data and present a new method that uses the full P and S adjoint wavefields
to image the micro-earthquake source locations. I separate the P and S waves from the
data, and extrapolate the P and S wavefields of each receiver subarray by solving the P
and S adjoint wave equations in parallel. I formulate three source imaging conditions by
multiplying over subarrays the adjoint P wavefield, S wavefield and cross-correlated P and S
wavefields. I perform numerical experiments on the highly realistic SEG SEAM4D reservoir
model using surface acquisition array geometries. I discuss the impacts of S-wave attenuation
and frequency bandwidth on the source location images. I perform noise tests to mimic the
surface monitoring data contaminated by ambient noise. I test the source imaging results
using smoothed velocity models and provide 90% confidence ellipse of the source location
due to Gaussian-distributed velocity model errors.
Furthermore, I have developed a P- and PS-wavefront imaging method to estimate the
source origin time sequentially, which overcomes the unknown variable of source origin time
in Kirchhoff-type imaging and helps to reduce the location uncertainties originating from
the source origin time. I also develop a 3D synthetic example by finite-difference modeling
the realistic elastic 3C data using the SEG SEAM4D earth model, and jointly compare the
reservoir and basement microearthquake source location uncertainties based on traveltime
inversion, wavefront imaging and full wavefield imaging methods. For each method, we
also investigate the source location uncertainties between the P- and PS-wave results. We
compare the source location uncertainties from data noise and velocity scaling errors, as well
as the computational costs based on different imaging methods.
Finally, since many observed induced seismicity events have characteristics that are similar
to natural earthquake events dominated by shear slip across a fault plane, it would be
interesting to find out the evidence if a certain type of induced seismicity involves the direct
interaction between the injected fluid and the fracture system through which the fluid flows.
Based on a continuously-recorded real data set from a fluid injection project in Texas, I use
a 7-layer U-Net autoencoder neural network (UANN) to observe and classify two distinct
types of long-duration microseismic events which are frequency-drop long-duration (FDLD)
events and low-frequency long-duration (LFLD) events. I perform Gaussian Mixture model
clustering to label the event signals based on the latent feature vectors from the UANN.
I discuss the potential causes and applications of LFLD events using proppant injection
histories, cumulative seismic moments, and spatiotemporal evolution of microseismic event
locations
Ultrafast Charge Recombination Mechanism in Single 0D All-inorganic Perovskite Nanocrystals
No full textNanoscale semiconductors possess many attractive properties as compared to bulk counterparts. Main advantages are tunable energy levels, size-controlled carrier-carrier interactions
and, often times, facile synthesis methods offering broad possibilities in optoelectronic applications. A rigorous understanding of the elemental physical properties in these nanos-
tructures would provide deep insights for designing and improving the quality of materials.
Among many spectroscopic detection methods, single particle spectroscopy is a powerful
and sensitive tool for understanding interactions of multiple charge-carrier species in a wide
range of materials, from bulk crystals down to individual nanoparticles . In this work, we
study various types of so-called “0D” cesium-based perovskite nanocrystals, whose photo
and environmental stability has been reported to exceed the conventional 3D perovskites
nanocrystals. Due to specific, nearly complete isolation of halide octahedra in 0D structures,
their optical properties bear strong resemblance to molecular-type defects, necessitating use
of single particle detection methods. The following work concerns with perovskites’ ultrafast
charge-carrier dynamics, stability and change of photoluminescence quantum yield (PLQY)
inferred from single particle blinking signatures and modified by application of nanoscale
alumina layers via the atomic layer deposition (ALD) encapsulation
Spherically Symmetric Static Solutions in General Relativity
No full textThis thesis studies spherically symmetric static solutions in general relativity.
The most general form of matter in general relativity compatible with staticity and spherical
symmetry is anisotropic fluid. We study all possible algorithms that can generate all solutions
of the anisotropic fluid system via quadrature using all possible pairs of the four basic
functions of the system as input functions. We also study sub-algorithms that generate all
solutions that are regular at the center and, for this, we revisit the conditions for central
regularity for both isotropic and anisotropic systems and obtain all possible sets of equivalent
initial conditions for regularity by combining the Einstein equations with the previouslyknown geometric conditions of regularity. Our study provides a reformulation of an existing
algorithm for the system and provides its first regularity analysis. A surprisingly simple
new algorithm for the anisotropic system follows from our study that aligns itself with the
regularity conditions. This concordance enables us to find solutions that satisfy all the
other hard-to-achieve conditions of physical acceptability. Anisotropy has increasingly been
shown to be physically relevant in recent times. We keep the well-studied isotropic system
as a special case and use it as a frame of reference for measuring the success of our study of
the anisotropic system.
We then study the hydrostatic equilibrium of static (an)isotropic fluid spheres. From the
condition of hydrostatic equilibrium, we explore maps between (an)isotropic solutions with
the same density profiles and develop solution-generating techniques to find new solutions
from existing ones. We compare and give physical interpretations of several equilibrium
configurations in terms of fluid variables and provide several examples where the solutiongenerating theorems can be utilized to find physically acceptable anisotropic solutions. This
include a new exact solution that satisfies all physically desirable conditions.
Finally, we study light propagation in Kottler, i.e., Schwarzschild-(anti-)de Sitter, spacetime.
The metric of this spacetime is known in canonical coordinates and, unlike its Λ = 0 version
(i.e, Schwarzschild metric), this metric was not known in isotropic coordinates (in which the
constant-time hypersurfaces are flat). We obtain the Kottler metric in isotropic coordinates.
This further enables us to plot the refractive indices of Kottler spacetime and show that the
invariance of Snell’s law in ordinary geometric optics is analogous to projective equivalence
in isotropic static coordinates.
We conclude with a summary and some future directions
Alpha-diimine Nickel (II) and Palladium (II) Complexes in Cross-coupling Reactions
No full textCross-couplings reactions are the most versatile synthetic tools and extensively applied for organic
syntheses in the industrial production plants. Traditionally established cross-coupling reactions,
including Suzuki–Miyaura, have been investigated over the last two decades because of synthetic
applicability for manufacturing valuable functionalized building blocks in organic electronics,
natural products, and drug discovery. Apart from Suzuki–Miyaura carbon-carbon cross-coupling,
carbon-sulfur cross-coupling has been established as a potential synthetic method for synthesizing
biologically and pharmaceutically active compounds. Remarkably, the introduction of
heteroaromatics through carbon-sulfur cross-coupling added a new dimension to the
pharmaceutical industries. Recently, direct arylation has gained much popularity for making πconjugated monomers and polymers through carbon-carbon bond formation that is an alternative
tool to the Suzuki–Miyaura cross-coupling technique. Nonetheless, these useful synthetic
procedures are facing enormous challenges arising from the catalytic systems. A significant
portion of the catalysts employed in these cross-coupling reactions are air- and moisture-sensitive.
Moreover, thermal instability is another drawback of implementing in elevated temperature.
Notably, ligand design plays a crucial role in catalytic outcomes. The existing ligand design for
the cross-coupling reactions lacks essential features, including steric and electronic requirements.
Consequently, these shortcomings are subject to the poor catalytic performance that significantly
hinders the industrial-scale application. In this dissertation, ligand design based on α-diimine
frameworks is investigated in the Suzuki–Miyaura cross-coupling, carbon-sulfur cross-coupling,
and direct arylation methods. Both nickel and palladium complexes with α-diimine cores were
synthesized and applied to examine their potential scope in the cross-coupling reactions.
Recent advances in the nickel and palladium-based catalytic systems in the cross-coupling
reactions are described in chapter 1. In situ and well-defined nickel and palladium catalytic systems
are discussed in this chapter. Moreover, existing challenges and possible solutions are also
explained.
Chapter 2 is designed to investigate the potential application of α-diimine-based nickel (II) and
palladium (II) complexes in the Suzuki–Miyaura cross-coupling reaction. Notably, ligand design
is extensively examined for making four different complexes by varying the ligand structure and
metal center. Notably, a wide variety of substrates having challenging functional moieties are
synthesized through carbon-carbon cross-coupling.
Chapter 3 describes the synthesis and application of α-diimine-based nickel (II) and palladium (II)
complexes in the carbon-sulfur cross-coupling. Both mono- and dinuclear complexes are
synthesized and practiced for making aryl/alkyl sulfides. Mostly, pharmaceutically relevant
heteroaryl moieties both from thiols and aryl halides are coupled.
Chapter 4 is dedicated to examining the α-diimine-based nickel (II) and palladium (II) complexes
in making valuable functionalized π-conjugated monomers through the direct arylation method.
Mainly, five-membered heteroaromatics, including thiazole and thiophene derivatives, are applied
with a wide variety of aryl halides. Moreover, the findings propose that α-diimine-based
complexes can deliver direct arylation as an alternative technique to the carbon-carbon bond
formation through Suzuki–Miyaura cross-coupling
Beyond Tiebout: Towards a Theory of Philanthropic Engagement in Education in Local Communities
No full textPhilanthropy has been a central component of the American experiment since its inception, and
philanthropic concern with education continues to be a central and accelerating theme among
national and local philanthropies. Scholarly study of philanthropy in the context of education
finance and student achievement is often limited to larger national foundations that attract public
scrutiny, leaving a gap in understanding influential local philanthropic entities. This dissertation
builds knowledge about local philanthropy by asking how philanthropic contributions influence
school district budgets and student achievement, and how philanthropists approach their efforts
to support and reform education. Through empirical analyses utilizing new data from the
National Center for Education Statistics, and through structured interviews with philanthropists
and philanthropic organizations who invest in education on a local scale, this dissertation finds
that philanthropic contributions are correlated with financial “extras” and with long-term student
achievement. Its core insight is the role of the relationship in mediating community consensus
around educational needs, investment strategies, and accountability mechanisms, building
towards a theory of how philanthropy engages in K-12 education at a local level
Personnel Policies, Educator Labor Markets and Student Achievement
No full textThe dissertation consists of three chapters on the impacts of personnel policies on educator labor
market outcomes and student achievements. The first two essays study effects on teachers and
students of an educational reform which dramatically alter the way how educators are evaluated
and compensated. These two papers introduce the integrated system which include two parts -
Teachers Excellence Initiative (TEI) and Principal Excellence Initiative (PEI) - and which were
introduced in the school year 2014-2015 and the school year 2012-2013, respectively. The system
links educator’s compensation with their effectiveness to improve student academic proficiency.
The goal of the school district is to bring highly effective teachers to every student to ensure their
success in the schools. By applying the regression discontinuity design (RDD) and constructing
the difference-in-discontinuities estimates, the first chapter finds that the lower salary increases
the likelihood of teacher leaving the school district. Second, receiving a lower salary because of a
lower rating shows a slightly positive effect on teacher’s subsequent performance. The second
chapter uses the method of synthetic control analysis to show that the educator reforms have a
significantly positive effect on grade 3 to 8 student math achievements. The last paper looks at the
effectiveness of principals who are believed to be an important factor to both teacher workforce
and student achievement. This chapter uses the administrative data across six states to examine
both variations in principal effectiveness and the relationship between principial effectiveness and
their pathways. It finds variation in principal effectiveness across states and that the prior
administrative or teaching experience is not related to the principal effectiveness that is measured
by the estimates of value-added
Modeling and Analysis of Stochastic Base Flow Uncertainties in Wall-bounded Shear Flows
No full textSpatially distributed dynamical systems arise in a variety of science and engineering problems
and are typically described by Partial Integro-Differential (P(I)DEs) equations. Important
examples of such systems include the wave equations, Maxwell equations, Burgers equations,
Schrodinger equations, and the Navier-Stokes equations. An appropriate way to study and
control such systems often involves the spatio-temporal analysis of linearized forms of these
equations around base profiles, which either describe a steady-state solution or a long-time
averaged mean of a simulation- or experiment-based field. In addition, deterministic or
stochastic forcing is commonly used to compensate for the neglected nonlinear terms and
evaluate the input-output features of the linearized dynamics. However, uncertainty in both
the base profile and nature of the inputs challenge the effectiveness of linearized models for
analysis and control design. Motivated by applications in the analysis and control of complex
fluid flows, this thesis demonstrates how modeling sources of stochastic base flow uncertainty
can enable physical discovery and statistical modeling of quantities of interest.
We provide an input-output framework to analyze the effect of base flow perturbations on
the stability and receptivity properties of transitional and turbulent channel flows. Such
base flow variations are modeled as persistent white-in-time stochastic excitations that enter
the linearized dynamics as multiplicative sources of uncertainty that can alter the stability of
the linearized dynamics and their receptivity to exogenous excitation. We provide verifiable
conditions for mean-square stability and study the frequency response of the flow subject
to additive and multiplicative sources of uncertainty using the solution to the generalized
Lyapunov equation. Our approach does not rely on costly stochastic simulations or adjointbased sensitivity analyses. We use our framework to uncover the Reynolds number scaling
of critically destabilizing variance levels of the base flow uncertainty, study the reliability
of numerically estimated mean velocity profiles in turbulent channel flows, and the robust
performance of a typical boundary control strategy for turbulence suppression in the wake
of parametric uncertainties. For small-amplitude base flow perturbations, we adopt a perturbation analysis to provide a computationally efficient method for computing the variance
amplification of velocity fluctuations around the uncertain base. Moreover, we study the flow
structures that are extracted from a modal decomposition of the resulting velocity covariance
matrix at energetically dominant locations of wall-parallel wavenumbers. In the final part of
this thesis, we use the developed input-output framework to evaluate the robust performance
transverse lower-wall oscillations as a flow control strategy when oscillations are subject to
imperfections in amplitude and phase. These imperfections, cause the nominally harmonic
flow control strategy to resemble a random oscillatory pattern
The Unique and Combined Impact of Mother and Child Temperamental Negative Reactivity on Mother-child Interactions: the Protective Role of Maternal Coping Strategies
No full textThe mother-child relationship can be influenced by individual characteristics of the mother and
child. Negative reactivity, a dimension of temperament, has been shown to be highly heritable,
yet research has only focused on the consequences of child negative reactivity. It is important to
understand if levels of negative reactivity are associated with displays of negative behavior in
mothers and their children, given these behaviors can be barriers to conflict resolution in familial
relationships. Additionally, it is important to understand if maternal positive coping skills may
act as a buffer between negative reactivity and negative behavior in mother-child interactions, as
these skills could offer protective benefits to the relationship. In this dissertation, I had three
principal aims. The first aim was to investigate if both maternal and child negative reactivity
would individually and jointly contribute to observed negativity in a discussion of conflict and
their associations with the type of resolution reached. The second aim was to investigate if
positive maternal coping behaviors would act as a buffer between negative reactivity and
observed negativity during a discussion of conflict. And lastly, the third aim was to identify
distinct mother-child dyads based on the negative affectivity domain of temperament, and
whether those dyad groupings had associations with observed negativity in the discussion of
conflict as well as the resolution outcomes. Participants included 189 mother-child dyads, where
the study child participant ranged in age between five and seven years old. Variable-centered
analyses were used to test the first two aims of the study and did not reveal significant
associations between mother or child negative reactivity and the observed negativity variables,
outside of the initial bivariate correlations. A person-centered approach was the focus of the third
aim and results revealed that there were two distinct mother-child negative reactivity profiles
among the study participants: a group where mothers reported moderate levels of negative
reactivity in themselves and slightly lower levels in their children (Moderate Mother/ Slightly
Low Child Negative Reactivity) and a group where mothers reported higher levels of negative
reactivity in themselves and slightly higher levels of negative reactivity in their children (High
Mother/Slightly High Child Negative Reactivity). There were no significant associations
between the dyadic reactivity groups and observed negativity in the conflict discussion.
However, a main effect emerged for the racial or ethnic group of children in these groups and the
resolution outcomes, where children that were identified as African American were more likely
to have the resolution outcome be a “win/loss” in favor of the mother when compared to children
identified as European American. Results are discussed in terms of temperament heritability and
the usefulness of person-centered analyses in conjunction with traditional variable-centered
approaches
Investigating the Functional Impacts of Tetrel Bonding in the Reaction Mechanism of Methyltransferases and Screening of Peptidomimetic Inhibitors
No full textWhile protein methyltransferases have important roles in many biological processes such as gene
regulation and RNA processing, their dysregulation has been implicated in the progression of a
number of diseases such as cancers and neurological conditions. These enzymes catalyze the
methylation of lysine and arginine residues of target proteins using the cofactor and methyl donor,
S-adenosyl methionine (SAM). A study of crystal structures of SAM-bound methyltransferases,
along with computational studies using small molecule models, have revealed the presence of a
type of non-covalent interaction termed a tetrel bond between the SAM methyl group and electron
donating atoms of the target substrate. Since the tetrel-bonded complex in methyltransferase active
site precedes the transition state in the SN2 methylation pathway, in this project it was hypothesized
that methyltransferase active site promotes the formation of the tetrel-bonded complex, which is
fundamental to the catalytic role of these enzymes. Using an optimized coupled fluorescent kinetic
assay and site-directed mutagenesis to change a tyrosine residue to a phenylalanine in the active
site of a model methyltransferase, SET7/9, a hydrogen bond which is believed to hold the tetrel-
bonded complex in the correct orientation was removed, resulting in a 15-fold decrease in enzyme
activity. Moreover, using this optimized fluorescence-based assay, ~80 peptidomimetic
compounds were screened for inhibition of SET7/9, with the most potent compound, B21-2,
having an IC50 value of 5.2 μM. Through understanding tetrel bonding and the use of lead
compounds discovered, inhibitors may be designed to exploit unique interactions yielding potent
and selective inhibitors for these enzymes