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UC Berkeley Electronic Theses and Dissertations

Cover page of Self Consistent Excited State Mean Field Theory: Development and Applications

Self Consistent Excited State Mean Field Theory: Development and Applications


In the wide spectrum of excited state quantum chemistry methods, there is no direct analogue to Hartree-Fock theory. This dissertation presents the theory and initial applications for a self consistent framework for Excited State Mean Field (ESMF) theory. This method presents a self consistent equation analogous to the Roothaan-Hall equation, that is constructed with mean-field one-electron operators. The convergence criteria is described by a commutator condition between Fock-type operators and density operators, just like in Hartree-Fock theory. Finally, this method is accelerated via direct inversion of the iterative subspace (DIIS), akin to acceleration in the ground state theory. Futhermore, this work discusses applications of ESMF to larger solvated systems, afforded by ESMF's scaling -- the method costs roughly twice the cost of a Hartree-Fock calculation. Getting an accurate physical picture of excited states in solvated systems is challenging, and the second half of this dissertation focuses on a comparative analysis of various methods, their degree of correlation, and their ability to qualitatively describe donor and acceptor regions for a charge transfer excitation. This comparison shows that ESMF can accurately describe the degree of participation of solvent water molecules in the excitation, unlike Density Functional Theory (DFT) based methods. However, when there is minimal participation from the solvent, Restricted Open-shell Kohn Sham methods fare better, indicating that the lack of correlation in ESMF prevents the method from providing a more quantitatively accurate picture. Using ESMF as a stepping rung for developing a hierarchy of excited state specific methods is a promising platform to achieve affordable excited state specific calculations.

Cover page of Learning from Justice-Oriented Teachers: The Makings and Significance of a University-Teacher Partnership Centered on Race and Housing

Learning from Justice-Oriented Teachers: The Makings and Significance of a University-Teacher Partnership Centered on Race and Housing


This dissertation tells the story of how an experiment in university-based teacher learning blossomed into a rigorous and deeply meaningful learning experience for teachers and a teacher-centered partnership between a university-based institute and a group of justice-oriented K-12 teachers. This ethnographic study followed a group of California Bay Area-based, K-12 justice-oriented teachers as they 1) learned about the racialized histories of housing in the Bay Area as well as restitution work through a university-based summer institute, and 2) as teachers implemented this content in their respective communities—both in and outside of school. As a way to highlight universities' roles in supporting justice-oriented teachers, particularly around the foundational racial justice issue of housing, this dissertation narrates the experiences of these teachers and the university-based staff involved in the university-teacher partnership. Through examining these phenomena, I make the case for supporting justice-oriented teachers' learning, and for learning from teachers in order to inform this support.

Using critical theoretical frameworks that focus on social/racial justice and transformation, this study illuminates significant topics, theoretical framings, and programmatic components that afforded powerful professional learning for teachers around issues of racial and social justice. More specifically, it provides insight into the potency of engaging teachers in what Freire (1970) calls “generative themes,” pertinent to participants’ personal and sociopolitical contexts. This dissertation brings forward the importance of addressing the generative theme of housing within teacher learning spaces, particularly as relevant to teachers’ personal lives, and as an understudied topic within such spaces. Notably, the framing of racial capitalism was resonant for teachers, pointing to the need for a racial capitalism framing in teacher learning spaces and engaging teachers in the explicit study of this theory.

The study 1) revealed teachers as expert pedagogues who benefit from rigorous content over a blueprint for teaching this content, 2) demonstrated the dynamism of teachers' creativity, and 3) showed the activist nature of justice-oriented teachers. Teachers' implementations provided insight into how they work, which furthers the field's understanding of their professional learning needs. As a study that examined the role that universities can play in meeting teachers' learning needs, this dissertation found a partnership approach to be key to such an endeavor, where core components of this work include respecting teachers’ expertise, taking an iterative approach, providing rigorous content and focusing on the experience of teachers rather than their curricular outputs, and involving former teachers as key participants. The study highlights the role that research/policy/interdisciplinary university-based institutes can play in supporting justice-oriented teachers, and the potential of these entities to positively impact and enrich teachers’ work as “transformative intellectuals” (Giroux, 1988). This study contributes to empirical research on teacher learning by offering a glimpse into one model for supporting and sustaining teachers, and, more specifically, highlights the role that universities can play in the work of supporting teachers who teach for racial and social justice.

Cover page of Control of Meiotic Entry by Dual Inhibition of the Key Mitotic Transcription Factor SBF

Control of Meiotic Entry by Dual Inhibition of the Key Mitotic Transcription Factor SBF


Transcription factors induce dynamic changes in gene expression to drive cellular differentiation. During the mitotic G1/S of budding yeast when the cell irreversibly commits to divide, transcription factors SBF(Swi4-Swi6) and MBF(Mbp1-Swi6) play essential roles by activating the expression of the G1/S transcriptome. While SBF and MBF act in parallel to mediate the mitotic G1/S transition, their regulation and function in meiosis have remained elusive. Here we characterize both the functional impact of SBF activation on meiotic entry and the molecular mechanisms restricting SBF activity in meiosis.

We first elucidated the functional significance of SBF activity restriction in meiosis and found that elevation of Swi4 protein levels was sufficient to activate SBF, resulting in mis-expression of SBF targets in meiosis. Further experimentation led us to discover that untimely SBF activation caused downregulation of early meiotic genes and delayed meiotic entry. Meiotic entry delays were caused by reduction in the function of Ime1, a master transcriptional regulator of meiosis. Among the SBF targets, G1 cyclins were the main driver of meiotic delays. We further found that G1 cyclins blocked the interaction between Ime1 and its cofactor Ume6.

We next investigated how SBF activity is restricted during meiosis and identified two parallel mechanisms: repression of the SBF-specific Swi4 subunit through LUTI-based regulation and inhibition of SBF by Whi5, a homolog of the Rb tumor suppressor. Our study provides insight into the role of SWI4LUTI in establishing the meiotic transcriptional program and demonstrates how the LUTI-based regulation is integrated into a larger regulatory network to ensure timely SBF activity.

Cover page of Some geometric methods in chromatic homotopy theory

Some geometric methods in chromatic homotopy theory


This thesis is a conglomerate of several results in algebraic topology united by the common thread of taking seriously the idea that geometric considerations can be useful for proving algebraic results in the field of chromatic homotopy theory. These results include a geometric construction of equivariant elliptic cohomology at the Tate curve, abstract derivations of the dual Steenrod algebras at all primes, and geometric presentations of higher algebraic structures.

Cover page of Embodying the Future: Modeling Visually Guided Planning as Prospective Mental Simulation

Embodying the Future: Modeling Visually Guided Planning as Prospective Mental Simulation


What would it feel like to run outside, right now, and attempt a somersault on the first surface you find? Taking seriously an invitation like this to imagine a (perhaps unlikely) future, prompts the activation of evolutionary machinery in the mind and body that took millions of years to emerge. The ability to answer this question depends upon a surprisingly complex model of yourself, the ecology you inhabit, and how you interact within it. Throughout the first several seconds of engaging with this prompt, you have likely tapped memories of a wide spatial vicinity around you, and the types of surfaces likely to be encountered. The season, today's weather, the existence of a lawn and the schedule of a sprinkler system, all brought to bear to produce simulations of the kinds of experience that might result, and the sorts of choices that might be required. Enactive and embodied views of cognition tell us that these simulated experiences are not unitary but parallel and overlapping (A. Clark, 2015), are unbound to typical temporal sequences and durations (Arnold, Iaria, & Ekstrom, 2016), and live not in your head as local neural traces, but leverage your entire body (Thompson, 2010) as you consider the sensory and motor consequences of an activity you may not have performed in quite a while, and certainly never in this particular context. These simulations are constructed under the guidance of past experiences (how fast do you typically run?), counterfactual contingencies (what if the lawn is too crowded?), and knowledge of complex causal relations and social dynamics (how would a passerby respond? what would a colleague think?).

Embodied, prospective simulations of this sort are not a rare occurrence prompted primarily by thought experiments in a thesis. They are ubiquitous in our daily experience. Our cognitive ability to predict how events may unfold in time, how the world will respond to our actions, and how our body will respond to the world, is likely one of the central, and perhaps unique (Bulley, Henry, & Suddendorf, 2016), competencies that allow members of our species to solve problems we've never before encountered, and construct, share, and run experiments on candidate actions and plans before committing to enact them.

This work focuses predominantly on the domain of spatial navigation. As a modeling target, navigation enjoys a long history in computer science, as well as the planning literature, and appears as one of four categories included in Buckner and Carrol's ontology of self-projection (Buckner & Carroll, 2007). Given its natural low-dimensional spatial state space, navigation is especially well-suited to behavioral study.

Psychologists have gathered a long list of effects outlining key features of the way we learn about and model the world. Tendencies to infer causal relations (Kushnir & Gopnik, 2005), to perceive patterns (even when none exists, e.g. Fyfe, Williams, Mason, and Pickup (2008)), to develop an intuitive understanding of physical systems (Krist, Fieberg, & Wilkening, 1993), to categorize, and hierarchically arrange novel stimuli and task environments (Collins & Frank, 2013), are all suggestive of the processes by which such a model are learned and employed. However, far less is known about the dynamics by which we navigate this internal model, its constraints and topology, or the mechanisms by which simulations traverse large spatial and temporal distances to most effectively instruct the action-oriented needs of the present. In short, we know little about the kinematics of mental simulation. I aim to pursue, then, the following claim: by studying behavior and sensory exploration during navigation, we may begin to characterize the human solution to planning in an uncertain world, and take steps towards a kinematics of prospective mental simulation---the dynamic process by which individuals embody and interact with multiple possible futures.

This work is guided by research questions that I categorize into three areas of inquiry: 1) embodied planning, 2) visual salience and simulation kinematics in navigation planning, and 3) prospection in joint planning.

Embodied planning

Questions in this area aim to explore the limits of classical approaches, and suggest avenues and opportunities to develop a more nuanced and naturalistic theory of planning in the real world. I will argue in Chapter 3 that this need to accommodate embodied dynamics---in decision-making as well as less explicitly choice-centered natural activities---requires us, as a scientific community, to develop new models better able to capture the richness of the mental processes that anticipate and drive action in the world. The reviewed work displays a range of approaches to bring embodied intelligence into communication with the classical literature on decision-making and planning. In particular, I'll develop the concept of the affordance landscape, with example applications in various naturalistic (and fundamentally embodied) tasks such as playing team sports, climbing, and crossing a river. These theoretical arguments and methodologies set a foundation for the next research area, in which a mode of embodiment particularly relevant to visual creatures like ourselves is explored.

Visual salience and simulation kinematics in navigation planning

This area captures the primary empirical questions of this dissertation, and motivates the use of an agent model designed to iteratively learn the sort of affordance landscapes discussed in Chapter 3. I'll tackle questions about attractors of visual attention, and temporal sampling dynamics, through a variety of behavioral analyses. Key findings in Chapters 4 and 5 include: the predictive relationship between planning-time biometrics and navigation-time decisions, geometric and map-geometry attributes most predictive of attention, as well as various hierarchical aspects of the sequential gaze patterns seen during planning. I also report behavioral differences between top and bottom performers in this task, which raise plausible explanations for how, and through what mechanisms, individuals differ in their spatial planning abilities.

Prospection in joint planning

In the third area of inquiry I'll look beyond the individual spatial navigation paradigm to explore the case of multiple collaborators who must, through a variety of techniques, converge on a shared strategy to jointly solve the task at hand. I propose that some of these techniques implicate a planning process driven by the simulation of (shared) counterfactual future trajectories. However, I also acknowledge the significant additional complexity that comes from introducing social interaction, even in relatively simple problem-solving paradigms, and even when verbal communication is limited. I report findings from a two-person collaborative task which suggests a history-dependence of strategy selection when task dynamics changed. Fairness (defined as the balance of effort) was found to be lower in imbalanced task environments, as well as during the more difficult blocks requiring greater partner monitoring. Finally, I find a persistent bias towards spatial separation (which likely helps avoid interaction and enhances decoupling between collaborators), even among dyads using strict color-based strategies, highlighting that non-trivial hybrid approaches which mix conventions can be productively adopted even in non-verbal collaborative settings.

This investigation of embodied prospection builds on a diverse multidisciplinary literature spanning work on mental simulation and episodic foresight in psychology, predictive processing in philosophy of mind, hippocampal preplay and internally generated sequences in neuroscience, embodied and enactive cognitive science, as well as a number of biologically inspired computational models of planning.


Building on this multidisciplinary foundation, I hope to make three contributions:

First is a conceptual extension made by projecting the body outwards into its likely future, and seeing this projection as a first class representation of the self within which simulations are continuously run. My claim is that this projection is the interface within which future-determining actions are enacted, and is therefore, in an important sense, cognitively inseparable from the individual. Furthermore, the sensorimotor patterns generated in these simulations are not fundamentally different from the inferential (and simulative) process of perception in the present, and therefore are equally constitutive of our moment-to-moment experience. Second, following Guest and Martin (2021), I propose an instantiation of this theoretical framing within a computational agent given control of a sensory apparatus similar to ours, and tasked with the same types of navigational challenges posed to the human participants in my studies. I argue that models like this one can help to achieve a unified conceptual framing of future-oriented dynamics that links both low-level predictive processing (which may operate over short temporal durations), with the kinds of dramatically extended episodic simulations typical when studying mental time travel. While a diversity of mechanisms are entailed in such a unified framework, I believe seeing these as two ends of a continuum with shared function, and more than likely, algorithmic and process-level correspondence as well.

Third, I share a series of empirical findings relating to visually guided planning and execution within spatial navigation problems. Some results are consistent with the more speculative ideas raised earlier in this section, and others highlight the remaining gaps in our understanding of the tremendously complex processes underlying visual search, prospection, and planning.

By pursuing the larger project within which this work sits, we can work towards a more nuanced understanding of the dynamics by which individuals generate and test expectations for the future. If successful, this project should help deepen our understanding of the way these prospective cognitive processes are embedded in a body, and a complex motor system, that grounds them in the world around us. If so, we may better appreciate the aspects of human intelligence that are truly unique, and defined by a complexity that is still far out of reach of replication in artificial systems. As such, perhaps our computational abilities will be better leveraged towards the design of tools personalized to individual preferences and idiosyncrasies, or even self-acknowledged oversights. Such systems may be able to externalize more legible beliefs, risks, and hypothetical futures, and by availing these to us, help enable more effective communication and collaboration. Finally, by better understanding how individuals project themselves into uncertain futures, and reason about long-term consequences, we might prepare ourselves, as a society, to more effectively face the challenges still ahead.

Cover page of Applications of Gene Editing for Improving Climate Change Resilience in Agriculture

Applications of Gene Editing for Improving Climate Change Resilience in Agriculture


Climate change imposes a severe threat to agricultural systems, food security, and human nutrition. Meanwhile, efforts in crop and livestock gene editing have been undertaken to improve performance across a range of traits. Gene editing applications for climate change specifically have converged on four major traits: nutritional quality improvement, yield enhancement, disease tolerance, and abiotic stress tolerance, with the fewest current applications directed towards abiotic stress tolerance. While only few applications of gene editing have been translated to agricultural production thus far, numerous studies in research settings have demonstrated the potential for potent gene editing based solutions to address climate change in the near future. Gene editing of rice (Oryza sativa) specifically holds promise for generating climate resilient foodscapes. Rice is of paramount importance for global nutrition, supplying at least 20% of global calories. However, water scarcity and increased drought severity are anticipated to reduce rice yields globally. Rice stomatal developmental genetics were explored as a mechanism to improve drought resilience while maintaining yield under climate stress. CRISPR/Cas9-mediated knockouts of EPFL10 and STOMAGEN yielded lines with c. 80% and 25% of wild-type stomatal density, respectively. epfl10 lines with moderate reductions in stomatal densities are able to conserve water to similar extents as stomagen lines, but do not suffer from the concomitant reductions in stomatal conductance, carbon assimilation, or thermoregulation observed in stomagen knockouts. Moderate reductions in stomatal densities achieved by editing EPFL10 may be a climate-adaptive approach in rice that can safeguard yield. Editing the paralog of STOMAGEN in other species may provide a means to tune stomatal density in agriculturally important crops beyond rice.

Negative pleiotropic effects of gene editing may be mitigated by editing a single copy of a duplicated gene underlying a trait of interest. However, this approach is limited by a narrow set of duplicated genes whose null phenotype is not deleterious to overall plant fitness. Promoter editing is emerging as an increasingly relevant tool to generate subtle trait variation while mitigating against harmful pleiotropy. We applied a multiplexed, guide design approach informed by bioinformatic analyses to generate genotypic variation in the promoter region of OsSTOMAGEN. Engineered genotypic variation corresponded to continuous variation stomatal density and size. This near-isogenic panel of stomatal variants was leveraged in physiological assays to establish discrete relationships of stomatal density with a range of gas exchange parameters. Developmental plasticity in response to vegetative drought was inhibited in some promoter alleles and in stomagen. Derived stomatal variants can be matched with similarly broad environmental conditions to optimize. Collectively our data suggest a role of promoter editing as a tool for establishing trait variation including phenotypic gain-of-function that can be leveraged for establishing relationships of anatomy and physiology and for crop improvement along diverse environmental clines.

In securing food systems against the severe implications of climate change, gene editing approaches towards the adaptation of rice to abiotic stress has shown promise. An additional approach makes use of gene editing for improving crop quality in crops with existing tolerance. To this end, we sought to improve the safety of the drought-stress-tolerant cassava crop, for human consumption using CRISPR/Cas9. Cassava accumulates cyanogenic glucosides which are human-toxic-metabolites that must be removed to avoid severe human health consequences. Cyanogenic glucosides may play an important physiological role in cassava plants, so eliminating their synthesis entirely may also limit overall productivity. Our work sought to engineer tissue specific accumulation of cyanogenic glucosides by editing, MeCGTR1, a putative systemic transporter using CRISPR/Cas9. cgtr1 lines exhibited depletions of cyanogenic glucosides in upper leaves while maintaining wild-type levels in tuberous roots. Together with a phloem girdling assay, our data indicated a root-to-shoot mode of cyanogenic transport which stands in contrast to previously documented modes of detected movement. Our work provides the first in-vivo validation of a cyanogenic glucoside transporter in cassava providing evidence for the de novo biosynthesis of cyanogenic glucosides in roots.

Cover page of Detection of waves in the Earth’s outer core using geomagnetic data-driven techniques

Detection of waves in the Earth’s outer core using geomagnetic data-driven techniques


Short-period fluctuations in the Earth’s geomagnetic field have been observed through satel- lite observations over the past 20 years. In this work, we explore the use of two data driven-techniques to quantify and interpret the short-period fluctuations. Complex empirical orthogonal functions (CEOFs) are applied to observations of the second time derivative of the geomagnetic field (secular acceleration) from several localized regions of the CHAOS6 model (Finlay et al., 2016). We found evidence of eastward and westward traveling waves with periods of 7.08 ± 0.58 and 15.73 ± 4.44 years, respectively, in the Atlantic and South Asia regions. Furthermore, we have applied dynamic mode decomposition (DMD) to investigate the temporal evolution of the radial magnetic field (Br) and secular variation (SV) at high latitudes using CHAOS7 (Finlay et al., 2020). Our results exhibit waves with periods of 19.1 and 58.4 years. A 60-year wave is compatible with prior predictions for zonal waves in a stratified fluid. The 20-year wave is consistent with previous findings at high latitudes, although the wave characteristics do not permit a simple interpretation. Finally, we study positive and negative geomagnetic acceleration patches moving westward at high latitudes. Magnetic Rossby waves offer one possible interpretation of the observations. This type of waves can account for the propagation direction and phase velocity. However, the predicted spatial pattern of the magnetic field variation is more complex than the observations. Zonal MAC waves, however, can explain the observed field with a stratified layer at the core’s top. In conclusion, these results are significant for comprehending the dynamics of the geomagnetic field and its impact on the Earth’s outer core structure.

Cover page of Deciphering Mechanisms of Early Meiotic Gene Expression Through Ume6 and Ime1

Deciphering Mechanisms of Early Meiotic Gene Expression Through Ume6 and Ime1


The process of gametogenesis is orchestrated by a dynamic gene expression program, where a vital subset constitutes the early meiotic genes (EMGs). In budding yeast, the transcription factor Ume6 represses EMG expression during mitotic growth. However, during the transition from mitotic to meiotic cell fate, EMGs are activated in response to the transcriptional regulator Ime1 through its interaction with Ume6. While it is known that binding of Ime1 to Ume6 promotes EMG expression, the mechanism of EMG activation remains elusive. Two competing models have been proposed whereby Ime1 either forms an activator complex with Ume6 or promotes Ume6 degradation. Here, we resolve this controversy using a combination of depletion and tethering strategies to functionally characterize both Ume6 and Ime1 (Chapter 2 and Chapter 3).

Much of the research surrounding Ume6 function, and the genes it regulates, has come from using a null allele (ume6∆). Accordingly, constitutive loss of UME6 function leads to derepression of several meiosis specific genes during mitosis. Expression of these meiotic genes during the mitotic cell cycle causes conflicts in cellular machinery and leads to pleiotropic consequences. Instead of ume6∆ to assess UME6 function, here we leverage the auxin inducible degron (AID) system to construct a depletable allele of UME6 (Ume6-AID). This allele of UME6 maintains repression of its targets during the mitotic cell cycle. Using this approach, we identify the set of genes that are directly regulated by Ume6, including UME6 itself (Chapter 2).

With the development of Ume6-AID, we next investigated the functional relationship between Ume6 and Ime1 by combining our Ume6-AID with a method of synchronizing expression for IME1, which encodes the meiotic transcription factor, and IME4, which encodes an mRNA N6-adenosine methyltransferase (Chapter 3). This increased control allowed careful monitoring of how Ume6 responds to IME1 and IME4 expression and allowed functional dissection of Ume6’s role in the mechanism of early meiotic gene (EMG) expression. We find that, while Ume6 protein levels increase in response to Ime1, Ume6 degradation occurs much later in meiosis, in a manner dependent on another meiotic transcription factor called Ndt80. Importantly, we found that depletion of Ume6 shortly before meiotic entry is detrimental to EMG activation and gamete formation. Finally, to explore the functional role of Ime1 in EMG expression, we employed a tethering strategy. We find that tethering of Ume6 to a heterologous activation domain is sufficient to trigger EMG expression and produce viable gametes in the absence of Ime1. These data indicate that Ime1 and Ume6 form an activator complex in meiosis. While Ume6 is indispensable for EMG expression, Ime1 primarily serves as a transactivator for Ume6.

This dissertation unifies observations from two disparate models involving Ime1 and Ume6 and their involvement in meiotic initiation. Our work unveils the impact Ime1 has on Ume6 through its binding to Ume6 and how this influences EMG expression. In doing so we elevate Ume6 to a primary determinant of cell state through its exchange of transcriptional cofactors and significantly advance our understanding of meiotic gene regulation.

Cover page of Development of Site-Selective Protein and Peptide Modification Strategies

Development of Site-Selective Protein and Peptide Modification Strategies


The goal of protein modification is to take advantage of the structural complexity and bindingspecificity of a protein and pair it with the additional properties that a synthetic molecule can provide. Many strategies have been developed that target native amino acids present on the protein surface, such as lysine, but these modification methods tend to produce heterogeneous mixtures of products since there are often multiples copies of the residue displayed. To better control the level of modification, the N-terminus has become a popular target since each protein has only one. Our lab has recently developed an N-terminal modification strategy that uses 2-pyridinecarboxaldehyde (2PCA) to form an imidazolidine product. The reaction proceeds through an imine intermediate, which is then cyclized with the second amino acid residue to form the product. The reaction can be performed with all 20 native amino acids at the N-terminus, and high levels of conversion can be obtained. Despite this generality, we have found that over time the imidazolidinone conjugate with 2PCA can reverse to liberate the free, unmodified protein, and that the rate of reversal is dependent on the identity of the N-terminal residue. To better understand the factors that influence product stability, we undertook a mechanistic study of the reaction, using NMR kinetics and DFT calculations, to explore the most likely pathway leading to product formation. Through these studies, we found that N-terminal proline residues create the most stable product, and that glycine at position two can also have a secondary stabilizing effect. DFT calculations supported these findings and allowed for structural analysis of the reactive species and transition states that contributed to this stabilization. With a better understanding of how the reaction proceeds, future goals will be toward the development of 2PCA derivatives that can capitalize on these effects to form irreversible conjugates.

In addition to N-terminal modification, our lab has also developed several methods forsite-selective tyrosine modification using a tyrosinase enzyme. Tyrosinase is able to oxidize the phenol of tyrosine to a reactive quinone intermediate, which can then be captured by a variety of nucleophiles. Our goal was to use this chemistry and apply it toward the synthesis of cyclic peptides. We have demonstrated that linear peptides bearing a tyrosine and cysteine residue are able to be oxidized with tyrosinase, and the subsequently formed quinone can be coupled with the cysteine thiol to form a cyclic product. In addition to peptide substrates, we have also demonstrated that this chemistry works on peptide sequences displayed at the N- or C-terminus of a protein. Initial work has shown that the level of tyrosinase activity and selectivity is heavily influenced by the identity of the amino acids next to the tyrosine residue, and future work will be focused on engineering new tyrosinase variants that are less sequence dependent.

Cover page of Atmospheric Rivers: Genesis, Representation, and Structure

Atmospheric Rivers: Genesis, Representation, and Structure


The goal of this dissertation is to advance atmospheric river (AR) research in 3 distinct areas: (i) genesis of ARs, (ii) model representation of ARs, and (iii) the impact of AR core structure on landfalling precipitation.In Chapter 2, the range of synoptic patterns that north Pacific landfalling ARs form under are objectively identified using genesis day 500 hPa geopotential height anomalies in a self- organizing map (SOM). The SOM arranges the synoptic patterns to differentiate between two groups of climate modes - the first group with ENSO (El Nin ̃o Southern Oscillation), PDO (Pacific Decadal Oscillation), PNA (Pacific North American) and NP (North Pacific index) and the second group with AO (Arctic Oscillation), EPO (East Pacific Oscillation), and WPO (West Pacific Oscillation). These two groups have their positive and negative modes organized in opposite corners of the SOM. The ARs produced in each of the syn- optic patterns have distinct lifecycle characteristics (such as genesis and landfall location, duration, velocity, meridional/zonal movement) and precipitation impacts (magnitude and spatial distribution). The conditions that favor AR trajectories closer to the tropics tend to produce higher amounts of precipitation. The large-scale circulation associated with AR genesis shows a close relationship between the genesis location and the location and intensity of the upper level jet in the west/central pacific as well as anomalous, low level southwesterly winds in the east pacific. Chapter 3 focuses on evaluating The Energy Exascale Earth System Model (E3SM) version v1.0 for its ability to represent ARs, which play significant roles in water vapor transport and precipitation. The E3SM Project is an ongoing, state-of-the-science Earth system modeling, simulation, and prediction project developed by the U.S. Department of Energy (DOE). With an emphasis on supporting DOE’s energy mission, understanding and quantifying how well the model simulates water cycle processes is of particular importance. The characteristics and precipitation associated with global ARs in E3SM at standard resolution (1◦ x 1◦) are compared to the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA2). Global patterns of AR frequencies in E3SM show high degrees of correlation (>=0.97) with MERRA2 and low mean absolute errors (<1 %) annually, seasonally, and across different ensemble members. However, some large-scale condition biases exist leading to AR biases - most significant of which are: the double-ITCZ, a stronger and/or equatorward shifted subtropical jet during boreal and austral winter, and enhanced northern hemisphere westerlies during summer. By comparing atmosphere-only and fully-coupled simulations, we attribute the sources of the biases to the atmospheric component or to a coupling response. Using relationships revealed in Dong et al., 2021, we provide evidence showing the stronger north Pacific jet in winter and enhanced northern hemisphere westerlies during summer associated with E3SM’s double-ITCZ and related weaker AMOC, respectively, are significant sources of the AR biases found in the coupled simulations. In Chapter 4, we explore how the vertical structure of ARs - specifically the core (the area of the strongest moisture transport) of an AR - can influence precipitation on the west coast states of the U.S.. The relationship between moisture transport intensity and precipitation impacts for ARs is currently well established. While vertically integrated moisture transport (IVT) is the most significant predictor in the intensity of precipitation for landfalling ARs, other aspects remain understudied. In this chapter, we find that the height of the AR core - defined as the height of the moisture flux maximum - can cause significant differences in precipitation even when controlling for IVT strength. Depending on the AR core height and the landfall terrain height, precipitation influences are varied. We find ARs with low (1000 - 950 hPa) core heights have enhanced precipitation over all terrain heights, ARs with medium heights (950 - 900 hPa) generally have reduced precipitation but particularly so over elevated terrain, and high (< 900 hPa) core heights deliver more precipitation to elevated terrain and into the interior of the U.S.. Looking at trends over the last 4 decades, the AR core height means are shifting to slightly higher altitudes with greater variance - i.e. low and high AR core heights will become more frequent while medium core heights become less frequent. In order to carry out the analysis on the AR core, we developed a novel algorithm used to identify AR sectors (core, cold sector, and warm sector) using IVT and geometric constraints. We compare characteristics of these detected sectors in 41 years of reanalysis data to recent dropsonde observations and find agreement in key characteristics for all sectors although there are lower moisture flux and windspeed values in the cold and warm sector due to threshold differences and reanalysis biases.