Using space geodesy to constrain variations in seismogenic behavior on subduction megathrusts

The concept of seismogenic asperities and aseismic barriers has become a useful paradigm within which to understand the seismogenic behavior of major faults. Since asperities and barriers can be thought of as defining the potential rupture area of large megathrust earthquakes, it is thus important to identify their respective spatial extents, constrain their temporal longevity, and to develop a physical understanding for their behavior. Space geodesy is making critical contributions to the identification of slip asperities and barriers but progress in many geographical regions depends on improving the accuracy and precision of the basic measurements. This thesis begins with technical developments aimed at improving satellite radar interferometric measurements of ground deformation whereby we introduce an empirical correction algorithm for unwanted effects due to interferometric path delays that are due to spatially and temporally variable radar wave propagation speeds in the atmosphere. In chapter 2, I combine geodetic datasets with complementary spatio-temporal resolutions to improve our understanding of the spatial distribution of crustal deformation sources and their associated temporal evolution – here we use observations from Long Valley Caldera (California) as our test bed. In the third chapter I apply the tools developed in the first two chapters to analyze postseismic deformation associated with the 2010 Mw=8.8 Maule (Chile) earthquake. The result delimits patches where afterslip occurs, explores their relationship to coseismic rupture, quantifies frictional properties associated with inferred patches of afterslip, and discusses the relationship of asperities and barriers to long-term topography. The final chapter investigates interseismic deformation of the eastern Makran subduction zone by using satellite radar interferometry only, and demonstrates that with state-of-art techniques it is possible to quantify tectonic signals with small amplitude and long wavelength. Portions of the eastern Makran for which we estimate low fault coupling correspond to areas where bathymetric features on the downgoing plate are presently subducting, whereas the region of the 1945 M=8.1 earthquake appears to be more highly coupled.

A genetic and biochemical analysis of pre-mRNA splicing in Saccharomyces cerevisiae

Pre-mRNA splicing requires interaction of cis- acting intron sequences with trans -acting factors: proteins and small nuclear ribonucleoproteins (snRNPs). The assembly of these factors into a large complex, the spliceosome, is essential for the subsequent two step splicing reaction. First, the 5' splice site is cleaved and free exon 1 and a lariat intermediate (intron- exon2) form. In the second reaction the 3' splice site is cleaved the exons ligated and lariat intron released. A combination of genetic and biochemical techniques have been used here to study pre-mRNA splicing in yeast.

Yeast introns have three highly conserved elements. We made point mutations within these elements and found that most of them affect splicing efficiency in vivo and in vitro, usually by inhibiting spliceosome assembly.

To study trans -acting splicing factors we generated and screened a bank of temperature- sensitive (ts) mutants. Eleven new complementation groups (prp17 to prp27) were isolated. The four phenotypic classes obtained affect different steps in splicing and accumulate either: 1) pre-mRNA, 2) lariat intermediate, 3) excised intron or 4) both pre-mRNA and intron. The latter three classes represent novel phenotypes. The excised intron observed in one mutant: prp26 is stabilized due to protection in a snRNP containing particle. Extracts from another mutant: prpl8 are heat labile and accumulate lariat intermediate and exon 1. This is especially interesting as it allows analysis of the second splicing reaction. In vitro complementation of inactivated prp18 extracts does not require intact snRNPs. These studies have also shown the mutation to be in a previously unknown splicing protein. A specific requirement for A TP is also observed for the second step of splicing. The PRP 18 gene has been cloned and its polyadenylated transcript identified.

Optimal design of building structures using genetic algorithms

A general framework for multi-criteria optimal design is presented which is well-suited for automated design of structural systems. A systematic computer-aided optimal design decision process is developed which allows the designer to rapidly evaluate and improve a proposed design by taking into account the major factors of interest related to different aspects such as design, construction, and operation.

The proposed optimal design process requires the selection of the most promising choice of design parameters taken from a large design space, based on an evaluation using specified criteria. The design parameters specify a particular design, and so they relate to member sizes, structural configuration, etc. The evaluation of the design uses performance parameters which may include structural response parameters, risks due to uncertain loads and modeling errors, construction and operating costs, etc. Preference functions are used to implement the design criteria in a "soft" form. These preference functions give a measure of the degree of satisfaction of each design criterion. The overall evaluation measure for a design is built up from the individual measures for each criterion through a preference combination rule. The goal of the optimal design process is to obtain a design that has the highest overall evaluation measure - an optimization problem.

Genetic algorithms are stochastic optimization methods that are based on evolutionary theory. They provide the exploration power necessary to explore high-dimensional search spaces to seek these optimal solutions. Two special genetic algorithms, hGA and vGA, are presented here for continuous and discrete optimization problems, respectively.

The methodology is demonstrated with several examples involving the design of truss and frame systems. These examples are solved by using the proposed hGA and vGA.

Origin of Th/U variations in chondritic meteorites

Isotope dilution thorium and uranium analyses of the Harleton chondrite show a larger scatter than previously observed in equilibrated ordinary chondrites (EOC). The linear correlation of Th/U with 1/U in Harleton (and all EOC data) is produced by variation in the chlorapatite to merrillite mixing ratio. Apatite variations control the U concentrations. Phosphorus variations are compensated by inverse variations in U to preserve the Th/U vs. 1/U correlation. Because the Th/U variations reflect phosphate ampling, a weighted Th/U average should converge to an improved solar system Th/U. We obtain Th/U=3.53 (1_-mean=0.10), significantly lower and more precise than previous estimates.

To test whether apatite also produces Th/U variation in CI and CM chondrites, we performed P analyses on the solutions from leaching experiments of Orgueil and Murchison meteorites.

A linear Th/U vs. 1/U correlation in CI can be explained by redistribution of hexavalent U by aqueous fluids into carbonates and sulfates.

Unlike CI and EOC, whole rock Th/U variations in CMs are mostly due to Th variations. A Th/U vs. 1/U linear correlation suggested by previous data for CMs is not real. We distinguish 4 components responsible for the whole rock Th/U variations: (1) P and actinide-depleted matrix containing small amounts of U-rich carbonate/sulfate phases (similar to CIs); (2) CAIs and (3) chondrules are major reservoirs for actinides, (4) an easily leachable phase of high Th/U. likely carbonate produced by CAI alteration. Phosphates play a minor role as actinide and P carrier phases in CM chondrites.

Using our Th/U and minimum galactic ages from halo globular clusters, we calculate relative supernovae production rates for ²³²Th/²³⁸U and ²³⁵U/²³⁸U for different models of r-process nucleosynthesis. For uniform galactic production, the beginning of the r-process nucleosynthesis must be less than 13 Gyr. Exponentially decreasing production is also consistent with a 13 Gyr age, but very slow decay times are required (less than 35 Gyr), approaching the uniform production. The 15 Gyr Galaxy requires either a fast initial production growth (infall time constant less than 0.5 Gyr) followed by very low decrease (decay time constant greater than 100 Gyr), or the fastest possible decrease (≈8 Gyr) preceded by slow in fall (≈7.5 Gyr).

Molecular genetic studies on voltage-gated ion channels

Several different methods have been employed in the study of voltage-gated ion channels. Electrophysiological studies on excitable cells in vertebrates and molluscs have shown that many different voltage-gated potassium (K⁺) channels and sodium channels may coexist in the same organism. Parallel genetic studies in Drosophila have identified mutations in several genes that alter the properties of specific subsets of physiologically identified ion channels. Chapter 2 describes molecular studies that identify two Drosophila homologs of vertebrate sodium-channel genes. Mutations in one of these Drosophila sodium-channel genes are shown to be responsible for the temperature-dependent paralysis of a behavioural mutant para^ts. Evolutionary arguments, based on the partial sequences of the two Drosophila genes, suggest that subfamilies of voltage-gated sodium channels in vertebrates remain to be identified.

In Drosophila, diverse voltage-gated K⁺ channels arise from alternatively spliced mRNAs generated at the Shaker locus. Chapter 3 and the Appendices describe the isolation and characterization of several human K⁺-channel genes, similar in sequence to Shaker. Each of these human genes has a highly conserved homolog in rodents; thus, this K⁺-channel gene family probably diversified prior to the mammalian radiation. Functional K⁺ channels encoded by these genes have been expressed in Xenopus oocytes and their properties have been analyzed by electrophysiological methods. These studies demonstrate that both transient and noninactivating voltage-gated K⁺ channels may be encoded by mammalian genes closely related to Shaker. In addition, results presented in Appendix 3 clearly demonstrate that independent gene products from two K⁺-channel genes may efficiently co-assemble into heterooligomeric K⁺ channels with properties distinct from either homomultimeric channel. This finding suggests yet another molecular mechanism for the generation of K⁺-channel diversity.

I. The effects of variations in certain parameters upon the efficiency of in vivo hemodialysis with a Kiil dialyzer. II. Interfacial structure of concurrent air-water flow in a two-inch diameter horizontal tube.

Part I

Regression analyses are performed on in vivo hemodialysis data for the transfer of creatinine, urea, uric acid and inorganic phosphate to determine the effects of variations in certain parameters on the efficiency of dialysis with a Kiil dialyzer. In calculating the mass transfer rates across the membrane, the effects of cell-plasma mass transfer kinetics are considered. The concept of the effective permeability coefficient for the red cell membrane is introduced to account for these effects. A discussion of the consequences of neglecting cell-plasma kinetics, as has been done to date in the literature, is presented.

A physical model for the Kiil dialyzer is presented in order to calculate the available membrane area for mass transfer, the linear blood and dialysate velocities, and other variables. The equations used to determine the independent variables of the regression analyses are presented. The potential dependent variables in the analyses are discussed.

Regression analyses were carried out considering overall mass-transfer coefficients, dialysances, relative dialysances, and relative permeabilities for each substance as the dependent variables. The independent variables were linear blood velocity, linear dialysate velocity, the pressure difference across the membrane, the elapsed time of dialysis, the blood hematocrit, and the arterial plasma concentrations of each substance transferred. The resulting correlations are tabulated, presented graphically, and discussed. The implications of these correlations are discussed from the viewpoint of a research investigator and from the viewpoint of patient treatment.

Recommendations for further experimental work are presented.

Part II

The interfacial structure of concurrent air-water flow in a two-inch diameter horizontal tube in the wavy flow regime has been measured using resistance wave gages. The median water depth, r.m.s. wave height, wave frequency, extrema frequency, and wave velocity have been measured as functions of air and water flow rates. Reynolds numbers, Froude numbers, Weber numbers, and bulk velocities for each phase may be calculated from these measurements. No theory for wave formation and propagation available in the literature was sufficient to describe these results.

The water surface level distribution generally is not adequately represented as a stationary Gaussian process. Five types of deviation from the Gaussian process function were noted in this work. The presence of the tube walls and the relatively large interfacial shear stresses precludes the use of simple statistical analyses to describe the interfacial structure. A detailed study of the behavior of individual fluid elements near the interface may be necessary to describe adequately wavy two-phase flow in systems similar to the one used in this work.

The variations and climatic significance of D/H ratios in the carbon-bound hydrogen of cellulose in trees

The σD values of nitrated cellulose from a variety of trees covering a wide geographic range have been measured. These measurements have been used to ascertain which factors are likely to cause σD variations in cellulose C-H hydrogen.

It is found that a primary source of tree σD variation is the σD variation of the environmental precipitation. Superimposed on this are isotopic variations caused by the transpiration of the leaf water incorporated by the tree. The magnitude of this transpiration effect appears to be related to relative humidity.

Within a single tree, it is found that the hydrogen isotope variations which occur for a ring sequence in one radial direction may not be exactly the same as those which occur in a different direction. Such heterogeneities appear most likely to occur in trees with asymmetric ring patterns that contain reaction wood. In the absence of reaction wood such heterogeneities do not seem to occur. Thus, hydrogen isotope analyses of tree ring sequences should be performed on trees which do not contain reaction wood.

Comparisons of tree σD variations with variations in local climate are performed on two levels: spatial and temporal. It is found that the σD values of 20 North American trees from a wide geographic range are reasonably well-correlated with the corresponding average annual temperature. The correlation is similar to that observed for a comparison of the σD values of annual precipitation of 11 North American sites with annual temperature. However, it appears that this correlation is significantly disrupted by trees which grew on poorly drained sites such as those in stagnant marshes. Therefore, site selection may be important in choosing trees for climatic interpretation of σD values, although proper sites do not seem to be uncommon.

The measurement of σD values in 5-year samples from the tree ring sequences of 13 trees from 11 North American sites reveals a variety of relationships with local climate. As it was for the spatial σD vs climate comparison, site selection is also apparently important for temporal tree σD vs climate comparisons. Again, it seems that poorly-drained sites are to be avoided. For nine trees from different "well-behaved" sites, it was found that the local climatic variable best related to the σD variations was not the same for all sites.

Two of these trees showed a strong negative correlation with the amount of local summer precipitation. Consideration of factors likely to influence the isotopic composition of summer rain suggests that rainfall intensity may be important. The higher the intensity, the lower the σD value. Such an effect might explain the negative correlation of σD vs summer precipitation amount for these two trees. A third tree also exhibited a strong correlation with summer climate, but in this instance it was a positive correlation of σD with summer temperature.

The remaining six trees exhibited the best correlation between σD values and local annual climate. However, in none of these six cases was it annual temperature that was the most important variable. In fact annual temperature commonly showed no relationship at all with tree σD values. Instead, it was found that a simple mass balance model incorporating two basic assumptions yielded parameters which produced the best relationships with tree σD values. First, it was assumed that the σD values of these six trees reflected the σD values of annual precipitation incorporated by these trees. Second, it was assumed that the σD value of the annual precipitation was a weighted average of two seasonal isotopic components: summer and winter. Mass balance equations derived from these assumptions yielded combinations of variables that commonly showed a relationship with tree σD values where none had previously been discerned.

It was found for these "well-behaved" trees that not all sample intervals in a σD vs local climate plot fell along a well-defined trend. These departures from the local σD VS climate norm were defined as "anomalous". Some of these anomalous intervals were common to trees from different locales. When such widespread commonalty of an anomalous interval occurred, it was observed that the interval corresponded to an interval in which drought had existed in the North American Great Plains.

Consequently, there appears to be a combination of both local and large scale climatic information in the σD variations of tree cellulose C-H hydrogen.

Constraining the interpretation of 2-methylhopanoids through genetic and phylogenetic methods

Hopanoids are a class of sterol-like lipids produced by select bacteria. Their preservation in the rock record for billions of years as fossilized hopanes lends them geological significance. Much of the structural diversity present in this class of molecules, which likely underpins important biological functions, is lost during fossilization. Yet, one type of modification that persists during preservation is methylation at C-2. The resulting 2-methylhopanoids are prominent molecular fossils and have an intriguing pattern over time, exhibiting increases in abundance associated with Ocean Anoxic Events during the Phanerozoic. This thesis uses diverse methods to address what the presence of 2-methylhopanes tells us about the microbial life and environmental conditions of their ancient depositional settings. Through an environmental survey of hpnP, the gene encoding the C-2 hopanoid methylase, we found that many different taxa are capable of producing 2-methylhopanoids in more diverse modern environments than expected. This study also revealed that hpnP is significantly overrepresented in organisms that are plant symbionts, in environments associated with plants, and with metabolisms that support plant-microbe interactions; collectively, these correlations provide a clue about the biological importance of 2-methylhopanoids. Phylogenetic reconstruction of the evolutionary history of hpnP revealed that 2-methylhopanoid production arose in the Alphaproteobacteria, indicating that the origin of these molecules is younger than originally thought. Additionally, we took genetic approach to understand the role of 2-methylhopanoids in Cyanobacteria using the filamentous symbiotic Nostoc punctiforme. We found that hopanoids likely aid in rigidifying the cell membrane but do not appear to provide resistance to osmotic or outer membrane stressors, as has been shown in other organisms. The work presented in this thesis supports previous findings that 2-methylhopanoids are not biomarkers for oxygenic photosynthesis and provides new insights by defining their distribution in modern environments, identifying their evolutionary origin, and investigating their role in Cyanobacteria. These efforts in modern settings aid the formation of a robust interpretation of 2-methylhopanes in the rock record.

Development of Microfluidic Devices with the Use of Nanotechnology to Aid in the Analysis of Biological Systems Including Membrane Protein Separation, Single Cell Analysis, and Genetic Markers

Computation technology has dramatically changed the world around us; you can hardly find an area where cell phones have not saturated the market, yet there is a significant lack of breakthroughs in the development to integrate the computer with biological environments. This is largely the result of the incompatibility of the materials used in both environments; biological environments and experiments tend to need aqueous environments. To help aid in these development chemists, engineers, physicists and biologists have begun to develop microfluidics to help bridge this divide. Unfortunately, the microfluidic devices required large external support equipment to run the device. This thesis presents a series of several microfluidic methods that can help integrate engineering and biology by exploiting nanotechnology to help push the field of microfluidics back to its intended purpose, small integrated biological and electrical devices. I demonstrate this goal by developing different methods and devices to (1) separate membrane bound proteins with the use of microfluidics, (2) use optical technology to make fiber optic cables into protein sensors, (3) generate new fluidic devices using semiconductor material to manipulate single cells, and (4) develop a new genetic microfluidic based diagnostic assay that works with current PCR methodology to provide faster and cheaper results. All of these methods and systems can be used as components to build a self-contained biomedical device.

Regional variations in upper mantle structure beneath North America

Several types of seismological data, including surface wave group and phase velocities, travel times from large explosions, and teleseismic travel time anomalies, have indicated that there are significant regional variations in the upper few hundred kilometers of the mantle beneath continental areas. Body wave travel times and amplitudes from large chemical and nuclear explosions are used in this study to delineate the details of these variations beneath North America.

As a preliminary step in this study, theoretical P wave travel times, apparent velocities, and amplitudes have been calculated for a number of proposed upper mantle models, those of Gutenberg, Jeffreys, Lehman, and Lukk and Nersesov. These quantities have been calculated for both P and S waves for model CIT11GB, which is derived from surface wave dispersion data. First arrival times for all the models except that of Lukk and Nersesov are in close agreement, but the travel time curves for later arrivals are both qualitatively and quantitatively very different. For model CIT11GB, there are two large, overlapping regions of triplication of the travel time curve, produced by regions of rapid velocity increase near depths of 400 and 600 km. Throughout the distance range from 10 to 40 degrees, the later arrivals produced by these discontinuities have larger amplitudes than the first arrivals. The amplitudes of body waves, in fact, are extremely sensitive to small variations in the velocity structure, and provide a powerful tool for studying structural details.

Most of eastern North America, including the Canadian Shield has a Pn velocity of about 8.1 km/sec, with a nearly abrupt increase in compressional velocity by ~ 0.3 km/sec near at a depth varying regionally between 60 and 90 km. Variations in the structure of this part of the mantle are significant even within the Canadian Shield. The low-velocity zone is a minor feature in eastern North America and is subject to pronounced regional variations. It is 30 to 50 km thick, and occurs somewhere in the depth range from 80 to 160 km. The velocity decrease is less than 0.2 km/sec.

Consideration of the absolute amplitudes indicates that the attenuation due to anelasticity is negligible for 2 hz waves in the upper 200 km along the southeastern and southwestern margins of the Canadian Shield. For compressional waves the average Q for this region is > 3000. The amplitudes also indicate that the velocity gradient is at least 2 x 10^-3 both above and below the low-velocity zone, implying that the temperature gradient is < 4.8°C/km if the regions are chemically homogeneous.

In western North America, the low-velocity zone is a pronounced feature, extending to the base of the crust and having minimum velocities of 7.7 to 7.8 km/sec. Beneath the Colorado Plateau and Southern Rocky Mountains provinces, there is a rapid velocity increase of about 0.3 km/sec, similar to that observed in eastern North America, but near a depth of 100 km.

Complicated travel time curves observed on profiles with stations in both eastern and western North America can be explained in detail by a model taking into account the lateral variations in the structure of the low-velocity zone. These variations involve primarily the velocity within the zone and the depth to the top of the zone; the depth to the bottom is, for both regions, between 140 and 160 km.

The depth to the transition zone near 400 km also varies regionally, by about 30-40 km. These differences imply variations of 250 °C in the temperature or 6 % in the iron content of the mantle, if the phase transformation of olivine to the spinel structure is assumed responsible. The structural variations at this depth are not correlated with those at shallower depths, and follow no obvious simple pattern.

The computer programs used in this study are described in the Appendices. The program TTINV (Appendix IV) fits spherically symmetric earth models to observed travel time data. The method, described in Appendix III, resembles conventional least-square fitting, using partial derivatives of the travel time with respect to the model parameters to perturb an initial model. The usual ill-conditioned nature of least-squares techniques is avoided by a technique which minimizes both the travel time residuals and the model perturbations.

Spherically symmetric earth models, however, have been found inadequate to explain most of the observed travel times in this study. TVT4, a computer program that performs ray theory calculations for a laterally inhomogeneous earth model, is described in Appendix II. Appendix I gives a derivation of seismic ray theory for an arbitrarily inhomogeneous earth model.

Robust Control of Evolutionary Dynamics

The application of principles from evolutionary biology has long been used to gain new insights into the progression and clinical control of both infectious diseases and neoplasms. This iterative evolutionary process consists of expansion, diversification and selection within an adaptive landscape - species are subject to random genetic or epigenetic alterations that result in variations; genetic information is inherited through asexual reproduction and strong selective pressures such as therapeutic intervention can lead to the adaptation and expansion of resistant variants. These principles lie at the center of modern evolutionary synthesis and constitute the primary reasons for the development of resistance and therapeutic failure, but also provide a framework that allows for more effective control.

A model system for studying the evolution of resistance and control of therapeutic failure is the treatment of chronic HIV-1 infection by broadly neutralizing antibody (bNAb) therapy. A relatively recent discovery is that a minority of HIV-infected individuals can produce broadly neutralizing antibodies, that is, antibodies that inhibit infection by many strains of HIV. Passive transfer of human antibodies for the prevention and treatment of HIV-1 infection is increasingly being considered as an alternative to a conventional vaccine. However, recent evolution studies have uncovered that antibody treatment can exert selective pressure on virus that results in the rapid evolution of resistance. In certain cases, complete resistance to an antibody is conferred with a single amino acid substitution on the viral envelope of HIV.

The challenges in uncovering resistance mechanisms and designing effective combination strategies to control evolutionary processes and prevent therapeutic failure apply more broadly. We are motivated by two questions: Can we predict the evolution to resistance by characterizing genetic alterations that contribute to modified phenotypic fitness? Given an evolutionary landscape and a set of candidate therapies, can we computationally synthesize treatment strategies that control evolution to resistance?

To address the first question, we propose a mathematical framework to reason about evolutionary dynamics of HIV from computationally derived Gibbs energy fitness landscapes -- expanding the theoretical concept of an evolutionary landscape originally conceived by Sewall Wright to a computable, quantifiable, multidimensional, structurally defined fitness surface upon which to study complex HIV evolutionary outcomes.

To design combination treatment strategies that control evolution to resistance, we propose a methodology that solves for optimal combinations and concentrations of candidate therapies, and allows for the ability to quantifiably explore tradeoffs in treatment design, such as limiting the number of candidate therapies in the combination, dosage constraints and robustness to error. Our algorithm is based on the application of recent results in optimal control to an HIV evolutionary dynamics model and is constructed from experimentally derived antibody resistant phenotypes and their single antibody pharmacodynamics. This method represents a first step towards integrating principled engineering techniques with an experimentally based mathematical model in the rational design of combination treatment strategies and offers predictive understanding of the effects of combination therapies of evolutionary dynamics and resistance of HIV. Preliminary in vitro studies suggest that the combination antibody therapies predicted by our algorithm can neutralize heterogeneous viral populations despite containing resistant mutations.

Stationary Eddies and Zonal Variations of the Global Hydrological Cycle in a Changing Climate

This thesis advances our physical understanding of the sensitivity of the hydrological cycle to global warming. Specifically, it focuses on changes in the longitudinal (zonal) variation of precipitation minus evaporation (P - E), which is predominantly controlled by planetary-scale stationary eddies. By studying idealized general circulation model (GCM) experiments with zonally varying boundary conditions, this thesis examines the mechanisms controlling the strength of stationary-eddy circulations and their role in the hydrological cycle. The overarching goal of this research is to understand the cause of changes in regional P - E with global warming. An understanding of such changes can be useful for impact studies focusing on water availability, ecosystem management, and flood risk.

Based on a moisture-budget analysis of ERA-Interim data, we establish an approximation for zonally anomalous P - E in terms of surface moisture content and stationary-eddy vertical motion in the lower troposphere. Part of the success of this approximation comes from our finding that transient-eddy moisture fluxes partially cancel the effect of stationary-eddy moisture advection, allowing divergent circulations to dominate the moisture budget. The lower-tropospheric vertical motion is related to horizontal motion in stationary eddies by Sverdrup and Ekman balance. These moisture- and vorticity-budget balances also hold in idealized and comprehensive GCM simulations across a range of climates.

By examining climate changes in the idealized and comprehensive GCM simulations, we are able to show the utility of the vertical motion P - E approximation for splitting changes in zonally anomalous P - E into thermodynamic and dynamic components. Shifts in divergent stationary-eddy circulations dominate changes in zonally anomalous P - E. This limits the local utility of the "wet gets wetter, dry gets drier” idea, where existing P - E patterns are amplified with warming by the increase in atmospheric moisture content, with atmospheric circulations held fixed. The increase in atmospheric moisture content manifests instead in an increase in the amplitude of the zonally anomalous hydrological cycle as measured by the zonal variance of P - E. However, dynamic changes, particularly the slowdown of divergent stationary-eddy circulations, limit the strengthening of the zonally anomalous hydrological cycle. In certain idealized cases, dynamic changes are even strong enough to reverse the tendency towards "wet gets wetter, dry gets drier” with warming.

Motivated by the importance of stationary-eddy vertical velocities in the moisture budget analysis, we examine controls on the amplitude of stationary eddies across a wide range of climates in an idealized GCM with simple topographic and ocean-heating zonal asymmetries. An analysis of the thermodynamic equation in the vicinity of topographic forcing reveals the importance of on-slope surface winds, the midlatitude isentropic slope, and latent heating in setting the amplitude of stationary waves. The response of stationary eddies to climate change is determined primarily by the strength of zonal surface winds hitting the mountain. The sensitivity of stationary-eddies to this surface forcing increases with climate change as the slope of midlatitude isentropes decreases. However, latent heating also plays an important role in damping the stationary-eddy response, and this damping becomes stronger with warming as the atmospheric moisture content increases. We find that the response of tropical overturning circulations forced by ocean heat-flux convergence is described by changes in the vertical structure of moist static energy and deep convection. This is used to derive simple scalings for the Walker circulation strength that capture the monotonic decrease with warming found in our idealized simulations.

Through the work of this thesis, the advances made in understanding the amplitude of stationary-waves in a changing climate can be directly applied to better understand and predict changes in the zonally anomalous hydrological cycle.

Proton magnetic resonance studies of ribonucleic acid complexes. I. Complexes of biological bases and oligonucleotides with RNA. II. Template recognition and the degeneracy of the genetic code

Part I. Complexes of Biological Bases and Oligonucleotides with RNA

The physical nature of complexes of several biological bases and oligonucleotides with single-stranded ribonucleic acids have been studied by high resolution proton magnetic resonance spectroscopy. The importance of various forces in the stabilization of these complexes is also discussed.

Previous work has shown that purine forms an intercalated complex with single-stranded nucleic acids. This complex formation led to severe and stereospecific broadening of the purine resonances. From the field dependence of the linewidths, T₁ measurements of the purine protons and nuclear Overhauser enhancement experiments, the mechanism for the line broadening was ascertained to be dipole-dipole interactions between the purine protons and the ribose protons of the nucleic acid.

The interactions of ethidium bromide (EB) with several RNA residues have been studied. EB forms vertically stacked aggregates with itself as well as with uridine, 3'-uridine monophosphate and 5'-uridine monophosphate and forms an intercalated complex with uridylyl (3' → 5') uridine and polyuridylic acid (poly U). The geometry of EB in the intercalated complex has also been determined.

The effect of chain length of oligo-A-nucleotides on their mode of interaction with poly U in D₂0 at neutral pD have also been studied. Below room temperatures, ApA and ApApA form a rigid triple-stranded complex involving a stoichiometry of one adenine to two uracil bases, presumably via specific adenine-uracil base pairing and cooperative base stacking of the adenine bases. While no evidence was obtained for the interaction of ApA with poly U above room temperature, ApApA exhibited complex formation of a 1:1 nature with poly U by forming Watson-Crick base pairs. The thermodynamics of these systems are discussed.

Part II. Template Recognition and the Degeneracy of the Genetic Code

The interaction of ApApG and poly U was studied as a model system for the codon-anticodon interaction of tRNA and mRNA in vivo. ApApG was shown to interact with poly U below ~20°C. The interaction was of a 1:1 nature which exhibited the Hoogsteen bonding scheme. The three bases of ApApG are in an anti conformation and the guanosine base appears to be in the lactim tautomeric form in the complex.

Due to the inadequacies of previous models for the degeneracy of the genetic code in explaining the observed interactions of ApApG with poly U, the "tautomeric doublet" model is proposed as a possible explanation of the degenerate interactions of tRNA with mRNA during protein synthesis in vivo.