1. Ultrasonic studies of binary liquid structure in the critical region. Theory and experiment for the 2,6-lutidine/water system. 2. Hartree-Fock calculations of electric polarizabilities of some simple atoms and molecules, and their practicality. 3. Calculation of vibrational transition probabilities in collinear atom-diatom and diatom-diatom collisions with Lennard-Jones interaction

<p><u>Part 1.</u> Many interesting visual and mechanical phenomena occur in the critical region of fluids, both for the gas-liquid and liquid-liquid transitions. The precise thermodynamic and transport behavior here has some broad consequences for the molecular theory of liquids. Previous studies in this laboratory on a liquid-liquid critical mixture via ultrasonics supported a basically classical analysis of fluid behavior by M. Fixman (e. g., the free energy is assumed analytic in intensive variables in the thermodynamics)--at least when the fluid is not too close to critical. A breakdown in classical concepts is evidenced close to critical, in some well-defined ways. We have studied herein a liquid-liquid critical system of complementary nature (possessing a <u>lower</u> critical mixing or consolute temperature) to all previous mixtures, to look for new qualitative critical behavior. We did not find such new behavior in the ultrasonic absorption ascribable to the critical fluctuations, but we did find extra absorption due to chemical processes (yet these are related to the mixing behavior generating the lower consolute point). We rederived, corrected, and extended Fixman's analysis to interpret our experimental results in these more complex circumstances. The entire account of theory and experiment is prefaced by an extensive introduction recounting the general status of liquid state theory. The introduction provides a context for our present work, and also points out problems deserving attention. Interest in these problems was stimulated by this work but also by work in Part 3.</p> <p><u>Part 2.</u> Among variational theories of electronic structure, the Hartree-Fock theory has proved particularly valuable for a practical understanding of such properties as chemical binding, electric multipole moments, and X-ray scattering intensity. It also provides the most tractable method of calculating first-order properties under external or internal one-electron perturbations, either developed explicitly in orders of perturbation theory or in the fully self-consistent method. The accuracy and consistency of first-order properties are poorer than those of zero-order properties, but this is most often due to the use of explicit approximations in solving the perturbed equations, or to inadequacy of the variational basis in size or composition. We have calculated the electric polarizabilities of H₂, He, Li, Be, LiH, and N₂ by Hartree-Fock theory, using exact perturbation theory or the fully self-consistent method, as dictated by convenience. By careful studies on total basis set composition, we obtained good approximations to limiting Hartree-Fock values of polarizabilities with bases of reasonable size. The values for all species, and for each direction in the molecular cases, are within 8% of experiment, or of best theoretical values in the absence of the former. Our results support the use of unadorned Hartree-Pock theory for static polarizabilities needed in interpreting electron-molecule scattering data, collision-induced light scattering experiments, and other phenomena involving experimentally inaccessible polarizabilities. </p> <p><u>Part 3.</u> Numerical integration of the close-coupled scattering equations has been carried out to obtain vibrational transition probabilities for some models of the electronically adiabatic H₂-H₂ collision. All the models use a Lennard-Jones interaction potential between nearest atoms in the collision partners. We have analyzed the results for some insight into the vibrational excitation process in its dependence on the energy of collision, the nature of the vibrational binding potential, and other factors. We conclude also that replacement of earlier, simpler models of the interaction potential by the Lennard-Jones form adds very little realism for all the complication it introduces. A brief introduction precedes the presentation of our work and places it in the context of attempts to understand the collisional activation process in chemical reactions as well as some other chemical dynamics.</p>

On the thermal budget of Pahoehoe lava flows

<p>In this thesis I investigate some aspects of the thermal budget of pahoehoe lava flows. This is done with a combination of general field observations, quantitative modeling, and specific field experiments. The results of this work apply to pahoehoe flows in general, even though the vast bulk of the work has been conducted on the lavas formed by the Pu'u 'O'o - Kupaianaha eruption of Kilauea Volcano on Hawai'i. The field observations rely heavily on discussions with the staff of the United States Geological Survey's Hawaiian Volcano Observatory (HVO), under whom I labored repeatedly in 1991-1993 for a period totaling about 10 months.</p> <p>The quantitative models I have constructed are based on the physical processes observed by others and myself to be active on pahoehoe lava flows. By building up these models from the basic physical principles involved, this work avoids many of the pitfalls of earlier attempts to fit field observations with "intuitively appropriate" mathematical expressions. Unlike many earlier works, my model results can be analyzed in terms of the interactions between the different physical processes. I constructed models to: (1) describe the initial cooling of small pahoehoe flow lobes and (2) understand the thermal budget of lava tubes.</p> <p>The field experiments were designed either to validate model results or to constrain key input parameters. In support of the cooling model for pahoehoe flow lobes, attempts were made to measure: (1) the cooling within the flow lobes, (2) the amount of heat transported away from the lava by wind, and (3) the growth of the crust on the lobes. Field data collected by Jones [1992], Hon et al. [1994b], and Denlinger [Keszthelyi and Denlinger, in prep.] were also particularly useful in constraining my cooling model for flow lobes. Most of the field observations I have used to constrain the thermal budget of lava tubes were collected by HVO (geological and geophysical monitoring) and the Jet Propulsion Laboratory (airborne infrared imagery [Realmuto et al., 1992]). I was able to assist HVO for part of their lava tube monitoring program and also to collect helicopterborne and ground-based IR video in collaboration with JPL [Keszthelyi et al., 1993].</p> <p>The most significant results of this work are (1) the quantitative demonstration that the emplacement of pahoehoe and 'a'a flows are the fundamentally different, (2) confirmation that even the longest lava flows observed in our Solar System could have formed as low effusion rate, tube-fed pahoehoe flows, and (3) the recognition that the atmosphere plays a very important role throughout the cooling of history of pahoehoe lava flows. In addition to answering specific questions about the thermal budget of tube-fed pahoehoe lava flows, this thesis has led to some additional, more general, insights into the emplacement of these lava flows. This general understanding of the tube-fed pahoehoe lava flow as a system has suggested foci for future research in this part of physical volcanology.</p>

Detailed properties of high redshift galaxies

<p>Galaxies evolve throughout the history of the universe from the first star-forming sources, through gas-rich asymmetric structures with rapid star formation rates, to the massive symmetrical stellar systems observed at the present day. Determining the physical processes which drive galaxy formation and evolution is one of the most important questions in observational astrophysics. This thesis presents four projects aimed at improving our understanding of galaxy evolution from detailed measurements of star forming galaxies at high redshift.</p> <p>We use resolved spectroscopy of gravitationally lensed z ��� 2 - 3 star forming galaxies to measure their kinematic and star formation properties. The combination of lensing with adaptive optics yields physical resolution of ��� 100 pc, sufficient to resolve giant Hii regions. We find that ~ 70 % of galaxies in our sample display ordered rotation with high local velocity dispersion indicating turbulent thick disks. The rotating galaxies are gravitationally unstable and are expected to fragment into giant clumps. The size and dynamical mass of giant Hii regions are in agreement with predictions for such clumps indicating that gravitational instability drives the rapid star formation. The remainder of our sample is comprised of ongoing major mergers. Merging galaxies display similar star formation rate, morphology, and local velocity dispersion as isolated sources, but their velocity fields are more chaotic with no coherent rotation.</p> <p>We measure resolved metallicity in four lensed galaxies at z = 2.0 ��� 2.4 from optical emission line diagnostics. Three rotating galaxies display radial gradients with higher metallicity at smaller radii, while the fourth is undergoing a merger and has an inverted gradient with lower metallicity at the center. Strong gradients in the rotating galaxies indicate that they are growing inside-out with star formation fueled by accretion of metal-poor gas at large radii. By comparing measured gradients with an appropriate comparison sample at z = 0, we demonstrate that metallicity gradients in isolated galaxies must flatten at later times. The amount of size growth inferred by the gradients is in rough agreement with direct measurements of massive galaxies. We develop a chemical evolution model to interpret these data and conclude that metallicity gradients are established by a gradient in the outflow mass loading factor, combined with radial inflow of metal-enriched gas.</p> <p>We present the first rest-frame optical spectroscopic survey of a large sample of low-luminosity galaxies at high redshift (L &#60; L*, 1.5 &lt; z &#60; 3.5). This population dominates the star formation density of the universe at high redshifts, yet such galaxies are normally too faint to be studied spectroscopically. We take advantage of strong gravitational lensing magnification to compile observations for a sample of 29 galaxies using modest integration times with the Keck and Palomar telescopes. Balmer emission lines confirm that the sample has a median SFR ��� 10 M_sun yr^���1 and extends to lower SFR than has been probed by other surveys at similar redshift. We derive the metallicity, dust extinction, SFR, ionization parameter, and dynamical mass from the spectroscopic data, providing the first accurate characterization of the star-forming environment in low-luminosity galaxies at high redshift. For the first time, we directly test the proposal that the relation between galaxy stellar mass, star formation rate, and gas phase metallicity does not evolve. We find lower gas phase metallicity in the high redshift galaxies than in local sources with equivalent stellar mass and star formation rate, arguing against a time-invariant relation. While our result is preliminary and may be biased by measurement errors, this represents an important first measurement that will be further constrained by ongoing analysis of the full data set and by future observations.</p> <p>We present a study of composite rest-frame ultraviolet spectra of Lyman break galaxies at z = 4 and discuss implications for the distribution of neutral outflowing gas in the circumgalactic medium. In general we find similar spectroscopic trends to those found at z = 3 by earlier surveys. In particular, absorption lines which trace neutral gas are weaker in less evolved galaxies with lower stellar masses, smaller radii, lower luminosity, less dust, and stronger Ly�� emission. Typical galaxies are thus expected to have stronger Ly�� emission and weaker low-ionization absorption at earlier times, and we indeed find somewhat weaker low-ionization absorption at higher redshifts. In conjunction with earlier results, we argue that the reduced low-ionization absorption is likely caused by lower covering fraction and/or velocity range of outflowing neutral gas at earlier epochs. This result has important implications for the hypothesis that early galaxies were responsible for cosmic reionization. We additionally show that fine structure emission lines are sensitive to the spatial extent of neutral gas, and demonstrate that neutral gas is concentrated at smaller galactocentric radii in higher redshift galaxies.</p> <p>The results of this thesis present a coherent picture of galaxy evolution at high redshifts 2 ��� z ��� 4. Roughly 1/3 of massive star forming galaxies at this period are undergoing major mergers, while the rest are growing inside-out with star formation occurring in gravitationally unstable thick disks. Star formation, stellar mass, and metallicity are limited by outflows which create a circumgalactic medium of metal-enriched material. We conclude by describing some remaining open questions and prospects for improving our understanding of galaxy evolution with future observations of gravitationally lensed galaxies.</p>

Sequence-function relationships in E. coli transcriptional regulation

<p>Understanding how transcriptional regulatory sequence maps to regulatory function remains a difficult problem in regulatory biology. Given a particular DNA sequence for a bacterial promoter region, we would like to be able to say which transcription factors bind there, how strongly they bind, and whether they interact with each other and/or RNA polymerase, with the ultimate objective of integrating knowledge of these parameters into a prediction of gene expression levels. The theoretical framework of statistical thermodynamics provides a useful framework for doing so, enabling us to predict how gene expression levels depend on transcription factor binding energies and concentrations. We used thermodynamic models, coupled with models of the sequence-dependent binding energies of transcription factors and RNAP, to construct a genotype to phenotype map for the level of repression exhibited by the lac promoter, and tested it experimentally using a set of promoter variants from E. coli strains isolated from different natural environments. For this work, we sought to ``reverse engineer'' naturally occurring promoter sequences to understand how variations in promoter sequence affects gene expression. The natural inverse of this approach is to ``forward engineer'' promoter sequences to obtain targeted levels of gene expression. We used a high precision model of RNAP-DNA sequence dependent binding energy, coupled with a thermodynamic model relating binding energy to gene expression, to predictively design and verify a suite of synthetic E. coli promoters whose expression varied over nearly three orders of magnitude.</p> <p>However, although thermodynamic models enable predictions of mean levels of gene expression, it has become evident that cell-to-cell variability or ``noise'' in gene expression can also play a biologically important role. In order to address this aspect of gene regulation, we developed models based on the chemical master equation framework and used them to explore the noise properties of a number of common E. coli regulatory motifs; these properties included the dependence of the noise on parameters such as transcription factor binding strength and copy number. We then performed experiments in which these parameters were systematically varied and measured the level of variability using mRNA FISH. The results showed a clear dependence of the noise on these parameters, in accord with model predictions.</p> <p>Finally, one shortcoming of the preceding modeling frameworks is that their applicability is largely limited to systems that are already well-characterized, such as the lac promoter. Motivated by this fact, we used a high throughput promoter mutagenesis assay called Sort-Seq to explore the completely uncharacterized transcriptional regulatory DNA of the E. coli mechanosensitive channel of large conductance (MscL). We identified several candidate transcription factor binding sites, and work is continuing to identify the associated proteins.</p>

Effects of self energy of the ions on the double layer structure and properties at the dielectric interface

<p>Although numerous theoretical efforts have been put forth, a systematic, unified and predictive theoretical framework that is able to capture all the essential physics of the interfacial behaviors of ions, such as the Hofmeister series effect, Jones-Ray effect and the salt effect on the bubble coalescence remain an outstanding challenge. The most common approach to treating electrostatic interactions in the presence of salt ions is the Poisson-Boltzmann (PB) theory. However, there are many systems for which the PB theory fails to offer even a qualitative explanation of the behavior, especially for ions distributed in the vicinity of an interface with dielectric contrast between the two media (like the water-vapor/oil interface). A key factor missing in the PB theory is the self energy of the ion.</p> <p>In this thesis, we develop a self-consistent theory that treats the electrostatic self energy (including both the short-range Born solvation energy and the long-range image charge interactions), the nonelectrostatic contribution of the self energy, the ion-ion correlation and the screening effect systematically in a single framework. By assuming a finite charge spread of the ion instead of using the point-charge model, the self energy obtained by our theory is free of the divergence problems and gives a continuous self energy across the interface. This continuous feature allows ions on the water side and the vapor/oil side of the interface to be treated in a unified framework. The theory involves a minimum set of parameters of the ion, such as the valency, radius, polarizability of the ions, and the dielectric constants of the medium, that are both intrinsic and readily available. The general theory is first applied to study the thermodynamic property of the bulk electrolyte solution, which shows good agreement with the experiment result for predicting the activity coefficient and osmotic coefficient.</p> <p>Next, we address the effect of local Born solvation energy on the bulk thermodynamics and interfacial properties of electrolyte solution mixtures. We show that difference in the solvation energy between the cations and anions naturally gives rise to local charge separation near the interface, and a finite Galvani potential between two coexisting solutions. The miscibility of the mixture can either increases or decreases depending on the competition between the solvation energy and translation entropy of the ions. The interfacial tension shows a non-monotonic dependence on the salt concentration: it increases linearly with the salt concentration at higher concentrations, and decreases approximately as the square root of the salt concentration for dilute solutions, which is in agreement with the Jones-Ray effect observed in experiment.</p> <p>Next, we investigate the image effects on the double layer structure and interfacial properties near a single charged plate. We show that the image charge repulsion creates a depletion boundary layer that cannot be captured by a regular perturbation approach. The correct weak-coupling theory must include the self-energy of the ion due to the image charge interaction. The image force qualitatively alters the double layer structure and properties, and gives rise to many non-PB effects, such as nonmonotonic dependence of the surface energy on concentration and charge inversion. The image charge effect is then studied for electrolyte solutions between two plates. For two neutral plates, we show that depletion of the salt ions by the image charge repulsion results in short-range attractive and long-range repulsive forces. If cations and anions are of different valency, the asymmetric depletion leads to the formation of an induced electrical double layer. For two charged plates, the competition between the surface charge and the image charge effect can give rise to like- charge attraction.</p> <p>Then, we study the inhomogeneous screening effect near the dielectric interface due to the anisotropic and nonuniform ion distribution. We show that the double layer structure and interfacial properties is drastically affected by the inhomogeneous screening if the bulk Debye screening length is comparable or smaller than the Bjerrum length. The width of the depletion layer is characterized by the Bjerrum length, independent of the salt concentration. We predict that the negative adsorption of ions at the interface increases linearly with the salt concentration, which cannot be captured by either the bulk screening approximation or the WKB approximation. For asymmetric salt, the inhomogeneous screening enhances the charge separation in the induced double layer and significantly increases the value of the surface potential.</p> <p>Finally, to account for the ion specificity, we study the self energy of a single ion across the dielectric interface. The ion is considered to be polarizable: its charge distribution can be self-adjusted to the local dielectric environment to minimize the self energy. Using intrinsic parameters of the ions, such as the valency, radius, and polarizability, we predict the specific ion effect on the interfacial affinity of halogen anions at the water/air interface, and the strong adsorption of hydrophobic ions at the water/oil interface, in agreement with experiments and atomistic simulations.</p> <p>The theory developed in this work represents the most systematic theoretical technique for weak-coupling electrolytes. We expect the theory to be more useful for studying a wide range of structural and dynamic properties in physicochemical, colloidal, soft-matter and biophysical systems.</p>

Topological strings, double affine Hecke algebras, and exceptional knot homology

<p>In this thesis, we consider two main subjects: refined, composite invariants and exceptional knot homologies of torus knots. The main technical tools are double affine Hecke algebras ("DAHA") and various insights from topological string theory.</p> <p>In particular, we define and study the composite DAHA-superpolynomials of torus knots, which depend on pairs of Young diagrams and generalize the composite HOMFLY-PT polynomials from the full HOMFLY-PT skein of the annulus. We also describe a rich structure of differentials that act on homological knot invariants for exceptional groups. These follow from the physics of BPS states and the adjacencies/spectra of singularities associated with Landau-Ginzburg potentials. At the end, we construct two DAHA-hyperpolynomials which are closely related to the Deligne-Gross exceptional series of root systems.</p> <p>In addition to these main themes, we also provide new results connecting DAHA-Jones polynomials to quantum torus knot invariants for Cartan types A and D, as well as the first appearance of quantum E6 knot invariants in the literature.</p>

A molecular dynamics study of the microscopic properties of simple dense fluids

<p>The microscopic properties of a two-dimensional model dense fluid of Lennard-Jones disks have been studied using the so-called "molecular dynamics" method. Analyses of the computer-generated simulation data in terms of "conventional" thermodynamic and distribution functions verify the physical validity of the model and the simulation technique.</p> <p>The radial distribution functions g(r) computed from the simulation data exhibit several subsidiary features rather similar to those appearing in some of the g(r) functions obtained by X-ray and thermal neutron diffraction measurements on real simple liquids. In the case of the model fluid, these "anomalous" features are thought to reflect the existence of two or more alternative configurations for local ordering.</p> <p>Graphical display techniques have been used extensively to provide some intuitive insight into the various microscopic phenomena occurring in the model. For example, "snapshots" of the instantaneous system configurations for different times show that the "excess" area allotted to the fluid is collected into relatively large, irregular, and surprisingly persistent "holes". Plots of the particle trajectories over intervals of 2.0 to 6.0 x 10^-12 sec indicate that the mechanism for diffusion in the dense model fluid is "cooperative" in nature, and that extensive diffusive migration is generally restricted to groups of particles in the vicinity of a hole.</p> <p>A quantitative analysis of diffusion in the model fluid shows that the cooperative mechanism is not inconsistent with the statistical predictions of existing theories of singlet, or self-diffusion in liquids. The relative diffusion of proximate particles is, however, found to be retarded by short-range dynamic correlations associated with the cooperative mechanism--a result of some importance from the standpoint of bimolecular reaction kinetics in solution.</p> <p>A new, semi-empirical treatment for relative diffusion in liquids is developed, and is shown to reproduce the relative diffusion phenomena observed in the model fluid quite accurately. When incorporated into the standard Smoluchowski theory of diffusion-controlled reaction kinetics, the more exact treatment of relative diffusion is found to lower the predicted rate of reaction appreciably.</p> <p>Finally, an entirely new approach to an understanding of the liquid state is suggested. Our experience in dealing with the simulation data--and especially, graphical displays of the simulation data--has led us to conclude that many of the more frustrating scientific problems involving the liquid state would be simplified considerably, were it possible to describe the microscopic structures characteristic of liquids in a concise and precise manner. To this end, we propose that the development of a formal language of partially-ordered structures be investigated.</p>

Phase transitions from the solid state of monatomic elements

<p>The principle aims of this thesis include the development of models of sublimation and melting from first principles and the application of these models to the rare gases.</p> <p>A simple physical model is constructed to represent the sublimation of monatomic elements. According to this model, the solid and gas phases are two states of a single physical system. The nature of the phase transition is clearly revealed, and the relations between the vapor pressure, the latent heat, and the transition temperature are derived. The resulting theory is applied to argon, krypton, and xenon, and good agreement with experiment is found.</p> <p>For the melting transition, the solid is represented by an anharmonic model and the liquid is described by the Percus-Yevick approximation. The behavior of the liquid at high densities is studied on the isotherms kT/��� = 1.3, 1.8, and 2.0, where k is Boltzmann's constant, T is the temperature, and e is the well depth of the Lennard-Jones 12-6 pair potential. No solutions of the PercusYevick equation were found for ����³ above 1.3, where �� is the particle density and �� is the radial parameter of the Lennard-Jones potential. The liquid structure is found to be very different from the solid structure near the melting line. The liquid pressures are about 50 percent low for experimental melting densities of argon. This discrepancy gives rise to melting pressures up to twice the experimental values.</p>

Reggeization of some unequal mass processes involving higher spins : the reactions pion-nucleon going to (V,Nucleon), pion-nucleon going to (V,delta-hyperon), and photon-proton going to (positive pion,neutron)

<p>Recent theoretical developments in the reggeization of inelastic processes involving particles with high spin are incorporated into a model of vector meson production. A number of features of experimental differential cross sections and density matrices are interpreted in terms of this model. </p> <p>The method chosen for reggeization of helicity amplitudes first separates kinematic zeros and singularities from the parity-conserving amplitudes and then applies results of Freedman and Wang on daughter trajectories to the remaining factors. Kinematic constraints on helicity amplitudes at t = 0 and t = (M ��� M_��)² are also considered.</p> <p>It is found that data for reactions of types ��N���VN and ��N���V�� are consistent with a model of this type in which all kinematic constraints at t = 0 are satisfied by evasion (vanishing of residue functions). As a quantitative test of the parametrization, experimental differential cross sections of vector meson production reactions dominated by pion trajectory exchange are compared with the theory. It is found that reduced residue functions are approximately constant, once the kinematic behavior near t = (M ��� M_��)² has been removed.</p> <p>The alternative possibility of conspiracy between amplitudes is also discussed; and it is shown that unless conspiracy is present, some amplitudes allowed by angular momentum conservation will not contribute with full strength in the forward direction. An example, ��p�����⁺n in which the data for d��/dt indicate conspiracy, is studied in detail.</p>