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

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.

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.

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.

Violence in the Medieval Church before the First Crusade

The attitude of the medieval church towards violence before the First Crusade in 1095 underwent a significant institutional evolution, from the peaceful tradition of the New Testament and the Roman persecution, through the prelate-led military campaigns of the Carolingian period and the Peace of God era. It would be superficially easy to characterize this transformation as the pragmatic and entirely secular response of a growing power to the changing world. However, such a simplification does not fully do justice to the underlying theology. While church leaders from the 5th Century to the 11th had vastly different motivations and circumstances under which to develop their responses to a variety of violent activities, the teachings of Augustine of Hippo provided a unifying theme. Augustine’s just war theology, in establishing which conflicts are acceptable in the eyes of God, focused on determining whether a proper causa belli or basis for war exists, and then whether a legitimate authority declares and leads the war. Augustine masterfully integrated aspects of the Old and New Testaments to create a lasting and compelling case for his definition of justified violence. Although at different times and places his theology has been used to support a variety of different attitudes, the profound influence of his work on the medieval church’s evolving position on violence is clear.

Quantum Interference and Entanglement of Surface Plasmons

Surface plasma waves arise from the collective oscillations of billions of electrons at the surface of a metal in unison. The simplest way to quantize these waves is by direct analogy to electromagnetic fields in free space, with the surface plasmon, the quantum of the surface plasma wave, playing the same role as the photon. It follows that surface plasmons should exhibit all of the same quantum phenomena that photons do, including quantum interference and entanglement.

Unlike photons, however, surface plasmons suffer strong losses that arise from the scattering of free electrons from other electrons, phonons, and surfaces. Under some circumstances, these interactions might also cause “pure dephasing,” which entails a loss of coherence without absorption. Quantum descriptions of plasmons usually do not account for these effects explicitly, and sometimes ignore them altogether. In light of this extra microscopic complexity, it is necessary for experiments to test quantum models of surface plasmons.

In this thesis, I describe two such tests that my collaborators and I performed. The first was a plasmonic version of the Hong-Ou-Mandel experiment, in which we observed two-particle quantum interference between plasmons with a visibility of 93 ± 1%. This measurement confirms that surface plasmons faithfully reproduce this effect with the same visibility and mutual coherence time, to within measurement error, as in the photonic case.

The second experiment demonstrated path entanglement between surface plasmons with a visibility of 95 ± 2%, confirming that a path-entangled state can indeed survive without measurable decoherence. This measurement suggests that elastic scattering mechanisms of the type that might cause pure dephasing must have been weak enough not to significantly perturb the state of the metal under the experimental conditions we investigated.

These two experiments add quantum interference and path entanglement to a growing list of quantum phenomena that surface plasmons appear to exhibit just as clearly as photons, confirming the predictions of the simplest quantum models.

Isolation of the murine interleukin 2 gene and characterization of its regulatory architecture

Interleukin 2 (IL2) is the primary growth hormone used by mature T cells and this lymphokine plays an important role in the magnification of cell-mediated immune responses. Under normal circumstances its expression is limited to antigen-activated type 1 helper T cells (T_H1) and the ability to transcribe this gene is often regarded as evidence for commitment to this developmental lineage. There is, however, abundant evidence than many non-T_H1 T cells, under appropriate conditions, possess the ability to express this gene. Of paramount interest in the study of T-cell development is the mechanisms by which differentiating thymocytes are endowed with particular combinations of cell surface proteins and response repertoires. For example, why do most helper T cells express the CD4 differentiation antigen?

As a first step in understanding these developmental processes the gene encoding IL2 was isolated from a mouse genomic library by probing with a conspecific IL2 cDNA. The sequence of the 5' flanking region from + 1 to -2800 was determined and compared to the previously reported human sequence. Extensive identity exists between +1 and -580 (86%) and sites previously shown to be crucial for the proper expression of the human gene are well conserved in both sequence location in the mouse counterpart.

Transient expression assays were used to evaluate the contribution of various genomic sequences to high-level gene expression mediated by a cloned IL2 promoter fragment. Differing lengths of 5' flanking DNA, all terminating in the 5' untranslated region, were linked to a reporter gene, bacterial chloramphenicol acetyltransferase (CAT) and enzyme activity was measured after introduction into IL2-producing cell lines. No CAT was ever detected without stimulation of the recipient cells. A cloned promoter fragment containing only 321 bp of upstream DNA was expressed well in both Jurkat and EL4.El cells. Addition of intragenic or downstream DNA to these 5' IL2-CAT constructs showed that no obvious regulatory regions resided there. However, increasing the extent of 5' DNA from -321 to -2800 revealed several positive and negative regulatory elements. One negative region that was well characterized resided between -750 and -1000 and consisted almost exclusively of alternating purine and pyrimidines. There is no sequence resembling this in the human gene now, but there is evidence that there may have once been.

No region, when deleted, could relax either the stringent induction-dependence on cell-type specificity displayed by this promoter. Reagents that modulated endogenous IL2 expression, such as cAMP, cyclosporin A, and IL1, affected expression of the 5' IL2-CAT constructs also. For a given reagent, expression from all expressible constructs was suppressed or enhanced to the same extent. This suggests that these modulators affect IL2 expression through perturbation of a central inductive signal rather than by summation of the effects of discrete, independently regulated, negative and positive transcription factors.

Storm track response to perturbations in climate

This thesis advances our understanding of midlatitude storm tracks and how they respond to perturbations in the climate system. The midlatitude storm tracks are regions of maximal turbulent kinetic energy in the atmosphere. Through them, the bulk of the atmospheric transport of energy, water vapor, and angular momentum occurs in midlatitudes. Therefore, they are important regulators of climate, controlling basic features such as the distribution of surface temperatures, precipitation, and winds in midlatitudes. Storm tracks are robustly projected to shift poleward in global-warming simulations with current climate models. Yet the reasons for this shift have remained unclear. Here we show that this shift occurs even in extremely idealized (but still three-dimensional) simulations of dry atmospheres. We use these simulations to develop an understanding of the processes responsible for the shift and develop a conceptual model that accounts for it.

We demonstrate that changes in the convective static stability in the deep tropics alone can drive remote shifts in the midlatitude storm tracks. Through simulations with a dry idealized general circulation model (GCM), midlatitude storm tracks are shown to be located where the mean available potential energy (MAPE, a measure of the potential energy available to be converted into kinetic energy) is maximal. As the climate varies, even if only driven by tropical static stability changes, the MAPE maximum shifts primarily because of shifts of the maximum of near-surface meridional temperature gradients. The temperature gradients shift in response to changes in the width of the tropical Hadley circulation, whose width is affected by the tropical static stability. Storm tracks generally shift in tandem with shifts of the subtropical terminus of the Hadley circulation.

We develop a one-dimensional diffusive energy-balance model that links changes in the Hadley circulation to midlatitude temperature gradients and so to the storm tracks. It is the first conceptual model to incorporate a dynamical coupling between the tropical Hadley circulation and midlatitude turbulent energy transport. Numerical and analytical solutions of the model elucidate the circumstances of when and how the storm tracks shift in tandem with the terminus of the Hadley circulation. They illustrate how an increase of only the convective static stability in the deep tropics can lead to an expansion of the Hadley circulation and a poleward shift of storm tracks.

The simulations with the idealized GCM and the conceptual energy-balance model demonstrate a clear link between Hadley circulation dynamics and midlatitude storm track position. With the help of the hierarchy of models presented in this thesis, we obtain a closed theory of storm track shifts in dry climates. The relevance of this theory for more realistic moist climates is discussed.

Manganese: Minerals, Microbes, and the Evolution of Oxygenic Photosynthesis

Oxygenic photosynthesis fundamentally transformed our planet by releasing molecular oxygen and altering major biogeochemical cycles, and this exceptional metabolism relies on a redox-active cubane cluster of four manganese atoms. Not only is manganese essential for producing oxygen, but manganese is also only oxidized by oxygen and oxygen-derived species. Thus the history of manganese oxidation provides a valuable perspective on our planet’s environmental past, the ancient availability of oxygen, and the evolution of oxygenic photosynthesis. Broadly, the general trends of the geologic record of manganese deposition is a chronicle of ancient manganese oxidation: manganese is introduced into the fluid Earth as Mn(II) and it will remain only a trace component in sedimentary rocks until it is oxidized, forming Mn(III,IV) insoluble precipitates that are concentrated in the rock record. Because these manganese oxides are highly favorable electron acceptors, they often undergo reduction in sediments through anaerobic respiration and abiotic reaction pathways.

The following dissertation presents five chapters investigating manganese cycling both by examining ancient examples of manganese enrichments in the geologic record and exploring the mineralogical products of various pathways of manganese oxide reduction that may occur in sediments. The first chapter explores the mineralogical record of manganese and reports abundant manganese reduction recorded in six representative manganese-enriched sedimentary sequences. This is followed by a second chapter that further analyzes the earliest significant manganese deposit 2.4 billon years ago, and determines that it predated the origin of oxygenic photosynthesis and thus is supporting evidence for manganese-oxidizing photosynthesis as an evolutionary precursor prior to oxygenic photosynthesis. The lack of oxygen during this early manganese deposition was partially established using oxygen-sensitive detrital grains, and so a third chapter delves into what these grains mean for oxygen constraints using a mathematical model. The fourth chapter returns to processes affecting manganese post-deposition, and explores the relationships between manganese mineral products and (bio)geochemical reduction processes to understand how various manganese minerals can reveal ancient environmental conditions and biological metabolisms. Finally, a fifth chapter considers whether manganese can be mobilized and enriched in sedimentary rocks and determines that manganese was concentrated secondarily in a 2.5 billion-year-old example from South Africa. Overall, this thesis demonstrates how microbial processes, namely photosynthesis and metal oxide-reducing metabolisms, are linked to and recorded in the rich complexity of the manganese mineralogical record.

Palladium-Catalyzed Decarboxylative and Decarbonylative Transformations in the Synthesis of Fine and Commodity Chemicals

Decarboxylation and decarbonylation are important reactions in synthetic organic chemistry, transforming readily available carboxylic acids and their derivatives into various products through loss of carbon dioxide or carbon monoxide. In the past few decades, palladium-catalyzed decarboxylative and decarbonylative reactions experienced tremendous growth due to the excellent catalytic activity of palladium. Development of new reactions in this category for fine and commodity chemical synthesis continues to draw attention from the chemistry community.

The Stoltz laboratory has established a palladium-catalyzed enantioselective decarboxylative allylic alkylation of β-keto esters for the synthesis of α-quaternary ketones since 2005. Recently, we extended this chemistry to lactams due to the ubiquity and importance of nitrogen-containing heterocycles. A wide variety of α-quaternary and tetrasubstituted α-tertiary lactams were obtained in excellent yields and exceptional enantioselectivities using our palladium-catalyzed decarboxylative allylic alkylation chemistry. Enantioenriched α-quaternary carbonyl compounds are versatile building blocks that can be further elaborated to intercept synthetic intermediates en route to many classical natural products. Thus our chemistry enables catalytic asymmetric formal synthesis of these complex molecules.

In addition to fine chemicals, we became interested in commodity chemical synthesis using renewable feedstocks. In collaboration with the Grubbs group, we developed a palladium-catalyzed decarbonylative dehydration reaction that converts abundant and inexpensive fatty acids into value-added linear alpha olefins. The chemistry proceeds under relatively mild conditions, requires very low catalyst loading, tolerates a variety of functional groups, and is easily performed on a large scale. An additional advantage of this chemistry is that it provides access to expensive odd-numbered alpha olefins.

Finally, combining features of both projects, we applied a small-scale decarbonylative dehydration reaction to the synthesis of α-vinyl carbonyl compounds. Direct α-vinylation is challenging, and asymmetric vinylations are rare. Taking advantage of our decarbonylative dehydration chemistry, we were able to transform enantioenriched δ-oxocarboxylic acids into quaternary α-vinyl carbonyl compounds in good yields with complete retention of stereochemistry. Our explorations culminated in the catalytic enantioselective total synthesis of (–)-aspewentin B, a terpenoid natural product featuring a quaternary α-vinyl ketone. Both decarboxylative and decarbonylative chemistries found application in the late stage of the total synthesis.

Normal structures and automorphism groups of t-designs

Combinatorial configurations known as t-designs are studied. These are pairs ˂B, ∏˃, where each element of B is a k-subset of ∏, and each t-design occurs in exactly λ elements of B, for some fixed integers k and λ. A theory of internal structure of t-designs is developed, and it is shown that any t-design can be decomposed in a natural fashion into a sequence of “simple” subdesigns. The theory is quite similar to the analysis of a group with respect to its normal subgroups, quotient groups, and homomorphisms. The analogous concepts of normal subdesigns, quotient designs, and design homomorphisms are all defined and used.

This structure theory is then applied to the class of t-designs whose automorphism groups are transitive on sets of t points. It is shown that if G is a permutation group transitive on sets of t letters and ф is any set of letters, then images of ф under G form a t-design whose parameters may be calculated from the group G. Such groups are discussed, especially for the case t = 2, and the normal structure of such designs is considered. Theorem 2.2.12 gives necessary and sufficient conditions for a t-design to be simple, purely in terms of the automorphism group of the design. Some constructions are given.

Finally, 2-designs with k = 3 and λ = 2 are considered in detail. These designs are first considered in general, with examples illustrating some of the configurations which can arise. Then an attempt is made to classify all such designs with an automorphism group transitive on pairs of points. Many cases are eliminated of reduced to combinations of Steiner triple systems. In the remaining cases, the simple designs are determined to consist of one infinite class and one exceptional case.

λ-designs and related combinatorial configurations

This thesis deals with two problems. The first is the determination of λ-designs, combinatorial configurations which are essentially symmetric block designs with the condition that each subset be of the same cardinality negated. We construct an infinite family of such designs from symmetric block designs and obtain some basic results about their structure. These results enable us to solve the problem for λ = 3 and λ = 4. The second problem deals with configurations related to both λ -designs and (ѵ, k, λ)-configurations. We have (n-1) k-subsets of {1, 2, ..., n}, S₁, ..., S_n-1 such that S_i ∩ S_j is a λ-set for i ≠ j. We obtain specifically the replication numbers of such a design in terms of n, k, and λ with one exceptional class which we determine explicitly. In certain special cases we settle the problem entirely.

On the uniqueness of singular solutions to boundary-initial value problems in linear elastodynamics

This investigation deals with certain generalizations of the classical uniqueness theorem for the second boundary-initial value problem in the linearized dynamical theory of not necessarily homogeneous nor isotropic elastic solids. First, the regularity assumptions underlying the foregoing theorem are relaxed by admitting stress fields with suitably restricted finite jump discontinuities. Such singularities are familiar from known solutions to dynamical elasticity problems involving discontinuous surface tractions or non-matching boundary and initial conditions. The proof of the appropriate uniqueness theorem given here rests on a generalization of the usual energy identity to the class of singular elastodynamic fields under consideration.

Following this extension of the conventional uniqueness theorem, we turn to a further relaxation of the customary smoothness hypotheses and allow the displacement field to be differentiable merely in a generalized sense, thereby admitting stress fields with square-integrable unbounded local singularities, such as those encountered in the presence of focusing of elastic waves. A statement of the traction problem applicable in these pathological circumstances necessitates the introduction of "weak solutions'' to the field equations that are accompanied by correspondingly weakened boundary and initial conditions. A uniqueness theorem pertaining to this weak formulation is then proved through an adaptation of an argument used by O. Ladyzhenskaya in connection with the first boundary-initial value problem for a second-order hyperbolic equation in a single dependent variable. Moreover, the second uniqueness theorem thus obtained contains, as a special case, a slight modification of the previously established uniqueness theorem covering solutions that exhibit only finite stress-discontinuities.

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

Part 1. 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 lower 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.

Part 2. 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.

Part 3. 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.

Estimation of catalyst activity profiles and deactivation parameters from reactor operating data with applications to naphtha reforming

Techniques are developed for estimating activity profiles in fixed bed reactors and catalyst deactivation parameters from operating reactor data. These techniques are applicable, in general, to most industrial catalytic processes. The catalytic reforming of naphthas is taken as a broad example to illustrate the estimation schemes and to signify the physical meaning of the kinetic parameters of the estimation equations. The work is described in two parts. Part I deals with the modeling of kinetic rate expressions and the derivation of the working equations for estimation. Part II concentrates on developing various estimation techniques.

Part I: The reactions used to describe naphtha reforming are dehydrogenation and dehydroisomerization of cycloparaffins; isomerization, dehydrocyclization and hydrocracking of paraffins; and the catalyst deactivation reactions, namely coking on alumina sites and sintering of platinum crystallites. The rate expressions for the above reactions are formulated, and the effects of transport limitations on the overall reaction rates are discussed in the appendices. Moreover, various types of interaction between the metallic and acidic active centers of reforming catalysts are discussed as characterizing the different types of reforming reactions.

Part II: In catalytic reactor operation, the activity distribution along the reactor determines the kinetics of the main reaction and is needed for predicting the effect of changes in the feed state and the operating conditions on the reactor output. In the case of a monofunctional catalyst and of bifunctional catalysts in limiting conditions, the cumulative activity is sufficient for predicting steady reactor output. The estimation of this cumulative activity can be carried out easily from measurements at the reactor exit. For a general bifunctional catalytic system, the detailed activity distribution is needed for describing the reactor operation, and some approximation must be made to obtain practicable estimation schemes. This is accomplished by parametrization techniques using measurements at a few points along the reactor. Such parametrization techniques are illustrated numerically with a simplified model of naphtha reforming.

To determine long term catalyst utilization and regeneration policies, it is necessary to estimate catalyst deactivation parameters from the the current operating data. For a first order deactivation model with a monofunctional catalyst or with a bifunctional catalyst in special limiting circumstances, analytical techniques are presented to transform the partial differential equations to ordinary differential equations which admit more feasible estimation schemes. Numerical examples include the catalytic oxidation of butene to butadiene and a simplified model of naphtha reforming. For a general bifunctional system or in the case of a monofunctional catalyst subject to general power law deactivation, the estimation can only be accomplished approximately. The basic feature of an appropriate estimation scheme involves approximating the activity profile by certain polynomials and then estimating the deactivation parameters from the integrated form of the deactivation equation by regression techniques. Different bifunctional systems must be treated by different estimation algorithms, which are illustrated by several cases of naphtha reforming with different feed or catalyst composition.