Topics in randomized numerical linear algebra

This thesis studies three classes of randomized numerical linear algebra algorithms, namely: (i) randomized matrix sparsification algorithms, (ii) low-rank approximation algorithms that use randomized unitary transformations, and (iii) low-rank approximation algorithms for positive-semidefinite (PSD) matrices.

Randomized matrix sparsification algorithms set randomly chosen entries of the input matrix to zero. When the approximant is substituted for the original matrix in computations, its sparsity allows one to employ faster sparsity-exploiting algorithms. This thesis contributes bounds on the approximation error of nonuniform randomized sparsification schemes, measured in the spectral norm and two NP-hard norms that are of interest in computational graph theory and subset selection applications.

Low-rank approximations based on randomized unitary transformations have several desirable properties: they have low communication costs, are amenable to parallel implementation, and exploit the existence of fast transform algorithms. This thesis investigates the tradeoff between the accuracy and cost of generating such approximations. State-of-the-art spectral and Frobenius-norm error bounds are provided.

The last class of algorithms considered are SPSD "sketching" algorithms. Such sketches can be computed faster than approximations based on projecting onto mixtures of the columns of the matrix. The performance of several such sketching schemes is empirically evaluated using a suite of canonical matrices drawn from machine learning and data analysis applications, and a framework is developed for establishing theoretical error bounds.

In addition to studying these algorithms, this thesis extends the Matrix Laplace Transform framework to derive Chernoff and Bernstein inequalities that apply to all the eigenvalues of certain classes of random matrices. These inequalities are used to investigate the behavior of the singular values of a matrix under random sampling, and to derive convergence rates for each individual eigenvalue of a sample covariance matrix.

Generalizations and extensions of the Fokker-Planck-Kolmogorov equations

The problem of determining probability density functions of general transformations of random processes is considered in this thesis. A method of solution is developed in which partial differential equations satisfied by the unknown density function are derived. These partial differential equations are interpreted as generalized forms of the classical Fokker-Planck-Kolmogorov equations and are shown to imply the classical equations for certain classes of Markov processes. Extensions of the generalized equations which overcome degeneracy occurring in the steady-state case are also obtained.

The equations of Darling and Siegert are derived as special cases of the generalized equations thereby providing unity to two previously existing theories. A technique for treating non-Markov processes by studying closely related Markov processes is proposed and is seen to yield the Darling and Siegert equations directly from the classical Fokker-Planck-Kolmogorov equations.

As illustrations of their applicability, the generalized Fokker-Planck-Kolmogorov equations are presented for certain joint probability density functions associated with the linear filter. These equations are solved for the density of the output of an arbitrary linear filter excited by Markov Gaussian noise and for the density of the output of an RC filter excited by the Poisson square wave. This latter density is also found by using the extensions of the generalized equations mentioned above. Finally, some new approaches for finding the output probability density function of an RC filter-limiter-RC filter system driven by white Gaussian noise are included. The results in this case exhibit the data required for complete solution and clearly illustrate some of the mathematical difficulties inherent to the use of the generalized equations.

Some constructions, related to noncommutative tori; Fredholm modules and the Beilinson-Bloch regulator

A noncommutative 2-torus is one of the main toy models of noncommutative geometry, and a noncommutative n-torus is a straightforward generalization of it. In 1980, Pimsner and Voiculescu in [17] described a 6-term exact sequence, which allows for the computation of the K-theory of noncommutative tori. It follows that both even and odd K-groups of n-dimensional noncommutative tori are free abelian groups on 2^n-1 generators. In 1981, the Powers-Rieffel projector was described [19], which, together with the class of identity, generates the even K-theory of noncommutative 2-tori. In 1984, Elliott [10] computed trace and Chern character on these K-groups. According to Rieffel [20], the odd K-theory of a noncommutative n-torus coincides with the group of connected components of the elements of the algebra. In particular, generators of K-theory can be chosen to be invertible elements of the algebra. In Chapter 1, we derive an explicit formula for the First nontrivial generator of the odd K-theory of noncommutative tori. This gives the full set of generators for the odd K-theory of noncommutative 3-tori and 4-tori.

In Chapter 2, we apply the graded-commutative framework of differential geometry to the polynomial subalgebra of the noncommutative torus algebra. We use the framework of differential geometry described in [27], [14], [25], [26]. In order to apply this framework to noncommutative torus, the notion of the graded-commutative algebra has to be generalized: the "signs" should be allowed to take values in U(1), rather than just {-1,1}. Such generalization is well-known (see, e.g., [8] in the context of linear algebra). We reformulate relevant results of [27], [14], [25], [26] using this extended notion of sign. We show how this framework can be used to construct differential operators, differential forms, and jet spaces on noncommutative tori. Then, we compare the constructed differential forms to the ones, obtained from the spectral triple of the noncommutative torus. Sections 2.1-2.3 recall the basic notions from [27], [14], [25], [26], with the required change of the notion of "sign". In Section 2.4, we apply these notions to the polynomial subalgebra of the noncommutative torus algebra. This polynomial subalgebra is similar to a free graded-commutative algebra. We show that, when restricted to the polynomial subalgebra, Connes construction of differential forms gives the same answer as the one obtained from the graded-commutative differential geometry. One may try to extend these notions to the smooth noncommutative torus algebra, but this was not done in this work.

A reconstruction of the Beilinson-Bloch regulator (for curves) via Fredholm modules was given by Eugene Ha in [12]. However, the proof in [12] contains a critical gap; in Chapter 3, we close this gap. More specifically, we do this by obtaining some technical results, and by proving Property 4 of Section 3.7 (see Theorem 3.9.4), which implies that such reformulation is, indeed, possible. The main motivation for this reformulation is the longer-term goal of finding possible analogs of the second K-group (in the context of algebraic geometry and K-theory of rings) and of the regulators for noncommutative spaces. This work should be seen as a necessary preliminary step for that purpose.

For the convenience of the reader, we also give a short description of the results from [12], as well as some background material on central extensions and Connes-Karoubi character.

The Riesz space structure of an Abelian W*-algebra

Let M be an Abelian W*-algebra of operators on a Hilbert space H. Let M₀ be the set of all linear, closed, densely defined transformations in H which commute with every unitary operator in the commutant M’ of M. A well known result of R. Pallu de Barriere states that if ɸ is a normal positive linear functional on M, then ɸ is of the form T → (Tx, x) for some x in H, where T is in M. An elementary proof of this result is given, using only those properties which are consequences of the fact that ReM is a Dedekind complete Riesz space with plenty of normal integrals. The techniques used lead to a natural construction of the class M₀, and an elementary proof is given of the fact that a positive self-adjoint transformation in M₀ has a unique positive square root in M₀. It is then shown that when the algebraic operations are suitably defined, then M₀ becomes a commutative algebra. If ReM₀ denotes the set of all self-adjoint elements of M₀, then it is proved that ReM₀ is Dedekind complete, universally complete Riesz spaces which contains ReM as an order dense ideal. A generalization of the result of R. Pallu de la Barriere is obtained for the Riesz space ReM₀ which characterizes the normal integrals on the order dense ideals of ReM₀. It is then shown that ReM₀ may be identified with the extended order dual of ReM, and that ReM₀ is perfect in the extended sense.

Some secondary questions related to the Riesz space ReM are also studied. In particular it is shown that ReM is a perfect Riesz space, and that every integral is normal under the assumption that every decomposition of the identity operator has non-measurable cardinal. The presence of atoms in ReM is examined briefly, and it is shown that ReM is finite dimensional if and only if every order bounded linear functional on ReM is a normal integral.

Relativistic quark models and the current algebra

In this thesis we are concerned with finding representations of the algebra of SU(3) vector and axial-vector charge densities at infinite momentum (the "current algebra") to describe the mesons, idealizing the real continua of multiparticle states as a series of discrete resonances of zero width. Such representations would describe the masses and quantum numbers of the mesons, the shapes of their Regge trajectories, their electromagnetic and weak form factors, and (approximately, through the PCAC hypothesis) pion emission or absorption amplitudes.

We assume that the mesons have internal degrees of freedom equivalent to being made of two quarks (one an antiquark) and look for models in which the mass is SU(3)-independent and the current is a sum of contributions from the individual quarks. Requiring that the current algebra, as well as conditions of relativistic invariance, be satisfied turns out to be very restrictive, and, in fact, no model has been found which satisfies all requirements and gives a reasonable mass spectrum. We show that using more general mass and current operators but keeping the same internal degrees of freedom will not make the problem any more solvable. In particular, in order for any two-quark solution to exist it must be possible to solve the "factorized SU(2) problem," in which the currents are isospin currents and are carried by only one of the component quarks (as in the K meson and its excited states).

In the free-quark model the currents at infinite momentum are found using a manifestly covariant formalism and are shown to satisfy the current algebra, but the mass spectrum is unrealistic. We then consider a pair of quarks bound by a potential, finding the current as a power series in 1/m where m is the quark mass. Here it is found impossible to satisfy the algebra and relativistic invariance with the type of potential tried, because the current contributions from the two quarks do not commute with each other to order 1/m³. However, it may be possible to solve the factorized SU(2) problem with this model.

The factorized problem can be solved exactly in the case where all mesons have the same mass, using a covariant formulation in terms of an internal Lorentz group. For a more realistic, nondegenerate mass there is difficulty in covariantly solving even the factorized problem; one model is described which almost works but appears to require particles of spacelike 4-momentum, which seem unphysical.

Although the search for a completely satisfactory model has been unsuccessful, the techniques used here might eventually reveal a working model. There is also a possibility of satisfying a weaker form of the current algebra with existing models.

Bifurcation theory of nonlinear boundary value problems

The theory of bifurcation of solutions to two-point boundary value problems is developed for a system of nonlinear first order ordinary differential equations in which the bifurcation parameter is allowed to appear nonlinearly. An iteration method is used to establish necessary and sufficient conditions for bifurcation and to construct a unique bifurcated branch in a neighborhood of a bifurcation point which is a simple eigenvalue of the linearized problem. The problem of bifurcation at a degenerate eigenvalue of the linearized problem is reduced to that of solving a system of algebraic equations. Cases with no bifurcation and with multiple bifurcation at a degenerate eigenvalue are considered.

The iteration method employed is shown to generate approximate solutions which contain those obtained by formal perturbation theory. Thus the formal perturbation solutions are rigorously justified. A theory of continuation of a solution branch out of the neighborhood of its bifurcation point is presented. Several generalizations and extensions of the theory to other types of problems, such as systems of partial differential equations, are described.

The theory is applied to the problem of the axisymmetric buckling of thin spherical shells. Results are obtained which confirm recent numerical computations.

Growth and characterization of novel, III-V semiconductor heterostructures

The material presented in this thesis concerns the growth and characterization of III-V semiconductor heterostructures. Studies of the interactions between bound states in coupled quantum wells and between well and barrier bound states in AlAs/GaAs heterostructures are presented. We also demonstrate the broad array of novel tunnel structures realizable in the InAs/GaSb/AlSb material system. Because of the unique broken-gap band alignment of InAs/GaSb these structures involve transport between the conduction- and valence-bands of adjacent layers. These devices possess a wide range of electrical properties and are fundamentally different from conventional AlAs/GaAs tunnel devices. We report on the fabrication of a novel tunnel transistor with the largest reported room temperature current gains. We also present time-resolved studies of the growth fronts of InAs/GainSb strained layer superlattices and investigations of surface anion exchange reactions.

Chapter 2 covers tunneling studies of conventional AlAs/GaAs RTD's. The results of two studies are presented: (i) A test of coherent vs. sequential tunneling in triple barrier heterostructures, (ii) An optical measurement of the effect of barrier X-point states on Γ-point well states. In the first it was found if two quantum wells are separated by a sufficiently thin barrier, then the eigenstates of the system extend coherently across both wells and the central barriers. For thicker barriers between the wells, the electrons become localized in the individual wells and transport is best described by the electrons hopping between the wells. In the second, it was found that Γ-point well states and X-point barrier states interact strongly. The barrier X-point states modify the energies of the well states and increase the escape rate for carriers in the quantum well.

The results of several experimental studies of a novel class of tunnel devices realized in the InAs/GaSb/AlSb material system are presented in Chapter 3. These interband tunnel structures involve transport between conduction- and valence-band states in adjacent material layers. These devices are compared and contrasted with the conventional AlAs/GaAs structures discussed in Chapter 2 and experimental results are presented for both resonant and nonresonant devices. These results are compared with theoretical simulations and necessary extensions to the theoretical models are discussed.

In chapter 4 experimental results from a novel tunnel transistor are reported. The measured current gains in this transistor exceed 100 at room temperature. This is the highest reported gain at room temperature for any tunnel transistor. The device is analyzed and the current conduction and gain mechanisms are discussed.

Chapters 5 and 6 are studies of the growth of structures involving layers with different anions. Chapter 5 covers the growth of InAs/GainSb superlattices for far infrared detectors and time resolved, in-situ studies of their growth fronts. It was found that the bandgap of superlattices with identical layer thicknesses and compositions varied by as much as 40 meV depending on how their internal interfaces are formed. The absorption lengths in superlattices with identical bandgaps but whose interfaces were formed in different ways varied by as much as a factor of two. First the superlattice is discussed including an explanation of the device and the complications involved in its growth. The experimental technique of reflection high energy electron diffraction (RHEED) is reviewed, and the results of RHEED studies of the growth of these complicated structures are presented. The development of a time resolved, in-situ characterization of the internal interfaces of these superlattices is described. Chapter 6 describes the result of a detailed study of some of the phenomena described in chapter 5. X-ray photoelectron spectroscopy (XPS) studies of anion exchange reactions on the growth fronts of these superlattices are reported. Concurrent RHEED studies of the same physical systems studied with XPS are presented. Using the RHEED and XPS results, a real-time, indirect measurement of surface exchange reactions was developed.

Descriptive set theory and the ergodic theory of countable groups

The primary focus of this thesis is on the interplay of descriptive set theory and the ergodic theory of group actions. This incorporates the study of turbulence and Borel reducibility on the one hand, and the theory of orbit equivalence and weak equivalence on the other. Chapter 2 is joint work with Clinton Conley and Alexander Kechris; we study measurable graph combinatorial invariants of group actions and employ the ultraproduct construction as a way of constructing various measure preserving actions with desirable properties. Chapter 3 is joint work with Lewis Bowen; we study the property MD of residually finite groups, and we prove a conjecture of Kechris by showing that under general hypotheses property MD is inherited by a group from one of its co-amenable subgroups. Chapter 4 is a study of weak equivalence. One of the main results answers a question of Abért and Elek by showing that within any free weak equivalence class the isomorphism relation does not admit classification by countable structures. The proof relies on affirming a conjecture of Ioana by showing that the product of a free action with a Bernoulli shift is weakly equivalent to the original action. Chapter 5 studies the relationship between mixing and freeness properties of measure preserving actions. Chapter 6 studies how approximation properties of ergodic actions and unitary representations are reflected group theoretically and also operator algebraically via a group's reduced C^*-algebra. Chapter 7 is an appendix which includes various results on mixing via filters and on Gaussian actions.

Dynamics of cell–matrix mechanical interactions in three dimensions

The forces cells apply to their surroundings control biological processes such as growth, adhesion, development, and migration. In the past 20 years, a number of experimental techniques have been developed to measure such cell tractions. These approaches have primarily measured the tractions applied by cells to synthetic two-dimensional substrates, which do not mimic in vivo conditions for most cell types. Many cell types live in a fibrous three-dimensional (3D) matrix environment. While studying cell behavior in such 3D matrices will provide valuable insights for the mechanobiology and tissue engineering communities, no experimental approaches have yet measured cell tractions in a fibrous 3D matrix.

This thesis describes the development and application of an experimental technique for quantifying cellular forces in a natural 3D matrix. Cells and their surrounding matrix are imaged in three dimensions with high speed confocal microscopy. The cell-induced matrix displacements are computed from the 3D image volumes using digital volume correlation. The strain tensor in the 3D matrix is computed by differentiating the displacements, and the stress tensor is computed by applying a constitutive law. Finally, tractions applied by the cells to the matrix are computed directly from the stress tensor.

The 3D traction measurement approach is used to investigate how cells mechanically interact with the matrix in biologically relevant processes such as division and invasion. During division, a single mother cell undergoes a drastic morphological change to split into two daughter cells. In a 3D matrix, dividing cells apply tensile force to the matrix through thin, persistent extensions that in turn direct the orientation and location of the daughter cells. Cell invasion into a 3D matrix is the first step required for cell migration in three dimensions. During invasion, cells initially apply minimal tractions to the matrix as they extend thin protrusions into the matrix fiber network. The invading cells anchor themselves to the matrix using these protrusions, and subsequently pull on the matrix to propel themselves forward.

Lastly, this thesis describes a constitutive model for the 3D fibrous matrix that uses a finite element (FE) approach. The FE model simulates the fibrous microstructure of the matrix and matches the cell-induced matrix displacements observed experimentally using digital volume correlation. The model is applied to predict how cells mechanically sense one another in a 3D matrix. It is found that cell-induced matrix displacements localize along linear paths. These linear paths propagate over a long range through the fibrous matrix, and provide a mechanism for cell-cell signaling and mechanosensing. The FE model developed here has the potential to reveal the effects of matrix density, inhomogeneity, and anisotropy in signaling cell behavior through mechanotransduction.

Completions of epsilon-dense partial Latin squares

A classical question in combinatorics is the following: given a partial Latin square $P$, when can we complete $P$ to a Latin square $L$? In this paper, we investigate the class of textbf{$epsilon$-dense partial Latin squares}: partial Latin squares in which each symbol, row, and column contains no more than $epsilon n$-many nonblank cells. Based on a conjecture of Nash-Williams, Daykin and H"aggkvist conjectured that all $frac{1}{4}$-dense partial Latin squares are completable. In this paper, we will discuss the proof methods and results used in previous attempts to resolve this conjecture, introduce a novel technique derived from a paper by Jacobson and Matthews on generating random Latin squares, and use this novel technique to study $ epsilon$-dense partial Latin squares that contain no more than $delta n^2$ filled cells in total.

In Chapter 2, we construct completions for all $ epsilon$-dense partial Latin squares containing no more than $delta n^2$ filled cells in total, given that $epsilon < frac{1}{12}, delta < frac{ left(1-12epsilonright)^{2}}{10409}$. In particular, we show that all $9.8 cdot 10^{-5}$-dense partial Latin squares are completable. In Chapter 4, we augment these results by roughly a factor of two using some probabilistic techniques. These results improve prior work by Gustavsson, which required $epsilon = delta leq 10^{-7}$, as well as Chetwynd and H"aggkvist, which required $epsilon = delta = 10^{-5}$, $n$ even and greater than $10^7$.

If we omit the probabilistic techniques noted above, we further show that such completions can always be found in polynomial time. This contrasts a result of Colbourn, which states that completing arbitrary partial Latin squares is an NP-complete task. In Chapter 3, we strengthen Colbourn's result to the claim that completing an arbitrary $left(frac{1}{2} + epsilonright)$-dense partial Latin square is NP-complete, for any $epsilon > 0$.

Colbourn's result hinges heavily on a connection between triangulations of tripartite graphs and Latin squares. Motivated by this, we use our results on Latin squares to prove that any tripartite graph $G = (V_1, V_2, V_3)$ such that begin{itemize} item $|V_1| = |V_2| = |V_3| = n$, item For every vertex $v in V_i$, $deg_+(v) = deg_-(v) geq (1- epsilon)n,$ and item $|E(G)| > (1 - delta)cdot 3n^2$ end{itemize} admits a triangulation, if $epsilon < frac{1}{132}$, $delta < frac{(1 -132epsilon)^2 }{83272}$. In particular, this holds when $epsilon = delta=1.197 cdot 10^{-5}$.

This strengthens results of Gustavsson, which requires $epsilon = delta = 10^{-7}$.

In an unrelated vein, Chapter 6 explores the class of textbf{quasirandom graphs}, a notion first introduced by Chung, Graham and Wilson cite{chung1989quasi} in 1989. Roughly speaking, a sequence of graphs is called "quasirandom"' if it has a number of properties possessed by the random graph, all of which turn out to be equivalent. In this chapter, we study possible extensions of these results to random $k$-edge colorings, and create an analogue of Chung, Graham and Wilson's result for such colorings.

Ordinary mod p representations of the metaplectic cover of p-adic SL_2

We classify the genuine ordinary mod p representations of the metaplectic group SL(2,F)-tilde, where F is a p-adic field, and compute its genuine mod p spherical and Iwahori Hecke algebras. The motivation is an interest in a possible correspondence between genuine mod p representations of SL(2,F)-tilde and mod p representations of the dual group PGL(2,F), so we also compare the two Hecke algebras to the mod p spherical and Iwahori Hecke algebras of PGL(2,F). We show that the genuine mod p spherical Hecke algebra of SL(2,F)-tilde is isomorphic to the mod p spherical Hecke algebra of PGL(2,F), and that one can choose an isomorphism which is compatible with a natural, though partial, correspondence of unramified ordinary representations via the Hecke action on their spherical vectors. We then show that the genuine mod p Iwahori Hecke algebra of SL(2,F)-tilde is a subquotient of the mod p Iwahori Hecke algebra of PGL(2,F), but that the two algebras are not isomorphic. This is in contrast to the situation in characteristic 0, where by work of Savin one can recover the local Shimura correspondence for representations generated by their Iwahori fixed vectors from an isomorphism of Iwahori Hecke algebras.

Voting games with incomplete information

We examine voting situations in which individuals have incomplete information over each others' true preferences. In many respects, this work is motivated by a desire to provide a more complete understanding of so-called probabilistic voting.

Chapter 2 examines the similarities and differences between the incentives faced by politicians who seek to maximize expected vote share, expected plurality, or probability of victory in single member: single vote, simple plurality electoral systems. We find that, in general, the candidates' optimal policies in such an electoral system vary greatly depending on their objective function. We provide several examples, as well as a genericity result which states that almost all such electoral systems (with respect to the distributions of voter behavior) will exhibit different incentives for candidates who seek to maximize expected vote share and those who seek to maximize probability of victory.

In Chapter 3, we adopt a random utility maximizing framework in which individuals' preferences are subject to action-specific exogenous shocks. We show that Nash equilibria exist in voting games possessing such an information structure and in which voters and candidates are each aware that every voter's preferences are subject to such shocks. A special case of our framework is that in which voters are playing a Quantal Response Equilibrium (McKelvey and Palfrey (1995), (1998)). We then examine candidate competition in such games and show that, for sufficiently large electorates, regardless of the dimensionality of the policy space or the number of candidates, there exists a strict equilibrium at the social welfare optimum (i.e., the point which maximizes the sum of voters' utility functions). In two candidate contests we find that this equilibrium is unique.

Finally, in Chapter 4, we attempt the first steps towards a theory of equilibrium in games possessing both continuous action spaces and action-specific preference shocks. Our notion of equilibrium, Variational Response Equilibrium, is shown to exist in all games with continuous payoff functions. We discuss the similarities and differences between this notion of equilibrium and the notion of Quantal Response Equilibrium and offer possible extensions of our framework.

Electron flow through cytochrome P450

The cytochromes P450 (P450s) are a remarkable class of heme enzymes that catalyze the metabolism of xenobiotics and the biosynthesis of signaling molecules. Controlled electron flow into the thiolate-ligated heme active site allows P450s to activate molecular oxygen and hydroxylate aliphatic C–H bonds via the formation of high-valent metal-oxo intermediates (compounds I and II). Due to the reactive nature and short lifetimes of these intermediates, many of the fundamental steps in catalysis have not been observed directly. The Gray group and others have developed photochemical methods, known as “flash-quench,” for triggering electron transfer (ET) and generating redox intermediates in proteins in the absence of native ET partners. Photo-triggering affords a high degree of temporal precision for the gating of an ET event; the initial ET and subsequent reactions can be monitored on the nanosecond-to-second timescale using transient absorption (TA) spectroscopies. Chapter 1 catalogues critical aspects of P450 structure and mechanism, including the native pathway for formation of compound I, and outlines the development of photochemical processes that can be used to artificially trigger ET in proteins. Chapters 2 and 3 describe the development of these photochemical methods to establish electronic communication between a photosensitizer and the buried P450 heme. Chapter 2 describes the design and characterization of a Ru-P450-BM3 conjugate containing a ruthenium photosensitizer covalently tethered to the P450 surface, and nanosecond-to-second kinetics of the photo-triggered ET event are presented. By analyzing data at multiple wavelengths, we have identified the formation of multiple ET intermediates, including the catalytically relevant compound II; this intermediate is generated by oxidation of a bound water molecule in the ferric resting state enzyme. The work in Chapter 3 probes the role of a tryptophan residue situated between the photosensitizer and heme in the aforementioned Ru-P450 BM3 conjugate. Replacement of this tryptophan with histidine does not perturb the P450 structure, yet it completely eliminates the ET reactivity described in Chapter 2. The presence of an analogous tryptophan in Ru-P450 CYP119 conjugates also is necessary for observing oxidative ET, but the yield of heme oxidation is lower. Chapter 4 offers a basic description of the theoretical underpinnings required to analyze ET. Single-step ET theory is first presented, followed by extensions to multistep ET: electron “hopping.” The generation of “hopping maps” and use of a hopping map program to analyze the rate advantage of hopping over single-step ET is described, beginning with an established rhenium-tryptophan-azurin hopping system. This ET analysis is then applied to the Ru-tryptophan-P450 systems described in Chapter 2; this strongly supports the presence of hopping in Ru-P450 conjugates. Chapter 5 explores the implementation of flash-quench and other phototriggered methods to examine the native reductive ET and gas binding events that activate molecular oxygen. In particular, TA kinetics that demonstrate heme reduction on the microsecond timescale for four Ru-P450 conjugates are presented. In addition, we implement laser flash-photolysis of P450 ferrous–CO to study the rates of CO rebinding in the thermophilic P450 CYP119 at variable temperature. Chapter 6 describes the development and implementation of air-sensitive potentiometric redox titrations to determine the solution reduction potentials of a series of P450 BM3 mutants, which were designed for non-native cyclopropanation of styrene in vivo. An important conclusion from this work is that substitution of the axial cysteine for serine shifts the wild type reduction potential positive by 130 mV, facilitating reduction by biological redox cofactors in the presence of poorly-bound substrates. While this mutation abolishes oxygenation activity, these mutants are capable of catalyzing the cyclopropanation of styrene, even within the confines of an E. coli cell. Four appendices are also provided, including photochemical heme oxidation in ruthenium-modified nitric oxide synthase (Appendix A), general protocols (Appendix B), Chapter-specific notes (Appendix C) and Matlab scripts used for data analysis (Appendix D).

Ortho-positronium annihilation: steps toward computing the first order radiative corrections

The 0.2% experimental accuracy of the 1968 Beers and Hughes measurement of the annihilation lifetime of ortho-positronium motivates the attempt to compute the first order quantum electrodynamic corrections to this lifetime. The theoretical problems arising in this computation are here studied in detail up to the point of preparing the necessary computer programs and using them to carry out some of the less demanding steps -- but the computation has not yet been completed. Analytic evaluation of the contributing Feynman diagrams is superior to numerical evaluation, and for this process can be carried out with the aid of the Reduce algebra manipulation computer program.

The relation of the positronium decay rate to the electronpositron annihilation-in-flight amplitude is derived in detail, and it is shown that at threshold annihilation-in-flight, Coulomb divergences appear while infrared divergences vanish. The threshold Coulomb divergences in the amplitude cancel against like divergences in the modulating continuum wave function.

Using the lowest order diagrams of electron-positron annihilation into three photons as a test case, various pitfalls of computer algebraic manipulation are discussed along with ways of avoiding them. The computer manipulation of artificial polynomial expressions is preferable to the direct treatment of rational expressions, even though redundant variables may have to be introduced.

Special properties of the contributing Feynman diagrams are discussed, including the need to restore gauge invariance to the sum of the virtual photon-photon scattering box diagrams by means of a finite subtraction.

A systematic approach to the Feynman-Brown method of Decomposition of single loop diagram integrals with spin-related tensor numerators is developed in detail. This approach allows the Feynman-Brown method to be straightforwardly programmed in the Reduce algebra manipulation language.

The fundamental integrals needed in the wake of the application of the Feynman-Brown decomposition are exhibited and the methods which were used to evaluate them -- primarily dis persion techniques are briefly discussed.

Finally, it is pointed out that while the techniques discussed have permitted the computation of a fair number of the simpler integrals and diagrams contributing to the first order correction of the ortho-positronium annihilation rate, further progress with the more complicated diagrams and with the evaluation of traces is heavily contingent on obtaining access to adequate computer time and core capacity.

Baryon number violation beyond the standard model

This thesis describes simple extensions of the standard model with new sources of baryon number violation but no proton decay. The motivation for constructing such theories comes from the shortcomings of the standard model to explain the generation of baryon asymmetry in the universe, and from the absence of experimental evidence for proton decay. However, lack of any direct evidence for baryon number violation in general puts strong bounds on the naturalness of some of those models and favors theories with suppressed baryon number violation below the TeV scale. The initial part of the thesis concentrates on investigating models containing new scalars responsible for baryon number breaking. A model with new color sextet scalars is analyzed in more detail. Apart from generating cosmological baryon number, it gives nontrivial predictions for the neutron-antineutron oscillations, the electric dipole moment of the neutron, and neutral meson mixing. The second model discussed in the thesis contains a new scalar leptoquark. Although this model predicts mainly lepton flavor violation and a nonzero electric dipole moment of the electron, it includes, in its original form, baryon number violating nonrenormalizable dimension-five operators triggering proton decay. Imposing an appropriate discrete symmetry forbids such operators. Finally, a supersymmetric model with gauged baryon and lepton numbers is proposed. It provides a natural explanation for proton stability and predicts lepton number violating processes below the supersymmetry breaking scale, which can be tested at the Large Hadron Collider. The dark matter candidate in this model carries baryon number and can be searched for in direct detection experiments as well. The thesis is completed by constructing and briefly discussing a minimal extension of the standard model with gauged baryon, lepton, and flavor symmetries.