New variational principles for systems of partial differential equations

The question of finding variational principles for coupled systems of first order partial differential equations is considered. Using a potential representation for solutions of the first order system a higher order system is obtained. Existence of a variational principle follows if the original system can be transformed to a self-adjoint higher order system. Existence of variational principles for all linear wave equations with constant coefficients having real dispersion relations is established. The method of adjoining some of the equations of the original system to a suitable Lagrangian function by the method of Lagrange multipliers is used to construct new variational principles for a class of linear systems. The equations used as side conditions must satisfy highly-restrictive integrability conditions. In the more difficult nonlinear case the system of two equations in two independent variables can be analyzed completely. For systems determined by two conservation laws the side condition must be a conservation law in addition to satisfying the integrability conditions.

Part I. On the breaking of nonlinear dispersive waves. Part II. Variational principles in continuum mechanics

A model equation for water waves has been suggested by Whitham to study, qualitatively at least, the different kinds of breaking. This is an integro-differential equation which combines a typical nonlinear convection term with an integral for the dispersive effects and is of independent mathematical interest. For an approximate kernel of the form e^(-b|x|) it is shown first that solitary waves have a maximum height with sharp crests and secondly that waves which are sufficiently asymmetric break into "bores." The second part applies to a wide class of bounded kernels, but the kernel giving the correct dispersion effects of water waves has a square root singularity and the present argument does not go through. Nevertheless the possibility of the two kinds of breaking in such integro-differential equations is demonstrated.

Difficulties arise in finding variational principles for continuum mechanics problems in the Eulerian (field) description. The reason is found to be that continuum equations in the original field variables lack a mathematical "self-adjointness" property which is necessary for Euler equations. This is a feature of the Eulerian description and occurs in non-dissipative problems which have variational principles for their Lagrangian description. To overcome this difficulty a "potential representation" approach is used which consists of transforming to new (Eulerian) variables whose equations are self-adjoint. The transformations to the velocity potential or stream function in fluids or the scaler and vector potentials in electromagnetism often lead to variational principles in this way. As yet no general procedure is available for finding suitable transformations. Existing variational principles for the inviscid fluid equations in the Eulerian description are reviewed and some ideas on the form of the appropriate transformations and Lagrangians for fluid problems are obtained. These ideas are developed in a series of examples which include finding variational principles for Rossby waves and for the internal waves of a stratified fluid.

I. Singular perturbation problems involving singular points and turning points. II. On the averaged Lagrangian technique for nonlinear dispersive waves

In Part I a class of linear boundary value problems is considered which is a simple model of boundary layer theory. The effect of zeros and singularities of the coefficients of the equations at the point where the boundary layer occurs is considered. The usual boundary layer techniques are still applicable in some cases and are used to derive uniform asymptotic expansions. In other cases it is shown that the inner and outer expansions do not overlap due to the presence of a turning point outside the boundary layer. The region near the turning point is described by a two-variable expansion. In these cases a related initial value problem is solved and then used to show formally that for the boundary value problem either a solution exists, except for a discrete set of eigenvalues, whose asymptotic behaviour is found, or the solution is non-unique. A proof is given of the validity of the two-variable expansion; in a special case this proof also demonstrates the validity of the inner and outer expansions.

Nonlinear dispersive wave equations which are governed by variational principles are considered in Part II. It is shown that the averaged Lagrangian variational principle is in fact exact. This result is used to construct perturbation schemes to enable higher order terms in the equations for the slowly varying quantities to be calculated. A simple scheme applicable to linear or near-linear equations is first derived. The specific form of the first order correction terms is derived for several examples. The stability of constant solutions to these equations is considered and it is shown that the correction terms lead to the instability cut-off found by Benjamin. A general stability criterion is given which explicitly demonstrates the conditions under which this cut-off occurs. The corrected set of equations are nonlinear dispersive equations and their stationary solutions are investigated. A more sophisticated scheme is developed for fully nonlinear equations by using an extension of the Hamiltonian formalism recently introduced by Whitham. Finally the averaged Lagrangian technique is extended to treat slowly varying multiply-periodic solutions. The adiabatic invariants for a separable mechanical system are derived by this method.

Techniques for strength measurement at high pressures and strain-rates using transverse waves

The study of the strength of a material is relevant to a variety of applications including automobile collisions, armor penetration and inertial confinement fusion. Although dynamic behavior of materials at high pressures and strain-rates has been studied extensively using plate impact experiments, the results provide measurements in one direction only. Material behavior that is dependent on strength is unaccounted for. The research in this study proposes two novel configurations to mitigate this problem.

The first configuration introduced is the oblique wedge experiment, which is comprised of a driver material, an angled target of interest and a backing material used to measure in-situ velocities. Upon impact, a shock wave is generated in the driver material. As the shock encounters the angled target, it is reflected back into the driver and transmitted into the target. Due to the angle of obliquity of the incident wave, a transverse wave is generated that allows the target to be subjected to shear while being compressed by the initial longitudinal shock such that the material does not slip. Using numerical simulations, this study shows that a variety of oblique wedge configurations can be used to study the shear response of materials and this can be extended to strength measurement as well. Experiments were performed on an oblique wedge setup with a copper impactor, polymethylmethacrylate driver, aluminum 6061-t6 target, and a lithium fluoride window. Particle velocities were measured using laser interferometry and results agree well with the simulations.

The second novel configuration is the y-cut quartz sandwich design, which uses the anisotropic properties of y-cut quartz to generate a shear wave that is transmitted into a thin sample. By using an anvil material to back the thin sample, particle velocities measured at the rear surface of the backing plate can be implemented to calculate the shear stress in the material and subsequently the strength. Numerical simulations were conducted to show that this configuration has the ability to measure the strength for a variety of materials.

A cocktail of thermally stable, chemically synthesized capture agents for the efficient detection of anti-gp41 antibodies from human sera and techniques

This thesis reports on a method to improve in vitro diagnostic assays that detect immune response, with specific application to HIV-1. The inherent polyclonal diversity of the humoral immune response was addressed by using sequential in situ click chemistry to develop a cocktail of peptide-based capture agents, the components of which were raised against different, representative anti-HIV antibodies that bind to a conserved epitope of the HIV-1 envelope protein gp41. The cocktail was used to detect anti-HIV-1 antibodies from a panel of sera collected from HIV-positive patients, with improved signal-to-noise ratio relative to the gold standard commercial recombinant protein antigen. The capture agents were stable when stored as a powder for two months at temperatures close to 60°C.

An investigation of techniques for the measurement and interpretation of cosmic ray isotopic abundances

An instrument, the Caltech High Energy Isotope Spectrometer Telescope (HEIST), has been developed to measure isotopic abundances of cosmic ray nuclei in the charge range 3 ≤ Z ≤ 28 and the energy range between 30 and 800 MeV/nuc by employing an energy loss -- residual energy technique. Measurements of particle trajectories and energy losses are made using a multiwire proportional counter hodoscope and a stack of CsI(TI) crystal scintillators, respectively. A detailed analysis has been made of the mass resolution capabilities of this instrument.

Landau fluctuations set a fundamental limit on the attainable mass resolution, which for this instrument ranges between ~.07 AMU for z~3 and ~.2 AMU for z~2b. Contributions to the mass resolution due to uncertainties in measuring the path-length and energy losses of the detected particles are shown to degrade the overall mass resolution to between ~.1 AMU (z~3) and ~.3 AMU (z~2b).

A formalism, based on the leaky box model of cosmic ray propagation, is developed for obtaining isotopic abundance ratios at the cosmic ray sources from abundances measured in local interstellar space for elements having three or more stable isotopes, one of which is believed to be absent at the cosmic ray sources. This purely secondary isotope is used as a tracer of secondary production during propagation. This technique is illustrated for the isotopes of the elements O, Ne, S, Ar and Ca.

The uncertainties in the derived source ratios due to errors in fragmentation and total inelastic cross sections, in observed spectral shapes, and in measured abundances are evaluated. It is shown that the dominant sources of uncertainty are uncorrelated errors in the fragmentation cross sections and statistical uncertainties in measuring local interstellar abundances.

These results are applied to estimate the extent to which uncertainties must be reduced in order to distinguish between cosmic ray production in a solar-like environment and in various environments with greater neutron enrichments.

Self-healing Techniques for RF and mm-Wave Transmitters and Receivers

With continuing advances in CMOS technology, feature sizes of modern Silicon chip-sets have gone down drastically over the past decade. In addition to desktops and laptop processors, a vast majority of these chips are also being deployed in mobile communication devices like smart-phones and tablets, where multiple radio-frequency integrated circuits (RFICs) must be integrated into one device to cater to a wide variety of applications such as Wi-Fi, Bluetooth, NFC, wireless charging, etc. While a small feature size enables higher integration levels leading to billions of transistors co-existing on a single chip, it also makes these Silicon ICs more susceptible to variations. A part of these variations can be attributed to the manufacturing process itself, particularly due to the stringent dimensional tolerances associated with the lithographic steps in modern processes. Additionally, RF or millimeter-wave communication chip-sets are subject to another type of variation caused by dynamic changes in the operating environment. Another bottleneck in the development of high performance RF/mm-wave Silicon ICs is the lack of accurate analog/high-frequency models in nanometer CMOS processes. This can be primarily attributed to the fact that most cutting edge processes are geared towards digital system implementation and as such there is little model-to-hardware correlation at RF frequencies.

All these issues have significantly degraded yield of high performance mm-wave and RF CMOS systems which often require multiple trial-and-error based Silicon validations, thereby incurring additional production costs. This dissertation proposes a low overhead technique which attempts to counter the detrimental effects of these variations, thereby improving both performance and yield of chips post fabrication in a systematic way. The key idea behind this approach is to dynamically sense the performance of the system, identify when a problem has occurred, and then actuate it back to its desired performance level through an intelligent on-chip optimization algorithm. We term this technique as self-healing drawing inspiration from nature's own way of healing the body against adverse environmental effects. To effectively demonstrate the efficacy of self-healing in CMOS systems, several representative examples are designed, fabricated, and measured against a variety of operating conditions.

We demonstrate a high-power mm-wave segmented power mixer array based transmitter architecture that is capable of generating high-speed and non-constant envelope modulations at higher efficiencies compared to existing conventional designs. We then incorporate several sensors and actuators into the design and demonstrate closed-loop healing against a wide variety of non-ideal operating conditions. We also demonstrate fully-integrated self-healing in the context of another mm-wave power amplifier, where measurements were performed across several chips, showing significant improvements in performance as well as reduced variability in the presence of process variations and load impedance mismatch, as well as catastrophic transistor failure. Finally, on the receiver side, a closed-loop self-healing phase synthesis scheme is demonstrated in conjunction with a wide-band voltage controlled oscillator to generate phase shifter local oscillator (LO) signals for a phased array receiver. The system is shown to heal against non-idealities in the LO signal generation and distribution, significantly reducing phase errors across a wide range of frequencies.

Injection Locked Clocking and Transmitter Equalization Techniques for Chip to Chip Interconnects

Semiconductor technology scaling has enabled drastic growth in the computational capacity of integrated circuits (ICs). This constant growth drives an increasing demand for high bandwidth communication between ICs. Electrical channel bandwidth has not been able to keep up with this demand, making I/O link design more challenging. Interconnects which employ optical channels have negligible frequency dependent loss and provide a potential solution to this I/O bandwidth problem. Apart from the type of channel, efficient high-speed communication also relies on generation and distribution of multi-phase, high-speed, and high-quality clock signals. In the multi-gigahertz frequency range, conventional clocking techniques have encountered several design challenges in terms of power consumption, skew and jitter. Injection-locking is a promising technique to address these design challenges for gigahertz clocking. However, its small locking range has been a major contributor in preventing its ubiquitous acceptance.

In the first part of this dissertation we describe a wideband injection locking scheme in an LC oscillator. Phase locked loop (PLL) and injection locking elements are combined symbiotically to achieve wide locking range while retaining the simplicity of the latter. This method does not require a phase frequency detector or a loop filter to achieve phase lock. A mathematical analysis of the system is presented and the expression for new locking range is derived. A locking range of 13.4 GHz–17.2 GHz (25%) and an average jitter tracking bandwidth of up to 400 MHz are measured in a high-Q LC oscillator. This architecture is used to generate quadrature phases from a single clock without any frequency division. It also provides high frequency jitter filtering while retaining the low frequency correlated jitter essential for forwarded clock receivers.

To improve the locking range of an injection locked ring oscillator; QLL (Quadrature locked loop) is introduced. The inherent dynamics of injection locked quadrature ring oscillator are used to improve its locking range from 5% (7-7.4GHz) to 90% (4-11GHz). The QLL is used to generate accurate clock phases for a four channel optical receiver using a forwarded clock at quarter-rate. The QLL drives an injection locked oscillator (ILO) at each channel without any repeaters for local quadrature clock generation. Each local ILO has deskew capability for phase alignment. The optical-receiver uses the inherent frequency to voltage conversion provided by the QLL to dynamically body bias its devices. A wide locking range of the QLL helps to achieve a reliable data-rate of 16-32Gb/s and adaptive body biasing aids in maintaining an ultra-low power consumption of 153pJ/bit.

From the optical receiver we move on to discussing a non-linear equalization technique for a vertical-cavity surface-emitting laser (VCSEL) based optical transmitter, to enable low-power, high-speed optical transmission. A non-linear time domain optical model of the VCSEL is built and evaluated for accuracy. The modelling shows that, while conventional FIR-based pre-emphasis works well for LTI electrical channels, it is not optimum for the non-linear optical frequency response of the VCSEL. Based on the simulations of the model an optimum equalization methodology is derived. The equalization technique is used to achieve a data-rate of 20Gb/s with power efficiency of 0.77pJ/bit.

A variational framework for spectral discretization of the density matrix in Kohn Sham density functional theory

Kohn-Sham density functional theory (KSDFT) is currently the main work-horse of quantum mechanical calculations in physics, chemistry, and materials science. From a mechanical engineering perspective, we are interested in studying the role of defects in the mechanical properties in materials. In real materials, defects are typically found at very small concentrations e.g., vacancies occur at parts per million, dislocation density in metals ranges from $10^{10} m^{-2}$ to $10^{15} m^{-2}$, and grain sizes vary from nanometers to micrometers in polycrystalline materials, etc. In order to model materials at realistic defect concentrations using DFT, we would need to work with system sizes beyond millions of atoms. Due to the cubic-scaling computational cost with respect to the number of atoms in conventional DFT implementations, such system sizes are unreachable. Since the early 1990s, there has been a huge interest in developing DFT implementations that have linear-scaling computational cost. A promising approach to achieving linear-scaling cost is to approximate the density matrix in KSDFT. The focus of this thesis is to provide a firm mathematical framework to study the convergence of these approximations. We reformulate the Kohn-Sham density functional theory as a nested variational problem in the density matrix, the electrostatic potential, and a field dual to the electron density. The corresponding functional is linear in the density matrix and thus amenable to spectral representation. Based on this reformulation, we introduce a new approximation scheme, called spectral binning, which does not require smoothing of the occupancy function and thus applies at arbitrarily low temperatures. We proof convergence of the approximate solutions with respect to spectral binning and with respect to an additional spatial discretization of the domain. For a standard one-dimensional benchmark problem, we present numerical experiments for which spectral binning exhibits excellent convergence characteristics and outperforms other linear-scaling methods.

Investigation of competitive antagonist binding to the nicotinic acetylcholine receptor using voltage-jump and light-flash techniques

1. The effect of 2,2’-bis-[α-(trimethylammonium)methyl]azobenzene (2BQ), a photoisomerizable competitive antagonist, was studied at the nicotinic acetycholine receptor of Electrophorus electroplaques using voltage-jump and light-flash techniques.

2. 2BQ, at concentrations below 3 μΜ, reduced the amplitude of voltage-jump relaxations but had little effect on the voltage-jump relaxation time constants under all experimental conditions. At higher concentrations and voltages more negative than -150 mV, 2BQ caused significant open channel blockade.

3. Dose-ratio studies showed that the cis and trans isomers of 2BQ have equilibrium binding constants (K _ᵢ) of .33 and 1.0 μΜ, respectively. The binding constants determined for both isomers are independent of temperature, voltage, agonist concentration, and the nature of the agonist.

4. In a solution of predominantly cis-2BQ, visible-light flashes led to a net cis→trans isomerization and caused an increase in the agonist-induced current. This increase had at least two exponential components; the larger amplitude component had the same time constant as a subsequent voltage-jump relaxation; the smaller amplitude component was investigated using ultraviolet light flashes.

5. In a solution of predominantly trans-2BQ, UV-light flashes led to a net trans→cis isomerization and caused a net decrease in the agonist-induced current. This effect had at least two exponential components. The smaller and faster component was an increase in agonist-induced current and had a similar time constant to the voltage-jump relaxation. The larger component was a slow decrease in the agonist-induced current with rate constant approximately an order of magnitude less than that of the voltage-jump relaxation. This slow component provided a measure of the rate constant for dissociation of cis-2BQ (k_ = 60/s at 20°C). Simple modelling of the slope of the dose-rate curves yields an association rate constant of 1.6 x 10⁸/M/s. This agrees with the association rate constant of 1.8 x 10⁸/M/s estimated from the binding constant (K_i). The Q₁₀ of the dissociation rate constant of cis-2BQ was 3.3 between 6° and 20°C. The rate constants for association and dissociation of cis-28Q at receptors are independent of voltage, agonist concentration, and the nature of the agonist.

6. We have measured the molecular rate constants of a competitive antagonist which has roughly the same K _ᵢ as d-tubocurarine but interacts more slowly with the receptor. This leads to the conclusion that curare itself has an association rate constant of 4 x 10⁹/M/s or roughly as fast as possible for an encounter-limited reaction.

Full and Model-Reduced Structure-Preserving Simulation of Incompressible Fluids

This thesis outlines the construction of several types of structured integrators for incompressible fluids. We first present a vorticity integrator, which is the Hamiltonian counterpart of the existing Lagrangian-based fluid integrator. We next present a model-reduced variational Eulerian integrator for incompressible fluids, which combines the efficiency gains of dimension reduction, the qualitative robustness to coarse spatial and temporal resolutions of geometric integrators, and the simplicity of homogenized boundary conditions on regular grids to deal with arbitrarily-shaped domains with sub-grid accuracy.

Both these numerical methods involve approximating the Lie group of volume-preserving diffeomorphisms by a finite-dimensional Lie-group and then restricting the resulting variational principle by means of a non-holonomic constraint. Advantages and limitations of this discretization method will be outlined. It will be seen that these derivation techniques are unable to yield symplectic integrators, but that energy conservation is easily obtained, as is a discretized version of Kelvin's circulation theorem.

Finally, we outline the basis of a spectral discrete exterior calculus, which may be a useful element in producing structured numerical methods for fluids in the future.

Algebraic Techniques in Coding Theory: Entropy Vectors, Frames, and Constrained Coding

The study of codes, classically motivated by the need to communicate information reliably in the presence of error, has found new life in fields as diverse as network communication, distributed storage of data, and even has connections to the design of linear measurements used in compressive sensing. But in all contexts, a code typically involves exploiting the algebraic or geometric structure underlying an application. In this thesis, we examine several problems in coding theory, and try to gain some insight into the algebraic structure behind them.

The first is the study of the entropy region - the space of all possible vectors of joint entropies which can arise from a set of discrete random variables. Understanding this region is essentially the key to optimizing network codes for a given network. To this end, we employ a group-theoretic method of constructing random variables producing so-called "group-characterizable" entropy vectors, which are capable of approximating any point in the entropy region. We show how small groups can be used to produce entropy vectors which violate the Ingleton inequality, a fundamental bound on entropy vectors arising from the random variables involved in linear network codes. We discuss the suitability of these groups to design codes for networks which could potentially outperform linear coding.

The second topic we discuss is the design of frames with low coherence, closely related to finding spherical codes in which the codewords are unit vectors spaced out around the unit sphere so as to minimize the magnitudes of their mutual inner products. We show how to build frames by selecting a cleverly chosen set of representations of a finite group to produce a "group code" as described by Slepian decades ago. We go on to reinterpret our method as selecting a subset of rows of a group Fourier matrix, allowing us to study and bound our frames' coherences using character theory. We discuss the usefulness of our frames in sparse signal recovery using linear measurements.

The final problem we investigate is that of coding with constraints, most recently motivated by the demand for ways to encode large amounts of data using error-correcting codes so that any small loss can be recovered from a small set of surviving data. Most often, this involves using a systematic linear error-correcting code in which each parity symbol is constrained to be a function of some subset of the message symbols. We derive bounds on the minimum distance of such a code based on its constraints, and characterize when these bounds can be achieved using subcodes of Reed-Solomon codes.

I. Electronic processes in α-sulfur. II. Polaron motion in a D.C. electric field

Part I: The mobilities of photo-generated electrons and holes in orthorhombic sulfur are determined by drift mobility techniques. At room temperature electron mobilities between 0.4 cm²/V-sec and 4.8 cm²/V-sec and hole mobilities of about 5.0 cm²/V-sec are reported. The temperature dependence of the electron mobility is attributed to a level of traps whose effective depth is about 0.12 eV. This value is further supported by both the voltage dependence of the space-charge-limited, D.C. photocurrents and the photocurrent versus photon energy measurements.

As the field is increased from 10 kV/cm to 30 kV/cm a second mechanism for electron transport becomes appreciable and eventually dominates. Evidence that this is due to impurity band conduction at an appreciably lower mobility (4.10^-4 cm²/V-sec) is presented. No low mobility hole current could be detected. When fields exceeding 30 kV/cm for electron transport and 35 kV/cm for hole transport are applied, avalanche phenomena are observed. The results obtained are consistent with recent energy gap studies in sulfur.

The theory of the transport of photo-generated carriers is modified to include the case of appreciable thermos-regeneration from the traps in one transit time.

Part II: An explicit formula for the electric field E necessary to accelerate an electron to a steady-state velocity v in a polarizable crystal at arbitrary temperature is determined via two methods utilizing Feynman Path Integrals. No approximation is made regarding the magnitude of the velocity or the strength of the field. However, the actual electron-lattice Coulombic interaction is approximated by a distribution of harmonic oscillator potentials. One may be able to find the “best possible” distribution of oscillators using a variational principle, but we have not been able to find the expected criterion. However, our result is relatively insensitive to the actual distribution of oscillators used, and our E-v relationship exhibits the physical behavior expected for the polaron. Threshold fields for ejecting the electron for the polaron state are calculated for several substances using numerical results for a simple oscillator distribution.

Part I. Approximate Hartree-Fock wavefunctions one-electron properties and electronic structure of the water molecule. Part II. Perturbation-variational calculation of the nuclear spin-spin isotope coupling constant in HD

Part I

Several approximate Hartree-Fock SCF wavefunctions for the ground electronic state of the water molecule have been obtained using an increasing number of multicenter s, p, and d Slater-type atomic orbitals as basis sets. The predicted charge distribution has been extensively tested at each stage by calculating the electric dipole moment, molecular quadrupole moment, diamagnetic shielding, Hellmann-Feynman forces, and electric field gradients at both the hydrogen and the oxygen nuclei. It was found that a carefully optimized minimal basis set suffices to describe the electronic charge distribution adequately except in the vicinity of the oxygen nucleus. Our calculations indicate, for example, that the correct prediction of the field gradient at this nucleus requires a more flexible linear combination of p-orbitals centered on this nucleus than that in the minimal basis set. Theoretical values for the molecular octopole moment components are also reported.

Part II

The perturbation-variational theory of R. M. Pitzer for nuclear spin-spin coupling constants is applied to the HD molecule. The zero-order molecular orbital is described in terms of a single 1s Slater-type basis function centered on each nucleus. The first-order molecular orbital is expressed in terms of these two functions plus one singular basis function each of the types e^-r/r and e^-r ln r centered on one of the nuclei. The new kinds of molecular integrals were evaluated to high accuracy using numerical and analytical means. The value of the HD spin-spin coupling constant calculated with this near-minimal set of basis functions is J_HD = +96.6 cps. This represents an improvement over the previous calculated value of +120 cps obtained without using the logarithmic basis function but is still considerably off in magnitude compared with the experimental measurement of J_HD = +43 0 ± 0.5 cps.