The flow between rotating coaxial disks

Numerical approximations of nonunique solutions of the Navier-Stokes equations are obtained for steady viscous incompressible axisymmetric flow between two infinite rotating coaxial disks. For example, nineteen solutions have been found for the case when the disks are rotating with the same speed but in opposite direction. Bifurcation and perturbed bifurcation phenomena are observed. An efficient method is used to compute solution branches. The stability of solutions is analyzed. The rate of convergence of Newton's method at singular points is discussed. In particular, recovery of quadratic convergence at "normal limit points" and bifurcation points is indicated. Analytical construction of some of the computed solutions using singular perturbation techniques is discussed.

Diffusion in glassy polymers

Fluid diffusion in glassy polymers proceeds in ways that are not explained by the standard diffusion model. Although the reasons for the anomalous effects are not known, much of the observed behavior is attributed to the long times that polymers below their glass transition temperature take to adjust to changes in their condition. The slow internal relaxations of the polymer chains ensure that the material properties are history-dependent, and also allow both local inhomogeneities and differential swelling to occur. Two models are developed in this thesis with the intent of accounting for these effects in the diffusion process.

In Part I, a model is developed to account for both the history dependence of the glassy polymer, and the dual sorption which occurs when gas molecules are immobilized by the local heterogeneities. A preliminary study of a special case of this model is conducted, showing the existence of travelling wave solutions and using perturbation techniques to investigate the effect of generalized diffusion mechanisms on their form. An integral averaging method is used to estimate the penetrant front position.

In Part II, a model is developed for particle diffusion along with displacements in isotropic viscoelastic materials. The nonlinear dependence of the materials on the fluid concentration is taken into account, while pure displacements are assumed to remain in the range of linear viscoelasticity. A fairly general model is obtained for three-dimensional irrotational movements, with the development of the model being based on the assumptions of irreversible thermodynamics. With the help of some dimensional analysis, this model is simplified to a version which is proposed to be studied for Case II behavior.

Some modified bifurcation problems with application to imperfection sensitivity in buckling

The branching theory of solutions of certain nonlinear elliptic partial differential equations is developed, when the nonlinear term is perturbed from unforced to forced. We find families of branching points and the associated nonisolated solutions which emanate from a bifurcation point of the unforced problem. Nontrivial solution branches are constructed which contain the nonisolated solutions, and the branching is exhibited. An iteration procedure is used to establish the existence of these solutions, and a formal perturbation theory is shown to give asymptotically valid results. The stability of the solutions is examined and certain solution branches are shown to consist of minimal positive solutions. Other solution branches which do not contain branching points are also found in a neighborhood of the bifurcation point.

The qualitative features of branching points and their associated nonisolated solutions are used to obtain useful information about buckling of columns and arches. Global stability characteristics for the buckled equilibrium states of imperfect columns and arches are discussed. Asymptotic expansions for the imperfection sensitive buckling load of a column on a nonlinearly elastic foundation are found and rigorously justified.

Nonlinear dispersive wave problems

The nonlinear partial differential equations for dispersive waves have special solutions representing uniform wavetrains. An expansion procedure is developed for slowly varying wavetrains, in which full nonlinearity is retained but in which the scale of the nonuniformity introduces a small parameter. The first order results agree with the results that Whitham obtained by averaging methods. The perturbation method provides a detailed description and deeper understanding, as well as a consistent development to higher approximations. This method for treating partial differential equations is analogous to the "multiple time scale" methods for ordinary differential equations in nonlinear vibration theory. It may also be regarded as a generalization of geometrical optics to nonlinear problems.

To apply the expansion method to the classical water wave problem, it is crucial to find an appropriate variational principle. It was found in the present investigation that a Lagrangian function equal to the pressure yields the full set of equations of motion for the problem. After this result is derived, the Lagrangian is compared with the more usual expression formed from kinetic minus potential energy. The water wave problem is then examined by means of the expansion procedure.

Non-linear dispersive waves with a small dissipation

The general theory of Whitham for slowly-varying non-linear wavetrains is extended to the case where some of the defining partial differential equations cannot be put into conservation form. Typical examples are considered in plasma dynamics and water waves in which the lack of a conservation form is due to dissipation; an additional non-conservative element, the presence of an external force, is treated for the plasma dynamics example. Certain numerical solutions of the water waves problem (the Korteweg-de Vries equation with dissipation) are considered and compared with perturbation expansions about the linearized solution; it is found that the first correction term in the perturbation expansion is an excellent qualitative indicator of the deviation of the dissipative decay rate from linearity.

A method for deriving necessary and sufficient conditions for the existence of a general uniform wavetrain solution is presented and illustrated in the plasma dynamics problem. Peaking of the plasma wave is demonstrated, and it is shown that the necessary and sufficient existence conditions are essentially equivalent to the statement that no wave may have an amplitude larger than the peaked wave.

A new type of fully non-linear stability criterion is developed for the plasma uniform wavetrain. It is shown explicitly that this wavetrain is stable in the near-linear limit. The nature of this new type of stability is discussed.

Steady shock solutions are also considered. By a quite general method, it is demonstrated that the plasma equations studied here have no steady shock solutions whatsoever. A special type of steady shock is proposed, in which a uniform wavetrain joins across a jump discontinuity to a constant state. Such shocks may indeed exist for the Korteweg-de Vries equation, but are barred from the plasma problem because entropy would decrease across the shock front.

Finally, a way of including the Landau damping mechanism in the plasma equations is given. It involves putting in a dissipation term of convolution integral form, and parallels a similar approach of Whitham in water wave theory. An important application of this would be towards resolving long-standing difficulties about the "collisionless" shock.

Nearly free molecular heat transfer from a sphere

Consider a sphere immersed in a rarefied monatomic gas with zero mean flow. The distribution function of the molecules at infinity is chosen to be a Maxwellian. The boundary condition at the body is diffuse reflection with perfect accommodation to the surface temperature. The microscopic flow of particles about the sphere is modeled kinetically by the Boltzmann equation with the Krook collision term. Appropriate normalizations in the near and far fields lead to a perturbation solution of the problem, expanded in terms of the ratio of body diameter to mean free path (inverse Knudsen number). The distribution function is found directly in each region, and intermediate matching is demonstrated. The heat transfer from the sphere is then calculated as an integral over this distribution function in the inner region. Final results indicate that the heat transfer may at first increase over its free flow value before falling to the continuum level.

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.

The cast net fishery, Kainji Lake, Nigeria 1970-1997

This study was carried out to establish trends in the cast net fishery of Kainji Lake, Nigeria. The cast net fishery was second in importance to the gillnet fishery in the early years after impoundment of the lake and still continues to be an important component of the fishery. Some of the economically important species such as Citharinus spp, Tilapia spp, Labeo spp, Alestes spp and Synodontis spp are exploited by cast nets. The study has not revealed any drastic perturbation in the species diversity, catch composition, and any real ecosystem overfishing. On the other hand, both the catfish, Auchenoglanis spp and the predator Hydrocynus spp appear to have increased in the catch in recent years. Never-the-less there is a decline in the mean weight of the major exploited fish species due to the capture of under sized fishes without allowing them to grow to 'legally' marketable sizes. The use of small meshed cast net and also fishing in the shallow waters of the lake can give rise to this situation. Thus, there are signs of growth overfishing in the fish stocks. It must also be acknowledged that the situation is complicated by the fact that in a multi-gear fishery as on Kainji Lake, the cast net fishery could not be managed in isolation without due regard to the other competing gears. The catch per unit of effort (CPUE) has declined in the cast net fishery possibly due to the increase in effort by the major fishing gears over the years. The ongoing extension campaigns by the KLFPP appears to be having the desired effect, as there was reduction in the number of the major fishing gears on the Lake in 1997. It can be anticipated that if this trend continues, the CPUE will recover in the long run. Yields observed from the mesh selectivity study revealed that for major species in the cast net fishery, both by number and weight, were maximal at 2.5 inch mesh, which contrasts with the fact that current minimum allowable mesh in the Fisheries Edict for the Lake is 2.0 inch. The adoption of 2.5 inch as the minimum allowable mesh in the cast net fishery is recommended to be included in future revision of existing regulations. It is also recommended that for this control to have a desired effect, the casting of the net from the shore should be prohibited so as to reduce the incidence of juvenile mortality in the nursery areas. (PDF contains 28 pages)

A dynamical systems analysis of vortex pinch-off

Vortex rings constitute the main structure in the wakes of a wide class of swimming and flying animals, as well as in cardiac flows and in the jets generated by some moss and fungi. However, there is a physical limit, determined by an energy maximization principle called the Kelvin-Benjamin principle, to the size that axisymmetric vortex rings can achieve. The existence of this limit is known to lead to the separation of a growing vortex ring from the shear layer feeding it, a process known as `vortex pinch-off', and characterized by the dimensionless vortex formation number. The goal of this thesis is to improve our understanding of vortex pinch-off as it relates to biological propulsion, and to provide future researchers with tools to assist in identifying and predicting pinch-off in biological flows.

To this end, we introduce a method for identifying pinch-off in starting jets using the Lagrangian coherent structures in the flow, and apply this criterion to an experimentally generated starting jet. Since most naturally occurring vortex rings are not circular, we extend the definition of the vortex formation number to include non-axisymmetric vortex rings, and find that the formation number for moderately non-axisymmetric vortices is similar to that of circular vortex rings. This suggests that naturally occurring vortex rings may be modeled as axisymmetric vortex rings. Therefore, we consider the perturbation response of the Norbury family of axisymmetric vortex rings. This family is chosen to model vortex rings of increasing thickness and circulation, and their response to prolate shape perturbations is simulated using contour dynamics. Finally, the response of more realistic models for vortex rings, constructed from experimental data using nested contours, to perturbations which resemble those encountered by forming vortices more closely, is simulated using contour dynamics. In both families of models, a change in response analogous to pinch-off is found as members of the family with progressively thicker cores are considered. We posit that this analogy may be exploited to understand and predict pinch-off in complex biological flows, where current methods are not applicable in practice, and criteria based on the properties of vortex rings alone are necessary.

Trapped ion magnetic resonance: concepts and designs

A novel spectroscopy of trapped ions is proposed which will bring single-ion detection sensitivity to the observation of magnetic resonance spectra. The approaches developed here are aimed at resolving one of the fundamental problems of molecular spectroscopy, the apparent incompatibility in existing techniques between high information content (and therefore good species discrimination) and high sensitivity. Methods for studying both electron spin resonance (ESR) and nuclear magnetic resonance (NMR) are designed. They assume established methods for trapping ions in high magnetic field and observing the trapping frequencies with high resolution (<1 Hz) and sensitivity (single ion) by electrical means. The introduction of a magnetic bottle field gradient couples the spin and spatial motions together and leads to a small spin-dependent force on the ion, which has been exploited by Dehmelt to observe directly the perturbation of the ground-state electron's axial frequency by its spin magnetic moment.

A series of fundamental innovations is described m order to extend magnetic resonance to the higher masses of molecular ions (100 amu = 2x 10^5 electron masses) and smaller magnetic moments (nuclear moments = 10^(-3) of the electron moment). First, it is demonstrated how time-domain trapping frequency observations before and after magnetic resonance can be used to make cooling of the particle to its ground state unnecessary. Second, adiabatic cycling of the magnetic bottle off between detection periods is shown to be practical and to allow high-resolution magnetic resonance to be encoded pointwise as the presence or absence of trapping frequency shifts. Third, methods of inducing spindependent work on the ion orbits with magnetic field gradients and Larmor frequency irradiation are proposed which greatly amplify the attainable shifts in trapping frequency.

The dissertation explores the basic concepts behind ion trapping, adopting a variety of classical, semiclassical, numerical, and quantum mechanical approaches to derive spin-dependent effects, design experimental sequences, and corroborate results from one approach with those from another. The first proposal presented builds on Dehmelt's experiment by combining a "before and after" detection sequence with novel signal processing to reveal ESR spectra. A more powerful technique for ESR is then designed which uses axially synchronized spin transitions to perform spin-dependent work in the presence of a magnetic bottle, which also converts axial amplitude changes into cyclotron frequency shifts. A third use of the magnetic bottle is to selectively trap ions with small initial kinetic energy. A dechirping algorithm corrects for undesired frequency shifts associated with damping by the measurement process.

The most general approach presented is spin-locked internally resonant ion cyclotron excitation, a true continuous Stern-Gerlach effect. A magnetic field gradient modulated at both the Larmor and cyclotron frequencies is devised which leads to cyclotron acceleration proportional to the transverse magnetic moment of a coherent state of the particle and radiation field. A preferred method of using this to observe NMR as an axial frequency shift is described in detail. In the course of this derivation, a new quantum mechanical description of ion cyclotron resonance is presented which is easily combined with spin degrees of freedom to provide a full description of the proposals.

Practical, technical, and experimental issues surrounding the feasibility of the proposals are addressed throughout the dissertation. Numerical ion trajectory simulations and analytical models are used to predict the effectiveness of the new designs as well as their sensitivity and resolution. These checks on the methods proposed provide convincing evidence of their promise in extending the wealth of magnetic resonance information to the study of collisionless ions via single-ion spectroscopy.

Conditional independence in quantum many-body systems

In this thesis, I will discuss how information-theoretic arguments can be used to produce sharp bounds in the studies of quantum many-body systems. The main advantage of this approach, as opposed to the conventional field-theoretic argument, is that it depends very little on the precise form of the Hamiltonian. The main idea behind this thesis lies on a number of results concerning the structure of quantum states that are conditionally independent. Depending on the application, some of these statements are generalized to quantum states that are approximately conditionally independent. These structures can be readily used in the studies of gapped quantum many-body systems, especially for the ones in two spatial dimensions. A number of rigorous results are derived, including (i) a universal upper bound for a maximal number of topologically protected states that is expressed in terms of the topological entanglement entropy, (ii) a first-order perturbation bound for the topological entanglement entropy that decays superpolynomially with the size of the subsystem, and (iii) a correlation bound between an arbitrary local operator and a topological operator constructed from a set of local reduced density matrices. I also introduce exactly solvable models supported on a three-dimensional lattice that can be used as a reliable quantum memory.

Preparation, characterization and intramolecular electron-transfer studies of ruthenium-modified cytochromes c

Redox-active ruthenium complexes have been covalently attached to the surface of a series of natural, semisynthetic and recombinant cytochromes c. The protein derivatives were characterized by a variety of spectroscopic techniques. Distant Fe^(2+) - Ru^(3+) electronic couplings were extracted from intramolecular electron-transfer rates in Ru(bpy)_2(im)HisX (where X= 33, 39, 62, and 72) derivatives of cyt c. The couplings increase according to 62 (0.0060) < 72 (0.057) < 33 (0.097) < 39 (0.11 cm^(-1)); however, this order is incongruent with histidine to heme edge-edge distances [62 (14.8) > 39 (12.3) > 33 (11.1) > =72 (8.4 Å)]. These results suggest the chemical nature of the intervening medium needs to be considered for a more precise evaluation of couplings. The rates (and couplings) correlate with the lengths of a-tunneling pathways comprised of covalent bonds, hydrogen bonds and through-space jumps from the histidines to the heme group. Space jumps greatly decrease couplings: one from Pro71 to Met80 extends the σ-tunneling length of the His72 pathway by roughly 10 covalent bond units. Experimental couplings also correlate well with those calculated using extended Hiickel theory to evaluate the contribution of the intervening protein medium.

Two horse heart cyt c variants incorporating the unnatural amino acids (S)-2- amino-3-(2,2'-bipyrid-6-yl)-propanoic acid (6Bpa) and (S)-2-amino-3-(2,2'-bipyrid-4-yl)propanoic acid ( 4Bpa) at position 72 have been prepared using semisynthetic protocols. Negligible perturbation of the protein structure results from this introduction of unnatural amino acids. Redox-active Ru(2,2'-bipyridine)_2^(2+) binds to 4Bpa72 cyt c but not to the 6Bpa protein. Enhanced ET rates were observed in the Ru(bpy)_2^(2+)-modified 4Bpa72 cyt c relative to the analogous His72 derivative. The rapid (< 60 nanosecond) photogeneration of ferrous Ru-modified 4Bpa72 cyt c in the conformationally altered alkaline state demonstrates that laser-induced ET can be employed to study submicrosecond protein-folding events.

Topology of toroidal helical fields in non-circular cross-sectional tokamaks

The ordinary differential magnetic field line equations are solved numerically; the tokamak magnetic structure is studied on Hefei Tokamak-7 Upgrade (HT-7U) when the equilibrium field with a monotonic q-profile is perturbed by a helical magnetic field. We find that a single mode (m, n) helical perturbation can cause the formation of islands on rational surfaces with q = m/n and q = (m +/- 1, +/- 2, +/- 3,...)/n due to the toroidicity and plasma shape (i.e. elongation and triangularity), while there are many undestroyed magnetic surfaces called Kolmogorov-Arnold-Moser (KAM) barriers on irrational surfaces. The islands on the same rational surface do not have the same size. When the ratio between the perturbing magnetic field B-r(r) and the toroidal magnetic field amplitude B(phi)0 is large enough, the magnetic island chains on different rational surfaces will overlap and chaotic orbits appear in the overlapping area, and the magnetic field becomes stochastic. It is remarkable that the stochastic layer appears first in the plasma edge region.

Polaronic correction to the first excited electronic energy level in an anisotropic semiconductor quantum dot

Within the framework of second-order Rayleigh-Schrodinger perturbation theory, the polaronic correction to the first excited state energy of an electron in an quantum dot with anisotropic parabolic confinements is presented. Compared with isotropic confinements, anisotropic confinements will make the degeneracy of the excited states to be totally or partly lifted. On the basis of a three-dimensional Frohlich's Hamiltonian with anisotropic confinements, the first excited state properties in two-dimensional quantum dots as well as quantum wells and wires can also be easily obtained by taking special limits. Calculations show that the first excited polaronic effect can be considerable in small quantum dots.

The electric field of a weakly electric fish

Freshwater fish of the genus Apteronotus (family Gymnotidae) generate a weak, high frequency electric field (< 100 mV/cm, 0.5-10 kHz) which permeates their local environment. These nocturnal fish are acutely sensitive to perturbations in their electric field caused by other electric fish, and nearby objects whose impedance is different from the surrounding water. This thesis presents high temporal and spatial resolution maps of the electric potential and field on and near Apteronotus. The fish's electric field is a complicated and highly stable function of space and time. Its characteristics, such as spectral composition, timing, and rate of attenuation, are examined in terms of physical constraints, and their possible functional roles in electroreception.

Temporal jitter of the periodic field is less than 1 µsec. However, electrocyte activity is not globally synchronous along the fish 's electric organ. The propagation of electrocyte activation down the fish's body produces a rotation of the electric field vector in the caudal part of the fish. This may assist the fish in identifying nonsymmetrical objects, and could also confuse electrosensory predators that try to locate Apteronotus by following its fieldlines. The propagation also results in a complex spatiotemporal pattern of the EOD potential near the fish. Visualizing the potential on the same and different fish over timescales of several months suggests that it is stable and could serve as a unique signature for individual fish.

Measurements of the electric field were used to calculate the effects of simple objects on the fish's electric field. The shape of the perturbation or "electric image" on the fish's skin is relatively independent of a simple object's size, conductivity, and rostrocaudal location, and therefore could unambiguously determine object distance. The range of electrolocation may depend on both the size of objects and their rostrocaudal location. Only objects with very large dielectric constants cause appreciable phase shifts, and these are strongly dependent on the water conductivity.