Pharmacology and pore-forming domains of the cystic fibrosis transmembrane conductance regulator

The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel member of the ATP-binding cassette (ABC) superfamily of membrane proteins. CFTR has two homologous halves, each consisting of six transmembrane spanning domains (TM) followed by a nucleotide binding fold, connected by a regulatory (R) domain. This thesis addresses the question of which domains are responsible for Cl^- selectivity, i.e., which domains line the channel pore.

To address this question, novel blockers of CFTR were characterized. CFTR was heterologously expressed in Xenopus oocytes to study the mechanism of block by two closely related arylaminobenzoates, diphenylamine-2-carboxylic acid (DPC) and flufenamic acid (FFA). Block by both is voltage-dependent, with a binding site ≈ 40% through the electric field of the membrane. DPC and FFA can both reach their binding site from either side of the membrane to produce a flickering block of CFTR single channels. In addition, DPC block is influenced by Cl^- concentration, and DPC blocks with a bimolecular forward binding rate and a unimolecular dissociation rate. Therefore, DPC and FFA are open-channel blockers of CFTR, and a residue of CFTR whose mutation affects their binding must line the pore.

Screening of site-directed mutants for altered DPC binding affinity reveals that TM-6 and TM-12 line the pore. Mutation of residue 5341 in TM-6 abolishes most DPC block, greatly reduces single-channel conductance, and alters the direction of current rectification. Additional residues are found in TM-6 (K335) and TM-12 (T1134) whose mutations weaken or strengthen DPC block; other mutations move the DPC binding site from TM-6 to TM-12. The strengthened block and lower conductance due to mutation T1134F is quantitated at the single-channel level. The geometry of DPC and of the residues mutated suggest α-helical structures for TM-6 and TM-12. Evidence is presented that the effects of the mutations are due to direct side-chain interaction, and not to allosteric effects propagated through the protein. Mutations are also made in TM-11, including mutation S1118F, which gives voltage-dependent current relaxations. The results may guide future studies on permeation through ABC transporters and through other Cl^- channels.

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.

Effects of particle size ratio on single particle motion in colloidal dispersions

The motion of a single Brownian particle of arbitrary size through a dilute colloidal dispersion of neutrally buoyant bath spheres of another characteristic size in a Newtonian solvent is examined in two contexts. First, the particle in question, the probe particle, is subject to a constant applied external force drawing it through the suspension as a simple model for active and nonlinear microrheology. The strength of the applied external force, normalized by the restoring forces of Brownian motion, is the Péclet number, Pe. This dimensionless quantity describes how strongly the probe is upsetting the equilibrium distribution of the bath particles. The mean motion and fluctuations in the probe position are related to interpreted quantities of an effective viscosity of the suspension. These interpreted quantities are calculated to first order in the volume fraction of bath particles and are intimately tied to the spatial distribution, or microstructure, of bath particles relative to the probe. For weak Pe, the disturbance to the equilibrium microstructure is dipolar in nature, with accumulation and depletion regions on the front and rear faces of the probe, respectively. With increasing applied force, the accumulation region compresses to form a thin boundary layer whose thickness scales with the inverse of Pe. The depletion region lengthens to form a trailing wake. The magnitude of the microstructural disturbance is found to grow with increasing bath particle size -- small bath particles in the solvent resemble a continuum with effective microviscosity given by Einstein's viscosity correction for a dilute dispersion of spheres. Large bath particles readily advect toward the minimum approach distance possible between the probe and bath particle, and the probe and bath particle pair rotating as a doublet is the primary mechanism by which the probe particle is able to move past; this is a process that slows the motion of the probe by a factor of the size ratio. The intrinsic microviscosity is found to force thin at low Péclet number due to decreasing contributions from Brownian motion, and force thicken at high Péclet number due to the increasing influence of the configuration-averaged reduction in the probe's hydrodynamic self mobility. Nonmonotonicity at finite sizes is evident in the limiting high-Pe intrinsic microviscosity plateau as a function of bath-to-probe particle size ratio. The intrinsic microviscosity is found to grow with the size ratio for very small probes even at large-but-finite Péclet numbers. However, even a small repulsive interparticle potential, that excludes lubrication interactions, can reduce this intrinsic microviscosity back to an order one quantity. The results of this active microrheology study are compared to previous theoretical studies of falling-ball and towed-ball rheometry and sedimentation and diffusion in polydisperse suspensions, and the singular limit of full hydrodynamic interactions is noted.

Second, the probe particle in question is no longer subject to a constant applied external force. Rather, the particle is considered to be a catalytically-active motor, consuming the bath reactant particles on its reactive face while passively colliding with reactant particles on its inert face. By creating an asymmetric distribution of reactant about its surface, the motor is able to diffusiophoretically propel itself with some mean velocity. The effects of finite size of the solute are examined on the leading order diffusive microstructure of reactant about the motor. Brownian and interparticle contributions to the motor velocity are computed for several interparticle interaction potential lengths and finite reactant-to-motor particle size ratios, with the dimensionless motor velocity increasing with decreasing motor size. A discussion on Brownian rotation frames the context in which these results could be applicable, and future directions are proposed which properly incorporate reactant advection at high motor velocities.

1. Astronomical photometry at wavelengths of 8.5, 10.5, and 11.6 µm. 2. Infrared emission from asteroids at wavelengths of 8.5, 10.5, and 11.6 µm

The purpose of this thesis is to present new observations of thermal-infrared radiation from asteroids. Stellar photometry was performed to provide standards for comparison with the asteroid data. The details of the photometry and the data reduction are discussed in Part 1. A system of standard stars is derived for wavelengths of 8.5, 10.5 and 11.6 µm and a new calibration is adopted. Sources of error are evaluated and comparisons are made with the data of other observers.

The observations and analysis of the thermal-emission observations of asteroids are presented in Part 2. Thermal-emission lightcurve and phase effect data are considered. Special color diagrams are introduced to display the observational data. These diagrams are free of any model-dependent assumptions and show that asteroids differ in their surface properties.

On the basis of photometric models, (4) Vesta is thought to have a bolometric Bond albedo of about 0.1, an emissivity greater than 0.7 and a true radius that is close to the model value of 300^(+50)_(-30)km. Model albedos and model radii are given for asteroids 1, 2, 4, 5, 6, 7, 15, 19, 20, 27, 39, 44, 68, 80, 324 and 674. The asteroid (324) Bamberga is extremely dark with a model (~bolometric Bond) albedo in the 0.01 - 0.02 range, which is thought to be the lowest albedo yet measured for any solar-system body. The crucial question about such low-albedo asteroids is their number and the distribution of their orbits.

A measurement of inclusive quasi-elastic electron scattering cross sections at high momentum transfer

We have measured inclusive electron-scattering cross sections for targets of ^(4)He, C, Al, Fe, and Au, for kinematics spanning the quasi-elastic peak, with squared, four­ momentum transfers (q^2) between 0.23 and 2.89 (GeV/c)^2. Additional data were measured for Fe with q^2's up to 3.69 (GeV/c)^2 These cross sections were analyzed for the y-scaling behavior expected from a simple, impulse-approximation model, and are found to approach a scaling limit at the highest q^2's. The q^2 approach to scaling is compared with a calculation for infinite nuclear matter, and relationships between the scaling function and nucleon momentum distributions are discussed. Deviations from perfect scaling are used to set limits on possible changes in the size of nucleons inside the nucleus.

The steady-state response of multidegree-of-freedom systems with a spatially localized nonlinearity

This thesis is concerned with the dynamic response of a General multidegree-of-freedom linear system with a one dimensional nonlinear constraint attached between two points. The nonlinear constraint is assumed to consist of rate-independent conservative and hysteretic nonlinearities and may contain a viscous dissipation element. The dynamic equations for general spatial and temporal load distributions are derived for both continuous and discrete systems. The method of equivalent linearization is used to develop equations which govern the approximate steady-state response to generally distributed loads with harmonic time dependence.

The qualitative response behavior of a class of undamped chainlike structures with a nonlinear terminal constraint is investigated. It is shown that the hardening or softening behavior of every resonance curve is similar and is determined by the properties of the constraint. Also examined are the number and location of resonance curves, the boundedness of the forced response, the loci of response extrema, and other characteristics of the response. Particular consideration is given to the dependence of the response characteristics on the properties of the linear system, the nonlinear constraint, and the load distribution.

Numerical examples of the approximate steady-state response of three structural systems are presented. These examples illustrate the application of the formulation and qualitative theory. It is shown that disconnected response curves and response curves which cross are obtained for base excitation of a uniform shear beam with a cubic spring foundation. Disconnected response curves are also obtained for the steady-state response to a concentrated load of a chainlike structure with a hardening hysteretic constraint. The accuracy of the approximate response curves is investigated.

Fluctuations in a tokamak plasma

An experimental investigation of low frequency floating potential fluctuations (f ≤ 200 kHz) in a research tokamak plasma using two spatially separated electrostatic probes has been performed. The spectra, correlation length, and the phase velocity of the fluctuations in both the radial and azimuthal direction have been determined. The propagation velocity in the toroidal direction was also measured and was found to be in the direction of electron current flow. The waves traveled azimuthally in the ion diamagnetic drift direction, even after the usual E x B rotation was taken into account. The electron density fluctuations associated with these oscillations were large, δn/n ≃ 0.35 - 0.50.

The spectra were found to have regularly spaced peaks which seemed to be related to specific azimuthal modes (m =1,2,3,...,etc. ) A parametric study was made to determine what effect plasma parameters had on these peaks. During periods of high electron density in the first 2 msec of the plasma lifetime, strong sawtooth type oscillations were observed. These oscillations typically had frequencies of approximately 10 kHz and were also present when large amounts of neutral gas were added during the discharge by a process called "gas puffing."

The results are compared with experimental observations made on other plasma devices with electric and magnetic probes and with microwave and CO₂ laser scattering techniques. (The scattering measurements are complimentary to the probe measurements since, in the former case, the wavelength is fixed by the scattering angle, but the oscillations could not be spatially localized.) The oscillations in the Caltech torus were probably related to a drift-tearing type instability which is thought to play a major role in the anomalous particle and energy flux observed in tokamaks. Comparisons are made between current theory and the experimental results. However, the theory for the observed oscillations is still in a rudimentary stage of development, and it is hoped that the present investigation will stimulate future analytical work.

Quantifying Earthquake Collapse Risk of Tall Steel Moment Frame Buildings Using Rupture-to-Rafters Simulations

There is a sparse number of credible source models available from large-magnitude past earthquakes. A stochastic source model generation algorithm thus becomes necessary for robust risk quantification using scenario earthquakes. We present an algorithm that combines the physics of fault ruptures as imaged in laboratory earthquakes with stress estimates on the fault constrained by field observations to generate stochastic source models for large-magnitude (Mw 6.0-8.0) strike-slip earthquakes. The algorithm is validated through a statistical comparison of synthetic ground motion histories from a stochastically generated source model for a magnitude 7.90 earthquake and a kinematic finite-source inversion of an equivalent magnitude past earthquake on a geometrically similar fault. The synthetic dataset comprises of three-component ground motion waveforms, computed at 636 sites in southern California, for ten hypothetical rupture scenarios (five hypocenters, each with two rupture directions) on the southern San Andreas fault. A similar validation exercise is conducted for a magnitude 6.0 earthquake, the lower magnitude limit for the algorithm. Additionally, ground motions from the Mw7.9 earthquake simulations are compared against predictions by the Campbell-Bozorgnia NGA relation as well as the ShakeOut scenario earthquake. The algorithm is then applied to generate fifty source models for a hypothetical magnitude 7.9 earthquake originating at Parkfield, with rupture propagating from north to south (towards Wrightwood), similar to the 1857 Fort Tejon earthquake. Using the spectral element method, three-component ground motion waveforms are computed in the Los Angeles basin for each scenario earthquake and the sensitivity of ground shaking intensity to seismic source parameters (such as the percentage of asperity area relative to the fault area, rupture speed, and risetime) is studied.

Under plausible San Andreas fault earthquakes in the next 30 years, modeled using the stochastic source algorithm, the performance of two 18-story steel moment frame buildings (UBC 1982 and 1997 designs) in southern California is quantified. The approach integrates rupture-to-rafters simulations into the PEER performance based earthquake engineering (PBEE) framework. Using stochastic sources and computational seismic wave propagation, three-component ground motion histories at 636 sites in southern California are generated for sixty scenario earthquakes on the San Andreas fault. The ruptures, with moment magnitudes in the range of 6.0-8.0, are assumed to occur at five locations on the southern section of the fault. Two unilateral rupture propagation directions are considered. The 30-year probabilities of all plausible ruptures in this magnitude range and in that section of the fault, as forecast by the United States Geological Survey, are distributed among these 60 earthquakes based on proximity and moment release. The response of the two 18-story buildings hypothetically located at each of the 636 sites under 3-component shaking from all 60 events is computed using 3-D nonlinear time-history analysis. Using these results, the probability of the structural response exceeding Immediate Occupancy (IO), Life-Safety (LS), and Collapse Prevention (CP) performance levels under San Andreas fault earthquakes over the next thirty years is evaluated.

Furthermore, the conditional and marginal probability distributions of peak ground velocity (PGV) and displacement (PGD) in Los Angeles and surrounding basins due to earthquakes occurring primarily on the mid-section of southern San Andreas fault are determined using Bayesian model class identification. Simulated ground motions at sites within 55-75km from the source from a suite of 60 earthquakes (Mw 6.0 − 8.0) primarily rupturing mid-section of San Andreas fault are considered for PGV and PGD data.

Theory of the positive column of a gas discharge

An attempt is made to provide a theoretical explanation of the effect of the positive column on the voltage-current characteristic of a glow or an arc discharge. Such theories have been developed before, and all are based on balancing the production and loss of charged particles and accounting for the energy supplied to the plasma by the applied electric field. Differences among the theories arise from the approximations and omissions made in selecting processes that affect the particle and energy balances. This work is primarily concerned with the deviation from the ambipolar description of the positive column caused by space charge, electron-ion volume recombination, and temperature inhomogeneities.

The presentation is divided into three parts, the first of which involved the derivation of the final macroscopic equations from kinetic theory. The final equations are obtained by taking the first three moments of the Boltzmann equation for each of the three species in the plasma. Although the method used and the equations obtained are not novel, the derivation is carried out in detail in order to appraise the validity of numerous approximations and to justify the use of data from other sources. The equations are applied to a molecular hydrogen discharge contained between parallel walls. The applied electric field is parallel to the walls, and the dependent variables—electron and ion flux to the walls, electron and ion densities, transverse electric field, and gas temperature—vary only in the direction perpendicular to the walls. The mathematical description is given by a sixth-order nonlinear two-point boundary value problem which contains the applied field as a parameter. The amount of neutral gas and its temperature at the walls are held fixed, and the relation between the applied field and the electron density at the center of the discharge is obtained in the process of solving the problem. This relation corresponds to that between current and voltage and is used to interpret the effect of space charge, recombination, and temperature inhomogeneities on the voltage-current characteristic of the discharge.

The complete solution of the equations is impractical both numerically and analytically, and in Part II the gas temperature is assumed uniform so as to focus on the combined effects of space charge and recombination. The terms representing these effects are treated as perturbations to equations that would otherwise describe the ambipolar situation. However, the term representing space charge is not negligible in a thin boundary layer or sheath near the walls, and consequently the perturbation problem is singular. Separate solutions must be obtained in the sheath and in the main region of the discharge, and the relation between the electron density and the applied field is not determined until these solutions are matched.

In Part III the electron and ion densities are assumed equal, and the complicated space-charge calculation is thereby replaced by the ambipolar description. Recombination and temperature inhomogeneities are both important at high values of the electron density. However, the formulation of the problem permits a comparison of the relative effects, and temperature inhomogeneities are shown to be important at lower values of the electron density than recombination. The equations are solved by a direct numerical integration and by treating the term representing temperature inhomogeneities as a perturbation.

The conclusions reached in the study are primarily concerned with the association of the relation between electron density and axial field with the voltage-current characteristic. It is known that the effect of space charge can account for the subnormal glow discharge and that the normal glow corresponds to a close approach to an ambipolar situation. The effect of temperature inhomogeneities helps explain the decreasing characteristic of the arc, and the effect of recombination is not expected to appear except at very high electron densities.

Part I: The abortive infection of bacteriophage øx174 at low temperatures. Part II: The early stages in the process of infection by bacteriophage øx174

Part I

The infection of E. coli by ΦX174 at 15°C is abortive; the cells are killed by the infection but neither mature phage nor SS (single-stranded) DNA are synthesized. Parental RF (replicative form) is formed and subsequently replicated at 15°C. The RF made at 15°C shows normal infectivity and full competence to act as precursor to progeny SS DNA after an increase in temperature to 37°C. The investigations suggest that all of the proteins required for SS DNA synthesis and phage maturation are present in the abortive infection at 15°C.

Three possible causes are suggested for the abortive infection at 15°C: (a) A virus-coded protein whose role is essential to the infection is made at 15°C and assumes its native conformation, but its rate of activity is too low at this temperature to sustain the infection process. (b) Virus maturation may involve the formation of a DNA-protein complex and conformational changes which have an energy threshold infrequently reached at 15°C. (c) A host-coded protein present in uninfected cells, and whose activity is essential to the infection at all temperatures, but not to the host at 15°C, is inactive at 15°C. An hypothesis of this type is offered which proposes that the temperature-limiting factor in SS DNA synthesis in vivo may reflect a temperature-dependent property of the host DNA polymerase.

Part II

Three distinct stages are demonstrated in the process whereby ΦX174 invades its host: (1) Attachment: The phage attach to the cell in a manner that does not irreversibly alter the phage particle and which exhibits "single-hit" kinetics. The total charge on the phage particle is demonstrated to be important in determining the rate at which stable attachment is effected. The proteins specified by ΦX cistrons II, III and VII play roles, which may be indirect, in the attachment reaction. (2) Eclipse: 'The attached phage undergo a conformational change. Some of the altered phage particles spontaneously detach from the cell (in a non-infective form) while the remainder are more tightly bound to the cell. The altered phage particles detached (spontaneously or chemically) from such complexes have at least 40% of their DNA extruded from the phage coat. It is proposed that this particle is, or derives from, a direct intermediate in the penetration of the viral DNA.

The kinetics for the eclipse of attached phage particles are first-order with respect to phage concentration and biphasic; about 85% of the phage eclipse at one rate (k = 0.86 min^-1) and the remainder do so at a distinctly lesser rate (k = 0.21 min^-1).

The eclipse event is very temperature-dependent and has the relatively high Arrhenius activation energy of 36.6 kcal/mole, indicating the cooperative nature of the process. The temperature threshold for eclipse is 17 to 18°C.

At present no specific ΦX cistron is identified as affecting the eclipse process. (3) DNA penetration: A fraction of the attached, eclipsed phage particles corresponding in number to the plaque-forming units complete DNA penetration. The penetrated DNA is found in the cell as RF, and the empty phage protein coat remains firmly attached to the exterior of the cell. This step is inhibited by prior irradiation of the phage with relatively high doses of UV light and is insensitive to the presence of KCN and NaN₃. Temporally excluded superinfecting phages do not achieve DNA penetration.

Both eclipsed phage particles and empty phage protein coats may be dissociated from infected cells; some of their properties are described.

Theoretical investigation of turbulent boundary layer over a wavy surface

The important features of the two-dimensional incompressible turbulent flow over a wavy surface of wavelength comparable with the boundary layer thickness are analyzed.

A turbulent field method using model equation for turbulent shear stress similar to the scheme of Bradshaw, Ferriss and Atwell (1967) is employed with suitable modification to cover the viscous sublayer. The governing differential equations are linearized based on the small but finite amplitude to wavelength ratio. An orthogonal wavy coordinate system, accurate to the second order in the amplitude ratio, is adopted to avoid the severe restriction to the validity of linearization due to the large mean velocity gradient near the wall. Analytic solution up to the second order is obtained by using the method of matched-asymptotic-expansion based on the large Reynolds number and hence the small skin friction coefficient.

In the outer part of the layer, the perturbed flow is practically "inviscid." Solutions for the velocity, Reynolds stress and also the wall pressure distributions agree well with the experimental measurement. In the wall region where the perturbed Reynolds stress plays an important role in the process of momentum transport, only a qualitative agreement is obtained. The results also show that the nonlinear second-order effect is negligible for amplitude ratio of 0.03. The discrepancies in the detailed structure of the velocity, shear stress, and skin friction distributions near the wall suggest modifications to the model are required to describe the present problem.

I. The effect of droplet solidification upon two-phase flow in a rocket nozzle. II. A kinetic theory investigation of some condensation-evaporation phenomena by a moment method

Part I:

The perturbation technique developed by Rannie and Marble is used to study the effect of droplet solidification upon two-phase flow in a rocket nozzle. It is shown that under certain conditions an equilibrium flow exists, where the gas and particle phases have the same velocity and temperature at each section of the nozzle. The flow is divided into three regions: the first region, where the particles are all in the form of liquid droplets; a second region, over which the droplets solidify at constant freezing temperature; and a third region, where the particles are all solid. By a perturbation about the equilibrium flow, a solution is obtained for small particle slip velocities using the Stokes drag law and the corresponding approximation for heat transfer between the particle and gas phases. Singular perturbation procedure is required to handle the problem at points where solidification first starts and where it is complete. The effects of solidification are noticeable.

Part II:

When a liquid surface, in contact with only its pure vapor, is not in the thermodynamic equilibrium with it, a net condensation or evaporation of fluid occurs. This phenomenon is studied from a kinetic theory viewpoint by means of moment method developed by Lees. The evaporation-condensation rate is calculated for a spherical droplet and for a liquid sheet, when the temperatures and pressures are not too far removed from their equilibrium values. The solutions are valid for the whole range of Knudsen numbers from the free molecule to the continuum limit. In the continuum limit, the mass flux rate is proportional to the pressure difference alone.

A multiple scattering problem

The present work deals with the problem of the interaction of the electromagnetic radiation with a statistical distribution of nonmagnetic dielectric particles immersed in an infinite homogeneous isotropic, non-magnetic medium. The wavelength of the incident radiation can be less, equal or greater than the linear dimension of a particle. The distance between any two particles is several wavelengths. A single particle in the absence of the others is assumed to scatter like a Rayleigh-Gans particle, i.e. interaction between the volume elements (self-interaction) is neglected. The interaction of the particles is taken into account (multiple scattering) and conditions are set up for the case of a lossless medium which guarantee that the multiple scattering contribution is more important than the self-interaction one. These conditions relate the wavelength λ and the linear dimensions of a particle a and of the region occupied by the particles D. It is found that for constant λ/a, D is proportional to λ and that |Δχ|, where Δχ is the difference in the dielectric susceptibilities between particle and medium, has to lie within a certain range.

The total scattering field is obtained as a series the several terms of which represent the corresponding multiple scattering orders. The first term is a single scattering term. The ensemble average of the total scattering intensity is then obtained as a series which does not involve terms due to products between terms of different orders. Thus the waves corresponding to different orders are independent and their Stokes parameters add.

The second and third order intensity terms are explicitly computed. The method used suggests a general approach for computing any order. It is found that in general the first order scattering intensity pattern (or phase function) peaks in the forward direction Θ = 0. The second order tends to smooth out the pattern giving a maximum in the Θ = π/2 direction and minima in the Θ = 0 , Θ = π directions. This ceases to be true if ka (where k = 2π/λ) becomes large (> 20). For large ka the forward direction is further enhanced. Similar features are expected from the higher orders even though the critical value of ka may increase with the order.

The first order polarization of the scattered wave is determined. The ensemble average of the Stokes parameters of the scattered wave is explicitly computed for the second order. A similar method can be applied for any order. It is found that the polarization of the scattered wave depends on the polarization of the incident wave. If the latter is elliptically polarized then the first order scattered wave is elliptically polarized, but in the Θ = π/2 direction is linearly polarized. If the incident wave is circularly polarized the first order scattered wave is elliptically polarized except for the directions Θ = π/2 (linearly polarized) and Θ = 0, π (circularly polarized). The handedness of the Θ = 0 wave is the same as that of the incident whereas the handedness of the Θ = π wave is opposite. If the incident wave is linearly polarized the first order scattered wave is also linearly polarized. The second order makes the total scattered wave to be elliptically polarized for any Θ no matter what the incident wave is. However, the handedness of the total scattered wave is not altered by the second order. Higher orders have similar effects as the second order.

If the medium is lossy the general approach employed for the lossless case is still valid. Only the algebra increases in complexity. It is found that the results of the lossless case are insensitive in the first order of k_imD where k_im = imaginary part of the wave vector k and D a linear characteristic dimension of the region occupied by the particles. Thus moderately extended regions and small losses make (k_imD)² ≪ 1 and the lossy character of the medium does not alter the results of the lossless case. In general the presence of the losses tends to reduce the forward scattering.

The ionic basis of frequency selectivity in hair cells of the bullfrog's sacculus

Hair cells from the bull frog's sacculus, a vestibular organ responding to substrate-borne vibration, possess electrically resonant membrane properties which maximize the sensitivity of each cell to a particular frequency of mechanical input. The electrical resonance of these cells and its underlying ionic basis were studied by applying gigohm-seal recording techniques to solitary hair cells enzymatically dissociated from the sacculus. The contribution of electrical resonance to frequency selectivity was assessed from microelectrode recordings from hair cells in an excised preparation of the sacculus.

Electrical resonance in the hair cell is demonstrated by damped membrane-potential oscillations in response to extrinsic current pulses applied through the recording pipette. This response is analyzed as that of a damped harmonic oscillator. Oscillation frequency rises with membrane depolarization, from 80-160 Hz at resting potential to asymptotic values of 200-250 Hz. The sharpness of electrical tuning, denoted by the electrical quality factor, Q_e, is a bell-shaped function of membrane voltage, reaching a maximum value around eight at a membrane potential slightly positive to the resting potential.

In whole cells, three time-variant ionic currents are activated at voltages more positive than -60 to -50 mV; these are identified as a voltage-dependent, non-inactivating Ca current (I_ca), a voltage-dependent, transient K current (I_a), and a Ca-dependent K current (I_c). The C channel is identified in excised, inside-out membrane patches on the basis of its large conductance (130-200 pS), its selective permeability to Kover Na or Cl, and its activation by internal Ca ions and membrane depolarization. Analysis of open- and closed-lifetime distributions suggests that the C channel can assume at least two open and three closed kinetic states.

Exposing hair cells to external solutions that inhibit the Ca or C conductances degrades the electrical resonance properties measured under current-clamp conditions, while blocking the A conductance has no significant effect, providing evidence that only the Ca and C conductances participate in the resonance mechanism. To test the sufficiency of these two conductances to account for electrical resonance, a mathematical model is developed that describes I_ca, I_c, and intracellular Ca concentration during voltage-clamp steps. I_ca activation is approximated by a third-order Hodgkin-Huxley kinetic scheme. Ca entering the cell is assumed to be confined to a small submembrane compartment which contains an excess of Ca buffer; Ca leaves this space with first-order kinetics. The Ca- and voltage-dependent activation of C channels is described by a five-state kinetic scheme suggested by the results of single-channel observations. Parameter values in the model are adjusted to fit the waveforms of I_ca and I_c evoked by a series of voltage-clamp steps in a single cell. Having been thus constrained, the model correctly predicts the character of voltage oscillations produced by current-clamp steps, including the dependencies of oscillation frequency and Q_e on membrane voltage. The model shows quantitatively how the Ca and C conductances interact, via changes in intracellular Ca concentration, to produce electrical resonance in a vertebrate hair cell.

Finite-Element Simulations of Earthquakes

This thesis discusses simulations of earthquake ground motions using prescribed ruptures and dynamic failure. Introducing sliding degrees of freedom led to an innovative technique for numerical modeling of earthquake sources. This technique allows efficient implementation of both prescribed ruptures and dynamic failure on an arbitrarily oriented fault surface. Off the fault surface the solution of the three-dimensional, dynamic elasticity equation uses well known finite-element techniques. We employ parallel processing to efficiently compute the ground motions in domains containing millions of degrees of freedom.

Using prescribed ruptures we study the sensitivity of long-period near-source ground motions to five earthquake source parameters for hypothetical events on a strike-slip fault (M_w 7.0 to 7.1) and a thrust fault (M_w 6.6 to 7.0). The directivity of the ruptures creates large displacement and velocity pulses in the ground motions in the forward direction. We found a good match between the severity of the shaking and the shape of the near-source factor from the 1997 Uniform Building Code for strike-slip faults and thrust faults with surface rupture. However, for blind thrust faults the peak displacement and velocities occur up-dip from the region with the peak near-source factor. We assert that a simple modification to the formulation of the near-source factor improves the match between the severity of the ground motion and the shape of the near-source factor.

For simulations with dynamic failure on a strike-slip fault or a thrust fault, we examine what constraints must be imposed on the coefficient of friction to produce realistic ruptures under the application of reasonable shear and normal stress distributions with depth. We found that variation of the coefficient of friction with the shear modulus and the depth produces realistic rupture behavior in both homogeneous and layered half-spaces. Furthermore, we observed a dependence of the rupture speed on the direction of propagation and fluctuations in the rupture speed and slip rate as the rupture encountered changes in the stress field. Including such behavior in prescribed ruptures would yield more realistic ground motions.