Variable-angle electron spectroscopic studies of various polyatomic molecular systems

The complementary techniques of low-energy, variable-angle electron-impact spectroscopy and ultraviolet variable-angle photoelectron spectroscopy have been used to study the electronic spectroscopy and structure of several series of molecules. Electron-impact studies were performed at incident beam energies between 25 eV and 100 eV and at scattering angles ranging from 0° to 90°. The energy-loss regions from 0 eV to greater than 15 eV were studied. Photoelectron spectroscopic studies were conducted using a HeI radiation source and spectra were measured at scattering angles from 45° to 90°. The molecules studied were chosen because of their spectroscopic, chemical, and structural interest. The operation of a new electron-impact spectrometer with multiple-mode target source capability is described. This spectrometer has been used to investigate the spin-forbidden transitions in a number of molecular systems.

The electron-impact spectroscopy of the six chloro-substituted ethylenes has been studied over the energy-loss region from 0-15 eV. Spin-forbidden excitations corresponding to the π → π*, N → T transition have been observed at excitation energies ranging from 4.13 eV in vinyl chloride to 3.54 eV in tetrachloroethylene. Symmetry-forbidden transitions of the type π → np have been oberved in trans-dichloroethyene and tetrachlor oethylene. In addition, transitions to many states lying above the first ionization potential were observed for the first time. Many of these bands have been assigned to Rydberg series converging to higher ionization potentials. The trends observed in the measured transition energies for the π → π*, N → T, and N → V as well as the π → 3s excitation are discussed and compared to those observed in the methyl- and fluoro- substituted ethylenes.

The electron energy-loss spectra of the group VIb transition metal hexacarbonyls have been studied in the 0 eV to 15 eV region. The differential cross sections were obtained for several features in the 3-7 eV energy-loss region. The symmetry-forbidden nature of the ¹A_1g → ¹A_1g, 2t_2g(π) → 3t_2g(π*) transition in these compounds was confirmed by the high-energy, low-angle behavior of their relative intensities. Several low lying transitions have been assigned to ligand field transitions on the basis of the energy and angular behavior of the differential cross sections for these transitions. No transitions which could clearly be assigned to singlet → triplet excitations involving metal orbitals were located. A number of states lying above the first ionization potential have been observed for the first time. A number of features in the 6-14 eV energy-loss region of the spectra of these compounds correspond quite well to those observed in free CO.

A number of exploratory studies have been performed. The π → π*, N → T, singlet → triplet excitation has been located in vinyl bromide at 4.05 eV. We have also observed this transition at approximately 3.8 eV in a cis-/trans- mixture of the 1,2-dibromoethylenes. The low-angle spectrum of iron pentacarbonyl was measured over the energy-loss region extending from 2-12 eV. A number of transitions of 8 eV or greater excitation energy were observed for the first time. Cyclopropane was also studied at both high and low angles but no clear evidence for any spin- forbidden transitions was found. The electron-impact spectrum of the methyl radical resulting from the pyrolysis of tetramethyl tin was obtained at 100 eV incident energy and at 0° scattering angle. Transitions observed at 5.70 eV and 8.30 eV agree well with the previous optical results. In addition, a number of bands were observed in the 8-14 eV region which are most likely due to Rydberg transitions converging to the higher ionization potentials of this molecule. This is the first reported electron-impact spectrum of a polyatomic free radical.

Variable-angle photoelectron spectroscopic studies were performed on a series of three-membered-ring heterocyclic compounds. These compounds are of great interest due to their highly unusual structure. Photoelectron angular distributions using HeI radiation have been measured for the first time for ethylene oxide and ethyleneimine. The measured anisotropy parameters, β, along with those measured for cyclopropane were used to confirm the orbital correlations and photoelectron band assignments. No high values of β similar to those expected for alkene π orbitals were observed for the Walsh or Forster-Coulson-Moffit type orbitals.

Structural Characterization of Pro-inflammatory and Anti-inflammatory Immunoglobulin G Fc Proteins

Immunoglobulin G (IgG) is central in mediating host defense due to its ability to target and eliminate invading pathogens. The fragment antigen binding (Fab) regions are responsible for antigen recognition; however the effector responses are encoded on the Fc region of IgG. IgG Fc displays considerable glycan heterogeneity, accounting for its complex effector functions of inflammation, modulation and immune suppression. Intravenous immunoglobulin G (IVIG) is pooled serum IgG from multiple donors and is used to treat individuals with autoimmune and inflammatory disorders such as rheumatoid arthritis and Kawasaki’s disease, respectively. It contains all the subtypes of IgG (IgG1-4) and over 120 glycovariants due to variation of an Asparagine 297-linked glycan on the Fc. The species identified as the activating component of IVIG is sialylated IgG Fc. Comparisons of wild type Fc and sialylated Fc X-ray crystal structures suggests that sialylation causes an increase in conformational flexibility, which may be important for its anti-inflammatory properties.

Although glycan modifications can promote the anti-inflammatory properties of the Fc, there are amino acid substitutions that cause Fcs to initiate an enhanced immune response. Mutations in the Fc can cause up to a 100-fold increase in binding affinity to activating Fc gamma receptors located on immune cells, and have been shown to enhance antibody dependent cell-mediated cytotoxicity. This is important in developing therapeutic antibodies against cancer and infectious diseases. Structural studies of mutant Fcs in complex with activating receptors gave insight into new protein-protein interactions that lead to an enhanced binding affinity.

Together these studies show how dynamic and diverse the Fc region is and how both protein and carbohydrate modifications can alter structure, leading to IgG Fc’s switch from a pro-inflammatory to an anti-inflammatory protein.

Brain type II calcium and calmodulin-dependent protein kinase: characterization of a brain-region specific isozyme and regulation by autophosphorylation

A variety of molecular approaches have been used to investigate the structural and enzymatic properties of rat brain type ll Ca^(2+) and calmodulin-dependent protein kinase (type ll CaM kinase). This thesis describes the isolation and biochemical characterization of a brain-region specific isozyme of the kinase and also the regulation the kinase activity by autophosphorylation.

The cerebellar isozyme of the type ll CaM kinase was purified and its biochemical properties were compared to the forebrain isozyme. The cerebellar isozyme is a large (500-kDa) multimeric enzyme composed of multiple copies of 50-kDa α subunits and 60/58-kDa β/β’ subunits. The holoenzyme contains approximately 2 α subunits and 8 β subunits. This contrasts to the forebrain isozyme, which is also composed of and β/β'subunits, but they are assembled into a holoenzyme of approximately 9 α subunits and 3 β/β ' subunits. The biochemical and enzymatic properties of the two isozymes are similar. The two isozymes differ in their association with subcellular structures. Approximately 85% of the cerebellar isozyme, but only 50% of the forebrain isozyme, remains associated with the particulate fraction after homogenization under standard conditions. Postsynaptic densities purified from forebrain contain the forebrain isozyme, and the kinase subunits make up about 16% of their total protein. Postsynaptic densities purified from cerebellum contain the cerebellar isozyme, but the kinase subunits make up only 1-2% of their total protein.

The enzymatic activity of both isozymes of the type II CaM kinase is regulated by autophosphorylation in a complex manner. The kinase is initially completely dependent on Ca^(2+)/calmodulin for phosphorylation of exogenous substrates as well as for autophosphorylation. Kinase activity becomes partially Ca^(2+) independent after autophosphorylation in the presence of Ca^(2+)/calmodulin. Phosphorylation of only a few subunits in the dodecameric holoenzyme is sufficient to cause this change, suggesting an allosteric interaction between subunits. At the same time, autophosphorylation itself becomes independent of Ca^(2+) These observations suggest that the kinase may be able to exist in at least two stable states, which differ in their requirements for Ca^(2+)/calmodulin.

The autophosphorylation sites that are involved in the regulation of kinase activity have been identified within the primary structure of the α and β subunits. We used the method of reverse phase-HPLC tryptic phosphopeptide mapping to isolate individual phosphorylation sites. The phosphopeptides were then sequenced by gas phase microsequencing. Phosphorylation of a single homologous threonine residue in the α and β subunits is correlated with the production of the Ca^(2+) -independent activity state of the kinase. In addition we have identified several sites that are phosphorylated only during autophosphorylation in the absence of Ca^(2+)/ calmodulin.

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.

Latent variable models for neural data analysis

The brain is perhaps the most complex system to have ever been subjected to rigorous scientific investigation. The scale is staggering: over 10^11 neurons, each making an average of 10^3 synapses, with computation occurring on scales ranging from a single dendritic spine, to an entire cortical area. Slowly, we are beginning to acquire experimental tools that can gather the massive amounts of data needed to characterize this system. However, to understand and interpret these data will also require substantial strides in inferential and statistical techniques. This dissertation attempts to meet this need, extending and applying the modern tools of latent variable modeling to problems in neural data analysis.

It is divided into two parts. The first begins with an exposition of the general techniques of latent variable modeling. A new, extremely general, optimization algorithm is proposed - called Relaxation Expectation Maximization (REM) - that may be used to learn the optimal parameter values of arbitrary latent variable models. This algorithm appears to alleviate the common problem of convergence to local, sub-optimal, likelihood maxima. REM leads to a natural framework for model size selection; in combination with standard model selection techniques the quality of fits may be further improved, while the appropriate model size is automatically and efficiently determined. Next, a new latent variable model, the mixture of sparse hidden Markov models, is introduced, and approximate inference and learning algorithms are derived for it. This model is applied in the second part of the thesis.

The second part brings the technology of part I to bear on two important problems in experimental neuroscience. The first is known as spike sorting; this is the problem of separating the spikes from different neurons embedded within an extracellular recording. The dissertation offers the first thorough statistical analysis of this problem, which then yields the first powerful probabilistic solution. The second problem addressed is that of characterizing the distribution of spike trains recorded from the same neuron under identical experimental conditions. A latent variable model is proposed. Inference and learning in this model leads to new principled algorithms for smoothing and clustering of spike data.

The relationship between the radio and gamma-ray emission of blazars

Blazars are active galaxies with a jet closely oriented to our line of sight. They are powerful, variable emitters from radio to gamma-ray wavelengths. Although the general picture of synchrotron emission at low energies and inverse Compton at high energies is well established, important aspects of blazars are not well understood. In particular, the location of the gamma-ray emission region is not clearly established, with some theories favoring a location close to the central engine, while others place it at parsec scales in the radio jet.

We developed a program to locate the gamma-ray emission site in blazars, through the study of correlated variations between their gamma-ray and radio-wave emission. Correlated variations are expected when there is a relation between emission processes at both bands, while delays tell us about the relative location of their energy generation zones. Monitoring at 15 GHz using the Owens Valley Radio Observatory 40 meter telescope started in mid-2007. The program monitors 1593 blazars twice per week, including all blazars detected by the Fermi Gamma-ray Space Telescope (Fermi) north of -20 degrees declination. This program complements the continuous monitoring of gamma-rays by Fermi.

Three year long gamma-ray light curves for bright Fermi blazars are cross-correlated with four years of radio monitoring. The significance of cross-correlation peaks is investigated using simulations that account for the uneven sampling and noise properties of the light curves, which are modeled as red-noise processes with a simple power-law power spectral density. We found that out of 86 sources with high quality data, only three show significant correlations (AO 0235+164, B2 2308+34 and PKS 1502+106). Additionally, we find a significant correlation for Mrk 421 when including the strong gamma-ray/radio flare of late 2012. In all four cases radio variations lag gamma-ray variations, suggesting that the gamma-ray emission originates upstream of the radio emission. For PKS 1502+106 we locate the gamma-ray emission site parsecs away from the central engine, thus disfavoring the model of Blandford and Levinson (1995), while other cases are inconclusive. These findings show that continuous monitoring over long time periods is required to understand the cross-correlation between gamma-ray and radio-wave variability in most blazars.

Using space geodesy to constrain variations in seismogenic behavior on subduction megathrusts

The concept of seismogenic asperities and aseismic barriers has become a useful paradigm within which to understand the seismogenic behavior of major faults. Since asperities and barriers can be thought of as defining the potential rupture area of large megathrust earthquakes, it is thus important to identify their respective spatial extents, constrain their temporal longevity, and to develop a physical understanding for their behavior. Space geodesy is making critical contributions to the identification of slip asperities and barriers but progress in many geographical regions depends on improving the accuracy and precision of the basic measurements. This thesis begins with technical developments aimed at improving satellite radar interferometric measurements of ground deformation whereby we introduce an empirical correction algorithm for unwanted effects due to interferometric path delays that are due to spatially and temporally variable radar wave propagation speeds in the atmosphere. In chapter 2, I combine geodetic datasets with complementary spatio-temporal resolutions to improve our understanding of the spatial distribution of crustal deformation sources and their associated temporal evolution – here we use observations from Long Valley Caldera (California) as our test bed. In the third chapter I apply the tools developed in the first two chapters to analyze postseismic deformation associated with the 2010 Mw=8.8 Maule (Chile) earthquake. The result delimits patches where afterslip occurs, explores their relationship to coseismic rupture, quantifies frictional properties associated with inferred patches of afterslip, and discusses the relationship of asperities and barriers to long-term topography. The final chapter investigates interseismic deformation of the eastern Makran subduction zone by using satellite radar interferometry only, and demonstrates that with state-of-art techniques it is possible to quantify tectonic signals with small amplitude and long wavelength. Portions of the eastern Makran for which we estimate low fault coupling correspond to areas where bathymetric features on the downgoing plate are presently subducting, whereas the region of the 1945 M=8.1 earthquake appears to be more highly coupled.

Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

Electron energy-loss spectroscopy study of polyatomic molecular systems under pyrolytic conditions

The technique of variable-angle, electron energy-loss spectroscopy has been used to study the electronic spectroscopy of the diketene molecule. The experiment was performed using incident electron beam energies of 25 eV and 50 eV, and at scattering angles between 10° and 90°. The energy-loss region from 2 eV to 11 eV was examined. One spin-forbidden transition has been observed at 4.36 eV and three others that are spin-allowed have been located at 5.89 eV, 6.88 eV and 7.84 eV. Based on the intensity variation of these transitions with impact energy and scattering angle, and through analogy with simpler molecules, the first three transitions are tentatively assigned to an n → π* transition, a π - σ* (3s) Rydberg transition and a π → π* transition.

Thermal decomposition of chlorodifluoromethane, chloroform, dichloromethane and chloromethane under flash-vacuum pyrolysis conditions (900-1100°C) was investigated by the technique of electron energy-loss spectroscopy, using the impact energy of 50 eV and a scattering angle of 10°. The pyrolytic reaction follows a hydrogen-chloride α-elimination pathway. The difluoromethylene radical was produced from chlorodifluoromethane pyrolysis at 900°C and identified by its X^1 A_1 → A^1B_1 band at 5.04 eV.

Finally, a number of exploratory studies have been performed. The thermal decomposition of diketene was studied under flash vacuum pressures (1-10 mTorr) and temperatures ranging from 500°C to 1000°C. The complete decomposition of the diketene molecule into two ketene molecules was achieved at 900°C. The pyrolysis of trifluoromethyl iodide molecule at 1000°C produced an electron energy-loss spectrum with several iodine-atom, sharp peaks and only a small shoulder at 8.37 eV as a possible trifluoromethyl radical feature. The electron energy-loss spectrum of trichlorobromomethane at 900°C mainly showed features from bromine atom, chlorine molecule and tetrachloroethylene. Hexachloroacetone decomposed partially at 900°C, but showed well-defined features from chlorine, carbon monoxide and tetrachloroethylene molecules. Bromodichloromethane molecule was investigated at 1000°C and produced a congested, electron energy-loss spectrum with bromine-atom, hydrogen-bromide, hydrogen-chloride and tetrachloroethylene features.

Metasomatism and magmatic assimilation at a gabbro-limestone contact, Christmas Mountains, Big Bend region, Texas

A composite stock of alkaline gabbro and syenite is intrusive into limestone of the Del Carmen, Sue Peake and Santa Elena Formations at the northwest end of the Christmas Mountains. There is abundant evidence of solution of wallrock by magma but nowhere are gabbro and limestone in direct contact. The sequence of lithologies developed across the intrusive contact and across xenoliths is gabbro, pyroxenite, calc-silicate skarn, marble. Pyroxenite is made up of euhedral crystals of titanaugite and sphene in a leucocratic matrix of nepheline, Wollastonite and alkali feldspar. The uneven modal distribution of phases in pyroxenite and the occurrence' of nepheline syenite dikes, intrusive into pyroxenite and skarn, suggest that pyroxenite represents an accumulation of clinopyroxene "cemented" together by late-solidifying residual magma of nepheline syenite composition. Assimilation of limestone by gabbroic magma involves reactions between calcite and magma and/or crystals in equilibrium with magma and crystallization of phases in which the magma is saturated, to supply energy for the solution reaction. Gabbroic magma was saturated with plagioclase and clinopyroxene at the time of emplacement. The textural and mineralogic features of pyroxenite can be produced by the reaction 2( 1-X) CALCITE + AN_XAB_l-X = (1-X) NEPHELINE+ 2(1-X) WOLLASTONITE+ X ANORTHITE+ 2(1-X) CO₂. Plagioclase in pyroxenite has corroded margins and is rimmed by nepheline, suggestive of resorption by magma. Anorthite and wollastonite enter solid solution in titanaugite. For each mole of calcite dissolved, approximately one mole of clinopyroxene was crystallized. Thus the amount of limestone that may be assimilated is limited by the concentration of potential clinopyroxene in the magma. Wollastonite appears as a phase when magma has been depleted in iron and magnesium by crystallization of titanaugite. The predominance of mafic and ultramafic compositions among contaminated rocks and their restriction to a narrow zone along the intrusive contact provides little evidence for the generation of a significant volume of desilicated magma as a result of limestone assimilation.

Within 60 m of the intrusive contact with the gabbro, nodular chert in the Santa Elena Limestone reacted with the enveloping marble to form spherical nodules of high-temperature calc-silicate minerals. The phases wollastonite, rankinite, spurrite, tilleyite and calcite, form a series of sharply-bounded, concentric monomineralic and two-phase shells which record a step-wise decrease in silica content from the core of a nodule to its rim. Mineral zones in the nodules vary 'with distance from the gabbro as follows:

0-5 m CALCITE + SPURRITE + RANKINITE + WOLLASTONITE
5-16 m CALCITE + TILLEYITE ± SPURRITE + RANKINITE + WOLLASTONITE
16-31 m CALCITE + TILLEYITE + WOLLASTONITE
31-60 m CALCITE + WOLLASTONITE
60-plus CALCITE + QUARTZ

The mineral of a one-phase zone is compatible with the phases bounding it on either side but these phases are incompatible in the same volume of P-T-X_CO2.

Growth of a monomineralio zone is initiated by reaction between minerals of adjacent one-phase zones which become unstable with rising temperature to form a thin layer of a new single phase that separates the reactants and is compatible with both of them. Because the mineral of the new zone is in equilibrium with the phases at both of its contacts, gradients in the chemical potentials of the exchangeable components are established across it. Although zone boundaries mark discontinuities in the gradients of bulk composition, two-phase equilibria at the contacts demonstrate that the chemical potentials are continuous. Hence, Ca, Si and CO₂ were redistributed in the growing nodule by diffusion. A monomineralic zone grows at the expense of an adjacent zone by reaction between diffusing components and the mineral of the adjacent zone. Equilibria between two phases at zone boundaries buffers the chemical potentials of the diffusing species. Thus, within a monomineralic zone, the chemical potentials of the diffusing components are controlled external to the local assemblage by the two-phase equilibria at the zone boundaries.

Mineralogically zoned calc-silicate skarn occurs as a narrow band that separates pyroxenite and marble along the intrusive contact and forms a rim on marble xenoliths in gabbro. Skarn consists of melilite or idocrase pseudomorphs of melili te, one or two . stoichiometric calcsilicate phases and accessory Ti-Zr garnet, perovskite and magnetite. The sequence of mineral zones from pyroxenite to marble, defined by a characteristic calc-silicate, is wollastonite, rankinite, spurrite, calcite. Mineral assemblages of adjacent skarn zones are compatible and the set of zones in a skarn band defines a facies type, indicating that the different mineral assemblages represent different bulk compositions recrystallized under identical conditions. The number of phases in each zone is less than the number that might be expected to result from metamorphism of a general bulk composition under conditions of equilibrium, trivariant in P, T and u_CO2. The "special" bulk composition of each zone is controlled by reaction between phases of the zones bounding it on either side. The continuity of the gradients of composition of melilite and garnet solid solutions across the skarn is consistent with the local equilibrium hypothesis and verifies that diffusion was the mechanism of mass transport. The formula proportions of Ti and Zr in garnet from skarn vary antithetically with that of Si Which systematically decreases from pyroxenite to marble. The chemical potential of Si in each skarn zone was controlled by the coexisting stoichiometric calc-silicate phases in the assemblage. Thus the formula proportion of Si in garnet is a direct measure of the chemical potential of Si from point to point in skarn. Reaction between gabbroic magma saturated with plagioclase and clinopyroxene produced nepheline pyroxenite and melilite-wollastonite skarn. The calcsilicate zones result from reaction between calcite and wollastonite to form spurrite and rankinite.

Protein-protein recognition: The neonatal Fe receptor and immunoglobulin G

The neonatal Fe receptor (FeRn) binds the Fe portion of immunoglobulin G (IgG) at the acidic pH of endosomes or the gut and releases IgG at the alkaline pH of blood. FeRn is responsible for the maternofetal transfer of IgG and for rescuing endocytosed IgG from a default degradative pathway. We investigated how FeRn interacts with IgG by constructing a heterodimeric form of the Fe (hdFc) that contains one FeRn binding site. This molecule was used to characterize the interaction between one FeRn molecule and one Fe and to determine under what conditions FeRn forms a dimer. The hdFc binds one FeRn molecule at pH 6.0 with a K_d of 80 nM. In solution and with FeRn anchored to solid supports, the heterodimeric Fe does not induce a dimer of FeRn molecules. FcRnhdFc complex crystals were obtained and the complex structure was solved to 2.8 Å resolution. Analysis of this structure refined the understanding of the mechanism of the pH-dependent binding, shed light on the role played by carbohydrates in the Fe binding, and provided insights on how to design therapeutic IgG antibodies with longer serum half-lives. The FcRn-hdFc complex in the crystal did not contain the FeRn dimer. To characterize the tendency of FeRn to form a dimer in a membrane we analyzed the tendency of the hdFc to induce cross-phosphorylation of FeRn-tyrosine kinase chimeras. We also constructed FeRn-cyan and FeRn-yellow fluorescent proteins and have analyzed the tendency of these molecules to exhibit fluorescence resonance energy transfer. As of now, neither of these analyses have lead to conclusive results. In the process of acquiring the context to appreciate the structure of the FcRn-hdFc interface, we developed a study of 171 other nonobligate protein-protein interfaces that includes an original principal component analysis of the quantifiable aspects of these interfaces.

Structural geology of the region between Pacoima and Little Tujunga Canyons, San Gabriel Mountains, California

An area of about 25 square miles in the western part of the San Gabriel Mountains was mapped on a scale of 1000 feet to the inch. Special attention was given to the structural geology, particularly the relations between the different systems of faults, of which the San Gabriel fault system and the Sierra Madre fault system are the most important ones. The present distribution and relations of the rocks suggests that the southern block has tilted northward against a more stable mass of old rocks which was raised up during a Pliocene or post-Pliocene orogeny. It is suggested that this northward tilting of the block resulted in the group of thrust faults which comprise the Sierra Madre fault system. It is show that this hypothesis fits the present distribution of the rocks and occupies a logical place in the geologic history of the region as well or better than any other hypothesis previously offered to explain the geology of the region.

Dynamic rupture simulation integrated with earthquake observations

Dynamic rupture simulations are unique in their contributions to the study of earthquake physics. The current rapid development of dynamic rupture simulations poses several new questions: Do the simulations reflect the real world? Do the simulations have predictive power? Which one should we believe when the simulations disagree? This thesis illustrates how integration with observations can help address these questions and reduce the effects of non-uniqueness of both dynamic rupture simulations and kinematic inversion problems. Dynamic rupture simulations with observational constraints can effectively identify non-physical features inferred from observations. Moreover, the integrative technique can also provide more physical insights into the mechanisms of earthquakes. This thesis demonstrates two examples of such kinds of integration: dynamic rupture simulations of the M_w 9.0 2011 Tohoku-Oki earthquake and of earthquake ruptures in damaged fault zones:

(1) We develop simulations of the Tohoku-Oki earthquake based on a variety of observations and minimum assumptions of model parameters. The simulations provide realistic estimations of stress drop and fracture energy of the region and explain the physical mechanisms of high-frequency radiation in the deep region. We also find that the overridding subduction wedge contributes significantly to the up-dip rupture propagation and large final slip in the shallow region. Such findings are also applicable to other megathrust earthquakes.

(2) Damaged fault zones are usually found around natural faults, but their effects on earthquake ruptures have been largely unknown. We simulate earthquake ruptures in damaged fault zones with material properties constrained by seismic and geological observations. We show that reflected waves in fault zones are effective at generating pulse-like ruptures and head waves tend to accelerate and decelerate rupture speeds. These mechanisms are robust in natural fault zones with large attenuation and off-fault plasticity. Moreover, earthquakes in damaged fault zones can propagate at super-Rayleigh speeds that are unstable in homogeneous media. Supershear transitions in fault zones do not require large fault stresses. In the end, we present observations in the Big Bear region, where variability of rupture speeds of small earthquakes correlates with the laterally variable materials in a damaged fault zone.

Investigation of bulk indium antimonide as heterodyne detector for the submillimeter wavelength region

Bulk n-lnSb is investigated at a heterodyne detector for the submillimeter wavelength region. Two modes or operation are investigated: (1) the Rollin or hot electron bolometer mode (zero magnetic field), and (2) the Putley mode (quantizing magnetic field). The highlight of the thesis work is the pioneering demonstration or the Putley mode mixer at several frequencies. For example, a double-sideband system noise temperature of about 510K was obtained using a 812 GHz methanol laser for the local oscillator. This performance is at least a factor or 10 more sensitive than any other performance reported to date at the same frequency. In addition, the Putley mode mixer achieved system noise temperatures of 250K at 492 GHz and 350K at 625 GHz. The 492 GHz performance is about 50% better and the 625 GHz is about 100% better than previous best performances established by the Rollin-mode mixer. To achieve these results, it was necessary to design a totally new ultra-low noise, room-temperature preamp to handle the higher source impedance imposed by the Putley mode operation. This preamp has considerably less input capacitance than comparably noisy, ambient designs.

In addition to advancing receiver technology, this thesis also presents several novel results regarding the physics of n-lnSb at low temperatures. A Fourier transform spectrometer was constructed and used to measure the submillimeter wave absorption coefficient of relatively pure material at liquid helium temperatures and in zero magnetic field. Below 4.2K, the absorption coefficient was found to decrease with frequency much faster than predicted by Drudian theory. Much better agreement with experiment was obtained using a quantum theory based on inverse-Bremmstrahlung in a solid. Also the noise of the Rollin-mode detector at 4.2K was accurately measured and compared with theory. The power spectrum is found to be well fit by a recent theory of non- equilibrium noise due to Mather. Surprisingly, when biased for optimum detector performance, high purity lnSb cooled to liquid helium temperatures generates less noise than that predicted by simple non-equilibrium Johnson noise theory alone. This explains in part the excellent performance of the Rollin-mode detector in the millimeter wavelength region.

Again using the Fourier transform spectrometer, spectra are obtained of the responsivity and direct detection NEP as a function of magnetic field in the range 20-110 cm^-1. The results show a discernable peak in the detector response at the conduction electron cyclotron resonance frequency tor magnetic fields as low as 3 KG at bath temperatures of 2.0K. The spectra also display the well-known peak due to the cyclotron resonance of electrons bound to impurity states. The magnitude of responsivity at both peaks is roughly constant with magnet1c field and is comparable to the low frequency Rollin-mode response. The NEP at the peaks is found to be much better than previous values at the same frequency and comparable to the best long wavelength results previously reported. For example, a value NEP=4.5x10^-13/Hz^1/2 is measured at 4.2K, 6 KG and 40 cm^-1. Study of the responsivity under conditions of impact ionization showed a dramatic disappearance of the impurity electron resonance while the conduction electron resonance remained constant. This observation offers the first concrete evidence that the mobility of an electron in the N=0 and N=1 Landau levels is different. Finally, these direct detection experiments indicate that the excellent heterodyne performance achieved at 812 GHz should be attainable up to frequencies of at least 1200 GHz.

Geochemistry and resonance ionization of platinum-group elements

Experimental studies were conducted with the goals of 1) determining the origin of Pt- group element (PGE) alloys and associated mineral assemblages in refractory inclusions from meteorites and 2) developing a new ultrasensitive method for the in situ chemical and isotopic analysis of PGE. A general review of the geochemistry and cosmochemistry of the PGE is given, and specific research contributions are presented within the context of this broad framework.

An important step toward understanding the cosmochemistry of the PGE is the determination of the origin of POE-rich metallic phases (most commonly εRu-Fe) that are found in Ca, AJ-rich refractory inclusions (CAI) in C3V meteorites. These metals occur along with γNi-Fe metals, Ni-Fe sulfides and Fe oxides in multiphase opaque assemblages. Laboratory experiments were used to show that the mineral assemblages and textures observed in opaque assemblages could be produced by sulfidation and oxidation of once homogeneous Ni-Fe-PGE metals. Phase equilibria, partitioning and diffusion kinetics were studied in the Ni-Fe-Ru system in order to quantify the conditions of opaque assemblage formation. Phase boundaries and tie lines in the Ni-Fe-Ru system were determined at 1273, 1073 and 873K using an experimental technique that allowed the investigation of a large portion of the Ni-Fe-Ru system with a single experiment at each temperature by establishing a concentration gradient within which local equilibrium between coexisting phases was maintained. A wide miscibility gap was found to be present at each temperature, separating a hexagonal close-packed εRu-Fe phase from a face-centered cubic γNi-Fe phase. Phase equilibria determined here for the Ni-Fe-Ru system, and phase equilibria from the literature for the Ni-Fe-S and Ni-Fe-O systems, were compared with analyses of minerals from opaque assemblages to estimate the temperature and chemical conditions of opaque assemblage formation. It was determined that opaque assemblages equilibrated at a temperature of ~770K, a sulfur fugacity 10 times higher than an equilibrium solar gas, and an oxygen fugacity 10⁶ times higher than an equilibrium solar gas.

Diffusion rates between -γNi-Fe and εRu-Fe metal play a critical role in determining the time (with respect to CAI petrogenesis) and duration of the opaque assemblage equilibration process. The diffusion coefficient for Ru in Ni (D^Ru_Ni) was determined as an analog for the Ni-Fe-Ru system by the thin-film diffusion method in the temperature range of 1073 to 1673K and is given by the expression:

D^Ru_Ni (cm² sec^-1) = 5.0(±0.7) x 10^-3 exp(-2.3(±0.1) x 10¹² erg mole^-1/RT) where R is the gas constant and T is the temperature in K. Based on the rates of dissolution and exsolution of metallic phases in the Ni-Fe-Ru system it is suggested that opaque assemblages equilibrated after the melting and crystallization of host CAI during a metamorphic event of ≥ 10³ years duration. It is inferred that opaque assemblages originated as immiscible metallic liquid droplets in the CAI silicate liquid. The bulk compositions of PGE in these precursor alloys reflects an early stage of condensation from the solar nebula and the partitioning of V between the precursor alloys and CAI silicate liquid reflects the reducing nebular conditions under which CAI were melted. The individual mineral phases now observed in opaque assemblages do not preserve an independent history prior to CAI melting and crystallization, but instead provide important information on the post-accretionary history of C3V meteorites and allow the quantification of the temperature, sulfur fugacity and oxygen fugacity of cooling planetary environments. This contrasts with previous models that called upon the formation of opaque assemblages by aggregation of phases that formed independently under highly variable conditions in the solar nebula prior to the crystallization of CAI.

Analytical studies were carried out on PGE-rich phases from meteorites and the products of synthetic experiments using traditional electron microprobe x-ray analytical techniques. The concentrations of PGE in common minerals from meteorites and terrestrial rocks are far below the ~100 ppm detection limit of the electron microprobe. This has limited the scope of analytical studies to the very few cases where PGE are unusually enriched. To study the distribution of PGE in common minerals will require an in situ analytical technique with much lower detection limits than any methods currently in use. To overcome this limitation, resonance ionization of sputtered atoms was investigated for use as an ultrasensitive in situ analytical technique for the analysis of PGE. The mass spectrometric analysis of Os and Re was investigated using a pulsed primary Ar⁺ ion beam to provide sputtered atoms for resonance ionization mass spectrometry. An ionization scheme for Os that utilizes three resonant energy levels (including an autoionizing energy level) was investigated and found to have superior sensitivity and selectivity compared to nonresonant and one and two energy level resonant ionization schemes. An elemental selectivity for Os over Re of ≥ 10³ was demonstrated. It was found that detuning the ionizing laser from the autoionizing energy level to an arbitrary region in the ionization continuum resulted in a five-fold decrease in signal intensity and a ten-fold decrease in elemental selectivity. Osmium concentrations in synthetic metals and iron meteorites were measured to demonstrate the analytical capabilities of the technique. A linear correlation between Os⁺ signal intensity and the known Os concentration was observed over a range of nearly 10⁴ in Os concentration with an accuracy of ~ ±10%, a millimum detection limit of 7 parts per billion atomic, and a useful yield of 1%. Resonance ionization of sputtered atoms samples the dominant neutral-fraction of sputtered atoms and utilizes multiphoton resonance ionization to achieve high sensitivity and to eliminate atomic and molecular interferences. Matrix effects should be small compared to secondary ion mass spectrometry because ionization occurs in the gas phase and is largely independent of the physical properties of the matrix material. Resonance ionization of sputtered atoms can be applied to in situ chemical analysis of most high ionization potential elements (including all of the PGE) in a wide range of natural and synthetic materials. The high useful yield and elemental selectivity of this method should eventually allow the in situ measurement of Os isotope ratios in some natural samples and in sample extracts enriched in PGE by fire assay fusion.

Phase equilibria and diffusion experiments have provided the basis for a reinterpretation of the origin of opaque assemblages in CAI and have yielded quantitative information on conditions in the primitive solar nebula and cooling planetary environments. Development of the method of resonance ionization of sputtered atoms for the analysis of Os has shown that this technique has wide applications in geochemistry and will for the first time allow in situ studies of the distribution of PGE at the low concentration levels at which they occur in common minerals.