Plasma inverse scattering theory

The object of this report is to calculate the electron density profile of plane stratified inhomogeneous plasmas. The electron density profile is obtained through a numerical solution of the inverse scattering algorithm.

The inverse scattering algorithm connects the time dependent reflected field resulting from a δ-function field incident normally on the plasma to the inhomogeneous plasma density.

Examples show that the method produces uniquely the electron density on or behind maxima of the plasma frequency.

It is shown that the δ-function incident field used in the inverse scattering algorithm can be replaced by a thin square pulse.

Spin wave resonance in ferromagnetic films

The objective of this investigation has been a theoretical and experimental understanding of ferromagnetic resonance phenomena in ferromagnetic thin films, and a consequent understanding of several important physical properties of these films. Significant results have been obtained by ferromagnetic resonance, hysteresis, torque magnetometer, He ion backscattering, and X-ray fluorescence measurements for nickel-iron alloy films.

Taking into account all relevant magnetic fields, including the applied, demagnetizing, effective anisotropy and exchange fields, the spin wave resonance condition applicable to the thin film geometry is presented. On the basis of the simple exchange interaction model it is concluded that the normal resonance modes of an ideal film are expected to be unpinned. The possibility of nonideality near the surface of a real film was considered by means of surface anisotropy field, inhomogeneity in demagnetizing field and inhomogeneity of magnetization models. Numerical results obtained for reasonable parameters in all cases show that they negligibly perturb the resonance fields and the higher order mode shapes from those of the unpinned modes of ideal films for thicknesses greater than 1000 Å. On the other hand for films thinner than 1000 Å the resonance field deviations can be significant even though the modes are very nearly unpinned. A previously unnoticed but important feature of all three models is that the interpretation of the first resonance mode as the uniform mode of an ideal film allows an accurate measurement of the average effective demagnetizing field over the film volume. Furthermore, it is demonstrated that it is possible to choose parameters which give indistinguishable predictions for all three models, making it difficult to uniquely ascertain the source of spin pinning in real films from resonance measurements alone.

Spin wave resonance measurements of 81% Ni-19% Fe coevaporated films 30 to 9000 Å thick, at frequencies from 1 to 8 GHz, at room temperature, and with the static magnetic field parallel and perpendicular to the film plane have been performed. A self-consistent analysis of the results for films thicker than 1000 Å, in which multiple excitations can be observed, shows for the first time that a unique value of exchange constant A can only be obtained by the use of unpinned mode assignments. This evidence and the resonance behavior of films thinner than 1000 Å strongly imply that the magnetization at the surfaces of permalloy films is very weakly pinned. However, resonance measurements alone cannot determine whether this pinning is due to a surface anisotropy, an inhomogeneous demagnetizing field or an inhomogeneous magnetization. The above analysis yields a value of 4πM=10,100 Oe and A = (1.03 ± .05) x 10^-6 erg/cm for this alloy. The ability to obtain a unique value of A suggests that spin wave resonance can be used to accurately characterize the exchange interaction in a ferromagnet.

In an effort to resolve the ambiguity of the source of pinning of the magnetization, a correlation of the ratio of magnetic moment and X-ray film thickness with the value of effective demagnetizing field 4πNM as determined from resonance, for films 45 to 300 Å has been performed. The remarkable agreement of both quantities and a comparison with the predictions of five distinct models, strongly imply that the thickness dependence of both quantities is related to a thickness dependent average saturation magnetization, which is far below 10,100 Oe for very thin films. However, a series of complementary experiments shows that this large decrease of average saturation magnetization cannot be simply explained by either oxidation or interdiffusion processes. It can only be satisfactorily explained by an intrinsic decrease of the average saturation magnetization for very thin films, an effect which cannot be justified by any simple physical considerations.

Recognizing that this decrease of average saturation magnetization could be due to an oxidation process, a correlation of resonance measurements, He ion backscattering, X-ray fluorescence and torque magnetometer measurements, for films 40 to 3500 Å thick has been performed. On basis of these measurements it is unambiguously established that the oxide layer on the surface of purposefully oxidized 81% Ni-19% Fe evaporated films is predominantly Fe-oxide, and that in the oxidation process Fe atoms are removed from the bulk of the film to depths of thousands of angstroms. Extrapolation of results for pure Fe films indicates that the oxide is most likely α-Fe₂O₃. These conclusions are in agreement with results from old metallurgical studies of high temperature oxidation of bulk Fe and Ni-Fe alloys. However, X-ray fluorescence results for films oxidized at room temperature, show that although the preferential oxidation of Fe also takes place in these films, the extent of this process is by far too small to explain the large variation of their average saturation magnetization with film thickness.

I. Quantal effects in biochemical cooperativity and a proposed mechanism for the differentiation of calcium signaling in synaptic plasticity. II. Evolutionary algorithms for the optimization of methods in computational chemistry

In Part 1 of this thesis, we propose that biochemical cooperativity is a fundamentally non-ideal process. We show quantal effects underlying biochemical cooperativity and highlight apparent ergodic breaking at small volumes. The apparent ergodic breaking manifests itself in a divergence of deterministic and stochastic models. We further predict that this divergence of deterministic and stochastic results is a failure of the deterministic methods rather than an issue of stochastic simulations.

Ergodic breaking at small volumes may allow these molecular complexes to function as switches to a greater degree than has previously been shown. We propose that this ergodic breaking is a phenomenon that the synapse might exploit to differentiate Ca$^{2+}$ signaling that would lead to either the strengthening or weakening of a synapse. Techniques such as lattice-based statistics and rule-based modeling are tools that allow us to directly confront this non-ideality. A natural next step to understanding the chemical physics that underlies these processes is to consider \textit{in silico} specifically atomistic simulation methods that might augment our modeling efforts.

In the second part of this thesis, we use evolutionary algorithms to optimize \textit{in silico} methods that might be used to describe biochemical processes at the subcellular and molecular levels. While we have applied evolutionary algorithms to several methods, this thesis will focus on the optimization of charge equilibration methods. Accurate charges are essential to understanding the electrostatic interactions that are involved in ligand binding, as frequently discussed in the first part of this thesis.

Epigenetic regulation in neural crest development : role of DNA methyltransferases 3A and 3B

The neural crest is a group of migratory, multipotent stem cells that play a crucial role in many aspects of embryonic development. This uniquely vertebrate cell population forms within the dorsal neural tube but then emigrates out and migrates long distances to different regions of the body. These cells contribute to formation of many structures such as the peripheral nervous system, craniofacial skeleton, and pigmentation of the skin. Why some neural tube cells undergo a change from neural to neural crest cell fate is unknown as is the timing of both onset and cessation of their emigration from the neural tube. In recent years, growing evidence supports an important role for epigenetic regulation as a new mechanism for controlling aspects of neural crest development. In this thesis, I dissect the roles of the de novo DNA methyltransferases (DNMTs) 3A and 3B in neural crest specification, migration and differentiation. First, I show that DNMT3A limits the spatial boundary between neural crest versus neural tube progenitors within the neuroepithelium. DNMT3A promotes neural crest specification by directly mediating repression of neural genes, like Sox2 and Sox3. Its knockdown causes ectopic Sox2 and Sox3 expression at the expense of neural crest territory. Thus, DNMT3A functions as a molecular switch, repressing neural to favor neural crest cell fate. Second, I find that DNMT3B restricts the temporal window during which the neural crest cells emigrate from the dorsal neural tube. Knockdown of DNMT3B causes an excess of neural crest emigration, by extending the time that the neural tube is competent to generate emigrating neural crest cells. In older embryos, this resulted in premature neuronal differentiation. Thus, DNMT3B regulates the duration of neural crest production by the neural tube and the timing of their differentiation. My results in avian embryos suggest that de novo DNA methylation, exerted by both DNMT3A and DNMT3B, plays a dual role in neural crest development, with each individual paralogue apparently functioning during a distinct temporal window. The results suggest that de novo DNA methylation is a critical epigenetic mark used for cell fate restriction of progenitor cells during neural crest cell fate specification. Our discovery provides important insights into the mechanisms that determine whether a cell becomes part of the central nervous system or peripheral cell lineages.

Faint Galaxies in the Megaparsec-Scale Environments of Hyperluminous QSOs at Redshifts 2 < z < 3

This thesis presents detailed observational studies of the extended distributions of gas, galaxies, and dark matter around hyperluminous quasars (HLQSOs) at high redshift. Taken together, these works aim to coherently describe the relationships between these massive, accreting black holes and their environments: the nature of the regions that give rise to such massive black holes, the effect of HLQSO radiation on their surrounding galaxies and gas, and the ability of both galaxies and black holes to shed new light on the formation and evolution of the other.

Chapter 2 focuses on the continuum-color-selected galaxies drawn from the Keck Baryonic Structure Survey (KBSS). The KBSS is a uniquely deep spectroscopic survey of star-forming galaxies in the same volumes of space as 15 HLQSOs at 2.5 < z < 2.9. The three-dimensional distribution of these galaxies among themselves and the nearby HLQSOs is used to infer the extent to which these black holes are associated with overdense peaks in the dark matter and galaxy distribution as quantified by clustering statistics. In conjunction with recent dark-matter simulations, these data provide the first estimates of the host dark-matter halo masses for HLQSOs, providing new insight into the formation and evolution of the most massive black holes at high redshift.

Chapter 3 describes the first results from a new survey (KBSS-Lyα) conducted for this thesis. The KBSS-Lyα survey uses narrowband imaging to identify Lyα-emitters (LAEs) in the ~Mpc regions around eight of the KBSS HLQSOs. Many of these LAEs show the effect of reprocessed HLQSO radiation in their emission through the process known as Lyα fluorescence. In this chapter, these fluorescent LAEs are used to generate a coarse map of the average HLQSO ionizing emission on Mpc scales, thereby setting the first direct constraints of the lifetime and angular distribution of activity for a population of these uniquely luminous black holes.

Chapter 4 contains a more detailed description of the KBSS-Lyα survey itself and the detailed properties of the star-forming and fluorescent objects selected therein. Using imaging and spectroscopic data covering rest-frame UV and optical wavelengths, including spectra from the new near-infrared spectrometer MOSFIRE, we characterize this population of nascent galaxies in terms of their kinematics, enrichment, gas properties, and luminosity distribution while comparing and contrasting them with previously-studied populations of continuum-selected galaxies and LAEs far from the effects of HLQSO emission.

At the conclusion of this thesis, I briefly present future directions for the continuation of this research. In Appendix A, I provide background information on the instrumentation used in this thesis, including my own contributions to MOSFIRE.

Tools For Spatiotemporally Specific Proteomic Analysis In Multicellular Organisms

The emergence of mass spectrometry-based proteomics has revolutionized the study of proteins and their abundances, functions, interactions, and modifications. However, in a multicellular organism, it is difficult to monitor dynamic changes in protein synthesis in a specific cell type within its native environment. In this thesis, we describe methods that enable the metabolic labeling, purification, and analysis of proteins in specific cell types and during defined periods in live animals. We first engineered a eukaryotic phenylalanyl-tRNA synthetase (PheRS) to selectively recognize the unnatural L-phenylalanine analog p-azido-L-phenylalanine (Azf). Using Caenorhabditis elegans, we expressed the engineered PheRS in a cell type of choice (i.e. body wall muscles, intestinal epithelial cells, neurons, pharyngeal muscles), permitting proteins in those cells -- and only those cells -- to be labeled with azides. Labeled proteins are therefore subject to "click" conjugation to cyclooctyne-functionalized affnity probes, separation from the rest of the protein pool and identification by mass spectrometry. By coupling our methodology with heavy isotopic labeling, we successfully identified proteins -- including proteins with previously unknown expression patterns -- expressed in targeted subsets of cells. While cell types like body wall or pharyngeal muscles can be targeted with a single promoter, many cells cannot; spatiotemporal selectivity typically results from the combinatorial action of multiple regulators. To enhance spatiotemporal selectivity, we next developed a two-component system to drive overlapping -- but not identical -- patterns of expression of engineered PheRS, restricting labeling to cells that express both elements. Specifically, we developed a split-intein-based split-PheRS system for highly efficient PheRS-reconstitution through protein splicing. Together, these tools represent a powerful approach for unbiased discovery of proteins uniquely expressed in a subset of cells at specific developmental stages.