Standing electron plasma wave mechanism of void array formation inside glass by femtosecond laser irradiation

We investigate the mechanism of formation of periodic void arrays inside fused silica and BK7 glass irradiated by a tightly focused femtosecond (fs) laser beam. Our results show that the period of each void array is not uniform along the laser propagation direction, and the average period of the void array decreases with increasing pulse number and pulse energy. We propose a mechanism in which a standing electron plasma wave created by the interference of a fs-laser-driven electron wave and its reflected wave is responsible for the formation of the periodic void arrays.

Functionalization of Si(111) surfaces and the formation of mixed monolayers for the covalent attachment of molecular catalysts in photoelectrochemical devices

The functionalization of silicon surfaces with molecular catalysts for proton reduction is an important part of the development of a solar-powered, water-splitting device for solar fuel formation. The covalent attachment of these catalysts to silicon without damaging the underlying electronic properties of silicon that make it a good photocathode has proven difficult. We report the formation of mixed monolayer-functionalized surfaces that incor- porate both methyl and vinylferrocenyl or vinylbipyridyl (vbpy) moieties. The silicon was functionalized using reaction conditions analogous to those of hydrosilylation, but instead of a H-terminated Si surface, a chlorine-terminated Si precursor surface was used to produce the linked vinyl-modified functional group. The functionalized surfaces were characterized by time-resolved photoconductivity decay, X-ray photoelectron spectroscopy (XPS), electro- chemical, and photoelectrochemical measurements. The functionalized Si surfaces were well passivated, exhibited high surface coverage and few remaining reactive Si atop sites, had a very low surface recombination velocity, and displayed little initial surface oxidation. The surfaces were stable toward atmospheric and electrochemical oxidation. The surface coverage of ferrocene or bipyridine was controllably varied from 0 up to 30% of a monolayer without loss of the underlying electronic properties of the silicon. Interfacial charge transfer to the attached ferrocene group was relatively rapid, and a photovoltage of 0.4 V was generated upon illumination of functionalized n-type silicon surfaces in CH₃CN. The immobilized bipyridine ligands bound transition metal ions, and thus enabled the assembly of metal complexes on the silicon surface. XPS studies demonstrated that [Cp∗Rh(vbpy)Cl]Cl, [Cp∗Ir(vbpy)Cl]Cl, and Ru(acac)₂vbpy were assembled on the surface. For the surface prepared with iridium, x-ray absorption spectroscopy at the Ir L_III edge showed an edge energy and post-edge features virtually identical to a powder sample of [Cp∗Ir(bipy)Cl]Cl (bipy is 2,2 ́-bipyridyl). Electrochemical studies on these surfaces confirmed that the assembled complexes were electrochemically active.

Nonlinear X-wave formation and conical emission at different powers of a femtosecond laser pulse in water

Nonlinear X-wave formation at different pulse powers in water is simulated using the standard model of nonlinear Schrodinger equation (NLSE). It is shown that in near field X-shape originally emerges from the interplay between radial diffraction and optical Kerr effect. At relatively low power group-velocity dispersion (GVD) arrests the collapse and leads to pulse splitting on axis. With high enough power, multi-photon ionization (NIPI) and multi-photon absorption (MPA) play great importance in arresting the collapse. The tailing part of pulse is first defocused by MPI and then refocuses. Pulse splitting on axis is a manifestation of this process. Double X-wave forms when the split sub-pulses are self-focusing. In the far field, the character of the central X structure of conical emission (CE) is directly related to the single or double X-shape in the near field. (c) 2007 Elsevier B.V. All rights reserved.

New insights into the formation and modification of carbonate-bearing minerals and methane gas in geological systems using multiply substituted isotopologues

This thesis describes the use of multiply-substituted stable isotopologues of carbonate minerals and methane gas to better understand how these environmentally significant minerals and gases form and are modified throughout their geological histories. Stable isotopes have a long tradition in earth science as a tool for providing quantitative constraints on how molecules, in or on the earth, formed in both the present and past. Nearly all studies, until recently, have only measured the bulk concentrations of stable isotopes in a phase or species. However, the abundance of various isotopologues within a phase, for example the concentration of isotopologues with multiple rare isotopes (multiply substituted or 'clumped' isotopologues) also carries potentially useful information. Specifically, the abundances of clumped isotopologues in an equilibrated system are a function of temperature and thus knowledge of their abundances can be used to calculate a sample’s formation temperature. In this thesis, measurements of clumped isotopologues are made on both carbonate-bearing minerals and methane gas in order to better constrain the environmental and geological histories of various samples.

Clumped-isotope-based measurements of ancient carbonate-bearing minerals, including apatites, have opened up paleotemperature reconstructions to a variety of systems and time periods. However, a critical issue when using clumped-isotope based measurements to reconstruct ancient mineral formation temperatures is whether the samples being measured have faithfully recorded their original internal isotopic distributions. These original distributions can be altered, for example, by diffusion of atoms in the mineral lattice or through diagenetic reactions. Understanding these processes quantitatively is critical for the use of clumped isotopes to reconstruct past temperatures, quantify diagenesis, and calculate time-temperature burial histories of carbonate minerals. In order to help orient this part of the thesis, Chapter 2 provides a broad overview and history of clumped-isotope based measurements in carbonate minerals.

In Chapter 3, the effects of elevated temperatures on a sample’s clumped-isotope composition are probed in both natural and experimental apatites (which contain structural carbonate groups) and calcites. A quantitative model is created that is calibrated by the experiments and consistent with the natural samples. The model allows for calculations of the change in a sample’s clumped isotope abundances as a function of any time-temperature history.

In Chapter 4, the effects of diagenesis on the stable isotopic compositions of apatites are explored on samples from a variety of sedimentary phosphorite deposits. Clumped isotope temperatures and bulk isotopic measurements from carbonate and phosphate groups are compared for all samples. These results demonstrate that samples have experienced isotopic exchange of oxygen atoms in both the carbonate and phosphate groups. A kinetic model is developed that allows for the calculation of the amount of diagenesis each sample has experienced and yields insight into the physical and chemical processes of diagenesis.

The thesis then switches gear and turns its attention to clumped isotope measurements of methane. Methane is critical greenhouse gas, energy resource, and microbial metabolic product and substrate. Despite its importance both environmentally and economically, much about methane’s formational mechanisms and the relative sources of methane to various environments remains poorly constrained. In order to add new constraints to our understanding of the formation of methane in nature, I describe the development and application of methane clumped isotope measurements to environmental deposits of methane. To help orient the reader, a brief overview of the formation of methane in both high and low temperature settings is given in Chapter 5.

In Chapter 6, a method for the measurement of methane clumped isotopologues via mass spectrometry is described. This chapter demonstrates that the measurement is precise and accurate. Additionally, the measurement is calibrated experimentally such that measurements of methane clumped isotope abundances can be converted into equivalent formational temperatures. This study represents the first time that methane clumped isotope abundances have been measured at useful precisions.

In Chapter 7, the methane clumped isotope method is applied to natural samples from a variety of settings. These settings include thermogenic gases formed and reservoired in shales, migrated thermogenic gases, biogenic gases, mixed biogenic and thermogenic gas deposits, and experimentally generated gases. In all cases, calculated clumped isotope temperatures make geological sense as formation temperatures or mixtures of high and low temperature gases. Based on these observations, we propose that the clumped isotope temperature of an unmixed gas represents its formation temperature — this was neither an obvious nor expected result and has important implications for how methane forms in nature. Additionally, these results demonstrate that methane-clumped isotope compositions provided valuable additional constraints to studying natural methane deposits.

Understanding planet formation through high precision photometry and spectroscopy

From studies of protoplanetary disks to extrasolar planets and planetary debris, we aim to understand the full evolution of a planetary system. Observational constraints from ground- and space-based instrumentation allows us to measure the properties of objects near and far and are central to developing this understanding. We present here three observational campaigns that, when combined with theoretical models, reveal characteristics of different stages and remnants of planet formation. The Kuiper Belt provides evidence of chemical and dynamical activity that reveals clues to its primordial environment and subsequent evolution. Large samples of this population can only be assembled at optical wavelengths, with thermal measurements at infrared and sub-mm wavelengths currently available for only the largest and closest bodies. We measure the size and shape of one particular object precisely here, in hopes of better understanding its unique dynamical history and layered composition.

Molecular organic chemistry is one of the most fundamental and widespread facets of the universe, and plays a key role in planet formation. A host of carbon-containing molecules vibrationally emit in the near-infrared when excited by warm gas, T~1000 K. The NIRSPEC instrument at the W.M. Keck Observatory is uniquely configured to study large ranges of this wavelength region at high spectral resolution. Using this facility we present studies of warm CO gas in protoplanetary disks, with a new code for precise excitation modeling. A parameterized suite of models demonstrates the abilities of the code and matches observational constraints such as line strength and shape. We use the models to probe various disk parameters as well, which are easily extensible to others with known disk emission spectra such as water, carbon dioxide, acetylene, and hydrogen cyanide.

Lastly, the existence of molecules in extrasolar planets can also be studied with NIRSPEC and reveals a great deal about the evolution of the protoplanetary gas. The species we observe in protoplanetary disks are also often present in exoplanet atmospheres, and are abundant in Earth's atmosphere as well. Thus, a sophisticated telluric removal code is necessary to analyze these high dynamic range, high-resolution spectra. We present observations of a hot Jupiter, revealing water in its atmosphere and demonstrating a new technique for exoplanet mass determination and atmospheric characterization. We will also be applying this atmospheric removal code to the aforementioned disk observations, to improve our data analysis and probe less abundant species. Guiding models using observations is the only way to develop an accurate understanding of the timescales and processes involved. The futures of the modeling and of the observations are bright, and the end goal of realizing a unified model of planet formation will require both theory and data, from a diverse collection of sources.

Engineered discoidin domain from factor VIII binds αvβ3 integrin with antibody-like affinity

Alternative scaffolds are non-antibody proteins that can be engineered to bind new targets. They have found useful niches in the therapeutic space due to their smaller size and the ease with which they can be engineered to be bispecific. We sought a new scaffold that could be used for therapeutic ends and chose the C2 discoidin domain of factor VIII, which is well studied and of human origin. Using yeast surface display, we engineered the C2 domain to bind to αvβ3 integrin with a 16 nM affinity while retaining its thermal stability and monomeric nature. We obtained a crystal structure of the engineered domain at 2.1 Å resolution. We have christened this discoidin domain alternative scaffold the “discobody.”

Silicide formation and the interaction of metals with polycrystalline Si

The main factors affecting solid-phase Si-metal interactions are reported in this work. The influence of the orientation of the Si substrates and the presence of impurities in metal films and at the Si-metal interface on the formation of nickel and chromium silicides have been demonstrated. We have observed that the formation and kinetic rate of growth of nickel silicides is strongly dependent on the orientation and crystallinity of the Si substrates; a fact which, up to date, has never been seriously investigated in silicide formation. Impurity contaminations in the Cr film and at the Si-Cr interface are the most dominant influencing factors in the formation and kinetic rate of growth of CrSi₂. The potentiality and use of silicides as a diffusion barrier in metallization on silicon devices were also investigated.

Two phases, Ni₂Si and NiSi, form simultaneously in two distinct sublayers in the reaction of Ni with amorphous Si, while only the former phase was observed on other substrates. On (111) oriented Si substrates the growth rate is about 2 to 3 times less than that on <100> or polycrystalline Si. Transmission electron micrographs establish-·that silicide layers grown on different substrates have different microcrystalline structures. The concept of grain-boundary diffusion is speculated to be an important factor in silicide formation.

The composition and kinetic rate of CrSi₂ formation are not influenced by the underlying Si substrate. While the orientation of the Si substrate does not affect the formation of CrSi₂ , the purity of the Cr film and the state of Si-Cr interface become the predominant factors in the reaction process. With an interposed layer of Pd₂Si between the Cr film and the Si substrate, CrSi₂ starts to form at a much lower temperature (400°C) relative to the Si-Cr system. However, the growth rate of CrSi₂ is observed to be independent of the thickness of the Pd2Si layer. For both Si-Cr and Si-Pd₂Si-Cr samples, the growth rate is linear with time with an activation energy of 1.7 ± 0.1 ev.

A tracer technique using radioactive ³¹Si (T_1/2 = 2.26 h) was used to study the formation of CrSi₂ on Pd₂Si. It is established from this experiment that the growth of CrSi₂ takes place partly by transport of Si directly from the Si substrate and partly by breaking Pd₂Si bonds, making free Si atoms available for the growth process.

The role of CrSi₂ in Pd-Al metallization on Si was studied. It is established that a thin CrSi₂ layer can be used as a diffusion barrier to prevent Al from interacting with Pd₂Si in the Pd-Al metallization on Si.

As a generalization of what has been observed for polycrystalline-Si-Al interaction, the reactions between polycrystalline Si (poly Si) and other metals were studied. The metals investigated include Ni, Cr, Pd, Ag and Au. For Ni, Cr and Pd, annealing results in silicide formation, at temperatures similar to those observed on single crystal Si substrates. For Al, Ag and Au, which form simple eutectics with Si annealing results in erosion of the poly Si layer and growth of Si crystallites in the metal films.

Backscattering spectrometry with 2.0 and 2.3 MeV ⁴He ions was the main analytical tool used in all our investigations. Other experimental techniques include the Read camera glancing angle x-ray diffraction, scanning electron, optical and transmission electron microscopy. Details of these analytical techniques are given in Chapter II.

DNA-mediated oxidation of transcription factor p53

Transcription factor p53 is the most commonly altered gene in human cancer. As a redox-active protein in direct contact with DNA, p53 can directly sense oxidative stress through DNA-mediated charge transport. Electron hole transport occurs with a shallow distance dependence over long distances through the π-stacked DNA bases, leading to the oxidation and dissociation of DNA-bound p53. The extent of p53 dissociation depends upon the redox potential of the response element DNA in direct contact with each p53 monomer. The DNA sequence dependence of p53 oxidative dissociation was examined by electrophoretic mobility shift assays using radiolabeled oligonucleotides containing both synthetic and human p53 response elements with an appended anthraquinone photooxidant. Greater p53 dissociation is observed from DNA sequences containing low redox potential purine regions, particularly guanine triplets, within the p53 response element. Using denaturing polyacrylamide gel electrophoresis of irradiated anthraquinone-modified DNA, the DNA damage sites, which correspond to locations of preferred electron hole localization, were determined. The resulting DNA damage preferentially localizes to guanine doublets and triplets within the response element. Oxidative DNA damage is inhibited in the presence of p53, however, only at DNA sites within the response element, and therefore in direct contact with p53. From these data, predictions about the sensitivity of human p53-binding sites to oxidative stress, as well as possible biological implications, have been made. On the basis of our data, the guanine pattern within the purine region of each p53-binding site determines the response of p53 to DNA-mediated oxidation, yielding for some sequences the oxidative dissociation of p53 from a distance and thereby providing another potential role for DNA charge transport chemistry within the cell.

To determine whether the change in p53 response element occupancy observed in vitro also correlates in cellulo, chromatin immunoprecipition (ChIP) and quantitative PCR (qPCR) were used to directly quantify p53 binding to certain response elements in HCT116N cells. The HCT116N cells containing a wild type p53 were treated with the photooxidant [Rh(phi)2bpy]³⁺, Nutlin-3 to upregulate p53, and subsequently irradiated to induce oxidative genomic stress. To covalently tether p53 interacting with DNA, the cells were fixed with disuccinimidyl glutarate and formaldehyde. The nuclei of the harvested cells were isolated, sonicated, and immunoprecipitated using magnetic beads conjugated with a monoclonal p53 antibody. The purified immounoprecipiated DNA was then quantified via qPCR and genomic sequencing. Overall, the ChIP results were significantly varied over ten experimental trials, but one trend is observed overall: greater variation of p53 occupancy is observed in response elements from which oxidative dissociation would be expected, while significantly less change in p53 occupancy occurs for response elements from which oxidative dissociation would not be anticipated.

The chemical oxidation of transcription factor p53 via DNA CT was also investigated with respect to the protein at the amino acid level. Transcription factor p53 plays a critical role in the cellular response to stress stimuli, which may be modulated through the redox modulation of conserved cysteine residues within the DNA-binding domain. Residues within p53 that enable oxidative dissociation are herein investigated. Of the 8 mutants studied by electrophoretic mobility shift assay (EMSA), only the C275S mutation significantly decreased the protein affinity (KD) for the Gadd45 response element. EMSA assays of p53 oxidative dissociation promoted by photoexcitation of anthraquinone-tethered Gadd45 oligonucleotides were used to determine the influence of p53 mutations on oxidative dissociation; mutation to C275S severely attenuates oxidative dissociation while C277S substantially attenuates dissociation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide labeled, while oxidized cysteines participating in disulfide bonds were ¹³C₂D₂-iodoacetamide labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed using a QTRAP 6500 LC-MS/MS system, quantified with Skyline, and directly compared. A distinct shift in peptide labeling toward ¹³C₂D₂-iodoacetamide labeled cysteines is observed in oxidized samples as compared to the respective controls. All of the observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds potentially among the C124, C135, C141, C182, C275, and C277. Based on these data it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA.