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Surface stress during electro-oxidation of carbon monoxide and bulk stress evolution during electrochemical intercalation of lithium

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This work investigates in-situ stress evolution of interfacial and bulk processes in electrochemical systems, and is divided into two projects. The first project examines the electrocapillarity of clean and CO-covered electrodes. It also investigates surface stress evolution during electro-oxidation of

This work investigates in-situ stress evolution of interfacial and bulk processes in electrochemical systems, and is divided into two projects. The first project examines the electrocapillarity of clean and CO-covered electrodes. It also investigates surface stress evolution during electro-oxidation of CO at Pt{111}, Ru/Pt{111} and Ru{0001} electrodes. The second project explores the evolution of bulk stress that occurs during intercalation (extraction) of lithium (Li) and formation of a solid electrolyte interphase during electrochemical reduction (oxidation) of Li at graphitic electrodes. Electrocapillarity measurements have shown that hydrogen and hydroxide adsorption are compressive on Pt{111}, Ru/Pt{111}, and Ru{0001}. The adsorption-induced surface stresses correlate strongly with adsorption charge. Electrocatalytic oxidation of CO on Pt{111} and Ru/Pt{111} gives a tensile surface stress. A numerical method was developed to separate both current and stress into background and active components. Applying this model to the CO oxidation signal on Ru{0001} gives a tensile surface stress and elucidates the rate limiting steps on all three electrodes. The enhanced catalysis of Ru/Pt{111} is confirmed to be bi-functional in nature: Ru provides adsorbed hydroxide to Pt allowing for rapid CO oxidation. The majority of Li-ion batteries have anodes consisting of graphite particles with polyvinylidene fluoride (PVDF) as binder. Intercalation of Li into graphite occurs in stages and produces anisotropic strains. As batteries have a fixed size and shape these strains are converted into mechanical stresses. Conventionally staging phenomena has been observed with X-ray diffraction and collaborated electrochemically with the potential. Work herein shows that staging is also clearly observed in stress. The Li staging potentials as measured by differential chronopotentiometry and stress are nearly identical. Relative peak heights of Li staging, as measured by these two techniques, are similar during reduction, but differ during oxidation due to non-linear stress relaxation phenomena. This stress relaxation appears to be due to homogenization of Li within graphite particles rather than viscous flow of the binder. The first Li reduction wave occurs simultaneously with formation of a passivating layer known as the solid electrolyte interphase (SEI). Preliminary experiments have shown the stress of SEI formation to be tensile (~+1.5 MPa).

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2011

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Analysis of nucleosome dynamics by fluorescence correlation spectroscopy

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Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and

Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and H4) around which 147 base pairs of DNA are wrapped in ~1.67 superhelical turns. Although the nucleosomes are stable protein-DNA complexes, they undergo spontaneous conformational changes that occur in an asynchronous fashion. This conformational dynamics, defined by the "site-exposure" model, involves the DNA unwrapping from the protein core and exposing itself transiently before wrapping back. Physiologically, this allows regulatory proteins to bind to their target DNA sites during cellular processes like replication, DNA repair and transcription. Traditional biochemical assays have stablished the equilibrium constants for the accessibility to various sites along the length of the nucleosomal DNA, from its end to the middle of the dyad axis. Using fluorescence correlation spectroscopy (FCS), we have established the position dependent rewrapping rates for nucleosomes. We have also used Monte Carlo simulation methods to analyze the applicability of FRET fluctuation spectroscopy towards conformational dynamics, specifically motivated by nucleosome dynamics. Another important conformational change that is involved in cellular processes is the disassembly of nucleosome into its constituent particles. The exact pathway adopted by nucleosomes is still not clear. We used dual color fluorescence correlation spectroscopy to study the intermediates during nucleosome disassembly induced by changing ionic strength. Studying the nature of nucleosome conformational change and the kinetics is very important in understanding gene expression. The results from this thesis give a quantitative description to the basic unit of the chromatin.

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2011

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Synthesis and characterization of thionated reduced graphene oxides and their thin films

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Thiol functionalization is one potentially useful way to tailor physical and chemical properties of graphene oxides (GOs) and reduced graphene oxides (RGOs). Despite the ubiquitous presence of thiol functional groups in diverse chemical systems, efficient thiol functionalization has been challenging

Thiol functionalization is one potentially useful way to tailor physical and chemical properties of graphene oxides (GOs) and reduced graphene oxides (RGOs). Despite the ubiquitous presence of thiol functional groups in diverse chemical systems, efficient thiol functionalization has been challenging for GOs and RGOs, or for carbonaceous materials in general. In this work, thionation of GOs has been achieved in high yield through two new methods that also allow concomitant chemical reduction/thermal reduction of GOs; a solid-gas metathetical reaction method with boron sulfides (BxSy) gases and a solvothermal reaction method employing phosphorus decasulfide (P4S10). The thionation products, called "mercapto reduced graphene oxides (m-RGOs)", were characterized by employing X-ray photoelectron spectroscopy, powder X-ray diffraction, UV-Vis spectroscopy, FT-IR spectroscopy, Raman spectroscopy, electron probe analysis, scanning electron microscopy, (scanning) transmission electron microscopy, nano secondary ion mass spectrometry, Ellman assay and atomic force microscopy. The excellent dispersibility of m-RGOs in various solvents including alcohols has allowed fabrication of thin films of m-RGOs. Deposition of m-RGOs on gold substrates was achieved through solution deposition and the m-RGOs were homogeneously distributed on gold surface shown by atomic force microscopy. Langmuir-Blodgett (LB) films of m-RGOs were obtained by transferring their Langmuir films, formed by simple drop casting of m-RGOs dispersion on water surface, onto various substrates including gold, glass and indium tin oxide. The m-RGO LB films showed low sheet resistances down to about 500 kΩ/sq at 92% optical transparency. The successful results make m-RGOs promising for applications in transparent conductive coatings, biosensing, etc.

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2013

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Novel strategies for producing proteins with non-proteinogenic amino acids

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The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using

The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using orthogonal aminoacyl-tRNA synthetase/tRNA pairs in conjunction with nonsense, rare, or 4-bp codons. There has been considerable progress in developing new types of amino acids, in identifying novel methods of tRNA aminoacylation, and in expanding the genetic code to direct their position. Chemical aminoacylation of tRNAs is accomplished by acylation and ligation of a dinucleotide (pdCpA) to the 3'-terminus of truncated tRNA. This strategy allows the incorporation of a wide range of natural and unnatural amino acids into pre-determined sites, thereby facilitating the study of structure-function relationships in proteins and allowing the investigation of their biological, biochemical and biophysical properties. Described in Chapter 1 is the current methodology for synthesizing aminoacylated suppressor tRNAs. Aminoacylated suppressor tRNACUAs are typically prepared by linking pre-aminoacylated dinucleotides (aminoacyl-pdCpAs) to 74 nucleotide (nt) truncated tRNAs (tRNA-COH) via a T4 RNA ligase mediated reaction. Alternatively, there is another route outlined in Chapter 1 that utilizes a different pre-aminoacylated dinucleotide, AppA. This dinucleotide has been shown to be a suitable substrate for T4 RNA ligase mediated coupling with abbreviated tRNA-COHs for production of 76 nt aminoacyl-tRNACUAs. The synthesized suppressor tRNAs have been shown to participate in protein synthesis in vitro, in an S30 (E. coli) coupled transcription-translation system in which there is a UAG codon in the mRNA at the position corresponding to Val10. Chapter 2 describes the synthesis of two non-proteinogenic amino acids, L-thiothreonine and L-allo-thiothreonine, and their incorporation into predetermined positions of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine. Here, the elaborated proteins were site-specifically derivitized with a fluorophore at the thiothreonine residue. The synthesis and incorporation of phosphorotyrosine derivatives into DHFR is illustrated in Chapter 3. Three different phosphorylated tyrosine derivatives were prepared: bis-nitrobenzylphosphoro-L-tyrosine, nitrobenzylphosphoro-L-tyrosine, and phosphoro-L-tyrosine. Their ability to participate in a protein synthesis system was also evaluated.

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2013

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Development of chip-based electrochemically- and light-directed peptide microarray synthesis

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ABSTRACT Peptide microarrays may prove to be a powerful tool for proteomics research and clinical diagnosis applications. Fodor et al. and Maurer et al. have shown proof-of-concept methods of light- and electrochemically-directed peptide microarray fabrication on glass and semiconductor microchips

ABSTRACT Peptide microarrays may prove to be a powerful tool for proteomics research and clinical diagnosis applications. Fodor et al. and Maurer et al. have shown proof-of-concept methods of light- and electrochemically-directed peptide microarray fabrication on glass and semiconductor microchips respectively. In this work, peptide microarray fabrication based on the abovementioned techniques were optimized. In addition, MALDI mass spectrometry based peptide synthesis characterization on semiconductor microchips was developed and novel applications of a CombiMatrix (CBMX) platform for electrochemically controlled synthesis were explored. We have investigated performance of 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) derivatives as photo-labile protecting group. Specifically, influence of substituents on 4 and 5 positions of phenyl ring of NPPOC group on the rate of photolysis and the yield of the amine was investigated. The results indicated that substituents capable of forming a π-network with the nitro group enhanced the rate of photolysis and yield. Once such properly substituted NPPOC groups were used, the rate of photolysis/yield depended on the nature of protected amino group indicating that a different chemical step during the photo-cleavage process became the rate limiting step. We also focused on electrochemically-directed parallel synthesis of high-density peptide microarrays using the CBMX technology referred to above which uses electrochemically generated acids to perform patterned chemistry. Several issues related to peptide synthesis on the CBMX platform were studied and optimized, with emphasis placed on the reactions of electro-generated acids during the deprotection step of peptide synthesis. We have developed a MALDI mass spectrometry based method to determine the chemical composition of microarray synthesis, directly on the feature. This method utilizes non-diffusional chemical cleavage from the surface, thereby making the chemical characterization of high-density microarray features simple, accurate, and amenable to high-throughput. CBMX Corp. has developed a microarray reader which is based on electro-chemical detection of redox chemical species. Several parameters of the instrument were studied and optimized and novel redox applications of peptide microarrays on CBMX platform were also investigated using the instrument. These include (i) a search of metal binding catalytic peptides to reduce overpotential associated with water oxidation reaction and (ii) an immobilization of peptide microarrays using electro-polymerized polypyrrole.

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2013

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Study of ribosomes having modifications in the peptidyltransferase center using non-alpha-L-amino acids and synthesis and biological evaluation of topopyrones

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The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino

The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino acids (2.1 - 2.5) into E. coli dihydrofolate reductase (DHFR). The second project (Chapter 3) focused on the study of the modified ribosomes facilitating the incorporation of the dipeptide glycylphenylalanine (3.25) and fluorescent dipeptidomimetic 3.26 into DHFR. These ribosomes also had modifications in the peptidyltransferase center in the 23S rRNA of the 50S ribosomal subunit. The modified DHFRs having beta-amino acids 2.3 and 2.5, dipeptide glycylphenylalanine (3.25) and dipeptidomimetic 3.26 were successfully characterized by the MALDI-MS analysis of the peptide fragments produced by "in-gel" trypsin digestion of the modified proteins. The fluorescent spectra of the dipeptidomimetic 3.26 and modified DHFR having fluorescent dipeptidomimetic 3.26 were also measured. The type I and II DNA topoisomerases have been firmly established as effective molecular targets for many antitumor drugs. A "classical" topoisomerase I or II poison acts by misaligning the free hydroxyl group of the sugar moiety of DNA and preventing the reverse transesterfication reaction to religate DNA. There have been only two classes of compounds, saintopin and topopyrones, reported as dual topoisomerase I and II poisons. Chapter 4 describes the synthesis and biological evaluation of topopyrones. Compound 4.10, employed at 20 µM, was as efficient as 0.5 uM camptothecin, a potent topoisomerase I poison, in stabilizing the covalent binary complex (~30%). When compared with a known topoisomerase II poison, etoposide (at 0.5 uM), topopyorone 4.10 produced similar levels of stabilized DNA-enzyme binary complex (~34%) at 5 uM concentration.

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2013

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Synthesis and application of porphyrin, phthalocyanine and perylene chromophores for solar energy conversion

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Photosynthesis, one of the most important processes in nature, has provided an energy basis for nearly all life on Earth, as well as the fossil fuels we use today to power modern society. This research aims to mimic the photosynthetic

Photosynthesis, one of the most important processes in nature, has provided an energy basis for nearly all life on Earth, as well as the fossil fuels we use today to power modern society. This research aims to mimic the photosynthetic process of converting incident solar energy into chemical potential energy in the form of a fuel via systems capable of carrying out photo-induced electron transfer to drive the production of hydrogen from water. Herein is detailed progress in using photo-induced stepwise electron transfer to drive the oxidation of water and reduction of protons to hydrogen. In the design, use of more blue absorbing porphyrin dyes to generate high-potential intermediates for oxidizing water and more red absorbing phthalocyanine dyes for forming the low potential charge needed for the production of hydrogen have been utilized. For investigating water oxidation at the photoanode, high potential porphyrins such as, bis-pyridyl porphyrins and pentafluorophenyl porphyrins have been synthesized and experiments have aimed at the co-immobilization of this dye with an IrO2-nH2O catalyst on TiO2. To drive the cathodic reaction of the water splitting photoelectrochemical cell, utilization of silicon octabutoxy-phthalocyanines have been explored, as they offer good absorption in the red to near infrared, coupled with low potential photo-excited states. Axially and peripherally substituted phthalocyanines bearing carboxylic anchoring groups for the immobilization on semiconductors such as TiO2 has been investigated. Ultimately, this work should culminate in a photoelectrochemical cell capable of splitting water to oxygen and hydrogen with the only energy input from light. A series of perylene dyes bearing multiple semi-conducting metal oxide anchoring groups have been synthesized and studied. Results have shown interfacial electron transfer between these perylenes and TiO2 nanoparticles encapsulated within reverse micelles and naked nanoparticles. The binding process was followed by monitoring the hypsochromic shift of the dye absorption spectra over time. Photoinduced electron transfer from the singlet excited state of the perylenes to the TiO2 conduction band is indicated by emission quenching of the TiO2-bound form of the dyes and confirmed by transient absorption measurements of the radical cation of the dyes and free carriers (injected electrons) in the TiO2.

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2013

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Application and study of water oxidation catalysts and molecular dyes for solar-fuel production

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Developing a system capable of using solar energy to drive the conversion of an abundant and available precursor to fuel would profoundly impact humanity's energy use and thereby the condition of the global ecosystem. Such is the goal of artificial

Developing a system capable of using solar energy to drive the conversion of an abundant and available precursor to fuel would profoundly impact humanity's energy use and thereby the condition of the global ecosystem. Such is the goal of artificial photosynthesis: to convert water to hydrogen using solar radiation as the sole energy input and ideally do so with the use of low cost, abundant materials. Constructing photoelectrochemical cells incorporating photoanodes structurally reminiscent of those used in dye sensitized photovoltaic solar cells presents one approach to establishing an artificial photosynthetic system. The work presented herein describes the production, integration, and study of water oxidation catalysts, molecular dyes, and metal oxide based photoelectrodes carried out in the pursuit of developing solar water splitting systems.

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2013

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Synthesis and band gap engineering in Ge₁-x-ySixSny Materials for Near-IR Wavelength Applications

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This thesis describes the fabrication of several new classes of Ge1-x-ySixSny materials with the required compositions and crystal quality to engineer the band gaps above and below that of elemental Ge (0.8 eV) in the near IR. The work initially

This thesis describes the fabrication of several new classes of Ge1-x-ySixSny materials with the required compositions and crystal quality to engineer the band gaps above and below that of elemental Ge (0.8 eV) in the near IR. The work initially focused on Ge1-x-ySixSny (1-5% Sn, 4-20% Si) materials grown on Ge(100) via gas-source epitaxy of Ge4H10, Si4H10 and SnD4. Both intrinsic and doped layers were produced with defect-free microstructure and viable thickness, allowing the fabrication of high-performance photodetectors. These exhibited low ideality factors, state-of-the-art dark current densities and adjustable absorption edges between 0.87 and 1.03 eV, indicating that the band gaps span a significant range above that of Ge. Next Sn-rich Ge1-x-ySixSny alloys (2-4% Si and 4-10% Sn) were fabricated directly on Si and were found to show significant optical emission using photoluminescence measurements, indicating that the alloys have direct band gaps below that of pure Ge in the range of 0.7-0.55 eV. A series of Sn-rich Ge1-x-ySixSny analogues (y>x) with fixed 3-4% Si content and progressively increasing Sn content in the 4-10% range were then grown on Ge buffered Si platforms for the purpose of improving the material's crystal quality. The films in this case exhibited lower defect densities than those grown on Si, allowing a meaningful study of both the direct and indirect gaps. The results show that the separation of the direct and indirect edges can be made smaller than in Ge even for non-negligible 3-4% Si content, confirming that with a suitable choice of Sn compositions the ternary Ge1-x-ySixSny reproduces all features of the electronic structure of binary Ge1-ySny, including the sought-after indirect-to-direct gap cross over. The above synthesis of optical quality Ge1-x-ySixSny on virtual Ge was made possible by the development of high quality Ge-on-Si buffers via chemical vapor deposition of Ge4H10. The resultant films exhibited structural and electrical properties significantly improved relative to state-of-the-art results obtained using conventional approaches. It was found that pure Ge4H10 facilitates the control of residual doping and enables p-i-n devices whose dark currents are not entirely determined by defects and whose zero-bias collection efficiencies are higher than those obtained from samples fabricated using alternative Ge-on-Si approaches.

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2013

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Epitaxy of group IV optical materials and synthesis of IV/III-V semiconductor analogs by designer hydride chemistries

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The thesis studies new methods to fabricate optoelectronic Ge1-ySny/Si(100) alloys and investigate their photoluminescence (PL) properties for possible applications in Si-based photonics including IR lasers. The work initially investigated the origin of the difference between the PL spectrum of bulk

The thesis studies new methods to fabricate optoelectronic Ge1-ySny/Si(100) alloys and investigate their photoluminescence (PL) properties for possible applications in Si-based photonics including IR lasers. The work initially investigated the origin of the difference between the PL spectrum of bulk Ge, dominated by indirect gap emission, and the PL spectrum of Ge-on-Si films, dominated by direct gap emission. It was found that the difference is due to the supression of self-absorption effects in Ge films, combined with a deviation from quasi-equilibrium conditions in the conduction band of undoped films. The latter is confirmed by a model suggesting that the deviation is caused by the shorter recombination lifetime in the films relative to bulk Ge. The knowledge acquired from this work was then utilized to study the PL properties of n-type Ge1-ySny/Si (y=0.004-0.04) samples grown via chemical vapor deposition of Ge2H6/SnD4/P(GeH3)3. It was found that the emission intensity (I) of these samples is at least 10x stronger than observed in un-doped counterparts and that the Idir/Iind ratio of direct over indirect gap emission increases for high-Sn contents due to the reduced gamma-L valley separation, as expected. Next the PL investigation was expanded to samples with y=0.05-0.09 grown via a new method using the more reactive Ge3H8 in place of Ge2H6. Optical quality, 1-um thick Ge1-ySny/Si(100) layers were produced using Ge3H10/SnD4 and found to exhibit strong, tunable PL near the threshold of the direct-indirect bandgap crossover. A byproduct of this study was the development of an enhanced process to produce Ge3H8, Ge4H10, and Ge5H12 analogs for application in ultra-low temperature deposition of Group-IV semiconductors. The thesis also studies synthesis routes of an entirely new class of semiconductor compounds and alloys described by Si5-2y(III-V)y (III=Al, V= As, P) comprising of specifically designed diamond-like structures based on a Si parent lattice incorporating isolated III-V units. The common theme of the two thesis topics is the development of new mono-crystalline materials on ubiquitous silicon platforms with the objective of enhancing the optoelectronic performance of Si and Ge semiconductors, potentially leading to the design of next generation optical devices including lasers, detectors and solar cells.

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2013