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Genome Project Standards in a New Era of Sequencing

Description: For over a decade, genome 43 sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole genome sequencing that requires a careful reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker 'draft', however these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and contributed to many wasted hours of (mis)interpretation. These same novel sequencing technologies have also brought an exponential leap in raw sequencing capability, and at greatly reduced prices that have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The resulting effect is an ever-widening gap between drafted and finished genomes that only promises to continue (Figure 1), hence there is an urgent need to distinguish good and poor datasets. The sequencing institutes in the authorship, along with the NIH's Human Microbiome Project Jumpstart Consortium (3), strongly believe that a new set of standards is required for genome sequences. The following represents a set of six community-defined categories of genome sequence standards that better ...
Date: June 1, 2009
Creator: Consortia, GSC; Consortia, HMP Jumpstart; Chain, P. S. G.; Grafham, D. V.; Fulton, R. S.; FitzGerald, M. G. et al.
Partner: UNT Libraries Government Documents Department

Conformational Diversity in (Octaethylporphinato) (trichloroacetato)iron(III) Derivatives

Description: Treatment of [Fe(OEP)]20 with trichloroacetic acid results in ruffled formation of (octaethylporphinato trichloroacetato)iron(HI). Various crystalline solvates can be isolated, depending on the crystallization solvent. Initial crystallization with CHC13/hexanes resulted in the isolation of an unsolvated form. [Fe(OEP)(02C2C13 )]. This form contains distinct porphyrin core conformations at the same site: one is domed and the other is ruffled. Crystal data for [Fe(OEP)(02C2C13 )]: Q = 14.734(4) .4. b = 13.674(1) .\. c = 17..541 [,.5] .~. 3 = 90.67(1)0, V = 35-!5.8(14) .\3. monoclinic. space group R1/ n. Z = 4. Subsequent crystallization with CHC13/hexanes resulted in a new crystalline form, [Fe(OEP)(OzC2C13 )~.- CHC13; the porphyrin core is slightly ruffled. Crystal data for [Fe(OEP)(OoC2C13 )]. CHC13: a =12.323(1) .~, 6 = 13.062(3) .\. C = 14.327(2) .$, Q = 89.32(1)", .3 = 113.36(2)0. :~ = 105.26(1)'. V = `2031.3(6) .\3. triclinic. space group Pi. Z = 2. Crystallization with CH2C12/hexanes resulted in the isolation of yet another form, [Fe(OEP) (02 C2C13)]. H02C2C13. which contains two independent molecules in the unit cell: molecule is slightly saddled and molecule B is modestly ruffled. Crystal data for [Fe(OEP)(02ClC13 )]. H02C2C13: a = 13.148(3) .\, b = 13.45.5(3) A, c = Q3.761(5) -& ~ = 90.72(3)", ~ = 91. ~4(3)". -y = 92.36(3)0, V = 4198.5(15) .\3, triclinic.space group PI, Z = 4. .+11 conformations form dimers in the solid state. Temperature-dependent manometic susceptibility measurements showed that [Fe(OEP)(02C2C13)] .CHC13 contains a high-spin iron(III) center; the data for {Fe(OEP)(02C2C13 )l.H02C2C13 are understood in terms of an admixed intermediate-spin state (S = 3/2, 5/2) and are readily fit to a faltempo model with a ground state multiplet containing about 78% S = 5/2 character and 22% S = 3/2 character. The structural data for [Fe(OEP)(02C2C13 )]. CHC13 are consistent with the observed high-spin state, while data for ...
Date: October 19, 1998
Creator: Cheng, B.; Ma, J.; Neal, T.J.; Scheidt, W.R.; Schulz, C.E. & Shelnutt, J.A.
Partner: UNT Libraries Government Documents Department

AEM investigation of tetrahedrally coordinated Ti{sup 4+} in nickel-titanate spinel

Description: Stoichiometry and site distribution of metastable nickel-titanate spinel was studied with AEM. Results of EDXS and EELS agree that the metastable spinel is nonstoichiometric and titanium-deficient relative to its hypothetical endmember composition, ``Ni{sub 2}TiO{sub 4}``. The titanium deficiency has been determined by EELS to be {Delta} = 0.025 {plus_minus} 0.005. Channeling-enhanced microanalysis and ELNES studies indicate that the Ti{sup 4+} and Ni{sup 2+} cations are in tetrahedral and octahedral coordination, respectively, so that the metastable spinel has the normal cation distribution: Ti{sub l-{Delta}}[Ni{sub 2(1+{Delta})}]O{sub 4}. This is consistent with neutron powder-diffraction studies and SiO{sub 2}-solubility measurements of similar equilibrated and quenched spinel-containing specimens. Metastable nickel-titanate spinel therefore contrasts with stable stoichiometric spinels which tend to the inverse cation distribution, Me[MeTi]O{sub 4}.
Date: December 31, 1994
Creator: Anderson, I.M.; Bentley, J. & Carter, C.B.
Partner: UNT Libraries Government Documents Department

Combining the Best of Bulk and Surface Micromaching Using Si(111) Substrates

Description: This process combines the best features of bulk ad surface micromachining. It enables the production of stress free, thick, virtually arbitrarily shaped structures with well defiti thick or thin sacrificial layers, high sacrificial layer selectivity and large undercuts using IC compatible, processes. The basis of this approach is the use of dy available {111} oriented substrates. anisotropic Si trench etching, S iN masking and KOH etching.
Date: November 30, 1998
Creator: Fleming, J.G.
Partner: UNT Libraries Government Documents Department

Porous networks derived from synthetic polymer-clay complexes

Description: Synthetic hectorites were hydrothermally crystallized with direct incorporation of a cationic polymer poly(dimethyl diallyl ammonium chloride) (PDDA), and two neutral cellulosic polymers hydroxypropyl methylcellulose (HPMC) and hydroxyethyl cellulose (HEC). Synthetic PDDA-hectorite displays the lowest d-spacing at 15.8 {Angstrom} along with less polymer incorporation (7.8 wt % organic) than the neutral polymers (18--22 wt % organic). Thermal analysis and small angle neutron scattering were used to further examine the polymer-clay systems. Clay platelets of the largest size and best stacking order occur when cationic PDDA polymer is used. PDDA also enhances these properties over the crystallites prepared for a control mineral, where no polymer is used. HEC acts to aggregate the silica, leaving less to react to form clay. The clay platelets which result from HEC are small, not stacked to a large degree, and oriented randomly. Neutral HPMC acts more like cationic PDDA in that larger clay platelets are allowed to form. The extended microstructure of the clay network remains undisturbed after polymer is removed by calcination. When no polymer is used, the synthetic hectorite has a N{sub 2} BET surface area of 200 M{sup 2}/gm, even after calcination. This increases by 20--50% for the synthetic polymer-hectorites after the polymer is removed by calcination.
Date: May 12, 1995
Creator: Carrado, K.A.; Thiyagarajan, P. & Elder, D.L.
Partner: UNT Libraries Government Documents Department

The Pathogenomic Sequence Analysis of B. cereus and B. Thuringiensis isolates closely related to Bacillus anthracis

Description: The sequencing and analysis of two close relatives of Bacillus anthracis are reported. AFLP analysis of over 300 isolates of B. cereus, B. thuringiensis and B. anthracis identified two isolates as being very closely related to B. anthracis. One, a B. cereus, BcE33L, was isolated from a zebra carcass in Nambia; the second, a B. thuringiensis, 97-27, was isolated from a necrotic human wound. The B. cereus appears to be the closest anthracis relative sequenced to date. A core genome of over 3,900 genes was compiled for the Bacillus cereus group, including B anthracis. Comparative analysis of these two genomes with other members of the B. cereus group provides insight into the evolutionary relationships among these organisms. Evidence is presented that differential regulation modulates virulence, rather than simple acquisition of virulence factors. These genome sequences provide insight into the molecular mechanisms contributing to the host range and virulence of this group of organisms.
Date: October 12, 2005
Creator: Han, C S; Xie, G; Challacombe, J F; Altherr, M R; Bhotika, S S; Bruce, D et al.
Partner: UNT Libraries Government Documents Department

Analysis and Annotation of Nucleic Acid Sequence

Description: The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.
Date: July 28, 2004
Creator: States, David J.
Partner: UNT Libraries Government Documents Department

Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond

Description: Genome sequence comparisons of exponentially growing data sets form the foundation for the comparative analysis tools provided by community biological data resources such as the Integrated Microbial Genome (IMG) system at the Joint Genome Institute (JGI). We present an example of how ScalaBLAST, a high-throughput sequence analysis program harnesses increasingly critical high-performance computing to perform sequence analysis which is a critical component of maintaining a state-of-the-art sequence data repository. The Integrated Microbial Genomes (IMG) system1 is a data management and analysis platform for microbial genomes hosted at the JGI. IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for interactive analysis of genomes, genes and functions, individually or in a comparative context. Most of these tools are based on pre-computed pairwise sequence similarities involving millions of genes. These computations are becoming prohibitively time consuming with the rapid increase in the number of newly sequenced genomes incorporated into IMG and the need to refresh regularly the content of IMG in order to reflect changes in the annotations of existing genomes. Thus, building IMG 2.0 (released on December 1st 2006) entailed reloading from NCBI's RefSeq all the genomes in the previous version of IMG (IMG 1.6, as of September 1st, 2006) together with 1,541 new public microbial,viral and eukaryal genomes, bringing the total of IMG genomes to 2,301. A critical part of building IMG 2.0 involved using PNNL ScalaBLAST software for computing pairwise similarities for over 2.2 million genes in under 26 hours on 1,000 processors, thus illustrating the impact that new generation bioinformatics tools are poised to make in biology. The BLAST algorithm2, 3 is a familiar bioinformatics application for computing sequence similarity, and has become a workhorse in large-scale genomics projects. The rapid ...
Date: June 1, 2007
Creator: Oehmen, Christopher S.; Sofia, Heidi J.; Baxter, Douglas; Szeto, Ernest; Hugenholtz, Philip; Kyrpides, Nikos et al.
Partner: UNT Libraries Government Documents Department

Determining physical constraints in transcriptional initiationcomplexes using DNA sequence analysis

Description: Eukaryotic gene expression is often under the control ofcooperatively acting transcription factors whose binding is limited bystructural constraints. By determining these structural constraints, wecan understand the "rules" that define functional cooperativity.Conversely, by understanding the rules of binding, we can inferstructural characteristics. We have developed an information theory basedmethod for approximating the physical limitations of cooperativeinteractions by comparing sequence analysis to microarray expressiondata. When applied to the coordinated binding of the sulfur amino acidregulatory protein Met4 by Cbf1 and Met31, we were able to create acombinatorial model that can correctly identify Met4 regulatedgenes.
Date: July 1, 2007
Creator: Shultzaberger, Ryan K.; Chiang, Derek Y.; Moses, Alan M. & Eisen,Michael B.
Partner: UNT Libraries Government Documents Department

Four-wave mixing using polarization grating induced thermal grating in liquids exhibiting circular dichroism

Description: A novel four-wave mixing technique for the detection of circular dichroism in optically active liquid samples is demonstrated. When two cross-polarized laser beams are crossed at a small angle in a circular dichroic liquid a weak thermal grating is produced with a phase depending on the sign of the circular dichroism. The authors show that the polarization of one of the beams can be modified to allow coherent interference with an intensity-grating induced thermal grating. A probe beam scattering from the composite grating results in a signal that reveals the sign and magnitude of the circular dichroism. The use of this technique to optimize the signal-to-noise ratio in the presence of scattered light and laser intensity noise is discussed.
Date: April 1, 1995
Creator: Nunes, J.A.; Tong, W.G.; Chandler, D.W. & Rahn, L.A.
Partner: UNT Libraries Government Documents Department

The in-situ generation of silica reinforcement in modified polydimethylsiloxane elastomers

Description: Structure and properties of a series of modified polydimethylsiloxane (PDMS) elastomers reinforced by {ital in situ} generated silic particles were investigated. The PDMS elastomer was modified by systematically varying the molecular weight between reactive groups incorporated into the backbone. Tetraethoxysilane (TEOS) and partial hydrolyzate of TEOS were used to generate silic particles. Chemistry and phase structure of the materials were investigated by {sup 29}Si magic angle spinning nuclear magnetic resonance spectroscopy and swelling experiments.
Date: June 1, 1996
Creator: Prabakar, S; Bates, S.E.; Black, E.P. & Ulibarri, T.A.
Partner: UNT Libraries Government Documents Department

Microstructures and Mechanical Properties of Two-Phase Alloys Based on NbCr(2)

Description: A two-phase, Nb-Cr-Ti alloy (bee+ C15 Laves phase) has been developed using several alloy design methodologies. In effort to understand processing-microstructure-property relationships, diffment processing routes were employed. The resulting microstructure and mechanical properties are discussed and compared. Plasma arc-melted samples served to establish baseline, . . . as-cast properties. In addition, a novel processing technique, involving decomposition of a supersaturated and metastable precursor phase during hot isostatic pressing (HIP), was used to produce a refined, equilibrium two-phase microstructure. Quasi-static compression tests as a ~ function of temperature were performed on both alloy types. Different deformation mechanisms were encountered based upon temperature and microstructure.
Date: December 7, 1998
Creator: Cady, C.M.; Chen, K.C.; Kotula, P.G.; Mauro, M.E. & Thoma, D.J.
Partner: UNT Libraries Government Documents Department

Preconversion catalytic deoxygenation of phenolic functional groups. July 1 - September 30, 1996

Description: Most industrial processes require the use hydrocarbon based solvents that have been shown to hurt the environment. Chlorine radicals from chlorine based hydrocarbons are considered to be a major factor in the depletion of the stratospheric ozone levels. Because of the health and environmental problems these solvents cause, there is renewed interest in water soluble organometallic complexes that can be used as catalysts in the industrially important reactions. Recently, the investigators completed an extensive study on the synthesis, characterization, and reactivity of a series of nickel trimers bridged by bis(diphenylphosphino)methane (dppm) ligands. They were able to synthesize the nickel trimers by two routes. The first route involves the synthesis of a nickel dimer Ni(CNCH{sub 3}){sub 3}({mu}CNCH{sub 3}) This dimer is then reacted with NiI{sub 2}, or CH{sub 2}I{sub 2}, to form a trimer with capping isocyanide and two terminal isocyanides, and then the terminal isocyanides are replaced with a third dppm (Scheme 1). The second procedure for the synthesis is the conproportionation of 2 equivalents of Ni(COD)2 (COD=1,5-cyclooctadiene) with 1 equivalent of NiI{sub 2} in the presence of dppm.
Date: December 31, 1996
Creator: Kubiak, C.P.
Partner: UNT Libraries Government Documents Department

Laser desorption mass spectrometry for DNA analysis and sequencing

Description: Laser desorption mass spectrometry has been considered as a potential new method for fast DNA sequencing. Our approach is to use matrix-assisted laser desorption to produce parent ions of DNA segments and a time-of-flight mass spectrometer to identify the sizes of DNA segments. Thus, the approach is similar to gel electrophoresis sequencing using Sanger`s enzymatic method. However, gel, radioactive tagging, and dye labeling are not required. In addition, the sequencing process can possibly be finished within a few hundred microseconds instead of hours and days. In order to use mass spectrometry for fast DNA sequencing, the following three criteria need to be satisfied. They are (1) detection of large DNA segments, (2) sensitivity reaching the femtomole region, and (3) mass resolution good enough to separate DNA segments of a single nucleotide difference. It has been very difficult to detect large DNA segments by mass spectrometry before due to the fragile chemical properties of DNA and low detection sensitivity of DNA ions. We discovered several new matrices to increase the production of DNA ions. By innovative design of a mass spectrometer, we can increase the ion energy up to 45 KeV to enhance the detection sensitivity. Recently, we succeeded in detecting a DNA segment with 500 nucleotides. The sensitivity was 100 femtomole. Thus, we have fulfilled two key criteria for using mass spectrometry for fast DNA sequencing. The major effort in the near future is to improve the resolution. Different approaches are being pursued. When high resolution of mass spectrometry can be achieved and automation of sample preparation is developed, the sequencing speed to reach 500 megabases per year can be feasible.
Date: March 1, 1995
Creator: Chen, C.H.; Taranenko, N.I.; Tang, K. & Allman, S.L.
Partner: UNT Libraries Government Documents Department

Determination of site-occupancies in aluminide intermetallics by ALCHEMI

Description: The site-distributions of Fe in four B2-ordered NiAl-based alloys with Fe concentrations of 10%, 2%, and 0.5% have been determined by ALCHEMI (atom-location by channeling-enhanced microanalysis). Site-distributions have been extracted with standard errors between {approximately} 1.5% (10% Fe concentration) and {approximately} 6% (0.5% Fe concentration). The results show that Fe has no strong site-preference in NiAl and tends to reside on the site of the stoichiometrically deficient host element. An improved ALCHEMI analysis procedure is outlined. The analysis explicitly addresses the phenomenon of ionization delocalization, which previously complicated the determination of site-distributions in aluminide intermetallics, leading to inaccurate and oftentimes nonphysical results. The improved ALCHEMI analysis also addresses the presence of anti-site defects. The data acquisition conditions have been optimized to minimize the sources of statistical and systematic error. This optimized procedure should be suitable for all analyses of B2-ordered alloys. Several analyses at different channeling orientations show that the extracted site-occupancies are robust as long as the data are acquired at orientations that are remote from any major pole of the crystal.
Date: April 1, 1995
Creator: Anderson, I. M.; Bentley, J. & Duncan, A. J.
Partner: UNT Libraries Government Documents Department

Al{sub 2}O{sub 3}/CeO{sub 2} Washcoats for three-way automotive emission catalysts

Description: Pt-Rh based three-way catalysts are the primary catalytic system for control of hydrocarbon, CO, and NO{sub x} automotive emissions. Mixed Al{sub 2}O{sub 3}/CeO{sub 2} oxides are often dispersed on a cordierite honeycomb monolith as a washcoat and act as a high-surface-area carrier for the heavy metal catalyst clusters. Conversion efficiency and lifetime of a converter is determined by the microstructure of the washcoat/monolith and its evolution during high-temperature exposure to the exhaust gas. SEM, electron microprobe analysis, and analytical electron microscopy were used to study these catalysts before and after engine dynamometer tests, with max monolith temperatures of 1000 and 1150 C.
Date: June 1, 1995
Creator: Kenik, E.A.; More, K.L.; LaBarge, W. & Beckmeyer, R.
Partner: UNT Libraries Government Documents Department

A characterization and evaluation of coal liquefaction process streams. Quarterly report, April 1--June 30, 1997

Description: This is the Technical Progress Report for the twelfth quarter of activities. Described in this report are the following activities: (1) Thirty-nine samples from four run conditions of HTI Run PB-07 were received. Appropriate samples were characterized by proton NMR spectroscopy, Fourier transform infrared spectroscopy, vacuum distillation, and solvent quality tests. (2) The University of Delaware completed their subcontract this quarter. A meeting was held on April 30, 1997 at the University to close out the subcontract. (3) Twelve sets of samples were chosen from the CONSOL sample bank for the study of the insoluble and presumed unreactive material from process stream samples. Each set consists of the whole process stream and the 454 C{sup +} (850 F{sup +}) distillation resid derived from that process stream. Processing data for all samples were compiled. The samples represent four Wilsonville pilot plant runs and two HTI runs.
Date: December 31, 1997
Creator: Brandes, S.D.; Robbins, G.A. & Winschel, R.A.
Partner: UNT Libraries Government Documents Department

EXAFS studies of lanthanide coordination in crystalline phosphates and amorphous phytates

Description: As part of the DOE Efficient Separations and Processing Integrated Program, techniques are being developed to stabilize radioactive and hazardous contaminants to prevent their migration from buried wastes. This report is part of a study to immobilize actinide ions in the near-surface environment by reacting them with organophosphorus complexants that decompose to phosphates. Nd and Gd ions were used as models for Pu, Am, and Cm ions; phytic acid was used as the complexant. Solid Nd and Gd phytates were prepared and the coordination characterized by EXAFS.
Date: December 31, 1995
Creator: Morss, L.R.; Schmidt, M.A.J. & Nash, K.L.
Partner: UNT Libraries Government Documents Department

Temperature effects on chemical structure and motion in coal. [Quarterly] report No. 9, [October 1--December 31, 1995]

Description: The temperature range from RF heating has been extended. {sup 1}H CRAMPS and NMR are being used to study structural changes that occur in coal at high temperatures. CRAMPS experiments under RF heating conditions proved to be difficult; other ways to solve this problem are being explored.
Date: December 31, 1995
Creator: Maciel, G.E.
Partner: UNT Libraries Government Documents Department

Characterization of polyxylylenes with solid state {sup 13}C nuclear magnetic resonance spectroscopy

Description: Polyxylylenes are thermoplastics used as encapsulants for electronic devices. Five polyxylylenes were prepared by pyrolysis of [2.2]paracyclophanes and characterized by solid state {sup 13}C NMR spectroscopy. The chemical shift data, in combination with interrupted decoupling experiments, allowed assignment of resonances to their carbon sources in the polymers. This confirmed the integrity of the xylylene building block in the polymers and is consistent with linear polymers. No crosslinking could be detected within the NMR sensitivity limits. Residual paracyclophane was detected by {sup 13}C CP MAS NMR spectroscopy in the polyxylylene samples prepared at room temperature; however discrete {sup 13}C resonances due to amorphous and crystalline phases in the polymers were not resolved.
Date: February 1, 1996
Creator: Loy, D.A.; Assink, R.A.; Jamison, G.M.; McNamara, W.F.; Schneider, D.A. & Prabakar, S.
Partner: UNT Libraries Government Documents Department

The chemical constitution of Pocahontas No. 3 coal

Description: A new method for the definition of the larger aromatic structural elements in high-rank coals has been developed. The procedure involves the oxidative decom-position of the coal with oxygen in basic solution and the subsequent decarboxylation of the aromatic arboxylic acids to yield a mixture of aromatic compounds that can readily be analyzed by conventional methods. This approach has been tested with pure compounds and applied to Pocahontas No. 3 coal.
Date: December 31, 1995
Creator: Stock, L.M. & Obeng, M.
Partner: UNT Libraries Government Documents Department

Photoelectron holography applied to surface structural determination

Description: Photoemitted electron waves are used as coherent source waves for angstrom-scale holographic imaging of local atomic geometry at surfaces. Electron angular distribution patterns are collected above a sample surface and serve as a record of the interference between source wave and waves scattered from surrounding ion cores. Using a mathematical imaging integral transformation, the three-dimensional structural information is obtained directly from these collected patterns. Patterns measured with different electron kinetic energies are phase-summed for image improvement. Pt (111) surface is used as a model system. A pattern 9.6{angstrom}{sup {minus}1} (351 eV) is used to generate a full 3-D image of atom locations around an emitter with nearest neighbors within 0.l{angstrom} of the expected bulk positions. Atoms several layers beyond the nearest neighbors are also apparent. Twin-image reduction and artifact suppression is obtained by phase-summing eight patterns measured from 8.8 to 10.2{angstrom}{sup {minus}1} (295 to 396 eV). 32 were measured in 0.2{angstrom}{sup {minus}1} steps from 6.0 to 12.2{angstrom}{sup {minus}1} (137 to 567 eV) are presented here. Simple models of two-slit interference are compared with electron scattering to illuminate understanding of holographic recording of the structural information. This also shows why it sometimes fails due to destructive interferences. Simple theoretical models of electron scattering are compared to experiment to show the origin of the structural information and the differences that result from atomic scattering and from the source wave. Experimental parameters and their relation to imaging is discussed. Comparison is made to the Pt pattern measured at 351 eV using the simple theoretical model. The remaining data set is also modeled, and the eight appropriate theoretical patterns are used to regenerate the multiple-wavenumber experimental result. A clean Cu (001) surface is also measured and imaged.
Date: May 1, 1995
Creator: Petersen, B.L.
Partner: UNT Libraries Government Documents Department

Characterization of carbon nitride films produced by pulsed laser deposition

Description: Carbon Nitride (CN{sub x}) films have been grown by ion-assisted pulsed-laser deposition (IAPLD). Graphite targets were laser ablated while bombarding the substrate with ions from a broad-beam Kaufman-type ion source. Ion voltage, current density, substrate temperature, and feed gas composition (N{sub 2} in Ar) were varied. Resultant films were characterized by Raman. Fourier transform infrared (FTIR), and Rutherford back scattering (RBS) spectroscopy. Samples with {approximately} 30% N/C ratio have been fabricated. The corresponding Raman and FTIR spectra indicate that nitrogen is incorporated into the samples by insertion into sp{sup 2}-bonded structures. A low level of C{identical_to}N triple bonds is also found. As the ion current and voltage are increased with a pure Ar ion beam, Raman peaks associated with nanocrystalline graphite appear in the spectra. Adding low levels of nitrogen to the ion beam first reduces the Raman intensity in the vicinity of the graphite disorder peak without adding detectable amounts of nitrogen to the films (as measured by RBS). At higher nitrogen levels in the ion beam, significant amounts of nitrogen are incorporated into the samples, and the magnitude of the ``disorder`` peak increases. By increasing the temperature of the substrate during deposition, the broad peak due mainly to sp{sup 2}-bonded C-N in the FTIR spectra is shifted to lower wavenumber. This could be interpreted as evidence of single-bonded C-N; however, it is more likely that the character of the sp{sup 2} bonding is changing.
Date: July 1, 1995
Creator: Friedmann, T.A.; Tallant, D.R.; Barbour, J.C.; Sullivan, J.P.; Siegal, M.P.; Simpson, R.L. et al.
Partner: UNT Libraries Government Documents Department