Digital Commons Network^™

Monte Carlo Simulation On The Indirect Exchange Interactions Of Co-Doped Zno Film, Abraham F. Jalbout, Hanning Chen, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

Monte Carlo simulations using a three-dimensional lattice model studied the Ruderman–Kittel–Kasuya–Yosida (RKKY) indirect exchange interaction of doped magnetic Co ions in ZnOfilms. The results of the calculations show that the RKKY interaction in Co-doped ZnO is long ranged and its magnitude is proportional to (inverse of the distance from a central ion). The sign oscillates with a frequency that depends on the concentration of the carrier. The long-distance sum of the RKKY indirect exchange energies is positive indicating that these materials are ferromagnetic, in direct correlation with previously reported results.

Creating Nanocavities Of Tunable Sizes: Hollow Helices, Bing Gong, Huaqiang Zeng, Jin Zhu, Lihua Yuan, Yaohua Han, Shizhi Cheng, Mako Furukawa, Ruben D. Parra, Audrey Y. Kovalevsky, Jeffrey L. Mills, Ewa Skrzypczak-Jankun, Suzana Martinovic, Richard D. Smith, Chong Zheng, Thomas Szyperski, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

A general strategy for creating nanocavities with tunable sizes based on the folding of unnatural oligomers is presented. The backbones of these oligomers are rigidified by localized, threecenter intramolecular hydrogen bonds, which lead to well-defined hollow helical conformations. Changing the curvature of the oligomer backbone leads to the adjustment of the interior cavity size. Helices with interior cavities of 10 Å to >30 Å across, the largest thus far formed by the folding of unnatural foldamers, are generated. Cavities of these sizes are usually seen at the tertiary and quaternary structural levels of proteins. The ability to tune molecular dimensions …

Preliminary Geochemical Evaluation Of Groundwaters From Wells Of The Nye County Early Warning Drilling Program, Irene Farnham, Klaus J. Stetzenbach, Amy J. Smiecinski

Publications (YM)

As part of the Yucca Mountain Oversight program, the Nye County Nuclear Waste Repository Project Office (NWRPO) has established a groundwater monitoring program to protect groundwater resources for the residents of Nye County in Amargosa and Pahrump Valleys. This groundwater monitoring program, referred to as the Nye County Early Warning Drilling Program (NCEWDP), involves drilling a series of wells down-gradient from Yucca Mountain for long term groundwater monitoring and also to provide much needed geologic and hydrologic information in this area. A comprehensive database of aquifer parameters in the alluvial, volcanic, and carbonate aquifers down-gradient hydrogeologically of Yucca Mountain is …

Synthesis And Characterization Of Hydroxyapatite-Collagen Biocomposite Materials, Vuk Uskoković, Nenad Ignjatović, Nadejda Petranović

Pharmacy Faculty Articles and Research

Hydroxyapatite-collagen composite is a prosperous biomaterial in reconstructive surgery for the reparation of defects within human hard tissue. Within this research, three-dimensional blocks of HAp/collagen composite biomaterial were synthesized by homogenizing the HAp/collagen mixture by cold and hot (T=60oC) pressing (P=49 MPa). The changes in the system were followed by using thermal analysis (DSC & TGA), FT-IR spectroscopy and scanning electron microscopy (SEM). The identification and kinetic analysis of appearing phase transition were done. FT-IR spectrum of the biocomposite shows that neither cold nor hot pressing had significant influence on the individual components of the composite. SEM of the fracture …

Holographic Analysis Of Diffraction Structure Factors, S. Marchesini, N. Mannella, C. S. Fadley, M. A. Van Hove, J. J. Bucher, D. K. Shuh, L. Fabris, M. J. Press, M. W. West, Wayne C. Stolte, Z. Hussain

Chemistry and Biochemistry Faculty Research

We combine the theory of inside-source/inside-detector x-ray fluorescence holography and Kossel lines/x ray standing waves in kinematic approximation to directly obtain the phases of the diffraction structure factors. The influence of Kossel lines and standing waves on holography is also discussed. We obtain partial phase determination from experimental data obtaining the sign of the real part of the structure factor for several reciprocal lattice vectors of a vanadium crystal.

A Microfabricated Microconcentrator For Sensors And Chromatography, Minhee Kim

Dissertations

The detection and quantitative measurement of trace components is a challenging task. The key component in such an instrument is the concentration step where the analytes are accumulated before the analysis. In this research, simple and inexpensive processes for the microfabrication of microconcentrator that can be used with sensors and as an injector in GC were developed. Analytes are selectively concentrated in the microconcentrator. Rapid electrical heating of the microconcentrator releases the adsorbed species as a 66 concentration pulse", which serves as an injection for the detection system. The relatively small size of the microconcentrator allows it to be heated …

Catalytic Reduction Of Nitric Oxide By Solid Carbonaceous Material Under Lean Condition, Shan Xiao

Dissertations

The reactions of O₂, NO_x and soot from Diesel exhaust over Cu containing catalysts can significantly reduce soot and NO_x emissions while producing N₂ and CO₂. The author has evaluated the performance of Cu ion exchanged ZSM-5 and Cu adsorbed on Granulated Activated Carbon (Cu-GAC) using GAC as a surrogate for soot in a packed bed reactor. CO, formed primarily by the oxidation of GAC with O₂, appears to be a stable intermediate in the reduction of NO. With experimental parameters chosen to simulate Diesel exhaust conditions, Cu-GAC is much more …

The Biophysical Basis Of Triplet Repeat Dna Expansion In Genetic Disease, Anthony M. Paiva

Seton Hall University Dissertations and Theses (ETDs)

.

The 1.20 Å Resolution Crystal Structure Of The Aminopeptidase From Aeromonas Proteolytica Complexed With Tris: A Tale Of Buffer Inhibition, William Desmarais, David L. Bienvenue, Krzysztof P. Bzymek, Richard C. Holz, Gregory A. Petsko, Dagmar Ringe

Chemistry Faculty Research and Publications

The aminopeptidase from Aeromonas proteolytica (AAP) is a bridged bimetallic enzyme that removes the N-terminal amino acid from a peptide chain. To fully understand the metal roles in the reaction pathway of AAP we have solved the 1.20 Å resolution crystal structure of native AAP (PDB ID = 1LOK). The high-quality electron density maps showed a single Tris molecule chelated to the active site Zn²⁺, alternate side chain conformations for some side chains, a sodium ion that mediates a crystal contact, a surface thiocyanate ion, and several potential hydrogen atoms. In addition, the high precision of the atomic …

44th Rocky Mountain Conference On Analytical Chemistry

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 44th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-endorsed by the Colorado Section of the American Chemical Society and the Society for Applied Spectroscopy. Held in Denver, Colorado, July 28 - August 1, 2002.

Preprogramming Of Porphyrin−Nucleic Acid Assemblies Via Variation Of The Alkyl/Aryl Substituents Of Phosphonium Tetratolylporphyrins, Pavel Kubat, Kamil Lang, Vladimir Kral, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Cationic alkyl/arylphosphonium meso-tetratolylporphyrins aggregate in an aqueous solution to form H-aggregates, J-aggregates, and long-range assemblies. The ratio between the monomer and various types of aggregates can be controlled by the substitution in the phosphonium units and by the ionic strength. A trimethylphosphonium derivative is predominantly monomeric, dimethylphenylphosphonium forms monomers as well as low-molecular-weight H- and J-aggregates, triphenylphosphonium forms mainly H- and J-aggregates, and tri(n-butyl)phosphonium forms mainly long-range assemblies. Porphyrin monomers associate with calf thymus DNA (binding constant Kb approximate to 10(7) M-1) and oligonucleotides (K-b approximate to 10(5-)10(6) M-1). The large size of the meso-substituents prevents the intercalation between base …

In-Situ X-Ray-Absorption Spectroscopy Study Of Hydrogen Absorption By Nickel-Magnesium Thin Films, B. Farangis, Ponnusamy Nachimuthu, T. J. Richardson, J. L. Slack, Rupert C. Perera, Eric M. Gullikson, Dennis W. Lindle, M. Rubin

Chemistry and Biochemistry Faculty Research

Structural and electronic properties of co-sputtered Ni-Mg thin films with varying Ni to Mg ratio were studied by in-situ x-ray absorption spectroscopy in the Ni L-edge and Mg K-edge regions. Co-deposition of the metals led to increased disorder and decreased coordination around Ni and Mg compared to pure metal films. Exposure of the metallic films to hydrogen resulted in formation of hydrides and increased disorder. The presence of hydrogen as a near neighbor around Mg caused a drastic reduction in the intensities of multiple scattering resonances at higher energies. The optical switching behavior and changes in the x-ray spectra varied …

Synthetic Studies Directed Toward The Phorboxazoles: Preparation Of The C3–C15 Bisoxane Segment And Two Stereoisomers, Patrick Bernard Greer, William A. Donaldson

Chemistry Faculty Research and Publications

A synthetic approach to the C3–C15 segment of the cytotoxic marine metabolite phorboxazoles is described. This segment consists of a methylene linked bisoxane structure. The first pyran ring was constructed by a Lewis acid catalyzed diene–aldehyde cyclocondensation. The β-C-glucoside substitution pattern of this ring was established by a stereoselective allylation. Ozonolysis of vinyl group and enantioselective allylation of the racemic aldehyde generated two separable homoallylic alcohols (−)-22 and (+)-23. The Mosher's esters of each alcohol were determined to be >90% de. Reaction of (−)-22 with acryloyl chloride, followed by ring closing metathesis gave the …

Synthesis Of The Abc Ring System Of Azaspiracid. 2. A Systematic Study Into The Effect Of C16 And C17 Substitution On Bis-Spirocyclization, Rich G. Carter, David E. Graves, Melissa A. Gronemeyer, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

(matrix presented) A systematic study into the effect of C16 and C17 substitution on the stereochemical outcome of bis-Spiro cyclization to form the ABC ring system of azaspiracid is disclosed. Successful construction of the natural 10R,13R bis-spirocyclic stereochemistry has been accomplished on the C16 benzyloxy-containing precursor.

Immobilization Of Fission Iodine By Reaction With A Fullerene Containing Carbon Compound And Insoluble Natural Organic Matrix, Spencer M. Steinberg

Separations Campaign (TRP)

The recovery of iodine released during the processing of used nuclear fuel poses a significant challenge to the transmutation of radioactive iodine. This proposal will develop and examine the use of Fullerene Containing Carbon (FCC) compounds as potential sorbents for iodine release from the reprocessing of nuclear fuel. This work will also include the development of bench-scale testing capabilities at UNLV to allow the testing of the FCC material in a simulated process off-gas environment. This experimental capability will also be used to test other potential sorbtion materials and processes, such as natural organic matter (NOM) and other promising alternatives. …

Computational Simulation Of The Docking Of Prochlorothrix Hollandica Plastocyanin To Photosystem I: Modeling The Electron Transfer Complex, Neocles B. Leontis, Eugene Myshkin, George S. Bullerjahn

Chemistry Faculty Publications

We have used several docking algorithms (GRAMM, FTDOCK, DOT, AUTODOCK) to examine protein-protein interactions between plastocyanin (Pc)/photosystem I (PSI) in the electron transfer reaction. Because of the large size and complexity of this system, it is faster and easier to use computer simulations than conduct x-ray crystallography or nuclear magnetic resonance experiments. The main criterion for complex selection was the distance between the copper ion of Pc and the P700 chlorophyll special pair. Additionally, the unique tyrosine residue (Tyr(12)) of the hydrophobic docking surface of Prochlorothrix hollandica Pc yields a specific interaction with the lumenal surface of PSI, thus providing …

Application Of Electrochemical Techniques To The Researches In Life Science, Jian-Tao Pang, Chun-Hai Fan, Gen-Xi Li

Journal of Electrochemistry

The research work of our group in the last two years is briefly reviewed in this paper. By using electrochemical method, and combining some other chemical and biological techniques, lots of achievements have been obtained. And these researches are towards some hot topics in life science, such as function conversion, interaction between signal molecules and proteins, electron-transfer of biomolecules, gene detection, structural biology, biochemical analysis and the third generation biosensors.

Magnetization Reversal Of Elliptical Co/Cu/Co Pseudo-Spin Valve Dots, Ngocnga Dao, Scott L. Whittenburg, Y. Hao, Leszek M. Malkinski, Jian Qing Wang, C. A. Ross

Chemistry and Biochemistry Faculty Publications

We present our recent simulated results on Cr (5 nm)/ Cu (5 nm)/ Co (5 nm)/ Cu (3 nm)/ Co (2 nm) pseudo-spin valve dots. The simulated results agree qualitatively with the experimental results. Three different sizes of elliptical dots, and were simulated. Our simulations show that in these types of dots magnetization reversal occurs by the formation of domain walls: for and for No domain wall was observed in the reversal of the dots. For such dots, the simulated loops show a small two-step reversal pattern with the thin upper layer partially reversing followed by complete reversal of both …

Synthesis And Dna Binding Of Cis And Trans-Rucl2 (Dmso)4, Thomas Curran

Honors Theses

The synthesis of both cis and trans-RuCl?(DMSO)? has been reported in literature, and is currently the only way of acquiring these compounds. Because these metallodrugs have shown similar antitumor properties to cisplatin, they are currently under investigation for use in clinical trials as potential chemotherapeutics. It is believed that these drugs act in a way similar to cisplatin by causing intrastrand crosslinking of adjacent guanine residues in DNA. In an attempt to better understand any Ru/DNA interaction for these compounds, both cis and trans-RuCl?(DMSO)? were synthesized with reasonable yields (~40%). The compounds were then characterized by nuclear magnetic resonance (NMR), …

Conformational Analysis Of Small Peptides By Circular Dichroism, Toni Bowie

Electronic Dissertations and Theses

Reports on peptides that are rich in D-alanine indicate that peptides with this structural motif adopt a specific secondary structure. In this study, two cyclic tetrapeptides cyclo[Leu-D-Ala], where Xaa is Glu or Lys, was studied by circular dichroism (CD). The conformational stability of these peptides was investigated by varying the temperature, solvent, pH, and concentration of the peptide solutions. When these conditions were varied, the CD measurements in each condition did not produce any significant changes. The CD of both peptides exhibits two positive CD bands at 211 nm and 222 nm and a third positive CD band below 190 …

Rnaml: A Standard Syntax For Exchanging Rna Information, Neocles B. Leontis, Allison Waugh, Patrick Gendron, Russ Altman, James W. Brown, David Case, Daniel Gautheret, Stephen C. Harvey, John Westbrook, Eric Westhof, Michael Zuker, François Major

Chemistry Faculty Publications

Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, …

Direct Haplotyping Of Kilobase-Size Dna Using Carbon Nanotube Probes, Adam T. Woolley, Chantal Guillemette, Chin Li Cheung, David E. Housman, Charles M. Lieber

Barry Chin Li Cheung Publications

We have implemented a method for multiplexed detection of polymorphic sites and direct determination of haplotypes in 10-kilobasesize DNA fragments using single-walled carbon nanotube (SWNT) atomic force microscopy (AFM) probes. Labeled oligonucleotides are hybridized specifically to complementary target sequences in template DNA, and the positions of the tagged sequences are detected by direct SWNT tip imaging. We demonstrated this concept by detecting streptavidin and IRD800 labels at two different sequences in M13mp18. Our approach also permits haplotype determination from simple visual inspection of AFM images of individual DNA molecules, which we have done on UGT1A7, a gene under study as …

Chemical Imaging Comes Of Age, John F. Turner Ii

Chemistry Faculty Publications

Sophisticated analysis techniques allow researchers to extract meaningful results from spectral imaging data.

1080 Summary Information, Department Of Agriculture, Western Australia, Department Of Conservation And Land Management, Western Australia, Department Of Health, Western Australia

Biosecurity research reports

Fluoroacetate, the active ingredient of 1080, occurs naturally in toxic plants in Australia, South Africa, and South America. Manufactured I080 underpins most vertebrate pest control programs in Australia and New Zealand. Fluoroacetate occurs naturally in about 40 plant species in Australia with most of these plants restricted to the south-west of WA.

I080 was introduced to rabbit control programs in the early 1950s and therefore has a long history of proven effectiveness and safety in Australia. There have been few repo1ted problems associated with human safety, environmental persistence, bioaccumulation or impact on populations of non-target species.

In particular, I080 baits …

The Chemistry Of Trifluoromethyl Indenes And Trifluoromethyl Indenyl Complexes, Maud J. Urbanski

Seton Hall University Dissertations and Theses (ETDs)

.

Dna Polymerase Iii Holoenzyme From Thermus Thermophilus Identification Expression Purification Of Components And Use To Reconstitute A Processive Replicase, James M. Bullard, Jennifer C. Williams, Wendy K. Acker, Carsten Jacobi, Nebojsa Janjic, Charles S. Mchenry

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

DNA replication in bacteria is performed by a specialized multicomponent replicase, the DNA polymerase III holoenzyme, that consist of three essential components: a polymerase, the β sliding clamp processivity factor, and the DnaX complex clamp-loader. We report here the assembly of the minimal functional holoenzyme from Thermus thermophilus (Tth), an extreme thermophile. The minimal holoenzyme consists of α (pol III catalytic subunit), β (sliding clamp processivity factor), and the essential DnaX (τ/γ), δ and δ′ components of the DnaX complex. We show with purified recombinant proteins that these five components are required for rapid and processive DNA synthesis …

A Three-Domain Structure For The Delta Subunit Of The Dna Polymerase Iii Holoenzyme Delta Domain Iii Binds Delta' And Assembles Into The Dnax Complex, James M. Bullard, Arthur E. Pritchard, Min Sun Song, Bradley P. Glover, Anna Wieczorek, Joe Chen, Nebojsa Janjic, Charles S. Mchenry

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Using ψ-BLAST, we have developed a method for identifying the poorly conserved δ subunit of the DNA polymerase III holoenzyme from all sequenced bacteria. This approach, starting withEscherichia coli δ, leads not only to the identification of δ but also to the DnaX and δ′ subunits of the DnaX complex and other AAA⁺-class ATPases. This suggests that, although not an ATPase, δ is related structurally to the other subunits of the DnaX complex that loads the β sliding clamp processivity factor onto DNA. To test this prediction, we aligned δ sequences with those of δ′ and, using …

Applications Of Nmr To Structure-Based Drug Design In Structural Genomics, Robert Powers

Robert Powers Publications

Structural genomics is poised to have a tremendous impact on traditional structure-based drug design programs. As a result, there is a growing need to obtain rapid structural information in a reliable form that is amenable to rational drug design. In this manner, NMR has been expanding and evolving its role in aiding the design process. A variety of NMR methodologies that cover a range of inherent resolution are described in the context of structure-based drug design in the era of structural genomics.

The Southern African Regional Science Initiative (Safari 2000): Overview Of The Dry Season Field Campaign, R. J. Swap, H. J. Annegarn, J. T. Suttles, J. Haywood, M. C. Helmlinger, C. Hely, Peter V. Hobbs, B. N. Holben, J. Ji, M. D. King, T. Landmann, W. Maenhaut, L. Otter, B. Pak, S. J. Piketh, S. Platnick, J. Privette, D. Roy, A. M. Thompson, Darold E. Ward, Robert J. Yokelson

Chemistry and Biochemistry Faculty Publications

The Southern African Regional Science Initiative (SAFARI 2000) is an international science project investigating the earth-atmosphere-human system in southern Africa. The programme was conducted over a two-year period from March 1999 to March 2001. The dry season field campaign (August-September 2000) was the most intensive activity and involved over 200 scientists from eighteen countries. The main objectives were to characterize and quantify biogenic, pyrogenic and anthropogenic aerosol and trace gas emissions and their transport and transformations in the atmosphere, and to validate NASA's Earth Observing System's satellite Terra within a scientific context. Five aircraft - two South African Weather Service …

Production Of A Monoclonal Antibody Against Benzo[Α]Pyrene Diol Epoxide Dna Adducts, Brian Peden Austin

Chemistry & Biochemistry Theses & Dissertations

Benzo[α]pyrene is a ubiquitous pollutant produced from the incomplete combustion of organic material such as fossil fuels. It is found in the workplace, urban air, drinking water, and the food supply. Recently, it has been proposed that benzo[α]pyrene may be the causative agent in the formation of lung adenocarcinomas among some Taiwanese women exposed to cooking oil fumes without adequate ventilation. In this study, calf thymus DNA was modified in vitro with benzo[α]pyrene-diol epoxide (BPDE) to a level consistent with that found in biological samples. This DNA of low modification was used as an immunogen in the production of a …