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A Quenchofluorometric Study of Polycyclic Aromatic Hydrocarbons in Molecularly Organized Media

Description: Detection, identification and separation of polycyclic aromatic compounds in environmental samples are of extreme importance since many of these compounds are well known for their potential carcinogenic and/or mutagenic activities. Selective quenching of molecular fluorescence can be utilized effectively to analyze mixtures containing different polycyclic aromatic hydrocarbons. Molecularly organized assemblies are used widely in detection and separation of these compounds mainly because of less toxicity and enhanced solubilization capabilities associated with these media. Feasibility of using nitromethane and the alkylpyridinium cation as selective fluorescence quenching agents for discriminating between alternant versus nonalternant polycyclic aromatic hydrocarbons (PAHs) is critically examined in several molecularly organized micellar solvent media. Fluorescence quenching is used to probe the structural features in mixed micelles containing the various combinations of anionic, cationic, nonionic and zwitterionic surfactants. Experimental results provide valuable information regarding molecular interactions between the dissimilar surfactants.
Date: May 1998
Creator: Pandey, Siddharth
Partner: UNT Libraries

Optical properties of fluids in microfabricated channels

Description: Microfabricated channels are widely thought to be the key to realizing chemical analysis on a microscopic scale. Chemical and biological information in the microchannels is often probed with optical techniques such as fluorescence, Raman and absorption spectroscopy. However, the optical effects of a microchannel are not well characterized. For example, it is important to understand the optics of the channel in order to optimize optical coupling efficiency. The authors consider various designs for enhancing the sensitivity of fluorescence detection in a microchannel.
Date: March 1, 1997
Creator: French, T.; Gourley, P.L. & McDonald, A.E.
Partner: UNT Libraries Government Documents Department

Laser physics research for KrF lasers - fluorescence suppression measurments. Final report

Description: This final report describes the work performed for Los Alamos National Laboratory (LANL) to measure the wavelength-dependent KrF fluorescence suppression as a function of intracavity flux. To our knowledge, this is the first time the wavelength-dependent suppresssion has been measured for KrF.
Date: October 1, 1991
Partner: UNT Libraries Government Documents Department

Structure of mix in a rayleigh-taylor unstable fuild cell

Description: Laser-induced fluorescence is used to image the central plane of the mix region of two immiscible liquids subject to the Rayleigh-Taylor instability. The familiar bubbles and spikes display a complex internal structure. This small-scale structure creates a large contact area whose density is constant in time. The size of the mixing zone, defined in a new way, grows with coefficient ab >= 0.054.
Date: September 2, 1997
Creator: Schneider, M.B.; Dimonte, G. & Remington, B.A.
Partner: UNT Libraries Government Documents Department

The self-supporting disc: A specimen geometry exhibiting low secondary characteristic fluorescence

Description: Secondary characteristic fluorescence, when expressed relative to the primary intensity of the fluorescing element, can be written as the product of three factors, which represent the probabilities of the various processes that govern the magnitude of fluorescence and thus have values between zero and one. Two of these factors are characteristic of the material being analyzed. The factor C{sub X}{sup Y} is the likelihood that the primary x ray of Y is absorbed by the element X if it is absorbed in the fluoresced volume of the specimen. The factor P{sub X} is the probability that element X, having absorbed the primary x ray, emits the secondary x ray of interest. The third factor is the likelihood that the primary x ray is absorbed in the fluoresced volume, and is denoted {Omega}{sub eff}/4{pi}. For critical microanalysis studies, thin-flake specimens are most desirable, especially if the size of individual flakes is small relative to the scale, {approximately}10 {mu}m, over which the primary x rays are typically absorbed. However, a specimen comprised of small flakes may be impractical for many studies. Such a geometry may not indicate the relative positions and orientations of important microstructural features. The lack of sampling volume may also inhibit microanalysis of a specific feature of the microstructure, such as an interface, which may not be represented within the small specimen volume. For such analyses, a specimen geometry that leaves the specimen intact, yet minimizes secondary fluorescence by virtue of having a small geometric factor, may be preferable. Because the geometric factor depends only on the absorption properties of the secondary x ray, a rule-of-thumb maximum secondary fluorescence of an elemental line can be calculated by assuming an extreme microanalysis situation: when the entire disc is composed of the fluoresced element.
Date: June 1, 1995
Creator: Anderson, I.M.; Bentley, J. & Carter, C.B.
Partner: UNT Libraries Government Documents Department

Directly labeled fluorescent DNA probes for chromosome mapping

Description: A new strategy is briefly described for employing nucleic acid probes that are directly labeled with fluorochromes in fluorescence in situ hybridization techniques. These probes will permit the detection, quantitation, and high-precision spatial analysis of multiple DNA sequences along a single chromosome using video-enhanced fluorescence microscopy and digital image processing and analysis. Potential advantages of direct labeled DNA probes for fluorescence in situ hybridization far surpass currently available, indirect DNA probe labeling techniques in ease of use, versatility, and increased signal- to-noise ratio.
Date: December 31, 1995
Creator: Marrone, B.L.; Deaven, L.L.; Chen, D.J.; Park, Min S.; MacInnes, M.A.; Salzman, G.C. et al.
Partner: UNT Libraries Government Documents Department

Preliminary evaluation of resinite recovery from Illinois coal. Technical report, December 1, 1994--February 28, 1995

Description: Resinite is a naturally occurring substance found in coal and derived from original plant resins. It is ubiquitous in North American coals. It makes up one to four percent by volume of most Illinois coals. It has been commercially exploited in the western USA for use in adhesives, varnishes and thermal setting inks. The overall objective of this project is to compare the properties of the resinite contained in Illinois Basin coals to resinite being commercially exploited in the western United States, and to recover the resinite from Illinois coals by microbubble column floatation techniques. This project is relevant to priority 1.4A identified in ICCI/RFP93-1. The significance of this study is that it has the potential to show the way to recover a valuable chemical, resinite, from coal using only physical processing techniques. The value of the resinite at $1.00/kg or $0.50/lb makes it about fifty times more valuable than steam coal. The removal of resinite from coal does not decrease the value of the remaining coal in any way. The unique aspects are that: (1) it is the first examination of the resinite recovery potential of Illinois coal, (2) it integrates the latest characterization techniques such as density gradient centrifugation, microspectrofluorometry, and gas chromatography-mass spectrometry, and (3) it uses microbubble column flotation to determine the resinite recovery potential. During this quarter samples were obtained, information from both the databases of both the Illinois State Geological Survey (ISGS) and the Pennsylvania State University (PSU) was obtained and evaluated, and IBCSP samples from the Herrin No. 6, the Springfield No. 5 and the Colchester No. 2 seams were analyzed petrographically and the resinites in these samples were characterized by fluorescence spectral analysis.
Date: December 31, 1995
Creator: Crelling, J.C.
Partner: UNT Libraries Government Documents Department

Near-field single molecule spectroscopy

Description: The high spatial resolution and sensitivity of near-field fluorescence microscopy allows one to study spectroscopic and dynamical properties of individual molecules at room temperature. Time-resolved experiments which probe the dynamical behavior of single molecules are discussed. Ground rules for applying near-field spectroscopy and the effect of the aluminum coated near-field probe on spectroscopic measurements are presented.
Date: February 1, 1995
Creator: Xie, X.S. & Dunn, R.C.
Partner: UNT Libraries Government Documents Department

Dispersion functions and factors that determine resolution for DNA sequencing by gel electrophoresis

Description: The number of bases that can be read in a single run by a DNA sequencing instrument that detects fluorophore labeled DNA arriving at a ``finish-line`` located a fixed distance from the starting wells is influenced by numerous parameters. Strategies for improving the length-of-read of a DNA sequencer can be based on quantitative models of the separation of DNA by gel electrophoresis. The dispersion function of the electrophoretic system--the relationship between molecular contour length and time of arrival at the detector--is useful in characterizing the performance of a DNA sequencer. We adapted analytical representations of dispersion functions, originally developed for snapshot imaging of DNA gels, (samples electrophoresed for constant time), to finish-line imaging, and demonstrated that a logistic-type function with non-integral exponent is required to describe the experimental data. We use this dispersion function to determine the resolution length and resolving power of a LI-COR DNA sequencing system and a custom built capillary gel electrophoresis system, and discuss the factors that presently limit the number of bases that can be determined reliably in a single sequencing run.
Date: April 1, 1996
Creator: Sutherland, J.C.; Reynolds, K.J. & Fisk, D.J.
Partner: UNT Libraries Government Documents Department

Advanced microinstrumentation for rapid DNA sequencing and large DNA fragment separation

Description: Our efforts to develop novel technology for a rapid DNA sequencer and large fragment analysis system based upon gel electrophoresis are described. We are using microfabrication technology to build dense arrays of high speed micro electrophoresis lanes that will ultimately increase the sequencing rate of DNA by at least 100 times the rate of current sequencers. We have demonstrated high resolution DNA fragment separation needed for sequencing in polyacrylamide microgels formed in glass microchannels. We have built prototype arrays of microchannels having up to 48 channels. Significant progress has also been made in developing a sensitive fluorescence detection system based upon a confocal microscope design that will enable the diagnostics and detection of DNA fragments in ultrathin microchannel gels. Development of a rapid DNA sequencer and fragment analysis system will have a major impact on future DNA instrumentation used in clinical, molecular and forensic analysis of DNA fragments.
Date: January 25, 1995
Creator: Balch, J.; Davidson, J.; Brewer, L.; Gingrich, J.; Koo, J.; Mariella, R. et al.
Partner: UNT Libraries Government Documents Department

Fabrication of High Performance Microlenses for an Integrated Capillary Channel Electrochromatograph with Fluorescence Detection

Description: We describe the microfabrication of an extremely compact optical system as a key element in an integrated capillary channel electrochromatograph with fluorescence detection. The optical system consists of a vertical cavity surface-emitting laser (VCSEL), two high performance microlenses and a commercial photodetector. The microlenses are multilevel diffractive optics patterned by electron beam lithography and etched by reactive ion etching in fused silica. The design uses substrate-mode propagation within the fused silica substrate. Two generations of optical subsystems are described. The first generation design has a 6 mm optical length and is integrated directly onto the capillary channel-containing substrate. The second generation design separates the optical system onto its own substrate module and the optical path length is further compressed to 3.5 mm. The first generation design has been tested using direct fluorescence detection with a 750 nm VCSEL pumping a 10{sup {minus}4}M solution of CY-7 dye. The observed signal-to-noise ratio of better than 100:1 demonstrates that the background signal from scattered pump light is low despite the compact size of the optical system and is adequate for system sensitivity requirements.
Date: July 7, 1999
Creator: Wendt, J.R.; Warren, M.E.; Sweatt, W.C.; Bailey, C.G.; Matzke, C.M.; Arnold, D.W. et al.
Partner: UNT Libraries Government Documents Department

Detection of lead in soil with excimer laser fragmentation fluorescence spectroscopy (ELFFS)

Description: Excimer laser fragmentation fluorescence spectroscopy (ELFFS) is used to monitor lead in soil sample and investigate laser-solid interactions. Pure lead nitrate salt and soil doped with lead nitrate are photolyzed with 193 nm light from an ArF excimer at fluences from 0.4 to 4 J/cm{sup 2}. Lead emission is observed at 357.2, 364.0, 368.3, 373.9 and 405.8 nm. Time-resolved data show the decay time of the lead emission at 405.8 nm grows with increasing fluence, and a plasma is formed above fluences of 2 J/cm{sup 2}, where a strong continuum emission interferes with the analyte signal. Fluences below this threshold allow us to achieve a detection limit of approximately 200 ppm in soil.
Date: March 1, 2004
Creator: Choi, J.H.; Damm, C.J.; O'Donovan, N.J.; Sawyer, R.F.; Koshland, C.P. & Lucas, D.
Partner: UNT Libraries Government Documents Department

Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair

Description: The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIII{beta} and the hLigIII{alpha}/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.
Date: May 11, 2009
Creator: Chen, Xi; Ballin, Jeff D.; Della-Maria, Julie; Tsai, Miaw-Sheue; White, Elizabeth J.; Tomkinson, Alan E. et al.
Partner: UNT Libraries Government Documents Department

1,2-Hydroxypyridonates as Contrast Agents for Magnetic ResonanceImaging: TREN-1,2-HOPO

Description: 1,2-Hydroxypyridinones (1,2-HOPO) form very stable lanthanide complexes that may be useful as contrast agents for Magnetic Resonance Imaging (MRI). X-ray diffraction of single crystals established that the solid state structures of the Eu(III) and the previously reported [Inorg. Chem. 2004, 43, 5452] Gd(III) complex are identical. The recently discovered sensitizing properties of 1,2-HOPO chelates for Eu(III) luminescence allow direct measurement of the number if water molecules in the metal complex. Fluorescence measurements of the Eu(III) complex corroborate that in solution two water molecules coordinate the lanthanide (q = 2) as proposed from the analysis of NMRD profiles. In addition, fluorescence measurements have verified the anion binding interactions of lanthanide TREN-1,2-HOPO complexes in solution, studied by relaxivity, revealing only very weak oxalate binding (K{sub A} = 82.7 {+-} 6.5 M{sup -1}). Solution thermodynamic studies of the metal complex and free ligand have been carried out using potentiometry, spectrophotometry and fluorescence spectroscopy. The metal ion selectivity of TREN-1,2-HOPO supports the feasibility of using 1,2-HOPO ligands for selective lanthanide binding [pGd = 19.3 (2); pZn = 15.2 (2), pCa = 8.8 (3)].
Date: May 8, 2007
Creator: Jocher, Christoph J.; Moore, Evan G.; Xu, Jide; Avedano, Stefano; Botta, Mauro; Aime, Silvio et al.
Partner: UNT Libraries Government Documents Department

Excited state carrier dynamics in CdS{sub x}Se{sub 1-x} semisconductor alloys as studied by ultrafast fluorescence spectroscopy

Description: This dissertation discusses studies of the electron-hole pair dynamics of CdS{sub x}Se{sub 1-x} semiconductor alloys for the entire compositional range from x = 1 to x = 0 as examined by the ultrafast fluorescence techniques of time correlated single photon counting and fluorescence upconversion. Specifically, samples with x = 1, .75, .5, .25, and 0 were studied each at a spread of wavelengths about its respective emission maximum which varies according to {lambda} = 718nm - 210x nm. The decays of these samples were found to obey a Kohlrausch distribution, exp [(t/{tau}){sup {beta}}], with the exponent 3 in the range .5-.7 for the alloys. These results are in agreement with those expected for localization due to local potential variations resulting from the random distribution of sulfur and selenium atoms on the element VI A sub-lattice. This localization can be understood in terms of Anderson localization of the holes in states whose energy distribution tails into the forbidden energy band-gap. Because these states have energy dependent lifetimes, the carriers can decay via many parallel channels. This distribution of channels is the ultimate source of the Kohlrausch form of the fluorescence decays.
Date: August 1, 1995
Creator: Gadd, S. E.
Partner: UNT Libraries Government Documents Department

Photoinduced degradation of PAHs in the presence of ozone

Description: Polycyclic Aromatic Hydrocarbons (PAH) are formed from both anthropogenic and natural sources. In order to assess the environmental impact caused by the surface-adsorbed PAHs, the chemical lifetimes of these compounds in the atmosphere must be determined. Although ozone is known to be a primary reactant in the chemical transformation of surface-adsorbed PAHs in the atmosphere, the kinetics of these reactions have not been investigated in detail. In addition to the experimental difficulties that arise in using an oxygen-ozone stream while monitoring the PAH with fluorescence, complications in analyzing the kinetic mechanism also exist. It is difficult to determine whether the ozone or oxygen initially quenches the excited state of PAH. Ozone could enhance the degradation rate by simply reacting with a product derived from the excited state of PAH and oxygen. The focus of this study is to demonstrate the use of fluorescence spectroscopy in monitoring the degradation of PAH adsorbed on a three dimensional particle in the presence of gaseous ozone free from the interference of oxygen. More specifically, the experimental procedure will involve the generation of an ozone-nitrogen gas stream to be used in the investigation of dark and photochemical reactions between ozone and naphthalene. The absence of oxygen in the system will allow for the accurate monitoring of PAH fluorescence decay due solely to ozone quenching. It will also aid in the determination of the reaction mechanism. This is the first time that the direct interaction of ozone with an excited state of PAH has been demonstrated.
Date: December 31, 1995
Creator: Schutt, W.S.; Li, Y. & Sigman, M.E.
Partner: UNT Libraries Government Documents Department

Laser induced fluorescence imaging of thermal damage in polymer matrix composites

Description: A simple, fluorescence-based imaging system was developed for identifying regions of thermal damage in polymer-matrix composites (PMCs). PMCs have important applications where low weight and high mechanical strength are needed. One concern in the aerospace industry is the tendency of some PMC materials to become irreversibly damaged when exposed to high temperatures. Traditional nondestructive evaluation (NDE) techniques are capable of detecting physical flaws, such as cracks and delaminations, but have not proven effective for detecting initial heat damage, which occurs on a molecular scale. Spectroscopic techniques such as laser-induced fluorescence provide an attractive means for detecting thermal damage on large, irregularly shaped surfaces. This paper describes instrumentation capable of rapidly detecting thermal damage in graphite/epoxy components.
Date: December 31, 1996
Creator: Wachter, E.A.; Fisher, W.G. & Meyer, K.E.
Partner: UNT Libraries Government Documents Department

Phytoplankton excretion revisited: healthy cells may not do it, but how many cells are healthy? Final report

Description: The goal of this project was to develop fluorescent probes that could be used on a individual cell basis to determine the physiological condition of phytoplankton cells in the field. Progress gained and problems encounter are described.
Date: August 6, 1996
Creator: Wood, A.M.
Partner: UNT Libraries Government Documents Department

Fluorescence spectroscopy of single molecules at room temperature and its applications

Description: We performed fluorescence spectroscopy of single and pairs of dye molecules on a surface at room temperature. Near field scanning optical microscope (NSOM) and far field scanning optical microscope with multi-color excitation/detection capability were built. The instrument is capable of optical imaging with 100nm resolution and has the sensitivity necessary for single molecule detection. A variety of dynamic events which cannot be observed from an ensemble of molecules is revealed when the molecules are probed one at a time. They include (1) spectral jumps correlated with dark states, (2) individually resolved quantum jumps to and from the meta-stable triplet state, (3) rotational jumps due to desorption/readsorption events of single molecules on the surface. For these studies, a computer controlled optical system which automatically and rapidly locates and performs spectroscopic measurements on single molecules was developed. We also studied the interaction between closely spaced pairs of molecules. In particular, fluorescence resonance energy transfer between a single resonant pair of donor and acceptor molecules was measured. Photodestruction dynamics of the donor or acceptor were used to determine the presence and efficiency of energy transfer Dual molecule spectroscopy was extended to a non-resonant pair of molecules to obtain high resolution differential distance information. By combining NSOM and dual color scheme, we studied the co-localization of parasite proteins and host proteins on a human red blood cell membrane infected with malaria. These dual-molecule techniques can be used to measure distances, relative orientations, and changes in distances/orientations of biological macromolecules with very good spatial, angular and temporal resolutions, hence opening new capabilities in the study of such systems.
Date: December 1, 1996
Creator: Ha, Taekjip
Partner: UNT Libraries Government Documents Department

Development of fluorescence lifetime diagnostic. Project accomplishments summary (Attachment 1), Revision 1

Description: Fiber-optic-based sensors are excellent candidates for detecting the presence and monitoring the levels of degradation products in stockpiled weapons. Specifically, fluorescence-based sensors are extremely sensitive, can have high specificity for compounds of interest, and are electrically inert. In addition to their applications in the enhanced surveillance program, fiber optic sensors are important for remote sensing, environmental remediation, and medical diagnostics. Optiphase Inc. has developed inexpensive technology for extremely precise measurement of phase shifts of interferometric optical and electrical signals. The company was interested in applying this capability in the rapidly expanding field of fluorescence lifetime spectroscopy, but lacked the expertise and resources associated with fluorescence chemistry and instrumentation. LLNL`s fiber-optic sensor group had significant expertise in these areas, but had previously concentrated its efforts on the chemistry, sensitivity, and selectivity of fluorescence amplitude-based sensors. Stability is a well known issue with this type of sensor whereas lifetime-based sensors exhibit excellent stability, a critical factor for the efficacy of sensors employed in the long-term monitoring of stockpiled weapons. Cooperation with the company afforded LLNL access to enabling, proprietary technology which could simplify and accelerate the transition to the next level of Enhanced Surveillance Program (ESP) sensor sophistication, namely fluorescence lifetime based sensors.
Date: February 18, 1998
Partner: UNT Libraries Government Documents Department