195 results on '"Sivanandan S"'
Search Results
2. Two-dimensional fluorescence spectroscopy of uranium isotopes in femtosecond laser ablation plumes
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Mark C. Phillips, Brian E. Brumfield, Nicole LaHaye, Sivanandan S. Harilal, Kyle C. Hartig, and Igor Jovanovic
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Medicine ,Science - Abstract
Abstract We demonstrate measurement of uranium isotopes in femtosecond laser ablation plumes using two-dimensional fluorescence spectroscopy (2DFS). The high-resolution, tunable CW-laser spectroscopy technique clearly distinguishes atomic absorption from 235U and 238U in natural and highly enriched uranium metal samples. We present analysis of spectral resolution and analytical performance of 2DFS as a function of ambient pressure. Simultaneous measurement using time-resolved absorption spectroscopy provides information on temporal dynamics of the laser ablation plume and saturation behavior of fluorescence signals. The rapid, non-contact measurement is promising for in-field, standoff measurements of uranium enrichment for nuclear safety and security.
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- 2017
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3. Progress towards machine learning methodologies for laser-induced breakdown spectroscopy with an emphasis on soil analysis
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Huang, Yingchao, Harilal, Sivanandan S., Bais, Abdul, and Hussein, Amina E.
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Electrical Engineering and Systems Science - Signal Processing - Abstract
Optical emission spectroscopy of laser-produced plasmas, commonly known as laser-induced breakdown spectroscopy (LIBS), is an emerging analytical tool for rapid soil analysis. However, specific challenges with LIBS exist, such as matrix effects and quantification issues, that require further study in the application of LIBS, particularly for analysis of heterogeneous samples such as soils. Advancements in the applications of Machine Learning (ML) methods can address some of these issues, advancing the potential for LIBS in soil analysis. This article aims to review the progress of LIBS application combined with ML methods, focusing on methodological approaches used in reducing matrix effect, feature selection, quantification analysis, soil classification, and self-absorption. The performance of various adopted ML approaches is discussed, including their shortcomings and advantages, to provide researchers with a clear picture of the current status of ML applications in LIBS for improving its analytical capability. The challenges and prospects of LIBS development in soil analysis are proposed, offering a path toward future research. This review article emphasize ML tools for LIBS soil analysis that are broadly relevant for other LIBS applications.
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- 2022
4. Spatiotemporal evolution of emission and absorption signatures in a laser-produced plasma
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Harilal, Sivanandan S., Kautz, Elizabeth J., and Phillips, Mark C.
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Physics - Plasma Physics - Abstract
We report spatiotemporal evolution of emission and absorption signatures of Al species in a nanosecond (ns) laser-produced plasma (LPP). The plasmas were generated from an Inconel target, which contained $\sim $ 0.4 wt.% Al, using 1064 nm, ~ 6 ns full width half maximum pulses from an Nd:YAG laser at an Ar cover gas pressure of ~ 34 Torr. The temporal distributions of the Al I (394.4 nm) transition were collected from various spatial points within the plasma employing time-of-flight (TOF) emission and laser absorption spectroscopy and they provide kinetics of the excited state and ground state population of the selected transition. The emission and absorption signatures showed multiple peaks in their temporal profiles, although they appeared at different spatial locations and times after the plasma onset. The absorption temporal profiles showed an early time signature representing shock wave propagation into the ambient gas. We also used emission and absorption spectral features for measuring various physical properties of the plasma. The absorption spectral profiles are utilized for measuring linewidths, column density, and kinetic temperature while emission spectra were used to measure excitation temperature. A comparison between excitation and the kinetic temperature was made at various spatial points in the plasma. Our results highlight that the TOF measurements provide a resourceful tool for showing the spatiotemporal LPP dynamics with higher spatial and temporal resolution than is possible with spectral measurements but are difficult to interpret without additional information on excitation temperatures and linewidths. The combination of absorption and emission TOF and spectral measurements thus provides a more complete picture of LPP spatiotemporal dynamics than is possible using any one technique alone., Comment: 22 Figures
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- 2022
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5. Dual-comb spectroscopy in the deep ultraviolet
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McCauley, John J., primary, Phillips, Mark C., additional, Weeks, Reagan R. D., additional, Zhang, Yu, additional, Harilal, Sivanandan S., additional, and Jones, R. Jason, additional
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- 2024
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6. Progress Toward Machine Learning Methodologies for Laser-Induced Breakdown Spectroscopy With an Emphasis on Soil Analysis
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Huang, Yingchao, primary, Harilal, Sivanandan S., additional, Bais, Abdul, additional, and Hussein, Amina E., additional
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- 2023
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7. Guest Editorial Special Issue on Plenary, Invited, and Tutorial Papers From ICOPS 2022
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Harilal, Sivanandan S., primary, Shumlak, Uri, additional, and Little, Justin, additional
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- 2023
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8. Influence of ambient gas on self-reversal in Li transitions relevant to isotopic analysis
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Kautz, Elizabeth J., primary, Xu, Annie, additional, Harilal, Ajay V., additional, Polek, Mathew P., additional, Casella, Andrew M., additional, Senor, David J., additional, and Harilal, Sivanandan S., additional
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- 2023
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9. Guest Editorial Special Issue on Plenary, Invited, and Tutorial Papers From ICOPS 2022
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Sivanandan S. Harilal, Uri Shumlak, and Justin Little
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Nuclear and High Energy Physics ,Condensed Matter Physics - Published
- 2023
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10. The role of ambient gas confinement, plasma chemistry, and focusing conditions on emission features of femtosecond laser-produced plasmas
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Bruce E. Bernacki, Sivanandan S. Harilal, Elizabeth J. Kautz, Mark C. Phillips, and Jeremy Yeak
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010302 applied physics ,Laser ablation ,Materials science ,Atomic emission spectroscopy ,02 engineering and technology ,Plasma ,Excitation temperature ,021001 nanoscience & nanotechnology ,Laser ,01 natural sciences ,Analytical Chemistry ,law.invention ,law ,Torr ,0103 physical sciences ,Femtosecond ,Atomic physics ,0210 nano-technology ,Spectroscopy ,Ambient pressure - Abstract
Ultrafast laser ablation coupled with optical emission spectroscopy is currently under development for standoff detection of elements and their isotopes for a wide range of application areas. In this work, we explore the role of ambient air pressure during the interaction of an ultrafast laser beam with two metallic targets (brass and uranium) with significantly different oxygen gas-phase reactivity. Plasma plumes were generated by focusing ∼800 nm, ∼35 fs pulses from an ultrafast laser system using a long focal length lens (f = 1 m). Two-dimensional spectral imaging was performed over the pressure range of 30 mTorr to 700 Torr air to evaluate emission dynamics, plasma chemistry, signal-to-background ratio, and characteristic parameters (i.e. excitation temperature, electron density). An increase in ambient air pressure during ultrafast laser ablation leads to plume confinement and subsequent changes in the emission dynamics due to plasma chemistry as well as changes in plasma generation conditions (i.e. focused fs laser ablation versus filament ablation). Ablation crater morphologies were also investigated via scanning electron microscopy. Results indicate atomic emission intensity and signal-to-background ratios peak at moderate pressure levels (∼50–100 Torr air) for both targets studied, although plasma chemistry influences uranium emission signatures. The emission features of the uranium plasma at pressures ≥10 Torr showed the presence of oxide molecules. We also find filament ablation leads to wider, more shallow craters compared to focused laser ablation. Our study provides unique insight into the interplay between plume dynamics, confinement, and plasma chemistry of fs laser-produced plasmas and how these phenomena evolve with changing ambient air pressure.
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- 2020
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11. A community effort to create standards for evaluating tumor subclonal reconstruction
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Salcedo, A., Tarabichi, M., Espiritu, S.M.G., Deshwar, A.G., David, M., Wilson, N.M., Dentro, S., Wintersinger, J.A., Liu, L.Y., Ko, M., Sivanandan, S., Zhang, H., Zhu, K., Ou Yang, T.-H., Chilton, J.M., Buchanan, A., Lalansingh, C.M., P’ng, C., Anghel, C.V., Umar, I., Lo, B., Zou, W., Jha, A., Huang, T., Yang, T.-P., Peifer, M., Sahinalp, C., Malikic, S., Vázquez-García, I., Mustonen, V., Yang, H.-T., Lee, K.-R., Ji, Y., Sengupta, Subhajit, Rudewicz, J., Nikolski, M., Schaeverbeke, Q., Yuan, K., Markowetz, F., Macintyre, G., Cmero, M., Chaudhary, B., Leshchiner, I., Livitz, D., Getz, G., Loher, P., Yu, K., Wang, W., Zhu, H., Simpson, J.T., Stuart, J.M., Anastassiou, D., Guan, Y., Ewing, A.D., Ellrott, K., Wedge, D.C., Morris, Q., Van Loo, P., Boutros, P.C., Department of Ecology and Evolutionary Biology [University of Toronto] (EEB), University of Toronto, Pennsylvania State University (Penn State), Penn State System, The Wellcome Trust Sanger Institute [Cambridge], Capital Normal University [Beijing], University of Queensland [Brisbane], Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford [Oxford], Department of Computer Science, Helsinki Institute for Information Technology, Bioinformatics, Institute of Biotechnology, and Organismal and Evolutionary Biology Research Programme
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DNA Copy Number Variations ,Tumour heterogeneity ,Computer science ,3122 Cancers ,Gene Dosage ,Biomedical Engineering ,Inference ,Bioengineering ,Computational biology ,Polymorphism, Single Nucleotide ,Applied Microbiology and Biotechnology ,Genome ,Tumor heterogeneity ,Article ,DNA sequencing ,03 medical and health sciences ,0302 clinical medicine ,GENOME SIMULATION ,Neoplasms ,Humans ,HETEROGENEITY ,Computer Simulation ,SOMATIC POINT MUTATIONS ,Evolutionary dynamics ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,318 Medical biotechnology ,IDENTIFICATION ,Manchester Cancer Research Centre ,ResearchInstitutes_Networks_Beacons/mcrc ,Reference Standards ,CANCER ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,EVOLUTION ,Clone Cells ,3. Good health ,Cancer evolution ,Mutation ,Mutation (genetic algorithm) ,Molecular Medicine ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Algorithms ,030217 neurology & neurosurgery ,Biotechnology - Abstract
Tumor DNA sequencing data can be interpreted by computational methods that analyse genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating tumor phylogenies are lacking. To address this need, we systematically assess methods for reconstructing tumor sub-clonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. We benchmark 580 tumor reconstructions, varying tumor read-depth, tumour type, and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity., Editors summary Methods for reconstructing tumor evolution are benchmarked in the DREAM Somatic Mutation Calling Tumour Heterogeneity Challenge using novel tools.
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- 2020
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12. Influence of ambient gas on self-reversal in Li transitions relevant to isotopic analysis
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Elizabeth J. Kautz, Annie Xu, Ajay V. Harilal, Mathew P. Polek, Andrew M. Casella, David J. Senor, and Sivanandan S. Harilal
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Atomic and Molecular Physics, and Optics - Abstract
Laser induced breakdown spectroscopy is a promising, rapid analysis method for the detection and quantification of Li and its isotopes needed in geochemical, nuclear, and energy storage applications. However, spectral broadening in laser produced plasmas, presence of fine and hyperfine structures, and self-reversal effects make Li isotopic analysis via laser induced breakdown spectroscopy challenging. The present study explores the influence of Ar, N2, and He ambient gases over the pressure range of 0.05 - 100 Torr on line broadening and self-reversal of the Li I transition with the greatest isotopic shift in the VIS spectral region (i.e., ≈670.8 nm, ≈15.8 pm isotopic shift). We perform spatially and temporally resolved optical emission spectroscopy of plasmas produced via laser ablation of LiAlO2 substrates. Our results show that the self-reversal and linewidth is reduced at lower pressures for all gases, and using optimized plasma conditions with chemometric methods, the 6Li/7Li isotopic ratios can be predicted.
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- 2023
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13. Time-resolved imaging of atoms and molecules in laser-produced uranium plasmas
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Mark C. Phillips, P. J. Skrodzki, Elizabeth J. Kautz, Milos Burger, Sivanandan S. Harilal, Igor Jovanovic, and Bruce E. Bernacki
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Argon ,Materials science ,010401 analytical chemistry ,Atoms in molecules ,Analytical chemistry ,Oxide ,chemistry.chemical_element ,Monoxide ,Partial pressure ,010501 environmental sciences ,Uranium ,01 natural sciences ,Oxygen ,0104 chemical sciences ,Analytical Chemistry ,chemistry.chemical_compound ,chemistry ,Molecule ,Physics::Chemical Physics ,Spectroscopy ,0105 earth and related environmental sciences - Abstract
Gas-phase oxidation of uranium (U), plume chemistry, and the corresponding impact on optical emission features of the U plasma are investigated. Plasmas were produced via nanosecond laser ablation of a natural U target in a chamber where U oxidation was controlled by varying the oxygen partial pressure in an argon cover gas. Monochromatic imaging of U atoms and monoxide (UO) molecules was performed using narrow bandpass optical filters. Results reveal the spatio-temporal evolution of atomic and molecular species in the plasma. U oxides are found to be formed further from the target (in comparison to U atoms), where lower temperatures favor molecular recombination. Segregation between the distribution of U atoms and UO species is observed at later times of plasma evolution, and is more apparent at lower oxygen partial pressures. At higher oxygen partial pressures, significant variation in plume morphology is noticed for UO species, which can be attributed to the higher oxide (UxOy) formation further from the target. The monochromatic images of U atoms and UO molecules and corresponding spectral features at various oxygen partial pressures presented here provide unique insight into gas-phase, high-temperature U oxidation and chemistry, with implications for a wide range of nuclear applications, from stand-off detection of radioisotopes to forensics and safeguards.
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- 2019
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14. Animal Salmonella Surveillance in Peninsular Malaysia, 1981-1985
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Joseph, P. G., Sivanandan, S. P., and Yee, Ham Thong
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- 1988
15. Hydrogen isotopic analysis of nuclear reactor materials using ultrafast laser-induced breakdown spectroscopy
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Sivanandan S. Harilal, Elizabeth J. Kautz, Arun Devaraj, and David J. Senor
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Laser ablation ,Argon ,Materials science ,Hydrogen ,business.industry ,chemistry.chemical_element ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,010309 optics ,Hydrogen storage ,Optics ,Deuterium ,chemistry ,0103 physical sciences ,Physics::Atomic Physics ,Laser-induced breakdown spectroscopy ,Atomic physics ,0210 nano-technology ,business ,Spectroscopy ,Doppler broadening - Abstract
Laser-induced breakdown spectroscopy is a promising method for rapidly measuring hydrogen and its isotopes, critical to a wide range of disciplines (e.g. nuclear energy, hydrogen storage). However, line broadening can hinder the ability to detect finely spaced isotopic shifts. Here, the effects of varying plasma generation conditions (nanosecond versus femtosecond laser ablation) and ambient environments (argon versus helium gas) on spectral features generated from Zircaloy-4 targets with varying hydrogen isotopic compositions were studied. Time-resolved 2D spectral imaging was employed to detail the spatial distribution of species throughout plasma evolution. Results highlight that hydrogen and deuterium isotopic shifts can be measured with minimal spectral broadening in a ∼ 10 Torr helium gas environment using ultrafast laser-produced plasmas.
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- 2021
16. Burst-mode dual-comb spectroscopy
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Yu Zhang, Sivanandan S. Harilal, Jeremy Yeak, R. Jason Jones, Caroline Lecaplain, Reagan R. D. Weeks, and Mark C. Phillips
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Laser ablation ,Materials science ,business.industry ,02 engineering and technology ,Burst mode (photography) ,021001 nanoscience & nanotechnology ,01 natural sciences ,Multiplexing ,Atomic and Molecular Physics, and Optics ,Fourier transform spectroscopy ,010309 optics ,Optics ,Transmission (telecommunications) ,0103 physical sciences ,Transient (oscillation) ,0210 nano-technology ,Absorption (electromagnetic radiation) ,business ,Spectroscopy - Abstract
We introduce a new, to the best of our knowledge, modality of dual-comb spectroscopy (DCS) that enables a simplified and powerful new approach for time-resolved measurements with increased acquisition rates. This “burst mode” form of DCS relies on the multiplexing of each probe pulse into a short train of pulses. With this approach we demonstrate a time-resolved series of absorption-based spectroscopic measurements of a laser-induced plasma using only a single laser ablation shot and identify 22 Nd lines not previously reported in the literature. The transmission spectra spanned 3.1 THz and were acquired at an effective acquisition rate of 25 kHz with 40 µs time resolution. This simple modification to ∼ 100 M H z level dual-comb systems provides a flexible approach for studying transient and low-duty-cycle events such as laser-induced plasmas, combustion, and explosive reactions.
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- 2021
17. Intermittent or daily short course chemotherapy for tuberculosis in children: Meta-analysis of randomized controlled trials
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Ramesh Menon, P., Lodha, R., Sivanandan, S., and Kabra, S. K.
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- 2010
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18. Screening for Anti-Dengue Leads from Euphorbia hirta L. through In Silico Methods.
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CHARUVIL, K. B., SIVANANDAN, S., and LEKSHMI, RADHA KESAVAN
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- *
DENGUE , *ARBOVIRUS diseases , *BIOACTIVE compounds , *DENGUE viruses , *EUPHORBIA , *VIRUS diseases , *METABOLITES - Abstract
Dengue is a vector-borne viral disease caused by Dengue virus. Current treatment and medicine are inadequate to eradicate the vector mosquitoes or to prevent the disease. Traditional healers have remedies for almost all ailments using natural products and plants. The well-known medicinal plant Euphorbia hirta L. is one of the herbs conventionally used for anti-dengue treatment even if the active compound responsible for the exact activity of the plant against the disease is not known. The plant is a rich source of various secondary metabolites. In silico screening of 76 small molecules of drug-value belongs to alkaloids, polyphenols and terpenes derived from the plant against dengue virus non-structural protein-5 Mtaseand human inosine 5'-monophosphate dehydrogenase-II determined 16 biologically active compounds with possible activity to fight against dengue virus. Based on the therapeutic importance and drug-likeness parameters, two best leads, 2-beta, 16-alpha, 19-trihydroxy-ent-kaurane and kaempferol were selected as promising candidates for developing anti-dengue drugs. [ABSTRACT FROM AUTHOR]
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- 2022
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19. Standoff chemical plume detection in turbulent atmospheric conditions with a swept-wavelength external cavity quantum cascade laser
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Mark C. Phillips, Sivanandan S. Harilal, Jeremy Yeak, R. Jason Jones, and Bruce E. Bernacki
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Freon ,Materials science ,Absorption spectroscopy ,Infrared ,business.industry ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,Spectral line ,Plume ,law.invention ,010309 optics ,Wavelength ,Optics ,law ,0103 physical sciences ,0210 nano-technology ,business ,Quantum cascade laser ,Noise (radio) - Abstract
Rapid and sensitive standoff measurement techniques are needed for detection of trace chemicals in outdoor plume releases, for example from industrial emissions, unintended chemical leaks or spills, burning of biomass materials, or chemical warfare attacks. Here, we present results from 235 m standoff detection of transient plumes for 5 gas-phase chemicals: Freon 152a (1,1-difluoroethane), Freon 134a (1,1,1,2-tetrafluoroethane), methanol (CH3OH), nitrous oxide (N2O), and ammonia (NH3). A swept-wavelength external cavity quantum cascade laser (ECQCL) measures infrared absorption spectra over the range 955-1195 cm−1 (8.37- 10.47 µm), from which chemical concentrations are determined via spectral fits. The fast 400 Hz scan rate of the swept-ECQCL enables measurement above the turbulence time-scales, reducing noise and allowing plume fluctuations to be measured. For high-speed plume detection, noise-equivalent column densities of 1-2 ppm*m are demonstrated with 2.5 ms time resolution, improving to 100-400 ppb*m with 100 ms averaging.
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- 2020
20. Expansion dynamics and chemistry evolution in ultrafast laser filament produced plasmas
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Sivanandan S. Harilal, Bruce E. Bernacki, Jeremy Yeak, Mark C. Phillips, and Elizabeth J. Kautz
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Laser ablation ,010401 analytical chemistry ,General Physics and Astronomy ,02 engineering and technology ,Plasma ,021001 nanoscience & nanotechnology ,Laser ,01 natural sciences ,0104 chemical sciences ,Plume ,law.invention ,Protein filament ,law ,Femtosecond ,Physical and Theoretical Chemistry ,Atomic physics ,0210 nano-technology ,Spectroscopy ,Ultrashort pulse - Abstract
Laser ablation in conjunction with optical emission spectroscopy is a potential non-contact, stand-off detection method for all elements in the periodic table and certain isotopes such as radionuclides. Currently, significant development efforts are on-going to use ultrafast laser filaments for remote detection of materials. The application of filaments is of particular interest in extending the range of stand-off capability associated with elemental and isotopic detection via laser-induced breakdown spectroscopy. In this study, we characterize the expansion dynamics and chemical evolution of filament-produced uranium (U) plasmas. Laser filaments are generated in the laboratory by loosely focusing 35 femtosecond (fs), 6 milli Joule (mJ) pulses in air. Time-resolved, two-dimensional plume and spectral imaging was performed to study hydrodynamics and evolution of U atomic and UO molecular emission in filament-produced U plasmas. Our results highlight that filament ablation of U plasmas gives a cylindrical plume morphology with an appearance of plume splitting into slow and fast moving components at later times of its evolution. Emission from the slow-moving component shows no distinct spectral features (i.e. broadband-like) and is contributed in part by nanoparticles generated during ultrafast laser ablation. Additionally, we find U atoms and U oxide molecules (i.e. UO, UxOy) co-exist in the filament produced plasma, which can be attributed to the generation of low-temperature plasma conditions during filament ablation.
- Published
- 2020
21. A community effort to create standards for evaluating tumor subclonal reconstruction
- Author
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Salcedo, A, Tarabichi, M, Espiritu, SMG, Deshwar, AG, David, M, Wilson, NM, Dentro, S, Wintersinger, JA, Liu, LY, Ko, M, Sivanandan, S, Zhang, H, Zhu, K, Ou Yang, T-H, Chilton, JM, Buchanan, A, Lalansingh, CM, P'ng, C, Anghel, CV, Umar, I, Lo, B, Zou, W, Simpson, JT, Stuart, JM, Anastassiou, D, Guan, Y, Ewing, AD, Ellrott, K, Wedge, DC, Morris, Q, Van Loo, P, Boutros, PC, Jha, A, Huang, T, Yang, T-P, Peifer, M, Sahinalp, C, Malikic, S, Vazquez-Garcia, I, Mustonen, V, Yang, H-T, Lee, K-R, Ji, Y, Sengupta, S, Rudewicz, J, Nikolski, M, Schaeverbeke, Q, Yuan, K, Markowetz, F, Macintyre, G, Cmero, M, Chaudhary, B, Leshchiner, I, Livitz, D, Getz, G, Loher, P, Yu, K, Wang, W, Zhu, H, Salcedo, A, Tarabichi, M, Espiritu, SMG, Deshwar, AG, David, M, Wilson, NM, Dentro, S, Wintersinger, JA, Liu, LY, Ko, M, Sivanandan, S, Zhang, H, Zhu, K, Ou Yang, T-H, Chilton, JM, Buchanan, A, Lalansingh, CM, P'ng, C, Anghel, CV, Umar, I, Lo, B, Zou, W, Simpson, JT, Stuart, JM, Anastassiou, D, Guan, Y, Ewing, AD, Ellrott, K, Wedge, DC, Morris, Q, Van Loo, P, Boutros, PC, Jha, A, Huang, T, Yang, T-P, Peifer, M, Sahinalp, C, Malikic, S, Vazquez-Garcia, I, Mustonen, V, Yang, H-T, Lee, K-R, Ji, Y, Sengupta, S, Rudewicz, J, Nikolski, M, Schaeverbeke, Q, Yuan, K, Markowetz, F, Macintyre, G, Cmero, M, Chaudhary, B, Leshchiner, I, Livitz, D, Getz, G, Loher, P, Yu, K, Wang, W, and Zhu, H
- Abstract
Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.
- Published
- 2020
22. Spatial and temporal evolution of argon sparks
- Author
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Harilal, Sivanandan S.
- Subjects
Optics -- Research ,Astronomy ,Physics - Abstract
Optical emission spectroscopic studies of laser-created argon sparks are carried out. Pulses of 532 nm and 8 ns from a frequency-doubled Nd:YAG laser are used to create an argon spark at 1 atm. Gated photography of 2 ns is used to investigate spark evolution at early times. Electron temperature and density measurements are made from the spectral data. The Stark broadening of emission lines is used to determine the electron density, and the Boltzmann plot of the singly ionized argon-line intensities is exploited for determination of the electron temperature. The dependence on electron temperature and density on different experimental parameters, such as distance from the focal point, delay time after the initiation of the spark, and laser energy, are discussed. OCIS codes: 140.3440, 300.6550, 300.6500, 300.2140.
- Published
- 2004
23. Standoff chemical plume detection in turbulent atmospheric conditions with a swept-wavelength external cavity quantum cascade laser
- Author
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Phillips, Mark C., primary, Bernacki, Bruce E., additional, Harilal, Sivanandan S., additional, Yeak, Jeremy, additional, and Jones, R. Jason, additional
- Published
- 2020
- Full Text
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24. Impact of oxygen chemistry on the emission and fluorescence spectroscopy of laser ablation plumes
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Sivanandan S. Harilal, K. C. Hartig, Brian E. Brumfield, and Mark C. Phillips
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Laser ablation ,Atmospheric pressure ,010401 analytical chemistry ,Analytical chemistry ,chemistry.chemical_element ,Partial pressure ,01 natural sciences ,Oxygen ,Emission intensity ,Atomic and Molecular Physics, and Optics ,Fluorescence spectroscopy ,0104 chemical sciences ,Analytical Chemistry ,010309 optics ,chemistry ,0103 physical sciences ,Laser-induced breakdown spectroscopy ,Spectroscopy ,Instrumentation - Abstract
Oxygen present in the ambient gas medium may affect both laser-induced breakdown spectroscopy (LIBS) and laser-induced fluorescence (LIF) emission through a reduction of emission intensity and persistence. In this study, an evaluation is made on the role of oxygen in the ambient environment under atmospheric pressure conditions in LIBS and laser ablation (LA)-LIF emission. To generate plasmas, 1064 nm, 10 ns pulses were focused on an aluminum alloy sample. LIF was performed by frequency scanning a CW laser over the 396.15 nm (3s 2 4s 2 S 1/2 → 3s 2 3p 2 P° 3/2 ) Al I transition. Time-resolved emission and fluorescence signals were recorded to evaluate the variation in emission intensity caused by the presence of oxygen. The oxygen partial pressure ( p o ) in the atmospheric pressure environment using N 2 as the makeup gas was varied from 0 to 400 Torr O 2 . 2D–fluorescence spectroscopy images were obtained for various oxygen concentrations for simultaneous evaluation of the emission and excitation spectral features. Results showed that the presence of oxygen in the ambient environment reduces the persistence of the LIBS and LIF emission through an oxidation process that depletes the density of atomic species within the resulting laser-produced plasma (LPP) plume.
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- 2017
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25. Physical conditions for UO formation in laser-produced uranium plumes
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Sivanandan S. Harilal, Mark C. Phillips, Bruce E. Bernacki, Elizabeth J. Kautz, P. J. Skrodzki, Milos Burger, and Igor Jovanovic
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Materials science ,Analytical chemistry ,General Physics and Astronomy ,chemistry.chemical_element ,Monoxide ,02 engineering and technology ,Partial pressure ,Plasma ,Atmospheric temperature range ,Uranium ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Redox ,Oxygen ,0104 chemical sciences ,chemistry ,Torr ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
We investigate the oxidation of uranium (U) species, the physical conditions leading to uranium monoxide (UO) formation and the interplay between plume hydrodynamics and plasma chemistry in a laser-produced U plasma. Plasmas are produced by ablation of metallic U using nanosecond laser pulses. An ambient gas environment with varying oxygen partial pressures in 100 Torr inert Ar gas is used for controlling the plasma oxidation chemistry. Optical emission spectroscopic analysis of U atomic and monoxide species shows a reduction in the emission intensity and persistence with increasing oxygen partial pressure. Spectral modelling is used for identifying the physical conditions in the plasma that favor UO formation. The optimal temperature for UO formation is found to be in the temperature range of ∼1500-5000 K. The spectrally integrated and spectrally filtered (monochromatic) imaging of U atomic and molecular species reveals the evolutionary paths of various species in the plasma. Our results also highlight that oxidation in U plasmas predominantly occurs at the cooler periphery and is delayed with respect to plasma formation, and the dissipation of molecular species strongly depends on oxygen partial pressure.
- Published
- 2019
26. Characterization of a Laser-Induced Plasma Using Time-Resolved Dual-Frequency-Comb Spectroscopy
- Author
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Yu Zhang, Caroline Lecaplain, Reagan R. D. Weeks, Jeremy Yeak, Sivanandan S. Harilal, Mark C. Phillips, and R. Jason Jones
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- 2019
- Full Text
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27. Time-Resolved Dual Frequency Comb Spectroscopy for Broadband Multi-Species Detection in Laser-Induced Plasmas
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Caroline Lecaplain, Yu Zhang, Reagan R. D. Weeks, Jeremy Yeak, Sivanandan S. Harilal, Mark C. Phillips, and R. Jason Jones
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- 2019
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28. Standoff 250 m Open-path Detection of Chemical Plumes Using a Broadband Swept-ECQCL
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Mark C. Phillips, Bruce E. Bernacki, Sivanandan S. Harilal, Jeremy Yeak, and R. Jason Jones
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- 2019
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29. Time-Resolved Dual Frequency Comb Phase Spectroscopy of Laser-Induced Plasmas
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Reagan R. D. Weeks, Yu Zhang, Caroline Lecaplain, Jeremy Yeak, Sivanandan S. Harilal, Mark C. Phillips, and R. Jason Jones
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- 2019
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30. Significance of ambient conditions in uranium absorption and emission features of laser ablation plasmas
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N.P. Shah, Brian E. Brumfield, Mark C. Phillips, N. L. LaHaye, P. J. Skrodzki, Sivanandan S. Harilal, K. C. Hartig, Nicholas Taylor, and Igor Jovanovic
- Subjects
education.field_of_study ,Laser ablation ,Absorption spectroscopy ,Chemistry ,010401 analytical chemistry ,Population ,Analytical chemistry ,02 engineering and technology ,Plasma ,021001 nanoscience & nanotechnology ,Laser ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Analytical Chemistry ,law.invention ,chemistry.chemical_compound ,law ,Uranium oxide ,Laser-induced breakdown spectroscopy ,0210 nano-technology ,education ,Absorption (electromagnetic radiation) ,Instrumentation ,Spectroscopy - Abstract
This study employs laser ablation (LA) to investigate mechanisms for U optical signal variation under various environmental conditions during laser absorption spectroscopy (LAS) and optical emission spectroscopy (OES). Potential mechanisms explored for signal quenching related to ambient conditions include plasma chemistry (e.g., uranium oxide formation), ambient gas confinement effects, and other collisional interactions between plasma constituents and the ambient gas. LA-LAS studies show that the persistence of the U ground state population is significantly reduced in the presence of air ambient compared to nitrogen. LA-OES yields congested spectra from which the U I 356.18 nm transition is prominent and serves as the basis for signal tracking. LA-OES signal and persistence vary negligibly between the test gases (air and N 2 ), unlike the LA-LAS results. The plume hydrodynamic features and plume fundamental properties showed similar results in both air and nitrogen ambient. Investigation of U oxide formation in the laser-produced plasma suggests that low U concentration in a sample hinders consistent detection of UO molecular spectra.
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- 2016
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31. Standoff detection of chemical plumes from high explosive open detonations using a swept-wavelength external cavity quantum cascade laser
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R. Jason Jones, Bruce E. Bernacki, Jeremy Yeak, Sonia Wharton, Sivanandan S. Harilal, and Mark C. Phillips
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010302 applied physics ,Materials science ,Explosive material ,business.industry ,Detonation ,General Physics and Astronomy ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Combustion ,01 natural sciences ,Spectral line ,Plume ,law.invention ,Wavelength ,Optics ,law ,0103 physical sciences ,0210 nano-technology ,Absorption (electromagnetic radiation) ,business ,Quantum cascade laser - Abstract
A swept-wavelength external cavity quantum cascade laser (ECQCL) is used to perform standoff detection of combustion gases in a plume generated from an outdoor high-explosive (HE) open detonation. The swept-ECQCL system was located at a standoff distance of 830 m from a 41 kg charge of LX-14 (polymer-bonded high explosive) and was used to measure the infrared transmission/absorption through the post-detonation plume as it propagated through the beam path. The swept-ECQCL was operated continuously to record broadband absorption spectra at a 200 Hz rate over a spectral range from 2050 to 2230 cm−1 (4.48–4.88 μm). Fitting of measured spectra was used to determine time-resolved column densities of CO, CO2, H2O, and N2O. Analysis of visible video imagery was used to provide timing correlations and to estimate plume dimensions, from which gas mixing ratios were estimated. Measured emission factors and modified combustion efficiency show good agreement with previously reported values.
- Published
- 2020
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32. Hyperfine structures and isotopic shifts of uranium transitions using tunable laser spectroscopy of laser ablation plumes
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J.B. Martin, C. M. Murzyn, Sivanandan S. Harilal, and Mark C. Phillips
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010302 applied physics ,Materials science ,Laser ablation ,Absorption spectroscopy ,010401 analytical chemistry ,Analytical chemistry ,Physics::Optics ,Laser ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Analytical Chemistry ,law.invention ,law ,0103 physical sciences ,Physics::Atomic Physics ,Spectroscopy ,Laser-induced fluorescence ,Absorption (electromagnetic radiation) ,Instrumentation ,Hyperfine structure ,Tunable laser - Abstract
We report isotopic shifts and hyperfine structures of selected U transitions employing tunable spectroscopy viz: laser-induced fluorescence and laser absorption spectroscopy of laser ablation plumes. The plasmas were produced during ns laser ablation on a natural U metal target which contains 0.73% 235U. Our results show that isotopic shifts between 238U and 235U are entangled with hyperfine structures of 235U. Measurements obtained using laser-induced fluorescence are affected by the high absorbance of 238U. Time-resolved laser absorption spectroscopy is carried out for evaluating the optical absorption and estimating the hyperfine constants.
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- 2020
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33. Elucidating uranium monoxide spectral features from a laser-produced plasma
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Brian E. Brumfield, Nick G Glumac, Sivanandan S. Harilal, and Mark C. Phillips
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inorganic chemicals ,Materials science ,Analytical chemistry ,chemistry.chemical_element ,complex mixtures ,01 natural sciences ,Pyrophoricity ,law.invention ,010309 optics ,chemistry.chemical_compound ,Optics ,law ,0103 physical sciences ,Uranium oxide ,Laser-induced fluorescence ,business.industry ,010401 analytical chemistry ,technology, industry, and agriculture ,Monoxide ,Plasma ,Uranium ,Laser ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,chemistry ,business ,Visible spectrum - Abstract
Uranium, because of its pyrophoricity, oxidizes rapidly in an oxygen-containing high-temperature environment. However, so far, the identification of uranium oxide (UO) emission from a laser-produced plasma system is limited to a spectral feature around 593.55 nm. The aim of this study is to elucidate UO emission features in the visible spectral regime from uranium plasmas generated in an environment with varying oxygen concentrations. The plasmas are produced by focusing nanosecond laser pulses on a uranium metal target in a controlled ambient environment. Space- and time-resolved optical emission spectroscopic investigations are used for isolating UO molecular emission structures from crowded U atomic line emission. Our studies highlight that the emission from a U plasma, even in the presence of trace oxygen is accompanied by a strong background-like emission with partially resolved bands from uranium monoxide and higher oxides. We also report several UO spectral emission bands in the visible spectral region.
- Published
- 2018
34. Dual-comb spectroscopy of laser-induced plasmas
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Jeremy Yeak, R. Jason Jones, Jenna Bergevin, Sivanandan S. Harilal, Tsung Han Wu, Mark C. Phillips, and Brian E. Brumfield
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Materials science ,Science ,Physics::Optics ,General Physics and Astronomy ,Atomic spectroscopy ,02 engineering and technology ,01 natural sciences ,Isotopes of rubidium ,Article ,General Biochemistry, Genetics and Molecular Biology ,law.invention ,010309 optics ,Frequency comb ,law ,0103 physical sciences ,Physics::Atomic Physics ,Spectral resolution ,lcsh:Science ,Spectroscopy ,Hyperfine structure ,Line (formation) ,Multidisciplinary ,Laser ablation ,Isotope ,business.industry ,General Chemistry ,Plasma ,021001 nanoscience & nanotechnology ,Laser ,Optoelectronics ,lcsh:Q ,Atomic physics ,0210 nano-technology ,Ground state ,business - Abstract
Dual-comb spectroscopy has become a powerful spectroscopic technique in applications that rely on its broad spectral coverage combined with high frequency resolution capabilities. Experiments to date have primarily focused on detection and analysis of multiple gas species under semi-static conditions, with applications ranging from environmental monitoring of greenhouse gases to high-resolution molecular spectroscopy. Here, we utilize dual-comb spectroscopy to demonstrate broadband, high-resolution, and time-resolved measurements in a laser-induced plasma. As a demonstration, we simultaneously detect trace amounts of Rb and K in solid samples with a single laser ablation shot, with transitions separated by over 6 THz (13 nm) and spectral resolution sufficient to resolve isotopic and ground state hyperfine splittings of the Rb D2 line. This new spectroscopic approach offers the broad spectral coverage found in the powerful techniques of laser-induced breakdown spectroscopy (LIBS) while providing the high-resolution and accuracy of cw laser-based spectroscopies., Dual-comb spectroscopy has become a valuable tool for broadband high-resolution measurements. Here Bergevin et al. apply this technique to a laser-induced plasma detecting different species in a solid sample with a spectral resolution sufficient to resolve hyperfine splitting of the Rb D2 line.
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- 2018
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35. Standoff analysis of laser-produced plasmas using laser-induced fluorescence
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Brian E. Brumfield, Mark C. Phillips, and Sivanandan S. Harilal
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Materials science ,Laser ablation ,business.industry ,010401 analytical chemistry ,Nanosecond ,Laser ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,law.invention ,010309 optics ,Optics ,law ,0103 physical sciences ,Continuous wave ,Spectral resolution ,business ,Spectroscopy ,Laser-induced fluorescence ,Tunable laser - Abstract
We report the use of laser-induced fluorescence (LIF) of laser ablation (LA) plumes for standoff applications. The standoff analysis of Al, as major and minor species in samples, is performed in a nanosecond laser-produced plasma created at a distance of ∼10 m. The LIF of LA plumes is carried out by resonantly exciting an Al transition at 394.4 nm (S1/22−P1/22) using a continuous wave (cw) tunable laser and by collecting the direct-line fluorescence signal at 396.15 nm. The spectral resolution of LIF is obtained by scanning the cw tunable LIF laser across the selected Al transition. Our results highlight that LIF provides enhanced signal intensity, emission persistence, and spectral resolution when compared to thermally excited emission.
- Published
- 2018
36. Spatio-temporal evolution of uranium emission in laser-produced plasmas
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Mark C. Phillips, N. L. LaHaye, Prasoon K. Diwakar, and Sivanandan S. Harilal
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Laser ablation ,Chemistry ,Laser ,Spectral line ,Atomic and Molecular Physics, and Optics ,law.invention ,Analytical Chemistry ,symbols.namesake ,Stark effect ,law ,Excited state ,symbols ,Emission spectrum ,Atomic physics ,Spectroscopy ,Instrumentation ,Ambient pressure - Abstract
Laser-induced plasma spectroscopy provides much impetus as a nuclear forensics tool because of its capability of standoff detection and real-time analysis. However, special nuclear materials like U, Pu, etc. provide very crowded spectra and, when combined with shifts and broadening of spectral lines caused by ambient atmospheric operation, generate a complex plasma spectroscopy system. We explored the spatio-temporal evolution of excited U species in a laser ablation plume under various ambient pressure conditions. Plasmas were generated using 1064 nm, 6 ns pulses from a Nd:YAG laser on a U containing glass matrix target. The role of air ambient pressure on U line intensities, signal-to-background ratios, and linewidths were investigated. Spatially and temporally resolved optical time-of-flight emission spectroscopy of excited uranium atoms were used for studying the expansion hydrodynamics and the persistence of U species in the plume. Our results showed that U emission linewidths increased with pressure due to increased Stark broadening; however, the broadening was less than that for Ca. A comparison with U emission features in the presence of an inert gas showed the persistence of U species in plasmas in ambient air is significantly reduced; this could be due to oxide and other reactive species formation.
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- 2015
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37. Collimation of laser-produced plasmas using axial magnetic field
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Sivanandan S. Harilal, Tomas Mocek, Ahmed Hassanein, S. M. Hassan, Akira Endo, and Amitava Roy
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Physics ,Field (physics) ,Field line ,business.industry ,Plasma ,Condensed Matter Physics ,Laser ,Atomic and Molecular Physics, and Optics ,Plume ,Magnetic field ,law.invention ,Optics ,law ,Electron temperature ,Emission spectrum ,Electrical and Electronic Engineering ,Atomic physics ,business - Abstract
We investigated the expansion dynamics of laser-produced plasmas expanding into an axial magnetic field. Plasmas were generated by focusing 1.064 μm Nd:YAG laser pulses onto a planar tin target in vacuum and allowed to expand into a 0.5 T magnetic field where the field lines were aligned along the plume expansion direction. Gated images employing an intensified charge-coupled device showed focusing of the plasma plume, which were also compared with results, obtained using particle-in-cell modeling methods. The estimated density and temperature of the plasma plumes employing emission spectroscopy revealed significant changes in the presence and absence of the 0.5 T magnetic field. In the presence of the field, the electron temperature is increased with distance from the target, while the density showed opposite effects.
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- 2015
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38. Helium bubble formation in ultrafine and nanocrystalline tungsten under different extreme conditions
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Khalid Hattar, Sivanandan S. Harilal, Graeme Greaves, Ahmed Hassanein, Jonathan A. Hinks, and Osman El-Atwani
- Subjects
Nuclear and High Energy Physics ,Materials science ,chemistry.chemical_element ,Tungsten ,Nanocrystalline material ,Condensed Matter::Materials Science ,Crystallography ,Materials Science(all) ,Nuclear Energy and Engineering ,chemistry ,Transmission electron microscopy ,Chemical physics ,Vacancy defect ,Physics::Atomic and Molecular Clusters ,General Materials Science ,Grain boundary ,Irradiation ,Liquid bubble ,QC ,Helium - Abstract
We have investigated the effects of helium ion irradiation energy and sample temperature on the performance of grain boundaries as helium sinks in ultrafine grained and nanocrystalline tungsten. Irradiations were performed at displacement and non-displacement energies and at temperatures above and below that required for vacancy migration. Microstructural investigations were performed using Transmission Electron Microscopy (TEM) combined with either in-situ or ex-situ ion irradiation. Under helium irradiation at an energy which does not cause atomic displacements in tungsten (70 eV), regardless of temperature and thus vacancy migration conditions, bubbles were uniformly distributed with no preferential bubble formation on grain boundaries. At energies that can cause displacements, bubbles were observed to be preferentially formed on the grain boundaries only at high temperatures where vacancy migration occurs. Under these conditions, the decoration of grain boundaries with large facetted bubbles occurred on nanocrystalline grains with dimensions less than 60 nm. We discuss the importance of vacancy supply and the formation and migration of radiation-induced defects on the performance of grain boundaries as helium sinks and the resulting irradiation tolerance of ultrafine grained and nanocrystalline tungsten to bubble formation.
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- 2015
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39. In-situ TEM/heavy ion irradiation on ultrafine-and nanocrystalline-grained tungsten: Effect of 3MeV Si, Cu and W ions
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Khalid Hattar, Anastassiya Suslova, T.J. Novakowski, Osman El-Atwani, Sivanandan S. Harilal, Mert Efe, and Ahmed Hassanein
- Subjects
Materials science ,Mechanical Engineering ,Radiochemistry ,Analytical chemistry ,chemistry.chemical_element ,Tungsten ,Condensed Matter Physics ,Fluence ,Nanocrystalline material ,Ion ,chemistry ,Materials Science(all) ,Mechanics of Materials ,Saturation (graph theory) ,General Materials Science ,Grain boundary ,Absorption (logic) ,Irradiation - Abstract
Plasma facing components for future fusion applications will experience helium- and neutron-induced structural damage. Direct observation of the in-situ dynamic response of such components during particle beam exposure assists in fundamental understanding of the physical phenomena that give rise to their irradiation resistance. We investigated the response of ultrafine and nanocrystalline-grained tungsten to 3 MeV heavy ion irradiations (Si{sup 2} {sup +}, Cu{sup 3} {sup +} and W{sup 4} {sup +}) for the simulation of neutron-induced damage through transmutation reactions via in-situ ion irradiation–transmission electron microscopy experiments. Defect densities as a function of irradiation dose (displacement per atom) and fluence were studied. Four stages of defect densities evolution were observed, as a function of irradiation dose: 1) increase in defect density at lower doses, 2) higher defect production rate at the intermediate doses (before saturation), 3) reaching the maximum value, and 4) drop of the defect density in the case of W{sup 4} {sup +}, possibly due to defect coalescence and grain boundary absorption of small defect clusters. The effect of grain size on defect densities was investigated and found that defect densities were independent of grain size in the ultrafine and nanocrystalline region (60–400 nm). These results were comparedmore » to other heavy ion irradiation studies of structural materials. - Graphical abstract: Bright-field TEM micrographs and defect densities of UF and NC tungsten grains irradiated with a) Si{sup +} {sup 2} at 1.03 dpa: 1) 140 nm — 7.2 × 10{sup −} {sup 3} defects/nm{sup 2}, 2) 122 nm — 6.9 × 10{sup −} {sup 3} defects/nm{sup 2}, 3) 63 nm — 4.7 × 10{sup −} {sup 3} defects/nm{sup 2}, and 4) 367 nm — 6.4 × 10{sup −} {sup 3} defects/nm{sup 2}; b) Cu{sup +} {sup 3} to 3.79 dpa: 1) 228 nm — 4.3 × 10{sup −} {sup 3} defects/nm{sup 2}; 2) 202 nm — 5.9 × 10{sup −} {sup 3} defects/nm{sup 2}; and 3) 137 nm — 6.1 × 10{sup −} {sup 3} defects/nm{sup 2}; and c) W{sup +} {sup 4} to 5.72 dpa: 1) 372 nm — 2.3 × 10{sup −} {sup 3} defects/nm{sup 2} and 2) 128 nm — 4.5 × 10{sup −} {sup 3} defects/nm{sup 2}. - Highlights: • Heavy ion irradiations were performed on UF and NC grained tungsten. • Irradiations were performed with 3 MeV (Si{sup 2} {sup +}, Cu{sup 3} {sup +} and W{sup 4} {sup +}) ions at RT. • Defect density vs. dpa demonstrated four different stages in the case of W{sup 4} {sup +} irradiation. • Defect coalescence and absorption by the grain boundaries were observed after a dose of 3 dpa during W{sup 4} {sup +} irradiation. • No correlation existed between the grain width and the defect density for the UF and NC region.« less
- Published
- 2015
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40. A Potential Lead from Acacia nilotica (L.) Delile Against Hepatitis C virus - An In silico Approach.
- Author
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LEKSHMI, RADHA KESAVAN, CHARUVIL, K. B., and SIVANANDAN, S.
- Subjects
HEPATITIS C virus ,ACACIA nilotica ,HEPATITIS C vaccines ,DRUG side effects ,RIBAVIRIN ,HEPATITIS C ,PHARMACEUTICAL chemistry - Abstract
Hepatitis C virus infection is the leading cause of chronic liver disease and hepatocellular carcinoma. There is no effective vaccine for hepatitis C virus prevention despite the fact that several vaccines are under development. Currently, the Unites States Food and drug administration approved combination drugs for all genotypes that would help to cure the infection more quickly and efficiently than ever before. However, the high costs, development of various side effects and emergence of drug resistant strains demand the need for new anti-viral to treat different stages of the hepatitis C virus life cycle. Focussing drug candidate from herbal ingredients is the novel approach of pharmaceutical science over the past few decades. In this perspective, the present study aimed to investigate the phytochemicals present in Acacia nilotica (L.) Delile against hepatitis C virus non-structural protein3-4A serine protease. The N-terminal Protease domain of non-structural protein3 along with non-structural protein4A protein is responsible for the cleavage of four polypeptide junctions' viz., non-structural protein3-4A, non-structural protein4A-non-structural protein4B, non-structural protein4B-non-structural protein5A and non-structural protein5A-5B that are essential for viral genome replication. Hence targeting non-structural protein3-4A blocks the replication process. Here, in silico molecular docking study was executed to estimate the efficacy of phytochemicals along with the two Food and drug administration approved hepatitis C virus non-structural protein3-4A inhibitors-Grazoprevir and simeprevir as reference compounds against the selected target. Docking results revealed that about six phytochemicals (+)-Catechin 5-Gallate, Acacetin, (+)-Mollisacacidin, Catechin, Acalinol A and Chlorogenic acid are better than the reference compounds and hence selected as hits. Further, the hit molecules were filtered through analysing druglikeness properties, pharmacokinetics, medicinal chemistry friendliness including pan assay interference compounds and Brenk structural alerts, leadlikeness and finally prediction of potential toxicity and toxic substructure to ascertain a lead molecule. The results obtained in the current study propose Acacetin as the lead molecule for further in vitro and in vivo study. [ABSTRACT FROM AUTHOR]
- Published
- 2021
41. Anti-Tuberculosis Activity in Punica granatum: In silico Validation and Identification of Lead Molecules.
- Author
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BASHEERA, SHEFIN, SIVANANDAN, S., and KAMALAN, B. C.
- Subjects
- *
POMEGRANATE , *MEDICAL botany , *MOLECULES , *PLANT species , *SYNTHETIC drugs , *SPINAL tuberculosis , *BINDING energy , *LEAD toxicology - Abstract
Discovery of novel drug against tuberculosis is inevitable since resistant bacterial strains are evolved against existing drugs and rapidly active single drug in short period is necessary for effective treatment. When compared to synthetic drugs, natural drugs particularly phytochemicals induce less side effects and long term stability. In Indian traditional medicine, several plant species have been used for treating tuberculosis and each plant species contains a plethora of phytochemicals. The efficacy of such treatment system and identification of the phytochemical with drug activity from plants has been seldom investigated scientifically. In this backdrop, the authors have validated the efficacy of anti-tuberculosis activity and identified lead molecule from a widely used plant species against several disease including tuberculosis, viz Punica granatum L. The four promising target proteins viz mycolyltransferase antigen protein 85C involved in cord factor synthesis, filamentous temperature sensitive protein Z involved in bacterial cell division, pantothenate kinase involved in co-enzyme A pathway and decaprenylphosphoryl β-D-ribofuranose-2 epimerase involved in the synthesis of virulent factor arabinan were docked with 243 phytochemicals derived from Punica granatum. The docked molecules having binding energy ≤-6 kcal/ mol were considered as active/hit molecules. The docked results showed that out of 243 phytochemicals, 126 have inhibitory activity on all selected target proteins. Further docking study using Glide and absorption, distribution, metabolism, excretion and toxicity studies revealed that the compound derived from the flowers, pomegranate can be recommended as the best lead compound against tuberculosis. [ABSTRACT FROM AUTHOR]
- Published
- 2021
42. Generation of nanoclusters by ultrafast laser ablation of Al: Molecular dynamics study
- Author
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Sivanandan S. Harilal, Alexander Miloshevsky, Phillip Dressman, Mark C. Phillips, and Gennady V. Miloshevsky
- Subjects
010302 applied physics ,Laser ablation ,Materials science ,Physics and Astronomy (miscellaneous) ,02 engineering and technology ,Plasma ,021001 nanoscience & nanotechnology ,Laser ,01 natural sciences ,Fluence ,Molecular physics ,law.invention ,Nanoclusters ,law ,Picosecond ,0103 physical sciences ,General Materials Science ,0210 nano-technology ,Ultrashort pulse ,Energy (signal processing) - Abstract
The laser ablation of materials induced by an ultrashort femtosecond pulse is a complex phenomenon, which depends on both the material properties and the properties of the laser pulse. A combination of molecular dynamics (MD) and momentum scaling model (MSM) methods is applied to a large atomic system to study the process of ultrafast laser-material interactions, behavior of matter in a highly nonequilibrium state, material disintegration, and formation of nanoclusters (NCs). Laser pulses with several fluences in the range from $500\phantom{\rule{0.16em}{0ex}}\mathrm{J}/{\mathrm{m}}^{2}$ to $5000\phantom{\rule{0.16em}{0ex}}\mathrm{J}/{\mathrm{m}}^{2}$ interacting with a large system of aluminum atoms are simulated. The response of Al to laser energy deposition is investigated within the finite-size laser spot. It is found that the shape of the plasma plume is dynamically changing during expansion. At several tens of picoseconds it can be characterized as a long hollow ellipsoid surrounded by Al atoms and NCs. The time evolution of NCs in the plume is investigated. The collisions between single Al atoms and generated NCs and fragmentation of large NCs determine the fractions of different-size NCs in the plume. The MD-MSM simulations show that laser fluence greatly affects the size distribution of NCs, their polar angles, and magnitude and direction vectors of NC velocities. These results and predictions are consistent, in many aspects, with the experimental data and previous MD simulations.
- Published
- 2017
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43. Evolution of uranium monoxide in femtosecond laser-induced uranium plasmas
- Author
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K. C. Hartig, Mark C. Phillips, Sivanandan S. Harilal, Igor Jovanovic, and Brian E. Brumfield
- Subjects
Laser ablation ,Materials science ,Atmospheric pressure ,business.industry ,010401 analytical chemistry ,Analytical chemistry ,Atomic emission spectroscopy ,chemistry.chemical_element ,Monoxide ,02 engineering and technology ,Uranium ,021001 nanoscience & nanotechnology ,Laser ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,law.invention ,Optics ,chemistry ,law ,Emission spectrum ,0210 nano-technology ,Spectroscopy ,business - Abstract
We report on the observation of uranium monoxide (UO) emission following fs laser ablation (LA) of a uranium metal sample. The formation and evolution of the molecular emission is studied under various ambient air pressures. Observation of UO emission spectra at a rarefied residual air pressure of ~1 Torr indicates that the UO molecule is readily formed in the expanding plasma with trace concentrations of oxygen present within the vacuum chamber. The persistence of the UO emission exceeded that of the atomic emission; however, the molecular emission was delayed in time compared to the atomic emission due to the necessary cooling and expansion of the plasma before the UO molecules can form.
- Published
- 2017
44. Characterization of uranium isotopes using laser ablation and tunable laser spectroscopy
- Author
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Sivanandan S. Harilal and Mark C. Phillips
- Subjects
X-ray laser ,Tunable diode laser absorption spectroscopy ,Materials science ,Laser ablation ,Isotopes of uranium ,Far-infrared laser ,Physics::Atomic and Molecular Clusters ,Analytical chemistry ,Physics::Optics ,Physics::Atomic Physics ,Laser-induced breakdown spectroscopy ,Atomic vapor laser isotope separation ,Tunable laser - Abstract
Recent results using nanosecond and femtosecond laser ablation combined with tunable laser absorption and fluorescence spectroscopy show the potential for rapid standoff characterization of uranium isotopes in solid samples at atmospheric pressure.
- Published
- 2017
- Full Text
- View/download PDF
45. Improvements in discrimination of bulk and trace elements in long-wavelength double pulse LIBS
- Author
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Sivanandan S. Harilal, Prasoon K. Diwakar, J. R. Freeman, and Ahmed Hassanein
- Subjects
Chemistry ,Pulse (signal processing) ,Analytical chemistry ,Plasma ,Laser ,Atomic and Molecular Physics, and Optics ,Analytical Chemistry ,law.invention ,Plume ,law ,Elemental analysis ,Figure of merit ,Laser-induced breakdown spectroscopy ,Instrumentation ,Spectroscopy ,Excitation - Abstract
In this work we study the effectiveness of long-wavelength heating in double pulse (DP) LIBS, quantitatively comparing figures of merit with those from traditional single pulse (SP) LIBS. The first laser pulse serves as the source of sample ablation, creating an aerosol-like plume that is subsequently reheated by the second laser pulse. At power densities used, the long-wavelength CO2 laser pulse does not ablate any of the solid sample in the atmospheric conditions investigated, meaning plasma emission and enhanced signal can be entirely attributed to the reheated plume rather than increased sample ablation. The signal discrimination was improved significantly using long-wavelength DP-LIBS. For bulk elemental analysis, DP-LIBS provided maximum enhancements of about 14 and 15 times for S/N and S/B, respectively, compared to SP-LIBS using the same quantity of ablated sample. For trace elemental analysis, maximum enhancements of about 7 and 4 times for S/N and S/B, respectively, were observed. These improvements are attributed to effective coupling between the second heating pulse and expanding plume and more efficient excitation of plume species than from the single pulse alone. Most significant improvements were observed in the case of low prepulse energy and minimal sample ablation. While bulk elemental analysis observed improvements for all prepulse energies studied, trace element discrimination only significantly improved for the lowest prepulse energy studied.
- Published
- 2014
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46. Characterization of high-explosive detonations using broadband infrared external cavity quantum cascade laser absorption spectroscopy
- Author
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Sivanandan S. Harilal, Brian E. Brumfield, Bruce E. Bernacki, Joel M. Schwallier, Mark C. Phillips, and Nick G Glumac
- Subjects
010302 applied physics ,Materials science ,Absorption spectroscopy ,Explosive material ,Opacity ,Infrared ,business.industry ,Far-infrared laser ,Detonation ,General Physics and Astronomy ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,law.invention ,Optics ,law ,0103 physical sciences ,0210 nano-technology ,Quantum cascade laser ,business ,Absorption (electromagnetic radiation) - Abstract
Infrared laser absorption spectroscopy provides a powerful tool for probing physical and chemical properties of high-explosive detonations. A broadly tunable swept-wavelength external cavity quantum cascade laser operating in the mid-wave infrared (MWIR) spectral region is used to measure transmission through explosive fireballs generated from 14 g charges of 4 different explosive types detonated in an enclosed chamber. Analysis of time-resolved transmission and emission at a 2 μs sampling rate shows the evolution of fireball infrared opacity in the first 10 ms after detonation. Broadband high-resolution absorption spectra acquired over the spectral range of 2050–2300 cm−1 (4.35–4.88 μm) at a 100 Hz rate are used to measure properties of fireball evolution over longer time scales out to 100 s. Path-integrated concentrations of combustion products CO, CO2, H2O, and N2O are measured and show evolutions over multiple time scales and significant differences between explosive types. Spectral analysis is used to characterize gas temperature and to measure broadband attenuation from absorption and scattering of particulates. Analysis of the results provides information on the MWIR optical properties, gaseous detonation/combustion products, and particulates throughout the explosive process including initial detonation, fireball expansion and cooling, and diffusive mixing in the chamber.
- Published
- 2019
- Full Text
- View/download PDF
47. Laser-produced uranium plasma characterization and Stark broadening measurements
- Author
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P. J. Skrodzki, Milos Burger, Mark C. Phillips, Sivanandan S. Harilal, and Igor Jovanovic
- Subjects
Physics ,Electron density ,chemistry.chemical_element ,Plasma ,Uranium ,Nanosecond ,Condensed Matter Physics ,Laser ,01 natural sciences ,010305 fluids & plasmas ,law.invention ,symbols.namesake ,chemistry ,Stark effect ,law ,0103 physical sciences ,symbols ,Emission spectrum ,Atomic physics ,010306 general physics ,Line (formation) - Abstract
This work reports the spatiotemporal diagnostics of uranium species in plasma plumes produced by nanosecond near-infrared laser pulses in a low-pressure environment. Spatially and temporally resolved emission spectroscopy experiments are combined with the modeling of uranium emission for investigating the dynamics of the plume. The Saha-Eggert equation and Boltzmann plots generated from numerous U I transitions are used to infer temperature. This work also reports the measurements of uranium Stark broadening parameters for U I 499.01 nm and U II 500.82 nm transitions. The Stark widths of select U transitions were measured by comparing their linewidths with the broadening of the O I 777.19 nm line. The electron density was found to be of the order of 1016 cm−3, while the temperature was found to be in the range of 3000–9000 K. In addition to enhancing the fundamental understanding of high-Z plasmas in reduced-pressure environments, the knowledge of Stark broadening parameters could improve the modeling capabilities and analytical performance of techniques that rely on emission plasma spectroscopy.
- Published
- 2019
- Full Text
- View/download PDF
48. Plume dynamics and gas-phase molecular formation in transient laser-produced uranium plasmas
- Author
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Brian E. Brumfield, Igor Jovanovic, Milos Burger, P. J. Skrodzki, Mark C. Phillips, Jeremy Yeak, and Sivanandan S. Harilal
- Subjects
inorganic chemicals ,Physics ,Argon ,Polyatomic ion ,technology, industry, and agriculture ,chemistry.chemical_element ,Monoxide ,Uranium ,Condensed Matter Physics ,complex mixtures ,Nitrogen ,Chemical reaction ,Oxygen ,Plume ,chemistry ,Chemical physics - Abstract
The dynamics of expansion, thermodynamics, and chemical reactions in laser-produced plasmas is of general interest for all laser ablation applications. This study investigates the complex morphology and behavior of reactive species in nanosecond laser-produced uranium plasmas. Comparing plasma morphology in various inert and reactive ambient gases provides information about the role of gas-phase chemistry in plume hydrodynamics. Background gases including nitrogen and argon foster collisional interactions leading to more significant plume confinement and the increase in persistence of uranium species. On the other hand, environments containing reactive gases such as oxygen promote chemical reactions between the plasma and ambient species. By comparing the expansion dynamics of uranium plumes in nitrogen, air, and argon, we discover that chemical reactions modify the hydrodynamics of the plume at later times of its evolution in the air background. Furthermore, we observe that varying the concentration of oxygen in the fill gas promotes different reaction pathways that lead to the formation of uranium oxides. The reaction pathways from atoms to diatomic to polyatomic molecules strongly vary with ambient oxygen concentration. Lower oxygen concentrations enhance the formation of uranium monoxide from atomic uranium, whereas higher oxygen concentrations tend to depopulate both atomic uranium and uranium monoxide concentrations through the formation of more complex uranium oxides.The dynamics of expansion, thermodynamics, and chemical reactions in laser-produced plasmas is of general interest for all laser ablation applications. This study investigates the complex morphology and behavior of reactive species in nanosecond laser-produced uranium plasmas. Comparing plasma morphology in various inert and reactive ambient gases provides information about the role of gas-phase chemistry in plume hydrodynamics. Background gases including nitrogen and argon foster collisional interactions leading to more significant plume confinement and the increase in persistence of uranium species. On the other hand, environments containing reactive gases such as oxygen promote chemical reactions between the plasma and ambient species. By comparing the expansion dynamics of uranium plumes in nitrogen, air, and argon, we discover that chemical reactions modify the hydrodynamics of the plume at later times of its evolution in the air background. Furthermore, we observe that varying the concentration of o...
- Published
- 2019
- Full Text
- View/download PDF
49. Time-resolved dual-comb measurement of number density and temperature in a laser-induced plasma
- Author
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Reagan R. D. Weeks, R. Jason Jones, Caroline Lecaplain, Jeremy Yeak, Yu Zhang, Mark C. Phillips, and Sivanandan S. Harilal
- Subjects
Materials science ,Population ,02 engineering and technology ,Excitation temperature ,01 natural sciences ,Molecular physics ,law.invention ,010309 optics ,Optics ,Physics::Plasma Physics ,law ,0103 physical sciences ,Laser-induced fluorescence ,education ,Spectroscopy ,education.field_of_study ,Laser ablation ,business.industry ,fungi ,Plasma ,021001 nanoscience & nanotechnology ,Laser ,Atomic and Molecular Physics, and Optics ,Time-resolved spectroscopy ,0210 nano-technology ,business - Abstract
We utilize time-resolved dual-comb spectroscopy to measure the temporal evolution of the population number densities and absorption excitation temperature of Fe in a laser-induced plasma. The spectra of three excited-state transitions of Fe around 533 nm are simultaneously measured at different time delays following laser ablation of a stainless steel sample. This Letter probes late-time behaviors of laser-induced ablation plumes during plasma cooling. The high spectral resolution and broad spectral coverage of the dual-comb technique, combined with the time-resolved measurement capability shown here, will aid in the characterization of laser induced plasmas, including species identification and molecule and particle formation that can occur at later times in the plasma evolution.
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- 2019
- Full Text
- View/download PDF
50. Single-shot, multi-signature remote detection of uranium by filament-induced breakdown spectroscopy
- Author
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L. A. Finney, Sivanandan S. Harilal, P. J. Skrodzki, Igor Jovanovic, Milos Burger, and John Nees
- Subjects
Materials science ,business.industry ,Analytical chemistry ,chemistry.chemical_element ,Monoxide ,02 engineering and technology ,Uranium ,021001 nanoscience & nanotechnology ,Laser ,01 natural sciences ,Signal ,Atomic and Molecular Physics, and Optics ,law.invention ,010309 optics ,chemistry.chemical_compound ,Optics ,Data acquisition ,chemistry ,law ,0103 physical sciences ,Uranium oxide ,Emission spectrum ,0210 nano-technology ,business ,Spectroscopy - Abstract
Filament-induced breakdown spectroscopy (FIBS) is an attractive remote detection approach that is potentially applicable to nuclear materials such as uranium (U). Simultaneous detection of atomic U and U monoxide features is demonstrated in a single laser shot with detection probabilities of 52.2% and 39.0%, respectively, and with a 1% false-alarm probability. It is shown that a nearly 100% detection probability can be reached with 1% false-alarm probability in ≲1 second when using an 80 Hz laser and data acquisition system. Atomic U and uranium oxide (UO) signal features are identifiable in the remote measurement with comparable signal-to-background ratios, suggesting that, despite being broader than the U I emission line, the UO band is also suitable for remote detection of U by FIBS.
- Published
- 2019
- Full Text
- View/download PDF
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