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. Hieu, Hoang Chi; Li, Hongyan; Miyauchi, Yoshihiro; Mizutani, Goro; Fujita, Naoko; Nakamura, Yasunori 2015-03-05 We report a sum frequency generation (SFG) spectroscopy study of d-glucose, d-fructose and sucrose in the CH stretching vibration regime. Wetting effect on the SFG spectra was investigated. The SFG spectrum of d-glucose changed from that of α-d-glucose into those of α-d-glucose monohydrate by wetting. The SFG spectra showed evidence of a small change of β-d-fructopyranose into other anomers by wetting. SFG spectra of sucrose did not change by wetting. Assignments of the vibrational peaks in the SFG spectra of the three sugars in the dry and wet states were performed in the CH stretching vibration region near 3000cm(-1).
Copyright © 2014 Elsevier B.V. All rights reserved. Zheng, Chen; Mathew, Kiran; Chen, Chi; Chen, Yiming; Tang, Hanmei; Dozier, Alan; Kas, Joshua J.; Vila, Fernando D.; Rehr, John J.; Piper, Louis F. J.; Persson, Kristin A.; Ong, Shyue Ping 2018-12-01 X-ray absorption spectroscopy (XAS) is a widely used materials characterization technique to determine oxidation states, coordination environment, and other local atomic structure information. Analysis of XAS relies on comparison of measured spectra to reliable reference spectra. However, existing databases of XAS spectra are highly limited both in terms of the number of reference spectra available as well as the breadth of chemistry coverage. In this work, we report the development of XASdb, a large database of computed reference XAS, and an Ensemble-Learned Spectra IdEntification (ELSIE) algorithm for the matching of spectra.
XASdb currently hosts more than 800,000 K-edge X-ray absorption near-edge spectra (XANES) for over 40,000 materials from the open-science Materials Project database. We discuss a high-throughput automation framework for FEFF calculations, built on robust, rigorously benchmarked parameters. FEFF is a computer program uses a real-space Green's function approach to calculate X-ray absorption spectra.
We will demonstrate that the ELSIE algorithm, which combines 33 weak 'learners' comprising a set of preprocessing steps and a similarity metric, can achieve up to 84.2% accuracy in identifying the correct oxidation state and coordination environment of a test set of 19 K-edge XANES spectra encompassing a diverse range of chemistries and crystal structures. The XASdb with the ELSIE algorithm has been integrated into a web application in the Materials Project, providing an important new public resource for the analysis of XAS to all materials researchers. Finally, the ELSIE algorithm itself has been made available as part of veidt, an open source machine-learning library for materials science.
Mavridis, Lazaros; Janes, Robert W 2017-01-01 Circular dichroism (CD) spectroscopy is extensively utilized for determining the percentages of secondary structure content present in proteins. However, although a large contributor, secondary structure is not the only factor that influences the shape and magnitude of the CD spectrum produced. Other structural features can make contributions so an entire protein structural conformation can give rise to a CD spectrum. There is a need for an application capable of generating protein CD spectra from atomic coordinates.
However, no empirically derived method to do this currently exists. PDB2CD has been created as an empirical-based approach to the generation of protein CD spectra from atomic coordinates. The method utilizes a combination of structural features within the conformation of a protein; not only its percentage secondary structure content, but also the juxtaposition of these structural components relative to one another, and the overall structure similarity of the query protein to proteins in our dataset, the SP175 dataset, the 'gold standard' set obtained from the Protein Circular Dichroism Data Bank (PCDDB). A significant number of the CD spectra associated with the 71 proteins in this dataset have been produced with excellent accuracy using a leave-one-out cross-validation process. The method also creates spectra in good agreement with those of a test set of 14 proteins from the PCDDB. The PDB2CD package provides a web-based, user friendly approach to enable researchers to produce CD spectra from protein atomic coordinates.
CONTACT: [email protected] information: Supplementary data are available at Bioinformatics online. © The Author 2016.
Published by Oxford University Press. Boone, J M; Seibert, J A 1997-11-01 A tungsten anode spectral model using interpolating polynomials (TASMIP) was used to compute x-ray spectra at 1 keV intervals over the range from 30 kV to 140 kV. The TASMIP is not semi-empirical and uses no physical assumptions regarding x-ray production, but rather interpolates measured constant potential x-ray spectra published by Fewell et al. Handbook of Computed Tomography X-ray Spectra (U.S. Government Printing Office, Washington, D.C., 1981).
X-ray output measurements (mR/mAs measured at 1 m) were made on a calibrated constant potential generator in our laboratory from 50 kV to 124 kV, and with 0-5 mm added aluminum filtration. The Fewell spectra were slightly modified (numerically hardened) and normalized based on the attenuation and output characteristics of a constant potential generator and metal-insert x-ray tube in our laboratory. Then, using the modified Fewell spectra of different kVs, the photon fluence phi at each 1 keV energy bin (E) over energies from 10 keV to 140 keV was characterized using polynomial functions of the form phi (E) = a0E + a1E kV + a2E kV2 +. + a(n)E kVn. A total of 131 polynomial functions were used to calculate accurate x-ray spectra, each function requiring between two and four terms. The resulting TASMIP algorithm produced x-ray spectra that match both the quality and quantity characteristics of the x-ray system in our laboratory. For photon fluences above 10% of the peak fluence in the spectrum, the average percent difference (and standard deviation) between the modified Fewell spectra and the TASMIP photon fluence was -1.43% (3.8%) for the 50 kV spectrum, -0.89% (1.37%) for the 70 kV spectrum, and for the 80, 90, 100, 110, 120, 130 and 140 kV spectra, the mean differences between spectra were all less than 0.20% and the standard deviations were less than approximately 1.1%.
The model was also extended to include the effects of generator-induced kV ripple. Finally, the x-ray photon fluence in the units of. Hummels, Cameron; Smith, Britton; Silvia, Devin; Peeples, Molly; Prochaska, X.; Tejos, Nicolas 2016-03-01 Astrophysical simulations are useful insofar as they aid in the interpretation of telescopic observations. Thus, a primary task in simulation analysis is in producing synthetic observations for direct comparison against observational data.
Furthermore, we as a field need an effective means for storing these synthetic observable data products, such that they are accessible and searchable by the entire population of researchers. In this talk, we present Trident, a universal pipeline for producing synthetic spectra from any of the major hydrodynamics codes, and MISTY, a means of storing these spectra on the HST MAST data archive. Trident and MISTY are our attempts to solve the difficult problems of synthetic data production and publicly-accessible storage for the scientific communities studying the intergalactic medium and circumgalactic medium. Niazi, Mansour; McLaughlin, Keith L. 1987-10-01 Short period recordings of PcP at the SRO station ANTO have been observed at epicentral distance of 13.5° from presumed underground explosions in western Kazahk, USSR. The core reflections are narrow band (0.6 to 2.4 Hz), short duration (3 sec) signals. Comparison of these near normally incident reflections to P waveforms observed at greater distances reveals that the PcP spectra are peaked with respect to the more representative P-wave spectra.
The 1.2 Hz spectral peak is also observed for PcP waves recorded at 50 degrees. Corrections for frequency independent mantle Q attnuation models only increase the high frequency deficiency of the PcP spectra at frequencies above 1.2 Hz. A plausible explanation calls for finer structural features of core-mantle boundary (CMB) than hitherto suggested. The influence of small scale lateral heterogeneities, however, cannot be completely ruled out. (Mantle-core boundary, near normal PcP reflection.). Tong, Yujin; Zhao, Yanbao; Li, Na; Ma, Yunsheng; Osawa, Masatoshi; Davies, Paul B; Ye, Shen 2010-07-21 In this paper, the results of the modeling calculations carried out for predicting the interference effects expected in the sum frequency generation (SFG) spectra of a specific thin-layer system, described in the accompanying paper, are tested by comparing them with the experimental spectra obtained for a real thin-layer film comprising an organic monolayer/variable thickness dielectric layer/gold substrate. In this system, two contributions to the SFG spectra arise, a resonant contribution from the organic film and a nonresonant contribution from the gold substrate.
The modeling calculations are in excellent agreement with the experimental spectra over a wide range of thicknesses and for different polarization combinations. The introduction of another resonant monolayer adjacent to the gold substrate and with the molecules having a reverse orientation has a significant affect on the spectral shapes which is predicted. If a dielectric substrate such as CaF(2) is used instead of a gold substrate, only the spectral intensities vary with the film thickness but not the spectral shapes. The counterpropagating beam geometry will change both the thickness dependent spectral shapes and the intensity of different vibrational modes in comparison with a copropagating geometry.
The influences of these experimental factors, i.e., the molecular orientational structure in the thin film, the nature of the substrate, and the selected incident beam geometry, on the experimental SFG spectra are quantitatively predicted by the calculations. The thickness effects on the signals from a SFG active monolayer contained in a thin liquid-layer cell of the type frequently used for in situ electrochemical measurements is also discussed. The modeling calculation is also valid for application to other thin-film systems comprising more than two resonant SFG active interfaces by appropriate choice of optical geometries and relevant optical properties.
Petschke, Danny; Staab, Torsten E. 2018-01-01 The quantitative analysis of lifetime spectra relevant in both life and materials sciences presents one of the ill-posed inverse problems and, hence, leads to most stringent requirements on the hardware specifications and the analysis algorithms.
Here we present DLTPulse Generator, a library written in native C 11, which provides a simulation of lifetime spectra according to the measurement setup. The simulation is based on pairs of non-TTL detector output-pulses. Those pulses require the Constant Fraction Principle (CFD) for the determination of the exact timing signal and, thus, the calculation of the time difference i.e. The lifetime. To verify the functionality, simulation results were compared to experimentally obtained data using Positron Annihilation Lifetime Spectroscopy (PALS) on pure tin. Jean, Pierre-Olivier; Bradley, Robert; Tremblay, Jean-Pierre 2015-04-01 An important asset for the management of wild ungulates is the ability to recognize the spatial distribution of forage quality across heterogeneous landscapes.
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To do so typically requires knowledge of which plant species are eaten, in what abundance they are eaten, and what their nutritional quality might be. Acquiring such data may be, however, difficult and time consuming. Here, we are proposing a rapid and cost-effective forage quality monitoring tool that combines near infrared (NIR) spectra of fecal samples and easily obtained data on plant community composition.
Our approach rests on the premise that NIR spectra of fecal samples collected within low population density exclosures reflect the optimal forage quality of a given landscape. Forage quality can thus be based on the Mahalanobis distance of fecal spectral scans across the landscape relative to fecal spectral scans inside exclosures (referred to as DISTEX). The Gi. spatial autocorrelation statistic can then be applied among neighbouring DISTEX values to detect and map 'hot-spots' and 'cold-spots' of nutritional quality over the landscape. We tested our approach in a heterogeneous boreal landscape on Anticosti Island (Qu.
Furer, V. L.; Vandyukov, A. E.; Tripathi, V.; Majoral, J. P.; Caminade, A.
M.; Kovalenko, V. 2018-06-01 A new phosphorus-containing dendrimer of the first- generation with potential pharmacological activity was synthesized and studied by spectral methods. The FTIR, FT Raman, 1H and 31P NMR spectra of the first generation dendrimer G1 with a cyclotriphosphazene core, six branches sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd P(S) 39.8% of 300 ha neighborhoods, whereas cold spots occur in laggs (i.e., transition zones from forest to peatland). In terms of ground-level indicator plant species, the presence of Canada bunchberry (Cornus canadensis) was highly correlated with hot spots, whereas tamarack (Larix laricina) was highly correlated with cold spots. Mean DISTEX values were positively and significantly correlated with the neutral detergent fiber and acid detergent lignin contents of feces. While our.
Raznikova, M O; Raznikov, V V 2015-01-01 In this work, information relating to charge states of biomolecule ions in solution obtained using the electrospray ionization mass spectrometry of different biopolymers is analyzed. The data analyses have mainly been carried out by solving an inverse problem of calculating the probabilities of retention of protons and other charge carriers by ionogenic groups of biomolecules with known primary structures. The approach is a new one and has no known to us analogues. A program titled 'Decomposition' was developed and used to analyze the charge distribution of ions of native and denatured cytochrome c mass spectra. The possibility of splitting of the charge-state distribution of albumin into normal components, which likely corresponds to various conformational states of the biomolecule, has been demonstrated.
The applicability criterion for using previously described method of decomposition of multidimensional charge-state distributions with two charge carriers, e.g., a proton and a sodium ion, to characterize the spatial structure of biopolymers in solution has been formulated. In contrast to known mass-spectrometric approaches, this method does not require the use of enzymatic hydrolysis or collision-induced dissociation of the biopolymers. Caratti 2006-01-01 The FIREMON Species Composition ( SC) method is used to provide ocular estimates of cover and height measurements for plant species on a macroplot. The SC method provides plant species composition and coverage estimates to describe a stand or plant community and can be used to document changes over time.
It is suited for a wide variety of vegetation types and is. Sawada, Hiroshi 2012-10-01 We report on the characterization of the in situ energy spectrum of fast electrons generated by ultra-intense (I˜10^19 W cm-2) short pulse (τ˜0.7 and 10 ps) laser-plasma interactions using the TITAN and OMEGA EP lasers. That in situ spectrum is a key component of ignition efficiency for the Fast Ignition (FI) Inertial Confinement Fusion (ICF) concept. It is challenging to model and, until now, has resisted direct experimental characterization; other techniques have very large error bars or measure the modified spectrum of escaped electrons. This technique also gives an indication of the forward coupling efficiency of the laser to fast electrons. This information is derived from the measurement of Cu Kα x-rays emitted from a 1.5 mm long Cu wire attached to the tip of Au or Al cone targets.
Fast electrons, generated in the cone, transport through the cone tip with a fraction of coupling to the wire. Electrons in the wire excite fluorescence measured by a monochromatic imager and an absolutely calibrated HOPG spectrometer. An implicit hybrid-PIC code, LSP, is applied to deduce electron parameters from the Kα measurements. Experiments on the TITAN laser with Au cones attached to wires show an increase in pre-pulse energy from 17 to 1000 mJ, decreases the fast electron fraction entering the wire from 8.4% to 2.5%. On OMEGA EP with Al cones attached to wires, total Kα yield, normalized to laser energy, drops ˜30% for laser pulse length increasing from 1 to 10 ps, indicative of a saturation mechanism.
For Au cones, Kα yields were 50% of that measured for Al cones indicating a strong material dependence. In all cases, the spatial distribution can only be fit with a two-temperature electron energy distribution, the relative fractions depending on prepulse level. These results are being used to develop an optimum cone design for integrated FI experiments. This work was performed under the auspices of the USDOE by LLNL under Contract DE-AC52-07NA27344 and DE-FG-02.
Evans, L.G.; Trombka, J.I.; Jensen, D.H.; Stephenson, W.A.; Hoover, R.A.; Mikesell, J.L.; Tanner, A.B.; Senftle, F.E. 1984-01-01 A neutron generator pulsed at 100 s-1 was suspended in an artificial borehole containing a 7.7 metric ton mixture of sand, aragonite, magnetite, sulfur, and salt. Two Ge(HP) gamma-ray detectors were used: one in a borehole sonde, and one at the outside wall of the sample tank opposite the neutron generator target. Gamma-ray spectra were collected by the outside detector during each of 10 discrete time windows during the 10 ms period following the onset of gamma-ray build-up after each neutron burst. The sample was measured first when dry and then when saturated with water. In the dry sample, gamma rays due to inelastic neutron scattering, neutron capture, and decay were counted during the first (150??s) time window.
Subsequently only capture and decay gamma rays were observed. In the wet sample, only neutron capture and decay gamma rays were observed.
Neutron capture gamma rays dominated the spectrum during the period from 150 to 400??s after the neutron burst in both samples, but decreased with time much more rapidly in the wet sample. A signal-to-noise-ratio (S/N) analysis indicates that optimum conditions for neutron capture analysis occurred in the 350-800??s window. A poor S/N in the first 100-150??s is due to a large background continuum during the first time interval. Time gating can be used to enhance gamma-ray spectra, depending on the nuclides in the target material and the reactions needed to produce them, and should improve the sensitivity of in situ well logging.??. Lakbub, Jude C; Su, Xiaomeng; Zhu, Zhikai; Patabandige, Milani W; Hua, David; Go, Eden P; Desaire, Heather 2017-08-04 The glycopeptide analysis field is tightly constrained by a lack of effective tools that translate mass spectrometry data into meaningful chemical information, and perhaps the most challenging aspect of building effective glycopeptide analysis software is designing an accurate scoring algorithm for MS/MS data.
We provide the glycoproteomics community with two tools to address this challenge. The first tool, a curated set of 100 expert-assigned CID spectra of glycopeptides, contains a diverse set of spectra from a variety of glycan types; the second tool, Glycopeptide Decoy Generator, is a new software application that generates glycopeptide decoys de novo. We developed these tools so that emerging methods of assigning glycopeptides' CID spectra could be rigorously tested. Software developers or those interested in developing skills in expert (manual) analysis can use these tools to facilitate their work. We demonstrate the tools' utility in assessing the quality of one particular glycopeptide software package, GlycoPep Grader, which assigns glycopeptides to CID spectra. We first acquired the set of 100 expert assigned CID spectra; then, we used the Decoy Generator (described herein) to generate 20 decoys per target glycopeptide.
The assigned spectra and decoys were used to test the accuracy of GlycoPep Grader's scoring algorithm; new strengths and weaknesses were identified in the algorithm using this approach. Both newly developed tools are freely available. The software can be downloaded at http://glycopro.chem.ku.edu/GPJ.jar.