Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra.

Science.gov (United States)

Mantini, Dante; Petrucci, Francesca; Del Boccio, Piero; Pieragostino, Damiana; Di Nicola, Marta; Lugaresi, Alessandra; Federici, Giorgio; Sacchetta, Paolo; Di Ilio, Carmine; Urbani, Andrea

2008-01-01

Independent component analysis (ICA) is a signal processing technique that can be utilized to recover independent signals from a set of their linear mixtures. We propose ICA for the analysis of signals obtained from large proteomics investigations such as clinical multi-subject studies based on MALDI-TOF MS profiling. The method is validated on simulated and experimental data for demonstrating its capability of correctly extracting protein profiles from MALDI-TOF mass spectra. The comparison on peak detection with an open-source and two commercial methods shows its superior reliability in reducing the false discovery rate of protein peak masses. Moreover, the integration of ICA and statistical tests for detecting the differences in peak intensities between experimental groups allows to identify protein peaks that could be indicators of a diseased state. This data-driven approach demonstrates to be a promising tool for biomarker-discovery studies based on MALDI-TOF MS technology. The MATLAB implementation of the method described in the article and both simulated and experimental data are freely available at http://www.unich.it/proteomica/bioinf/.

A Simple Spreadsheet Program to Simulate and Analyze the Far-UV Circular Dichroism Spectra of Proteins

Science.gov (United States)

Abriata, Luciano A.

2011-01-01

A simple algorithm was implemented in a spreadsheet program to simulate the circular dichroism spectra of proteins from their secondary structure content and to fit [alpha]-helix, [beta]-sheet, and random coil contents from experimental far-UV circular dichroism spectra. The physical basis of the method is briefly reviewed within the context of…

Absolute nutrient concentration measurements in cell culture media: 1H q-NMR spectra and data to compare the efficiency of pH-controlled protein precipitation versus CPMG or post-processing filtering approaches

Directory of Open Access Journals (Sweden)

Luca Goldoni

2016-09-01

Full Text Available The NMR spectra and data reported in this article refer to the research article titled “A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using q-NMR” [1]. We provide the 1H q-NMR spectra of cell culture media (DMEM after removal of serum proteins, which show the different efficiency of various precipitating solvents, the solvent/DMEM ratios, and pH of the solution. We compare the data of the absolute nutrient concentrations, measured by PULCON external standard method, before and after precipitation of serum proteins and those obtained using CPMG (Carr-Purcell-Meiboom-Gill sequence or applying post-processing filtering algorithms to remove, from the 1H q-NMR spectra, the proteins signal contribution. For each of these approaches, the percent error in the absolute value of every measurement for all the nutrients is also plotted as accuracy assessment. Keywords: 1H NMR, pH-controlled serum removal, PULCON, Accuracy, CPMG, Deconvolution

Study on the Interaction between Cadmium Sulphide Nanoparticles and Proteins by Resonance Rayleigh Scattering Spectra

Directory of Open Access Journals (Sweden)

Weiwei Zhu

2013-01-01

Full Text Available The interaction of cadmium sulphide nanoparticles [(CdSn] with proteins has been studied by resonance Rayleigh scattering spectra (RRS. Below the isoelectric point, proteins such as bovine serum albumin (BSA, human serum albumin (HSA, lysozyme (Lys, hemoglobin (HGB, and ovalbumin (OVA can bind with CdSn to form macromolecules by virtue of electrostatic attraction and hydrophobic force. It can result in the enhancement of resonance Rayleigh scattering spectra (RRS intensity. Their maximum scattering peaks were 280 nm, and there was a smaller peak at 370 nm. The scattering enhancement (ΔIRRS is directly proportional to the concentration of proteins. A new RRS method for the determination of trace proteins using uncapped CdSn nanoparticles probe has been developed. The detection limits are 19.6 ng/mL for HSA, 16.7 ng/mL for BSA, 18.5 ng/mL for OVA, 80.2 ng/mL for HGB, and 67.4 ng/mL for Lys, separately. In this work, the optimum condition of reaction, the effect of foreign, and the analytical application had been investigated.

ARTSY-J: Convenient and precise measurement of 3JHNHα couplings in medium-size proteins from TROSY-HSQC spectra

Science.gov (United States)

Roche, Julien; Ying, Jinfa; Shen, Yang; Torchia, Dennis A.; Bax, Ad

2016-07-01

A new and convenient method, named ARTSY-J, is introduced that permits extraction of the 3JHNHα couplings in proteins from the relative intensities in a pair of 15N-1H TROSY-HSQC spectra. The pulse scheme includes 3JHNHα dephasing of the narrower TROSY 1HN-{15N} doublet component during a delay, integrated into the regular two-dimensional TROSY-HSQC pulse scheme, and compares the obtained intensity with a reference spectrum where 3JHNHα dephasing is suppressed. The effect of passive 1Hα spin flips downscales the apparent 3JHNHα coupling by a uniform factor that depends approximately linearly on both the duration of the 3JHNHα dephasing delay and the 1H-1H cross relaxation rate. Using such a correction factor, which accounts for the effects of both inhomogeneity of the radiofrequency field and 1Hα spin flips, agreement between prior and newly measured values for the small model protein GB3 is better than 0.3 Hz. Measurement for the HIV-1 protease homodimer (22 kDa) yields 3JHNHα values that agree to better than 0.7 Hz with predictions made on the basis of a previously parameterized Karplus equation. Although for Gly residues the two individual 3JHNHα couplings cannot be extracted from a single set of ARTSY-J spectra, the measurement provides valuable ϕ angle information.

Obtaining of interspecific hybrids for pea introgressive breeding

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Sergey Vasilevich Bobkov

2015-09-01

Full Text Available Background. Overcoming of reproductive isolation, identification and transfer of agronomic value genes from wild relatives into cultivated pea genomes is an important task for pea introgressive breeding. Materials and methods. Reciprocal hybridization of cultivated pea with wide set of P. fulvum accessions was conducted. Identification of hybrids was carried out with use of biochemical and morphological markers. Identification of unique protein was conducted with use of electrophoretic spectra of mature seeds. Results. Pea interspecific hybrids were obtained in two reciprocal directions of crosses. Cross efficiency in Р. sativum × P. fulvum and P. fulvum × Р. sativum combinations was 36 % and 7 %, respectively. All tested seeds in crosses Р. sativum × P. fulvum were hybrids. Crosses in direction P. fulvum × Р. sativum led to formation of puny seeds restricted in embryo growth. Protein markers of one seed derived in cross P. fulvum × Р. sativum proved its hybrid nature. Morphological markers demonstrated that plant derived from another cross was also a hybrid. Culture of immature embryos was developed for recovering plants in interspecific crosses. Morphogenic calli and regenerated plants were obtained in culture of immature embryos P. fulvum (И592589 × Р. sativum (Aest. Identification of unique protein 7 of P. fulvum was conducted. Inheritance of that protein was proved as monogenic dominant. Conclusion. Efficiency of hybridization in combination P. fulvum × Р. sativum was significantly less in compare to reciprocal one. All products of that cross combination were tested as hybrids. Unique protein 7 of P. fulvum was revealed as a result of mature seed electrophoretic spectra analysis. Inheritance of that protein was determined as monogenic dominant.

Facilitated assignment of large protein NMR signals with covariance sequential spectra using spectral derivatives.

Science.gov (United States)

Harden, Bradley J; Nichols, Scott R; Frueh, Dominique P

2014-09-24

Nuclear magnetic resonance (NMR) studies of larger proteins are hampered by difficulties in assigning NMR resonances. Human intervention is typically required to identify NMR signals in 3D spectra, and subsequent procedures depend on the accuracy of this so-called peak picking. We present a method that provides sequential connectivities through correlation maps constructed with covariance NMR, bypassing the need for preliminary peak picking. We introduce two novel techniques to minimize false correlations and merge the information from all original 3D spectra. First, we take spectral derivatives prior to performing covariance to emphasize coincident peak maxima. Second, we multiply covariance maps calculated with different 3D spectra to destroy erroneous sequential correlations. The maps are easy to use and can readily be generated from conventional triple-resonance experiments. Advantages of the method are demonstrated on a 37 kDa nonribosomal peptide synthetase domain subject to spectral overlap.

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm

International Nuclear Information System (INIS)

Yang, Yu; Fritzsching, Keith J.; Hong, Mei

2013-01-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra (“good connections”), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra (“bad connections”), and minimizing the number of assigned peaks that have no matching peaks in the other spectra (“edges”). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.

Science.gov (United States)

Yang, Yu; Fritzsching, Keith J; Hong, Mei

2013-11-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra ("good connections"), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra ("bad connections"), and minimizing the number of assigned peaks that have no matching peaks in the other spectra ("edges"). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct assignment for a

Comparison of hard X-ray spectra obtained by spectrometers on Hinotori and SMM and detection of 'superhot' component

Science.gov (United States)

Nitta, Nariaki

1988-01-01

Hard X-ray spectra in solar flares obtained by the broadband spectrometers aboard Hinotori and SMM are compared. Within the uncertainty brought about by assuming the typical energy of the background X-rays, spectra by the Hinotori spectrometer are usually consistent with those by the SMM spectrometer for flares in 1981. On the contrary, flares in 1982 persistently show 20-50-percent higher flux by Hinotori than by SMM. If this discrepancy is entirely attributable to errors in the calibration of energy ranges, the errors would be about 10 percent. Despite such a discrepancy in absolute flux, in the the decay phase of one flare, spectra revealed a hard X-ray component (probably a 'superhot' component) that could be explained neither by emission from a plasma at about 2 x 10 to the 7th K nor by a nonthermal power-law component. Imaging observations during this period show hard X-ray emission nearly cospatial with soft X-ray emission, in contrast with earlier times at which hard and soft X-rays come from different places.

Design spectra development considering short time histories

International Nuclear Information System (INIS)

Weiner, E.O.

1983-01-01

The need for generation of seismic acceleration histories to prescribed response spectra arises several ways in structural dynamics. For example, one way of obtaining floor spectra is to generate a history from a foundation spectra and then solve for the floor motion from which a floor spectrum can be obtained. Two separate programs, MODQKE and MDOF, were written to provide a capability of obtaining equipment spectra from design spectra. MODQKE generates or modifies acceleration histories to conform with design spectra pertaining to, say, a foundation. MDOF is a simple linear modal superposition program that solves for equipment support histories using the design spectra conforming histories as input. Equipment spectra, then, are obtained from the support histories using MODQKE

The effects of general anesthetics on ESR spectra of spin labels in phosphatidylcholine vesicles containing purified Na,K-ATPase or microsomal protein

Energy Technology Data Exchange (ETDEWEB)

Shibuya, Makiko, E-mail: shibu@den.hokudai.ac.jp [Department of Dental Anesthesiology, Graduate School of Dental Medicine, Hokkaido University (Japan); Hiraoki, Toshifumi [Division of Applied Physics, Graduate School of Engineering, Hokkaido University (Japan); Kimura, Kunie; Fukushima, Kazuaki [Department of Dental Anesthesiology, Graduate School of Dental Medicine, Hokkaido University (Japan); Suzuki, Kuniaki [Department of Molecular Cell Pharmacology, Graduate School of Dental Medicine, Hokkaido University (Japan)

2012-12-01

Highlights: Black-Right-Pointing-Pointer We studied the effects of general anesthetics on liposome using ESR spectra. Black-Right-Pointing-Pointer Two spin labels, 5-DSA and 16-DSA, were located in different position in liposome. Black-Right-Pointing-Pointer Anesthetics did not change the environment around the spin labels in the liposome. Black-Right-Pointing-Pointer Anesthetics remained on the surface of the lipid bilayer of liposome. Black-Right-Pointing-Pointer Proteins in the liposome did not change the effects of anesthetics on liposome. - Abstract: We investigated the effects of general anesthetics on liposome containing spin labels, 5-doxyl stearic acid (5-DSA) and 16-doxyl stearic acid (16-DSA), and purified Na,K-ATPase or membrane protein of microsome using an electron spin resonance (ESR) spectroscopy. The spectra of 16-DSA in liposomes with both proteins showed three sharp signals compared with 5-DSA. The difference in the order parameter S value of 5-DSA and 16-DSA suggested that the nitroxide radical location of 5-DSA and 16-DSA were different in the membrane bilayer. The results were almost the same as those obtained in liposomes without proteins. The addition of sevoflurane, isoflurane, halothane, ether, ethanol and propofol increased the intensity of the signals, but the clinical concentrations of anesthetics did not significantly alter the S and {tau} values, which are indices of the fluidity of the membrane. These results suggest that anesthetics remain on the surface of the lipid bilayer and do not act on both the inside hydrophobic area and the relatively hydrophilic area near the surface. These results and others also suggest that the existence of Na,K-ATPase and microsomal proteins did not affect the environment around the spin labels in the liposome and the effects of anesthetics on liposome as a model membrane.

Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins

International Nuclear Information System (INIS)

Englander, S.W.; Wand, A.J.

1987-01-01

A strategy for assigning the resonances in two-dimensional (2D) NMR spectra of proteins is described. The method emphasizes the analysis of through-space relationships between protons by use of the two-dimensional nuclear Overhauser effect (NOE) experiment. NOE patterns used in the algorithm were derived from a statistical analysis of the combinations of short proton-proton distances observed in the high-resolution crystal structures of 21 proteins. One starts with a search for authentic main-chain NH-C/sub α/H-C/sub β/H J-coupled units, which can be found with high reliability. The many main-chain units of a protein are then placed in their proper juxtaposition by recognition of predefined NOE connectivity patterns. To discover these connectivities, the 2D NOE spectrum is examined, in a prescribed order, for the distinct NOE patterns characteristic of helices, sheets, turns, and extended chain. Finally, the recognition of a few amino acid side-chain types places the discovered secondary structure elements within the polypeptide sequences. Unlike the sequential assignment approach, the main-chain-directed strategy does not rely on the difficult task of recognizing many side-chain spin systems in J-correlated spectra, the assignment process is not in general sequential with the polypeptide chain, and the prescribed connectivity patterns are cyclic rather than linear. The latter characteristic avoids ambiguous branch points in the analysis and imposed an internally confirmatory property on each forward step

Diversity in C-Xanes Spectra Obtained from Carbonaceous Solid Inclusions from Monahans Halite

Science.gov (United States)

Kebukawa, Y.; Zolensky, M. E.; Fries, M.; Kilcoyne, A. L. D.; Rahman, Z.; Cody, G. D.

2014-01-01

Monahans meteorite (H5) contains fluid inclusion- bearing halite (NaCl) crystals [1]. Microthermometry and Raman spectroscopy showed that the fluid in the inclusions is an aqueous brine and they were trapped near 25degC [1]. Their continued presence in the halite grains requires that their incorporation into the H chondrite asteroid was post metamorphism [2]. Abundant solid inclusions are also present in the halites. The solid inclusions include abundant and widely variable organics [2]. Analyses by Raman microprobe, SEM/EDX, synchrotron X-ray diffraction and TEM reveal that these grains include macromolecular carbon similar in structure to CV3 chondrite matrix carbon, aliphatic carbon compounds, olivine (Fo99-59), high- and low-Ca pyroxene, feldspars, magnetite, sulfides, lepidocrocite, carbonates, diamond, apatite and possibly the zeolite phillipsite [3]. Here we report organic analyses of these carbonaceous residues in Monahans halite using C-, N-, and O- X-ray absorption near edge structure (XANES). Samples and Methods: Approximately 100 nm-thick sections were extracted with a focused ion beam (FIB) at JSC from solid inclusions from Monahans halite. The sections were analyzed using the scanning transmission X-ray microscope (STXM) on beamline 5.3.2.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory for XANES spectroscopy. Results and Discussion: C-XANES spectra of the solid inclusions show micrometer-scale heterogeneity, indicating that the macromolecular carbon in the inclusions have complex chemical variations. C-XANES features include 284.7 eV assigned to aromatic C=C, 288.4-288.8 eV assigned to carboxyl, and 290.6 eV assigned to carbonate. The carbonyl features obtained by CXANES might have been caused by the FIB used in sample preparation. No specific N-XANES features are observed. The CXANES spectra obtained from several areas in the FIB sections include type 1&2 chondritic IOM like, type 3 chondritic IOM like, and none of the above

Spectra of alkali atoms

International Nuclear Information System (INIS)

Santoso, Budi; Arumbinang, Haryono.

1981-01-01

Emission spectra of alkali atoms has been determined by using spectrometer at the ultraviolet to infra red waves range. The spectra emission can be obtained by absorption spectrophotometric analysis. Comparative evaluations between experimental data and data handbook obtained by spark method were also presented. (author tr.)

Temperature dependence of Q-band electron paramagnetic resonance spectra of nitrosyl heme proteins

Energy Technology Data Exchange (ETDEWEB)

Flores, Marco; Wajnberg, Eliane; Bemski, George

1997-11-01

The Q-band (35 GHz) electron paramagnetic resonance (EPR) spectra of nitrosyl hemoglobin (Hb N O) and nitrosyl myoglobin (Mb NO) were studied as a function of temperature between 19 K and 200 K. The spectra of both heme proteins show classes of variations as a function of temperature. The first one has previously been associated with the existence of two paramagnetic species, one with rhombic and the other with axial symmetry. The second one manifests itself in changes in the g-factors and linewidths of each species. These changes are correlated with the conformational substates model and associate the variations of g-values with changes in the angle of the N(his)-Fe-N (NO) bond in the rhombic species and with changes in the distance between Fe and N of the proximal (F8) histidine in the axial species. (author) 24 refs., 6 figs.

Analysis of neutron spectra and fluxes obtained with cold and thermal moderators at IBR-2 reactor: experimental and computer modeling studies at small-angle scattering YuMO setup

International Nuclear Information System (INIS)

Kuklin, A.I.; Rogov, A.D.; Gorshkova, Yu.E.; Kovalev, Yu.S.; Kutuzov, S.A.; Utrobin, P.K.; Rogachev, A.V.; Ivan'kov, O.I.; Solov'ev, D.V.; Gordelij, V.I.

2011-01-01

Results of experimental and computer modeling investigations of neutron spectra and fluxes obtained with cold and thermal moderators at the IBR-2 reactor (JINR, Dubna) are presented. The studies are done for small-angle neutron scattering (SANS) spectrometer YuMO (beamline number 4 of the IBR-2). The measurements of neutron spectra for two methane cold moderators are done for the standard configuration of the SANS instrument. The data from both moderators under different conditions of their operation are compared. The ratio of experimentally determined neutron fluxes of cold and thermal moderators at different wavelength is shown. Monte Carlo simulations are done to determine spectra for cold methane and thermal moderators. The results of the calculations of the ratio of neutron fluxes of cold and thermal moderators at different wavelength are demonstrated. In addition, the absorption of neutrons in the air gaps on the way from the moderator to the investigated sample is presented. SANS with the protein apoferritin was done in the case of cold methane as well as a thermal moderator and the data were compared. The perspectives for the use of the cold moderator for a SANS spectrometer at the IBR-2 are discussed. The advantages of the YuMO spectrometer with the thermal moderator with respect to the tested cold moderator are shown

Thermal denaturation of protein studied by terahertz time-domain spectroscopy

Science.gov (United States)

Fu, Xiuhua; Li, Xiangjun; Liu, Jianjun; Du, Yong; Hong, Zhi

2012-12-01

In this study, the absorption spectra of native or thermal protein were measured in 0.2-1.4THz using terahertz time-domain spectroscopy (THz-TDS) system at room temperature, their absorption spectra and the refractive spectra were obtained. Experimental results indicate that protein both has strong absorption but their characteristics were not distinct in the THz region, and the absorption decreased during thermal denatured state. In order to prove protein had been denatured, we used Differential scanning calorimeter (DSC) measured their denatured temperature, from their DSC heating traces, collagen Td=101℃, Bovine serum albumin Td=97℃. While we also combined the Fourier transform infrared spectrometer (FTIR) to investigate their secondary and tertiary structure before and after denatuation, but the results did not have the distinct changes. We turned the absorption spectra and the refractive spectra to the dielectric spectra, and used the one-stage Debye model simulated the terahertz dielectric spectra of protein before and after denaturation. This research proved that the terahertz spectrum technology is feasible in testing protein that were affected by temperature or other factors which can provide theoretical foundation in the further study about the THz spectrum of protein and peptide temperature stability.

Determination of the optical absorption spectra of thin layers from their photoacoustic spectra

Science.gov (United States)

Bychto, Leszek; Maliński, Mirosław; Patryn, Aleksy; Tivanov, Mikhail; Gremenok, Valery

2018-05-01

This paper presents a new method for computations of the optical absorption coefficient spectra from the normalized photoacoustic amplitude spectra of thin semiconductor samples deposited on the optically transparent and thermally thick substrates. This method was tested on CuIn(Te0.7Se0.3)2 thin films. From the normalized photoacoustic amplitude spectra, the optical absorption coefficient spectra were computed with the new formula as also with the numerical iterative method. From these spectra, the value of the energy gap of the thin film material and the type of the optical transitions were determined. From the experimental optical transmission spectra, the optical absorption coefficient spectra were computed too, and compared with the optical absorption coefficient spectra obtained from photoacoustic spectra.

Plasma Emission Spectra of Opuntia Nopalea Obtained with Microsecond Laser Pulses

International Nuclear Information System (INIS)

Ponce, L.; Flores, T.; Arronte, A.; Flores, A.

2008-01-01

Laser-induced Plasma Spectroscopy was performed during the spines ablation of Opuntia by using Nd:YAG microsecond laser pulses. The results show strong absorption in Glochids that causes the intense electronic noise on the spectra. This process is consider suitable for practical elimination of spines in alimentary products like opuntia

Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage.

Science.gov (United States)

Zhao, Panpan; Zhong, Jiayong; Liu, Wanting; Zhao, Jing; Zhang, Gong

2017-12-01

Multiple search engines based on various models have been developed to search MS/MS spectra against a reference database, providing different results for the same data set. How to integrate these results efficiently with minimal compromise on false discoveries is an open question due to the lack of an independent, reliable, and highly sensitive standard. We took the advantage of the translating mRNA sequencing (RNC-seq) result as a standard to evaluate the integration strategies of the protein identifications from various search engines. We used seven mainstream search engines (Andromeda, Mascot, OMSSA, X!Tandem, pFind, InsPecT, and ProVerB) to search the same label-free MS data sets of human cell lines Hep3B, MHCCLM3, and MHCC97H from the Chinese C-HPP Consortium for Chromosomes 1, 8, and 20. As expected, the union of seven engines resulted in a boosted false identification, whereas the intersection of seven engines remarkably decreased the identification power. We found that identifications of at least two out of seven engines resulted in maximizing the protein identification power while minimizing the ratio of suspicious/translation-supported identifications (STR), as monitored by our STR index, based on RNC-Seq. Furthermore, this strategy also significantly improves the peptides coverage of the protein amino acid sequence. In summary, we demonstrated a simple strategy to significantly improve the performance for shotgun mass spectrometry by protein-level integrating multiple search engines, maximizing the utilization of the current MS spectra without additional experimental work.

High resolution solid-state NMR spectroscopy of the Yersinia pestis outer membrane protein Ail in lipid membranes

International Nuclear Information System (INIS)

Yao, Yong; Dutta, Samit Kumar; Park, Sang Ho; Rai, Ratan; Fujimoto, L. Miya; Bobkov, Andrey A.; Opella, Stanley J.; Marassi, Francesca M.

2017-01-01

The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail’s biological activity. Here, we demonstrate that high-resolution solid-state NMR spectra can be obtained from samples of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The spectra, obtained with 13 C or 1 H detection, have very narrow line widths (0.40–0.60 ppm for 13 C, 0.11–0.15 ppm for 1 H, and 0.46–0.64 ppm for 15 N) that are consistent with a high level of sample homogeneity. The spectra enable resonance assignments to be obtained for N, CO, CA and CB atomic sites from 75 out of 156 residues in the sequence of Ail, including 80% of the transmembrane region. The 1 H-detected solid-state NMR 1 H/ 15 N correlation spectra obtained for Ail in liposomes compare very favorably with the solution NMR 1 H/ 15 N TROSY spectra obtained for Ail in nanodiscs prepared with a similar lipid to protein molar ratio. These results set the stage for studies of the molecular basis of the functional interactions of Ail with its protein partners from human host cells, as well as the development of drugs targeting Ail.

Identifying inter-residue resonances in crowded 2D {sup 13}C-{sup 13}C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Miao Yimin; Cross, Timothy A. [Florida State University, Department of Chemistry and Biochemistry (United States); Fu Riqiang, E-mail: rfu@magnet.fsu.edu [National High Magnet Field Lab (United States)

2013-07-15

The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially enhanced resolution in crowded two-dimensional {sup 13}C-{sup 13}C chemical shift correlation spectra is presented. With the analyses of {sup 13}C-{sup 13}C spin diffusion in simple spin systems, difference spectroscopy is proposed to partially separate the spin diffusion resonances of relatively short intra-residue distances from the longer inter-residue distances, leading to a better identification of the inter-residue resonances. Here solid-state magic-angle-spinning NMR spectra of the full length M2 protein embedded in synthetic lipid bilayers have been used to illustrate the resolution enhancement in the difference spectra. The integral membrane M2 protein of Influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Based on known amino acid resonance assignments from amino acid specific labeled samples of truncated M2 sequences or from time-consuming 3D experiments of uniformly labeled samples, some inter-residue resonances of the full length M2 protein can be identified in the difference spectra of uniformly {sup 13}C labeled protein that are consistent with the high resolution structure of the M2 (22-62) protein (Sharma et al., Science 330(6003):509-512, 2010)

The effects of general anesthetics on ESR spectra of spin labels in phosphatidylcholine vesicles containing purified Na,K-ATPase or microsomal protein

Science.gov (United States)

Shibuya, Makiko; Hiraoki, Toshifumi; Kimura, Kunie; Fukushima, Kazuaki; Suzuki, Kuniaki

2012-12-01

We investigated the effects of general anesthetics on liposome containing spin labels, 5-doxyl stearic acid (5-DSA) and 16-doxyl stearic acid (16-DSA), and purified Na,K-ATPase or membrane protein of microsome using an electron spin resonance (ESR) spectroscopy. The spectra of 16-DSA in liposomes with both proteins showed three sharp signals compared with 5-DSA. The difference in the order parameter S value of 5-DSA and 16-DSA suggested that the nitroxide radical location of 5-DSA and 16-DSA were different in the membrane bilayer. The results were almost the same as those obtained in liposomes without proteins. The addition of sevoflurane, isoflurane, halothane, ether, ethanol and propofol increased the intensity of the signals, but the clinical concentrations of anesthetics did not significantly alter the S and τ values, which are indices of the fluidity of the membrane. These results suggest that anesthetics remain on the surface of the lipid bilayer and do not act on both the inside hydrophobic area and the relatively hydrophilic area near the surface. These results and others also suggest that the existence of Na,K-ATPase and microsomal proteins did not affect the environment around the spin labels in the liposome and the effects of anesthetics on liposome as a model membrane.

High resolution solid-state NMR spectroscopy of the Yersinia pestis outer membrane protein Ail in lipid membranes

Energy Technology Data Exchange (ETDEWEB)

Yao, Yong; Dutta, Samit Kumar [Sanford Burnham Prebys Medical Discovery Institute (United States); Park, Sang Ho; Rai, Ratan [University of California San Diego, Department of Chemistry and Biochemistry (United States); Fujimoto, L. Miya; Bobkov, Andrey A. [Sanford Burnham Prebys Medical Discovery Institute (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbp.edu [Sanford Burnham Prebys Medical Discovery Institute (United States)

2017-03-15

The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail’s biological activity. Here, we demonstrate that high-resolution solid-state NMR spectra can be obtained from samples of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The spectra, obtained with {sup 13}C or {sup 1}H detection, have very narrow line widths (0.40–0.60 ppm for {sup 13}C, 0.11–0.15 ppm for {sup 1}H, and 0.46–0.64 ppm for {sup 15}N) that are consistent with a high level of sample homogeneity. The spectra enable resonance assignments to be obtained for N, CO, CA and CB atomic sites from 75 out of 156 residues in the sequence of Ail, including 80% of the transmembrane region. The {sup 1}H-detected solid-state NMR {sup 1}H/{sup 15}N correlation spectra obtained for Ail in liposomes compare very favorably with the solution NMR {sup 1}H/{sup 15}N TROSY spectra obtained for Ail in nanodiscs prepared with a similar lipid to protein molar ratio. These results set the stage for studies of the molecular basis of the functional interactions of Ail with its protein partners from human host cells, as well as the development of drugs targeting Ail.

Scikit-spectra: Explorative Spectroscopy in Python

Directory of Open Access Journals (Sweden)

Adam Hughes

2015-06-01

Full Text Available Scikit-spectra is an intuitive framework for explorative spectroscopy in Python. Scikit-spectra leverages the Pandas library for powerful data processing to provide datastructures and an API designed for spectroscopy. Utilizing the new IPython Notebook widget system, scikit-spectra is headed towards a GUI when you want it, API when you need it approach to spectral analysis. As an application, analysis is presented of the surface-plasmon resonance shift in a solution of gold nanoparticles induced by proteins binding to the gold’s surface. Please refer to the scikit-spectra website for full documentation and support: http://hugadams.github.io/scikit-spectra/

Photoelectron and Auger-electron spectra of Cl{sub 3}SiSi(CH{sub 3}){sub 3} obtained by using monochromatized synchrotron radiation

Energy Technology Data Exchange (ETDEWEB)

Nagaoka, Shin-ichi, E-mail: nagaoka@ehime-u.ac.jp [Department of Chemistry, Faculty of Science and Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577 (Japan); Endo, Hikaru; Nagai, Kanae [Department of Chemistry, Faculty of Science and Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577 (Japan); Takahashi, Osamu [Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima 739-8511 (Japan); Tamenori, Yusuke [Synchrotron Radiation Research Institute/SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun 679-5198 (Japan); Suzuki, Isao H. [Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba 305-0801 (Japan); Advanced Institute of Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba 305-8568 (Japan)

2014-08-15

Highlights: • Various photo- and Auger-electron spectra of Cl{sub 3}SiSi(CH{sub 3}){sub 3} vapor were measured. • The measured spectra were interpreted with the aid of some calculations. • The spectra showed profiles close to those expected from SiCl{sub 4} and Si(CH{sub 3}){sub 4}. • These results were discussed in conjunction with site-specific fragmentation. - Abstract: A variety of photoelectron and Auger-electron spectra of 1,1,1-trimethyltrichlorodisilane vapor (Cl{sub 3}SiSi(CH{sub 3}){sub 3}) were measured by using monochromatized synchrotron radiation and a hemispherical electron energy analyzer. The measured spectra were interpreted with the aid of some calculations by means of the outer valence Green's function (OVGF) method or the density-functional-theory (DFT) method. Since Cl{sub 3}SiSi(CH{sub 3}){sub 3} consists of -SiCl{sub 3} and -Si(CH{sub 3}){sub 3} moieties, the experimental core-electron binding-energies were compared with those of tetrachlorosilane and tetramethylsilane (SiCl{sub 4} and Si(CH{sub 3}){sub 4}, respectively). This comparison showed that electronic properties of Cl{sub 3}SiSi(CH{sub 3}){sub 3} hold a close correlation with those of SiCl{sub 4} and Si(CH{sub 3}){sub 4}. Si:L{sub 23}VV, Cl:L{sub 23}VV and C:KVV Auger-electron spectra of Cl{sub 3}SiSi(CH{sub 3}){sub 3} also showed profiles close to those expected from the spectra of SiCl{sub 4} and Si(CH{sub 3}){sub 4}. The results obtained here were discussed in conjunction with electronic relaxation leading to site-specific fragmentation.

Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation

Directory of Open Access Journals (Sweden)

Haruki Nakamura

2012-09-01

Full Text Available We have developed a method for estimating protein-ligand binding free energy (DG based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the DG value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA and dihedral angles of the protein-ligand complex system as the entropy terms of the DG estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated DG values was 0.81, and the average error of DG was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation.

Medium-range structural properties of vitreous germania obtained through first-principles analysis of vibrational spectra.

Science.gov (United States)

Giacomazzi, Luigi; Umari, P; Pasquarello, Alfredo

2005-08-12

We analyze the principal vibrational spectra of vitreous GeO(2) and derive therefrom structural properties referring to length scales beyond the basic tetrahedral unit. We generate a model structure that yields a neutron structure factor in accord with experiment. The inelastic-neutron, the infrared, and the Raman spectra, calculated within a density-functional approach, also agree with respective experimental spectra. The accord for the Raman spectrum supports a Ge-O-Ge angle distribution centered at 135 degrees. The Raman feature X(2) is found to result from vibrations in three-membered rings, and therefore constitutes a distinctive characteristic of the medium-range structure.

Conformational aspects of proteins at the air/water interface studied by infrared reflection-adsorption spectroscopy

NARCIS (Netherlands)

Martin, A.H.; Meinders, M.B.J.; Bos, M.A.; Cohen Stuart, M.A.; Vliet, van T.

2003-01-01

From absorption spectra obtained with infrared reflection-absorption spectroscopy (IRRAS), it is possible to obtain information on conformational changes at a secondary folding level of proteins adsorbed at the air/water interface. In addition, information on protein concentration at the interface

Conformational aspects of proteins at the air/water interface studied by infrared reflection-absorption spectroscopy

NARCIS (Netherlands)

Martin, A.H.; Meinders, M.B.J.; Bos, M.A.; Cohen Stuart, M.A.; Vliet, T. van

2003-01-01

From absorption spectra obtained with infrared reflection - absorption spectroscopy (IRRAS), it is possible to obtain information on conformational changes at a secondary folding level of proteins adsorbed at the air/water interface. In addition, information on protein concentration at the interface

Improving interpretation of infrared spectra for OM characterization by subtraction of spectra from incinerated samples

Science.gov (United States)

Ellerbrock, Ruth H.; Gerke, Horst H.; Leue, Martin

2017-04-01

Non-destructive methods such as diffuse reflectance infrared Fourier transform spectroscopy (DRIFT) have been applied to characterize organic matter (OM) at intact structural surfaces among others. However, it is often difficult to distinguish effects of organic components on DRIFT signal intensities from those of mineral components. The objective of this study was to re-evaluate DRIFT spectra from intact earthworm burrow walls and coated cracks to improve the interpretation of C-H and C=O bands. We compared DRIFT and transmission Fourier transform infrared (FTIR) spectra of entire samples that were from the same pedogenetic soil horizon, but different in mineral composition and texture (i.e., glacial till versus loess). Spectra of incinerated samples were subtracted from the original spectra. Transmission FTIR and DRIFT spectra were almost identical for entire soil samples. However, the DRIFT spectra were affected by the bulk mode bands (i.e., wavenumbers 2000 to 1700 cm-1) that affected spectral resolution and reproducibility. The ratios between C-H and C=O band intensities as indicator for OM quality obtained with DRIFT were smaller than those obtained from transmission FTIR. A spectral subtraction procedure was found to reduce effects of mineral absorption bands on DRIFT spectra allowing an improved interpretation. DRIFT spectroscopy as a non-destructive method for analyzing OM composition at intact surfaces in structured soils could be calibrated with information obtained with the more detailed transmission FTIR and complementary methods.

Response spectra in alluvial soils

International Nuclear Information System (INIS)

Chandrasekharan, A.R.; Paul, D.K.

1975-01-01

For aseismic design of structures, the ground motion data is assumed either in the form of ground acceleration as a function of time or indirectly in the form of response spectra. Though the response spectra approach has limitations like not being applicable for nonlinear problems, it is usually used for structures like nuclear power plants. Fifty accelerograms recorded at alluvial sites have been processed. Since different empirical formulas relating acceleration with magnitude and distance give a wide scatter of values, peak ground acceleration alone cannot be the parameter as is assumed by a number of authors. The spectra corresponding to 5% damping have been normalised with respect to three parameters, namely, peak ground acceleration, peak ground velocity and a nondimensional quantity ad/v 2 . Envelopee of maxima and minima as well as average response spectra has been obtained. A comparison with the USAEC spectra has been made. A relation between ground acceleration, ground velocity and ad/v 2 has been obtained which would nearly give the same magnification of the response. A design response spectra for alluvial soils has been recommended. (author)

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

International Nuclear Information System (INIS)

Bellstedt, Peter; Herbst, Christian; Häfner, Sabine; Leppert, Jörg; Görlach, Matthias; Ramachandran, Ramadurai

2012-01-01

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC′C and 3D C′NCA with sequential 13 C acquisitions, 3D NHH and 3D NC′H with sequential 1 H acquisitions and 3D CANH and 3D C’NH with broadband 13 C– 15 N mixing are demonstrated using microcrystalline samples of the β1 immunoglobulin binding domain of protein G (GB1) and the chicken α-spectrin SH3 domain.

FITPULS: a code for obtaining analytic fits to aggregate fission-product decay-energy spectra

International Nuclear Information System (INIS)

LaBauve, R.J.; George, D.C.; England, T.R.

1980-03-01

The operation and input to the FITPULS code, recently updated to utilize interactive graphics, are described. The code is designed to retrieve data from a library containing aggregate fine-group spectra (150 energy groups) from fission products, collapse the data to few groups (up to 25), and fit the resulting spectra along the cooling time axis with a linear combination of exponential functions. Also given in this report are useful results for aggregate gamma and beta spectra from the decay of fission products released from 235 U irradiated with a pulse (10 -4 s irradiation time) of thermal neutrons. These fits are given in 22 energy groups that are the first 22 groups of the LASL 25-group decay-energy group structure, and the data are expressed both as MeV per fission second and particles per fission second; these pulse functions are readily folded into finite fission histories. 65 figures, 11 tables

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

Energy Technology Data Exchange (ETDEWEB)

Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

2012-12-15

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

Generation of synthetic gamma spectra with MATLAB

International Nuclear Information System (INIS)

Palmerio, Julian J.; Coppo, Anibal D.

2009-01-01

Objectives: The aim of this work is the simulation of gamma spectra using the MATLAB program to generate the calibration curves in efficiency, which will be used to measure radioactive waste in drums. They are necessary for the proper characterization of these drums. A Monte Carlo simulation was basically developed with the random number generator Mersenne Twister and nuclear data obtained from NIST. This paper shows the results obtained and difficulties encountered until today. The physical correction of the simulated spectra has been the only aspect we have been working, up to this moment. Procedures: A simplified representation of the 'Laboratorio de Verificacion y Control de la Calidad' was chosen. Drums with cemented liquid waste are routinely measured in this laboratory. The commercial program MCNP was also used to get a valid reference in the field of simulation of spectra. We analyzed the spectra obtained by MATLAB in the light of classical literature photon detection and the spectrum obtained by MCNP. Conclusions: Currently the program developed seems adequate to simulate a measurement in the 'Laboratorio de Verificacion y Control de la Calidad'. The spectra obtained by MATLAB seem to physically represent what is observed in real spectra. However, it is a slow program. The current development efforts are directed to improve the speed of simulation. An alternative is to use the CUDA language for NVIDIA video cards to parallelized the simulation. An adequate simulation of the electronic measuring chain is also needed to obtain better representations of the shapes of the peaks. (author)

SimLabel: a graphical user interface to simulate continuous wave EPR spectra from site-directed spin labeling experiments.

Science.gov (United States)

Etienne, E; Le Breton, N; Martinho, M; Mileo, E; Belle, V

2017-08-01

Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the residue level, structural transitions in proteins. SDSL-EPR is based on the selective grafting of a paramagnetic label on the protein under study, followed by cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give reliable interpretation on biological system dynamics, numerical simulations of the spectra are required. Such spectral simulations can be carried out by coding in MATLAB using functions from the EasySpin toolbox. For non-expert users of MATLAB, this could be a complex task or even impede the use of such simulation tool. We developed a graphical user interface called SimLabel dedicated to run cw EPR spectra simulations particularly coming from SDSL-EPR experiments. Simlabel provides an intuitive way to visualize, simulate, and fit such cw EPR spectra. An example of SDSL-EPR spectra simulation concerning the study of an intrinsically disordered region undergoing a local induced folding is described and discussed. We believe that this new tool will help the users to rapidly obtain reliable simulated spectra and hence facilitate the interpretation of their results. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Prediction of peak overlap in NMR spectra

International Nuclear Information System (INIS)

Hefke, Frederik; Schmucki, Roland; Güntert, Peter

2013-01-01

Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.

Resonance Raman and surface-enhanced resonance Raman spectra of LH2 antenna complex from Rhodobacter sphaeroides and Ectothiorhodospira sp. excited in the Qx and Qy transitions.

Science.gov (United States)

Chumanov, G; Picorel, R; Ortiz de Zarate, I; Cotton, T M; Seibert, M

2000-05-01

Well-resolved vibrational spectra of LH2 complex isolated from two photosynthetic bacteria, Rhodobacter sphaeroides and Ectothiorhodospira sp., were obtained using surface-enhanced resonance Raman scattering (SERRS) exciting into the Qx and the Qy transitions of bacteriochlorophyll a. High-quality SERRS spectra in the Qy region were accessible because the strong fluorescence background was quenched near the roughened Ag surface. A comparison of the spectra obtained with 590 nm and 752 nm excitation in the mid- and low-frequency regions revealed spectral differences between the two LH2 complexes as well as between the LH2 complexes and isolated bacteriochlorophyll a. Because peripheral modes of pigments contribute mainly to the low-frequency spectral region, frequencies and intensities of many vibrational bands in this region are affected by interactions with the protein. The results demonstrate that the microenvironment surrounding the pigments within the two LH2 complexes is somewhat different, despite the fact that the complexes exhibit similar electronic absorption spectra. These differences are most probably due to specific pigment-pigment and pigment-protein interactions within the LH2 complexes, and the approach might be useful for addressing subtle static and dynamic structural variances between pigment-protein complexes from different sources or in complexes altered chemically or genetically.

In-cell NMR spectroscopy of proteins inside Xenopus laevis oocytes

International Nuclear Information System (INIS)

Sakai, Tomomi; Tochio, Hidehito; Tenno, Takeshi; Ito, Yutaka; Kokubo, Tetsuro; Hiroaki, Hidekazu; Shirakawa, Masahiro

2006-01-01

In-cell NMR is an application of solution NMR that enables the investigation of protein conformations inside living cells. We have measured in-cell NMR spectra in oocytes from the African clawed frog Xenopus laevis. 15 N-labeled ubiquitin, its derivatives and calmodulin were injected into Xenopus oocytes and two-dimensional 1 H- 15 N correlation spectra of the proteins were obtained. While the spectrum of wild-type ubiquitin in oocytes had rather fewer cross-peaks compared to its in vitro spectrum, ubiquitin derivatives that are presumably unable to bind to ubiquitin-interacting proteins gave a markedly larger number of cross-peaks. This observation suggests that protein-protein interactions between ubiquitin and ubiquitin-interacting proteins may cause NMR signal broadening, and hence spoil the quality of the in-cell HSQC spectra. In addition, we observed the maturation of ubiquitin precursor derivative in living oocytes using the in-cell NMR technique. This process was partly inhibited by pre-addition of ubiquitin aldehyde, a specific inhibitor for ubiquitin C-terminal hydrolase (UCH). Our work demonstrates the potential usefulness of in-cell NMR with Xenopus oocytes for the investigation of protein conformations and functions under intracellular environmental conditions

A setup for simultaneous measurement of infrared spectra and light scattering signals: Watching amyloid fibrils grow from intact proteins

Energy Technology Data Exchange (ETDEWEB)

Li, Yang; Maurer, Jürgen; Roth, Andreas; Vogel, Vitali; Winter, Ernst; Mäntele, Werner, E-mail: maentele@biophysik.uni-frankfurt.de [Institut für Biophysik, Goethe-Universität Frankfurt am Main, Max-von Laue-Straße 1, D-60438 Frankfurt am Main (Germany)

2014-08-15

A setup for the simultaneous measurement of mid-infrared spectra and static light scattering is described that can be used for the analysis of the formation of nanoscale and microscopic aggregates from smaller molecules to biopolymers. It can be easily integrated into sample chambers of infrared spectrometers or combined with laser beams from tunable infrared lasers. Here, its use for the analysis of the formation of amyloid fibrils from intact proteins is demonstrated. The formation of amyloid fibrils or plaques from proteins is a widespread and pathogenetic relevant process, and a number of diseases are caused and correlated with the deposition of amyloid fibrils in cells and tissues. The molecular mechanisms of these transformations, however, are still unclear. We report here the simultaneous measurement of infrared spectra and static light scattering for the analysis of fibril formation from egg-white lysozyme. The transformation of the native form into non-native forms rich in β-sheet structure is measured by analysis of the amide I spectral region in the infrared spectra, which is sensitive for local structures. At the same time, light scattering signals at forward direction as well as the forward/backward ratio, which are sensitive for the number of scattering centers and their approximate sizes, respectively, are collected for the analysis of fibril growth. Thermodynamic and kinetic parameters as well as mechanistic information are deduced from the combination of the two complementary techniques.

A setup for simultaneous measurement of infrared spectra and light scattering signals: Watching amyloid fibrils grow from intact proteins

Science.gov (United States)

Li, Yang; Maurer, Jürgen; Roth, Andreas; Vogel, Vitali; Winter, Ernst; Mäntele, Werner

2014-08-01

A setup for the simultaneous measurement of mid-infrared spectra and static light scattering is described that can be used for the analysis of the formation of nanoscale and microscopic aggregates from smaller molecules to biopolymers. It can be easily integrated into sample chambers of infrared spectrometers or combined with laser beams from tunable infrared lasers. Here, its use for the analysis of the formation of amyloid fibrils from intact proteins is demonstrated. The formation of amyloid fibrils or plaques from proteins is a widespread and pathogenetic relevant process, and a number of diseases are caused and correlated with the deposition of amyloid fibrils in cells and tissues. The molecular mechanisms of these transformations, however, are still unclear. We report here the simultaneous measurement of infrared spectra and static light scattering for the analysis of fibril formation from egg-white lysozyme. The transformation of the native form into non-native forms rich in β-sheet structure is measured by analysis of the amide I spectral region in the infrared spectra, which is sensitive for local structures. At the same time, light scattering signals at forward direction as well as the forward/backward ratio, which are sensitive for the number of scattering centers and their approximate sizes, respectively, are collected for the analysis of fibril growth. Thermodynamic and kinetic parameters as well as mechanistic information are deduced from the combination of the two complementary techniques.

Covariance NMR Processing and Analysis for Protein Assignment.

Science.gov (United States)

Harden, Bradley J; Frueh, Dominique P

2018-01-01

During NMR resonance assignment it is often necessary to relate nuclei to one another indirectly, through their common correlations to other nuclei. Covariance NMR has emerged as a powerful technique to correlate such nuclei without relying on error-prone peak peaking. However, false-positive artifacts in covariance spectra have impeded a general application to proteins. We recently introduced pre- and postprocessing steps to reduce the prevalence of artifacts in covariance spectra, allowing for the calculation of a variety of 4D covariance maps obtained from diverse combinations of pairs of 3D spectra, and we have employed them to assign backbone and sidechain resonances in two large and challenging proteins. In this chapter, we present a detailed protocol describing how to (1) properly prepare existing 3D spectra for covariance, (2) understand and apply our processing script, and (3) navigate and interpret the resulting 4D spectra. We also provide solutions to a number of errors that may occur when using our script, and we offer practical advice when assigning difficult signals. We believe such 4D spectra, and covariance NMR in general, can play an integral role in the assignment of NMR signals.

Quantitative surface studies of protein adsorption by infrared spectroscopy. II. Quantification of adsorbed and bulk proteins

International Nuclear Information System (INIS)

Fink, D.J.; Hutson, T.B.; Chittur, K.K.; Gendreau, R.M.

1987-01-01

Attenuated total reflectance Fourier transform infrared spectra of surface-adsorbed proteins are correlated with concentration measurements determined by 125 I-labeled proteins. This paper demonstrates that linear correlations between the intensity of the major bands of proteins and the quantity of proteins can be obtained for human albumin and immunoglobulin G up to surface concentrations of approximately 0.25 microgram/cm2. A poorer correlation was observed for human fibrinogen. A linear correlation was also observed between the concentration in the bulk solution and the major bands of albumin up to a concentration of 60 mg/ml

The amino-terminal structure of human fragile X mental retardation protein obtained using precipitant-immobilized imprinted polymers

Science.gov (United States)

Hu, Yufeng; Chen, Zhenhang; Fu, Yanjun; He, Qingzhong; Jiang, Lun; Zheng, Jiangge; Gao, Yina; Mei, Pinchao; Chen, Zhongzhou; Ren, Xueqin

2015-03-01

Flexibility is an intrinsic property of proteins and essential for their biological functions. However, because of structural flexibility, obtaining high-quality crystals of proteins with heterogeneous conformations remain challenging. Here, we show a novel approach to immobilize traditional precipitants onto molecularly imprinted polymers (MIPs) to facilitate protein crystallization, especially for flexible proteins. By applying this method, high-quality crystals of the flexible N-terminus of human fragile X mental retardation protein are obtained, whose absence causes the most common inherited mental retardation. A novel KH domain and an intermolecular disulfide bond are discovered, and several types of dimers are found in solution, thus providing insights into the function of this protein. Furthermore, the precipitant-immobilized MIPs (piMIPs) successfully facilitate flexible protein crystal formation for five model proteins with increased diffraction resolution. This highlights the potential of piMIPs for the crystallization of flexible proteins.

Design spectra development considering short time histories

International Nuclear Information System (INIS)

Weiner, E.O.

1983-01-01

Two separate programs, MODQKE and MDOF, were written to provide a capability of obtaining equipment spectra from design spectra. MODQKE generates or modifies acceleration histories to conform with design spectra pertaining to, say, a foundation. MDOF is a simple linear modal superposition program that solves for equipment support histories using the design spectra conforming histories as input. Equipment spectra, then, are obtained from the support histories using MODQKE. MODQKE was written to modify or provide new histories with special attention paid to short seismic records. A technique from the open literature was borrowed to generate an initial history that approximates a given response spectrum. Further refinement is done with smoothing cycles in which several correction signals are added to the history in a way that produces a least squares fit between actual and prescribed spectra. Provision is made for history shaping, a baseline correction, and final scaling. MODQKE performance has been demonstrated with seven examples having zero to ten percent damping ratios, and 2.5 seconds to 20 seconds durations and a variety of target spectra. The examples show the program is inexpensive to use. MDOF is a simple modal superposition program. It has no eigensolver, and the user supplies mode shapes, frequencies, and participation factors as input. Floor spectra can be generated from design spectra by using a history from MODQKE that conforms to the design spectrum as input to MDOF. Floor motions from MDOF can be fed back to MODQKE without modification to obtain the floor spectra. A simple example is given to show how equipment mass effects can be incorporated into the MDOF solution. Any transient solution capability can be used to replace MDOF. For example, a direct transient approach may be desirable if both the equipment and floor structures are to be included in the model with different damping fractions. (orig./HP)

Identification of membrane proteins by tandem mass spectrometry of protein ions

Science.gov (United States)

Carroll, Joe; Altman, Matthew C.; Fearnley, Ian M.; Walker, John E.

2007-01-01

The most common way of identifying proteins in proteomic analyses is to use short segments of sequence (“tags”) determined by mass spectrometric analysis of proteolytic fragments. The approach is effective with globular proteins and with membrane proteins with significant polar segments between membrane-spanning α-helices, but it is ineffective with other hydrophobic proteins where protease cleavage sites are either infrequent or absent. By developing methods to purify hydrophobic proteins in organic solvents and by fragmenting ions of these proteins by collision induced dissociation with argon, we have shown that partial sequences of many membrane proteins can be deduced easily by manual inspection. The spectra from small proteolipids (1–4 transmembrane α-helices) are dominated usually by fragment ions arising from internal amide cleavages, from which internal sequences can be obtained, whereas the spectra from larger membrane proteins (5–18 transmembrane α-helices) often contain fragment ions from N- and/or C-terminal parts yielding sequences in those regions. With these techniques, we have, for example, identified an abundant protein of unknown function from inner membranes of mitochondria that to our knowledge has escaped detection in proteomic studies, and we have produced sequences from 10 of 13 proteins encoded in mitochondrial DNA. They include the ND6 subunit of complex I, the last of its 45 subunits to be analyzed. The procedures have the potential to be developed further, for example by using newly introduced methods for protein ion dissociation to induce fragmentation of internal regions of large membrane proteins, which may remain partially folded in the gas phase. PMID:17720804

Case study on human α1-antitrypsin: Recombinant protein titers obtained by commercial ELISA kits are inaccurate

DEFF Research Database (Denmark)

Hansen, Henning Gram; Kildegaard, Helene Faustrup; Min Lee, Gyun

2016-01-01

Accurate titer determination of recombinant proteins is crucial for evaluating protein production cell lines and processes. Even though enzyme-linked immunosorbent assay (ELISA) is the most widely used assay for determining protein titer, little is known about the accuracy of commercially available...... ELISA kits. We observed that estimations of recombinant human ø1-antitrypsin (rø1AT) titer by Coomassie-stained SDS-PAGE gels did not correspond to previously obtained titers obtained by a commercially available ELISA kit. This prompted us to develop two independent quantification assays based...... on biolayer interferometry and reversed-phase high-performance liquid chromatography. We compared the rø1AT titer obtained by these assays with three different off-the-shelf ELISA kits and found that the ELISA kits led to inconsistent results. The data presented here show that recombinant protein titers...

Protein-observed (19)F-NMR for fragment screening, affinity quantification and druggability assessment.

Science.gov (United States)

Gee, Clifford T; Arntson, Keith E; Urick, Andrew K; Mishra, Neeraj K; Hawk, Laura M L; Wisniewski, Andrea J; Pomerantz, William C K

2016-08-01

NMR spectroscopy can be used to quantify the binding affinity between proteins and low-complexity molecules, termed 'fragments'; this versatile screening approach allows researchers to assess the druggability of new protein targets. Protein-observed (19)F-NMR (PrOF NMR) using (19)F-labeled amino acids generates relatively simple spectra that are able to provide dynamic structural information toward understanding protein folding and function. Changes in these spectra upon the addition of fragment molecules can be observed and quantified. This protocol describes the sequence-selective labeling of three proteins (the first bromodomains of Brd4 and BrdT, and the KIX domain of the CREB-binding protein) using commercially available fluorinated aromatic amino acids and fluorinated precursors as example applications of the method developed by our research group. Fragment-screening approaches are discussed, as well as Kd determination, ligand-efficiency calculations and druggability assessment, i.e., the ability to target these proteins using small-molecule ligands. Experiment times on the order of a few minutes and the simplicity of the NMR spectra obtained make this approach well-suited to the investigation of small- to medium-sized proteins, as well as the screening of multiple proteins in the same experiment.

Blood proteins analysis by Raman spectroscopy method

Science.gov (United States)

Artemyev, D. N.; Bratchenko, I. A.; Khristoforova, Yu. A.; Lykina, A. A.; Myakinin, O. O.; Kuzmina, T. P.; Davydkin, I. L.; Zakharov, V. P.

2016-04-01

This work is devoted to study the possibility of plasma proteins (albumin, globulins) concentration measurement using Raman spectroscopy setup. The blood plasma and whole blood were studied in this research. The obtained Raman spectra showed significant variation of intensities of certain spectral bands 940, 1005, 1330, 1450 and 1650 cm-1 for different protein fractions. Partial least squares regression analysis was used for determination of correlation coefficients. We have shown that the proposed method represents the structure and biochemical composition of major blood proteins.

Automation of peak-tracking analysis of stepwise perturbed NMR spectra

Energy Technology Data Exchange (ETDEWEB)

Banelli, Tommaso; Vuano, Marco [Università di Udine, Dipartimento di Area Medica (Italy); Fogolari, Federico [INBB (Italy); Fusiello, Andrea [Università di Udine, Dipartimento Politecnico di Ingegneria e Architettura (Italy); Esposito, Gennaro [INBB (Italy); Corazza, Alessandra, E-mail: alessandra.corazza@uniud.it [Università di Udine, Dipartimento di Area Medica (Italy)

2017-02-15

We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TinT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak.The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered. TinT was applied successfully to several protein systems during a temperature ramp in isotope exchange experiments. A comparison with a state-of-the-art algorithm showed promising results for great numbers of spectra and low signal to noise ratios, when the graduality of the perturbation is appropriate. TinT can be applied to different kinds of high throughput chemical shift mapping experiments, with quasi-continuous variations, in which a quantitative automated recognition is crucial.

Monitoring Protein Fouling on Polymeric Membranes Using Ultrasonic Frequency-Domain Reflectometry

Directory of Open Access Journals (Sweden)

Robin Fong

2011-08-01

Full Text Available Novel signal-processing protocols were used to extend the in situ sensitivity of ultrasonic frequency-domain reflectometry (UFDR for real-time monitoring of microfiltration (MF membrane fouling during protein purification. Different commercial membrane materials, with a nominal pore size of 0.2 µm, were challenged using bovine serum albumin (BSA and amylase as model proteins. Fouling induced by these proteins was observed in flat-sheet membrane filtration cells operating in a laminar cross-flow regime. The detection of membrane-associated proteins using UFDR was determined by applying rigorous statistical methodology to reflection spectra of ultrasonic signals obtained during membrane fouling. Data suggest that the total power reflected from membrane surfaces changes in response to protein fouling at concentrations as low as 14 μg/cm2, and results indicate that ultrasonic spectra can be leveraged to detect and monitor protein fouling on commercial MF membranes.

Interpreting peptide mass spectra by VEMS

DEFF Research Database (Denmark)

Mathiesen, Rune; Lundsgaard, M.; Welinder, Karen G.

2003-01-01

the calculated and the experimental mass spectrum of the called peptide. The program package includes four accessory programs. VEMStrans creates protein databases in FASTA format from EST or cDNA sequence files. VEMSdata creates a virtual peptide database from FASTA files. VEMSdist displays the distribution......Most existing Mass Spectra (MS) analysis programs are automatic and provide limited opportunity for editing during the interpretation. Furthermore, they rely entirely on publicly available databases for interpretation. VEMS (Virtual Expert Mass Spectrometrist) is a program for interactive analysis...... of peptide MS/MS spectra imported in text file format. Peaks are annotated, the monoisotopic peaks retained, and the b-and y-ion series identified in an interactive manner. The called peptide sequence is searched against a local protein database for sequence identity and peptide mass. The report compares...

Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra

International Nuclear Information System (INIS)

Oezguen, Numan; Adamian, Larisa; Xu Yuan; Rajarathnam, Krishna; Braun, Werner

2002-01-01

The NOAH/DIAMOD suite uses feedback filtering and self-correcting distance geometry to generate 3D structures from unassigned NOESY spectra. In this study we determined the minimum set of experiments needed to generate a high quality structure bundle. Different combinations of 3D 15 N-edited, 13 C-edited HSQC-NOESY and 2D homonuclear 1 H- 1 H NOESY spectra of the 77 amino acid protein, myeloid progenitor inhibitory factor-1 (MPIF-1) were used as input for NOAH/DIAMOD calculations. The quality of the assignments of NOESY cross peaks and the accuracy of the automatically generated 3D structures were compared to those obtained with a conventional manual procedure. Combining data from two types of experiments synergistically increased the number of peaks assigned unambiguously in both individual spectra. As a general trend for the accuracy of the structures we observed structural variations in the backbone fold of the final structures of about 2 A for single spectral data, of 1 A to 1.5 A for double spectral data, and of 0.6 A for triple spectral data sets. The quality of the assignments and 3D structures from the optimal data using all three spectra were similar to those obtained from traditional assignment methods with structural variations within the bundle of 0.6 A and 1.3 A for backbone and heavy atoms, respectively. Almost all constraints (97%) of the automatic NOESY cross peak assignments were cross compatible with the structures from the conventional manual assignment procedure, and an even larger proportion (99%) of the manually derived constraints were compatible with the automatically determined 3D structures. The two mean structures determined by both methods differed only by 1.3 A rmsd for the backbone atoms in the well-defined regions of the protein. Thus NOAD/DIAMOD analysis of spectra from labeled proteins provides a reliable method for high throughput analysis of genomic targets

Surface-enhanced Raman spectroscopy of saliva proteins for the noninvasive differentiation of benign and malignant breast tumors

Science.gov (United States)

Feng, Shangyuan; Huang, Shaohua; Lin, Duo; Chen, Guannan; Xu, Yuanji; Li, Yongzeng; Huang, Zufang; Pan, Jianji; Chen, Rong; Zeng, Haishan

2015-01-01

The capability of saliva protein analysis, based on membrane protein purification and surface-enhanced Raman spectroscopy (SERS), for detecting benign and malignant breast tumors is presented in this paper. A total of 97 SERS spectra from purified saliva proteins were acquired from samples obtained from three groups: 33 healthy subjects; 33 patients with benign breast tumors; and 31 patients with malignant breast tumors. Subtle but discernible changes in the mean SERS spectra of the three groups were observed. Tentative assignments of the saliva protein SERS spectra demonstrated that benign and malignant breast tumors led to several specific biomolecular changes of the saliva proteins. Multiclass partial least squares–discriminant analysis was utilized to analyze and classify the saliva protein SERS spectra from healthy subjects, benign breast tumor patients, and malignant breast tumor patients, yielding diagnostic sensitivities of 75.75%, 72.73%, and 74.19%, as well as specificities of 93.75%, 81.25%, and 86.36%, respectively. The results from this exploratory work demonstrate that saliva protein SERS analysis combined with partial least squares–discriminant analysis diagnostic algorithms has great potential for the noninvasive and label-free detection of breast cancer. PMID:25609959

Obtaining classical swine fever virus E2 recombinant protein and DNA-vaccine on the basis of one subunit

International Nuclear Information System (INIS)

Deryabin, O.; Deryabina, O.; Verbitskiy, P.; Kordyum, V.

2005-01-01

Three forms of E2 recombinant protein were expressed in E. coli. Swine sera obtained against different forms of the recombinant protein were cross-studied with indirect ELISA. Using individual proteins as an antigen, only 15% of sera against other forms of protein reacted positively, while 100% of heterologous sera showed positive reaction with fused protein. Challenge experiments showed the existence of protective action only from the individual protein. Specificity and activity of sera obtained from the animals after control challenge was confirmed in a blocking variant of ELISA. Genetic construction used a eukaryotic vector that contained the E2 protein gene. Immunization of mice with the resulting DNA induced synthesis of specific antibodies, the titre of which increased considerably after additional single immunization with the E2 recombinant protein, expressed in E. coli. This demonstrated the effectiveness of animal priming by DNA vaccine, and the possibility of using the E2 recombinant protein in E. coli for booster vaccination. (author)

Obtaining a citric tristeza virus p65 protein antibody and preliminary results of p65 in vivo expression

Directory of Open Access Journals (Sweden)

Yanneth Torres

2003-07-01

Full Text Available The citric tristeza virus (CTV belongs to the Closteroviridae family which indudes the only vegetal viruses possessing genes homologous to HSP70 thermal cellular shock proteins in their genome. Such is the case of the gene encoding for the CTV p65 protein which presents high homology with the HSP70 protein family. It has been shown recently that HSP70h viral proteins (such as CTV p65 are involved both in viral assembly, as a microtubule binding protein, and in cell-cell movement. Since CTV is the most deleterious citrus pathogen, understanding this protein's role in the pathogenesis process is important. Rabbits were immunised with four synthetic peptides (corresponding to CTV p65 thermal shock protein's carboxyl-terminal region to obtain polyclonal antibodies. All the peptides used were immunogenic, even though two of them showed greater response. Whilst none of the antibodies obtained reacted to non-infected plant extract, the p65 proteins was detected in extracts taken from citric plants infected with CTV Based on the antibody's reaction to two Colombian isolates having different serological characteristics, the p65 antibody's immunological behaviour appeared to be independent of the symptomatic severity of the CTV isolates. It was shown that the ORF encoded for the HSP70 homologue in CTV was expressed in vivo, even though the p65 antibody was only detected in concentrated protein extracts taken from infected plants, supporting reports from other studies that the concentration of this protein in plants infected with CTV is low. This is the first time that a polyclonal CTV antibody has been obtained in Colombia against p65 (a protein intervening in viral assembly and movement. Adapting a technique for obtaining p65 antibodies by using synthetic peptides as immunogens could be useful in the future for detecting or diagnosing p65 proteins present in different Colombian CTV isolates, especially in developing studies contributing towards greater

Amide or Amine: Determining the Origin of the 3300 cm−1 NH Mode in Protein SFG Spectra Using 15N Isotope Labels

Science.gov (United States)

Weidner, Tobias; Breen, Nicholas F.; Drobny, Gary P.; Castner, David G.

2009-01-01

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases a strong NH mode near 3300 cm−1 is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode we studied 15N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an α-helical secondary structure (LKα14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. 15N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm−1 on SiO2 and 13 cm−1 on CaF2. This clearly shows the 3300 cm−1 NH feature is associated with side chain NH stretches and not with backbone amide modes. PMID:19873996

Amide or amine: determining the origin of the 3300 cm(-1) NH mode in protein SFG spectra using 15N isotope labels.

Science.gov (United States)

Weidner, Tobias; Breen, Nicholas F; Drobny, Gary P; Castner, David G

2009-11-26

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases, a strong NH mode near 3300 cm(-1) is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain, since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode, we studied (15)N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an alpha-helical secondary structure (LKalpha14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. (15)N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm(-1) on SiO(2) and 13 cm(-1) on CaF(2). This clearly shows the 3300 cm(-1) NH feature is associated with side chain NH stretches and not with backbone amide modes.

Biosynthetically directed fractional 13C labeling facilitates identification of Phe and Tyr aromatic signals in proteins

International Nuclear Information System (INIS)

Jacob, Jaison; Louis, John M.; Nesheiwat, Issa; Torchia, Dennis A.

2002-01-01

Analysis of 2D [ 13 C, 1 H]-HSQC spectra of biosynthetic fractionally 13 C labeled proteins is a reliable, straightforward means to obtain stereospecific assignments of Val and Leu methyl sites in proteins. Herein we show that the same fractionally labeled protein sample facilitates observation and identification of Phe and Tyr aromatic signals. This is the case, in part, because the fractional 13 C labeling yields aromatic rings in which some of the 13 C- 13 C J-couplings, present in uniformly labeled samples, are absent. Also, the number of homonuclear J-coupling partners differs for the δ-, ε- and ζ-carbons. This enabled us to vary their signal intensities in distinctly different ways by appropriately setting the 13 C constant-time period in 2D [ 13 C, 1 H]-HSQC spectra. We illustrate the application of this approach to an 18 kDa protein, c-VIAF, a modulator of apoptosis. In addition, we show that cancellation of the aromatic 13 C CSA and 13 C- 1 H dipolar interactions can be fruitfully utilized in the case of the fractionally labeled sample to obtain high resolution 13 C constant-time spectra with good sensitivity

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system

Energy Technology Data Exchange (ETDEWEB)

Ikeya, Teppei [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany); Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune [Tokyo Metropolitan University, Graduate School of Science (Japan)], E-mail: kainosho@nmr.chem.metro-u.ac.jp; Guentert, Peter [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany)], E-mail: guentert@em.uni-frankfurt.de

2009-08-15

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly {sup 13}C/{sup 15}N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional 'through-bond' spectrum (and 2D HSQC spectra) in addition to the {sup 13}C-edited and {sup 15}N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system

International Nuclear Information System (INIS)

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Guentert, Peter

2009-01-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13 C/ 15 N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional 'through-bond' spectrum (and 2D HSQC spectra) in addition to the 13 C-edited and 15 N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

Science.gov (United States)

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

2009-08-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Study of the hydration of globular proteins by broad NMR lines method

Energy Technology Data Exchange (ETDEWEB)

Blicharska, B [Uniwersytet Jagiellonski, Krakow (Poland). Instytut Fizyki

1973-01-01

Spectra of proteins and polypeptides obtained by means of a NMR broad line spectrometer consist of broad and thin lines. These broad and thin lines are attributed to proteins and to water absorbed on the surfaces of proteins respectively. The behaviour of the thin line in the spectra of lyophilizated albumin of the egg white has been studied in the temperature range from -42 to 20/sup 0/C. The amount of water has been found by the simple method of weighing and has been equal about 7% of the total weight. It has been found that the water absorbed on the surface of the lyophilizated proteins gives a thinner line in comparison to the water absorbed on molecules of proteins in water solutions and that the correlation time is about 10/sup 3/ times greater.

Automated Peak Picking and Peak Integration in Macromolecular NMR Spectra Using AUTOPSY

Science.gov (United States)

Koradi, Reto; Billeter, Martin; Engeli, Max; Güntert, Peter; Wüthrich, Kurt

1998-12-01

A new approach for automated peak picking of multidimensional protein NMR spectra with strong overlap is introduced, which makes use of the program AUTOPSY (automatedpeak picking for NMRspectroscopy). The main elements of this program are a novel function for local noise level calculation, the use of symmetry considerations, and the use of lineshapes extracted from well-separated peaks for resolving groups of strongly overlapping peaks. The algorithm generates peak lists with precise chemical shift and integral intensities, and a reliability measure for the recognition of each peak. The results of automated peak picking of NOESY spectra with AUTOPSY were tested in combination with the combined automated NOESY cross peak assignment and structure calculation routine NOAH implemented in the program DYANA. The quality of the resulting structures was found to be comparable with those from corresponding data obtained with manual peak picking.

Identification of ultramodified proteins using top-down spectra

Energy Technology Data Exchange (ETDEWEB)

Liu, Xiaowen; Hengel, Shawna M.; Wu, Si; Tolic, Nikola; Pasa-Tolic, Ljiljana; Pevzner, Pavel A.

2013-04-10

Post-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some ultramodified proteins (like histones) have multiple PTMs forming PTM patterns that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying individual PTMs within short peptides, it is unable to identify PTM patterns spread along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many protein forms of histone H4 and benchmark it against the currently accepted software tools.

Reconstruction of neutron spectra through neural networks

International Nuclear Information System (INIS)

Vega C, H.R.; Hernandez D, V.M.; Manzanares A, E.

2003-01-01

A neural network has been used to reconstruct the neutron spectra starting from the counting rates of the detectors of the Bonner sphere spectrophotometric system. A group of 56 neutron spectra was selected to calculate the counting rates that would produce in a Bonner sphere system, with these data and the spectra it was trained the neural network. To prove the performance of the net, 12 spectra were used, 6 were taken of the group used for the training, 3 were obtained of mathematical functions and those other 3 correspond to real spectra. When comparing the original spectra of those reconstructed by the net we find that our net has a poor performance when reconstructing monoenergetic spectra, this attributes it to those characteristic of the spectra used for the training of the neural network, however for the other groups of spectra the results of the net are appropriate with the prospective ones. (Author)

Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK

International Nuclear Information System (INIS)

Würz, Julia M.; Güntert, Peter

2017-01-01

The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity. The performance of CYPICK was evaluated for a variety of spectra from different proteins by systematic comparison with peak lists obtained by other, manual or automated, peak picking methods, as well as by analyzing the results of automated chemical shift assignment and structure calculation based on input peak lists from CYPICK. The results show that CYPICK yielded peak lists that compare in most cases favorably to those obtained by other automated peak pickers with respect to the criteria of finding a maximal number of real signals, a minimal number of artifact peaks, and maximal correctness of the chemical shift assignments and the three-dimensional structure obtained by fully automated assignment and structure calculation.

Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK

Energy Technology Data Exchange (ETDEWEB)

Würz, Julia M.; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany)

2017-01-15

The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity. The performance of CYPICK was evaluated for a variety of spectra from different proteins by systematic comparison with peak lists obtained by other, manual or automated, peak picking methods, as well as by analyzing the results of automated chemical shift assignment and structure calculation based on input peak lists from CYPICK. The results show that CYPICK yielded peak lists that compare in most cases favorably to those obtained by other automated peak pickers with respect to the criteria of finding a maximal number of real signals, a minimal number of artifact peaks, and maximal correctness of the chemical shift assignments and the three-dimensional structure obtained by fully automated assignment and structure calculation.

Climatology of tropospheric vertical velocity spectra

Science.gov (United States)

Ecklund, W. L.; Gage, K. S.; Balsley, B. B.; Carter, D. A.

1986-01-01

Vertical velocity power spectra obtained from Poker Flat, Alaska; Platteville, Colorado; Rhone Delta, France; and Ponape, East Caroline Islands using 50-MHz clear-air radars with vertical beams are given. The spectra were obtained by analyzing the quietest periods from the one-minute-resolution time series for each site. The lengths of available vertical records ranged from as long as 6 months at Poker Flat to about 1 month at Platteville. The quiet-time vertical velocity spectra are shown. Spectral period ranging from 2 minutes to 4 hours is shown on the abscissa and power spectral density is given on the ordinate. The Brunt-Vaisala (B-V) periods (determined from nearby sounding balloons) are indicated. All spectra (except the one from Platteville) exhibit a peak at periods slightly longer than the B-V period, are flat at longer periods, and fall rapidly at periods less than the B-V period. This behavior is expected for a spectrum of internal waves and is very similar to what is observed in the ocean (Eriksen, 1978). The spectral amplitudes vary by only a factor of 2 or 3 about the mean, and show that under quiet conditions vertical velocity spectra from the troposphere are very similar at widely different locations.

Raman spectra of lithium compounds

Science.gov (United States)

Gorelik, V. S.; Bi, Dongxue; Voinov, Y. P.; Vodchits, A. I.; Gorshunov, B. P.; Yurasov, N. I.; Yurasova, I. I.

2017-11-01

The paper is devoted to the results of investigating the spontaneous Raman scattering spectra in the lithium compounds crystals in a wide spectral range by the fibre-optic spectroscopy method. We also present the stimulated Raman scattering spectra in the lithium hydroxide and lithium deuteride crystals obtained with the use of powerful laser source. The symmetry properties of the lithium hydroxide, lithium hydroxide monohydrate and lithium deuteride crystals optical modes were analyzed by means of the irreducible representations of the point symmetry groups. We have established the selection rules in the Raman and infrared absorption spectra of LiOH, LiOH·H2O and LiD crystals.

Assessment of nonenzymatic glycation in protein by FTIR spectroscopy

Science.gov (United States)

Otero de Joshi, Virginia; Joshi, Narahari V.; Gil, Herminia; Velasquez, William; Contreras, Silvia; Marquez, Glevis

1999-04-01

Detection of nonenzymatic glycated proteins is a very significant feature in diabetes, aging and related diseases, therefore we have carried out an FTIR spectroscopic study for glycated and native proteins such as (gamma) -globulin, human serum albumin. For this purpose, commercially available proteins were glycated by a usual procedure and their FTIR spectra were recorded together with that of the native ones. In order to follow the changes in time, (gamma) -globulin was glycated during 1, 2, 3, 5 and 8 weeks and their spectra were recorded. Direct verification was obtained by examining a model unit where the -NH2 group was attached to glucose. The spectrum shows a strong peak at 3500 cm-1 confirming the observed variation in time dependent spectra. The general features of the spectra are very similar and there was no additional structure or change in the peaks. This is understandable as not all the lysine residues are glycated, only a small fraction. Glucose is attached to the (epsilon) -amino group of lysine to form Amadori products, and therefore, the vibrational modes corresponding to the (epsilon) -NH2 unit of lysine are expected to be altered. This region exactly lies in the Amide I region of protein structure. Careful investigation of this part, indeed, shows a complex structure originated from alternations of -NH2 group. Thus, the present investigation indicates that an optical approach could be a rapid and effective method to identify the nonenzymatic glycation process.

Time-of-flight neutron spectra measurements in Zenith

Energy Technology Data Exchange (ETDEWEB)

Barclay, F R; Coates, M S; Diment, K M; Durrani, S A; Gayther, D B; Poole, M J; Reed, D L

1962-01-15

Neutron spectra in the second core loading of ZENITH have been measured using a neutron chopper. Spectra at two positions in the reactore core were obtained over a range of temperatures extending to 650 deg C.

Adjusted neutron spectra of STEK cores for reactivity calculations

International Nuclear Information System (INIS)

Dekker, J.W.M.; Dragt, J.B.; Janssen, A.J.; Heijboer, R.J.; Klippel, H.Th.

1978-02-01

Neutron flux and adjoint flux spectra form a pre-requisite in the analysis of reactivity worth data measured in the STEK facility. First, a survey of all available information about these spectra is given. Next a special application of a general adjustment method is described. This method has been used to obtain adjusted STEK group flux and adjoint flux spectra, starting from calculated spectra. These theoretical spectra were adjusted to reactivity worths of natural boron (nat. B) and 235 U as well as a number of fission reaction rates. As a by-product in this adjustment calculation adjusted fission group cross sections of 235 U were obtained. The results, viz. group fluxes and adjoint fluxes and adjusted fission cross sections of 235 U are given. They have been used for the interpretation of fission product reactivity worth measurements made in STEK

Tchebichef image moment approach to the prediction of protein secondary structures based on circular dichroism.

Science.gov (United States)

Li, Sha Sha; Li, Bao Qiong; Liu, Jin Jin; Lu, Shao Hua; Zhai, Hong Lin

2018-04-20

Circular dichroism (CD) spectroscopy is a widely used technique for the evaluation of protein secondary structures that has a significant impact for the understanding of molecular biology. However, the quantitative analysis of protein secondary structures based on CD spectra is still a hard work due to the serious overlap of the spectra corresponding to different structural motifs. Here, Tchebichef image moment (TM) approach is introduced for the first time, which can effectively extract the chemical features in CD spectra for the quantitative analysis of protein secondary structures. The proposed approach was applied to analyze reference set. and the obtained results were evaluated by the strict statistical parameters such as correlation coefficient, cross-validation correlation coefficient and root mean squared error. Compared with several specialized prediction methods, TM approach provided satisfactory results, especially for turns and unordered structures. Our study indicates that TM approach can be regarded as a feasible tool for the analysis of the secondary structures of proteins based on CD spectra. An available TMs package is provided and can be used directly for secondary structures prediction. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

A Hybrid Dry and Aqueous Fractionation Method to Obtain Protein-Rich Fractions from Quinoa (Chenopodium quinoa Willd)

NARCIS (Netherlands)

Avila Ruiz, Geraldine; Arts, Anke; Minor, Marcel; Schutyser, Maarten

2016-01-01

Combination of dry and aqueous fractionation is investigated to obtain protein-rich fractions from quinoa in a milder and more sustainable way compared to conventional wet fractionation. Dry fractionation of quinoa involved milling and subsequent air classification, generating a protein-enriched

Spectra and depth-dose deposition in a polymethylmethacrylate breast phantom obtained by experimental and Monte Carlo method; Espectros e deposicao de dose em profundidade em phantom de mama de polimetilmetacrilato: obtencao experimental e por metodo de Monte Carlo

Energy Technology Data Exchange (ETDEWEB)

David, Mariano G.; Pires, Evandro J.; Magalhaes, Luis A.; Almeida, Carlos E. de; Alves, Carlos F.E., E-mail: marianogd08@gmail.com [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Lab. Ciencias Radiologicas; Albuquerque, Marcos A. [Coordenacao dos Programas de Pos-Graduacao de Engenharia (COPPE/UFRJ), RJ (Brazil). Instituto Alberto Luiz Coimbra; Bernal, Mario A. [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Instituto de Fisica Gleb Wataghin; Peixoto, Jose G. [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

2012-08-15

This paper focuses on the obtainment, using experimental and Monte Carlo-simulated (MMC) methods, of the photon spectra at various depths and depth-dose deposition curves for x-rays beams used in mammography, obtained on a polymethylmethacrylate (PMMA) breast phantom. Spectra were obtained for 28 and 30 kV quality-beams and the corresponding average energy values (Emed) were calculated. For the experimental acquisition was used a Si-PIN photodiode spectrometer and for the MMC simulations the PENELOPE code was employed. The simulated and the experimental spectra show a very good agreement, which was corroborated by the low differences found between the Emed values. An increase in the Emed values and a strong attenuation of the beam through the depth of the PMMA phantom was also observed. (author)

Study on Properties of Energy Spectra of the Molecular Crystals

Science.gov (United States)

Pang, Xiao-Feng; Chen, Xiang-Rong

The energy-spectra of nonlinear vibration of molecular crystals such as acetanilide have been calculated by using discrete nonlinear Schrödinger equation appropriate to the systems, containing various interactions. The energy levels including higher excited states are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. We further give the features of distribution of the energy-spectra for the acetanilide. Using the energy spectra we also explained well experimental results obtained by Careri et al..

Aircraft Measurements of Atmospheric Kinetic Energy Spectra

DEFF Research Database (Denmark)

Lundtang Petersen, Erik; Lilly, D. K.

1983-01-01

Wind velocity data obtained from a jet airliner are used to construct kinetic energy spectra over the range of wavelengths from 2.5 to 2500 km. The spectra exhibit an approximate -5/3 slope for wavelengths of less than about 150 km, steepening to about -2.2 at larger scales. These results support...

Egg-yolk protein by-product as a source of ACE-inhibitory peptides obtained with using unconventional proteinase from Asian pumpkin (Cucurbita ficifolia).

Science.gov (United States)

Eckert, Ewelina; Zambrowicz, Aleksandra; Pokora, Marta; Setner, Bartosz; Dąbrowska, Anna; Szołtysik, Marek; Szewczuk, Zbigniew; Polanowski, Antoni; Trziszka, Tadeusz; Chrzanowska, Józefa

2014-10-14

In the present study angiotensin I-converting enzyme (ACE) inhibitory peptides were isolated from egg-yolk protein preparation (YP). Enzymatic hydrolysis conducted using unconventional enzyme from Cucurbita ficifolia (dose: 1000 U/mg of hydrolyzed YP (E/S (w/w)=1:7.52)) was employed to obtain protein hydrolysates. The 4-h hydrolysate exhibited a significant (IC₅₀=482.5 μg/mL) ACE inhibitory activity. Moreover, hydrolysate showed no cytotoxic activity on human and animal cell lines which makes it a very useful multifunctional method for peptide preparation. The compiled isolation procedure (ultrafiltration, size-exclusion chromatography and RP-HPLC) of bioactive peptides from YP hydrolysate resulted in obtaining peptides with the strong ACE inhibitory activity. One homogeneous and three heterogeneous peptide fractions were identified. The peptides were composed of 9-18 amino-acid residues, including mainly arginine and leucine at the N-terminal positions. To confirm the selected bioactive peptide sequences their analogs were chemically synthesized and tested. Peptide LAPSLPGKPKPD showed the strongest ACE inhibitory activity, with IC₅₀ value of 1.97 μmol/L. Peptides with specific biological activity can be used in pharmaceutical, cosmetic or food industries. Because of their potential role as physiological modulators, as well as theirhigh safety profile, they can be used as natural pharmacological compounds or functional food ingredients. The development of biotechnological solutions to obtain peptides with desired biological activity is already in progress. Studies in this area are focused on using unconventional highly specific enzymes and more efficient methods developed to conduct food process technologies. Natural peptides have many advantages. They are mainly toxicologically safe, have wide spectra of therapeutic actions, exhibit less side effects compared to synthetic drugs and are more efficiently absorbed in the intestinal tract. The complexity of

Calculation of neutron spectra produced in neutron generator target: Code testing.

Science.gov (United States)

Gaganov, V V

2018-03-01

DT-neutron spectra calculated using the SRIANG code was benchmarked against the results obtained by widely used Monte Carlo codes: PROFIL, SHORIN, TARGET, ENEA-JSI, MCUNED, DDT and NEUSDESC. The comparison of the spectra obtained by different codes confirmed the correctness of SRIANG calculations. The cross-checking of the compared spectra revealed some systematic features and possible errors of analysed codes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determination of the secondary structure content of proteins in aqueous solutions from their amide I and amide II infrared bands. Comparison between classical and partial least-squares methods

International Nuclear Information System (INIS)

Dousseau, F.; Pezolet, M.

1990-01-01

A method for estimating protein secondary structure from infrared spectra has been developed. The infrared spectra of H 2 O solutions of 13 proteins of known crystal structure have been recorded and corrected for the spectral contribution of water in the amide I and II region by using the algorithm of Dousseau et al. This calibration set of proteins has been analyzed by using either a classical least-squares (CLS) method or the partial least-squares (PLS) method. The pure-structure spectra calculated by the classical least-squares method are in good agreement with spectra of poly(L-lysine) in the α-helix, β-sheet, and undefined conformations. The results show that the best agreement between the secondary structure determined by X-ray crystal-lography and that predicted by infrared spectroscopy is obtained when both the amide I and II bands are used to generate the calibration set, when the PLS method is used, and when it is assumed that the secondary structure of proteins is composed of only four types of structure: ordered and disordered α-helices, β-sheet, and undefined conformation. Attempts to include turns in the secondary structure estimation have led to a loss of accuracy. The spectra of the calibration proteins were also recorded in 2 H 2 O solution. After correction for the contribution of the combination band of 2 H 2 O in the amide I' band region, the spectra were analyzed with PLS, but the results were not as good as for the spectra obtained in H 2 O, especially for the α-helical conformation

Protein Analysis by Mass Spectrometry

Directory of Open Access Journals (Sweden)

Cindic, M.

2008-04-01

Full Text Available Soft ionization techniques, electrospray (ESI and matrix-assisted laser desorption/ionization (MALDI make the analysis of biomolecules by mass spectrometry (MS possible. MS is used for determination of the molecular weight of peptides and protein, sequence analysis, characterization of protein-ligand interactions etc. The detection limit, resolution and mass accuracy depend on instrument used (Table 1. Impurities (buffers, salts, detergents can reduce the ion intensities or even totally suppress them, so a separation method (chromatography, 2D-gel electrophoresis must be used for purification of the sample.Molecular mass of intact protein can be determined by ESI or MALDI MS. Multiply charged ions are produced by ESI MS, while singly charged ions are predominant in MALDI spectra (Fig. 2.Sequence analysis of proteins by MS can be performed using peptide mass fingerprint. In this method, proteins are separated by 2-D gel electrophoresis and digested with specific protease (Table 2 or digested and then separated by two-dimensional chromatography (Fig. 1. The obtained peptide mixtures are analyzed by MS or MALDI-TOF technique. The masses determined by MS are compared with calculated masses from database entries. Different algorithms have been developed for protein identification. Example of posttranslational modifications (N- and O-glycosylation and protein sequence complex analysis after dual digestion (endoproteinase digestion followed by endoglycosidase digestion is shown in Fig. 3.It is known that detection of peptides by MS is influenced by intrinsic properties like amino acid composition, the basicity of the C-terminal amino acid, hydrophobicity, etc. Arginine-containing peptides dominate in MS spectra of tryptic digest, so the chemical derivatization of lysine terminal residue by O-methilisourea or 2-methoxy-4,5-1H-imidazole was suggested (Fig. 4.The peptide mass fingerprint method can be improved further by peptide fragmentation using tandem

Theoretical analysis of time-dependent neutron spectra in bulk assemblies

International Nuclear Information System (INIS)

Akimoto, Tadashi; Ogawa, Yuichi; Togawa, Orihiko.

1988-01-01

Time-dependent neutron spectra in an iron assembly and in a graphite assembly are obtained with the one-dimensional S N calculation, in order an attempt to investigate the availability of these spectra to the benchmark test by the LINAC-TOF method for evaluation of nuclear data and numerical methods. The group constants are taken from the JAERI FAST SET Version 1, 2 and the ABBN SET. It was demonstrated by a sensitivity test that the time-dependent neutron spectra are sensitive to changes in the inelastic scattering cross section data in the iron assembly and to changes in the elastic scattering cross section data in the graphite assembly. Moreover, it is shown that the time-dependent spectra in the graphite assembly are sensitive to the group structure. Because some information about the neutron transport phenomena which has not been obtained in the stationary spectra is observed in the time-dependent spectra, the availability of the benchmark test based on the time-dependent spectra is indicated from the theoretical analysis. (author)

Vibronic spectra of Gd3+ in metaphosphate glasses: Comparison with Raman and infrared spectra

International Nuclear Information System (INIS)

Hall, D.W.; Brawer, S.A.; Weber, M.J.

1982-01-01

Vibronic sidebands associated with the 6 P/sub 7/2/→ 8 S/sub 7/2/ transition of Gd 3+ -doped metaphosphate glasses are observed using line-narrowed fluorescence techniques. Glasses having metal cations of different mass and charge (La,Al,Mg,Ba) are examined. Vibronic spectra, which probe vibrations about the rare-earth element site, are compared with polarized Raman scattering data and the infrared dielectric constant obtained from near-normal reflectance measurements. Results indicate that in metaphosphate glasses vibronic selection rules are similar to HV (vertical height) Raman selection rules. The wavelengths and relative intensities of peaks in the high-frequency portion of the vibronic spectra change with respect to corresponding peaks in the Raman spectra when the mass and/or charge of Gd 3+ differs significantly from that of the metal cation

Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.

Science.gov (United States)

Woys, Ann Marie; Almeida, Aaron M; Wang, Lu; Chiu, Chi-Cheng; McGovern, Michael; de Pablo, Juan J; Skinner, James L; Gellman, Samuel H; Zanni, Martin T

2012-11-21

protected inside the macrocycle. This work provides calculated and experimentally verified couplings for parallel β-sheets that can be used in structure-based models to simulate and interpret the infrared spectra of β-sheet containing proteins and protein assemblies, such as amyloid fibers.

Deconvolution of Complex 1D NMR Spectra Using Objective Model Selection.

Directory of Open Access Journals (Sweden)

Travis S Hughes

Full Text Available Fluorine (19F NMR has emerged as a useful tool for characterization of slow dynamics in 19F-labeled proteins. One-dimensional (1D 19F NMR spectra of proteins can be broad, irregular and complex, due to exchange of probe nuclei between distinct electrostatic environments; and therefore cannot be deconvoluted and analyzed in an objective way using currently available software. We have developed a Python-based deconvolution program, decon1d, which uses Bayesian information criteria (BIC to objectively determine which model (number of peaks would most likely produce the experimentally obtained data. The method also allows for fitting of intermediate exchange spectra, which is not supported by current software in the absence of a specific kinetic model. In current methods, determination of the deconvolution model best supported by the data is done manually through comparison of residual error values, which can be time consuming and requires model selection by the user. In contrast, the BIC method used by decond1d provides a quantitative method for model comparison that penalizes for model complexity helping to prevent over-fitting of the data and allows identification of the most parsimonious model. The decon1d program is freely available as a downloadable Python script at the project website (https://github.com/hughests/decon1d/.

Decomposition of continuum {gamma}-ray spectra using synthesized response matrix

Energy Technology Data Exchange (ETDEWEB)

Jandel, M.; Morhac, M.; Kliman, J.; Krupa, L.; Matousek, V. E-mail: vladislav.matousek@savba.sk; Hamilton, J.H.; Ramayya, A.V

2004-01-01

The efficient methods of decomposition of {gamma}-ray spectra, based on the Gold algorithm, are presented. They use a response matrix of Gammasphere, which was obtained by synthesis of simulated and interpolated response functions using a new developed interpolation algorithm. The decomposition method has been applied to the measured spectra of {sup 152}Eu and {sup 56}Co. The results show a very effective removal of the background counts and their concentration into the corresponding photopeaks. The peak-to-total ratio in the spectra achieved after applying the decomposition method is in the interval 0.95-0.99. In addition, a new advanced algorithm of the 'boosted' decomposition has been proposed. In the spectra obtained after applying the boosted decomposition to the measured spectra, very narrow photopeaks are observed with the counts concentrated to several channels.

Antioxidant and antimicrobial activity of lecithin free egg yolk protein preparation hydrolysates obtained with digestive enzymes

Directory of Open Access Journals (Sweden)

Aleksandra Zambrowicz

2012-12-01

Full Text Available ABSTRACT:Several biological activities have now been associated with egg protein- derived peptides, including antihypertensive, antimicrobial, immunomodulatory, anticancer and antioxidantactivities, highlighting the importance of these biopeptides in human health, and disease prevention and treatment. Special attention has been given to peptides with antioxidant and antimicrobial activities as a new source of natural preservatives in food industry. In this study, the antioxidant properties of the egg-yolk protein by-product (YP hydrolysates were evaluated based on their radical scavenging capacity (DPPH, Fe2+chelating effect and ferric reducing power (FRAP. Furthermore, antimicrobial properties of obtained hydrolysates against Bacillus species were studied. The degrees (DHs of hydrolysis for 4h hydrolysates were: 19.1%, 13.5% and 13.0%, for pepsin, chymotrypsin and trypsin, respectively. Pepsin was the most effective in producing the free amino groups (1410.3 μmolGly/g. The RP-HPLC profiles of the protein hydrolysates showed differences in the hydrophobicity of the generated peptides.Trypsin hydrolysate obtained after 4h reaction demonstrated the strongest DPPH free radical scavenging activity (0.85 µmol Troloxeq/mg. Trypsin and chymotrypsin hydrolysates obtained after 4h reaction exhibited 4 times higher ferric reducing capacity than those treated bypepsin. The hydrolysis products obtained from YP exhibited significant chelating activity. The 4h trypsin hydrolysate exhibited weak antimicrobial activity against B. subtilis B3; B. cereus B512; B. cereus B 3p and B. laterosporum B6.

Identification of Ultramodified Proteins Using Top-Down Mass Spectra

Energy Technology Data Exchange (ETDEWEB)

Liu, Xiaowen; Hengel, Shawna M.; Wu, Si; Tolic, Nikola; Pasa-Tolic, Ljiljana; Pevzner, Pavel A.

2013-11-05

Post-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some ultramodified proteins (like histones) have multiple PTMs forming PTM patterns that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying individual PTMs within short peptides, it is unable to identify PTM patterns spread along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many protein forms of histone H4 and benchmark it against the currently accepted software tools.

Infrared spectra of mineral species

CERN Document Server

Chukanov, Nikita V

2014-01-01

This book details more than 3,000 IR spectra of more than 2,000 mineral species collected during last 30 years. It features full descriptions and analytical data of each sample for which IR spectrum was obtained.

Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

Science.gov (United States)

Vendruscolo, M; Najmanovich, R; Domany, E

2000-02-01

We present a method to derive contact energy parameters from large sets of proteins. The basic requirement on which our method is based is that for each protein in the database the native contact map has lower energy than all its decoy conformations that are obtained by threading. Only when this condition is satisfied one can use the proposed energy function for fold identification. Such a set of parameters can be found (by perceptron learning) if Mp, the number of proteins in the database, is not too large. Other aspects that influence the existence of such a solution are the exact definition of contact and the value of the critical distance Rc, below which two residues are considered to be in contact. Another important novel feature of our approach is its ability to determine whether an energy function of some suitable proposed form can or cannot be parameterized in a way that satisfies our basic requirement. As a demonstration of this, we determine the region in the (Rc, Mp) plane in which the problem is solvable, i.e., we can find a set of contact parameters that stabilize simultaneously all the native conformations. We show that for large enough databases the contact approximation to the energy cannot stabilize all the native folds even against the decoys obtained by gapless threading.

Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases

International Nuclear Information System (INIS)

Nigsch, Florian; Mitchell, John B.O.

2008-01-01

The combination of models for protein target prediction with large databases containing toxicological information for individual molecules allows the derivation of 'toxiclogical' profiles, i.e., to what extent are molecules of known toxicity predicted to interact with a set of protein targets. To predict protein targets of drug-like and toxic molecules, we built a computational multiclass model using the Winnow algorithm based on a dataset of protein targets derived from the MDL Drug Data Report. A 15-fold Monte Carlo cross-validation using 50% of each class for training, and the remaining 50% for testing, provided an assessment of the accuracy of that model. We retained the 3 top-ranking predictions and found that in 82% of all cases the correct target was predicted within these three predictions. The first prediction was the correct one in almost 70% of cases. A model built on the whole protein target dataset was then used to predict the protein targets for 150 000 molecules from the MDL Toxicity Database. We analysed the frequency of the predictions across the panel of protein targets for experimentally determined toxicity classes of all molecules. This allowed us to identify clusters of proteins related by their toxicological profiles, as well as toxicities that are related. Literature-based evidence is provided for some specific clusters to show the relevance of the relationships identified

Library search with regular reflectance IR spectra

International Nuclear Information System (INIS)

Staat, H.; Korte, E.H.; Lampen, P.

1989-01-01

Characterisation in situ for coatings and other surface layers is generally favourable, but a prerequisite for precious items such as art objects. In infrared spectroscopy only reflection techniques are applicable here. However for attenuated total reflection (ATR) it is difficult to obtain the necessary optical contact of the crystal with the sample, when the latter is not perfectly plane or flexible. The measurement of diffuse reflectance demands a scattering sample and usually the reflectance is very poor. Therefore in most cases one is left with regular reflectance. Such spectra consist of dispersion-like feature instead of bands impeding their interpretation in the way the analyst is used to. Furthermore for computer search in common spectral libraries compiled from transmittance or absorbance spectra a transformation of the reflectance spectra is needed. The correct conversion is based on the Kramers-Kronig transformation. This somewhat time - consuming procedure can be speeded up by using appropriate approximations. A coarser conversion may be obtained from the first derivative of the reflectance spectrum which resembles the second derivative of a transmittance spectrum. The resulting distorted spectra can still be used successfully for the search in peak table libraries. Experiences with both transformations are presented. (author)

Temperatures of fragment kinetic energy spectra

International Nuclear Information System (INIS)

Bauer, W.

1995-01-01

Multifragmentation reactions without large compression in the initial state (proton-induced reactions, reverse kinematics, projectile fragmentation) are examined, and it is verified quantitatively that the high temperatures obtained from fragment kinetic energy spectra and lower temperatures obtained from observables such as level population or isotope ratios can be understood in a common framework

Pulse radiolysis experiments: synthesis and analysis of composite spectra

Energy Technology Data Exchange (ETDEWEB)

Schuler, R H; Buzzard, G K [Carnegie-Mellon Univ., Pittsburgh, Pa. (USA). Dept. of Chemistry

1976-01-01

Methods are outlined for compiling optical spectra obtained in pulse radiolysis experiments in a form suitable for detailed synthesis and analysis of composite spectra. The experimental data are processed with a programmable calculator having a cassette recorder for the storage of the output data files and a peripheral plotter. The spectra are first smoothed by fitting them parabolically segment by segment. The overall spectrum is then assembled in digital form by interpolating the fitted data on a 1 nm grid and the results are stored on cassette files for further processing. Composite spectra can be readily calculated and plotted from the data on these files or known components can be subtracted from observed spectra to examine underlying contributions. The use of the fairly simple data processing methods described here permits an interactive mode of operation by the investigator which can maximize insight into details of the various contributions to an observed spectrum. Several examples of the use of these methods in conjunction with data obtained with a computer controlled pulse radiolysis data acquisition system are given.

Determination of the fast neutrons spectra by the Elastic scattering method (n, p)

International Nuclear Information System (INIS)

Elizalde D, J.

1973-01-01

This work consists in determining the fast neutron spectra emitted by a Pu-Be isotopic source. The implemented technique is based in the spectrometry (n, p). This consists in making to fall on a fast neutrons beams (polyenergetic) over a thin film of hydrogenated material, detecting the spectra of emitted protons at a fix angle. The polyethylene film and the used solid state detector are inside of a vacuum chamber. The detector is placed at 30 degree with respect to direction of the incident neutrons beam. The protons spectra is stored in a multichannel. the energy is obtained with the prior calibration of the system. The data processing involves the transformation of the protons spectra observed at the falling on neutrons spectra over the film. The energy of the neutrons is related with that of the protons, according to the collision kinematical equations. The cross section of elastic collision of the neutrons with the hydrogen atoms is obtained from literature. Applying these relations to the observed spectra it is obtained the falling on neutron spectra over the film. (Author)

Graphics of diffraction spectra for PC

International Nuclear Information System (INIS)

Macias B, L.R.

1991-09-01

The materials can be studied by means of diffraction if these are crystalline; of the type of study will depend the technique to apply, the first step is the obtaining of a digital register that allows to build the corresponding spectra. The digital register should have well-known the initial and final angular data. The main objective of this work, is starting of a digital register of data or an arrangement CPSi type (counts per second measured by the detection system) generated by means of the diffractometer, to create the graph of the corresponding spectra in visual form in the screen of a microcomputer and if is required, to obtain the graph in printed form by means of the same computer program for microcomputer. (Author)

MoFi: A Software Tool for Annotating Glycoprotein Mass Spectra by Integrating Hybrid Data from the Intact Protein and Glycopeptide Level.

Science.gov (United States)

Skala, Wolfgang; Wohlschlager, Therese; Senn, Stefan; Huber, Gabriel E; Huber, Christian G

2018-04-18

Hybrid mass spectrometry (MS) is an emerging technique for characterizing glycoproteins, which typically display pronounced microheterogeneity. Since hybrid MS combines information from different experimental levels, it crucially depends on computational methods. Here, we describe a novel software tool, MoFi, which integrates hybrid MS data to assign glycans and other post-translational modifications (PTMs) in deconvoluted mass spectra of intact proteins. Its two-stage search algorithm first assigns monosaccharide/PTM compositions to each peak and then compiles a hierarchical list of glycan combinations compatible with these compositions. Importantly, the program only includes those combinations which are supported by a glycan library as derived from glycopeptide or released glycan analysis. By applying MoFi to mass spectra of rituximab, ado-trastuzumab emtansine, and recombinant human erythropoietin, we demonstrate how integration of bottom-up data may be used to refine information collected at the intact protein level. Accordingly, our software reveals that a single mass frequently can be explained by a considerable number of glycoforms. Yet, it simultaneously ranks proteoforms according to their probability, based on a score which is calculated from relative glycan abundances. Notably, glycoforms that comprise identical glycans may nevertheless differ in score if those glycans occupy different sites. Hence, MoFi exposes different layers of complexity that are present in the annotation of a glycoprotein mass spectrum.

Raman spectra of thiolated arsenicals with biological importance.

Science.gov (United States)

Yang, Mingwei; Sun, Yuzhen; Zhang, Xiaobin; McCord, Bruce; McGoron, Anthony J; Mebel, Alexander; Cai, Yong

2018-03-01

Surface enhanced Raman scattering (SERS) has great potential as an alternative tool for arsenic speciation in biological matrices. SERS measurements have advantages over other techniques due to its ability to maintain the integrity of arsenic species and its minimal requirements for sample preparation. Up to now, very few Raman spectra of arsenic compounds have been reported. This is particularly true for thiolated arsenicals, which have recently been found to be widely present in humans. The lack of data for Raman spectra in arsenic speciation hampers the development of new tools using SERS. Herein, we report the results of a study combining the analysis of experimental Raman spectra with that obtained from density functional calculations for some important arsenic metabolites. The results were obtained with a hybrid functional B3LYP approach using different basis sets to calculate Raman spectra of the selected arsenicals. By comparing experimental and calculated spectra of dimethylarsinic acid (DMA V ), the basis set 6-311++G** was found to provide computational efficiency and precision in vibrational frequency prediction. The Raman frequencies for the rest of organoarsenicals were studied using this basis set, including monomethylarsonous acid (MMA III ), dimethylarsinous acid (DMA III ), dimethylmonothioarinic acid (DMMTA V ), dimethyldithioarsinic acid (DMDTA V ), S-(Dimethylarsenic) cysteine (DMA III (Cys)) and dimethylarsinous glutathione (DMA III GS). The results were compared with fingerprint Raman frequencies from As─O, As─C, and As─S obtained under different chemical environments. These fingerprint vibrational frequencies should prove useful in future measurements of different species of arsenic using SERS. Copyright © 2017 Elsevier B.V. All rights reserved.

Denaturation and in Vitro Gastric Digestion of Heat-Treated Quinoa Protein Isolates Obtained at Various Extraction pH

NARCIS (Netherlands)

Ruiz, Geraldine Avila; Opazo-Navarrete, Mauricio; Meurs, Marlon; Minor, Marcel; Sala, Guido; Boekel, van Tiny; Stieger, Markus; Janssen, Anja E.M.

2016-01-01

The aim of this study was to determine the influence of heat processing on denaturation and digestibility properties of protein isolates obtained from sweet quinoa (Chenopodium quinoa Willd) at various extraction pH values (8, 9, 10 and 11). Pretreatment of suspensions of protein isolates at 60,

Bench mark spectra for high-energy neutron dosimetry

International Nuclear Information System (INIS)

Dierckx, R.

1986-01-01

To monitor radiation damage experiments, activation detectors are commonly used. The precision of the results obtained by the multiple foil analysis is largely increased by the intercalibration in bench-mark spectra. This technique is already used in dosimetry measurements for fission reactors. To produce neutron spectra similar to fusion reactor and high-energy high-intensity neutron sources (d-Li or spallation), accelerators can be used. Some possible solutions as p-Be and d-D 2 O neutron sources, useful as bench-mark spectra are described. (author)

Sequentially Integrated Optimization of the Conditions to Obtain a High-Protein and Low-Antinutritional Factors Protein Isolate from Edible Jatropha curcas Seed Cake.

Science.gov (United States)

León-López, Liliana; Dávila-Ortiz, Gloria; Jiménez-Martínez, Cristian; Hernández-Sánchez, Humberto

2013-01-01

Jatropha curcas seed cake is a protein-rich byproduct of oil extraction which could be used to produce protein isolates. The purpose of this study was the optimization of the protein isolation process from the seed cake of an edible provenance of J. curcas by an alkaline extraction followed by isoelectric precipitation method via a sequentially integrated optimization approach. The influence of four different factors (solubilization pH, extraction temperature, NaCl addition, and precipitation pH) on the protein and antinutritional compounds content of the isolate was evaluated. The estimated optimal conditions were an extraction temperature of 20°C, a precipitation pH of 4, and an amount of NaCl in the extraction solution of 0.6 M for a predicted protein content of 93.3%. Under these conditions, it was possible to obtain experimentally a protein isolate with 93.21% of proteins, 316.5 mg 100 g(-1) of total phenolics, 2891.84 mg 100 g(-1) of phytates and 168 mg 100 g(-1) of saponins. The protein content of the this isolate was higher than the content reported by other authors.

Electron impact spectra of some mono-olefinic hydrocarbonsa)

International Nuclear Information System (INIS)

Johnson, K.E.; Johnston, D.B.; Lipsky, S.

1979-01-01

Electron impact spectra of ethylene, propylene, isobutene, trans-butene, cis-butene, trimethylethylene, and tetramethylethylene have been obtained at scattering angles of 0 0 and 90 0 and at impact energies from approx. =20 to 150 eV. The spectra scan an energy-loss region from 2.5--15 eV. All of the observed Rydberg transitions of the methyl derivatives are correlated to corresponding Rydberg transitions of ethylene. The missing π→3p transitions of ethylene are tentatively located via this correlation. Evidence is also presented for assigning the N→3R' system of ethylene (at 8.26 eV) to a π→3p/sub x/ transition. Possible assignments of some broad continua above approx. =8--9eV as sigma→π* and sigma→sigma* transitions are considered. In agreement with other reported large-angle electron impact spectra, no evidence is obtained for transitions that could be assigned to triplet Rydberg states. However the π→π* triplet transitions are all clearly located with transition energies in good agreement with those obtained by a variety of other techniques

Functional and antioxidant properties of protein hydrolysates obtained from white shrimp (Litopenaeus vannamei).

Science.gov (United States)

Latorres, J M; Rios, D G; Saggiomo, G; Wasielesky, W; Prentice-Hernandez, C

2018-02-01

Protein hydrolysates from white shrimp ( Litopenaeus vannamei ) with different degrees of hydrolysis (DH-10 and 20%) were prepared using the enzymes Alcalase 2.4 L and Protamex. The hydrolysates were evaluated for amino acid composition, solubility, foaming properties, emulsifying and antioxidant activity. All the hydrolysates showed high concentrations of Glutamic Acid, Aspartic acid, Arginine, Glycine, Lysine, Proline. It was found that the increase in the production of negatively charged amino acids was related to increase in DH. The hydrophobic amino acids were higher for hydrolysates obtained with Alcalase (10% DH) and Protamex (20% DH). The results indicated that higher degree of hydrolysis showed positive relation with the protein solubility of the hydrolysates, while negatively influenced foam and emulsification properties. The antioxidant properties presented by the white shrimp protein hydrolysates were influenced by the composition and peptides size. Hydrolysates with higher peptide chain showed the highest antioxidant power for the 2,2-Diphenyl-1-picrylhydrazyl radical scavenging and reducing power, while hydrolysates with lower peptide chain showed higher antioxidant power for 2,2'-azinobis (3-ethylbenzothiazoline sulfonic acid) radical scavenging. All hydrolysates showed dose-dependent antioxidant activities. Therefore, the results of the present study suggest that white shrimp is a potential source of protein hydrolysates as bioactive ingredients for the use in the formulation of functional foods as well as natural antioxidants in lipid food systems.

Biomimetic mineralization of recombinant collagen type I derived protein to obtain hybrid matrices for bone regeneration.

Science.gov (United States)

Ramírez-Rodríguez, Gloria Belén; Delgado-López, José Manuel; Iafisco, Michele; Montesi, Monica; Sandri, Monica; Sprio, Simone; Tampieri, Anna

2016-11-01

Understanding the mineralization mechanism of synthetic protein has recently aroused great interest especially in the development of advanced materials for bone regeneration. Herein, we propose the synthesis of composite materials through the mineralization of a recombinant collagen type I derived protein (RCP) enriched with RGD sequences in the presence of magnesium ions (Mg) to closer mimic bone composition. The role of both RCP and Mg ions in controlling the precipitation of the mineral phase is in depth evaluated. TEM and X-ray powder diffraction reveal the crystallization of nanocrystalline apatite (Ap) in all the evaluated conditions. However, Raman spectra point out also the precipitation of amorphous calcium phosphate (ACP). This amorphous phase is more evident when RCP and Mg are at work, indicating the synergistic role of both in stabilizing the amorphous precursor. In addition, hybrid matrices are prepared to tentatively address their effectiveness as scaffolds for bone tissue engineering. SEM and AFM imaging show an homogeneous mineral distribution on the RCP matrix mineralized in presence of Mg, which provides a surface roughness similar to that found in bone. Preliminary in vitro tests with pre-osteoblast cell line show good cell-material interaction on the matrices prepared in the presence of Mg. To the best of our knowledge this work represents the first attempt to mineralize recombinant collagen type I derived protein proving the simultaneous effect of the organic phase (RCP) and Mg on ACP stabilization. This study opens the possibility to engineer, through biomineralization process, advanced hybrid matrices for bone regeneration. Copyright © 2016 Elsevier Inc. All rights reserved.

Decomposition of spectra in EPR dosimetry using the matrix method

International Nuclear Information System (INIS)

Sholom, S.V.; Chumak, V.V.

2003-01-01

The matrix method of EPR spectra decomposition is developed and adapted for routine application in retrospective EPR dosimetry with teeth. According to this method, the initial EPR spectra are decomposed (using methods of matrix algebra) into several reference components (reference matrices) that are specific for each material. Proposed procedure has been tested on the example of tooth enamel. Reference spectra were a spectrum of an empty sample tube and three standard signals of enamel (two at g=2.0045, both for the native signal and one at g perpendicular =2.0018, g parallel =1.9973 for the dosimetric signal). Values of dosimetric signals obtained using the given method have been compared with data obtained by manual manipulation of spectra, and good coincidence was observed. This allows considering the proposed method as potent for application in routine EPR dosimetry

Method for the deconvolution of incompletely resolved CARS spectra in chemical dynamics experiments

International Nuclear Information System (INIS)

Anda, A.A.; Phillips, D.L.; Valentini, J.J.

1986-01-01

We describe a method for deconvoluting incompletely resolved CARS spectra to obtain quantum state population distributions. No particular form for the rotational and vibrational state distribution is assumed, the population of each quantum state is treated as an independent quantity. This method of analysis differs from previously developed approaches for the deconvolution of CARS spectra, all of which assume that the population distribution is Boltzmann, and thus are limited to the analysis of CARS spectra taken under conditions of thermal equilibrium. The method of analysis reported here has been developed to deconvolute CARS spectra of photofragments and chemical reaction products obtained in chemical dynamics experiments under nonequilibrium conditions. The deconvolution procedure has been incorporated into a computer code. The application of that code to the deconvolution of CARS spectra obtained for samples at thermal equilibrium and not at thermal equilibrium is reported. The method is accurate and computationally efficient

THE UTILISATION OF GRAPE MARC FOR OBTAINING FEED PROTEIN WITH ETHANOL CONSUMING YEASTS

Directory of Open Access Journals (Sweden)

Steliana RODINO

2014-11-01

Full Text Available The research presented in this work has been directed to achieve an optimal and economic medium, for the protein biosynthesis. The carbon source and the mineral elements are provided by the fresh marc diffusion solution and the source of organic nitrogen and growth factors are provided by proteic wine yeast extract. For the alcoholic fermentation it was used a strain of Saccharomyces ellipsoideus and for obtaining the biomass, a strain of Candida robusta. There were performed two series of experiments in which the alcoholic fermentation progress was monitored as follows: by titration of the carbohydrates, at the beginning and respectively at the end of the fermentation; by determining the optical density of the culture medium and by the determination of alcohol in the fermented solution. Protein biosynthesis was monitored by measurement of the alcohol concentration at the beginning and end of the process, by the determination of the optical density of the culture medium, by the determination of residual sugar, and by determining wet and dry biomass. The wet biomass was used for the protein titration. At the termination of the bioprocess was determined the dry matter in the culture medium.

Floor response spectra of buildings with uncertain structural properties

International Nuclear Information System (INIS)

Chen, P.C.

1975-01-01

All Category I equipment, such as reactors, vessels, and major piping systems of nuclear power plants, is required to withstand earthquake loadings in order to minimize risk of seismic damage. The equipment is designed by using response spectra of the floor on which the equipment is mounted. The floor response spectra are constructed usually from the floor response time histories which are obtained through a deterministic dynamic analysis. This analysis assumes that all structural parameters, such as mass, stiffness, and damping have been calculated precisely, and that the earthquakes are known. However, structural parameters are usually difficult to determine precisely if the structures are massive and/or irregular, such as nuclear containments and its internal structures with foundation soil incorporated into the analysis. Faced with these uncertainties, it has been the practice to broaden the floor response spectra peaks by +-10 percent of the peak frequencies on the basis of conservatism. This approach is based on engineering judgement and does not have an analytical basis to provide a sufficient level of confidence in using these spectra for equipment design. To insure reliable design, it is necessary to know structural response variations due to variations in structural properties. This consideration leads to the treatment of structural properties as random variables and the use of probabilistic methods to predict structural response more accurately. New results on floor response spectra of buildings with uncertain structural properties obtained by determining the probabilistic dynamic response from the deterministic dynamic response and its standard deviation are presented. The resulting probabilistic floor response spectra are compared with those obtained deterministically, and are shown to provide a more reliable method for determining seismic forces

Analysis of X-Ray (L) spectra of heavy elements

International Nuclear Information System (INIS)

Souza Coelho, L.F. de.

1976-08-01

The general problem of obtaining and analysing spectra is presented, with emphasis in the comparison of methods for the analysis of gamma rays and X rays. The method proposed to obtain a standard and later the intensities of lines of an X-ray (L) spectrum is discussed. The good eesults obtained by the program RAIOXL, when simulated spectra are used, and by the program RAIXL1, when doublets are decomposed, are shown. In annex A, the listings of the programs used are presented, and in annex B a review is made of the analytical formulae used for adjustment of the pulses. (I.C.R.) [pt

[Establishment of optimun conditions in order to obtain a protein isolate from Chilean Hazelnut].

Science.gov (United States)

Villarroel, Mario; Zapata, Constanza; Pino, Leonardo; Rubilar, Mónica

2012-03-01

An alternative to solve the problem of the overall deficit of proteins has been the use ofdefatted cakes generated by the extraction of oil from vegetable sources such as rapeseed, soybean, lupin, etc. This process at the same time increases the protein content, making this feasible to be used to enrich some types of food. This is the case of the chilean hazelnut (Gevuina avellana, Mol), monotypic species characterized by their high percentage of oil (50%) and whose defatted cake isolated protein could be used to obtain an isolated protein. For this purpose optimized conditions of extraction of protein were carried out using the surface response methodology (SRM) and a central composite design with three independent variables: time of contact of the cake with the solvent, sample/solvent ratio and pH was used. All variables were controlled at five different levels. The data were subjected to an analysis of regression and ANOVA, the first to determine the polynomial equation and the second to select the control factors with significant effect on the extraction of the protein. The best combination of factors turned out to be: time between 30 and 40 minutes, pH between 9 and 9.5 and a relationship sample/solvent between 1/15 to 1/16 with a final yield of 76%. The physical characteristics were: density 0,504 g/cm3, compaction 43, 34% apparent and pale yellow. Proximal analysis showed a concentration of protein of 76%, 13%, raw fiber carbohydrate 0.68% and oil 1.29%. With regard to the functional properties emphasized water absorption (320 g/100 g), absorption of oil (410 g/100 g) and foaming capacity (221%).

A simple method for generation of back-ground-free gamma-ray spectra

International Nuclear Information System (INIS)

Kawarasaki, Y.

1976-01-01

A simple and versatile method of generating background-free γ-ray spectra is presented. This method is equivalent to the generation of a continuous background baseline over the entire energy range of spectra corresponding to the original ones obtained with a Ge(Li) detector. These background curves can not be generally expressed in a single and simple analytic form nor in the form of a power series. These background-free spectra thus obtained make it feasible to assign many tiny peaks at the stage of visual inspection of the spectra, which is difficult to do with the original ones. The automatic peak-finding and peak area calculation procedures are both applicable to these background-free spectra. Examples of the application are illustrated. The effect of the peak-shape distortion is also discussed. (Auth.)

Systematic evaluation of prompt neutron spectra in fission

International Nuclear Information System (INIS)

Osawa, Takaaki

1995-01-01

To create the nuclear data fail JEND-32, the prompt fission neutron spectra X(E) of 233 U, 235 U, 238 U and 239 Pu were reevaluated and some improvement were added to the calculation models. We tried to extend the calculation method of fission spectra of nuclides with poor measurement data in consideration of increasing the importance of nuclear data of minor actinoids. We improved and extended the following five points. (1) On JENDL-3.1, the fission spectra of principal fissible materials had been calculated by the Modland-Nix model which the neutron emissions of fragments were calculated under the approximation of the constant inverse process cross section. In the paper, the spectra were calculated by the use of the inverse process cross section depend on the energy obtained by the calculation of the optical model. The result showed the increase of low energy components and the softening effect of spectra (2) On JENDL-3.1, the all fission processes were assumed to undergo (n,f) reaction. In the paper, they were calculated by the multi-chance fission such as (n, n'f), (n, 2nf) and (n, 3nf) etc. Softening of the spectra (En > 6 MeV) was obtained by this method. (3) The level density parameter (LDP) has been assumed as a = A/C in either case of light fragment (LF) and heavy fragment (HF) in the original Madland-Nix model. But we used LDP based on the Ignatyuk model under consideration of the shell effects of nuclear fragments, hence the neutron spectra of heavy fragments were hardening. (4) Nuclear temperature of both fragments had been assumed to be the same at original model, but now R T = Tm/TmH was derived to calculate them. The ratio of middle/both side components of spectra was changed. (5) Unknown neutron fission spectra of minor actinide were able to the assumed on the basis of Moriyama-Ohnishi model. (S.Y.)

Properties of Energy Spectra of Molecular Crystals Investigated by Nonlinear Theory

Science.gov (United States)

Pang, Xiao-Feng; Zhang, Huai-Wu

We calculate the quantum energy spectra of molecular crystals, such as acetanilide, by using discrete nonlinear Schrodinger equation, containing various interactions, appropriate to the systems. The energy spectra consist of many energy bands, in each energy band there are a lot of energy levels including some higher excited states. The result of energy spectrum is basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide and can also explain some experimental results obtained by Careri et al. Finally, we further discuss the influences of variously characteristic parameters on the energy spectra of the systems.

Protein profiles of Taenia solium cysts obtained from skeletal muscles and the central nervous system of pigs: Search for tissue-specific proteins.

Science.gov (United States)

Navarrete-Perea, José; Moguel, Bárbara; Bobes, Raúl José; Villalobos, Nelly; Carrero, Julio César; Sciutto, Edda; Soberón, Xavier; Laclette, Juan Pedro

2017-01-01

Taeniasis/cysticercosis caused by the tapeworm Taenia solium is a parasite disease transmitted among humans and pigs, the main intermediate host. The larvae/cysts can lodge in several tissues of the pig, i.e. skeletal muscles and different locations of the central nervous system. The molecular mechanisms associated to tissue preferences of the cysts remain poorly understood. The major public health concern about this zoonosis is due to the human infections by the larval form in the central nervous system, causing a highly pleomorphic and debilitating disease known as neurocysticercosis. This study was aimed to explore the 2DE protein maps of T. solium cysts obtained from skeletal muscles and central nervous system of naturally infected pigs. The gel images were analyzed through a combination of PDQuest™ and multivariate analysis. Results showed that differences in the protein patterns of cysts obtained from both tissues were remarkably discrete. Only 7 protein spots were found specifically associated to the skeletal muscle localization of the cysts; none was found significantly associated to the central nervous system. The use of distinct protein fractions of cysts allowed preliminary identification of several tissue-specific antigenic bands. The implications of these findings are discussed, as well as several strategies directed to achieve the complete characterization of this parasite's proteome, in order to extend our understanding of the molecular mechanisms underlying tissue localization of the cysts and to open avenues for the development of immunological tissue-specific diagnosis of the disease. Copyright © 2016 Elsevier Inc. All rights reserved.

Algal autolysate medium to label proteins for NMR in mammalian cells.

Science.gov (United States)

Fuccio, Carmelo; Luchinat, Enrico; Barbieri, Letizia; Neri, Sara; Fragai, Marco

2016-04-01

In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a homemade growth medium from Spirulina platensis autolysate, suitable to express uniformly labeled proteins inside mammalian cells at a reduced cost-per-sample. The human proteins SOD1 and Mia40 were overexpressed in human cells grown in (15)N-enriched S. platensis algal-derived medium, and high quality in-cell NMR spectra were obtained.

Algal autolysate medium to label proteins for NMR in mammalian cells

Energy Technology Data Exchange (ETDEWEB)

Fuccio, Carmelo; Luchinat, Enrico; Barbieri, Letizia [University of Florence, Magnetic Resonance Center (CERM) (Italy); Neri, Sara [Giotto Biotech S.R.L. (Italy); Fragai, Marco, E-mail: fragai@cerm.unifi.it [University of Florence, Magnetic Resonance Center (CERM) (Italy)

2016-04-15

In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a homemade growth medium from Spirulina platensis autolysate, suitable to express uniformly labeled proteins inside mammalian cells at a reduced cost-per-sample. The human proteins SOD1 and Mia40 were overexpressed in human cells grown in {sup 15}N-enriched S. platensis algal-derived medium, and high quality in-cell NMR spectra were obtained.

Spectral fitting for signal assignment and structural analysis of uniformly {sup 13}C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

Energy Technology Data Exchange (ETDEWEB)

Matsuki, Yoh; Akutsu, Hideo; Fujiwara, Toshimichi [Osaka University, Institute for Protein Research (Japan)], E-mail: tfjwr@protein.osaka-u.ac.jp

2007-08-15

We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional {sup 13}C-{sup 13}C magic-angle-spinning solid-state NMR spectra of uniformly {sup 13}C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C{sup {alpha}} and C{sup {beta}} chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 deg. from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.

UV-Visible intensity ratio (aggregates/single particles) as a measure to obtain stability of gold nanoparticles conjugated with protein A

Energy Technology Data Exchange (ETDEWEB)

Rios-Corripio, M. A. [Instituto Politecnico Nacional, CIBA-Tlaxcala (Mexico); Garcia-Perez, B. E. [Instituto Politecnico Nacional, Departamento de Inmunologia, ENCB (Mexico); Jaramillo-Flores, M. E. [Instituto Politecnico Nacional, Departamento de Ingenieria Bioquimica, ENCB (Mexico); Gayou, V. L.; Rojas-Lopez, M., E-mail: marlonrl@yahoo.com.mx [Instituto Politecnico Nacional, CIBA-Tlaxcala (Mexico)

2013-05-15

We have analyzed the titration process of gold nanoparticles with several amounts of protein A (0.3, 0.5, 1, 3, 6, and 9 {mu}g/ml) in the presence of NaCl, which induces aggregation if the surface of particles is not fully covered with protein A. The colloidal solutions with different particle size (16, 18, 20, 33 nm) were synthesized by citrate reduction to be conjugated with protein A. UV-Visible spectroscopy was used to measure the absorption of the surface plasmon resonance of gold nanoparticles as a function of the concentration of protein A. Such dependence shows an aggregation region (0 < x<6 {mu}g/ml), where the amount of protein A was insufficient to cover the surface of particles, obtaining aggregation caused by NaCl. The next part is the stability region (x {>=} 6 {mu}g/ml), where the amount of protein used covers the surface of particles and protects it from the aggregation. In addition to that the ratio between the intensities of both: the aggregates and of the gold nanoparticle bands was plotted as a function of the concentration of protein A. It was determined that 6 {mu}g/ml is a sufficient value of protein A to stabilize the gold nanoparticle-protein A system. This method provides a simple way to stabilize gold nanoparticles obtained by citrate reduction, with protein A.

Kinetic energy and scalar spectra in high Rayleigh number axially homogeneous buoyancy driven turbulence

Science.gov (United States)

Pawar, Shashikant S.; Arakeri, Jaywant H.

2016-06-01

Kinetic energy and scalar spectra from the measurements in high Rayleigh number axially homogeneous buoyancy driven turbulent flow are presented. Kinetic energy and concentration (scalar) spectra are obtained from the experiments wherein density difference is created using brine and fresh water and temperature spectra are obtained from the experiments in which heat is used. Scaling of the frequency spectra of lateral and longitudinal velocity near the tube axis is closer to the Kolmogorov-Obukhov scaling, while the scalar spectra show some evidence of dual scaling, Bolgiano-Obukhov scaling followed by Obukhov-Corrsin scaling. These scalings are also observed in the corresponding second order spatial structure functions of velocity and concentration fluctuations.

Geal: A general program for the analysis of alpha spectra

International Nuclear Information System (INIS)

Garcia-Torano, E.; Acena Barrenechea, M.L.

1978-01-01

A computing program for analysis and representation of alpha spectra obtained with surface barrier detectors is described. Several methods for fitting spectra are studied. A monoenergetic line or a doublet previously fitted has been used as a standard for the analyses of all kind of spectra. Some examples of application as well as a list of the program are shown. The program has been written in Fortran V language. (author)

Secondary graviton spectra and waterfall-like fields

OpenAIRE

Giovannini, Massimo

2010-01-01

The secondary spectra of the gravitons induced by a waterfall-like field are computed and the general bounds on the spectral energy density of the tensor modes of the geometry are translated into explicit constraints on the amplitude and slope of the waterfall spectrum. The obtained results are compared with the primary gravitational wave spectra of the concordance model and of its neighboring extensions as well as with the direct Ligo/Virgo bounds on stochastic backgrounds of relic gravitons...

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

Science.gov (United States)

Chamrad, Daniel C; Körting, Gerhard; Schäfer, Heike; Stephan, Christian; Thiele, Herbert; Apweiler, Rolf; Meyer, Helmut E; Marcus, Katrin; Blüggel, Martin

2006-09-01

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Calculation of ground vibration spectra from heavy military vehicles

Science.gov (United States)

Krylov, V. V.; Pickup, S.; McNuff, J.

2010-07-01

The demand for reliable autonomous systems capable to detect and identify heavy military vehicles becomes an important issue for UN peacekeeping forces in the current delicate political climate. A promising method of detection and identification is the one using the information extracted from ground vibration spectra generated by heavy military vehicles, often termed as their seismic signatures. This paper presents the results of the theoretical investigation of ground vibration spectra generated by heavy military vehicles, such as tanks and armed personnel carriers. A simple quarter car model is considered to identify the resulting dynamic forces applied from a vehicle to the ground. Then the obtained analytical expressions for vehicle dynamic forces are used for calculations of generated ground vibrations, predominantly Rayleigh surface waves, using Green's function method. A comparison of the obtained theoretical results with the published experimental data shows that analytical techniques based on the simplified quarter car vehicle model are capable of producing ground vibration spectra of heavy military vehicles that reproduce basic properties of experimental spectra.

Beta spectra. II-Positron spectra

International Nuclear Information System (INIS)

Grau, A.; Garcia-Torano, E.

1981-01-01

Using the Fermi theory of beta decay, the beta spectra for 30 positron emitters have been computed, introducing a correction factor for unique forbidden transitions. The spectra are ploted vs. energy, once normalised, and tabulated with the related Fermi functions. The average and median energies are calculated. (author)

Deconvoluting double Doppler spectra

International Nuclear Information System (INIS)

Ho, K.F.; Beling, C.D.; Fung, S.; Chan, K.L.; Tang, H.W.

2001-01-01

The successful deconvolution of data from double Doppler broadening of annihilation radiation (D-DBAR) spectroscopy is a promising area of endeavour aimed at producing momentum distributions of a quality comparable to those of the angular correlation technique. The deconvolution procedure we test in the present study is the constrained generalized least square method. Trials with computer simulated DDBAR spectra are generated and deconvoluted in order to find the best form of regularizer and the regularization parameter. For these trials the Neumann (reflective) boundary condition is used to give a single matrix operation in Fourier space. Experimental D-DBAR spectra are also subject to the same type of deconvolution after having carried out a background subtraction and using a symmetrize resolution function obtained from an 85 Sr source with wide coincidence windows. (orig.)

BETA SPECTRA. I. Negatrons spectra

International Nuclear Information System (INIS)

Grau Malonda, A.; Garcia-Torano, E.

1978-01-01

Using the Fermi theory of beta decay, the beta spectra for 62 negatrons emitters have been computed introducing a correction factor for unique forbidden transitions. These spectra are plotted vs. energy, once normal i sed, and tabulated with the related Fermi functions. The average and median energies are calculated. (Author)

THE Be STAR SPECTRA (BeSS) DATABASE

International Nuclear Information System (INIS)

Neiner, C.; De Batz, B.; Cochard, F.; Floquet, M.; Mekkas, A.; Desnoux, V.

2011-01-01

Be stars vary on many timescales, from hours to decades. A long time base of observations to analyze certain phenomena in these stars is therefore necessary. Collecting all existing and future Be star spectra into one database has thus emerged as an important tool for the Be star community. Moreover, for statistical studies, it is useful to have centralized information on all known Be stars via an up-to-date catalog. These two goals are what the Be Star Spectra (BeSS, http://basebe.obspm.fr) database proposes to achieve. The database contains an as-complete-as-possible catalog of known Be stars with stellar parameters, as well as spectra of Be stars from all origins (any wavelength, any epoch, any resolution, etc.). It currently contains over 54,000 spectra of more than 600 different Be stars among the ∼2000 Be stars in the catalog. A user can access and query this database to retrieve information on Be stars or spectra. Registered members can also upload spectra to enrich the database. Spectra obtained by professional as well as amateur astronomers are individually validated in terms of format and science before being included in BeSS. In this paper, we present the database itself as well as examples of the use of BeSS data in terms of statistics and the study of individual stars.

Generate tri-directional spectra-compatible time histories using HHT method

Energy Technology Data Exchange (ETDEWEB)

Li, Bo; Xie, Wei-Chau, E-mail: xie@uwaterloo.ca; Pandey, Mahesh D.

2016-11-15

Highlights: • Hilbert–Huang Transform are applied to modify real earthquake records. • Generate tri-directional time histories compatible with target spectra. • Both GRS and FRS are considered as target spectra. • Target spectra with multiple damping ratios are considered. - Abstract: This paper proposes two algorithms to generate spectrum-compatible time histories based on two approaches recommended by USNRC Standard Review Plan 3.7.1. Hilbert–Huang Transform technique is used to analyze frequency contents and amplitudes of seed motions. Through adjusting the frequency contents and amplitudes of seed motions, spectrum-compatible time histories are obtained. The first algorithm is to generate tri-directional time histories compatible with multi-damping target design spectra (ground response spectra or floor response spectra). The second algorithm is to generate tri-directional time histories compatible with single-damping target design spectra. Examples are presented to demonstrate versatility of these two proposed algorithms to generate spectra-compatible time histories.

Generate tri-directional spectra-compatible time histories using HHT method

International Nuclear Information System (INIS)

Li, Bo; Xie, Wei-Chau; Pandey, Mahesh D.

2016-01-01

Highlights: • Hilbert–Huang Transform are applied to modify real earthquake records. • Generate tri-directional time histories compatible with target spectra. • Both GRS and FRS are considered as target spectra. • Target spectra with multiple damping ratios are considered. - Abstract: This paper proposes two algorithms to generate spectrum-compatible time histories based on two approaches recommended by USNRC Standard Review Plan 3.7.1. Hilbert–Huang Transform technique is used to analyze frequency contents and amplitudes of seed motions. Through adjusting the frequency contents and amplitudes of seed motions, spectrum-compatible time histories are obtained. The first algorithm is to generate tri-directional time histories compatible with multi-damping target design spectra (ground response spectra or floor response spectra). The second algorithm is to generate tri-directional time histories compatible with single-damping target design spectra. Examples are presented to demonstrate versatility of these two proposed algorithms to generate spectra-compatible time histories.

Preservation of information in Fourier theory based deconvolved nuclear spectra

International Nuclear Information System (INIS)

Madan, V.K.; Gopalakrishnan, K.R.; Sharma, R.C.; Rattan, S.S.

1995-01-01

Nuclear spectroscopy is extremely useful to the internal radiation dosimetry for the estimation of body burden due to gamma emitters. Analysis of nuclear spectra is concerned with the extraction of qualitative and quantitative information embedded in the spectra. A spectral deconvolution method based on Fourier theory is probably the simplest method of deconvolving nuclear spectra. It is proved mathematically that the deconvolution method preserves the qualitative information. It is shown by using simulated spectra and an observed gamma ray spectrum that the method preserves the quantitative information. This may provide a novel approach of information extraction from a deconvolved spectrum. The paper discusses the methodology, mathematical analysis, and the results obtained by deconvolving spectra. (author). 6 refs., 2 tabs

Cancerous tissue mapping from random lasing emission spectra

International Nuclear Information System (INIS)

Polson, R C; Vardeny, Z V

2010-01-01

Random lasing emission spectra have been collected from both healthy and cancerous tissues. The two types of tissue with optical gain have different light scattering properties as obtained from an average power Fourier transform of their random lasing emission spectra. The difference in the power Fourier transform leads to a contrast between cancerous and benign tissues, which is utilized for tissue mapping of healthy and cancerous regions of patients

Biological activity of egg-yolk protein by-product hydrolysates obtained with the use of non-commercial plant protease

Directory of Open Access Journals (Sweden)

A. Zambrowicz

2015-12-01

Full Text Available Enzymatic hydrolysis leads to improved functional and biological properties of protein by-products, which can be further used as nutraceuticals and protein ingredients for food applications.The present study evaluated ACE-inhibitory, antioxidant and immunostimulating activities in hydrolysates of egg-yolk protein by-product (YP, generated during industrial process of delipidation of yolk. The protein substrate was hydrolyzed using non-commercial protease from Asian pumpkin (Cucurbita ficifolia. The reaction was conducted in 0.1 M Tris-HCl buffer (pH 8.0 at temperature of 37°C for 4 hours using different enzyme doses (100-1000 U/mg of substrate. The protein degradation was monitored by the determination of the degree of hydrolysis (DH, release of free amino groups (FAG and by RP-HPLC. In the obtained hydrolysates we also evaluated biological activities. It was shown that the highest DH of substrate (46.6% was obtained after 4h of reaction at the highest amount of enzyme. This hydrolysate exhibited antioxidant activity, including ferricion reducing (FRAP (56.41 μg Fe2+/mg, ferric ion chelating (695.76 μg Fe2+/mg and DPPH free radical scavenging (0.89 μmol troloxeq/mg as well as ACE-inhibitory (IC50=837.75 μg/mL activities.The research showed improved biological properties of enzymatically modified YP by-product.

Virtual photon spectra for finite nuclei

International Nuclear Information System (INIS)

Wolynec, E.; Martins, M.N.

1988-01-01

The experimental results of an isochromat of the virtual photon spectrum, obtained by measuring the number of ground-state protons emitted by the 16.28 MeV isobaric analogue state in 90 Zr as a function of electron incident energy in the range 17-105 MeV, are compared with the values predicted by a calculation of the E1 DWBA virtual photon spectra for finite nuclei. It is found that the calculations are in excellent agreement with the experimental results. The DWBA virtual photon spectra for finite nuclei for E2 and M1 multipoles are also assessed. (author) [pt

Interpretation of tandem mass spectra of posttranslationally modified peptides

DEFF Research Database (Denmark)

Bunkenborg, J.; Matthiesen, R.

2013-01-01

spectra and protein database search engines have been developed to match the experimental data to peptide candidates. In most studies there is a schism between discarding perfectly valid data and including nonsensical peptide identifications-this is currently a major bottleneck in data...

X-ray absorption spectra and emission spectra of plasmas

International Nuclear Information System (INIS)

Peng Yonglun; Yang Li; Wang Minsheng; Li Jiaming

2002-01-01

The author reports a theoretical method to calculate the resolved absorption spectra and emission spectra (optically thin) of hot dense plasmas. Due to its fully relativistic treatment incorporated with the quantum defect theory, it calculates the absorption spectra and emission spectra for single element or multi-element plasmas with little computational efforts. The calculated absorption spectra of LTE gold plasmas agree well with the experimental ones. It also calculates the optical thin emission spectra of LTE gold plasmas, which is helpful to diagnose the plasmas of relevant ICF plasmas. It can also provide the relevant parameters such as population density of various ionic stages, precise radiative properties for ICF studies

Moessbauer spectra of some complex compounds of Fe(II) with pyridine

International Nuclear Information System (INIS)

Teodorescu, M.; Filoti, G.

1975-01-01

The Moessbauer spectra of [Fe(II)py 6 ]Br 2 at 298 and 80 K and the reflectance spectra of the same compound at room temperature are presented. Isomer shift and quadrupole splitting were determined for [Fe(II)py 6 ]Br 2 at 298 and 80 K, their values being correlated with those obtained from electronic spectra measured in the solid state. (Z.S.)

Genetic parameters of blood β-hydroxybutyrate predicted from milk infrared spectra and clinical ketosis, and their associations with milk production traits in Norwegian Red cows.

Science.gov (United States)

Belay, T K; Svendsen, M; Kowalski, Z M; Ådnøy, T

2017-08-01

The aim of this study was to estimate genetic parameters for blood β-hydroxybutyrate (BHB) predicted from milk spectra and for clinical ketosis (KET), and to examine genetic association of blood BHB with KET and milk production traits (milk, fat, protein, and lactose yields, and milk fat, protein, and lactose contents). Data on milk traits, KET, and milk spectra were obtained from the Norwegian Dairy Herd Recording System with legal permission from TINE SA (Ås, Norway), the Norwegian Dairy Association that manages the central database. Data recorded up to 120 d after calving were considered. Blood BHB was predicted from milk spectra using a calibration model developed based on milk spectra and blood BHB measured in Polish dairy cows. The predicted blood BHB was grouped based on days in milk into 4 groups and each group was considered as a trait. The milk components for test-day milk samples were obtained by Fourier transform mid-infrared spectrometer with previously developed calibration equations from Foss (Hillerød, Denmark). Veterinarian-recorded KET data within 15 d before calving to 120 d after calving were used. Data were analyzed using univariate or bivariate linear animal models. Heritability estimates for predicted blood BHB at different stages of lactation were moderate, ranging from 0.250 to 0.365. Heritability estimate for KET from univariate analysis was 0.078, and the corresponding average estimate from bivariate analysis with BHB or milk production traits was 0.002. Genetic correlations between BHB traits were higher for adjacent lactation intervals and decreased as intervals were further apart. Predicted blood BHB at first test day was moderately genetically correlated with KET (0.469) and milk traits (ranged from -0.367 with protein content to 0.277 with milk yield), except for milk fat content from across lactation stages that had near zero genetic correlation with BHB (0.033). These genetic correlations indicate that a lower BHB is genetically

Cross-correlation analysis of Ge/Li/ spectra

International Nuclear Information System (INIS)

MacDonald, R.; Robertson, A.; Kennett, T.J.; Prestwich, W.V.

1974-01-01

A sensitive technique is proposed for activation analysis using cross-correlation and improved spectral orthogonality achieved through use of a rectangular zero area digital filter. To test the accuracy and reliability of the cross-correlation procedure five spectra obtained with a Ge/Li detector were combined in different proportions. Gaussian distributed statistics were then added to the composite spectra by means of a pseudo-random number generator. The basis spectra used were 76 As, 82 Br, 72 Ga, 77 Ge, and room background. In general, when the basis spectra were combined in roughly comparable proportions the accuracy of the techique proved to be excelent (>1%). However, of primary importance was the ability of the correlation technique to identify low intensity components in the presence of high intensity components. It was found that the detection threshold for Ge, for example, was not reached until the Ge content in the unfiltered spectrum was <0.16%. (T.G.)

Examination of segmental average mass spectra from liquid chromatography-tandem mass spectrometric (LC-MS/MS) data enables screening of multiple types of protein modifications.

Science.gov (United States)

Liu, Nai-Yu; Lee, Hsiao-Hui; Chang, Zee-Fen; Tsay, Yeou-Guang

2015-09-10

It has been observed that a modified peptide and its non-modified counterpart, when analyzed with reverse phase liquid chromatography, usually share a very similar elution property [1-3]. Inasmuch as this property is common to many different types of protein modifications, we propose an informatics-based approach, featuring the generation of segmental average mass spectra ((sa)MS), that is capable of locating different types of modified peptides in two-dimensional liquid chromatography-mass spectrometric (LC-MS) data collected for regular protease digests from proteins in gels or solutions. To enable the localization of these peptides in the LC-MS map, we have implemented a set of computer programs, or the (sa)MS package, that perform the needed functions, including generating a complete set of segmental average mass spectra, compiling the peptide inventory from the Sequest/TurboSequest results, searching modified peptide candidates and annotating a tandem mass spectrum for final verification. Using ROCK2 as an example, our programs were applied to identify multiple types of modified peptides, such as phosphorylated and hexosylated ones, which particularly include those peptides that could have been ignored due to their peculiar fragmentation patterns and consequent low search scores. Hence, we demonstrate that, when complemented with peptide search algorithms, our approach and the entailed computer programs can add the sequence information needed for bolstering the confidence of data interpretation by the present analytical platforms and facilitate the mining of protein modification information out of complicated LC-MS/MS data. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of phase correction to improve the interpretation of crude oil spectra obtained using 7 T Fourier transform ion cyclotron resonance mass spectrometry.

Science.gov (United States)

Cho, Yunju; Qi, Yulin; O'Connor, Peter B; Barrow, Mark P; Kim, Sunghwan

2014-01-01

In this study, a phase-correction technique was applied to the study of crude oil spectra obtained using a 7 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). 7 T FT-ICR MS had not been widely used for oil analysis due to the lower resolving power compared with high field FT-ICR MS. For low field instruments, usage of data that has not been phase-corrected results in an inability to resolve critical mass splits of C3 and SH4 (3.4 mDa), and (13)C and CH (4.5 mDa). This results in incorrect assignments of molecular formulae, and discontinuous double bond equivalents (DBE) and carbon number distributions of S1, S2, and hydrocarbon classes are obtained. Application of phase correction to the same data, however, improves the reliability of assignments and produces continuous DBE and carbon number distributions. Therefore, this study clearly demonstrates that phase correction improves data analysis and the reliability of assignments of molecular formulae in crude oil anlayses.

Emission Spectra of Hydrogen-Seeded Helium Arcjets

National Research Council Canada - National Science Library

Welle, R

2000-01-01

.... This work reports on a recent set of experiments in which emission spectra of the plume of a helium arcjet were acquired and analyzed to obtain information on the internal energy modes of the arcjet...

Molecular absorption spectra of beryllium, cerium, lanthanum, iron, and platinum salts

International Nuclear Information System (INIS)

Daidoji, Hidehiro

1980-01-01

The absorption spectra of some salts of beryllium, cerium, lanthanum, iron and platinum in air-acetylene flame were measured in the wavelength range from 200 to 400 nm. A Hitachi 207 type atomic absorption spectrophotometer was used. A deuterium lamp, a home-made continuous radiation lamp and some hollow cathode lamps were used as light sources. The new molecular absorption spectra of cerium, lanthanum and platinum and the absorption spectra due to Be(OH) 2 , LaO, PtH, FeO and FeCl in 200-400 nm region were obtained. Emission spectra of CeO, LaO and FeOH were also obtained. These molecular absorption bands were estimated as absorption errors of maximum 15 times to the sensitivity of each elements in atomic absorption spectrometry. In addition, spectral line interferences of iron were observed in atomic absorption spectrometry of Zn, Cd, Ni, Cu and Cr. (author)

Vibrational infrared and Raman spectra of polypeptides: Fragments-in-fragments within molecular tailoring approach

Energy Technology Data Exchange (ETDEWEB)

Sahu, Nityananda; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016 (India)

2016-03-21

The present work reports the calculation of vibrational infrared (IR) and Raman spectra of large molecular systems employing molecular tailoring approach (MTA). Further, it extends the grafting procedure for the accurate evaluation of IR and Raman spectra of large molecular systems, employing a new methodology termed as Fragments-in-Fragments (FIF), within MTA. Unlike the previous MTA-based studies, the accurate estimation of the requisite molecular properties is achieved without performing any full calculations (FC). The basic idea of the grafting procedure is implemented by invoking the nearly basis-set-independent nature of the MTA-based error vis-à-vis the respective FCs. FIF has been tested out for the estimation of the above molecular properties for three isomers, viz., β-strand, 3{sub 10}- and α-helix of acetyl(alanine){sub n}NH{sub 2} (n = 10, 15) polypeptides, three conformers of doubly protonated gramicidin S decapeptide and trpzip2 protein (PDB id: 1LE1), respectively, employing BP86/TZVP, M06/6-311G**, and M05-2X/6-31G** levels of theory. For most of the cases, a maximum difference of 3 cm{sup −1} is achieved between the grafted-MTA frequencies and the corresponding FC values. Further, a comparison of the BP86/TZVP level IR and Raman spectra of α-helical (alanine){sub 20} and its N-deuterated derivative shows an excellent agreement with the existing experimental spectra. In view of the requirement of only MTA-based calculations and the ability of FIF to work at any level of theory, the current methodology provides a cost-effective solution for obtaining accurate spectra of large molecular systems.

Measurements of Wiener spectra of laser printer in a computed radiography

International Nuclear Information System (INIS)

Yamauchi, Syuichi; Ueda, Katsuhiko; Nishihara, Sadamitsu; Ohtsuka, Akiyoshi; Fujita, Hiroshi; Morishita, Junji; Fujikawa, Tsuyoshi.

1992-01-01

Sources of noise in a computed radiography (CR) were investigated by measuring three different Wiener spectra: 1) laser printer Wiener spectra including CR film, 2) Wiener spectrum of CR film (single emulsion), and 3) overall Wiener spectra. To measure the noise contributed by the laser printer, 'image data' (i.e., image having a constant pixel value) were produced on a personal computer and were sent to the laser printer in the CR system. The noise level of laser printer was comparable to that of the CR film at low spatial frequencies ( 4 cycle/mm) was higher than that of the film. Laser printer Wiener spectra obtained in the perpendicular direction relative to the laser beam scanning direction were comparable at low spatial frequencies, but greater at high spatial frequencies, to those obtained in the parallel direction. And a spectral peak around 10 cycle/mm was obtained in the Wiener spectrum in the perpendicular direction. The peak is caused mainly by a banding artifact. Overall Wiener spectra in the parallel and perpendicular directions show the same tendency as those of the laser printer, but the noise level of the overall Wiener spectrum was increased mainly by X-ray quantum mottle at low spatial frequencies. In conclusion, the noise of laser printer greatly increases the overall Wiener spectrum at high spatial frequencies. (author)

Protein dynamics revealed in the excitonic spectra of single LH2 complexes

International Nuclear Information System (INIS)

Valkunas, Leonas; Janusonis, Julius; Rutkauskas, Danielis; Grondelle, Rienk van

2007-01-01

The fluorescence emission spectrum of single peripheral light-harvesting (LH2) complexes of the photosynthetic purple bacterium Rhodopseudomonas acidophila exhibits remarkable dynamics on a time scale of several minutes. Often the spectral properties are quasi-stable; sometimes large spectral jumps to the blue or to the red are observed. To explain the dynamics, every pigment is proposed to be in two conformational substates with different excitation energies, which originate from the conformational state of the protein as a result of pigment-protein interaction. Due to the excitonic coupling in the ring of 18 pigments, the two-state assumption generates a substantial amount of distinct spectroscopic states, which reflect part of the inhomogeneous distributed spectral properties of LH2. To describe the observed dynamics, spontaneous and light-induced transitions are introduced between the two states. For each 'realization of the disorder', the spectral properties are calculated using a disordered exciton model combined with the modified Redfield theory to obtain realistic spectral line shapes. The single-molecule fluorescence peak (FLP) distribution, the distribution dependence on the excitation intensity, and the FLP time traces are well described within the framework of this model

[Apply fourier transform infrared spectra coupled with two-dimensional correlation analysis to study the evolution of humic acids during composting].

Science.gov (United States)

Bu, Gui-jun; Yu, Jing; Di, Hui-hui; Luo, Shi-jia; Zhou, Da-zhai; Xiao, Qiang

2015-02-01

The composition and structure of humic acids formed during composting play an important influence on the quality and mature of compost. In order to explore the composition and evolution mechanism, municipal solid wastes were collected to compost and humic and fulvic acids were obtained from these composted municipal solid wastes. Furthermore, fourier transform infrared spectra and two-dimensional correlation analysis were applied to study the composition and transformation of humic and fulvic acids during composting. The results from fourier transform infrared spectra showed that, the composition of humic acids was complex, and several absorbance peaks were observed at 2917-2924, 2844-2852, 2549, 1662, 1622, 1566, 1454, 1398, 1351, 990-1063, 839 and 711 cm(-1). Compared to humic acids, the composition of fulvci acids was simple, and only three peaks were detected at 1725, 1637 and 990 cm(-1). The appearance of these peaks showed that both humic and fulvic acids comprised the benzene originated from lignin and the polysaccharide. In addition, humic acids comprised a large number of aliphatic and protein which were hardly detected in fulvic acids. Aliphatic, polysaccharide, protein and lignin all were degraded during composting, however, the order of degradation was different between humic and fulvci acids. The result from two-dimensional correlation analysis showed that, organic compounds in humic acids were degraded in the following sequence: aliphatic> protein> polysaccharide and lignin, while that in fulvic acids was as following: protein> polysaccharide and aliphatic. A large number of carboxyl, alcohols and ethers were formed during the degradation process, and the carboxyl was transformed into carbonates. It can be concluded that, fourier transform infrared spectra coupled with two-dimensional correlation analysis not only can analyze the function group composition of humic substances, but also can characterize effectively the degradation sequence of these

Diversity of soft X-ray spectra in quasars

International Nuclear Information System (INIS)

Elvis, M.; Wilkes, B.J.; Tananbaum, H.

1985-01-01

Soft X-ray spectra for three quasars obtained with the Einstein Imaging Proportional Counter covering the 0.1-4.0 keV band are reported. Power-law fits to these spectra have best-fit energy indices of 1.2 +0.6 or -0.2, for the quasar NAB 0205 + 024, 0.6 +0.3 or -0.2 for the quasar B2 1028 + 313, and 2.2 + or -0.4 for the quasar PG 1211 + 143. None of the quasars shows any evidence for a column density of cold matter in excess of the galactic values. The derived spectra demonstrate that there is no single universal power law slope for quasar X-ray spectra. The implications of these results for the X-ray background, X-ray continuum emission mechanisms, and the production of the optical/UV emission lines are briefly discussed. 46 references

Diagnostic x-ray spectra measurements using a silicon surface barrier detector

International Nuclear Information System (INIS)

Pani, R.; Laitano, R.F.

1987-01-01

A silicon surface barrier detector having a low efficiency for x-ray is used to analyse diagnostic x-ray spectra. This characteristic is advantageous in overcoming experimental problems caused by high fluence rates typical of diagnostic x-ray beams. The pulse height distribution obtained with silicon surface barrier detectors is very different from the true photon spectra because of the presence of escaped Compton photons and the fact that detection efficiency falls abruptly when photon energy increases. A detailed analysis of the spurious effects involved in detection is made by a Monte Carlo method. A stripping procedure is described for implementation on a personal computer. The validity of this method is tested by comparison with experimental results obtained with a Ge detector. The spectra obtained with the Si detector are in fairly good agreement with the analogous spectra measured with a Ge detector. The advantages of using Si as opposed to Ge detectors in x-ray spectrometry are: its simplicity of use, its greater economy for use in routine diagnostic x-ray spectroscopy and the possibility that the stripping procedure can be implemented on a personal computer. (author)

QUALITATIVE INTERPRETATION OF GALAXY SPECTRA

Energy Technology Data Exchange (ETDEWEB)

Sanchez Almeida, J.; Morales-Luis, A. B. [Instituto de Astrofisica de Canarias, E-38205 La Laguna, Tenerife (Spain); Terlevich, R.; Terlevich, E. [Instituto Nacional de Astrofisica, Optica y Electronica, Tonantzintla, Puebla (Mexico); Cid Fernandes, R., E-mail: jos@iac.es, E-mail: abml@iac.es, E-mail: rjt@ast.cam.ac.uk, E-mail: eterlevi@inaoep.mx, E-mail: cid@astro.ufsc.br [Departamento de Fisica-CFM, Universidade Federal de Santa Catarina, P.O. Box 476, 88040-900 Florianopolis, SC (Brazil)

2012-09-10

We describe a simple step-by-step guide to qualitative interpretation of galaxy spectra. Rather than an alternative to existing automated tools, it is put forward as an instrument for quick-look analysis and for gaining physical insight when interpreting the outputs provided by automated tools. Though the recipe is for general application, it was developed for understanding the nature of the Automatic Spectroscopic K-means-based (ASK) template spectra. They resulted from the classification of all the galaxy spectra in the Sloan Digital Sky Survey data release 7, thus being a comprehensive representation of the galaxy spectra in the local universe. Using the recipe, we give a description of the properties of the gas and the stars that characterize the ASK classes, from those corresponding to passively evolving galaxies, to H II galaxies undergoing a galaxy-wide starburst. The qualitative analysis is found to be in excellent agreement with quantitative analyses of the same spectra. We compare the mean ages of the stellar populations with those inferred using the code STARLIGHT. We also examine the estimated gas-phase metallicity with the metallicities obtained using electron-temperature-based methods. A number of byproducts follow from the analysis. There is a tight correlation between the age of the stellar population and the metallicity of the gas, which is stronger than the correlations between galaxy mass and stellar age, and galaxy mass and gas metallicity. The galaxy spectra are known to follow a one-dimensional sequence, and we identify the luminosity-weighted mean stellar age as the affine parameter that describes the sequence. All ASK classes happen to have a significant fraction of old stars, although spectrum-wise they are outshined by the youngest populations. Old stars are metal-rich or metal-poor depending on whether they reside in passive galaxies or in star-forming galaxies.

LSD-based analysis of high-resolution stellar spectra

Science.gov (United States)

Tsymbal, V.; Tkachenko, A.; Van, Reeth T.

2014-11-01

We present a generalization of the method of least-squares deconvolution (LSD), a powerful tool for extracting high S/N average line profiles from stellar spectra. The generalization of the method is effected by extending it towards the multiprofile LSD and by introducing the possibility to correct the line strengths from the initial mask. We illustrate the new approach by two examples: (a) the detection of astroseismic signatures from low S/N spectra of single stars, and (b) disentangling spectra of multiple stellar objects. The analysis is applied to spectra obtained with 2-m class telescopes in the course of spectroscopic ground-based support for space missions such as CoRoT and Kepler. Usually, rather high S/N is required, so smaller telescopes can only compete successfully with more advanced ones when one can apply a technique that enables a remarkable increase in the S/N of the spectra which they observe. Since the LSD profiles have a potential for reconstruction what is common in all the spectral profiles, it should have a particular practical application to faint stars observed with 2-m class telescopes and whose spectra show remarkable LPVs.

Nonlinear FMR spectra in yttrium iron garnet

Directory of Open Access Journals (Sweden)

Yu.M. Bunkov, P.M. Vetoshko, I.G. Motygullin, T.R. Safin, M.S. Tagirov, N.A. Tukmakova

2015-12-01

Full Text Available Results of demagnetizing effect studies in yttrium iron garnet Y3Fe5O12 thin films are reported. Experiments were performed on X-Band of electron paramagnetic resonance spectrometer at room temperature. The ferromagnetic resonance (FMR spectra were obtained for one-layer single crystal YIG films for different values of the applied microwave power. Nonlinear FMR spectra transformation by the microwave power increasing in various directions of magnetic field sweep was observed. It is explained by the influence of the demagnetization action of nonequilibrium magnons.

Combined analysis of the S and W parameters obtained from positron annihilation spectra

International Nuclear Information System (INIS)

Fedorov, A.V.; Veen, A. van; Schut, H.

2001-01-01

Variable energy positron beam analysis (PBA) has proven to be a very useful and powerful technique for the study of nanosize layer structures and point defects in various materials. Analysis of the positron annihilation spectra is usually performed with the help of the S and W parameters. By mapping the experimental points in the S-W plane the cluster points characteristic for the layers or defects can be derived. We have developed the program SWAN (S-W analysis) to enable to trace these cluster points and to calculate the fractions of the positrons annihilated at the layers or defects ascribed to the cluster points. In combination with the known computer code VEPFIT, program SWAN was successfully used for analyzing the S and W- curves for a number of samples. As an example, the analysis of SIMOX sample measured by PBA is presented. The program runs on a PC, has a user-friendly interface and is available for distribution. (orig.)

Stationary spectra in a quasi neutral current-carrying plasma

International Nuclear Information System (INIS)

Vakulenko, M.O.

1992-01-01

The low-frequency short-wave equilibrium spectra of electromagnetic fluctuations are obtained, accounting for cross-field correlations. The statistical analysis shows that a longitudinal current in a dense quasi neutral (α e ≡4πnomec 2 /Bo 2 >>1) plasma destroys the stationary of fluctuation spectra corresponding to zero fluxes of motion invariants, and may alter also the anomalous electron heat conductivity. 2 refs. (author)

Application of Wavelets and Quaternions to NIR Spectra Classification

International Nuclear Information System (INIS)

Barcala Riveira, J. M.; Fernandez Marron, J. L.; Alberdi Primicia, J.; Navarrete Marin, J. J.; Oller Gonzalez, J.C.

2003-01-01

This document describes how multi resolution analysis can combine with the use of quaternions to identify near infrared spectra. The method is applied to spectra of plastics usually present in domestic wastes. First, Haar wavelet is applied to spectrum. With the coefficients obtained, a quaternion is built. We named this quaternion a characteristic quaternion. Distances to characteristic quaternions are used to classify new quaternions. (Author) 54 refs

Study of Gamma spectra by Monte Carlo simulation

International Nuclear Information System (INIS)

Cantaragiu, A.; Gheorghies, A.; Borcia, C.

2008-01-01

The purpose of this paper is obtaining gamma ray spectra by means of a scintillation detector applying the Monte Carlo statistic simulation method using the EGS4 program. The Monte Carlo algorithm implies that the physical system is described by the probability density function which allows generating random figures and the result is taken as an average of numbers which were observed. The EGS4 program allows the simulation of the following physical processes: the photo-electrical effect, the Compton effect, the electron positron pairs generation and the Rayleigh diffusion. The gamma rays recorded by the detector are converted into electrical pulses and the gamma ray spectra are acquired and processed by means of the Nomad Plus portable spectrometer connected to a computer. As a gamma ray sources 137Cs and 60Co are used whose spectra drawn and used for study the interaction of the gamma radiations with the scintillation detector. The parameters which varied during the acquisition of the gamma ray spectra are the distance between source and detector and the measuring time. Due to the statistical processes in the detector, the peak looks like a Gauss distribution. The identification of the gamma quantum energy value is achieved by the experimental spectra peaks, thus gathering information about the position of the peak, the width and the area of the peak respectively. By means of the EGS4 program a simulation is run using these parameters and an 'ideal' spectrum is obtained, a spectrum which is not influenced by the statistical processes which take place inside the detector. Then, the convolution of the spectra is achieved by means of a normalised Gauss function. There is a close match between the experimental results and those simulated in the EGS4 program because the interactions which occurred during the simulation have a statistical behaviour close to the real one. (authors)

Analysis of COSIMA spectra: Bayesian approach

Directory of Open Access Journals (Sweden)

H. J. Lehto

2015-06-01

secondary ion mass spectrometer (TOF-SIMS spectra. The method is applied to the COmetary Secondary Ion Mass Analyzer (COSIMA TOF-SIMS mass spectra where the analysis can be broken into subgroups of lines close to integer mass values. The effects of the instrumental dead time are discussed in a new way. The method finds the joint probability density functions of measured line parameters (number of lines, and their widths, peak amplitudes, integrated amplitudes and positions. In the case of two or more lines, these distributions can take complex forms. The derived line parameters can be used to further calibrate the mass scaling of TOF-SIMS and to feed the results into other analysis methods such as multivariate analyses of spectra. We intend to use the method, first as a comprehensive tool to perform quantitative analysis of spectra, and second as a fast tool for studying interesting targets for obtaining additional TOF-SIMS measurements of the sample, a property unique to COSIMA. Finally, we point out that the Bayesian method can be thought of as a means to solve inverse problems but with forward calculations, only with no iterative corrections or other manipulation of the observed data.

The eclipse of CI Cygni in 1980 on the objective prism spectra

International Nuclear Information System (INIS)

Mikolajewska, J.; Mikolajewski, M.

1982-01-01

The observations of CI Cyg were carried out with the Torun 60/90 cm Schmidt telescope with the objective prism giving a dispersion of 250 A/mm at H-gamma. Intensity traces of 20 selected spectra, made on the Kodak IIa-O plates, were made. The results were corrected for all instrumental effects and the interstellar extinction. The relative emission lines intensities have been obtained from the tracings after normalization to H-beta = 100. The spectra were typical for the quiet symbiotic star. So, all changes in the spectrum were caused by geometrical effects (eclipse). A preliminary analysis of the obtained spectra is presented. (Auth.)

On joint spectra of families of unbounded operators

International Nuclear Information System (INIS)

Mirotin, A R

2015-01-01

We consider several types of joint spectra of a finite set of commuting closed operators in a Banach space. We establish new relations between these spectra (it was previously known only that the Taylor spectrum is contained in the commutant spectrum) and prove spectral mapping theorems in the case of generators of semigroups. Some of these theorems generalize previous results of the author. The results obtained are applied to stability issues for multi-parameter semigroups

Creation of n-dimension spectra, projection and visualization of sub-volumes

International Nuclear Information System (INIS)

Be, M.M.

1980-06-01

A data base has been created which allows the processing of multiparameter data (five at most) resulting from nuclear physics experiments, with help of a CII 10 020 computer. From this basis one can set conditions on the various parameters and thus obtain one to five monoparametric spectra and one to four bidimensional spectra which are created simultaneously. These mono- and bidimensional spectra can be visualized as soon as their extraction ends up [fr

Digital dewaxing of Raman signals: discrimination between nevi and melanoma spectra obtained from paraffin-embedded skin biopsies.

Science.gov (United States)

Tfayli, Ali; Gobinet, Cyril; Vrabie, Valeriu; Huez, Regis; Manfait, Michel; Piot, Olivier

2009-05-01

Malignant melanoma (MM) is the most severe tumor affecting the skin and accounts for three quarters of all skin cancer deaths. Raman spectroscopy is a promising nondestructive tool that has been increasingly used for characterization of the molecular features of cancerous tissues. Different multivariate statistical analysis techniques are used in order to extract relevant information that can be considered as functional spectroscopic descriptors of a particular pathology. Paraffin embedding (waxing) is a highly efficient process used to conserve biopsies in tumor banks for several years. However, the use of non-dewaxed formalin-fixed paraffin-embedded tissues for Raman spectroscopic investigations remains very restricted, limiting the development of the technique as a routine analytical tool for biomedical purposes. This is due to the highly intense signal of paraffin, which masks important vibrations of the biological tissues. In addition to being time consuming and chemical intensive, chemical dewaxing methods are not efficient and they leave traces of the paraffin in tissues, which affects the Raman signal. In the present study, we use independent component analysis (ICA) on Raman spectral images collected on melanoma and nevus samples. The sources obtained from these images are then used to eliminate, using non-negativity constrained least squares (NCLS), the paraffin contribution from each individual spectrum of the spectral images of nevi and melanomas. Corrected spectra of both types of lesion are then compared and classified into dendrograms using hierarchical cluster analysis (HCA).

VizieR Online Data Catalog: BD+46 442 optical spectra (Bollen+, 2017)

Science.gov (United States)

Bollen, D.; van Winckel, H.; Kamath, D.

2017-08-01

Reduced high-resolution (R~85000) optical spectra of BD+46 442. These 104 spectra were obtained between July 2009 and January 2016 from the HERMES spectrograph, mounted on the 1.2m Flemish Mercator telescope at La Palma, Canary Islands, Spain. The spectra cover a wavelength range from 3770 to 9000 angstrom in logscale. The flux is given in arbitrary units. The spectra are collected as FITS files. The numbering of the spectra corresponds to the numbering in Table B.1 in the article (e.g. spec_15.fits corresponds to N=15). (2 data files).

RCI Simulation for EUV spectra from Sn ions

International Nuclear Information System (INIS)

Kagawa, T; Tanuma, H; Ohashi, H; Nishihara, K

2007-01-01

Using the relativistic-configuration-interaction atomic structure code, RCI simulations for EUV spectra from Sn 10+ , Sn 11+ and Sn 12+ ions are carried out, where it is assumed that each ion is embedded in a LTE plasma with the electron temperature of 30 eV. To make clear assignment of the measured spectra, the value of the excitation energy limit, which is introduced to limit the number of excited states in the simulation, is changed to see the excitation-energy-limit dependence of the spectral shape. The simulated spectra are obtained as a superposition of line intensities due to all possible transitions between two states whose excitation energy from the ground state is lower than the excitation energy limit assumed. The RCI simulated spectra are compared to the spectra measured with the chargeexchange- collision experiment in which a rare gas such as Xe or He as a target is bombarded by a charge-selected tin ion. Applicability of the LTE model to a decay model in the charge exchange collision experiment is also discussed

A digital processing method for the analysis of complex nuclear spectra

International Nuclear Information System (INIS)

Madan, V.K.; Abani, M.C.; Bairi, B.R.

1994-01-01

This paper describes a digital processing method using frequency power spectra for the analysis of complex nuclear spectra. The power spectra were estimated by employing modified discrete Fourier transform. The method was applied to observed spectral envelopes. The results for separating closely-spaced doublets in nuclear spectra of low statistical precision compared favorably with those obtained by using a popular peak fitting program SAMPO. The paper also describes limitations of the peak fitting methods. It describes the advantages of digital processing techniques for type II digital signals including nuclear spectra. A compact computer program occupying less than 2.5 kByte of memory space was written in BASIC for the processing of observed spectral envelopes. (orig.)

APSY-NMR for protein backbone assignment in high-throughput structural biology

Energy Technology Data Exchange (ETDEWEB)

Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

2015-01-15

A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

Usefulness of in-house obtained recombinant proteins Yop of Yersinia enterocolitica as highly specific antigens in ELISA and recom-dot performed in the serodiagnosis of yersiniosis.

Science.gov (United States)

Rastawicki, Waldemar; Smietafiska, Karolina; Chrost, Anna; Wolkowicz, Tomasz; Rokosz-Chudziak, Natalia

Proper analysis of the human immune response is crucial in the laboratory diagnosis of many bacterial infections-The current serological diagnosis of yersiniosis often is carried out using ELISA with native antigens. However, recombinant proteins increase the specificity of the serological assays, particularly in patients with chronic, non- specific infections. The aim of the present study was to evaluate the usefulness of in-house obtained recombinant proteins Yop of Yersinia enterocolitica as highly specific antigens in ELISA and recom-dot performed in the serodiagnosis of yersiniosis. Recombinant YopD, YopB, YopE and V-Ag proteins of Y enterocolitica were expressing in E. coli BL21 (DE3) using the pET-30 Ek/LIC expression vector (Novagen). Purification was accomplished by immobilized metal (Ni2) affinity column chromatography (His-trap). The proteins were used as antigens in standard ELISA and recom-dot assay, which was performed on nitrocellulose strips. The study population, used for characterization of the humoral immune response to the recombinant proteins, consisted of 74 patients suspected for Y enterocolitica infection and 41 clinically healthy blood donors. Some of the results obtained by ELISA and recom-dot were compared with results obtained by commercial western-blot Yersinia (Virotech). In the group of patients suspected for yersiniosis in clinical investigation the most positive results were obtained in ELISA with the recombinant protein YopD (IgA respectively 25 (42.4%), IgG 41 (69.5%), IgM 24 (40.7%). The percentage ofpositive results in the group of blood donors did not exceed 10.0% in IgG and 5.0% in IgA/IgM classes of immunoglobulin. The results obtained in the recom-dot assay showed that among 74 tested serum samples obtained from individuals suspected of yersiniosis the most common IgA, IgG and IgM antibodies were found for recombinant protein YopD (respectively IgG in 60.8%, IgA in 37.8% and IgM in 33.8% of serum samples). IgG antibodies to

A systematic approach to obtain validated Partial Least Square models for predicting lipoprotein subclasses from serum NMR spectra

NARCIS (Netherlands)

Mihaleva, V.V.; van Schalkwijk, D.B.; de Graaf, A.A.; van Duynhoven, J.; van Dorsten, F.A.; Vervoort, J.; Smilde, A.; Westerhuis, J.A.; Jacobs, D.M.

2014-01-01

A systematic approach is described for building validated PLS models that predict cholesterol and triglyceride concentrations in lipoprotein subclasses in fasting serum from a normolipidemic, healthy population. The PLS models were built on diffusion-edited 1H NMR spectra and calibrated on

A systematic approach to obtain validated partial least square models for predicting lipoprotein subclasses from serum NMR spectra

NARCIS (Netherlands)

Mihaleva, V.V.; Schalkwijk, van D.B.; Graaf, de A.A.; Duynhoven, van J.P.M.; Dorsten, van F.A.; Vervoort, J.J.M.; Smilde, A.K.; Westerhuis, J.A.; Jacobs, D.M.

2014-01-01

A systematic approach is described for building validated PLS models that predict cholesterol and triglyceride concentrations in lipoprotein subclasses in fasting serum from a normolipidemic, healthy population. The PLS models were built on diffusion-edited (1)H NMR spectra and calibrated on

A systematic approach to obtain validated partial least square models for predicting lipoprotein subclasses from serum nmr spectra

NARCIS (Netherlands)

Mihaleva, V.V.; Schalkwijk, D.B. van; Graaf, A.A. de; Duynhoven, J. van; Dorsten, F.A. van; Vervoort, J.; Smilde, A.; Westerhuis, J.A.; Jacobs, D.M.

2014-01-01

A systematic approach is described for building validated PLS models that predict cholesterol and triglyceride concentrations in lipoprotein subclasses in fasting serum from a normolipidemic, healthy population. The PLS models were built on diffusion-edited 1H NMR spectra and calibrated on

Simultaneous in-bore rail and insulator spectra from a railgun plasma armature

International Nuclear Information System (INIS)

Keefer, D.; Sedghinasah, A.; Crawford, R.

1991-01-01

This paper reports on absolute spectral radiance measurements obtained simultaneously at the rail and insulator surface of the UTSI 1 cm square-bore railgun. The emission spectra were obtained through the use of quartz optical fibers which penetrated both the rail and the insulator walls. The spectral characteristics of the rail and insulator emission are quite similar but differ significantly in magnitude. A detailed plasma radiation model was used to analyze these spectra. In order to obtain reasonable agreement between the model predictions and the experimental spectra, it was necessary to assume that these existed a broadband absorbing layer at the insulator surface. This result suggests a new physical model of the plasma armature in which insulator ablation leads to significant 3-dimensional flow and affects the shape of the current emission pattern on the rail surfaces

Mössbauer spectra linearity improvement by sine velocity waveform followed by linearization process

Science.gov (United States)

Kohout, Pavel; Frank, Tomas; Pechousek, Jiri; Kouril, Lukas

2018-05-01

This note reports the development of a new method for linearizing the Mössbauer spectra recorded with a sine drive velocity signal. Mössbauer spectra linearity is a critical parameter to determine Mössbauer spectrometer accuracy. Measuring spectra with a sine velocity axis and consecutive linearization increases the linearity of spectra in a wider frequency range of a drive signal, as generally harmonic movement is natural for velocity transducers. The obtained data demonstrate that linearized sine spectra have lower nonlinearity and line width parameters in comparison with those measured using a traditional triangle velocity signal.

Crystallographically-based analysis of the NMR spectra of maghemite

International Nuclear Information System (INIS)

Spiers, K.M.; Cashion, J.D.

2012-01-01

All possible iron environments with respect to nearest neighbour vacancies in vacancy-ordered and vacancy-disordered maghemite have been evaluated and used as the foundation for a crystallographically-based analysis of the published NMR spectra of maghemite. The spectral components have been assigned to particular configurations and excellent agreement obtained in comparing predicted spectra with published spectra taken in applied magnetic fields. The broadness of the published NMR lines has been explained by calculations of the magnetic dipole fields at the various iron sites and consideration of the supertransferred hyperfine fields. - Highlights: ► Analysis of 57 Fe NMR of maghemite based on vacancy ordering and nearest neighbour vacancies. ► Assignment of NMR spectral components based on crystallographic analysis of unique iron sites. ► Strong agreement between predicted spectra and published spectra taken in applied magnetic fields. ► Maghemite NMR spectral broadening due to various iron sites and supertransferred hyperfine field.

Larger red-shift in optical emissions obtained from the thin films of globular proteins (BSA, lysozyme) – polyelectrolyte (PAA) complexes

Energy Technology Data Exchange (ETDEWEB)

Talukdar, Hrishikesh [Physical Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati 781035, Assam (India); Kundu, Sarathi, E-mail: sarathi.kundu@gmail.com [Physical Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati 781035, Assam (India); Basu, Saibal [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 (India)

2016-09-30

Graphical abstract: Thin films of protein-polyelectrolyte complexes show larger red-shift in optical emission. - Highlights: • Globular proteins (lysozyme and BSA) and polyelectrolyte (sodium polyacrylic acid) are used to form protein-polyelectrolyte complexes (PPC). • Larger red-shift in optical emission is obtained from the thin films of PPC. • Red-shift is not obtained from the solution of PPC and pure protein thin films. • Larger red-shift from PPC films is due to the energy dissipation as non-radiative form through interactions with nearby atoms. • Red-shift in optical emission is independent on the thickness of the PPC film. - Abstract: Globular proteins (lysozyme and BSA) and polyelectrolyte (sodium polyacrylic acid) are used to form protein-polyelectrolyte complexes (PPC). Out-of-plane structures of ≈30–60 nm thick PPC films and their surface morphologies have been studied by using X-ray reflectivity and atomic force microscopy, whereas optical behaviors of PPC and protein conformations have been studied by using UV–vis, photoluminescence and FTIR spectroscopy respectively. Our study reveals that thin films of PPC show a larger red-shift of 23 and 16 nm in the optical emissions in comparison to that of pure protein whereas bulk PPC show a small blue-shift of ≈3 nm. A small amount of peak-shift is found to occur due to the heat treatment or concentration variation of the polyelectrolyte/protein in bulk solution but cannot produce such film thickness independent larger red-shift. Position of the emission peak remains nearly unchanged with the film thickness. Mechanism for such larger red-shift has been proposed.

The Spectra Count Label-free Quantitation in Cancer Proteomics

OpenAIRE

Zhou, Weidong; Liotta, Lance A.; Petricoin, Emanuel F.

2012-01-01

Mass spectrometry is used routinely for large-scale protein identification from complex biological mixtures. Recently, relative quantitation approach on the basis of spectra count has been applied in several cancer proteomic studies. In this review, we examine the mechanism of this technique and highlight several important parameters associated with its application.

Determination of crystal oscillatory spectra by internal friction data spectroscopic analysis

International Nuclear Information System (INIS)

Zaykin, Yu.A.

1998-01-01

Technique for relaxation spectra determination on the basis of internal friction averaging over relaxation frequencies is developed. It is shown that mathematically the problem is reduced to solution of the first type Fredholm integral equation. Impurity oscillatory spectra in alpha-iron, molybdenum and Fe-Cr-Ni alloy are obtained. (author)

Automatic processing of gamma ray spectra employing classical and modified Fourier transform approach

International Nuclear Information System (INIS)

Rattan, S.S.; Madan, V.K.

1994-01-01

This report describes methods for automatic processing of gamma ray spectra acquired with HPGe detectors. The processing incorporated both classical and signal processing approach. The classical method was used for smoothing, detecting significant peaks, finding peak envelope limits and a proposed method of finding peak limits, peak significance index, full width at half maximum, detecting doublets for further analysis. To facilitate application of signal processing to nuclear spectra, Madan et al. gave a new classification of signals and identified nuclear spectra as Type II signals, mathematically formalized modified Fourier transform and pioneered its application to process doublet envelopes acquired with modern spectrometers. It was extended to facilitate routine analysis of the spectra. A facility for energy and efficiency calibration was also included. The results obtained by analyzing observed gamma-ray spectra using the above approach compared favourably with those obtained with SAMPO and also those derived from table of radioisotopes. (author). 15 refs., 3 figs., 3 tabs

A chemometric method for correcting FTIR spectra of biomaterials for interference from water in KBr discs

Science.gov (United States)

FTIR analysis of solid biomaterials by the familiar KBr disc technique is very often frustrated by water interference in the important protein (amide I) and carbohydrate (hydroxyl) regions of their spectra. A method was therefore devised that overcomes the difficulty and measures FTIR spectra of so...

Secondary graviton spectra and waterfall-like fields

CERN Document Server

Giovannini, Massimo

2010-01-01

The secondary spectra of the gravitons induced by a waterfall-like field are computed and the general bounds on the spectral energy density of the tensor modes of the geometry are translated into explicit constraints on the amplitude and slope of the waterfall spectrum. The obtained results are compared with the primary gravitational wave spectra of the concordance model and of its neighboring extensions as well as with the direct Ligo/Virgo bounds on stochastic backgrounds of relic gravitons. Space-borne interferometers (such as Lisa, Bbo, Decigo) seem to be less relevant but their potential implications are briefly outlined.

Algorithms for classification of astronomical object spectra

Science.gov (United States)

Wasiewicz, P.; Szuppe, J.; Hryniewicz, K.

2015-09-01

Obtaining interesting celestial objects from tens of thousands or even millions of recorded optical-ultraviolet spectra depends not only on the data quality but also on the accuracy of spectra decomposition. Additionally rapidly growing data volumes demands higher computing power and/or more efficient algorithms implementations. In this paper we speed up the process of substracting iron transitions and fitting Gaussian functions to emission peaks utilising C++ and OpenCL methods together with the NOSQL database. In this paper we implemented typical astronomical methods of detecting peaks in comparison to our previous hybrid methods implemented with CUDA.

Data on xylem sap proteins from Mn- and Fe-deficient tomato plants obtained using shotgun proteomics.

Science.gov (United States)

Ceballos-Laita, Laura; Gutierrez-Carbonell, Elain; Takahashi, Daisuke; Abadía, Anunciación; Uemura, Matsuo; Abadía, Javier; López-Millán, Ana Flor

2018-04-01

This article contains consolidated proteomic data obtained from xylem sap collected from tomato plants grown in Fe- and Mn-sufficient control, as well as Fe-deficient and Mn-deficient conditions. Data presented here cover proteins identified and quantified by shotgun proteomics and Progenesis LC-MS analyses: proteins identified with at least two peptides and showing changes statistically significant (ANOVA; p ≤ 0.05) and above a biologically relevant selected threshold (fold ≥ 2) between treatments are listed. The comparison between Fe-deficient, Mn-deficient and control xylem sap samples using a multivariate statistical data analysis (Principal Component Analysis, PCA) is also included. Data included in this article are discussed in depth in the research article entitled "Effects of Fe and Mn deficiencies on the protein profiles of tomato ( Solanum lycopersicum) xylem sap as revealed by shotgun analyses" [1]. This dataset is made available to support the cited study as well to extend analyses at a later stage.

Electron impact spectra of methane, ethane, and neopentane

International Nuclear Information System (INIS)

Johnson, K.E.; Kim, K.; Johnston, D.B.; Lipsky, S.

1979-01-01

Electron impact spectra of methane, ethane, and neopentane have been obtained at scattering angles of 0 0 and 90 0 and at impact energies from approx. =30 to 250 eV. The data are consistent with the lowest excitation in all of these systems to involve promotion of an electron to a 3s Rydberg-like orbital. Differences between 0 0 and 90 0 onsets are attributed to large-angle intensity enhancements of transitions to the 3s Rydberg triplets. At 90 0 all of the spectra exhibit very similar intensity redistributions with strong enhancement of transitions in the 12 and 15 eV region as compared to lower-lying transitions. Assignments of the spectra and possible origins of the angular dependence are discussed

Photoinduced Effects in the ZnO Luminescence Spectra

Science.gov (United States)

Akopyan, I. Kh.; Labzovskaya, M. E.; Novikov, B. V.; Lisachenko, A. A.; Serov, A. Yu.; Filosofov, N. G.

2018-02-01

The effect of intense UV irradiation on the photoluminescence (PL) spectra of ZnO powders and nanocrystalline films obtained by atomic layer deposition (ALD) was investigated. At room temperature, the behavior of the spectra under continuous UV irradiation in multiple vacuum-atmosphere cycles was studied. The changes in the intensities of exciton radiation and radiation in the "green" band region, associated with the phenomena of oxygen photodesorption and photoadsorption, are discussed. In the temperature range of 5-300 K, the effect of strong UV irradiation on the near-edge luminescence spectrum of ZnO films was studied. The nature of a new line arising in the photoluminescence spectra of an irradiated film in the region of emission of bound excitons is discussed.

Analytical investigation of different mathematical approaches utilizing manipulation of ratio spectra

Science.gov (United States)

Osman, Essam Eldin A.

2018-01-01

This work represents a comparative study of different approaches of manipulating ratio spectra, applied on a binary mixture of ciprofloxacin HCl and dexamethasone sodium phosphate co-formulated as ear drops. The proposed new spectrophotometric methods are: ratio difference spectrophotometric method (RDSM), amplitude center method (ACM), first derivative of the ratio spectra (1DD) and mean centering of ratio spectra (MCR). The proposed methods were checked using laboratory-prepared mixtures and were successfully applied for the analysis of pharmaceutical formulation containing the cited drugs. The proposed methods were validated according to the ICH guidelines. A comparative study was conducted between those methods regarding simplicity, limitations and sensitivity. The obtained results were statistically compared with those obtained from the reported HPLC method, showing no significant difference with respect to accuracy and precision.

Langmuir-Blodgett nanotemplates for protein crystallography.

Science.gov (United States)

Pechkova, Eugenia; Nicolini, Claudio

2017-12-01

The new generation of synchrotrons and microfocused beamlines has enabled great progress in X-ray protein crystallography, resulting in new 3D atomic structures for proteins of high interest to the pharmaceutical industry and life sciences. It is, however, often still challenging to produce protein crystals of sufficient size and quality (order, intensity of diffraction, radiation stability). In this protocol, we provide instructions for performing the Langmuir-Blodgett (LB) nanotemplate method, a crystallization approach that can be used for any protein (including membrane proteins). We describe how to produce highly ordered 2D LB protein monolayers at the air-water interface and deposit them on glass slides. LB-film formation can be observed by surface-pressure measurements and Brewster angle microscopy (BAM), although its quality can be characterized by atomic force microscopy (AFM) and nanogravimetry. Such films are then used as a 2D template for triggering 3D protein crystal formation by hanging-drop vapor diffusion. The procedure for forming the 2D template takes a few minutes. Structural information about the protein reorganization in the LB film during the crystallization process on the nano level can be obtained using an in situ submicron GISAXS (grazing-incidence small-angle X-ray scattering) method. MicroGISAXS spectra, measured directly at the interface of the LB films and protein solution in real time, as described in this protocol, can be interpreted in terms of the buildup of layers, islands, or holes. In our experience, the obtained LB crystals take 1-10 d to prepare and they are more ordered and radiation stable as compared with those produced using other crystallization methods.

Infrared spectra of lunar soils. [using a Michelson interferometer

Science.gov (United States)

Aronson, J. R.; Emslie, A. G.; Smith, E. M.

1979-01-01

Measured data obtained by Michelson interferometer spectrometer were stored in a computer file and smoothed by being passed forward and backward through a digital four-pole low pass filter. Infrared spectra of the 10 lunar samples are presented in the format of brightness temperature versus frequency. The mol % of feldspar, pyroxene, olivine, ilmenite and ferromagnetic silicate in each sample is presented in tables. The reflectance spectra of ilmenite and enstatite are shown in graphs.

Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

Science.gov (United States)

Laszlo, Kenneth J.; Bush, Matthew F.

2015-12-01

Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/ z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/ z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

Microdosimetric spectra measurements of JANUS neutrons

Energy Technology Data Exchange (ETDEWEB)

Marshall, I.R.; Williamson, F.S.

1985-01-01

Neutron radiation from the JANUS reactor at Argonne National Laboratory is being used with increasing frequency for major biological experiments. The fast neutron spectrum has a Kerma-weighted mean energy of 0.8 MeV and low gamma-ray contamination. In 1984 the JANUS fission converter plate of highly enriched uranium was replaced by one made of low-enriched uranium. We recorded microdosimetric spectra at several different positions in the high-flux irradiation room of JANUS before the change of the converter plate. Each set of measurements consisted of spectra taken at three different site diameters (0.5, 1.0, and 5.0 ..mu..m) and in both ''attenuator up'' and ''attenuator down'' configurations. At two conventional dosimetry reference positions, two sets of measurements were recorded. At three biological reference positions, measurements simulating several biological irradiation conditions, were taken. The dose rate at each position was estimated and compared with dose rates obtained previously by conventional dosimetry. Comparison of the different measurements showed no major change in spectra as a function of position or irradiation condition. First results from similar sets of measurements recorded after the installment of the new converter plate indicate no major change in the spectra. 11 refs., 4 figs., 5 tabs.

Microdosimetric spectra measurements of JANUS neutrons

International Nuclear Information System (INIS)

Marshall, I.R.; Williamson, F.S.

1985-01-01

Neutron radiation from the JANUS reactor at Argonne National Laboratory is being used with increasing frequency for major biological experiments. The fast neutron spectrum has a Kerma-weighted mean energy of 0.8 MeV and low gamma-ray contamination. In 1984 the JANUS fission converter plate of highly enriched uranium was replaced by one made of low-enriched uranium. We recorded microdosimetric spectra at several different positions in the high-flux irradiation room of JANUS before the change of the converter plate. Each set of measurements consisted of spectra taken at three different site diameters (0.5, 1.0, and 5.0 μm) and in both ''attenuator up'' and ''attenuator down'' configurations. At two conventional dosimetry reference positions, two sets of measurements were recorded. At three biological reference positions, measurements simulating several biological irradiation conditions, were taken. The dose rate at each position was estimated and compared with dose rates obtained previously by conventional dosimetry. Comparison of the different measurements showed no major change in spectra as a function of position or irradiation condition. First results from similar sets of measurements recorded after the installment of the new converter plate indicate no major change in the spectra. 11 refs., 4 figs., 5 tabs

Food Protein-polysaccharide Conjugates Obtained via the Maillard Reaction: A Review.

Science.gov (United States)

de Oliveira, Fabíola Cristina; Coimbra, Jane Sélia Dos Reis; de Oliveira, Eduardo Basílio; Zuñiga, Abraham Damian Giraldo; Rojas, Edwin E Garcia

2016-05-18

The products formed by glycosylation of food proteins with carbohydrates via the Maillard reaction, also known as conjugates, are agents capable of changing and improving techno-functional characteristics of proteins. The Maillard reaction uses the covalent bond between a group of a reducing carbohydrates and an amino group of a protein. This reaction does not require additional chemicals as it occurs naturally under controlled conditions of temperature, time, pH, and moisture. Moreover, there is growing interest in modifying proteins for industrial food applications. This review analyses the current state of art of the Maillard reaction on food protein functionalities. It also discusses the influence of the Maillard reaction on the conditions and formulation of reagents that improve desirable techno-functional characteristics of food protein.

Physicochemical and functional properties of protein isolate obtained from cottonseed meal.

Science.gov (United States)

Ma, Mengting; Ren, Yanjing; Xie, Wei; Zhou, Dayun; Tang, Shurong; Kuang, Meng; Wang, Yanqin; Du, Shuang-Kui

2018-02-01

To investigate the effect of preparation methods of cottonseed meals on protein properties, the physicochemical and functional properties of proteins isolated from hot-pressed solvent extraction cottonseed meal (HCM), cold-pressed solvent extraction cottonseed meal (CCM) and subcritical fluid extraction cottonseed meal (SCM) were investigated. Cottonseed proteins had two major bands (at about 45 and 50kD), two X-ray diffraction peaks (8.5° and 19.5°) and one endothermic peak (94.31°C-97.72°C). Proteins of HCM showed relatively more β-sheet (38.3%-40.5%), and less β-turn (22.2%-25.8%) and α-helix (15.8%-19.5%), indicating the presence of highly denatured protein molecules. Proteins of CCM and SCM exhibited high water/oil absorption capacity, emulsifying abilities, surface hydrophobicity and fluorescence intensity, suggesting that the proteins have potential as functional ingredients in the food industry. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation.

Science.gov (United States)

Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

2017-08-30

A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.

A Probabilistic Framework for Detection of Skin Cancer by Raman Spectra

DEFF Research Database (Denmark)

Sigurdsson, Sigurdur

2003-01-01

. These identified important features are shown to originate from molecular structure changes in lipids and proteins. While the theme of this dissertation is skin cancer diagnosis from Raman spectra, the dimension reduction and the neural network classifier can be applied in general to other types of pattern...... melanoma. The neural network classifier visualization showed that frequency bands, previously identified by visual inspection of Raman spectra by medical experts, were considered important for classification. Moreover, frequency band not previously used for skin lesion classification were identified...... brugt til diagnosering af hudkræft. Disse vigtige frekvensbånd stammer fra forskel i molekyle struktur i lipider og proteiner. Selv om temaet for denne afhandling er hudkræft diagnosering fra Raman spektra, kan dimensions reduceringen og det neurale netværk bruges til andre mønster genkendelses...

He-like spectra from laboratory plasmas and solar flares

International Nuclear Information System (INIS)

Kato, Takako

1990-01-01

The X-ray spectra of He-like ions from tokamaks and solar flares have been measured. Several physical parameters of plasma can be derived from the X-ray spectra of He-like ions. The ion temperature can be derived from the doppler width of a resonance line. The electron temperature is obtained from the intensity ratio of dielectronic satellite lines to a resonance line. The energy level for the prominent lines is shown. The line q is produced mainly by the inner-shell excitation of Li-like ions, and line beta is produced by the inner-shell excitation of Be-like ions. The intensity ratios give the ion density ratios. The intensities of the intercombination and the forbidden lines are affected by the recombination from H-like ions. The synthetic spectra including excitation, ionization and recombination processes are fitted to the measurement. In this paper, the He-like X-ray spectra of the titanium ions from TFTR tokamak plasma and of the iron ions from solar flares are discussed, paying attention to the presence of high energy electrons which affect the spectra and ionization balance. Atomic data, the spectra from the TFTR tokamak, the spectra from solar flares and so on are described. (K.I.)

Formation of protein-birnessite complex: XRD, FTIR, and AFM analysis.

Science.gov (United States)

Naidja, A; Liu, C; Huang, P M

2002-07-01

Limited information is available on formation chemistry of enzyme-Mn oxide complexes. Adsorption isotherm of protein molecules (tyrosinase) on birnessite (delta-MnO(2)) at pH 6.0 and room temperature (23 degrees C) was of H type, indicating a very high affinity of the enzyme protein molecules to the birnessite mineral surfaces. After thorough washing of the protein-mineral complex with deionized-distilled water, up to 89% of adsorbed protein molecules remained bound to the mineral surfaces. When a high amount of the protein was immobilized, the X-ray diffractogram shows a significant decrease in the intensity of characteristic d-spacings of birnessite. No shift to higher values of the d-spacings of protein-birnessite complex was observed, indicating that the enzyme molecules were not intercalated in the mineral structure but immobilized at the external surfaces and the edges of the mineral oxide. By comparison to the free enzyme, infrared absorption spectra of the protein-birnessite complexes show a shift by up to 11 cm(-1) to lower frequencies in the absorption bands characteristic of amide I and II modes of the polypeptides chains. The mineral surfaces exerted some strain on the protein structure, resulting in an alteration of the protein molecular conformation after binding to the mineral colloid surfaces. In the free state, the globular protein molecules had a spheroid shape with an average cross-sectional diameter of 70+/-6 nm. The unfolding and flattening of the protein molecules after immobilization is clearly shown in atomic force micrographs. Compared to the tyrosinase-birnessite complex, similar FTIR spectra and atomic force micrographs were observed for the pure protein, bovine serum albumin (BSA), after immobilization on birnessite. The information obtained in this study is of fundamental significance for understanding birnessite as an adsorbent of biopolymers and the catalytic role of the enzyme-birnessite complex.

VizieR Online Data Catalog: Sulamitis and Clarissa asteroids spectra (Morate+, 2018)

Science.gov (United States)

Morate, D.; de, Leon J.; de Pra, M.; Licandro, J.; Cabrera-Lavers, A.; Campins, H.; Pinilla-Alonso, N.

2017-11-01

A total of 97 low-resolution visible spectra were obtained for the asteroids in the Sulamitis and Clarissa families (64 and 33 objects, respectively), using the Optical System for Imaging and Low Resolution Integrated Spectroscopy (OSIRIS) camera spectrograph at the 10.4m Gran Telescopio Canarias (GTC), located at the El Roque de los Muchachos Observatory (ORM) in La Palma, Canary Islands, Spain. In addition, we obtained three spectra of (752) Sulamitis using the Intermediate Dispersion Spectrograph (IDS) at the 2.5m Isaac Newton Telescope, also located at the ORM in La Palma, as part of program C97 (2015), on July 22, 2015. All the spectra files included here are named ast_ASTEROIDNUMBER.txt, except for the spectra of (752) taken with the INT (named ast752INT.txt). The first column is the wavelength, expressed in microns, and the second column is the reflectance value (which is normalized at 1 at 0.55 microns). (3 data files).

Program LEPS to addition of gamma spectra from germanium detectors

International Nuclear Information System (INIS)

Romero, L.

1986-01-01

The LEP program, written in FORTRAN IV, performs the addition of two spectra, collected with different detectors, from the same sample. This application, adds the two gamma spectra obtained from two opposite LEPS Germanium Detectors (Low Energy Photon Spectrometer), correcting the differences (channel/energy) between both two spectra, and fitting them before adding. The total-spectrum is recorded at the computer memory as a single spectrum. The necessary equipment, to run this program is: - Two opposite germanium detectors, with their associate electronics. - Multichannel analyzer (2048 memory channel minimum) - Computer on-line interfacing to multichannel analyzer. (Author) 4 refs

Modeling a gamma spectroscopy system and predicting spectra with Geant-4

International Nuclear Information System (INIS)

Sahin, D.; Uenlue, K.

2009-01-01

An activity predictor software was previously developed to foresee activities, exposure rates and gamma spectra of activated samples for Radiation Science and Engineering Center (RSEC), Penn State Breazeale Reactor (PSBR), Neutron Activation Analysis (NAA) measurements. With Activity Predictor it has been demonstrated that the predicted spectra were less than satisfactory. In order to obtain better predicted spectra, a new detailed model for the RSEC NAA spectroscopy system with High Purity Germanium (HPGe) detector is developed using Geant-4. The model was validated with a National Bureau of Standards certified 60 Co source and tree activated high purity samples at PSBR. The predicted spectra agreed well with measured spectra. Error in net photo peak area values were 8.6-33.6%. Along with the previously developed activity predictor software, this new model in Geant-4 provided realistic spectra prediction for NAA experiments at RSEC PSBR. (author)

Synthesis of audio spectra using a diffraction model.

Science.gov (United States)

Vijayakumar, V; Eswaran, C

2006-12-01

It is shown that the intensity variations of an audio signal in the frequency domain can be obtained by using a mathematical function containing a series of weighted complex Bessel functions. With proper choice of values for two parameters, this function can transform an input spectrum of discrete frequencies of unit intensity into the known spectra of different musical instruments. Specific examples of musical instruments are considered for evaluating the performance of this method. It is found that this function yields musical spectra with a good degree of accuracy.

Analysis of gamma spectra with a HP calcultor

International Nuclear Information System (INIS)

Rocc, H.C.

1978-01-01

Three programs for the analysis of gamma spectra, specially useful for neutron activation analysis, were adapted and tested. The equipment used is a Hewlett-Packard, model 9810-A desk-computer, supplied with punched tape reader, additional memory in magnetic tape and plotter, being the system capacity 111 numerical registers and 2036 programme steps. The first programme allows automatic photopeak detection in spectra up to 4096 channels, obtained with Ge(Li) detectors,generating the corresponding background radiation line. The areas and their standard deviations are calculated and the spectrum and background can be plotted [pt

A Simple Approach for Obtaining High Resolution, High Sensitivity ¹H NMR Metabolite Spectra of Biofluids with Limited Mass Supply

Energy Technology Data Exchange (ETDEWEB)

Hu, Jian Zhi; Rommereim, Donald N.; Wind, Robert A.; Minard, Kevin R.; Sears, Jesse A.

2006-11-01

A simple approach is reported that yields high resolution, high sensitivity ¹H NMR spectra of biofluids with limited mass supply. This is achieved by spinning a capillary sample tube containing a biofluid at the magic angle at a frequency of about 80Hz. A 2D pulse sequence called ¹H PASS is then used to produce a high-resolution ¹H NMR spectrum that is free from magnetic susceptibility induced line broadening. With this new approach a high resolution ¹H NMR spectrum of biofluids with a volume less than 1.0 µl can be easily achieved at a magnetic field strength as low as 7.05T. Furthermore, the methodology facilitates easy sample handling, i.e., the samples can be directly collected into inexpensive and disposable capillary tubes at the site of collection and subsequently used for NMR measurements. In addition, slow magic angle spinning improves magnetic field shimming and is especially suitable for high throughput investigations. In this paper first results are shown obtained in a magnetic field of 7.05T on urine samples collected from mice using a modified commercial NMR probe.

Skyshine spectra of gamma rays

International Nuclear Information System (INIS)

Swarup, Janardan

1980-01-01

A study of the spectra of gamma photons back-scattered in vertical direction by infinite air above ground (skyshine) is presented. The source for these measurements is a 650 Ci Cobalt-60 point-source and the skyshine spectra are reported for distances from 150 m to 325 m from the source, measured with a 5 cm x 5 cm NaI(Tl) detector collimated with collimators of 12 mm and 20 mm diameter and 5 cm length. These continuous spectra are unfolded with Gold's iterative technique. The photon-spectra so obtained have a distinct line at 72 keV due to multiply-scattered photons. This is an energy where photoelectric and Compton cross-sections for multiply-scattered photons balance each other. The intensity of the line(I) decreases exponentially with distance (d) from the source obeying a relation of the type I = Isub(o)esup(-μd) where μ is called as ''Multiply-Scatter Coefficient'', a constant of the medium which is air in these measurements. This relationship is explained in terms of a halo around the source comprising of multiply-scattered gamma photons, Isub(0) being the intensity of these scattered photons at the location of cobalt-source. A fraction called as ''Back-scattered Fraction'', the ratio of Isub(0) to the number of original photons from the cobalt-source entering the infinite air, is also calculated. It is shown that with a properly calibrated detector system, this fraction can be used to determine the strength of a large gamma source, viz. a nuclear explosion in air, and for mineral prospecting. These conclusions are general and can be applied to any other infinite medium. Some forward-scatter (transmission) spectra of cobalt-60 source through 10 cm of Pb and 2.5 cm of Al are also reported. (auth.)

The mechanism and properties of bio-photon emission and absorption in protein molecules in living systems

Science.gov (United States)

Pang, Xiao-feng

2012-05-01

The mechanism and properties of bio-photon emission and absorption in bio-tissues were studied using Pang's theory of bio-energy transport, in which the energy spectra of protein molecules are obtained from the discrete dynamic equation. From the energy spectra, it was determined that the protein molecules could both radiate and absorb bio-photons with wavelengths of energy level transitions of the excitons. These results were consistent with the experimental data; this consisted of infrared absorption data from collagen, bovine serum albumin, the protein-like molecule acetanilide, plasma, and a person's finger, and the laser-Raman spectra of acidity I-type collagen in the lungs of a mouse, and metabolically active Escherichia coli. We further elucidated the mechanism responsible for the non-thermal biological effects produced by the infrared light absorbed by the bio-tissues, using the above results. No temperature rise was observed; instead, the absorbed infrared light promoted the vibrations of amides as well the transport of the bio-energy from one place to other in the protein molecules, which changed their conformations. These experimental results, therefore, not only confirmed the validity of the mechanism of bio-photon emission, and the newly developed theory of bio-energy transport mentioned above, but also explained the mechanism and properties of the non-thermal biological effects produced by the absorption of infrared light by the living systems.

Variable valence ion spectra in a crystal field

International Nuclear Information System (INIS)

Ghiordanescu, V.

1979-01-01

Using the Cadmium chloride as a host lattice, the optical spectra and RES of Mnsup(2+) were studied and the following results were obtained: a) By controlled dopings, the absorbtion and excitation spectra of ion Mnsup(2+) in CdCl 2 within the concentration range between 0.01 M and 25 M were plotted. Thus, the band structure for small concentrations was pointed out to differ from the structure observed for high concentrations. In the literature, this effect has not been observed on similar compounds, due to the small intensity values of the absorbtion spectra. b) Considering that for CdCl 2 :Mnsup(2+) 0.1 M, the optical spectra correspond to the isolated ion in the lattice, the energy levels were evaluated using electrostatic and spin-orbit terms in a perturbation calculation of the crystal field approximation. c) The calculation of parameter a which represents the effect of the cubic field in the spjn Hamiltonian of Mnsup(2+), is closer to the experjmental value -0.5.10 -4 cm -1 of the crystal field Dq and zeta parameters are used, respectively, parameters of the spin-orbit interaction obtained under b). d) The coupling effects of spins into more concentrated crystals with Mn 2+ are a function of temperature. The emjssion yield was given a quasi-cantitative evaluation in thjs paper as a function of temperature and concentratjon on the basis of which the isolated centers of Mn 2+ were found to display ectra whose intensity vary with temperature according to the Laporte forbidden transitions and spin rule theory, and the clusters including Mn 2+ - Mn 2+ pairs provide spectra whose intensity vary with the strength of the spin-spin coupling. (author)

Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

Science.gov (United States)

Pak, Huisong; Nikitin, Frederic; Gluck, Florent; Lisacek, Frederique; Scherl, Alexander; Muller, Markus

2013-12-01

Data-independent mass spectrometry activates all ion species isolated within a given mass-to-charge window ( m/z) regardless of their abundance. This acquisition strategy overcomes the traditional data-dependent ion selection boosting data reproducibility and sensitivity. However, several tandem mass (MS/MS) spectra of the same precursor ion are acquired during chromatographic elution resulting in large data redundancy. Also, the significant number of chimeric spectra and the absence of accurate precursor ion masses hamper peptide identification. Here, we describe an algorithm to preprocess data-independent MS/MS spectra by filtering out noise peaks and clustering the spectra according to both the chromatographic elution profiles and the spectral similarity. In addition, we developed an approach to estimate the m/z value of precursor ions from clustered MS/MS spectra in order to improve database search performance. Data acquired using a small 3 m/z units precursor mass window and multiple injections to cover a m/z range of 400-1400 was processed with our algorithm. It showed an improvement in the number of both peptide and protein identifications by 8 % while reducing the number of submitted spectra by 18 % and the number of peaks by 55 %. We conclude that our clustering method is a valid approach for data analysis of these data-independent fragmentation spectra. The software including the source code is available for the scientific community.

Investigation of relations between skin cancer lesions' images and their fluorescent spectra

Science.gov (United States)

Pavlova, P.; Borisova, E.; Avramov, L.; Petkova, El.; Troyanova, P.

2010-03-01

This investigation is based on images obtained from healthy tissue and skin cancer lesions and their fluorescent spectra of cutaneous lesions derived after optical stimulation. Our analyses show that the lesions’ spectra of are different of those, obtained from normal tissue and the differences depend on the type of cancer. We use a comparison between these “healthy” and “unhealthy” spectra to define forms of variations and corresponding diseases. However, the value of the emitted light varies not only between the patients, but also depending on the position of the tested area inside of one lesion. These variations could be result from two reasons: different degree of damaging and different thickness of the suspicious lesion area. Regarded to the visible image of the lesion, it could be connected with the chroma of colour of the tested area and the lesion homogeneity that corresponds to particular disease. For our investigation, images and spectra of three non-melanoma cutanous malignant tumors are investigated, namely—basal cell carcinoma, squamous cell carcinoma, and keratoacanthoma. The images were processed obtaining the chroma by elimination of the background—healthy tissue, and applying it as a basic signal for transformation from RGB to Lab colorimetric model. The chroma of the areas of emission is compared with the relative value of fluorescence spectra. Specific spectral features are used to develop hybrid diagnostic algorithm (including image and spectral features) for differentiation of these three kinds of malignant cutaneous pathologies.

Analysis of X-ray Spectra of High-Z Elements obtained on Nike with high spectral and spatial resolution

Science.gov (United States)

Aglitskiy, Yefim; Weaver, J. L.; Karasik, M.; Serlin, V.; Obenschain, S. P.; Ralchenko, Yu.

2014-10-01

The spectra of multi-charged ions of Hf, Ta, W, Pt, Au and Bi have been studied on Nike krypton-fluoride laser facility with the help of two kinds of X-ray spectrometers. First, survey instrument covering a spectral range from 0.5 to 19.5 angstroms which allows simultaneous observation of both M- and N- spectra of above mentioned elements with high spectral resolution. Second, an imaging spectrometer with interchangeable spherically bent Quartz crystals that added higher efficiency, higher spectral resolution and high spatial resolution to the qualities of the former one. Multiple spectral lines with X-ray energies as high as 4 keV that belong to the isoelectronic sequences of Fe, Co, Ni, Cu and Zn were identified with the help of NOMAD package developed by Dr. Yu. Ralchenko and colleagues. In our continuous effort to support DOE-NNSA's inertial fusion program, this campaign covered a wide range of plasma conditions that result in production of relatively energetic X-rays. Work supported by the US DOE/NNSA.

Neutron spectra unfolding in Bonner spheres spectrometry using neural networks

International Nuclear Information System (INIS)

Kardan, M.R.; Setayeshi, S.; Koohi-Fayegh, R.; Ghiassi-Nejad, M.

2003-01-01

The neural network method has been used for the unfolding of neutron spectra in neutron spectrometry by Bonner spheres. A back propagation algorithm was used for training of neural networks 4mm x 4 mm bare LiI(Eu) and in a polyethylene sphere set: 2, 3, 4, 5, 6, 7, 8, 10, 12, 18 inch diameter have been used for unfolding of neutron spectra. Neural networks were trained by 199 sets of neutron spectra, which were subdivided into 6, 8, 10, 12, 15 and 20 energy bins and for each of them an appropriate neural network was designed and trained. The validation was performed by the 21 sets of neutron spectra. A neural network with 10 energy bins which had a mean value of error of 6% for dose equivalent estimation of spectra in the validation set showed the best results. The obtained results show that neural networks can be applied as an effective method for unfolding neutron spectra especially when the main target is neutron dosimetry. (author)

New Fe i Level Energies and Line Identifications from Stellar Spectra. II. Initial Results from New Ultraviolet Spectra of Metal-poor Stars

Energy Technology Data Exchange (ETDEWEB)

Peterson, Ruth C. [SETI Institute and Astrophysical Advances, 607 Marion Place, Palo Alto, CA 94301 (United States); Kurucz, Robert L. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Ayres, Thomas R., E-mail: peterson@ucolick.org [Center for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, CO 80309-0389 (United States)

2017-04-01

The Fe i spectrum is critical to many areas of astrophysics, yet many of the high-lying levels remain uncharacterized. To remedy this deficiency, Peterson and Kurucz identified Fe i lines in archival ultraviolet and optical spectra of metal-poor stars, whose warm temperatures favor moderate Fe i excitation. Sixty-five new levels were recovered, with 1500 detectable lines, including several bound levels in the ionization continuum of Fe i. Here, we extend the previous work by identifying 59 additional levels, with 1400 detectable lines, by incorporating new high-resolution UV spectra of warm metal-poor stars recently obtained by the Hubble Space Telescope Imaging Spectrograph. We provide gf values for these transitions, both computed as well as adjusted to fit the stellar spectra. We also expand our spectral calculations to the infrared, confirming three levels by matching high-quality spectra of the Sun and two cool stars in the H -band. The predicted gf values suggest that an additional 3700 Fe i lines should be detectable in existing solar infrared spectra. Extending the empirical line identification work to the infrared would help confirm additional Fe i levels, as would new high-resolution UV spectra of metal-poor turnoff stars below 1900 Å.

Assisted Interpretation of Laser-Induced Fluorescence Spectra of Egg-Based Binding Media Using Total Emission Fluorescence Spectroscopy

International Nuclear Information System (INIS)

Anglos, D.; Nevin, A.

2006-01-01

Laser-induced fluorescence (LIF) spectroscopy can provide nondestructive, qualitative analysis of protein-based binding media found in artworks. Fluorescence emissions from proteins in egg yolk and egg white are due to auto fluorescent aromatic amino acids as well as other native and age-related fluorophores, but the potential of fluorescence spectroscopy for the differentiation between binding media is dependent on the choice of a suitable excitation wavelength and limited by problems in interpretation. However, a better understanding of emission spectra associated with LIF can be achieved following comparisons with total emission fluorescence spectra where a series of consecutive emission spectra are recorded over a specific range. Results using nanosecond UV laser sources for LIF of egg-based binding media are presented which are rationalised following comparisons with total emission spectra. Specifically, fluorescence is assigned to tryptophan and oxidation products of amino acids; in the case of egg yolk, fatty-acid polymerisation and age-related degradation products account for the formation of fluorophores.

Comparison of exit time moment spectra for extrinsic metric balls

DEFF Research Database (Denmark)

Hurtado, Ana; Markvorsen, Steen; Palmer, Vicente

2012-01-01

We prove explicit upper and lower bounds for the $L^1$-moment spectra for the Brownian motion exit time from extrinsic metric balls of submanifolds $P^m$ in ambient Riemannian spaces $N^n$. We assume that $P$ and $N$ both have controlled radial curvatures (mean curvature and sectional curvature...... obtain new intrinsic comparison results for the exit time spectra for metric balls in the ambient manifolds $N^n$ themselves....

Portable microcomputer unit for the analysis of plutonium gamma-ray spectra

International Nuclear Information System (INIS)

Ruhter, W.D.; Camp, D.C.

1981-10-01

A portable microcomputer has been developed for the IAEA to perform in-field analysis of plutonium gamma-ray spectra. The unit includes a 16-bit LSI-11/2 microprocessor, 32K words of memory, a 20-character display for user prompting, and a 20-character thermal printer for hardcopy output. Only the positions of the 148-keV Pu-241 and 208-keV U-237 peaks are required for spectral analysis. The unit was tested against gamma-ray spectra taken of NBS plutonium standards and IAEA spectra. Results obtained are presented

Electronic structure of beta-FeSi sub 2 obtained by maximum entropy method and photoemission spectroscopy

CERN Document Server

Kakemoto, H; Makita, Y; Kino, Y; Tsukamoto, T; Shin, S; Wada, S; Tsurumi, T

2003-01-01

The electronic structure of beta-FeSi sub 2 was investigated by maximum entropy method (MEM) and photoemission spectroscopy. The electronic structure obtained by MEM using X-ray diffraction data at room temperature (RT) showed covalent bonds of Fe-Si and Si-Si electrons. The photoemission spectra of beta-FeSi sub 2 at RT were changed by incidence photon energies. For photon energies between 50 and 100 eV, resonant photoemission spectra caused by a super Coster-Kronig transition were observed. In order to reduce resonant effect about Fe(3d) for obtained photoemission spectra, difference spectrum between 53 and 57 eV was calculated, and it was compared with ab-initio band calculation and spectra function.

Analysis of low-intensity scintillation spectra

International Nuclear Information System (INIS)

Muravsky, V.; Tolstov, S.A.

2002-01-01

The maximum likelihood algorithms for nuclides activities estimation from low intensity scintillation γ-ray spectra have been created. The algorithms treat full energy peaks and Compton parts of spectra, and they are more effective than least squares estimators. The factors that could lead to the bias of activity estimates are taken into account. Theoretical analysis of the problem of choosing the optimal set of initial spectra for the spectrum model to minimize errors of the activities estimation has been carried out for the general case of the N-components with Gaussian or Poisson statistics. The obtained criterion allows to exclude superfluous initial spectra of nuclides from the model. A special calibration procedure for scintillation γ-spectrometers has been developed. This procedure is required for application of the maximum likelihood activity estimators processing all the channels of the scintillation γ-spectrum, including the Compton part. It allows one to take into account the influence of the sample mass density variation. The algorithm for testing the spectrum model adequacy to the processed scintillation spectrum has been developed. The algorithms are realized in Borland Pascal 7 as a library of procedures and functions. The developed library is compatible with Delphi 1.0 and higher versions. It can be used as the algorithmic basis for analysis of highly sensitive scintillation γ- and β-spectrometric devices. (author)

Ga+ TOF-SIMS lineshape analysis for resolution enhancement of MALDI MS spectra of a peptide mixture

International Nuclear Information System (INIS)

Malyarenko, D.I.; Chen, H.; Wilkerson, A.L.; Tracy, E.R.; Cooke, W.E.; Manos, D.M.; Sasinowski, M.; Semmes, O.J.

2004-01-01

The use of mass spectrometry to obtain molecular profiles indicative of alteration of concentrations of peptides in body fluids is currently the subject of intense investigation. For surface-based time-of-flight mass spectrometry the reliability and specificity of such profiling methods depend both on the resolution of the measuring instrument and on the preparation of samples. The present work is a part of a program to use Ga + beam TOF-SIMS alone, and as an adjunct to MALDI, in the development of reliable protein and peptide markers for diseases. Here, we describe techniques to prepare samples of relatively high-mass peptides, which serve as calibration standards and proxies for biomarkers. These are: Arg8-vasopressin, human angiotensin II, and somatostatin. Their TOF-SIMS spectra show repeatable characteristic features, with mass resolution exceeding 2000, including parent peaks and chemical adducts. The lineshape analysis for high-resolution parent peaks is shown to be useful for filter construction and deconvolution of inferior resolution SELDI-TOF spectra of calibration peptide mixture

Flare stars of the Orion Nebula - spectra of an outburst

International Nuclear Information System (INIS)

Carter, B.D.; O'Mara, B.J.; Ross, J.E.

1988-01-01

For the first time, detailed, time-resolved spectra of a flare event of an Orion cluster flare star are presented. These spectra, covering ∼ λλ3600-4600, were obtained by using the Anglo-Australian Telescope with a fibre coupler to simultaneously monitor 23 flare stars in the region of the Orion Nebula. The flare spectra reveal continuous emission which filled in the photospheric Ca I 4226 A absorption, and hydrogen Balmer, Ca II H and K, He I 4026 A and He I 4471 A line emission. Overall, the spectral behaviour indicates similarities to strong outbursts of the classical dMe flare stars. (author)

Genetic multivariate calibration for near infrared spectroscopic determination of protein, moisture, dry mass, hardness and other residues of wheat

OpenAIRE

Özdemir, Durmuş

2006-01-01

Determination of wheat flour quality parameters, such as protein, moisture, dry mass by wet chemistry analyses takes long time. Near infrared spectroscopy (NIR) coupled with multivariate calibration offers a fast and nondestructive alternative to obtain reliable results. However, due to the complexity of the spectra obtained from NIR, some wavelength selection is generally required to improve the predictive ability of multivariate calibration methods. In this study, two different wheat data s...

Measurements of impurity spectra using UV/visible spectroscopic system in a GAMMA 10 plasma

International Nuclear Information System (INIS)

Matama, K.; Yoshikawa, M.; Kobayashi, T.; Kubota, Y.; Cho, T.

2006-01-01

Impurity spectra have been measured and identified using a newly designed ultraviolet and visible (UV/visible) spectroscopic system in the tandem mirror GAMMA 10. It is constructed using two spectrometers to obtain an entire wavelength range of UV/visible impurity spectra with a high wavelength resolution in one plasma shot. We successfully obtained the emission intensities of the radiation spectra in detail and information on the time-varying population densities of the impurities. We evaluate radiation loss from the GAMMA 10 plasma in the UV/visible range; further we estimate the electron density and temperature after applying the measured spectral intensity to a collisional-radiative model

Optical Spectra of Candidate International Celestial Reference Frame (ICRF) Flat-spectrum Radio Sources. III

Energy Technology Data Exchange (ETDEWEB)

Titov, O.; Stanford, Laura M. [Geoscience Australia, P.O. Box 378, Canberra, ACT 2601 (Australia); Pursimo, T. [Nordic Optical Telescope, Nordic Optical Telescope Apartado 474E-38700 Santa Cruz de La Palma, Santa Cruz de Tenerife (Spain); Johnston, Helen M.; Hunstead, Richard W. [Sydney Institute for Astronomy, School of Physics, University of Sydney, NSW 2006 (Australia); Jauncey, David L. [CSIRO Astronomy and Space Science, ATNF and Mount Stromlo Observatory, Cotter Road, Weston, ACT 2611 (Australia); Zenere, Katrina A., E-mail: oleg.titov@ga.gov.au [School of Physics, University of Sydney, NSW 2006 (Australia)

2017-04-01

In extending our spectroscopic program, which targets sources drawn from the International Celestial Reference Frame (ICRF) Catalog, we have obtained spectra for ∼160 compact, flat-spectrum radio sources and determined redshifts for 112 quasars and radio galaxies. A further 14 sources with featureless spectra have been classified as BL Lac objects. Spectra were obtained at three telescopes: the 3.58 m European Southern Observatory New Technology Telescope, and the two 8.2 m Gemini telescopes in Hawaii and Chile. While most of the sources are powerful quasars, a significant fraction of radio galaxies is also included from the list of non-defining ICRF radio sources.

Bacterial expression and one-step purification of an isotope-labeled heterotrimeric G-protein α-subunit

International Nuclear Information System (INIS)

Abdulaev, Najmoutin G.; Zhang Cheng; Dinh, Andy; Ngo, Tony; Bryan, Philip N.; Brabazon, Danielle M.; Marino, John P.; Ridge, Kevin D.

2005-01-01

Heterologous expression systems are often employed to generate sufficient quantities of isotope-labeled proteins for high-resolution NMR studies. Recently, the interaction between the prodomain region of subtilisin and an active, mutant form of the mature enzyme has been exploited to develop a cleavable affinity tag fusion system for one-step generation and purification of full-length soluble proteins obtained by inducible prokaryotic expression. As a first step towards applying high-resolution NMR methods to study heterotrimeric G-protein α-subunit (G α ) conformation and dynamics, the utility of this subtilisin prodomain fusion system for expressing and purifying an isotope-labeled G α chimera (∼40 kDa polypeptide) has been tested. The results show that a prodomain fused G α chimera can be expressed to levels approaching 6-8 mg/l in minimal media and that the processed, mature protein exhibits properties similar to those of G α isolated from natural sources. To assay for the functional integrity of the purified G α chimera at NMR concentrations and probe for changes in the structure and dynamics of G α that result from activation, 15 N-HSQC spectra of the GDP/Mg 2+ bound form of G α obtained in the absence and presence of aluminum fluoride, a well known activator of the GDP bound state, have been acquired. Comparisons of the 15 N-HSQC spectra reveals a number of changes in chemical shifts of the 1 HN, 15 N crosspeaks that are discussed with respect to expected changes in the protein conformation associated with G α activation

Honey bee odorant-binding protein 14: effects on thermal stability upon odorant binding revealed by FT-IR spectroscopy and CD measurements.

Science.gov (United States)

Schwaighofer, Andreas; Kotlowski, Caroline; Araman, Can; Chu, Nam; Mastrogiacomo, Rosa; Becker, Christian; Pelosi, Paolo; Knoll, Wolfgang; Larisika, Melanie; Nowak, Christoph

2014-03-01

In the present work, we study the effect of odorant binding on the thermal stability of honey bee (Apis mellifera L.) odorant-binding protein 14. Thermal denaturation of the protein in the absence and presence of different odorant molecules was monitored by Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD). FT-IR spectra show characteristic bands for intermolecular aggregation through the formation of intermolecular β-sheets during the heating process. Transition temperatures in the FT-IR spectra were evaluated using moving-window 2D correlation maps and confirmed by CD measurements. The obtained results reveal an increase of the denaturation temperature of the protein when bound to an odorant molecule. We could also discriminate between high- and low-affinity odorants by determining transition temperatures, as demonstrated independently by the two applied methodologies. The increased thermal stability in the presence of ligands is attributed to a stabilizing effect of non-covalent interactions between odorant-binding protein 14 and the odorant molecule.

A successful strategy for the recovering of active P21, an insoluble recombinant protein of Trypanosoma cruzi

Science.gov (United States)

Santos, Marlus Alves Dos; Teixeira, Francesco Brugnera; Moreira, Heline Hellen Teixeira; Rodrigues, Adele Aud; Machado, Fabrício Castro; Clemente, Tatiana Mordente; Brigido, Paula Cristina; Silva, Rebecca Tavares E.; Purcino, Cecílio; Gomes, Rafael Gonçalves Barbosa; Bahia, Diana; Mortara, Renato Arruda; Munte, Claudia Elisabeth; Horjales, Eduardo; da Silva, Claudio Vieira

2014-03-01

Structural studies of proteins normally require large quantities of pure material that can only be obtained through heterologous expression systems and recombinant technique. In these procedures, large amounts of expressed protein are often found in the insoluble fraction, making protein purification from the soluble fraction inefficient, laborious, and costly. Usually, protein refolding is avoided due to a lack of experimental assays that can validate correct folding and that can compare the conformational population to that of the soluble fraction. Herein, we propose a validation method using simple and rapid 1D 1H nuclear magnetic resonance (NMR) spectra that can efficiently compare protein samples, including individual information of the environment of each proton in the structure.

MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

Science.gov (United States)

Reid, Deseree J.; Diesing, Jessica M.; Miller, Matthew A.; Perry, Scott M.; Wales, Jessica A.; Montfort, William R.; Marty, Michael T.

2018-04-01

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. [Figure not available: see fulltext.

Proposed Site-Specific Response Spectra for Surabaya-Madura Bridge

Directory of Open Access Journals (Sweden)

Dyah Kusumastuti

2008-01-01

Full Text Available This paper presents a site-specific seismic hazard study to determine the recommended seismic design criteria for Suramadu Bridge. The study is performed using probabilistic seismic hazard approach to determine maximum acceleration and response spectra at bedrock and followed by local site effect analysis to determine maximum acceleration and response spectra at ground surface. The probabilistic seismic hazard analysis (PSHA is carried out using 3-dimension (3-D seismic source models (fault source model. Two hazard levels are analysed to represent 150 and 3,300 years return period of ground motion around site location. The local site effect analysis is performed using 1-dimension (1-D shear wave propagation theory to obtain peak ground acceleration and response spectra at ground surface. Finally, the site-specific surface response spectra with 5 percent damping are developed based on the mean plus one standard deviation concept from the result of local site effect analysis.

Infrared spectra of jennite and tobermorite from first-principles

Energy Technology Data Exchange (ETDEWEB)

Vidmer, Alexandre, E-mail: alexandre@vidmer.com; Sclauzero, Gabriele; Pasquarello, Alfredo

2014-06-01

The infrared absorption spectra of jennite, tobermorite 14 Å, anomalous tobermorite 11 Å, and normal tobermorite 11 Å are simulated within a density-functional-theory scheme. The atomic coordinates and the cell parameters are optimized resulting in structures which agree with previous studies. The vibrational frequencies and modes are obtained for each mineral. The vibrational density of states is analyzed through extensive projections on silicon tetrahedra, oxygen atoms, OH groups, and water molecules. The coupling with the electric field is achieved through the use of density functional perturbation theory, which yields Born effective charges and dielectric constants. The simulated absorption spectra reproduce well the experimental spectra, thereby allowing for a detailed interpretation of the spectral features in terms of the underlying vibrational modes. In the far-infrared part of the absorption spectra, the interplay between Ca and Si related vibrations leads to differences which are sensitive to the calcium/silicon ratio of the mineral.

Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography*

Science.gov (United States)

Paixão, Lucas; Oliveira, Bruno Beraldo; Viloria, Carolina; de Oliveira, Marcio Alves; Teixeira, Maria Helena Araújo; Nogueira, Maria do Socorro

2015-01-01

Objective Derive filtered tungsten X-ray spectra used in digital mammography systems by means of Monte Carlo simulations. Materials and Methods Filtered spectra for rhodium filter were obtained for tube potentials between 26 and 32 kV. The half-value layer (HVL) of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F & MAM Detector Platinum and 8201023-C Xi Base unit Platinum Plus w mAs in a Hologic Selenia Dimensions system using a direct radiography mode. Results Calculated HVL values showed good agreement as compared with those obtained experimentally. The greatest relative difference between the Monte Carlo calculated HVL values and experimental HVL values was 4%. Conclusion The results show that the filtered tungsten anode X-ray spectra and the EGSnrc Monte Carlo code can be used for mean glandular dose determination in mammography. PMID:26811553

Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography

Directory of Open Access Journals (Sweden)

Lucas Paixão

2015-12-01

Full Text Available Abstract Objective: Derive filtered tungsten X-ray spectra used in digital mammography systems by means of Monte Carlo simulations. Materials and Methods: Filtered spectra for rhodium filter were obtained for tube potentials between 26 and 32 kV. The half-value layer (HVL of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F & MAM Detector Platinum and 8201023-C Xi Base unit Platinum Plus w mAs in a Hologic Selenia Dimensions system using a direct radiography mode. Results: Calculated HVL values showed good agreement as compared with those obtained experimentally. The greatest relative difference between the Monte Carlo calculated HVL values and experimental HVL values was 4%. Conclusion: The results show that the filtered tungsten anode X-ray spectra and the EGSnrc Monte Carlo code can be used for mean glandular dose determination in mammography.

EPR spectra of synthetic, and natural Australian opals - A pilot study

International Nuclear Information System (INIS)

Hutton, D.R.; Troup, G.J.

1996-01-01

Full text: The EPR spectra of some synthetic opals, and of some Australian natural opals of various provenance, have been obtained, with the use of a Varian E-12 EPR spectrometer operating at ∼9.2 Ghz. The synthetic opals, from Swiss Gilson showed here a broad ESR signal in the g =2 region, with little identifiable structure . The natural Australian opals from Coober Pedy, Lightning Ridge, and Mintabie all showed the clear presence of Fe 3+ , Mn 2+ and a free radical like signal, suspected to be localised on an Al atom. Examples of the various spectra will be presented. It is not yet certain how the spectra correlate with provenance, but the synthetic spectra are quite different from the natural ones

Secondary graviton spectra and waterfall-like fields

International Nuclear Information System (INIS)

Giovannini, Massimo

2010-01-01

The secondary spectra of the gravitons induced by a waterfall-like field are computed and the general bounds on the spectral energy density of the tensor modes of the geometry are translated into explicit constraints on the amplitude and slope of the waterfall spectrum. The obtained results are compared with the primary gravitational wave spectra of the concordance model and of its neighboring extensions as well as with the direct LIGO/Virgo bounds on stochastic backgrounds of relic gravitons. Space-borne interferometers [such as LISA (Laser Interferometer Space Antenna), BBO (Big Bang Observer), and DECIGO (Deci-hertz Interferometer Gravitational Wave Observatory)] seem to be less relevant but their potential implications are briefly outlined.

Secondary graviton spectra and waterfall-like fields

Science.gov (United States)

Giovannini, Massimo

2010-10-01

The secondary spectra of the gravitons induced by a waterfall-like field are computed and the general bounds on the spectral energy density of the tensor modes of the geometry are translated into explicit constraints on the amplitude and slope of the waterfall spectrum. The obtained results are compared with the primary gravitational wave spectra of the concordance model and of its neighboring extensions as well as with the direct LIGO/Virgo bounds on stochastic backgrounds of relic gravitons. Space-borne interferometers [such as LISA (Laser Interferometer Space Antenna), BBO (Big Bang Observer), and DECIGO (Deci-hertz Interferometer Gravitational Wave Observatory)] seem to be less relevant but their potential implications are briefly outlined.

Electronic and oscillation absorption spectra of blood plamsa at surgical diseases of thyroid gland

Science.gov (United States)

Guminetskiy, S. G.; Motrich, A. V.; Poliansky, I. Y.; Hyrla, Ya. V.

2012-01-01

The results of investigating the absorption spectra of blood plasma in the visible and infrared parts of spectra obtained using the techniques of spherical photometer and spectrophotometric complex "Specord IR75" are presented. The possibility of using these spectra for diagnoses the cases of diffuse toxic goiter and nodular goiter and control of treatment process in postsurgical period in the cases of thyroid gland surgery is estimated.

Trajectory resolved analysis of LEIS energy spectra: Neutralization and surface structure

International Nuclear Information System (INIS)

Beikler, Robert; Taglauer, Edmund

2001-01-01

For a quantitative evaluation of low-energy ion scattering (LEIS) data with respect to surface composition and structure a detailed analysis of the energy spectra is required. This includes the identification of multiple scattering processes and the determination of ion survival probabilities. We analyzed scattered ion energy spectra by using the computer code MARLOWE for which we developed a new analysis routine that allows to record energy distributions in dependence of the number of projectile-target atom collisions, in dependence of the distance of closest approach, or in dependence of the scattering crystalline layer. This procedure also permits the determination of ion survival probabilities by applying simple collision-dependent neutralization models. Experimental energy spectra for various projectile (He + , Ne + , Na + ) and target (transition metals, oxides) combinations are well reproduced and quantitative results for ion survival probabilities are obtained. These are largely in agreement with results obtained for bimetallic crystal surfaces obtained in a different way. Such MARLOWE calculations are also useful for the identification of structure relevant processes. This is shown exemplarily for the reconstructed Au(1 1 0) surface including a possibility to determine the (1x2)→(1x1) transition temperature

Dynamical and Radiative Properties of X-Ray Pulsar Accretion Columns: Phase-averaged Spectra

Energy Technology Data Exchange (ETDEWEB)

West, Brent F. [Department of Electrical and Computer Engineering, United States Naval Academy, Annapolis, MD (United States); Wolfram, Kenneth D. [Naval Research Laboratory (retired), Washington, DC (United States); Becker, Peter A., E-mail: bwest@usna.edu, E-mail: kswolfram@gmail.com, E-mail: pbecker@gmu.edu [Department of Physics and Astronomy, George Mason University, Fairfax, VA (United States)

2017-02-01

The availability of the unprecedented spectral resolution provided by modern X-ray observatories is opening up new areas for study involving the coupled formation of the continuum emission and the cyclotron absorption features in accretion-powered X-ray pulsar spectra. Previous research focusing on the dynamics and the associated formation of the observed spectra has largely been confined to the single-fluid model, in which the super-Eddington luminosity inside the column decelerates the flow to rest at the stellar surface, while the dynamical effect of gas pressure is ignored. In a companion paper, we have presented a detailed analysis of the hydrodynamic and thermodynamic structure of the accretion column obtained using a new self-consistent model that includes the effects of both gas and radiation pressures. In this paper, we explore the formation of the associated X-ray spectra using a rigorous photon transport equation that is consistent with the hydrodynamic and thermodynamic structure of the column. We use the new model to obtain phase-averaged spectra and partially occulted spectra for Her X-1, Cen X-3, and LMC X-4. We also use the new model to constrain the emission geometry, and compare the resulting parameters with those obtained using previously published models. Our model sheds new light on the structure of the column, the relationship between the ionized gas and the photons, the competition between diffusive and advective transport, and the magnitude of the energy-averaged cyclotron scattering cross-section.

Spectroscopic studies of model photo-receptors: validation of a nanosecond time-resolved micro-spectrophotometer design using photoactive yellow protein and α-phycoerythrocyanin.

Science.gov (United States)

Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh; Schmidt, Marius

2013-09-13

Time-resolved spectroscopic experiments have been performed with protein in solution and in crystalline form using a newly designed microspectrophotometer. The time-resolution of these experiments can be as good as two nanoseconds (ns), which is the minimal response time of the image intensifier used. With the current setup, the effective time-resolution is about seven ns, determined mainly by the pulse duration of the nanosecond laser. The amount of protein required is small, on the order of 100 nanograms. Bleaching, which is an undesirable effect common to photoreceptor proteins, is minimized by using a millisecond shutter to avoid extensive exposure to the probing light. We investigate two model photoreceptors, photoactive yellow protein (PYP), and α-phycoerythrocyanin (α-PEC), on different time scales and at different temperatures. Relaxation times obtained from kinetic time-series of difference absorption spectra collected from PYP are consistent with previous results. The comparison with these results validates the capability of this spectrophotometer to deliver high quality time-resolved absorption spectra.

Computer simulation of RBS spectra from samples with surface roughness

Energy Technology Data Exchange (ETDEWEB)

Malinský, P., E-mail: malinsky@ujf.cas.cz [Nuclear Physics Institute of the Academy of Sciences of the Czech Republic, v. v. i., 250 68 Rez (Czech Republic); Department of Physics, Faculty of Science, J. E. Purkinje University, Ceske mladeze 8, 400 96 Usti nad Labem (Czech Republic); Hnatowicz, V., E-mail: hnatowicz@ujf.cas.cz [Nuclear Physics Institute of the Academy of Sciences of the Czech Republic, v. v. i., 250 68 Rez (Czech Republic); Macková, A., E-mail: mackova@ujf.cas.cz [Nuclear Physics Institute of the Academy of Sciences of the Czech Republic, v. v. i., 250 68 Rez (Czech Republic); Department of Physics, Faculty of Science, J. E. Purkinje University, Ceske mladeze 8, 400 96 Usti nad Labem (Czech Republic)

2016-03-15

A fast code for the simulation of common RBS spectra including surface roughness effects has been written and tested on virtual samples comprising either a rough layer deposited on a smooth substrate or smooth layer deposited on a rough substrate and simulated at different geometries. The sample surface or interface relief has been described by a polyline and the simulated RBS spectrum has been obtained as the sum of many particular spectra from randomly chosen particle trajectories. The code includes several procedures generating virtual samples with random and regular (periodical) roughness. The shape of the RBS spectra has been found to change strongly with increasing sample roughness and an increasing angle of the incoming ion beam.

Calculation of quantum-mechanical system energy spectra using path integrals

International Nuclear Information System (INIS)

Evseev, A.M.; Dmitriev, V.P.

1977-01-01

A solution of the Feynman quantum-mechanical integral connecting a wave function (psi (x, t)) at a moment t+tau (tau → 0) with the wave function at the moment t is provided by complex variable substitution and subsequent path integration. Time dependence of the wave function is calculated by the Monte Carlo method. The Fourier inverse transformation of the wave function by path integration calculated has been applied to determine the energy spectra. Energy spectra are presented of a hydrogen atom derived from wave function psi (x, t) at different x, as well as boson energy spectra of He, Li, and Be atoms obtained from psi (x, t) at X = O

Distribution and Spectroscopy of Green Fluorescent Protein and Acyl-CoA: Cholesterol Acytransferase in Sf21 Insect Cells

Science.gov (United States)

Richmond, R. C.; Mahtani, H.; Lu, X.; Chang, T. Y.; Malak, H.; Rose, M. Franklin (Technical Monitor)

2001-01-01

Acyl-CoA: cholesterol acyltransferase (ACAT) is thought to significantly participate in the pathway of cholesterol esterification that underlies the pathology of artherosclerosis. This enzyme is a membrane protein known to be preferentially bound within the endoplasmic reticulum of mammalian cells, from which location it esterifies cholesterol derived from low density lipoprotein. Cultures of insect cells were separately infected with baculovirus containing the gene for green fluroescent protein (GFP) and with baculovirus containing tandem genes for GFP and ACAT. These infected cultures expressed GFP and the fusion protein GCAT, respectively, with maximum expression occurring on the fourth day after infection. Extraction of GFP- and of GCAT-expressing cells with urea and detergent resulted in recovery of fluorescent protein in aqueous solution. Fluorescence spectra at neutral pH were identical for both GFP and GCAT extracts in aqueous solution, indicating unperturbed tertiary structure for the GFP moiety within GCAT. In a cholesterol esterification assay, GCAT demonstrated ACAT activity, but with less efficiency compared to native ACAT. It was hypothesized that the membrane protein ACAT would lead to differences in localization of GCAT compared to GFP within the respective expressing insect cells. The GFP marker directly and also within the fusion protein GCAT was accordingly used as the intracellular probe that was fluorescently analyzed by the new biophotonics technique of hyperspectral imaging. In that technique, fluorescence imaging was obtained from two dimensional arrays of cells, and regions of interest from within those images were then retrospectively analyzed for the emission spectra that comprises the image. Results of hyperspectral imaging of insect cells on day 4 postinfection showed that GCAT was preferentially localized to the cytoplasm of these cells compared to GFP. Furthermore, the emission spectra obtained for the localized GCAT displayed a peak

A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.

Science.gov (United States)

Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li

2013-01-21

A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments.

Modeling of A-DLTS Spectra of MOS Structures

Directory of Open Access Journals (Sweden)

Peter Hockicko

2008-01-01

Full Text Available Acquisition of basic characteristic of defects has become possible through a wide class of measurement techniqueswhich probe the interface, the near interface, as well as the bulk of semiconductor. Results presented here are basedessentially on the acoustic version of Deep Level Transient Spectroscopy (A-DLTS measurements. This method is based onthe acoustoelectric response effect observed at the interface. The A-DLTS uses the acoustoelectric response signal (ARSproduced by MOS structure interface when a longitudal acoustic wave propagates through a structure. The ARS is extremelysensitive to external conditions of the structure and reflects any changes in the charge distribution connected with chargedtraps. The temperature dependence of ARS after bias voltage step application is investigated and the activation energies andsome other parameters of traps at the insulator – semiconductor interface are determined. The results obtained formArrhenius plots of A-DLTS spectra of selected MOS structures are compared with results obtained from modeling of ADLTS spectra using theoretical model.

C-X neutral spectra from ZT-40M

International Nuclear Information System (INIS)

Munson, C.; Carolan, P.G.; Bunting, C.A.

1988-01-01

A series of experiments have recently been completed on the ZT-40M Reversed Field Pinch at Los Alamos for which Neutral Charge Exchange (C-X) spectra have been measured using both the previously reported Time-of-Flight (TOF) system, and a 5 channel electrostatic Neutral Particle Analyzer (NPA). The experiments involved measurements of ion and electron temperatures for a variety of discharge conditions including scans of flat-top current levels, different values of the toroidal field reversal parameter (F = B phi (a)/ phi >), ramped current discharges, discharges with a movable graphite paddle limiter inserted into the edge of the plasma from above, and discharges with Deuterium pellet injection. Both the TOF and NPA systems view the plasma along chords from the outside midplane, and are separated by 60 0 toroidally. Core ion temperatures are obtained by examining the asymptotic tail of the neutral particle efflux spectrum. Detailed comparisons of the neutral particle spectra obtained with these two systems for the various operating conditions will be presented

Analysis of secreted proteins from Aspergillus flavus.

Science.gov (United States)

Medina, Martha L; Haynes, Paul A; Breci, Linda; Francisco, Wilson A

2005-08-01

MS/MS techniques in proteomics make possible the identification of proteins from organisms with little or no genome sequence information available. Peptide sequences are obtained from tandem mass spectra by matching peptide mass and fragmentation information to protein sequence information from related organisms, including unannotated genome sequence data. This peptide identification data can then be grouped and reconstructed into protein data. In this study, we have used this approach to study protein secretion by Aspergillus flavus, a filamentous fungus for which very little genome sequence information is available. A. flavus is capable of degrading the flavonoid rutin (quercetin 3-O-glycoside), as the only source of carbon via an extracellular enzyme system. In this continuing study, a proteomic analysis was used to identify secreted proteins from A. flavus when grown on rutin. The growth media glucose and potato dextrose were used to identify differentially expressed secreted proteins. The secreted proteins were analyzed by 1- and 2-DE and MS/MS. A total of 51 unique A. flavus secreted proteins were identified from the three growth conditions. Ten proteins were unique to rutin-, five to glucose- and one to potato dextrose-grown A. flavus. Sixteen secreted proteins were common to all three media. Fourteen identifications were of hypothetical proteins or proteins of unknown functions. To our knowledge, this is the first extensive proteomic study conducted to identify the secreted proteins from a filamentous fungus.

The Mossbauer spectra of carbon nanotubes synthesize using ferrite catalyst

International Nuclear Information System (INIS)

Zhang Haiyan; Lin Jiapeng; Peng Zuxiong; Zeng Guoxun; Pang Jinshan; Chen Yiming

2009-01-01

The ferrite powder with honeycombed structure obtained by chemical combustion was used as catalyst to synthesize multi-walled carbon nanotubes by chemical vapor deposition. The magnetic components and characters of the the carbon nanotubes synthesized were investigated by X-ray diffraction (XRD), Mossbauer spectra and vibrating-sample magnetometer (VSM). The ferric components of the carbon nanotubes samples can be identified by Mossbauer spectra. The Mossbauer spectra of carbon nanotubes sample after purification contains two ferromagnetic sextet components corresponding to α-Fe species and Fe 3 C (cementite) species. While the Mossbauer spectra of the carbon nanotubes sample before purification contains three ferromagnetic sextet components corresponding to α-Fe species, Fe 3 C species and γ-Fe 2 O 3 . The saturation magnetization intensity Ms of carbon nanotubes sample after purification is decreased from 46.61 to 2.94 emu/g, but the coercive force increasd and reached 328Oe.

A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins

International Nuclear Information System (INIS)

Plevin, Michael J.; Hamelin, Olivier; Boisbouvier, Jérôme; Gans, Pierre

2011-01-01

A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-[ 13 C]glucose and subsaturating amounts of 2-[ 13 C]methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional 1 H- 13 C correlation spectra. Protein samples are conveniently prepared using the same media composition as the main uniformly-labeled sample and contain higher levels of isotope-enrichment than fractional labeling approaches. This new strategy thus represents an economically-attractive, robust alternative for obtaining isotopically-encoded stereospecific NMR assignments of prochiral methyl groups.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples

Energy Technology Data Exchange (ETDEWEB)

Gopinath, T. [University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics (United States); Mote, Kaustubh R. [University of Minnesota, Department of Chemistry (United States); Veglia, Gianluigi, E-mail: vegli001@umn.edu [University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics (United States)

2015-05-15

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living {sup 15}N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through {sup 15}N–{sup 15}N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish {sup 15}N–{sup 15}N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI–HETCOR and 3D PISEMAI–HETCOR-mixing experiments.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples.

Science.gov (United States)

Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi

2015-05-01

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples

International Nuclear Information System (INIS)

Gopinath, T.; Mote, Kaustubh R.; Veglia, Gianluigi

2015-01-01

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living 15 N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through 15 N– 15 N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish 15 N– 15 N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI–HETCOR and 3D PISEMAI–HETCOR-mixing experiments

Sensitivity of NMR spectra properties to different inversion algorithms. Abstract 97

International Nuclear Information System (INIS)

Bryan, J.; Wang, G.; Vargas, S.; Kantzas, A.

2004-01-01

'Full text:' Low field NMR technology has many applications in the petroleum industry. NMR spectra obtained from logging tools or laboratory instruments can be used to provide an incredible wealth of useful information for formation evaluation and reservoir fluid characterization purposes. In recent years, research performed at the University of Calgary has been instrumental in developing this technology for heavy oil and bitumen related problems. Specifically, low field NMR has been used in several niche applications: in-situ viscosity estimates of heavy oil and bitumen, water-in-oil emulsion and solvent-bitumen mixture viscosity, water cut in produced fluid streams, and oil-water-solids content in oil sands mining samples. The majority of all NMR analyses are based on the interpretation of NMR spectra. These spectra are inverted numerically from the measured NMR decay data. The mathematics of the inversion is generally assumed to be correct, and the analyses revolve around interpretations of how the spectra relate to physical properties of the samples. However, when measuring high viscosity fluids or clay-bound water, the NMR signal relaxes very quickly and it becomes extremely important to ensure that the spectrum obtained is accurate before relating its properties to physics. This work investigates the effect of different inversion algorithms on the generated spectra, and attempts to quantify the magnitude of the errors that can be associated with the mathematics of inversion. This leads to a better understanding of the accuracy of NMR estimates of rock and fluid properties. (author)

Communications: On artificial frequency shifts in infrared spectra obtained from centroid molecular dynamics: Quantum liquid water

Science.gov (United States)

Ivanov, Sergei D.; Witt, Alexander; Shiga, Motoyuki; Marx, Dominik

2010-01-01

Centroid molecular dynamics (CMD) is a popular method to extract approximate quantum dynamics from path integral simulations. Very recently we have shown that CMD gas phase infrared spectra exhibit significant artificial redshifts of stretching peaks, due to the so-called "curvature problem" imprinted by the effective centroid potential. Here we provide evidence that for condensed phases, and in particular for liquid water, CMD produces pronounced artificial redshifts for high-frequency vibrations such as the OH stretching band. This peculiar behavior intrinsic to the CMD method explains part of the unexpectedly large quantum redshifts of the stretching band of liquid water compared to classical frequencies, which is improved after applying a simple and rough "harmonic curvature correction."

Redox sensor proteins for highly sensitive direct imaging of intracellular redox state.

Science.gov (United States)

Sugiura, Kazunori; Nagai, Takeharu; Nakano, Masahiro; Ichinose, Hiroshi; Nakabayashi, Takakazu; Ohta, Nobuhiro; Hisabori, Toru

2015-02-13

Intracellular redox state is a critical factor for fundamental cellular functions, including regulation of the activities of various metabolic enzymes as well as ROS production and elimination. Genetically-encoded fluorescent redox sensors, such as roGFP (Hanson, G. T., et al. (2004)) and Redoxfluor (Yano, T., et al. (2010)), have been developed to investigate the redox state of living cells. However, these sensors are not useful in cells that contain, for example, other colored pigments. We therefore intended to obtain simpler redox sensor proteins, and have developed oxidation-sensitive fluorescent proteins called Oba-Q (oxidation balance sensed quenching) proteins. Our sensor proteins derived from CFP and Sirius can be used to monitor the intracellular redox state as their fluorescence is drastically quenched upon oxidation. These blue-shifted spectra of the Oba-Q proteins enable us to monitor various redox states in conjunction with other sensor proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

Measurements of fast neutron spectra in iron, uranium and sodium-iron assemblies

International Nuclear Information System (INIS)

Kappler, F.; Pieroni, N.; Rusch, D.; Schmidt, A.; Wattecamps, E.; Werle, H.

1979-01-01

Spectrum measurements were performed at the fast subcritical facility SUAK to test nuclear data and computer codes used in fast reactor calculations. In order to obtain a specific and quantitative interpretation of discrepancies between measured and calculated spectrum, homogeneous assemblies consisting of single materials were investigated. The leakage spectrum of iron and uranium cylinders was measured by time-of-flight and proportional counters. Time-dependent leakage spectra were measured by a NE 213 liquid scintillator. It was demonstrated that the investigation of time-dependent spectra is a sensitive test of inelastic scattering cross section data. The effect of an interface on fast neutron spectra was also investigated by measuring space dependent spectra across a sodium-iron interface. The measured spectra of these assemblies are suitable for testing the adequacy of computational approximations and cross section data. (author)

Interpretation of Tandem Mass Spectrometry (MSMS) Spectra for Peptide Analysis

DEFF Research Database (Denmark)

Hjernø, Karin; Højrup, Peter

2015-01-01

The aim of this chapter is to give a short introduction to peptide analysis by mass spectrometry (MS) and interpretation of fragment mass spectra. Through examples and guidelines we demonstrate how to understand and validate search results and how to perform de novo sequencing based on the often...... very complex fragmentation pattern obtained by tandem mass spectrometry (also referred to as MSMS). The focus is on simple rules for interpretation of MSMS spectra of tryptic as well as non-tryptic peptides....

Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition

Directory of Open Access Journals (Sweden)

André Melo

2008-09-01

Full Text Available In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT terms, was introduced to evaluate the magnitude of the interaction between each amino acid and the ligand. In this case study, the nonbonding–PLCT noncompensation characterizes the stabilization energy of the association process in study. The main residues (Gly29, Cys3 and Arg5 with net attractive effects and Arg1 (with a net repulsive effect, responsible by the stability of protein-ligand complex, are associated with large nonbonding energies non-compensated by PLCT effects. The results obtained enable us to conclude that the present decomposition scheme can be used for understanding the cohesive phenomena in proteins.

Fourier evaluation of broad Moessbauer spectra

International Nuclear Information System (INIS)

Vincze, I.

1981-01-01

It is shown by the Fourier analysis of broad Moessbauer spectra that the even part of the distribution of the dominant hyperfine interaction (hyperfine field or quadrupole splitting) can be obtained directly without using least-square fitting procedures. Also the odd part of this distribution correlated with other hyperfine parameters (e.g. isomer shift) can be directly determined. Examples for amorphous magnetic and paramagnetic iron-based alloys are presented. (author)

Radio synchrotron spectra of star-forming galaxies

Science.gov (United States)

Klein, U.; Lisenfeld, U.; Verley, S.

2018-03-01

We investigated the radio continuum spectra of 14 star-forming galaxies by fitting nonthermal (synchrotron) and thermal (free-free) radiation laws. The underlying radio continuum measurements cover a frequency range of 325 MHz to 24.5 GHz (32 GHz in case of M 82). It turns out that most of these synchrotron spectra are not simple power-laws, but are best represented by a low-frequency spectrum with a mean slope αnth = 0.59 ± 0.20 (Sν ∝ ν-α), and by a break or an exponential decline in the frequency range of 1-12 GHz. Simple power-laws or mildly curved synchrotron spectra lead to unrealistically low thermal flux densities, and/or to strong deviations from the expected optically thin free-free spectra with slope αth = 0.10 in the fits. The break or cutoff energies are in the range of 1.5-7 GeV. We briefly discuss the possible origin of such a cutoff or break. If the low-frequency spectra obtained here reflect the injection spectrum of cosmic-ray electrons, they comply with the mean spectral index of Galactic supernova remnants. A comparison of the fitted thermal flux densities with the (foreground-corrected) Hα fluxes yields the extinction, which increases with metallicity. The fraction of thermal emission is higher than believed hitherto, especially at high frequencies, and is highest in the dwarf galaxies of our sample, which we interpret in terms of a lack of containment in these low-mass systems, or a time effect caused by a very young starburst.

Magnetic polymeric microspheres for protein adsorption

International Nuclear Information System (INIS)

Felinto, M.C.F.C.; Parra, D.F.; Lugao, A.B.; Batista, M.P.; Higa, O.Z.; Yamaura, M.; Camilo, R.L.; Ribela, M.T.C.P.; Sampaio, L.C.

2005-01-01

Magnetic beads consisting of polymer-coated manganese ferrite nanoparticles were prepared by the precipitation reaction of manganese ferrite into the channels of methyl methacrylate polymer beads by sodium hydroxide, resulting in MnMagBead. MnMagBead was characterized by infrared spectra (FTIR), thermogravimetric analysis of TGA/DTG and indicates the presence of -CO (carbonyl) groups and the MnFe 2 O 4 on the beads. Magnetization measurements were obtained at room temperature in magnetic fields up to 10 KOe using a vibrating sample magnetometer. Introductory Protein adsorption biological tests were processed using labeled I-125 albumin (BSA), and the activity was measured in a gamma counting spectrometer. These superparamagnetic beads exhibit the capacity to bind biological molecules such as proteins like albumin, with a good capability (5 x 10 -6 ) μg/100 mg of beads as compared with other magnetic resins studied in our group

Moessbauer spectroscopic studies of iron-storage proteins

Energy Technology Data Exchange (ETDEWEB)

St. Pierre, T.G.

1986-01-01

/sup 57/Fe Moessbauer spectroscopy was used to study iron storage proteins. Various cryostats and a superconducting magnet were used to obtain sample environment temperatures from 1.3 to 200K and applied magnetic fields of up to 10T. The Moessbauer spectra of ferritins isolated from iron-overloaded human spleen, limpet (Patella vulgata), giant limpet (Patella laticostata) and chiton (Clavarizona hirtosa) hemolymph, and bacterial (Pseudomonas aeruginosa) cells are used to gain information on the magnetic ordering- and superparamagnetic transition temperatures of the microcrystalline cores of the proteins. Investigations were made about the cause of the difference in the magnetic anisotropy constants of the cores of iron-overloaded human spleen ferritin and hemosiderin. Livers taken from an iron-overloaded hornbill and artificially iron-loaded rats showed no component with a superparamagnetic transition temperature approaching that of the human spleen hemosiderin.

Bacterial expression and one-step purification of an isotope-labeled heterotrimeric G-protein {alpha}-subunit

Energy Technology Data Exchange (ETDEWEB)

Abdulaev, Najmoutin G. [University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology (United States); Zhang Cheng; Dinh, Andy [University of Texas Health Science Center, Center for Membrane Biology, Department of Biochemistry and Molecular Biology (United States); Ngo, Tony; Bryan, Philip N. [University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology (United States); Brabazon, Danielle M. [Loyola College in Maryland, Department of Chemistry (United States); Marino, John P. [University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology (United States)], E-mail: marino@carb.nist.gov; Ridge, Kevin D. [University of Texas Health Science Center, Center for Membrane Biology, Department of Biochemistry and Molecular Biology (United States)

2005-05-15

Heterologous expression systems are often employed to generate sufficient quantities of isotope-labeled proteins for high-resolution NMR studies. Recently, the interaction between the prodomain region of subtilisin and an active, mutant form of the mature enzyme has been exploited to develop a cleavable affinity tag fusion system for one-step generation and purification of full-length soluble proteins obtained by inducible prokaryotic expression. As a first step towards applying high-resolution NMR methods to study heterotrimeric G-protein {alpha}-subunit (G{sub {alpha}}) conformation and dynamics, the utility of this subtilisin prodomain fusion system for expressing and purifying an isotope-labeled G{sub {alpha}} chimera ({approx}40 kDa polypeptide) has been tested. The results show that a prodomain fused G{sub {alpha}} chimera can be expressed to levels approaching 6-8 mg/l in minimal media and that the processed, mature protein exhibits properties similar to those of G{sub {alpha}} isolated from natural sources. To assay for the functional integrity of the purified G{sub {alpha}} chimera at NMR concentrations and probe for changes in the structure and dynamics of G{sub {alpha}} that result from activation, {sup 15}N-HSQC spectra of the GDP/Mg{sup 2+} bound form of G{sub {alpha}} obtained in the absence and presence of aluminum fluoride, a well known activator of the GDP bound state, have been acquired. Comparisons of the {sup 15}N-HSQC spectra reveals a number of changes in chemical shifts of the {sup 1}HN, {sup 15}N crosspeaks that are discussed with respect to expected changes in the protein conformation associated with G{sub {alpha}} activation.

Photoabsorption spectra in the perturbative regime for atoms in crossed electric and magnetic fields

International Nuclear Information System (INIS)

Marxer, H.; Moser, I.; O'Mahony, P.F.; Mota-Furtado, F.

1994-01-01

We calculate photoabsorption spectra of atoms in crossed electric and magnetic fields using a truncated basis of Coulomb eigenfunctions. The method yields spectra in the regime where inter-n-mixing is not dominant and allows for the treatment of non-hydrogenic atoms via a simple recourse to quantum defects. We compare results for hydrogen to those obtained in second order perturbation theory where the residual degeneracy left in first order perturbation theory is completely lifted and we show that only a very small basis size is needed to achieve convergence to within the accuracy of second order perturbation theory. In the case of lithium the coupling of an incomplete hydrogen-like manifold to states with non-negligible quantum defects substantially modifies the spectra obtained in comparison to the purely hydrogenic spectra. In the inter-n-mixing regime we also compare our convoluted results directly with an experimental spectrum for hydrogen and find good agreement below the saddle point. (Author)

Analysis of Earthquake Source Spectra in Salton Trough

Science.gov (United States)

Chen, X.; Shearer, P. M.

2009-12-01

Previous studies of the source spectra of small earthquakes in southern California show that average Brune-type stress drops vary among different regions, with particularly low stress drops observed in the Salton Trough (Shearer et al., 2006). The Salton Trough marks the southern end of the San Andreas Fault and is prone to earthquake swarms, some of which are driven by aseismic creep events (Lohman and McGuire, 2007). In order to learn the stress state and understand the physical mechanisms of swarms and slow slip events, we analyze the source spectra of earthquakes in this region. We obtain Southern California Seismic Network (SCSN) waveforms for earthquakes from 1977 to 2009 archived at the Southern California Earthquake Center (SCEC) data center, which includes over 17,000 events. After resampling the data to a uniform 100 Hz sample rate, we compute spectra for both signal and noise windows for each seismogram, and select traces with a P-wave signal-to-noise ratio greater than 5 between 5 Hz and 15 Hz. Using selected displacement spectra, we isolate the source spectra from station terms and path effects using an empirical Green’s function approach. From the corrected source spectra, we compute corner frequencies and estimate moments and stress drops. Finally we analyze spatial and temporal variations in stress drop in the Salton Trough and compare them with studies of swarms and creep events to assess the evolution of faulting and stress in the region. References: Lohman, R. B., and J. J. McGuire (2007), Earthquake swarms driven by aseismic creep in the Salton Trough, California, J. Geophys. Res., 112, B04405, doi:10.1029/2006JB004596 Shearer, P. M., G. A. Prieto, and E. Hauksson (2006), Comprehensive analysis of earthquake source spectra in southern California, J. Geophys. Res., 111, B06303, doi:10.1029/2005JB003979.

A rapid method to screen for cell-wall mutants using discriminant analysis of Fourier transform infrared spectra

International Nuclear Information System (INIS)

Chen LiMei; Carpita, N.C.; Reiter, W.D.; Wilson, R.H.; Jeffries, C.; McCann, M.C.

1998-01-01

We have developed a rapid method to screen large numbers of mutant plants for a broad range of cell wall phenotypes using Fourier transform infrared (FTIR) microspectroscopy of leaves. We established and validated a model that can discriminate between the leaves of wild-type and a previously defined set of cell-wall mutants of Arabidopsis. Exploratory principal component analysis indicated that mutants deficient in different cell-wall sugars can be distinguished from each other. Discrimination of cell-wall mutants from wild-type was independent of variability in starch content or additional unrelated mutations that might be present in a heavily mutagenised population. We then developed an analysis of FTIR spectra of leaves obtained from over 1000 mutagenised flax plants, and selected 59 plants whose spectral variation from wild-type was significantly out of the range of a wild-type population, determined by Mahalanobis distance. Cell wall sugars from the leaves of selected putative mutants were assayed by gas chromatography-mass spectrometry and 42 showed significant differences in neutral sugar composition. The FTIR spectra indicated that six of the remaining 17 plants have altered ester or protein content. We conclude that linear discriminant analysis of FTIR spectra is a robust method to identify a broad range of structural and architectural alterations in cell walls, appearing as a consequence of developmental regulation, environmental adaptation or genetic modification. (author)

COLORED DISSOLVED ORGANIC MATTER (CDOM) CHARACTERIZATION BY ABSORPTION AND FLUORESCENCE SPECTRA

OpenAIRE

Goncalves Araujo, Rafael; Ramirez-Perez, Marta; Kraberg, Alexandra; Piera, Jaume; Bracher, Astrid

2014-01-01

Colored dissolved organic matter (CDOM) absorption and fluorescence spectra were analyzed from samples collected in the Lena River Delta region (Siberia, Russia; summer-2013) and in the Alfacs Bay (Ebro River Delta, Spain; summer-2013/winter-2014) in order to use optical measurements to infer loading and origin of CDOM. Absorbance spectra and Excitation-Emission matrices (EEMs) were obtained with a HORIBA Aqualog® spectrofluorometer. CDOM absorption at 443nm (a443) and terrestrial absorption ...

Spectroscopic analysis on the binding interaction between tetracycline hydrochloride and bovine proteins β-casein, α-lactalbumin

Energy Technology Data Exchange (ETDEWEB)

Bi, Hongna; Tang, Lin, E-mail: tanglin@sdnu.edu.cn; Gao, Xin; Jia, Jingjing; Lv, Henghui

2016-10-15

We investigated the binding interaction between tetracycline hydrochloride (TCH) and bovine proteins β-casein (β-CN), α-lactalbumin (α-LA) in aqueous solution by multi-spectroscopic methods and molecular modeling techniques. Fluorescence and time-resolved fluorescence showed that TCH effectively quenched the intrinsic fluorescence of bovine proteins via static quenching, while there was a single class of binding site on protein. Thermodynamic parameters revealed that electrostatic forces played major roles in the interaction between β-CN and TCH, whereas α-LA-TCH complex were stabilized by hydrogen bonds and van der Waals forces. Moreover, circular dichroism spectra (CD spectra), ultraviolet visible absorption spectra (UV–vis absorption spectra), and fluorescence Excitation-Emission Matrix (EEM) spectra results indicated the secondary structure of bovine proteins was changed in the presence of TCH with the α-helix percentage of protein-TCH complexes decreased. Molecular modeling analysis supported the experimental results well. In addition, the research of surface hydrophobicity further verified tertiary structure of proteins was changed in the presence of TCH and the possible changes of protein function. These results achieved from experiments may be valuable in the milk industry and food safety.

Spectroscopic analysis on the binding interaction between tetracycline hydrochloride and bovine proteins β-casein, α-lactalbumin

International Nuclear Information System (INIS)

Bi, Hongna; Tang, Lin; Gao, Xin; Jia, Jingjing; Lv, Henghui

2016-01-01

We investigated the binding interaction between tetracycline hydrochloride (TCH) and bovine proteins β-casein (β-CN), α-lactalbumin (α-LA) in aqueous solution by multi-spectroscopic methods and molecular modeling techniques. Fluorescence and time-resolved fluorescence showed that TCH effectively quenched the intrinsic fluorescence of bovine proteins via static quenching, while there was a single class of binding site on protein. Thermodynamic parameters revealed that electrostatic forces played major roles in the interaction between β-CN and TCH, whereas α-LA-TCH complex were stabilized by hydrogen bonds and van der Waals forces. Moreover, circular dichroism spectra (CD spectra), ultraviolet visible absorption spectra (UV–vis absorption spectra), and fluorescence Excitation-Emission Matrix (EEM) spectra results indicated the secondary structure of bovine proteins was changed in the presence of TCH with the α-helix percentage of protein-TCH complexes decreased. Molecular modeling analysis supported the experimental results well. In addition, the research of surface hydrophobicity further verified tertiary structure of proteins was changed in the presence of TCH and the possible changes of protein function. These results achieved from experiments may be valuable in the milk industry and food safety.

ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data.

Science.gov (United States)

Winkler, Robert

2010-02-01

Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI-MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI-MS data. The resulting software ESIprot was tested with ESI-MS data of six intact reference proteins between 12.4 and 66.7 kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between -0.2 and 1.2 Da, the relative errors below 30 ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open-source GPLv3 license to support future developments of mass spectrometry software. Copyright 2010 John Wiley & Sons, Ltd.

Spectra of chemical trees

International Nuclear Information System (INIS)

Balasubramanian, K.

1982-01-01

A method is developed for obtaining the spectra of trees of NMR and chemical interests. The characteristic polynomials of branched trees can be obtained in terms of the characteristic polynomials of unbranched trees and branches by pruning the tree at the joints. The unbranched trees can also be broken down further until a tree containing just two vertices is obtained. The effectively reduces the order of the secular determinant of the tree used at the beginning to determinants of orders atmost equal to the number of vertices in the branch containing the largest number of vertices. An illustrative example of a NMR graph is given for which the 22 x 22 secular determinant is reduced to determinants of orders atmost 4 x 4 in just the second step of the algorithm. The tree pruning algorithm can be applied even to trees with no symmetry elements and such a factoring can be achieved. Methods developed here can be elegantly used to find if two trees are cospectral and to construct cospectral trees

Investigating the fermentation of cocoa by correlating denaturing gradient gel electrophoresis profiles and near infrared spectra

DEFF Research Database (Denmark)

Nielsen, Dennis Sandris; Snitkjær, Pia; van der Berg, Franciscus Winfried J

2008-01-01

demonstrating the microbial succession taking place during the fermentation. Subsequently the DGGE spectra were correlated to the NIR spectra using Partial Least Squares regression models (PLS2). Correlations of 0.87 (bacterial derived DGGE spectra) and 0.81 (yeast derived DGGE spectra) were obtained indicating......Raw cocoa has an astringent, unpleasant taste and flavour, and has to be fermented, dried and roasted in order to obtain the characteristic cocoa flavour and taste. During the fermentation microbial activity outside the cocoa beans induces biochemical and physical changes inside the beans...... of the beans and the chemical processes inside the beans have been carried out previously. Recently it has been shown that Denaturing Gradient Gel Electrophoresis (DGGE) offers an efficient tool for monitoring the microbiological changes taking place during the fermentation of cocoa. Near Infrared (NIR...

Calculations of oscillation spectra of disordered interstitial solid solutions of vanadium-oxygen system

International Nuclear Information System (INIS)

Danilkin, S.A.

1978-01-01

The frequency spectra calculation of disordered solid interstitial solutions of a vanadium-oxygen system for oxygen concentration of 5.9% and 15.8% (V 16 O and V 16 O 3 ) is carried out. The axially-symmetric model of crystal lattice dinamics with consideration of vanadium-oxygen and vanadium-vanadium interactions up to the second coordination sphere is used. On the whole, the obtained spectra are in qualitative agreement with experiment and reflect correctly all the changes in frequency spectra of pure vanadium on doping with oxygen

Delin and Delog codes for graphic representation of gamma ray spectra

International Nuclear Information System (INIS)

Travesi, A.; Romero, L.

1983-01-01

Two FORTRAN IV Codes have been developed for graphic representation of the gamma-ray spectra obtained with GeLi detectors and multichannel analyzers. The graphic plotting is carried out with the H.P. Graphic Plotter Mod HP-7221 A, using the graphic package software GRAPHICS-1000 from Hewlett-Packard. The codes have a great versatility and the representation of gamma spectra can be done in a lineal, semilog, or log-log scale, as desired. The gamma ray spectra data are fed into the computer through magnetic tape or perforated paper tape. The different output options and complementary data are given in a conversational way through a terminal with TV display. Among the options that can be selected by the user are the following: 1) smoothing the spectra; 2) drawing the spectra point by point or continuous; 3) output drawing in 1, 2 or 4 sheets with automatic division of the energy scale; 4) overlapping of selected spectra regions in γ-scale ampliation with automatic printout of the region limits and ampliation factor; 5) printing spectra data and identifications of selected photopeaks. The codes can be employed with any computer using printing devices, HP-GRAPHICS 1000 software compatible, but are easily modified for another printing software since their modular structure with FORTRAN IV written subroutines. (author)

DELIN and DELOG codes for graphic representation of gamma ray spectra

International Nuclear Information System (INIS)

Romero, L.; Travesi, A.

1983-01-01

Two Fortran IV Codes has been developed for graphic representation of the gamma-ray spectra obtained with Ge Li detectors and multichannel analyzers. The grafic plotting es carried out with the H.P. Graphic Plotter Mod HP-7221 A, using the graphic package software GRAPHICS-1000 from Hewlett-Packard. The codes have a great versatility and the representation of gamma spectra can ba done in a lineal, semi log, or log-log scale, as desired. The gamma ray spectra data are feed into the computer through magnetic tape or perfored paper tape. The different out-put options and complementary data are given in a conversational way through a terminal with T.V. displays. Among the options that can be selected by the user are the following: - smoothing the spectra - drawing the spectra point by point or continuous - out-put drawing an 1, 2, or 4 sheet with automatic division of the energy scale. - overlapping of selected spectra regions in Y scale ampliation with automatic print-out of the region limits and ampliation factor. - Printing spectra data and identifications of selected photo peaks. The codes can be employed with any computer using printing devices, HP-Graphics 1000 software compatible, but are easily modified for another printing software since their modular structure with Fortran IV written

Protein-resistant polymer coatings obtained by matrix assisted pulsed laser evaporation

Energy Technology Data Exchange (ETDEWEB)

Rusen, L. [National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor Street, PO Box MG-16, 077125, Magurele, Bucharest (Romania); Mustaciosu, C. [Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH, Magurele, Bucharest (Romania); Mitu, B.; Filipescu, M.; Dinescu, M. [National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor Street, PO Box MG-16, 077125, Magurele, Bucharest (Romania); Dinca, V., E-mail: dinali@nipne.ro [National Institute for Lasers, Plasma and Radiation Physics, 409 Atomistilor Street, PO Box MG-16, 077125, Magurele, Bucharest (Romania)

2013-08-01

Adsorption of proteins and polysaccharides is known to facilitate microbial attachment and subsequent formation of biofilm on surfaces that ultimately results in its biofouling. Therefore, protein repellent modified surfaces are necessary to block the irreversible attachment of microorganisms. Within this context, the feasibility of using the Poly(ethylene glycol)-block-poly(ε-caprolactone) methyl ether (PEG-block-PCL Me) copolymer as potential protein-resistant coating was explored in this work. The films were deposited using Matrix Assisted Pulsed Laser Evaporation (MAPLE), a technique that allows good control of composition, thickness and homogeneity. The chemical and morphological characteristics of the films were examined using Fourier Transform Infrared Spectroscopy (FTIR), contact angle measurements and Atomic Force Microscopy (AFM). The FTIR data demonstrates that the functional groups in the MAPLE-deposited films remain intact, especially for fluences below 0.5 J cm{sup −2}. Optical Microscopy and AFM images show that the homogeneity and the roughness of the coatings are related to both laser parameters (fluence, number of pulses) and target composition. Protein adsorption tests were performed on the PEG-block-PCL Me copolymer coated glass and on bare glass surface as a control. The results show that the presence of copolymer as coating significantly reduces the adsorption of proteins.

Fitting PAC spectra with a hybrid algorithm

Energy Technology Data Exchange (ETDEWEB)

Alves, M. A., E-mail: mauro@sepn.org [Instituto de Aeronautica e Espaco (Brazil); Carbonari, A. W., E-mail: carbonar@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (Brazil)

2008-01-15

A hybrid algorithm (HA) that blends features of genetic algorithms (GA) and simulated annealing (SA) was implemented for simultaneous fits of perturbed angular correlation (PAC) spectra. The main characteristic of the HA is the incorporation of a selection criterion based on SA into the basic structure of GA. The results obtained with the HA compare favorably with fits performed with conventional methods.

Statistical detection of the hidden distortions in diffusive spectra

CERN Document Server

Nigmatullin, R R; Smith, G; Butler, P

2003-01-01

The detection of an unknown substance in small concentration represents an important problem in spectroscopy. Usually this detection is based on the recognition of specific 'labels' i.e. the visual appearance of new resonance lines that appear in the spectrograms analysed. But if the concentration of the unknown substance is small and visual indications (e.g. resonance peaks in diffusive spectra) are absent then the detection of the unknown substance constitutes a problem. We suggest a new methodology for the statistical detection of an unknown substance, based on the transformation of fluctuations obtained from initial spectrograms into ordered quantized histograms (QHs). The QHs obtained help to detect, statistically, the presence of unknown substances using the characteristics of conventional quantum spectra adopted from quantum mechanics. The averaging of the QHs helps to calculate the ordered 'fluctuation fork' (FF), which provides a specific 'noise ruler' for the detection and quantification of the trac...

Transverse energy and neutral pion spectra obtained from 16O- and 32S-induced reactions at 200 GeV/nucleon

International Nuclear Information System (INIS)

Plasil, F.; Albrecht, R.; Awes, T.C.

1989-01-01

The main goal of the CERN heavy-ion experiments is the search for an indication that the predicted state of deconfined quarks and gluons, the quark-gluon plasma (QGP), has been produced. The most promising indication that this may, in fact, be the case comes from the NA38 dimuon measurements, which are focused on the question of J//psi/ suppression. This effect was predicted to be one of the signatures of QGP formation before any measurements were made, and it is the subject of the two other talks at this conference that deal with nucleus-nucleus reactions at ultrarelativistic energies. In this presentation we consider the general (global) features of heavy-ion reactions at CERN energies, and we examine the degree to which they differ from mere superpositions of nucleon-nucleon collisions. We discuss the present status of our data analysis and our main conclusions from the first round of CERN experiments with emphasis on transverse energy measurements, on attained energy densities, and on the spectra of produced neutral pions. Because of time limitations we will not discuss our measurements of distributions of charged particles and the analysis of these distributions in terms of fluctuations nor the results that we have obtained with the Plastic Ball on the behavior of target spectator matter. 20 refs., 5 figs

Efficient DNP NMR of Membrane Proteins: Sample Preparation Protocols, Sensitivity, and Radical Location

Science.gov (United States)

Liao, Shu Y.; Lee, Myungwoon; Wang, Tuo; Sergeyev, Ivan V.; Hong, Mei

2016-01-01

Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surprisingly limited enhancement factors. This motivated us to carry out a systematic evaluation of sample preparation protocols for optimizing the sensitivity of DNP NMR spectra of membrane-bound peptides and proteins at cryogenic temperatures of ~110 K. We show that mixing the radical with the membrane by direct titration instead of centrifugation gives a significant boost to DNP enhancement. We quantify the relative sensitivity enhancement between AMUPol and TOTAPOL, two commonly used radicals, and between deuterated and protonated lipid membranes. AMUPol shows ~4 fold higher sensitivity enhancement than TOTAPOL, while deuterated lipid membrane does not give net higher sensitivity for the membrane peptides than protonated membrane. Overall, a ~100 fold enhancement between the microwave-on and microwave-off spectra can be achieved on lipid-rich membranes containing conformationally disordered peptides, and absolute sensitivity gains of 105–160 can be obtained between low-temperature DNP spectra and high-temperature non-DNP spectra. We also measured the paramagnetic relaxation enhancement of lipid signals by TOTAPOL and AMUPol, to determine the depths of these two radicals in the lipid bilayer. Our data indicate a bimodal distribution of both radicals, a surface-bound fraction and a membrane-bound fraction where the nitroxides lie at ~10 Å from the membrane surface. TOTAPOL appears to have a higher membrane-embedded fraction than AMUPol. These results should be useful for membrane-protein solid-state NMR studies under DNP conditions and provide insights into how biradicals interact with phospholipid membranes. PMID:26873390

Efficient DNP NMR of membrane proteins: sample preparation protocols, sensitivity, and radical location

Energy Technology Data Exchange (ETDEWEB)

Liao, Shu Y.; Lee, Myungwoon; Wang, Tuo [Massachusetts Institute of Technology, Department of Chemistry (United States); Sergeyev, Ivan V. [Bruker Biospin (United States); Hong, Mei, E-mail: meihong@mit.edu [Massachusetts Institute of Technology, Department of Chemistry (United States)

2016-03-15

Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surprisingly limited enhancement factors. This motivated us to carry out a systematic evaluation of sample preparation protocols for optimizing the sensitivity of DNP NMR spectra of membrane-bound peptides and proteins at cryogenic temperatures of ~110 K. We show that mixing the radical with the membrane by direct titration instead of centrifugation gives a significant boost to DNP enhancement. We quantify the relative sensitivity enhancement between AMUPol and TOTAPOL, two commonly used radicals, and between deuterated and protonated lipid membranes. AMUPol shows ~fourfold higher sensitivity enhancement than TOTAPOL, while deuterated lipid membrane does not give net higher sensitivity for the membrane peptides than protonated membrane. Overall, a ~100 fold enhancement between the microwave-on and microwave-off spectra can be achieved on lipid-rich membranes containing conformationally disordered peptides, and absolute sensitivity gains of 105–160 can be obtained between low-temperature DNP spectra and high-temperature non-DNP spectra. We also measured the paramagnetic relaxation enhancement of lipid signals by TOTAPOL and AMUPol, to determine the depths of these two radicals in the lipid bilayer. Our data indicate a bimodal distribution of both radicals, a surface-bound fraction and a membrane-bound fraction where the nitroxides lie at ~10 Å from the membrane surface. TOTAPOL appears to have a higher membrane-embedded fraction than AMUPol. These results should be useful for membrane-protein solid-state NMR studies under DNP conditions and provide insights into how biradicals interact with phospholipid membranes.

Study of different filtering techniques applied to spectra from airborne gamma spectrometry

Energy Technology Data Exchange (ETDEWEB)

Wilhelm, Emilien; Gutierrez, Sebastien; Reboli, Anne; Menard, Stephanie; Nourreddine, Abdel-Mjid [Commissariat a l' Energie Atomique et aux energies alternatives - CEA, DAM, DIF F-91297 Arpajon (France); Arbor, Nicolas [Institut Pluridisciplinaire Hubert Curien, UMR 7178 Universite de Strasbourg-CNRS, 23 rue du Loess, BP 28, F-67037 Strasbourg Cedex 2 (France)

2015-07-01

One of the features of spectra obtained by airborne gamma spectrometry is low counting statistics due to the short acquisition time (1 s) and the large source-detector distance (40 m). It leads to considerable uncertainty in radionuclide identification and determination of their respective activities from the windows method recommended by the IAEA, especially for low-level radioactivity. The present work compares the results obtained with filters in terms of errors of the filtered spectra with the window method and over the whole gamma energy range. The results are used to determine which filtering technique is the most suitable in combination with some method for total stripping of the spectrum. (authors)

Fourier evaluation of broad Moessbauer spectra

International Nuclear Information System (INIS)

Vincze, I.

1981-09-01

It is shown by the Fourier analysis of broad Moessbauer spectra that the even part of the distribution of the dominant hyperfine interaction (hyperfine field or quadrupole splitting) can be obtained directly without using least-square fitting procedures. Also the odd part of this distribution correlated with other hyperfine parameters (e.g. isomer shift) can be directly determined. Examples covering the case of amorphous magnetic and paramagnetic iron-based alloys are presented. (author)

X-ray spectra of He-like ions of Ga and Ge, excited in the low-inductance spark plasma

International Nuclear Information System (INIS)

Aglitsky, E.V.; Antsiferov, P.S.; Panin, A.M.

1984-01-01

The spectra of Ga XXX and Ge XXXI ions in the interval 1.2-1.4 A excited in the low-inductance vacuum spark plasma have been obtained for the first time. The resonance line 1s 2 -1s2p of Ga XXX and Ge XXXI and a group of satellites, corresponding to transitions in Ga XXIX and Ge XXX can be seen distinctly in the spectra. The spectra were obtained by an electronic-optical image-intensifier tube for one discharge. (orig.)

Reconstruction of neutron spectra through neural networks; Reconstruccion de espectros de neutrones mediante redes neuronales

Energy Technology Data Exchange (ETDEWEB)

Vega C, H.R.; Hernandez D, V.M.; Manzanares A, E. [Cuerpo Academico de Radiobiologia, Estudios Nucleares, Universidad Autonoma de Zacatecas, A.P. 336, 98000 Zacatecas (Mexico)] e-mail: rvega@cantera.reduaz.mx [and others

2003-07-01

A neural network has been used to reconstruct the neutron spectra starting from the counting rates of the detectors of the Bonner sphere spectrophotometric system. A group of 56 neutron spectra was selected to calculate the counting rates that would produce in a Bonner sphere system, with these data and the spectra it was trained the neural network. To prove the performance of the net, 12 spectra were used, 6 were taken of the group used for the training, 3 were obtained of mathematical functions and those other 3 correspond to real spectra. When comparing the original spectra of those reconstructed by the net we find that our net has a poor performance when reconstructing monoenergetic spectra, this attributes it to those characteristic of the spectra used for the training of the neural network, however for the other groups of spectra the results of the net are appropriate with the prospective ones. (Author)

Derivation of electron and photon energy spectra from electron beam central axis depth dose curves

Energy Technology Data Exchange (ETDEWEB)

Deng Jun [Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305 (United States)]. E-mail: jun@reyes.stanford.edu; Jiang, Steve B.; Pawlicki, Todd; Li Jinsheng; Ma, C.M. [Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305 (United States)

2001-05-01

A method for deriving the electron and photon energy spectra from electron beam central axis percentage depth dose (PDD) curves has been investigated. The PDD curves of 6, 12 and 20 MeV electron beams obtained from the Monte Carlo full phase space simulations of the Varian linear accelerator treatment head have been used to test the method. We have employed a 'random creep' algorithm to determine the energy spectra of electrons and photons in a clinical electron beam. The fitted electron and photon energy spectra have been compared with the corresponding spectra obtained from the Monte Carlo full phase space simulations. Our fitted energy spectra are in good agreement with the Monte Carlo simulated spectra in terms of peak location, peak width, amplitude and smoothness of the spectrum. In addition, the derived depth dose curves of head-generated photons agree well in both shape and amplitude with those calculated using the full phase space data. The central axis depth dose curves and dose profiles at various depths have been compared using an automated electron beam commissioning procedure. The comparison has demonstrated that our method is capable of deriving the energy spectra for the Varian accelerator electron beams investigated. We have implemented this method in the electron beam commissioning procedure for Monte Carlo electron beam dose calculations. (author)

Parallel of semi-empirical results simulated by MCNP of X-ray spectra with a semiconductor

International Nuclear Information System (INIS)

Santos, L.R.; Vivolo, V.; Potiens, M.P.A.; Navarro, M.V.T.; Santos, W.S.

2016-01-01

The aim of this study was to use the MCNPX radiation transport code to simulate X-ray spectra generated by a constant voltage system in a CdTe semiconductor detector. As part of the validation process, we obtained a series of experimental spectra. Comparatively, in all cases there is a good correlation between the two spectra. There were no statistically significant differences between the experimental results with the simulated. (author)

The laser desorption/laser ionization mass spectra of some methylated xanthines and the laser desorption of caffeine and theophylline from thin layer chromatography plates

Science.gov (United States)

Rogers, Kevin; Milnes, John; Gormally, John

1993-02-01

Laser desorption/laser ionization time-of-flight mass spectra of caffeine, theophylline, theobromine and xanthine are reported. These mass spectra are compared with published spectra obtained using electron impact ionization. Mass spectra of caffeine and theophylline obtained by IR laser desorption from thin layer chromatography plates are also described. The laser desorption of materials from thin layer chromatography plates is discussed.

Are neutral loss and internal product ions useful for top-down protein identification?

Science.gov (United States)

Xiao, Kaijie; Yu, Fan; Fang, Houqin; Xue, Bingbing; Liu, Yan; Li, Yunhui; Tian, Zhixin

2017-05-08

Neutral loss and internal product ions have been found to be significant in both peptide and protein tandem mass spectra and they have been proposed to be included in database search and for protein identification. In addition to common canonical b/y ions in collision-based dissociation or c/z ions in electron-based dissociation, inclusion of neutral loss and internal product ions would certainly make better use of tandem mass spectra data; however, their ultimate utility for protein identification with false discovery rate control remains unclear. Here we report our proteome-level utility benchmarking of neutral loss and internal product ions with tandem mass spectra of intact E. coli proteome. Utility of internal product ions was further evaluated at the protein level using selected tandem mass spectra of individual E. coli proteins. We found that both neutral loss and internal products ions do not have direct utility for protein identification when they were used for scoring of P Score; but they do have indirect utility for provision of more canonical b/y ions when they are included in the database search and overlapping ions between different ion types are resolved. Tandem mass spectrometry has evolved to be a state-of-the-art method for characterization of protein primary structures (including amino acid sequence, post-translational modifications (PTMs) as well as their site location), where full study and utilization tandem mass spectra and product ions are indispensable. This primary structure information is essential for higher order structure and eventual function study of proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

A high-throughput 2D-analytical technique to obtain single protein parameters from complex cell lysates for in silico process development of ion exchange chromatography.

Science.gov (United States)

Kröner, Frieder; Elsäßer, Dennis; Hubbuch, Jürgen

2013-11-29

The accelerating growth of the market for biopharmaceutical proteins, the market entry of biosimilars and the growing interest in new, more complex molecules constantly pose new challenges for bioseparation process development. In the presented work we demonstrate the application of a multidimensional, analytical separation approach to obtain the relevant physicochemical parameters of single proteins in a complex mixture for in silico chromatographic process development. A complete cell lysate containing a low titre target protein was first fractionated by multiple linear salt gradient anion exchange chromatography (AEC) with varying gradient length. The collected fractions were subsequently analysed by high-throughput capillary gel electrophoresis (HT-CGE) after being desalted and concentrated. From the obtained data of the 2D-separation the retention-volumes and the concentration of the single proteins were determined. The retention-volumes of the single proteins were used to calculate the related steric-mass action model parameters. In a final evaluation experiment the received parameters were successfully applied to predict the retention behaviour of the single proteins in salt gradient AEC. Copyright © 2013 Elsevier B.V. All rights reserved.

Gas-Phase Infrared Spectra of Vinyl Selenol and Vinyl Tellurol

Science.gov (United States)

Benidar, Abdessamad; Khater, Brahim; Guillemin, Jean-Claude; Gámez, José A.; Yáñez, Manuel

2009-10-01

The infrared spectra (3500-500 cm-1) of gaseous vinyl selenol and vinyl tellurol have been recorded at 0.1 cm-1 resolution. For the latter the spectra were obtained at room temperature, but for the former a temperature of -40 °C was required because of the chemical instability of vinyl selenol at room temperature. To compensate the very weak vapor pressure of vinyl tellurol at room temperature, a long optical path up to 136 m was necessary to record its spectrum. B3LYP density functional theory (DFT) calculations have been performed to assign the different absorption bands. Since an unambiguous assignment of the absorption bands requires a precise knowledge on the relative abundance of the syn and gauche rotamers of these compounds, their relative energies and their anharmonic vibrational frequencies were obtained using a very extended Def2-QZVP basis set. Two rotamers, the syn, which is planar, and a nonplanar gauche, were found to be local minima for both compounds. The gauche rotamer presents two degenerate conformers, which differ by the position of the SeH (TeH) hydrogen atom above or below the molecular plane. Our theoretical results are in good agreement with the main features of the experimental spectra. Fundamental bands and some combination bands of vinyl selenol and vinyl tellurol were assigned and compared with those of vinyl alcohol and vinyl thiol, whose spectra had been reported previously in the literature.

Extending the McDonald Observatory Serendipitous Survey of UV/Blue Asteroid Spectra

Science.gov (United States)

Vilas, Faith; Cochran, A. L.

1999-01-01

Moderate resolution asteroid spectra in the 350 - 650 nm spectral range acquired randomly over many years (Cochran and Vilas, Icarus v 127, 121, 1997) identified absorption features in spectra of some of the asteroids. A feature centered at 430 nm was identified in the spectra of some low-albedo asteroids (C class and subclass), similar to the feature identified by Vilas et al. (Icarus, v. 102, 225,1993) in other low-albedo asteroid spectra and attributed to a ferric iron spin-forbidden transition in iron alteration minerals such as jarosite. Features at 505 nm and 430 nm were identified in the spectrum of 4 Vesta. The 505-nm feature is highly diagnostic of the amount and form of calcium in pyroxenes. This suggested further research on the sharpness and spectral placement of this feature in the spectra of Vesta and Vestoids (e.g., Cochran and Vilas, Icarus v. 134, 207, 1998). In 1997 and 1998, additional UV/blue spectra were obtained at the 2.7-m Harlan J. Smith telescope with a facility cassegrain spectrograph. These included spectra of low-albedo asteroids, the R-class asteroid 349 Dembowska, and the M-class asteroid 135 Hertha. These spectra will be presented and identified features will be discussed.

Vibration-rotation band intensities in the IR spectra of polyatomic molecules

International Nuclear Information System (INIS)

El'kin, M.D.; Kosterina, E.K.; Berezin

1995-01-01

Using the curvilinear vibrational coordinates for a nuclear subsystem, expressions for the effective dipole-moment operators are derived in order to analyze the vibrational-rotational transitions in the IR spectra of polyatomic rigid molecules. The explicit expressions obtained for the intensities of hot bands allow one to estimate the influence of the vibration-rotation interaction within the framework of the adopted molecular-vibration model. The suggested method is shown to be suitable for Raman spectra analysis. 12 refs

Calculation of the correlation coefficients between the numbers of counts (peak areas and backgrounds) obtained from gamma-ray spectra

International Nuclear Information System (INIS)

Korun, M.; Vodenik, B.; Zorko, B.

2016-01-01

Two simple methods for calculating the correlations between peaks appearing in gamma-ray spectra are described. We show how the areas are correlated when the peaks do not overlap, but the spectral regions used for the calculation of the background below the peaks do. When the peaks overlap, the correlation can be stronger than in the case of the non-overlapping peaks. The methods presented are simplified to the extent of allowing their implementation with manual calculations. They are intended for practitioners as additional tools to be used when the correlations between the areas of the peaks in the gamma-ray spectra are to be calculated. Also, the correlation coefficient between the number of counts in the peak and the number of counts in the continuous background below the peak is derived. - Highlights: • The correlation coefficients between areas of closely spaced peaks are assessed. • For isolated peaks the correlation arises from the common continuous background. • If peaks overlap the correlation coefficient depends on how much they overlap. • If peaks overlap also the background height affects the correlation coefficient. • The correlation coefficient between the peak area and its background is −1.

Structure and behaviour of proteins, nucleic acids and viruses from vibrational Raman optical activity

DEFF Research Database (Denmark)

Barron, L.D.; Blanch, E.W.; McColl, I.H.

2003-01-01

stacking arrangement and the mutual orientation of the sugar and base rings around the C-N glycosidic link. The ROA spectra of intact viruses provide information on the folds of the coat proteins and the nucleic acid structure. The large number of structure-sensitive bands in protein ROA spectra...... is especially favourable for fold determination using pattern recognition techniques. This article gives a brief account of the ROA technique and presents the ROA spectra of a selection of proteins, nucleic acids and viruses that illustrate the applications of ROA spectroscopy in biomolecular research....

A method to unfold the efficiency of gaseous detectors exposed to broad X-ray spectra

International Nuclear Information System (INIS)

Almeida, Gevaldo L. de; Souza, Maria Ines S. de; Lopes, Ricardo T.

2000-01-01

A method to obtain the efficiency of a gaseous detector exposed to broad energy X-ray spectra was developed. It consists in the de-convolution of the integrated detector response using the shapes of those spectra as a tool to unfold the aimed detector efficiency curve. For this purpose, the spectra emitted by a X-ray tube under several anode voltages, were properly characterized through measurements with a NaI(Tl) spectrometer. A Lorentz function was then fitted to each of the spectra, and their parameters expressed as a function of the anode voltage, by using polynomial and gaussian fittings. The integral of the product of each Lorentz function, by another unknown Lorentz function, expressing the detector efficiency curve, represents the response of the detector for each anode tension, e.g., each X-ray spectrum. The symbolical integration of that product, produces a general function containing the unknown parameters of the unknown efficiency curve. A non-linear fitting of this general function, to the detector response points, as experimentally obtained, generates the aimed parameters for the efficiency curve. The final detector efficiency curve is obtained after normalization procedures. (author)

New user-friendly approach to obtain an Eisenberg plot and its use as a practical tool in protein sequence analysis.

Science.gov (United States)

Keller, Rob C A

2011-01-01

The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein-lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein-lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides.

RDANN a new methodology to solve the neutron spectra unfolding problem

Energy Technology Data Exchange (ETDEWEB)

Ortiz R, J.M.; Martinez B, M.R.; Vega C, H.R. [UAZ, Av. Ramon Lopez Velarde No. 801, 98000 Zacatecas (Mexico)

2006-07-01

The optimization processes known as Taguchi method and DOE methodology are applied to the design, training and testing of Artificial Neural Networks in the neutron spectrometry field, which offer potential benefits in the evaluation of the behavior of the net as well as the ability to examine the interaction of the weights and neurons inside the same one. In this work, the Robust Design of Artificial Neural Networks methodology is used to solve the neutron spectra unfolding problem, designing, training and testing an ANN using a set of 187 neutron spectra compiled by the International Atomic Energy Agency, to obtain the better neutron spectra unfolded from the Bonner spheres spectrometer's count rates. (Author)

RDANN a new methodology to solve the neutron spectra unfolding problem

International Nuclear Information System (INIS)

Ortiz R, J.M.; Martinez B, M.R.; Vega C, H.R.

2006-01-01

The optimization processes known as Taguchi method and DOE methodology are applied to the design, training and testing of Artificial Neural Networks in the neutron spectrometry field, which offer potential benefits in the evaluation of the behavior of the net as well as the ability to examine the interaction of the weights and neurons inside the same one. In this work, the Robust Design of Artificial Neural Networks methodology is used to solve the neutron spectra unfolding problem, designing, training and testing an ANN using a set of 187 neutron spectra compiled by the International Atomic Energy Agency, to obtain the better neutron spectra unfolded from the Bonner spheres spectrometer's count rates. (Author)

PDB2CD visualises dynamics within protein structures.

Science.gov (United States)

Janes, Robert W

2017-10-01

Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

OSL, TL and IRSL emission spectra of sedimentary quartz and feldspar samples

International Nuclear Information System (INIS)

Lomax, Johanna; Mittelstraß, Dirk; Kreutzer, Sebastian; Fuchs, Markus

2015-01-01

This contribution presents a variety of different luminescence emission spectra from sedimentary feldspar and quartz samples under various stimulation modes. These are green stimulated quartz (OSL-) spectra, quartz TL spectra, feldspar IRSL and post-IR IRSL spectra. A focus was set at recording OSL and IRSL spectra at elevated stimulation temperatures such as routinely applied in luminescence dating. This was to test whether optical stimulation at elevated temperatures results in a shift of emission peaks. For OSL emissions of quartz, this has so far not been tested. In case of feldspar emissions, post-IR IRSL conditions, hence IRSL emissions at a low temperature, directly followed by high temperature post-IRSL emissions, are explicitly investigated. All spectra were recorded using a new system incorporated into a Lexsyg luminescence reader. Thus, this study, besides presenting new spectral data, also serves as a feasibility study for this new device. It is shown that (a) the new device is capable of automatically measuring different sorts of spectra, also at elevated temperatures, (b) known thermally and optically stimulated peak emissions of quartz and feldspar are confirmed, (c) obtained IRSL and OSL spectra indicate that there is no significant relation between peak emission and stimulation temperature. - Highlights: • We have measured OSL, IRSL and TL emission spectra of sedimentary quartz and feldspar samples. • Spectral analyses were performed at elevated stimulation temperatures. • Emission spectra show very little variation with stimulation temperatures.

Modelling of oscillations in two-dimensional echo-spectra of the Fenna-Matthews-Olson complex

International Nuclear Information System (INIS)

Hein, Birgit; Kreisbeck, Christoph; Kramer, Tobias; Rodríguez, Mirta

2012-01-01

Recent experimental observations of time-dependent beatings in the two-dimensional echo-spectra of light-harvesting complexes at ambient temperatures have opened up the question of whether coherence and wave-like behaviour play a significant role in photosynthesis. We carry out a numerical study of the absorption and echo-spectra of the Fenna-Matthews-Olson (FMO) complex in Chlorobium tepidum and analyse the requirements in the theoretical model needed to reproduce beatings in the calculated spectra. The energy transfer in the FMO pigment-protein complex is theoretically described by an exciton Hamiltonian coupled to a phonon bath which accounts for the pigments' electronic and vibrational excitations, respectively. We use the hierarchical equations of motions method to treat the strong couplings in a non-perturbative way. We show that the oscillations in the two-dimensional echo-spectra persist in the presence of thermal noise and static disorder. (paper)

The Utilization of Low Frequency Raman Spectra of Gases for the Study of Molecules with Large Amplitude Vibration

Institute of Scientific and Technical Information of China (English)

James R. Durig; Sarah Xiao-hua Zhou; Joshua Klaassen; Arindam Ganguly

2009-01-01

The utilization of the Raman spectra of the low frequency bending mode for three quasi-linear molecules, disiloxane, (SiH3)2 O; methylisocyanate, CH3NCO; and dimethy lisocyanate, (CH3)2SiHNCO for observing the low frequency anharmonic bending vibration is demonstrated which is superior to the corresponding far infrared spectra. From the observed frequencies from the Raman spectra the potential function governing the heavy atom motion to linearity has been obtained from which the barrier has been determined. These experimental values are compared to the ab ini-tio predicted values. Also low frequency Raman spectra of the ring puckering vibration of chlorocy-clobutane, c-C4H7Cl, bromocyclobutane, c-C4H7Br, and aminocyclobutane, c-C4H7NH2, have been utilized to obtain the potential function governing the ring inversion for these molecules. The deter-mined barriers to planarity are compared to those obtained from MP2 (full) ab initio and density functional theory B3LYP calculations by utilizing a variety of basis sets. For all of these studies it is shown that the Raman spectra are superior to the infrared spectra for determining the frequencies of the excited state transitions.

Raman spectra of SDW superconductors

Energy Technology Data Exchange (ETDEWEB)

Rout, G.C. [Condensed Matter Physics Group, Department of Physics, Government Science College, Chatrapur, Orissa 761 020 (India)]. E-mail: gcr@iopb.res.in; Bishoyi, K.C. [P.G. Department of Physics, F.M. College (Autonomous), Balasore, Orissa 756 001 (India); Behera, S.N. [Institute of Physics, Bhubaneswar 751 005 (India)

2005-03-15

We report the calculation of the phonon response of the coexistent spin density wave (SDW) and superconducting (SC) state and predict the observation of SC gap in the Raman spectra of rare-earth nickel borocarbide superconductors. The SDW state normally does not couple to the lattice and hence, the phonons in the system are not expected to be affected by the SDW state. But there is a possibility of observing SC gap mode in the Raman spectra of a SDW superconductor due to the coupling of the SC gap excitation to the Raman active phonons in the system via the electron-phonon (e-p) interaction. A theoretical model is used for the coexistent phase and electron-phonon interaction. Phonon Green's function is calculated by Zubarev's technique and the phonon self-energy due to e-p interaction which is given by electron density response function in the coexistent state corresponding to the SDW wave vector q = Q is evaluated. The results so obtained exhibit agreement with the experimental observations.

Raman spectra of SDW superconductors

International Nuclear Information System (INIS)

Rout, G.C.; Bishoyi, K.C.; Behera, S.N.

2005-01-01

We report the calculation of the phonon response of the coexistent spin density wave (SDW) and superconducting (SC) state and predict the observation of SC gap in the Raman spectra of rare-earth nickel borocarbide superconductors. The SDW state normally does not couple to the lattice and hence, the phonons in the system are not expected to be affected by the SDW state. But there is a possibility of observing SC gap mode in the Raman spectra of a SDW superconductor due to the coupling of the SC gap excitation to the Raman active phonons in the system via the electron-phonon (e-p) interaction. A theoretical model is used for the coexistent phase and electron-phonon interaction. Phonon Green's function is calculated by Zubarev's technique and the phonon self-energy due to e-p interaction which is given by electron density response function in the coexistent state corresponding to the SDW wave vector q = Q is evaluated. The results so obtained exhibit agreement with the experimental observations

Diffuse reflectance infrared Fourier-Transform spectra of selected organic compounds

Energy Technology Data Exchange (ETDEWEB)

Harmon, S.H.; Caton, J.E.

1982-05-01

Diffuse reflectance infrared spectra of a variety of different organic compounds have been determined. Profiles of the spectra along with the location and relative intensity of the principal bands have been included for each compound studied. In addition both diffuse reflectance and transmittance infrared spectra were obtained for the same samples, and the spectral results were compared. Although some minor variations are observed between a diffuse reflectance spectrum and the corresponding transmittance spectrum, the diffuse reflectance is quite useful and may be a superior technique for the study of many samples because it possesses an inherently higher signal-to-noise response, requires less sample preparation and allows a very wide range of samples (solids, liquids of low volatility, neat sample, or sample diluted in a reflecting medium) to be studied under very similar conditions.

An analysis of scattered light in low dispersion IUE spectra

Science.gov (United States)

Basri, G.; Clarke, J. T.; Haisch, B. M.

1985-01-01

A detailed numerical simulation of light scattering from the low-resolution grating in the short wavelength spectrograph of the IUE Observatory was developed, in order to quantitatively analyze the effects of scattering on both continuum and line emission spectra. It is found that: (1) the redistribution of light by grating scattering did not appreciably alter either the shape or the absolute flux level of continuum spectra for A-F stars; (2) late-type stellar continua showed a tendency to flatten when observed in scattered light toward the shorter wavelengths; and (3) the effect of grating scattering on emission lines is to decrease measured line intensities by an increasing percentage toward the shorter wavelengths. The spectra obtained from scattering experiments for solar-type and late type stars are reproduced in graphic form.

Preliminary observations on differences in the Raman spectra of cancerous and noncancerous cells and connective tissue of human skin

Science.gov (United States)

Short, Michael A.; Lui, Harvey; McLean, David I.; Zeng, Haishan; Alajlan, Abdulmajeed; Chen, Michael X.

2005-04-01

A less invasive method of reliably detecting skin cancers is required. Raman spectroscopy is just one of several spectroscopic methods that look promising, but are not yet sufficiently reliable. More information is needed on how and why the Raman spectra of cancerous skin tissue is different from its normal counterpart. We have used confocal micro-Raman spectroscopy with a spatial resolution of about a micron to obtain spectra of unstained thin sections of human skin. We found that there were clear differences in the Raman spectra between cancerous and non-cancerous tissue both in cells and in the connective tissue. The DNA contribution to the spectra was generally stronger in malignant cells than normal ones. In regions of the dermis far away from the tumor one obtains the usual collagen spectra of normal skin, but adjacent to the tumor the spectra no longer appeared to be those of native collagen.

Gamma-ray burst spectra

International Nuclear Information System (INIS)

Teegarden, B.J.

1982-01-01

A review of recent results in gamma-ray burst spectroscopy is given. Particular attention is paid to the recent discovery of emission and absorption features in the burst spectra. These lines represent the strongest evidence to date that gamma-ray bursts originate on or near neutron stars. Line parameters give information on the temperature, magnetic field and possibly the gravitational potential of the neutron star. The behavior of the continuum spectrum is also discussed. A remarkably good fit to nearly all bursts is obtained with a thermal-bremsstrahlung-like continuum. Significant evolution is observed of both the continuum and line features within most events

High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field

International Nuclear Information System (INIS)

Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Lipton, Andrew S.; Berthold, Deborah A.; Rienstra, Chad M.

2010-01-01

Magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy of uniformly- 13 C, 15 N labeled protein samples provides insight into atomic-resolution chemistry and structure. Data collection efficiency has advanced remarkably in the last decade; however, the study of larger proteins is still challenged by relatively low resolution in comparison to solution NMR. In this study, we present a systematic analysis of SSNMR protein spectra acquired at 11.7, 17.6 and 21.1 Tesla ( 1 H frequencies of 500, 750, and 900 MHz). For two protein systems-GB1, a 6 kDa nanocrystalline protein and DsbA, a 21 kDa nanocrystalline protein-line narrowing is demonstrated in all spectral regions with increasing field. Resolution enhancement is greatest in the aliphatic region, including methine, methylene and methyl sites. The resolution for GB1 increases markedly as a function of field, and for DsbA, resolution in the C-C region increases by 42%, according to the number of peaks that can be uniquely picked and integrated in the 900 MHz spectra when compared to the 500 MHz spectra. Additionally, chemical exchange is uniquely observed in the highest field spectra for at least two isoleucine Cδ1 sites in DsbA. These results further illustrate the benefits of high-field MAS SSNMR spectroscopy for protein structural studies.

Spitzer mid-infrared spectra of cool-core galaxy clusters

NARCIS (Netherlands)

de Messières, G.E.; O'Connell, R.W.; McNamara, B.R.; Donahue, M.; Nulsen, P.E.J.; Voit, G.M.; Wise, M.W.; Smith, B.; Higdon, J.; Higdon, S.; Bastian, N.

2010-01-01

We have obtained mid-infrared spectra of nine cool-core galaxy clusters with the Infrared Spectrograph aboard the Spitzer Space Telescope. X-ray, ultraviolet and optical observations have demonstrated that each of these clusters hosts a cooling flow which seems to be fueling vigorous star formation

Photonic reagents for concentration measurement of flu-orescent proteins with overlapping spectra

Science.gov (United States)

Goun, Alexei; Bondar, Denys I.; Er, Ali O.; Quine, Zachary; Rabitz, Herschel A.

2016-05-01

By exploiting photonic reagents (i.e., coherent control by shaped laser pulses), we employ Optimal Dynamic Discrimination (ODD) as a novel means for quantitatively characterizing mixtures of fluorescent proteins with a large spectral overlap. To illustrate ODD, we simultaneously measured concentrations of in vitro mixtures of Enhanced Blue Fluorescent Protein (EBFP) and Enhanced Cyan Fluorescent Protein (ECFP). Building on this foundational study, the ultimate goal is to exploit the capabilities of ODD for parallel monitoring of genetic and protein circuits by suppressing the spectral cross-talk among multiple fluorescent reporters.

Fourier Transform and Photoacoustic Absorption Spectra of Ethylene within 6035 6210 cm-1: Comparative Measurements

International Nuclear Information System (INIS)

Kapitanov, V.A.; Solodov, A.M.; Petrova, T.M.; Ponomarev, Y.N.

2010-01-01

Measurements of ethylene absorption spectra with Fourier Transform (FT) and Photoacoustic (PA) spectrometers within 6035-6210 cm -1 are described. The methodology used for building the frequency scale for both spectrometers is presented. The methane absorption spectrum, included into the HITRAN database, was used in both cases to calibrate the frequency scale. Ethylene absorption spectra were obtained with the two recording methods; a coincidence of the measured line center positions was obtained with an accuracy of 0.0005 cm -1

Spatial power-spectra from Yohkoh soft X-ray images

Science.gov (United States)

Martens, Petrus C. H.; Gomez, Daniel O.

1992-01-01

We analyze three sequences of images from active regions, and a full disk image obtained by Yohkoh's Soft X-ray Telescope. Two sequences are from a region at center disk observed through different filters, and one sequence is from the limb. After Fourier-transforming the X-ray intensity of the images we find nearly isotropic power-spectra with an azimuthally integrated slope of -2.1 for the center disk, and -2.8 for the limb images. The full-disk picture yields a spectrum of -2.4. These results are different from the active region spectra obtained with the Normal Incidence X-ray Telescope which have a slope of the order of -3.0, and we ascribe this to the difference in temperature response between the instruments. However, both the SXT and NIXT results are consistent with coronal heating as the end result of a downward quasistatic cascade (in lengthscales) of free magnetic energy in the corona, driven by footpoint motions in the photosphere.

Steady-state and accident analyses of PBMR with the computer code SPECTRA

International Nuclear Information System (INIS)

Stempniewicz, Marek M.

2002-01-01

The SPECTRA code is an accident analysis code developed at NRG. It is designed for thermal-hydraulic analyses of nuclear or conventional power plants. The code is capable of analysing the whole power plant, including reactor vessel, primary system, various control and safety systems, containment and reactor building. The aim of the work presented in this paper was to prepare a preliminary thermal-hydraulic model of PBMR for SPECTRA, and perform steady state and accident analyses. In order to assess SPECTRA capability to model the PBMR reactors, a model of the INCOGEN system has been prepared first. Steady state and accident scenarios were analyzed for INCOGEN configuration. Results were compared to the results obtained earlier with INAS and OCTOPUS/PANTHERMIX. A good agreement was obtained. Results of accident analyses with PBMR model showed qualitatively good results. It is concluded that SPECTRA is a suitable tool for analyzing High Temperature Reactors, such as INCOGEN or for example PBMR (Pebble Bed Modular Reactor). Analyses of INCOGEN and PBMR systems showed that in all analyzed cases the fuel temperatures remained within the acceptable limits. Consequently there is no danger of release of radioactivity to the environment. It may be concluded that those are promising designs for future safe industrial reactors. (author)

Hemoglobin protein hollow shells fabricated through covalent layer-by-layer technique

International Nuclear Information System (INIS)

Duan Li; He Qiang; Yan Xuehai; Cui Yue; Wang Kewei; Li Junbai

2007-01-01

Hemoglobin (Hb) protein microcapsules held together by cross-linker, glutaraldehyde (GA), were successfully fabricated by covalent layer-by-layer (LbL) technique. The Schiff base reaction occurred on the colloid templates between the aldehyde groups of GA and free amino sites of Hb results in the formation of GA/Hb microcapsules after the removal of the templates. The structure of obtained monodisperse protein microcapsule was characterized by transmission electron microscopy (TEM) and confocal laser scanning microscopy (CLSM). The UV-Vis spectra measurements demonstrate the existence of Hb in the assembled capsules. Cyclic voltammetry (CV) and potential-controlled amperometric measurements (I-t curve) confirm that hemoglobin microcapsules after fabrication remain their heme electroactivity. Moreover, direct electron transfer process from protein to electrode surface was performed to detect the heme electrochemistry without using any mediator or promoter. The experiments of fluorescence recovery after photobleaching (FRAP) by CLSM demonstrate that the hemoglobin protein microcapsules have an improved permeability comparing to the conventional polyelectrolyte microcapsules

Principal component analysis for the forensic discrimination of black inkjet inks based on the Vis-NIR fibre optics reflection spectra.

Science.gov (United States)

Gál, Lukáš; Oravec, Michal; Gemeiner, Pavol; Čeppan, Michal

2015-12-01

Nineteen black inkjet inks of six different brands were examined by fibre optics reflection spectroscopy in Visible and Near Infrared Region (Vis-NIR FORS) directly on paper with a view to achieving good resolution between them. These different inks were tested on nineteen different inkjet printers from three brands. Samples were obtained from prints by reflection probe. Processed reflection spectra in the range 500-1000 nm were used as samples in principal component analysis. Variability between spectra of the same ink obtained from different prints, as well as between spectra of square areas and lines was examined. For both spectra obtained from square areas and lines reference, Principal Component Analysis (PCA) models were created. According to these models, the inkjet inks were divided into clusters. PCA method is able to separate inks containing carbon black as main colorant from the other inks using other colorants. Some spectra were recorded from another piece of printer and used as validation samples. Spectra of validation samples were projected onto reference PCA models. According to position of validation samples in score plots it can be concluded that PCA based on Vis-NIR FORS can reliably differentiate inkjet inks which are included in the reference database. The presented method appears to be a suitable tool for forensic examination of questioned documents containing inkjet inks. Inkjet inks spectra were obtained without extraction or cutting sample with possibility to measure out of the laboratory. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Application of work load spectra for estimative of the skin entrance dose

International Nuclear Information System (INIS)

Pereira, P.A.A.; Furquim, T.A.C.; Costa, P.R.

2004-01-01

The present work refers to obtaining data for the determination of workload spectra related to the use of different radiological equipment. The obtained information was stored in a data base developed for this working program. Values of skin entrance dose were obtained bu using the results of the field research (performed in radiological clinics and hospitals of Sao Paulo). (author)

Automatic storage of single gamma spectra on magnetic tape. Programs Longo, Dire

International Nuclear Information System (INIS)

Los Arcos Merino, J.M.

1978-01-01

The program Longo provides the block size and the black number in a binary file on magnetic tape. It has been applied to analyse the structure of the nine-track magnetic tapes storing single or coincidence gamma spectra files, recorded in octet form by a Multi-8 minicomputer in the Nuclear Spectrometry Laboratory of J.E.N. Then the program Dire has been written to transform the single gamma spectra into a new Fastrand disk file, storing the information in 36 bit words. A copy of this file is obtained on magnetic tape and the single gamma spectra are then availables by standard Fortran V reading sentences. (author)

Automatic storing of single gamma spectra on magnetic tape. Programs LONGO, DIRE

International Nuclear Information System (INIS)

Los Arcos Merino, J. M.

1978-01-01

The program LONGO provides the block size and the block number in a binary file on magnetic tape. It has been applied to analyse the structure of the nine-track magnetic tapes storing single or coincidence gamma spectra files, recorded in octet form by a MULTI-8 minicomputer in the Nuclear Spectrometry Laboratory of J.E.N. Then the program DIRE has been written to transform the single gamma spectra into a new FASTRAND disk file, storing the information in-36 bit words. A copy of this file is obtained on magnetic tape and the single gamma spectra are then available by standard FORTRAN V reading sentences. (Author) 3 refs

Effect of Enzymatic Digestion of Protein Derivatives Obtained from Mucuna pruriens L. on Production of Proinflammatory Mediators by BALB/c Mouse Macrophages.

Science.gov (United States)

Martínez Leo, Edwin E; Arana Argáez, Victor E; Acevedo Fernández, Juan J; Puc, Rosa Moo; Segura Campos, Maira R

2018-04-25

Inflammation is considered to be a major risk factor for the pathogenesis of chronic non-communicable diseases. Macrophages are important immune cells, which regulate inflammation and host defense by secretion of proinflammatory mediators. Obtaining biopeptides by enzymatic hydrolysis adds value to proteins of vegetative origin, such as Mucuna pruriens L. The present study evaluated the effect of enzymatic digestion of protein derivatives obtained from M. pruriens L. on the production of proinflammatory mediators by BALB/c mouse macrophages. Five different molecular weight peptide fractions were obtained (F > 10, 5-10, 3-5, 1-3, and < 1 kDa, respectively). At 300 μg/mL, F5-10 kDa inhibited 50.26 and 61.00% NO and H 2 O 2 production, respectively. Moreover, F5-10 kDa reduced the IL-6 and TNFα levels to 60.25 and 69.54%, respectively. After enzymatic digestive simulation, F5-10 kDa decreased the inflammatory mediators.

Protein resonance assignment at MAS frequencies approaching 100 kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods

Energy Technology Data Exchange (ETDEWEB)

Penzel, Susanne; Smith, Albert A.; Agarwal, Vipin; Hunkeler, Andreas [ETH Zürich, Physical Chemistry (Switzerland); Org, Mai-Liis; Samoson, Ago, E-mail: ago.samoson@ttu.ee [Tallinn University of Technology, NMR Instituut, Tartu Teadus, Tehnomeedikum (Estonia); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Université de Lyon 1, Institut de Biologie et Chimie des Protéines (France); Ernst, Matthias, E-mail: maer@ethz.ch; Meier, Beat H., E-mail: beme@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland)

2015-10-15

We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T{sub 2}′ times and a site-specific comparison of T{sub 2}′ at 93 kHz versus 60 kHz MAS frequency. A quantitative analysis of transfer efficiencies of building blocks, as they are used for typical 3D experiments, was performed. To do this, we compared dipolar-coupling and J-coupling based transfer steps. The building blocks were then combined into 3D experiments for sequential resonance assignment, where we evaluated signal-to-noise ratio and information content of the different 3D spectra in order to identify the best assignment strategy. Based on this comparison, six experiments were selected to optimally assign the model protein ubiquitin, solely using spectra acquired at 93 kHz MAS. Within 3 days of instrument time, the required spectra were recorded from which the backbone resonances have been assigned to over 96 %.

Energy spectra of primary knock-on atoms under neutron irradiation

International Nuclear Information System (INIS)

Gilbert, M.R.; Marian, J.; Sublet, J.-Ch.

2015-01-01

Materials subjected to neutron irradiation will suffer from a build-up of damage caused by the displacement cascades initiated by nuclear reactions. Previously, the main “measure” of this damage accumulation has been through the displacements per atom (dpa) index, which has known limitations. This paper describes a rigorous methodology to calculate the primary atomic recoil events (often called the primary knock-on atoms or PKAs) that lead to cascade damage events as a function of energy and recoiling species. A new processing code SPECTRA-PKA combines a neutron irradiation spectrum with nuclear recoil data obtained from the latest nuclear data libraries to produce PKA spectra for any material composition. Via examples of fusion relevant materials, it is shown that these PKA spectra can be complex, involving many different recoiling species, potentially differing in both proton and neutron number from the original target nuclei, including high energy recoils of light emitted particles such as α-particles and protons. The variations in PKA spectra as a function of time, neutron field, and material are explored. The application of PKA spectra to the quantification of radiation damage is exemplified using two approaches: the binary collision approximation and stochastic cluster dynamics, and the results from these different models are discussed and compared. - Highlights: • Recoil cross-section matrices under neutron irradiation are generated. • Primary knock-on atoms (PKA) spectra are calculated for fusion relevant materials. • Variation in PKA spectra due to changes in geometry are considered. • Inventory simulations to consider time-evolution in PKA spectra. • Damage quantification using damage functions from different approximations.

Optimizing Methods of Obtaining Stellar Parameters for the H3 Survey

Science.gov (United States)

Ivory, KeShawn; Conroy, Charlie; Cargile, Phillip

2018-01-01

The Stellar Halo at High Resolution with Hectochelle Survey (H3) is in the process of observing and collecting stellar parameters for stars in the Milky Way's halo. With a goal of measuring radial velocities for fainter stars, it is crucial that we have optimal methods of obtaining this and other parameters from the data from these stars.The method currently developed is The Payne, named after Cecilia Payne-Gaposchkin, a code that uses neural networks and Markov Chain Monte Carlo methods to utilize both spectra and photometry to obtain values for stellar parameters. This project was to investigate the benefit of fitting both spectra and spectral energy distributions (SED). Mock spectra using the parameters of the Sun were created and noise was inserted at various signal to noise values. The Payne then fit each mock spectrum with and without a mock SED also generated from solar parameters. The result was that at high signal to noise, the spectrum dominated and the effect of fitting the SED was minimal. But at low signal to noise, the addition of the SED greatly decreased the standard deviation of the data and resulted in more accurate values for temperature and metallicity.

Low-frequency vibrational spectra of crystals of tutton salts

Science.gov (United States)

Barashkov, M. V.; Zazhogin, A. A.; Komyak, A. I.; Shashkov, S. N.

2000-07-01

IR absorption spectra and polarized Raman spectra of crystals of Tutton salts K2M(SO4)26H2O and (NH4)2M(SO4)2·6H2O, where M=Co, Ni, Zn, have been obtained by experiment at 93 K and at room temperature. The frequencies and forms of normal modes of the [Zn(H2O)6]2+ octahedral complex have been calculated. The observed lines are assigned to the internal modes of the [M(H2O)6]2+ complex and external modes of the crystal lattice in accordance with the results of the calculations and factor-group analysis.

Authentication of Whey Protein Powders by Portable Mid-Infrared Spectrometers Combined with Pattern Recognition Analysis.

Science.gov (United States)

Wang, Ting; Tan, Siow Ying; Mutilangi, William; Aykas, Didem P; Rodriguez-Saona, Luis E

2015-10-01

The objective of this study was to develop a simple and rapid method to differentiate whey protein types (WPC, WPI, and WPH) used for beverage manufacturing by combining the spectral signature collected from portable mid-infrared spectrometers and pattern recognition analysis. Whey protein powders from different suppliers are produced using a large number of processing and compositional variables, resulting in variation in composition, concentration, protein structure, and thus functionality. Whey protein powders including whey protein isolates, whey protein concentrates and whey protein hydrolysates were obtained from different suppliers and their spectra collected using portable mid-infrared spectrometers (single and triple reflection) by pressing the powder onto an Attenuated Total Reflectance (ATR) diamond crystal with a pressure clamp. Spectra were analyzed by soft independent modeling of class analogy (SIMCA) generating a classification model showing the ability to differentiate whey protein types by forming tight clusters with interclass distance values of >3, considered to be significantly different from each other. The major bands centered at 1640 and 1580 cm(-1) were responsible for separation and were associated with differences in amide I and amide II vibrations of proteins, respectively. Another important band in whey protein clustering was associated with carboxylate vibrations of acidic amino acids (∼1570 cm(-1)). The use of a portable mid-IR spectrometer combined with pattern recognition analysis showed potential for discriminating whey protein ingredients that can help to streamline the analytical procedure so that it is more applicable for field-based screening of ingredients. A rapid, simple and accurate method was developed to authenticate commercial whey protein products by using portable mid-infrared spectrometers combined with chemometrics, which could help ensure the functionality of whey protein ingredients in food applications. © 2015

Beta-energy averaging and beta spectra

International Nuclear Information System (INIS)

Stamatelatos, M.G.; England, T.R.

1976-07-01

A simple yet highly accurate method for approximately calculating spectrum-averaged beta energies and beta spectra for radioactive nuclei is presented. This method should prove useful for users who wish to obtain accurate answers without complicated calculations of Fermi functions, complex gamma functions, and time-consuming numerical integrations as required by the more exact theoretical expressions. Therefore, this method should be a good time-saving alternative for investigators who need to make calculations involving large numbers of nuclei (e.g., fission products) as well as for occasional users interested in restricted number of nuclides. The average beta-energy values calculated by this method differ from those calculated by ''exact'' methods by no more than 1 percent for nuclides with atomic numbers in the 20 to 100 range and which emit betas of energies up to approximately 8 MeV. These include all fission products and the actinides. The beta-energy spectra calculated by the present method are also of the same quality

A consensus successive projections algorithm--multiple linear regression method for analyzing near infrared spectra.

Science.gov (United States)

Liu, Ke; Chen, Xiaojing; Li, Limin; Chen, Huiling; Ruan, Xiukai; Liu, Wenbin

2015-02-09

The successive projections algorithm (SPA) is widely used to select variables for multiple linear regression (MLR) modeling. However, SPA used only once may not obtain all the useful information of the full spectra, because the number of selected variables cannot exceed the number of calibration samples in the SPA algorithm. Therefore, the SPA-MLR method risks the loss of useful information. To make a full use of the useful information in the spectra, a new method named "consensus SPA-MLR" (C-SPA-MLR) is proposed herein. This method is the combination of consensus strategy and SPA-MLR method. In the C-SPA-MLR method, SPA-MLR is used to construct member models with different subsets of variables, which are selected from the remaining variables iteratively. A consensus prediction is obtained by combining the predictions of the member models. The proposed method is evaluated by analyzing the near infrared (NIR) spectra of corn and diesel. The results of C-SPA-MLR method showed a better prediction performance compared with the SPA-MLR and full-spectra PLS methods. Moreover, these results could serve as a reference for combination the consensus strategy and other variable selection methods when analyzing NIR spectra and other spectroscopic techniques. Copyright © 2014 Elsevier B.V. All rights reserved.

Microscopic study of low-lying yrast spectra and deformation systematics of even-even barium isotopes

International Nuclear Information System (INIS)

Sarswat, S.P.; Bharti, Arun; Khosa, S.K.

1996-01-01

The yrast spectra has been obtained in the variation-after-projection framework using pairing-plus-quadrupole- quadrupole model for the two body interaction. Besides the low-lying yrast spectra, the calculated values of intrinsic quadrupole moments of some of the barium isotopes i.e. 124-134 Ba are presented

Mid-IR Spectra of Refractory Minerals Relevant to Comets

Science.gov (United States)

Jauhari, Shekeab

2008-09-01

On 4 July 2005 the Spitzer Space Telescope obtained mid-IR ( 5-40 µm) spectra of the ejecta from the hypervelocity impact of the Deep Impact projectile with comet 9P/Tempel 1. Spectral modeling demonstrates that there are abundant minerals present in the ejecta including Ca/Fe/Mg-rich silicates, carbonates, phyllosilicates, water ice, amorphous carbon, and sulfides [1]. However, precise mineralogical identifications are hampered by the lack of comprehensive 5 - 40 µm spectral measurements of the emissivity for a broad compositional range of these materials. Here, we present our initial results for 2 - 50 µm transmission spectra and absorption constants for materials relevant to comets, including pyrrhotite, pyrite, and several phyllosilicate (clay) minerals. Measuring the transmission of materials over the full spectral range sensitive by Spitzer requires grinding the minerals into submicron powders and then mixing them with KBr (for the 1-25 um region) and polyethylene (16-50 um region) to form pellets. Transmission measurements of sub-micron sulfides are particularly difficult to obtain because the minerals oxidize rapidly upon grinding and subsequent handling unless special care is taken. A detailed description of our sample preparation and measurement technique will be provided to assist other researchers in their attempts to acquire similar spectra. References: [1] Lisse, C.M. et al., Science 313, 635 - 640 (2006)

Research of electronic absorption spectra of benzazols derivatives by ab initio calculations

Science.gov (United States)

Irgibaeva, I. S.; Birimzhanova, D. A.; Barashkov, N. N.

Using the method of density functional theory in approximating B3LYP with the basis set 6-31G* the computations of structures and UV-vis spectra (TDDFT method) of benzazols derivatives were performed. The comparison of estimated electron spectra with the observed ones was made indicating good agreement of theoretically obtained results with experiment. Moreover these compounds have distinctive spectral-luminescent properties (large stokes shift) because of intramolecular proton transfer in excited state.

Essential spectra and exponential estimates of eigenfunctions of lattice operators of quantum mechanics

International Nuclear Information System (INIS)

Rabinovich, Vladimir S; Roch, Steffen

2009-01-01

This paper is devoted to estimates of the exponential decay of eigenfunctions of difference operators on the lattice Z n which are discrete analogs of the Schroedinger, Dirac and square-root Klein-Gordon operators. Our investigation of the essential spectra and the exponential decay of eigenfunctions of the discrete spectra is based on the calculus of pseudodifference operators (i.e., pseudodifferential operators on the group Z n with analytic symbols), and the limit operators method. We obtain a description of the location of the essential spectra and estimates of the eigenfunctions of the discrete spectra of the main lattice operators of quantum mechanics, namely: matrix Schroedinger operators on Z n , Dirac operators on Z 3 and square root Klein-Gordon operators on Z n .

Simulation of attenuated total reflection infrared absorbance spectra: applications to automotive clear coat forensic analysis.

Science.gov (United States)

Lavine, Barry K; Fasasi, Ayuba; Mirjankar, Nikhil; Nishikida, Koichi; Campbell, Jay

2014-01-01

Attenuated total reflection (ATR) is a widely used sampling technique in infrared (IR) spectroscopy because minimal sample preparation is required. Since the penetration depth of the ATR analysis beam is quite shallow, the outer layers of a laminate or multilayered paint sample can be preferentially analyzed with the entire sample intact. For this reason, forensic laboratories are taking advantage of ATR to collect IR spectra of automotive paint systems that may consist of three or more layers. However, the IR spectrum of a paint sample obtained by ATR will exhibit distortions, e.g., band broadening and lower relative intensities at higher wavenumbers, compared with its transmission counterpart. This hinders library searching because most library spectra are measured in transmission mode. Furthermore, the angle of incidence for the internal reflection element, the refractive index of the clear coat, and surface contamination due to inorganic contaminants can profoundly influence the quality of the ATR spectrum obtained for automotive paints. A correction algorithm to allow ATR spectra to be searched using IR transmission spectra of the paint data query (PDQ) automotive database is presented. The proposed correction algorithm to convert transmission spectra from the PDQ library to ATR spectra is able to address distortion issues such as the relative intensities and broadening of the bands, and the introduction of wavelength shifts at lower frequencies, which prevent library searching of ATR spectra using archived IR transmission data.

Investigation of two blood proteins binding to Cantharidin and Norcantharidin by multispectroscopic and chemometrics methods

Energy Technology Data Exchange (ETDEWEB)

Liu, Rong; Cheng, Zhengjun, E-mail: ncczj1112@126.com; Li, Tian; Jiang, Xiaohui

2015-01-15

The interactions of Cantharidin/Norcantharidin (CTD/NCTD) with two blood proteins, i.e., bovine serum albumin (BSA) and bovine hemoglobin (BHb), have been investigated by the fluorescence, UV–vis absorption, and FT-IR spectra under imitated physiological condition. The binding characteristics between CTD/NCTD and BSA/BHb were determined by fluorescence emission and resonance light scattering (RLS) spectra. The quenching mechanism of two blood proteins with CTD/NCTD is a static quenching. Moreover, the experimental data were further analyzed based on multivariate curve resolution-alternating least squares (MCR-ALS) technique to obtain the concentration profiles and pure spectra for three species (BSA/BHb, CTD/NCTD and CTD/NCTD–BSA/BHb complexes) which existed in the interaction procedure. The number of binding sites n and binding constants K{sub b} were calculated at various temperatures. The thermodynamic parameters (such as, ΔG, ΔH, and ΔS) for BSA–CTD/NCTD and BHb–CTD/NCTD systems were calculated by the Van’t Hoff equation and also discussed. The distance r between CTD/NCTD and BSA/BHb were evaluated according to Förster no-radiation energy transfer theory. The results of Fourier transform infrared (FT-IR), synchronous fluorescence and three-dimensional fluorescence spectra showed that the conformations of BSA/BHb altered with the addition of CTD/NCTD. In addition, the effects of common ions on the binding constants of BSA–CTD/NCTD and BHb–CTD/NCTD systems were also discussed.

Medium-resolution isaac newton telescope library of empirical spectra

NARCIS (Netherlands)

Sanchez-Blazquez, P.; Peletier, R. F.; Jimenez-Vicente, J.; Cardiel, N.; Cenarro, A. J.; Falcon-Barroso, J.; Gorgas, J.; Selam, S.; Vazdekis, A.

2006-01-01

A new stellar library developed for stellar population synthesis modelling is presented. The library consists of 985 stars spanning a large range in atmospheric parameters. The spectra were obtained at the 2.5-m Isaac Newton Telescope and cover the range lambda lambda 3525-7500 angstrom at 2.3

Neutron spectra due 13N production in a PET cyclotron

International Nuclear Information System (INIS)

Benavente, J.A.; Vega-Carrillo, H.R.; Lacerda, M.A.S.; Fonseca, T.C.F.; Faria, F.P.; Silva, T.A. da

2015-01-01

Monte Carlo and experimental methods have been used to characterize the neutron radiation field around PET (Positron Emission Tomography) cyclotrons. In this work, the Monte Carlo code MCNPX was used to estimate the neutron spectra, the neutron fluence rates and the ambient dose equivalent (H*(10)) in seven locations around a PET cyclotron during 13 N production. In order to validate these calculations, H*(10) was measured in three sites and were compared with the calculated doses. All the spectra have two peaks, one above 0.1 MeV due to the evaporation neutrons and another in the thermal region due to the room-return effects. Despite the relatively large difference between the measured and calculated H*(10) for one point, the agreement was considered good, compared with that obtained for 18 F production in a previous work. - Highlights: • MCNPX code was used to estimate the neutron spectra in a PET cyclotron. • Neutrons were estimated when 13 N is produced. • Neutron spectra show evaporation and room-return neutrons. • Calculated H*(10) were compared with measured H*(10)

Optical properties of Cd Se thin films obtained by pyrolytic dew

International Nuclear Information System (INIS)

Perez G, A.M.; Tepantlan, C.S.; Renero C, F.

2006-01-01

In this paper the optical properties of Cd Se thin films obtained by spray pyrolysis are presented. The films are prepared by Sodium Seleno sulphate (Na 2 SSeO 3 ) and Cadmium Chloride (CdC 12 ) mixing in aqueous environment. Optical parameters of the films (refractive index, absorption coefficient and optical ban gap) were calculated from transmittance spectra. The obtained values of the optical ban gap are compared with the result obtained by other deposition method. (Author)

A method to reproduce alpha-particle spectra measured with semiconductor detectors.

Science.gov (United States)

Timón, A Fernández; Vargas, M Jurado; Sánchez, A Martín

2010-01-01

A method is proposed to reproduce alpha-particle spectra measured with silicon detectors, combining analytical and computer simulation techniques. The procedure includes the use of the Monte Carlo method to simulate the tracks of alpha-particles within the source and in the detector entrance window. The alpha-particle spectrum is finally obtained by the convolution of this simulated distribution and the theoretical distributions representing the contributions of the alpha-particle spectrometer to the spectrum. Experimental spectra from (233)U and (241)Am sources were compared with the predictions given by the proposed procedure, showing good agreement. The proposed method can be an important aid for the analysis and deconvolution of complex alpha-particle spectra. Copyright 2009 Elsevier Ltd. All rights reserved.

Gamma-ray continuum spectra from heavy ion reactions

International Nuclear Information System (INIS)

Beene, J.R.; Halbert, M.L.; Hensley, D.C.; Sarantites, D.G.; Westerberg, L.W.; Geoffroy, K.; Woodward, R.

1979-01-01

A detailed quantitative analysis of the yrast continuum was attempted by subtracting the underlying statistical continnuum in a way that makes allowance for ignorance of its detailed shape. This procedure makes it possible to obtain the moment of inertia as a function of spin over a wide range of spins. The results of this continuum spectra shape analysis can be used to calculate the first and second moments of the continuum multiplicity distribution. Continuum spectra were taken during the bombardment of 150 Nd by 115- and 130-MeV beams of 20 Ne, also the first and second moments of the γ-ray multiplicity distribution as a function of the gamma energy. The moment of inertia versus spin and the deduced Yrast continuua are shown. 10 references

Benchmarking statistical averaging of spectra with HULLAC

Science.gov (United States)

Klapisch, Marcel; Busquet, Michel

2008-11-01

Knowledge of radiative properties of hot plasmas is important for ICF, astrophysics, etc When mid-Z or high-Z elements are present, the spectra are so complex that one commonly uses statistically averaged description of atomic systems [1]. In a recent experiment on Fe[2], performed under controlled conditions, high resolution transmission spectra were obtained. The new version of HULLAC [3] allows the use of the same model with different levels of details/averaging. We will take advantage of this feature to check the effect of averaging with comparison with experiment. [1] A Bar-Shalom, J Oreg, and M Klapisch, J. Quant. Spectros. Rad. Transf. 65, 43 (2000). [2] J. E. Bailey, G. A. Rochau, C. A. Iglesias et al., Phys. Rev. Lett. 99, 265002-4 (2007). [3]. M. Klapisch, M. Busquet, and A. Bar-Shalom, AIP Conference Proceedings 926, 206-15 (2007).

Polarization-dependent spectra in the photoassociative ionization of cold atoms in a bright sodium beam

International Nuclear Information System (INIS)

Ramirez-Serrano, Jaime; DeGraffenreid, William; Weiner, John

2002-01-01

We report measurements of cold photoassociative ionization (PAI) spectra obtained from collisions within a slow, bright Na atomic beam. A high-brightness atom flux, obtained by optical cooling and focusing of the atom beam, permits a high degree of alignment and orientation of binary collisions with respect to the laboratory atom-beam axis. The results reveal features of PAI spectra not accessible in conventional magneto-optical trap studies. We take advantage of this high degree of alignment to selectively excite autoionizing doubly excited states of specific symmetry

High-resolution n = 3 to n = 2 spectra of neonlike silver

International Nuclear Information System (INIS)

Beiersdorfer, P.; Bitter, M.; von Goeler, S.

1986-01-01

Spectra of the n = 3 to n = 2 transitions in neonlike silver emitted from the Princeton Large Torus have been recorded with a high-resolution Bragg-crystal spectrometer. The measurements cover the wavelength region 3.3--4.1 A-circle and include the forbidden 3p→2p electric quadrupole lines. Transitions in the adjacent sodiumlike, magnesiumlike, and aluminumlike charge states of silver have also been observed and identified. The Ly-α spectra of hydrogenlike argon and iron, the Kα spectra of heliumlike argon, potassium, manganese, and iron, and the Kβ spectrum of heliumlike argon fall in the same wavelength region in first or second order and have been measured concurrently. These spectra provide a coherent set of wavelength reference data obtained with the same spectrometer and from the same tokamak. This set is used as a basis to compare wavelength predictions for one- and two-electron systems to each other and to determine the transition energies of the silver lines with great accuracy

Vibrationally resolved photoelectron spectra of lower diamondoids: A time-dependent approach

Science.gov (United States)

Xiong, Tao; Włodarczyk, Radosław; Gallandi, Lukas; Körzdörfer, Thomas; Saalfrank, Peter

2018-01-01

Vibrationally resolved lowest-energy bands of the photoelectron spectra (PES) of adamantane, diamantane, and urotropine were simulated by a time-dependent correlation function approach within the harmonic approximation. Geometries and normal modes for neutral and cationic molecules were obtained from B3LYP hybrid density functional theory (DFT). It is shown that the simulated spectra reproduce the experimentally observed vibrational finestructure (or its absence) quite well. Origins of the finestructure are discussed and related to recurrences of autocorrelation functions and dominant vibrations. Remaining quantitative and qualitative errors of the DFT-derived PES spectra refer to (i) an overall redshift by ˜0.5 eV and (ii) the absence of satellites in the high-energy region of the spectra. The former error is shown to be due to the neglect of many-body corrections to ordinary Kohn-Sham methods, while the latter has been argued to be due to electron-nuclear couplings beyond the Born-Oppenheimer approximation [Gali et al., Nat. Commun. 7, 11327 (2016)].

Effects of NMR spectral resolution on protein structure calculation.

Directory of Open Access Journals (Sweden)

Suhas Tikole

Full Text Available Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.

An Inverse Modeling Approach to Estimating Phytoplankton Pigment Concentrations from Phytoplankton Absorption Spectra

Science.gov (United States)

Moisan, John R.; Moisan, Tiffany A. H.; Linkswiler, Matthew A.

2011-01-01

Phytoplankton absorption spectra and High-Performance Liquid Chromatography (HPLC) pigment observations from the Eastern U.S. and global observations from NASA's SeaBASS archive are used in a linear inverse calculation to extract pigment-specific absorption spectra. Using these pigment-specific absorption spectra to reconstruct the phytoplankton absorption spectra results in high correlations at all visible wavelengths (r(sup 2) from 0.83 to 0.98), and linear regressions (slopes ranging from 0.8 to 1.1). Higher correlations (r(sup 2) from 0.75 to 1.00) are obtained in the visible portion of the spectra when the total phytoplankton absorption spectra are unpackaged by multiplying the entire spectra by a factor that sets the total absorption at 675 nm to that expected from absorption spectra reconstruction using measured pigment concentrations and laboratory-derived pigment-specific absorption spectra. The derived pigment-specific absorption spectra were further used with the total phytoplankton absorption spectra in a second linear inverse calculation to estimate the various phytoplankton HPLC pigments. A comparison between the estimated and measured pigment concentrations for the 18 pigment fields showed good correlations (r(sup 2) greater than 0.5) for 7 pigments and very good correlations (r(sup 2) greater than 0.7) for chlorophyll a and fucoxanthin. Higher correlations result when the analysis is carried out at more local geographic scales. The ability to estimate phytoplankton pigments using pigment-specific absorption spectra is critical for using hyperspectral inverse models to retrieve phytoplankton pigment concentrations and other Inherent Optical Properties (IOPs) from passive remote sensing observations.

Statistical properties of spectra in harmonically trapped spin-orbit coupled systems

DEFF Research Database (Denmark)

V. Marchukov, O.; G. Volosniev, A.; V. Fedorov, D.

2014-01-01

We compute single-particle energy spectra for a one-body Hamiltonian consisting of a two-dimensional deformed harmonic oscillator potential, the Rashba spin-orbit coupling and the Zeeman term. To investigate the statistical properties of the obtained spectra as functions of deformation, spin......-orbit and Zeeman strengths we examine the distributions of the nearest neighbor spacings. We find that the shapes of these distributions depend strongly on the three potential parameters. We show that the obtained shapes in some cases can be well approximated with the standard Poisson, Brody and Wigner...... distributions. The Brody and Wigner distributions characterize irregular motion and help identify quantum chaotic systems. We present a special choices of deformation and spin-orbit strengths without the Zeeman term which provide a fair reproduction of the fourth-power repelling Wigner distribution. By adding...

Investigation of experimental pole-figure errors by simulation of individual spectra

International Nuclear Information System (INIS)

Lychagina, T. A.; Nikolaev, D. I.

2007-01-01

The errors in measuring the crystallographic texture described by pole figures are studied. A set of diffraction spectra for a sample of the MA2-1 alloy (Mg + 4.5% Al + 1% Zn) are measured, simulation of individual spectra on the basis of which the pole figures were obtained is performed, and their errors are determined. The conclusion about the possibility of determining the effect of errors of the diffraction peak half-width on the pole figure errors that was drawn in our previous studies is confirmed

GRETEL, Ge(Li) Gamma Spectra Unfolding

International Nuclear Information System (INIS)

1975-01-01

1 - Nature of physical problem solved: The program performs the quantitative analysis of gamma-ray spectra obtained by Ge(Li) detectors, using special libraries which are prepared for each particular problem. 2 - Method of solution: The computer routines which detect and evaluate peak areas perform the following operations: - local smoothing of the spectrum; - first derivative of the smoothed spectrum, - peak location according to the change of sign of the first derivative; - computation of the net area of each peak found

Induced synthesis of toroid-like lead sulfide nanocomposites in ethanol solution through a protein templating route

International Nuclear Information System (INIS)

Zhang, Li; Qin, Dezhi; Yang, Guangrui; Du, Xian; Zhang, Qiuxia; Li, Feng

2015-01-01

The toroid-like PbS nanocrystals have been prepared in zein ethanol solution based on self-assembly template of protein molecules. From transmission electron microscopy observation, the obtained samples were monodispersed with an average size of about 47 nm. The chemical composition and crystal structure of nanocomposites were determined by X-ray diffraction and energy-dispersive X-ray spectrum measurements. The interaction between PbS and zein was investigated through Fourier transform infrared, photoluminescence, circular dichroism (CD) spectra, and thermogravimetric analysis. The PbS nanocrystals could react with nitrogen and oxygen atoms of zein molecules through coordination and electrostatic force. The CD spectra results suggested that PbS nanocrystals induced the conformational transition of protein from α-helix to β-sheet and then self-assembled into ring or toroid nanostructure. The quenching of zein fluorescence induced by PbS nanocrystals also showed the change in the chemical microenvironments of the fluorescent amino acid residues in the protein structure. The key step of this facile, biomimetic route was the formation of self-assembly nanostructure of zein, which could regulate the nucleation and growth of toroid-like PbS nanocrystals

Non-Hermitian systems of Euclidean Lie algebraic type with real energy spectra

Science.gov (United States)

Dey, Sanjib; Fring, Andreas; Mathanaranjan, Thilagarajah

2014-07-01

We study several classes of non-Hermitian Hamiltonian systems, which can be expressed in terms of bilinear combinations of Euclidean-Lie algebraic generators. The classes are distinguished by different versions of antilinear (PT)-symmetries exhibiting various types of qualitative behaviour. On the basis of explicitly computed non-perturbative Dyson maps we construct metric operators, isospectral Hermitian counterparts for which we solve the corresponding time-independent Schrödinger equation for specific choices of the coupling constants. In these cases general analytical expressions for the solutions are obtained in the form of Mathieu functions, which we analyze numerically to obtain the corresponding energy spectra. We identify regions in the parameter space for which the corresponding spectra are entirely real and also domains where the PT symmetry is spontaneously broken and sometimes also regained at exceptional points. In some cases it is shown explicitly how the threshold region from real to complex spectra is characterized by the breakdown of the Dyson maps or the metric operator. We establish the explicit relationship to models currently under investigation in the context of beam dynamics in optical lattices.

FIER: Software for analytical modeling of delayed gamma-ray spectra

Science.gov (United States)

Matthews, E. F.; Goldblum, B. L.; Bernstein, L. A.; Quiter, B. J.; Brown, J. A.; Younes, W.; Burke, J. T.; Padgett, S. W.; Ressler, J. J.; Tonchev, A. P.

2018-05-01

A new software package, the Fission Induced Electromagnetic Response (FIER) code, has been developed to analytically predict delayed γ-ray spectra following fission. FIER uses evaluated nuclear data and solutions to the Bateman equations to calculate the time-dependent populations of fission products and their decay daughters resulting from irradiation of a fissionable isotope. These populations are then used in the calculation of γ-ray emission rates to obtain the corresponding delayed γ-ray spectra. FIER output was compared to experimental data obtained by irradiation of a 235U sample in the Godiva critical assembly. This investigation illuminated discrepancies in the input nuclear data libraries, showcasing the usefulness of FIER as a tool to address nuclear data deficiencies through comparison with experimental data. FIER provides traceability between γ-ray emissions and their contributing nuclear species, decay chains, and parent fission fragments, yielding a new capability for the nuclear science community.

[Non-invasive analysis of proteins in living cells using NMR spectroscopy].

Science.gov (United States)

Tochio, Hidehito; Murayama, Shuhei; Inomata, Kohsuke; Morimoto, Daichi; Ohno, Ayako; Shirakawa, Masahiro

2015-01-01

NMR spectroscopy enables structural analyses of proteins and has been widely used in the structural biology field in recent decades. NMR spectroscopy can be applied to proteins inside living cells, allowing characterization of their structures and dynamics in intracellular environments. The simplest "in-cell NMR" approach employs bacterial cells; in this approach, live Escherichia coli cells overexpressing a specific protein are subjected to NMR. The cells are grown in an NMR active isotope-enriched medium to ensure that the overexpressed proteins are labeled with the stable isotopes. Thus the obtained NMR spectra, which are derived from labeled proteins, contain atomic-level information about the structure and dynamics of the proteins. Recent progress enables us to work with higher eukaryotic cells such as HeLa and HEK293 cells, for which a number of techniques have been developed to achieve isotope labeling of the specific target protein. In this review, we describe successful use of electroporation for in-cell NMR. In addition, (19)F-NMR to characterize protein-ligand interactions in cells is presented. Because (19)F nuclei rarely exist in natural cells, when (19)F-labeled proteins are delivered into cells and (19)F-NMR signals are observed, one can safely ascertain that these signals originate from the delivered proteins and not other molecules.

Rotation-vibrational spectra of diatomic molecules and nuclei with Davidson interactions

CERN Document Server

Rowe, D J

1998-01-01

Complete rotation-vibrational spectra and electromagnetic transition rates are obtained for Hamiltonians of diatomic molecules and nuclei with Davidson interactions. Analytical results are derived by dynamical symmetry methods for diatomic molecules and a liquid-drop model of the nucleus. Numerical solutions are obtained for a many-particle nucleus with quadrupole Davidson interactions within the framework of the microscopic symplectic model. (author)

The photoluminescence spectra of micropowder of aromatic compounds under ultraviolet laser excitation

International Nuclear Information System (INIS)

Rakhmatullaev, I.A.; Kurbonov, A.K. et al.; Gorelik, V.S.

2016-01-01

The method of diagnostics of aromatic compounds on the example of novocaine, aspirin and anthracene is presented. The method is based on optical detection of photoluminescence spectra at ultraviolet laser (266 nm) excitation. Employing this method the photoluminescence spectra are obtained which allows one to establish the differences of the composition and structure of compounds. The developed method can be used for analysis the quality of the large class of luminescent bioactive structures under the ultraviolet radiation. (authors)

A feedback framework for protein inference with peptides identified from tandem mass spectra

Directory of Open Access Journals (Sweden)

Shi Jinhong

2012-11-01

Full Text Available Abstract Background Protein inference is an important computational step in proteomics. There exists a natural nest relationship between protein inference and peptide identification, but these two steps are usually performed separately in existing methods. We believe that both peptide identification and protein inference can be improved by exploring such nest relationship. Results In this study, a feedback framework is proposed to process peptide identification reports from search engines, and an iterative method is implemented to exemplify the processing of Sequest peptide identification reports according to the framework. The iterative method is verified on two datasets with known validity of proteins and peptides, and compared with ProteinProphet and PeptideProphet. The results have shown that not only can the iterative method infer more true positive and less false positive proteins than ProteinProphet, but also identify more true positive and less false positive peptides than PeptideProphet. Conclusions The proposed iterative method implemented according to the feedback framework can unify and improve the results of peptide identification and protein inference.

Fluorescence of Bacteria, Pollens, and Naturally Occurring Airborne Particles: Excitation/Emission Spectra

Science.gov (United States)

2009-02-01

35 Figure 29. EEM spectra of kaolin particles, dry...Warrington, PA. Glass beads were obtained from Peirce Chemical Co., Rockford, IL. Kaolin particles were obtained from Particle Information Services...solution concentration of 1 mg/ml. The samples were vortexed and pipetted vigorously to disperse aggregates. Stock bacteria solutions were diluted to a

A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: sample preparation, reproducibility, and differential protein expression patterns.

Science.gov (United States)

Azzam, Sausan; Broadwater, Laurie; Li, Shuo; Freeman, Ernest J; McDonough, Jennifer; Gregory, Roger B

2013-05-01

Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears to play a role in the development of neuropathology in MS and may also play a role in disease pathology in EAE. Here, surface enhanced laser desorption ionization mass spectrometry (SELDI-MS) has been employed to obtain protein expression profiles from mitochondrially enriched fractions derived from EAE and control mouse brain. To gain insight into experimental variation, the reproducibility of sub-cellular fractionation, anion exchange fractionation as well as spot-to-spot and chip-to-chip variation using pooled samples from brain tissue was examined. Variability of SELDI mass spectral peak intensities indicates a coefficient of variation (CV) of 15.6% and 17.6% between spots on a given chip and between different chips, respectively. Thinly slicing tissue prior to homogenization with a rotor homogenizer showed better reproducibility (CV = 17.0%) than homogenization of blocks of brain tissue with a Teflon® pestle (CV = 27.0%). Fractionation of proteins with anion exchange beads prior to SELDI-MS analysis gave overall CV values from 16.1% to 18.6%. SELDI mass spectra of mitochondrial fractions obtained from brain tissue from EAE mice and controls displayed 39 differentially expressed proteins (p≤ 0.05) out of a total of 241 protein peaks observed in anion exchange fractions. Hierarchical clustering analysis showed that protein fractions from EAE animals with severe disability clearly segregated from controls. Several components of electron transport chain complexes (cytochrome c oxidase subunit 6b1, subunit 6C, and subunit 4; NADH dehydrogenase flavoprotein 3, alpha subcomplex subunit 2, Fe-S protein 4, and Fe-S protein 6; and ATP synthase subunit e) were identified as possible differentially expressed proteins. Myelin Basic Protein isoform 8 (MBP8) (14.2 k

Prompt fission neutron spectra of n + 235U above the (n, nf) fission threshold

International Nuclear Information System (INIS)

Shu Nengchuan; Chen Yongjing; Liu Tingjin; Jia Min

2015-01-01

Calculations of prompt fission neutron spectra (PFNS) from the 235 U(n, f) reaction were performed with a semi-empirical method for En = 7.0 and 14.7 MeV neutron energies. The total PFNS were obtained as a superposition of (n, xnf) pre-fission neutron spectra and post-fission spectra of neutrons which were evaporated from fission fragments, and these two kinds of spectra were taken as an expression of the evaporation spectrum. The contributions of (n, xnf) fission neutron spectra on the calculated PFNS were discussed. The results show that emission of one or two neutrons in the (n, nf) or (n, 2nf) reactions influences the PFNS shape, and the neutron spectra of the (n, xnf) fission-channel are soft compared with the neutron spectra of the (n, f) fission channel. In addition, analysis of the multiple-chance fission component showed that second-chance fission dominates the PFNS with an incident neutron energy of 14.7 MeV whereas first-chance fission dominates the 7 MeV case. (authors)

Fluorescence spectra of blood plasma treated with ultraviolet irradiation in vivo

Science.gov (United States)

Zalesskaya, G. A.; Maslova, T. O.

2010-09-01

We have studied the fluorescence spectra of blood plasma from patients with acute coronary syndrome, and also the effect of therapeutic doses of in vivo ultraviolet blood irradiation (UBI) on the spectra. We have established that the maxima in the fluorescence spectra of the original plasma samples, obtained from unirradiated blood, are located in the wavelength interval 330-340 nm, characteristic for the fluorescence of tryptophan residues. In extracorporeal UBI ( λ = 254 nm), we observed changes in the shape and also both a blue and a red shift in the maxima of the fluorescence spectra, differing in magnitude for blood plasma samples from different patients in the test group. We show that UBI-initiated changes in the fluorescence spectra of the plasma depend on the original pathological disturbances of metabolite levels, and also on the change in the oxygen-transport function of the blood and the acid-base balance, affecting the oxidative stability of the plasma. We have concluded that UV irradiation, activating buffer systems in the blood, has an effect on the universal and specific interactions of the tryptophan residue with the amino acid residues and water surrounding it.

High-resolution spectra of comet C/2013 R1 (Lovejoy)

Science.gov (United States)

Rousselot, P.; Decock, A.; Korsun, P. P.; Jehin, E.; Kulyk, I.; Manfroid, J.; Hutsemékers, D.

2015-08-01

Context. High-resolution spectra of comets permit deriving the physical properties of the coma. In the optical range, relative production rates can be computed, and information about isotopic ratios and the origin of oxygen atoms can be obtained. Aims: The main objective of the work presented here was to obtain information about the chemical composition of comet C/2013 R1 (Lovejoy), a bright and long-period comet that passed perihelion (0.81 au) on 22 December 2013. Methods: We used the HARPS-North echelle spectrograph at the 3.5 m telescope TNG to obtain high-resolution spectra of comet C/2013 R1 (Lovejoy) in the optical range immediately after its perihelion passage during four consecutive nights in the period December 23 to 26, 2013. Results: Our results demonstrate the ability of HARPS-North to efficiently obtain cometary spectra. Very faint emission lines, such as those of 15NH2, have been detected, leading to a rough estimate of the 14N/15N ratio in NH2. The 12C/13C ratio was measured in the C2 lines and is equal to 80 ± 30. The oxygen lines were studied as well (green to red line intensity ratios and widths), confirming that H2O is the main parent molecule that photodissociates to produce oxygen atoms. This suggests that this comet has a high CO2 abundance. Relative production rates for C2 and NH2 were computed, but we found no significant deviation from a typical NH2/C2 ratio. Based on observations made with the Italian Telescopio Nazionale Galileo (TNG) operated on the island of La Palma by the Fundación Galileo Galilei of the INAF (Istituto Nazionale di Astrofisica) at the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias.

Application of Principal Component Analysis in Prompt Gamma Spectra for Material Sorting

Energy Technology Data Exchange (ETDEWEB)

Im, Hee Jung; Lee, Yun Hee; Song, Byoung Chul; Park, Yong Joon; Kim, Won Ho

2006-11-15

For the detection of illicit materials in a very short time by comparing unknown samples' gamma spectra to pre-programmed material signatures, we at first, selected a method to reduce the noise of the obtained gamma spectra. After a noise reduction, a pattern recognition technique was applied to discriminate the illicit materials from the innocuous materials in the noise reduced data. Principal component analysis was applied for a noise reduction and pattern recognition in prompt gamma spectra. A computer program for the detection of illicit materials based on PCA method was developed in our lab and can be applied to the PGNAA system for the baggage checking at all ports of entry at a very short time.

Coherent manipulation of spontaneous emission spectra in coupled semiconductor quantum well structures.

Science.gov (United States)

Chen, Aixi

2014-11-03

In triple coupled semiconductor quantum well structures (SQWs) interacting with a coherent driving filed, a coherent coupling field and a weak probe field, spontaneous emission spectra are investigated. Our studies show emission spectra can easily be manipulated through changing the intensity of the driving and coupling field, detuning of the driving field. Some interesting physical phenomena such as spectral-line enhancement/suppression, spectral-line narrowing and spontaneous emission quenching may be obtained in our system. The theoretical studies of spontaneous emission spectra in SQWS have potential application in high-precision spectroscopy. Our studies are based on the real physical system [Appl. Phys. Lett.86(20), 201112 (2005)], and this scheme might be realizable with presently available techniques.

Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

International Nuclear Information System (INIS)

Zuiderweg, E.R.P.; Fesik, S.W.

1989-01-01

The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of 1 H and 15 N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with 15 N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the 15 N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that 15 N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques

Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

Energy Technology Data Exchange (ETDEWEB)

Zuiderweg, E.R.P.; Fesik, S.W. (Abbott Laboratories, Abbott Park, IL (USA))

1989-03-21

The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of {sup 1}H and {sup 15}N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with {sup 15}N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the {sup 15}N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that {sup 15}N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques.

Spectra of Graphs

NARCIS (Netherlands)

Brouwer, A.E.; Haemers, W.H.

2012-01-01

This book gives an elementary treatment of the basic material about graph spectra, both for ordinary, and Laplace and Seidel spectra. The text progresses systematically, by covering standard topics before presenting some new material on trees, strongly regular graphs, two-graphs, association

Nanocomposite biofilms obtained from Whitemouth croaker (Micropogonias furnieri) protein isolate and Montmorillonite: evaluation of the physical, mechanical and barrier properties

International Nuclear Information System (INIS)

Cortez-Vega, William Renzo; Bagatini, Daniela Cardozo; Souza, Juliana Tais Andreghetto de; Prentice, Carlos

2013-01-01

The objective of this study was to evaluate the properties of nanocomposite biofilms based on Whitemouth croaker (Micropogonias furnieri) protein isolate with organophilic clays. Initially the croaker protein isolate (CPI) was obtained using the pH shifting process from by-products of croaker industrialization. A Box and Behnken experimental design was used to develop the films, with three levels of CPI (2, 3.5 and 5 g.100 g -1 solution), montmorillonite MMT clay (0.3, 0.5 and 0.7 g.100 g -1 solution) and glycerol (25, 30 and 35 g.100g -1 CPI). The polymeric films were produced by the 'casting technique'. The tensile strength values ranged from 7.2 to 10.7 MPa and the elongation values from 39.6 to 45.8 %. The water vapor permeability (WVP) values ranged from 3.2 to 5.5 (g.mm.m -2 .d -1 ) and the CPI had an average protein content of 97.87 % protein (d. b.). It was concluded that the nanocomposite films produced from CPI with MMT were promising from the standpoint of their mechanical properties, visual appearance and easy handling, as well as for their low water vapor permeability and low water solubility. With respect to their mechanical properties, the concentrations of CPI and MMT were the main factors influencing the development of the nanocomposite films. The results obtained from the experimental design indicated that 3.5 g of CPI.100 g -1 solution, 0.5 g of MMT.100 g -1 solution and 30 g of glycerol.100 g -1 CPI would be the ideal parameters for the development of nanocomposite films by 'casting'. (author)

Deconvolution analysis to determine relaxation time spectra of internal friction peaks

International Nuclear Information System (INIS)

Cost, J.R.

1985-01-01

A new method for analysis of an internal friction vs temperature peak to obtain an approximation of the spectrum of relaxation time responsible for the peak is described. This method, referred to as direct spectrum analysis (DSA), is shown to provide an accurate estimate of the distribution of relaxation times. The method is validated for various spectra, and it is shown that: (1) It provides approximations to known input spectra which replicate the position, amplitude, width and shape with good accuracy (typically 10%). (2) It does not yield approximations which have false spectral peaks

CompAZ Parametrization of the Luminosity Spectra for the Photon Collider

CERN Document Server

Zarnecki, A F

2003-01-01

A simple model, based on the analytical formula for the Compton scattering, is proposed to describe the realistic photon-energy spectra for the Photon Collider at TESLA. Parameters of the model are obtained from the full simulation of the beam by V. Telnov, which includes nonlinear corrections and contributions of higher order processes. Photon energy distribution and polarization, in the high energy part of the spectra, are well reproduced. Our model can be used for a Monte Carlo simulation of gamma-gamma events at various energies and for direct cross-section calculations.

Raman optical activity of proteins and glycoproteins

International Nuclear Information System (INIS)

Smyth, E.

2000-03-01

Raman optical activity (ROA), measured in this project as a small difference in the intensity of Raman scattering from chiral molecules in right- and left-circularly polarised incident laser light, offers the potential to provide more information about the structure of biological molecules in aqueous solution than conventional spectroscopic techniques. Chapter one contains a general discussion of the relative merits of different spectroscopic techniques for structure determination of biomolecules, as well as a brief introduction to ROA. In Chapter two a theoretical analysis of ROA is developed, which extends the discussion in chapter one. The spectrometer setup and sample preparation is then discussed in chapter three. Instrument and sample conditions are monitored to ensure that the best results are obtained. As with any experimental project problems occur, which may result in a degradation of the spectra obtained. The cause of these problems was explored and remedied whenever possible. Chapter four introduces a brief account of protein, glycoprotein and carbohydrate structure and function, with a particular emphasis on the structure of proteins. In the remaining chapters experimental ROA results on proteins and glycoproteins, with some carbohydrate samples, from a wide range of sources are examined. For example, in chapter five some β-sheet proteins are examined. Structural features in these proteins are examined in the extended amide III region of their ROA spectra, revealing that ROA is sensitive to the rigidity or flexibility inherent in proteins. Chapter six concentrates on a group of proteins (usually glycoproteins) known as the serine proteinase inhibitors (serpins). Medically, the serpins are one of the most important groups of proteins of current interest, with wide-ranging implications in conditions such as Down's syndrome, Alzheimer's disease, and emphysema with associated cirrhosis of the liver. With favourable samples and conditions ROA may offer the

The mechanical spectra of deposited materials by a composite reed vibration method

International Nuclear Information System (INIS)

Ying, X.N.; Zhang, L.; Yuan, Y.H.

2010-01-01

Recently a composite reed vibration method has been designed to measure the mechanical spectra (complex Young's modulus) of materials from liquid to solid state. The mechanical spectra of materials can be obtained from a composite system consisting of a substrate reed and of materials deposited on it. In this report, two sets of formulas to calculate the mechanical spectra of deposited materials are further analyzed. The proof is given for the previous named 'approximate formulas' (labeled as Formula II). Then the composite reed vibration method can be safely used as an extension of the mechanical spectrum method of the thin solid film. At the same time, some comments are made on previous analytical formulas (labeled as Formula I). At last, more experiments with a small amount of deposited materials are performed. It is found that smaller quantity is more favorable to achieve the intrinsic mechanical spectra of deposited materials.

Multifractal spectra in homogeneous shear flow

Science.gov (United States)

Deane, A. E.; Keefe, L. R.

1988-01-01

Employing numerical simulations of 3-D homogeneous shear flow, the associated multifractal spectra of the energy dissipation, scalar dissipation and vorticity fields were calculated. The results for (128) cubed simulations of this flow, and those obtained in recent experiments that analyzed 1- and 2-D intersections of atmospheric and laboratory flows, are in some agreement. A two-scale Cantor set model of the energy cascade process which describes the experimental results from 1-D intersections quite well, describes the 3-D results only marginally.

Alkaline transition of pseudoazurin Met16X mutant proteins: protein stability influenced by the substitution of Met16 in the second sphere coordination.

Science.gov (United States)

Abdelhamid, Rehab F; Obara, Yuji; Kohzuma, Takamitsu

2008-01-01

Several blue copper proteins are known to change the active site structure at alkaline pH (alkaline transition). Spectroscopic studies of Met16Phe, Met16Tyr, Met16Trp, and Met16Val pseudoazurin variants were performed to investigate the second sphere role through alkaline transition. The visible electronic absorption and resonance Raman spectra of Met16Phe, Met16Tyr, and Met16Trp variants showed the increasing of axial component at pH approximately 11 like wild-type PAz. The visible electronic absorption and far-UV CD spectra of Met16Val demonstrated that the destabilization of the protein structure was triggered at pH>11. Resonance Raman (RR) spectra of PAz showed that the intensity-weighted averaged Cu-S(Cys) stretching frequency was shifted to higher frequency region at pH approximately 11. The higher frequency shift of Cu-S(Cys) bond is implied the stronger Cu-S(Cys) bond at alkaline transition pH approximately 11. The visible electronic absorption and far-UV CD spectra of Met16X PAz revealed that the Met16Val variant is denatured at pH>11, but Met16Phe, Met16Tyr, and Met16Trp mutant proteins are not denatured even at pH>11. These observations suggest that Met16 is important to maintain the protein structure through the possible weak interaction between methionine -SCH3 part and coordinated histidine imidazole moiety. The introduction of pi-pi interaction in the second coordination sphere may be contributed to the enhancement of protein structure stability.

Behavior of lambda 2800 Mg II in stellar spectra

International Nuclear Information System (INIS)

Gurzadyan, G.A.

1975-01-01

The results of measurements of the equivalent widths of the resonance doublet of ionized magnesium lambda 2800 Mg II in the spectra of 51 relatively faint stars, up to 10/sup m/, of the spectral classes B1-K5 are presented. The observed material has been obtained by means of the space observatory ''Orion-2''. Some regularities in the behavior of lambda 2800 Mg II in stellar spectra have been revealed: wide and deep depression of the continuous spectra at 2800 A in F-G type stars; the presence of the doublet lambda 2800 Mg II in the form of weak emission in the spectra of cold stars (K2-K5); the presence both of the multiplet lambda 3080 Ti II and the doublet lambda 2800 Mg II simultaneously either in emission--in the late-type stars--or in absorption in earlier types; the existence of combined profiles of lambda 2800 Mg II, i.e., a wide absorption line with a weak emission in the center, in stars of the transitional class (G5-K0), etc. A well-defined empirical relationship between the equivalent width of lambda 2800 Mg II and the spectral class of the star has been established (Fig. 8). (U.S.)

Seismic analysis of a PWR 900 reactor: study of reactor building with soil-structure interaction and evaluation of floor spectra

International Nuclear Information System (INIS)

Gantenbein, F.; Aguilar, J.

1983-08-01

The purpose of this paper is the evaluation of seismic response and floor spectra for a typical PWR 900 reactor building with respect to soil-structure interaction for soil stiffness). The typical PWR 900 reactor building consists of a concrete cylindrical external building and roof dome, a concrete internal structure (internals) on a common foundation mat as illustrated. The seismic response is obtained by SRSS method and floor spectra directly from ground spectrum and modal properties of the structure. Seismic responses and floor spectra computation is performed in the case of two different ground spectra: EDF spectrum (mean of oscillator spectra obtained from 8 californian records) normalized to 0.2 g, and DSN spectrum (typical of shallow seism) normalized to 0.3 g. The first section is devoted to internals' modelisation, the second one to the axisymmetric model of the reactor, the third one to the seismic response, the fourth one to floor spectra

Compound complex enzymes and proteins of Stipa capillata from Semipalatinsk polygon

International Nuclear Information System (INIS)

Sarsenbaev, K.N.; Esnazarov, U.; Sarsenbaeva, M.V.; Seisebaev, A.

2002-01-01

The effects of low and high doses of irradiation near Semipalatinsk Atomic lake on the compound complex of different enzymes and proteins of leaves from different population of Stipa capillata are considered. 36 samples of Stipa capillata were analyzed by the iso-electrofocusing methods, native and SDS-electrophoresis. Levels of radioactivity effect on compound complex of peroxidase, esterase, acid phosphates and soluble proteins were found. SDS-PAGE and IEF methods did not show difference in peptides spectra between 36 populations of examined species. It means, that difference between contaminated and non-contaminated populations not so big as was expected. Compound complex soluble protein of Stipa capillata leaves changes under chronic doses of radioactivity. The difference in spectra between control and contaminated leaves make up 3-6 bands. Control leaves have more high molecular weight proteins than contaminated ones. Appearance of new bands is one of ways of plant adaptation. New components of enzymes spectra and soluble proteins were found. It was suggested, that gene mutation or post-translation modification of these proteins are result of chronic irradiation. To prove exactly genetic nature of this alteration aminoacids sequence for these proteins the DNA sequence of different Stipa capillata populations genomes were compared

Use of electrophoretic analysis of grain proteins in the identification of wheat radiomutant ST 7750

International Nuclear Information System (INIS)

Sasek, A.; Kubanek, J.; Hanis, M.; Cerny, J.

1977-01-01

For a more precise comparison of the protein complexes of the grain of the 'Jubilar' cv. and of its radiomutant ST 7750, the methods of the electrophoresis in starch gel in various buffer systems and of disc electrophoresis in polyacrylamide gel were used for the study of anodal isoperoxidases. A determination was made of the total protein content, of the basic protein fractions, and of the quantitative proportion of amino acids. Basic qualitative correspondence of the albumin-globulin and gliadin spectrum of the examined variants was found and only in some zones of both spectra certain differences were observed in the quantitative content which may of course, indicate genotypic differentiation of the mutant SF 7750 and of the starting 'Jubilar' cv. Analogous findings were confirmed also by the results of isoperoxidases. Complementary analyses of the protein fractions confirmed the correspondence of the content of albumins, globulins, and gliadins of the investigated variants. Differences were found in the content of glutelin fractions and of insoluble residue. The ascertained changes were confirmed by amino acid analysis where higher methionine, valine, leucine, and isoleucine levels were found in the ST 7750 mutant. The results obtained have shown that especially the analysis of gliadin spectra by electrophoresis in starch gel is a suitable method of differentiating and unifying wheat genotypes as it reveals the differences between the initial and the mutated genotype. (author)

The dynamic method for time-of-flight measurement of thermal neutron spectra from pulsed sources

International Nuclear Information System (INIS)

Pepyolyshev, Yu.N.; Chuklyaev, S.V.; Tulaev, A.B.; Bobrakov, V.F.

1995-01-01

A time-of-flight method for measurement of thermal neutron spectra in pulsed neutron sources with an efficiency more than 10 5 times higher than the standard method is described. The main problems associated with the electric current technique for time-of-flight spectra measurement are examined. The methodical errors, problems of special neutron detector design and other questions are discussed. Some experimental results for spectra from the surfaces of water and solid methane moderators obtained at the IBR-2 pulsed reactor (Dubna, Russia) are presented. (orig.)

On Descriptions of Particle Transverse Momentum Spectra in High Energy Collisions

Directory of Open Access Journals (Sweden)

Fu-Hu Liu

2014-01-01

is obtained that, at a given set of parameters, the standard distributions show a narrower shape than their Tsallis forms which result in wide and/or multicomponent spectra with the Tsallis distribution in between. A comparison among the temperatures obtained from the distributions is made with a possible relation to the Boltzmann temperature. An example of the angular distributions of projectile fragments in nuclear collisions is given.

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method

International Nuclear Information System (INIS)

Douglas, Justin T.; Latham, Michael P.; Armstrong, Geoffrey S.; Bendiak, Brad; Pardi, Arthur

2008-01-01

The NMR spectra of nucleic acids suffer from severe peak overlap, which complicates resonance assignments. 4D NMR experiments can overcome much of the degeneracy in 2D and 3D spectra; however, the linear increase in acquisition time with each new dimension makes it impractical to acquire high-resolution 4D spectra using standard Fourier transform (FT) techniques. The filter diagonalization method (FDM) is a numerically efficient algorithm that fits the entire multi-dimensional time-domain data to a set of multi-dimensional oscillators. Selective 4D constant-time HCCH-COSY experiments that correlate the H5-C5-C6-H6 base spin systems of pyrimidines or the H1'-C1'-C2'-H2' spin systems of ribose sugars were acquired on the 13 C-labeled iron responsive element (IRE) RNA. FDM-processing of these 4D experiments recorded with only 8 complex points in the indirect dimensions showed superior spectral resolution than FT-processed spectra. Practical aspects of obtaining optimal FDM-processed spectra are discussed. The results here demonstrate that FDM-processing can be used to obtain high-resolution 4D spectra on a medium sized RNA in a fraction of the acquisition time normally required for high-resolution, high-dimensional spectra

Raman light scattering in nanoporous carbon obtained from carbides of silicon and titanium

International Nuclear Information System (INIS)

Danishevskij, A.M.; Smorgonskaya, Eh.A.; Gordeev, S.K.; Grechinskaya, A.V.

2001-01-01

The Raman spectra in nanoporous carbon obtained through the chemical reaction from the polycrystal α-SiC and TiC are studied. It is shown that the spectra have a multicomponent character differentiating the considered group of materials from graphites and disordered carbon structures. The series of low-frequency modes is registered. The anisotropy and dispersion effects are identified. The results testify to the cluster structure of nanoporous carbon and dimensional quantization of electron and vibrational spectra in the carbon nanoclusters. The fine fragments of curved or fractures graphed sheets are the basic structural elements of nanoclusters in the porous skeleton. The presence of fragments close by structure to the tense cubic or hexagonal diamond is also notes [ru

Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins

Science.gov (United States)

2013-01-01

Background Biomarker discovery datasets created using mass spectrum protein profiling of complex mixtures of proteins contain many peaks that represent the same protein with different charge states. Correlated variables such as these can confound the statistical analyses of proteomic data. Previously we developed an algorithm that clustered mass spectrum peaks that were biologically or technically correlated. Here we demonstrate an algorithm that clusters correlated technical aliases only. Results In this paper, we propose a preprocessing algorithm that can be used for grouping technical aliases in mass spectrometry protein profiling data. The stringency of the variance allowed for clustering is customizable, thereby affecting the number of peaks that are clustered. Subsequent analysis of the clusters, instead of individual peaks, helps reduce difficulties associated with technically-correlated data, and can aid more efficient biomarker identification. Conclusions This software can be used to pre-process and thereby decrease the complexity of protein profiling proteomics data, thus simplifying the subsequent analysis of biomarkers by decreasing the number of tests. The software is also a practical tool for identifying which features to investigate further by purification, identification and confirmation. PMID:24010718

Protein nanocrystallography: growth mechanism and atomic structure of crystals induced by nanotemplates.

Science.gov (United States)

Pechkova, E; Vasile, F; Spera, R; Fiordoro, S; Nicolini, C

2005-11-01

Protein nanocrystallography, a new technology for crystal growth based on protein nanotemplates, has recently been shown to produce diffracting, stable and radiation-resistant lysozyme crystals. This article, by computing these lysozyme crystals' atomic structures, obtained by the diffraction patterns of microfocused synchrotron radiation, provides a possible mechanism for this increased stability, namely a significant decrease in water content accompanied by a minor but significant alpha-helix increase. These data are shown to be compatible with the circular dichroism and two-dimensional Fourier transform spectra of high-resolution H NMR of proteins dissolved from the same nanotemplate-based crystal versus those from a classical crystal. Finally, evidence for protein direct transfer from the nanotemplate to the drop and the participation of the template proteins in crystal nucleation and growth is provided by high-resolution NMR spectrometry and mass spectrometry. Furthermore, the lysozyme nanotemplate appears stable up to 523 K, as confirmed by a thermal denaturation study using spectropolarimetry. The overall data suggest that heat-proof lysozyme presence in the crystal provides a possible explanation of the crystal's resistance to synchrotron radiation.

Study on the man-operator characteristics in the peak identification problem in line spectra

International Nuclear Information System (INIS)

Gopych, P.M.; Sorokin, V.I.; Sotnikov, V.V.

1992-01-01

ATOS program complex (automatical test spectra processing) realizing all stages of investigation necessary to obtain qualitative characteristics of the man-operator in the peak identification problem is developed. Qualitative characteristics of identitication ion quality of peaks by operators searching for peaks in line spectra are determined due to simulation experiment. It is shown, that for trained operators reference possibility of false detection of peaks is equal to F=0.012±0.004, while for untrained ones - F≅0.3. Comparison of results with analogous data on on-line programs for identification of peaks in γ-spectra is conducted

A model for quasi parity-doublet spectra with strong coriolis mixing

International Nuclear Information System (INIS)

Minkov, N.; Drenska, S.; Strecker, M.

2013-01-01

The model of coherent quadrupole and octupole motion (CQOM) is combined with the reflection-asymmetric deformed shell model (DSM) in a way allowing fully microscopic description of the Coriolis decoupling and K-mixing effects in the quasi parity-doublet spectra of odd-mass nuclei. In this approach the even-even core is considered within the CQOM model, while the odd nucleon is described within DSM with pairing interaction. The Coriolis decoupling/mixing factors are calculated through a parity-projection of the single-particle wave function. Expressions for the Coriolis mixed quasi parity-doublet levels are obtained in the second order of perturbation theory, while the K-mixed core plus particle wave function is obtained in the first order. Expressions for the B(E1), B(E2) and B(E3) reduced probabilities for transitions within and between different quasi-doublets are obtained by using the total K-mixed wave function. The model scheme is elaborated in a form capable of describing the yrast and non-yrast quasi parity-doublet spectra in odd-mass nuclei. (author)

Electronic energy transfer through non-adiabatic vibrational-electronic resonance. II. 1D spectra for a dimer

Science.gov (United States)

Tiwari, Vivek; Jonas, David M.

2018-02-01

Vibrational-electronic resonance in photosynthetic pigment-protein complexes invalidates Förster's adiabatic framework for interpreting spectra and energy transfer, thus complicating determination of how the surrounding protein affects pigment properties. This paper considers the combined effects of vibrational-electronic resonance and inhomogeneous variations in the electronic excitation energies of pigments at different sites on absorption, emission, circular dichroism, and hole-burning spectra for a non-degenerate homodimer. The non-degenerate homodimer has identical pigments in different sites that generate differences in electronic energies, with parameters loosely based on bacteriochlorophyll a pigments in the Fenna-Matthews-Olson antenna protein. To explain the intensity borrowing, the excited state vibrational-electronic eigenvectors are discussed in terms of the vibrational basis localized on the individual pigments, as well as the correlated/anti-correlated vibrational basis delocalized over both pigments. Compared to those in the isolated pigment, vibrational satellites for the correlated vibration have the same frequency and precisely a factor of 2 intensity reduction through vibrational delocalization in both absorption and emission. Vibrational satellites for anti-correlated vibrations have their relaxed emission intensity reduced by over a factor 2 through vibrational and excitonic delocalization. In absorption, anti-correlated vibrational satellites borrow excitonic intensity but can be broadened away by the combination of vibronic resonance and site inhomogeneity; in parallel, their vibronically resonant excitonic partners are also broadened away. These considerations are consistent with photosynthetic antenna hole-burning spectra, where sharp vibrational and excitonic satellites are absent. Vibrational-excitonic resonance barely alters the inhomogeneously broadened linear absorption, emission, and circular dichroism spectra from those for a

Inclusive spectra of hadrons in proton-nucleus collisions

International Nuclear Information System (INIS)

Gevorkyan, S.R.; Gulkanyan, G.R.; Kotzinyan, A.M.; Zhamkochyan, V.M.

1985-01-01

A model is proposed, which allows one to describe all exprimental data on inclusive spectra of different hadrons produced on nuclei. The model is based on the following assumptions. After the first inelastic collision with nucleon in the nucleus the proton transforms into some excited system H, which collides with the other nucleons during its passage through the nucleus. Since in inelastic collisions the slow sea partons play the dominant role, the valence quarks of this system H coincide with those of proton. Fragmentation of H into hadrons (as well as into proton) is dilated in the lab system by the Lorentz factor E/m >> 1 and so it takes place out of the nucleus. Using the methods of multiple scattering theory one can receive the connection between inclusive spectra on nuclei and those on nucleons. The calculations of inclusive spectra of different hadrons (p, p, πsup(-+), ksup(+-)) were done, and a satisfactory description of the experimental data was obtained. It should be noted that this description was done without introduction of any free parameters. Analogous models are discussed, and their diffference from the method proposed is outlined

Comparative analysis of quasi-linear spectra of organic boron compounds and their heterocyclic and aromatic analogs

International Nuclear Information System (INIS)

Klimova, L.A.; Volkova, V.P.; Kugemova, M.E.; Mikhajlov, B.M.

1976-01-01

Quasiline absorption and luminescence spectra of polycyclic compounds containing boron, nitrogen, or oxygen atoms have been obtained and studied for the first time. Electron-vibrating spectra of these compounds have been compared with the corresponding spectra of nitrogen- and oxygen-containing heterocycles as well as with spectra of their aromatic analog - phenanthrene. Vibrational analysis of the spectra of all the compounds reveals, within the accuracy limit of measurements, the relative closeness of the vibrational frequencies. However, the great difference between the positions of electron transitions points to a change in π-electron structure of the molecules when heteroatoms are introduced. High sensitivity of the frequency of electron transition to structural changes makes it possible to determine the degree of influence of separate heteroatoms

Raman spectra of zirconium tetrachloride in molten and evaporational states

International Nuclear Information System (INIS)

Salyuev, A.B.; Kornyakova, I.D.

1994-01-01

For the first time raman spectra of ZrCl 4 are obtained in the temperature range of its existence in molten state as well as in vapors near the critical point. It is shown, that rupture of zigzag chains is taking place when ZrCl 4 is melting

Emission spectra of Rb*Hen exciplexes in a cold 4He gas

International Nuclear Information System (INIS)

Hirano, K.; Enomoto, K.; Kumakura, M.; Takahashi, Y.; Yabuzaki, T.

2003-01-01

We report on the systematic observation of emission spectra of Rb * He n exciplexes (n=1,2,...,6), realized by exciting Rb atoms to the 5 2 P states (Rb * ) in a cold 4 He gas. The observed broad spectral components are assigned to Rb * He n (n=1-6) using theoretical spectra obtained from ab initio potential curves. The dynamics of the exciplex formation is discussed, based on the observed temperature dependence of the spectra. The He gas density dependence of the spectra of Rb * He is understood as a change in the population distribution over the vibrational levels. The present results are compared with our previous work with Cs [K. Enomoto et al., Phys. Rev. A 66, 042505 (2002)], and differences are explained in terms of the difference in the fine-structure splitting. Furthermore, we show the emission spectrum observed after the excitation of Rb in liquid He and conclude that it is the fluorescence from the exciplex Rb * He 6

Smoothed Spectra, Ogives, and Error Estimates for Atmospheric Turbulence Data

Science.gov (United States)

Dias, Nelson Luís

2018-01-01

A systematic evaluation is conducted of the smoothed spectrum, which is a spectral estimate obtained by averaging over a window of contiguous frequencies. The technique is extended to the ogive, as well as to the cross-spectrum. It is shown that, combined with existing variance estimates for the periodogram, the variance—and therefore the random error—associated with these estimates can be calculated in a straightforward way. The smoothed spectra and ogives are biased estimates; with simple power-law analytical models, correction procedures are devised, as well as a global constraint that enforces Parseval's identity. Several new results are thus obtained: (1) The analytical variance estimates compare well with the sample variance calculated for the Bartlett spectrum and the variance of the inertial subrange of the cospectrum is shown to be relatively much larger than that of the spectrum. (2) Ogives and spectra estimates with reduced bias are calculated. (3) The bias of the smoothed spectrum and ogive is shown to be negligible at the higher frequencies. (4) The ogives and spectra thus calculated have better frequency resolution than the Bartlett spectrum, with (5) gradually increasing variance and relative error towards the low frequencies. (6) Power-law identification and extraction of the rate of dissipation of turbulence kinetic energy are possible directly from the ogive. (7) The smoothed cross-spectrum is a valid inner product and therefore an acceptable candidate for coherence and spectral correlation coefficient estimation by means of the Cauchy-Schwarz inequality. The quadrature, phase function, coherence function and spectral correlation function obtained from the smoothed spectral estimates compare well with the classical ones derived from the Bartlett spectrum.

Time resolved EUV spectra from Zpinching capillary discharge plasma

Science.gov (United States)

Jancarek, Alexandr; Nevrkla, Michal; Nawaz, Fahad

2015-09-01

We developed symmetrically charged driver to obtain high voltage, high current Z-pinching capillary discharge. Plasma is created by up to 70 kA, 29 ns risetime current pulse passing through a 5 mm inner diameter, 224 mm long capillary filled with gas to initial pressure in the range of 1 kPa. Due to the low inductance design of the driver, the pinch is observable directly from the measured current curve. Time-integrated and time-resolved spectra of discharge plasma radiation are recorded together with the capillary current and analyzed. The most encouraging spectra were captured in the wavelength range 8.3 ÷ 14 nm. This spectral region contains nitrogen Balmer series lines including potentially lasing NVII 2 - 3 transition. Spectral lines are identified in the NIST database using the FLY kinetic code. The line of 13.38 nm wavelength, transition NVII 2 - 3, was observed in gated, and also in time-integrated spectra for currents >60 kA. This work has been supported by the Ministry of Education, Youth and Sports of the Czech Republic grants LG13029.

Nanostructured films of metal particles obtained by laser ablation

Energy Technology Data Exchange (ETDEWEB)

Muniz-Miranda, M., E-mail: muniz@unifi.it [Dipartimento di Chimica “U. Schiff”, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Italy); Gellini, C. [Dipartimento di Chimica “U. Schiff”, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Italy); Giorgetti, E.; Margheri, G.; Marsili, P. [Istituto Sistemi Complessi (CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Lascialfari, L.; Becucci, L. [Dipartimento di Chimica “U. Schiff”, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Italy); Trigari, S. [Istituto Sistemi Complessi (CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Giammanco, F. [Dipartimento di Fisica “E. Fermi”, Università di Pisa, Largo Pontecorvo 3, 56127 Pisa (Italy)

2013-09-30

Colloidal dispersions of silver and gold nanoparticles were obtained in pure water by ablation with nanosecond pulsed laser. Then, by filtration of the metal particles on alumina, we fabricated nanostructured films, whose surface morphology was examined by atomic force microscopy (AFM) and related to surface-enhanced Raman scattering (SERS) after adsorption of adenine. - Highlights: • Ag and Au colloidal nanoparticles were obtained by laser ablation. • Nanostructured Ag and Au films were fabricated by filtration of metal nanoparticles. • Surface morphology of metal films was investigated by atomic force microscopy. • Surface-enhanced Raman spectra (SERS) of adenine on metal films were obtained. • SERS enhancements were related to the surface roughness of the metal films.

A improved method for the analysis of alpha spectra

International Nuclear Information System (INIS)

Equillor, Hugo E.

2004-01-01

In this work we describe a methodology, developed in the last years, for the analysis of alpha emitters spectra, obtained with implanted ion detectors, that tend to solve some of the problems that shows this type of spectra. This is an improved methodology respect to that described in a previous publication. The method is based on the application of a mathematical function that allows to model the tail of an alpha peak, to evaluate the part of the peak that is not seen in the cases of partial superposition with another peak. Also, a calculation program that works in a semiautomatic way, with the possibility of interactive intervention of the analyst, has been developed simultaneously and is described in detail. (author)

Ni-doped zinc oxide nanocombs and phonon spectra properties

International Nuclear Information System (INIS)

Zhang Bin; Zhang Xingtang; Gong Hechun; Wu Zhishen; Zhou Shaomin; Du Zuliang

2008-01-01

Ni-doped comb-like zinc oxide (ZnO) semiconductor nanostructures have been synthesized by a simple chemical vapor-deposition method (CVD) at relatively low temperature. The as-synthesized ZnO nanocombs consist of an array of very uniform, perfectly aligned, evenly spaced and long single-crystalline nanobelts (nanowires) with periods of about several tens of nanometers. X-ray diffraction and Raman spectra results provide the evidence that Ni is incorporated into the ZnO lattice at Zn site. Photoluminescence spectra of the as-obtained samples have been detected, in which the incorporation of donor Ni leads to the increases of the ultraviolet emission intensity and a blueshift of emission peak. This technique can be used to prepare other semiconductors and morphology-controlled doping nanocombs

Annotating and Interpreting Linear and Cyclic Peptide Tandem Mass Spectra.

Science.gov (United States)

Niedermeyer, Timo Horst Johannes

2016-01-01

Nonribosomal peptides often possess pronounced bioactivity, and thus, they are often interesting hit compounds in natural product-based drug discovery programs. Their mass spectrometric characterization is difficult due to the predominant occurrence of non-proteinogenic monomers and, especially in the case of cyclic peptides, the complex fragmentation patterns observed. This makes nonribosomal peptide tandem mass spectra annotation challenging and time-consuming. To meet this challenge, software tools for this task have been developed. In this chapter, the workflow for using the software mMass for the annotation of experimentally obtained peptide tandem mass spectra is described. mMass is freely available (http://www.mmass.org), open-source, and the most advanced and user-friendly software tool for this purpose. The software enables the analyst to concisely annotate and interpret tandem mass spectra of linear and cyclic peptides. Thus, it is highly useful for accelerating the structure confirmation and elucidation of cyclic as well as linear peptides and depsipeptides.

Precise Wavelengths and Energy Levels for the Spectra of Cr I, Mn I, and Mn III, and Branching Fractions for the Spectra of Fe II and Cr II

Science.gov (United States)

Nave, Gillian

I propose to measure wavelengths and energy levels for the spectra of Cr I, Mn I, and Mn III covering the wavelength range 80 nm to 5500 nm, and oscillator strengths for Fe II and Cr II in the region 120 nm to 2500 nm. I shall also produce intensity calibrated atlases and linelists of the iron-neon and chromium-neon hollow cathode lamps that can be compared with astrophysical spectra. The spectra will be obtained from archival data from spectrometers at NIST and Kitt Peak National Observatory and additional experimental observations as necessary from Fourier transform (FT) and grating spectrometers at NIST. The wavelength uncertainty of the strong lines will be better than 1 part in 10^7. The radiometric calibration of the spectra will be improved in order to reduce the uncertainty of measured oscillator strengths in the near UV region and extend the wavelength range of these measurements down to 120 nm. These will complement and support the measurements of lifetimes and branching fractions by J. E. Lawler in the near UV region. An intensive effort by NIST and Imperial College London that was partly funded by previous NASA awards has resulted in comprehensive analyses of the spectra of Fe II, Cr II and Cu II, with similar analyses of Mn II, Ni II, and Sc II underway. The species included in this proposal will complete the analysis of the first two ionization stages of the elements titanium through nickel using the same techniques, and add the spectrum of Mn III - one of the most important doubly-ionized elements. The elements Cr I and Mn I give large numbers of spectral lines in spectra of cool stars and important absorption lines in the interstellar medium. The spectrum of Mn III is important in chemically peculiar stars and can often only be studied in the UV region. Analyses of many stellar spectra depend on comprehensive analyses of iron-group elements and are hampered by incomplete spectroscopic data. As a result of many decades of work by the group at the

Influence of fluctuating strain on exciton reflection spectra

DEFF Research Database (Denmark)

Skettrup, Torben

1982-01-01

The influence of an internal distribution of strain on the exciton reflection spectra is investigated. The resulting fluctuating optical constants give rise to a fluctuating phase of reflectivity. The standard deviation σ of these phase fluctuations is the quantity which can be observed...... to derive the dependence of the phase of reflectivity on the direction of the fluctuating optical axis. The results obtained for σ are compared with the experimental depolarization spectra of ZnO. The only fitting parameter is the common standard deviation of the strain components. It is found......, for example, between crossed polarizers or from ellipsometric measurements. Assuming the phase fluctuations to obey a Gaussian distribution, σ can be expressed in a simple way in terms of the degree of polarization or the depolarization of the reflected light. σ is then derived in terms of the standard...

[Progress in the spectral library based protein identification strategy].

Science.gov (United States)

Yu, Derui; Ma, Jie; Xie, Zengyan; Bai, Mingze; Zhu, Yunping; Shu, Kunxian

2018-04-25

Exponential growth of the mass spectrometry (MS) data is exhibited when the mass spectrometry-based proteomics has been developing rapidly. It is a great challenge to develop some quick, accurate and repeatable methods to identify peptides and proteins. Nowadays, the spectral library searching has become a mature strategy for tandem mass spectra based proteins identification in proteomics, which searches the experiment spectra against a collection of confidently identified MS/MS spectra that have been observed previously, and fully utilizes the abundance in the spectrum, peaks from non-canonical fragment ions, and other features. This review provides an overview of the implement of spectral library search strategy, and two key steps, spectral library construction and spectral library searching comprehensively, and discusses the progress and challenge of the library search strategy.

Oxygen infrared spectra of oxyhemoglobins and oxymyoglobins. Evidence of two major liganded O2 structures

International Nuclear Information System (INIS)

Potter, W.T.; Tucker, M.P.; Houtchens, R.A.; Caughey, W.S.

1987-01-01

The dioxygen stretch bands in infrared spectra for solutions of oxy species of human hemoglobin A and its separated subunits, human mutant hemoglobin Zurich (β63His to Arg), rabbit hemoglobin, lamprey, hemoglobin, sperm whale myoglobin, bovine myoglobin, and a sea worm chlorocruorin are examined. Each protein exhibits multiple isotope-sensitive bands between 1160 and 1060 cm -1 for the liganded 16 O 2 , 17 O 2 , and 18 O 2 . The O-O stretch bands for each of the mammalian myoglobins and hemoglobins are similar, with frequencies that differ between proteins by only 3-5 cm -1 . The spectra for the lamprey and sea worm hemoglobins exhibit greater diversity. For all proteins an O-O stretch band expected to occur near 1125 cm -1 for 16 O 2 and 17 O 2 , but not 18 O 2 , appears split by ∼25 cm -1 due to an unidentified perturbation. The spectrum for each dioxygen isotope, if unperturbed, would contain two strong bands for the mammalian myoglobins (1150 and 1120 cm -1 ) and hemoglobins (1155 and 1125 cm -1 ). Two strong bands separated by ∼30 cm -1 for each oxy heme protein subunit indicate that two major protein conformations (structure) that differ substantially in O 2 bonding are present. The two dioxygen structures can result from a combination of dynamic distal and proximal effects upon the O 2 ligand bound in a bent-end-on stereochemistry

Non-Hermitian systems of Euclidean Lie algebraic type with real energy spectra

International Nuclear Information System (INIS)

Dey, Sanjib; Fring, Andreas; Mathanaranjan, Thilagarajah

2014-01-01

We study several classes of non-Hermitian Hamiltonian systems, which can be expressed in terms of bilinear combinations of Euclidean–Lie algebraic generators. The classes are distinguished by different versions of antilinear (PT)-symmetries exhibiting various types of qualitative behaviour. On the basis of explicitly computed non-perturbative Dyson maps we construct metric operators, isospectral Hermitian counterparts for which we solve the corresponding time-independent Schrödinger equation for specific choices of the coupling constants. In these cases general analytical expressions for the solutions are obtained in the form of Mathieu functions, which we analyze numerically to obtain the corresponding energy spectra. We identify regions in the parameter space for which the corresponding spectra are entirely real and also domains where the PT symmetry is spontaneously broken and sometimes also regained at exceptional points. In some cases it is shown explicitly how the threshold region from real to complex spectra is characterized by the breakdown of the Dyson maps or the metric operator. We establish the explicit relationship to models currently under investigation in the context of beam dynamics in optical lattices. -- Highlights: •Different PT-symmetries lead to qualitatively different systems. •Construction of non-perturbative Dyson maps and isospectral Hermitian counterparts. •Numerical discussion of the eigenvalue spectra for one of the E(2)-systems. •Established link to systems studied in the context of optical lattices. •Setup for the E(3)-algebra is provided

Measurement of characteristic to total spectrum ratio of tungsten X-ray spectra for the validation of the modified Tbc model

International Nuclear Information System (INIS)

Lopez G, A. H.; Costa, P. R.; Tomal, A.

2014-08-01

Primary X-ray spectra were measured in the range of 80 to 150 kV in order to validate a computer program based on a semiempirical model for X-ray spectra evaluation(tbc and mod). The ratio between the characteristic lines and total spectrum was considered for comparing the simulated results and experimental data. The raw spectra measured by the Cd Te detector were corrected by the detector efficiency, Compton effects and characteristic Cd and Te X-rays escape peaks, using a software specifically developed. The software Origin 8.5.1 was used to calculate the spectra and characteristic peaks areas. The obtained result shows that the experimental spectra have higher effective energy than the simulated spectra computed with tbc and mod software. The behavior of the ratio between the characteristic lines and total spectrum for simulated data presents discrepancy with the experimental result. Computed results are in good agreement with theoretical data published by Green, for spectra obtained with 3.04 mm of additional aluminum filtration. The difference of characteristic to total spectrum ratio between experimental and simulated data increases with the tube voltage. (Author)

Measurement of characteristic to total spectrum ratio of tungsten X-ray spectra for the validation of the modified Tbc model

Energy Technology Data Exchange (ETDEWEB)

Lopez G, A. H.; Costa, P. R. [University of Sao Paulo, Institute of Physics, Laboratory of Radiation Dosimetry and Medical Physics, Matao Street, alley R, 187, 66318 Sao Paulo (Brazil); Tomal, A., E-mail: ahlopezg@usp.br [Universidade Federal de Goias, Physics Institute, Campus Samambaia, 131 Goiania, Goias (Brazil)

2014-08-15

Primary X-ray spectra were measured in the range of 80 to 150 kV in order to validate a computer program based on a semiempirical model for X-ray spectra evaluation(tbc and mod). The ratio between the characteristic lines and total spectrum was considered for comparing the simulated results and experimental data. The raw spectra measured by the Cd Te detector were corrected by the detector efficiency, Compton effects and characteristic Cd and Te X-rays escape peaks, using a software specifically developed. The software Origin 8.5.1 was used to calculate the spectra and characteristic peaks areas. The obtained result shows that the experimental spectra have higher effective energy than the simulated spectra computed with tbc and mod software. The behavior of the ratio between the characteristic lines and total spectrum for simulated data presents discrepancy with the experimental result. Computed results are in good agreement with theoretical data published by Green, for spectra obtained with 3.04 mm of additional aluminum filtration. The difference of characteristic to total spectrum ratio between experimental and simulated data increases with the tube voltage. (Author)

Contribution of recently measured nuclear data to reactor antineutrino energy spectra predictions

Directory of Open Access Journals (Sweden)

Fallot M.

2013-12-01

Full Text Available This paper attempts to summarize the actual problematic of reactor antineutrino energy spectra in the frame of fundamental and applied neutrino physics. Nuclear physics is an important ingredient of reactor antineutrino experiments. These experiments are motivated by neutrino oscillations, i.e. the measure of the θ13 mixing angle. In 2011, after a new computation of the reactor antineutrino energy spectra, based on the conversion of integral data of the beta spectra from 235U, and 239;241Pu, a deficit of reactor antineutrinos measured by short baseline experiments was pointed out. This is called the “reactor anomaly”, a new puzzle in the neutrino physics area. Since then, numerous new experimental neutrino projects have emerged. In parallel, computations of the antineutrino spectra independant from the ILL data would be desirable. One possibility is the use of the summation method, summing all the contributions of the fission product beta decay branches that can be found in nuclear databases. Studies have shown that in order to obtain reliable summation antineutrino energy spectra, new nuclear physics measurements of selected fission product beta decay properties are required. In these proceedings, we will present the computation methods of reactor antineutrino energy spectra and the impact of recent beta decay measurements on summation method spectra. The link of these nuclear physics studies with short baseline line oscillation search will be drawn and new neutrino physics projects at research reactors will be briefly presented.

Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography

Energy Technology Data Exchange (ETDEWEB)

Paixao, L.; Oliveira, B. B.; Nogueira, M. do S. [Centro de Desenvolvimento da Tecnologia Nuclear, Post-graduation in Science and Technology of Radiations, Minerals and Materials, Pte. Antonio Carlos 6.627, Pampulha, 31270-901 Belo Horizonte (Brazil); Viloria, C. [UFMG, Departamento de Engenharia Nuclear, Post-graduation in Nuclear Sciences and Techniques, Pte. Antonio Carlos 6.627, Pampulha, 31270-901 Belo Horizonte (Brazil); Alves de O, M. [UFMG, Department of Anatomy and Imaging, Prof. Alfredo Balena 190, 30130-100 Belo Horizonte (Brazil); Araujo T, M. H., E-mail: lpr@cdtn.br [Dr Maria Helena Araujo Teixeira Clinic, Guajajaras 40, 30180-100 Belo Horizonte (Brazil)

2014-08-15

It is widely accepted that the mean glandular dose (D{sub G}) for the glandular tissue is the more useful magnitude for characterizing the breast cancer risk. The procedure to estimate the D{sub G}, for being difficult to measure it directly in the breast, it is to make the use of conversion factors that relate incident air kerma (K{sub i}) at this dose. Generally, the conversion factors vary with the x-ray spectrum half-value layer and the breast composition and thickness. Several authors through computer simulations have calculated such factors by the Monte Carlo (Mc) method. Many spectral models for D{sub G} computer simulations purposes are available in the diagnostic range. One of the models available generates unfiltered spectra. In this work, the Monte Carlo EGSnrc code package with the C++ class library (eg spp) was employed to derive filtered tungsten x-ray spectra used in digital mammography systems. Filtered spectra for rhodium and aluminium filters were obtained for tube potentials between 26 and 32 kV. The half-value layer of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F and Mam Detector Platinum and 8201023-C Xi Base unit Platinum Plus w m As in a Hologic Selenia Dimensions system using a Direct Radiography mode. Calculated half-value layer values showed good agreement compared to those obtained experimentally. These results show that the filtered tungsten anode x-ray spectra and the EGSnrc Mc code can be used for D{sub G} determination in mammography. (Author)

Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography

International Nuclear Information System (INIS)

Paixao, L.; Oliveira, B. B.; Nogueira, M. do S.; Viloria, C.; Alves de O, M.; Araujo T, M. H.

2014-08-01

It is widely accepted that the mean glandular dose (D G ) for the glandular tissue is the more useful magnitude for characterizing the breast cancer risk. The procedure to estimate the D G , for being difficult to measure it directly in the breast, it is to make the use of conversion factors that relate incident air kerma (K i ) at this dose. Generally, the conversion factors vary with the x-ray spectrum half-value layer and the breast composition and thickness. Several authors through computer simulations have calculated such factors by the Monte Carlo (Mc) method. Many spectral models for D G computer simulations purposes are available in the diagnostic range. One of the models available generates unfiltered spectra. In this work, the Monte Carlo EGSnrc code package with the C++ class library (eg spp) was employed to derive filtered tungsten x-ray spectra used in digital mammography systems. Filtered spectra for rhodium and aluminium filters were obtained for tube potentials between 26 and 32 kV. The half-value layer of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F and Mam Detector Platinum and 8201023-C Xi Base unit Platinum Plus w m As in a Hologic Selenia Dimensions system using a Direct Radiography mode. Calculated half-value layer values showed good agreement compared to those obtained experimentally. These results show that the filtered tungsten anode x-ray spectra and the EGSnrc Mc code can be used for D G determination in mammography. (Author)

Earthquake response spectra for seismic design of nuclear power plants in the UK

International Nuclear Information System (INIS)

Bommer, Julian J.; Papaspiliou, Myrto; Price, Warren

2011-01-01

Highlights: → Seismic design of UK nuclear power plants usually based on PML response spectra. → We review derivation of PML spectra in terms of earthquake data used and procedure. → The data include errors and represent a small fraction of what is now available. → Seismic design loads in current practice are derived as mean uniform hazard spectra. → The need to capture epistemic uncertainty makes use of single equation indefensible. - Abstract: Earthquake actions for the seismic design of nuclear power plants in the United Kingdom are generally based on spectral shapes anchored to peak ground acceleration (PGA) values obtained from a single predictive equation. Both the spectra and the PGA prediction equation were derived in the 1980s. The technical bases for these formulations of seismic loading are now very dated if compared with the state-of-the-art in this field. Alternative spectral shapes are explored and the options, and the associated benefits and challenges, for generating uniform hazard response spectra instead of fixed shapes anchored to PGA are discussed.

Vibronic effects and destruction of exciton coherence in optical spectra of J-aggregates: A variational polaron transformation approach

Energy Technology Data Exchange (ETDEWEB)

Bloemsma, E.A.; Silvis, M.H.; Stradomska, A.; Knoester, J., E-mail: j.knoester@rug.nl

2016-12-20

Using a symmetry adapted polaron transformation of the Holstein Hamiltonian, we study the interplay of electronic excitation-vibration couplings, resonance excitation transfer interactions, and temperature in the linear absorption spectra of molecular J-aggregates. Semi-analytical expressions for the spectra are derived and compared with results obtained from direct numerical diagonalization of the Hamiltonian in the two-particle basis set representation. At zero temperature, we show that our polaron transformation reproduces both the collective (exciton) and single-molecule (vibrational) optical response associated with the appropriate standard perturbation limits. Specifically, for the molecular dimer excellent agreement with the spectra from the two-particle approach for the entire range of model parameters is obtained. This is in marked contrast to commonly used polaron transformations. Upon increasing the temperature, the spectra show a transition from the collective to the individual molecular features, which results from the thermal destruction of the exciton coherence.

Assessment of electron propagator methods for the simulation of vibrationally-resolved valence and core photoionization spectra

Science.gov (United States)

Baiardi, A.; Paoloni, L.; Barone, V.; Zakrzewski, V.G.; Ortiz, J.V.

2017-01-01

The analysis of photoelectron spectra is usually facilitated by quantum mechanical simulations. Due to the recent improvement of experimental techniques, the resolution of experimental spectra is rapidly increasing, and the inclusion of vibrational effects is usually mandatory to obtain a reliable reproduction of the spectra. With the aim of defining a robust computational protocol, a general time-independent formulation to compute different kinds of vibrationally-resolved electronic spectra has been generalized to support also photoelectron spectroscopy. The electronic structure data underlying the simulation are computed using different electron propagator approaches. In addition to the more standard approaches, a new and robust implementation of the second-order self-energy approximation of the electron propagator based on a transition operator reference (TOEP2) is presented. To validate our implementation, a series of molecules has been used as test cases. The result of the simulations shows that, for ultraviolet photoionization spectra, the more accurate non-diagonal approaches are needed to obtain a reliable reproduction of vertical ionization energies, but diagonal approaches are sufficient for energy gradients and pole strengths. For X-ray photoelectron spectroscopy, the TOEP2 approach, besides being more efficient, is also the most accurate in the reproduction of both vertical ionization energies and vibrationally-resolved bandshapes. PMID:28521087

Adsorption geometry and core excitation spectra of three phenylpropene isomers on Cu(111)

International Nuclear Information System (INIS)

Kolczewski, C.; Williams, F. J.; Cropley, R. L.; Vaughan, O. P. H.; Urquhart, A. J.; Tikhov, M. S.; Lambert, R. M.; Hermann, K.

2006-01-01

Theoretical C 1s near edge x-ray absorption fine structure (NEXAFS) spectra for the C 9 H 10 isomers trans-methylstyrene, α-methylstyrene, and allylbenzene in gas phase and adsorbed at Cu(111) surfaces have been obtained from density functional theory calculations where adsorbate geometries were determined by corresponding total energy optimizations. The three species show characteristic differences in widths and peak shapes of the lowest C 1s→π* transitions which are explained by different coupling of the π-electron system of the C 6 ring with that of the side chain in the molecules as well as by the existence of nonequivalent carbon centers. The adsorbed molecules bind only weakly with the substrate which makes the use of theoretical NEXAFS spectra of the oriented free molecules meaningful for an interpretation of experimental angle-resolved NEXAFS spectra of the adsorbate systems obtained in this work. However, a detailed quantitative account of relative peak intensities requires theoretical angle-resolved NEXAFS spectra of the complete adsorbate systems which have been evaluated within the surface cluster approach. The comparison with experiment yields almost perfect agreement and confirms the reliability of the calculated equilibrium geometries of the adsorbates. This can help to explain observed differences in the catalytic epoxidation of the three molecules on Cu(111) based on purely geometric considerations

The Rovibronic Spectra of the Cyclopentadienyl Radical

Science.gov (United States)

Sharma, Ketan; Miller, Terry A.; Stanton, John F.; Nesbitt, David

2017-06-01

Cyclopentadienyl (Cp) radical has been subject to numerous studies for the greater part of half a century. Experimental work has involved photo-electron spectroscopy, laser induced fluorescence excitation and emission, infrared absorption spectroscopy, and recently rotationally resolved spectra in the CH stretch region taken at JILA. Even more theoretical works appear in the literature, but substantial advances in computation have occurred since their completion. Cp's highly symmetric (D_{5h}) structure and doubly degenerate electronic ground (˜{X}^2E_1^{''}), which is subject to linear Jahn-Teller distortion, have been a great motivation for work on it. We have commenced new computational work to obtain a broad understanding of the electronic, vibrational, and rotational, i.e. rovibronic, structure of the Cp radical as revealed by its spectra, with particular emphasis on the new infrared spectra. The goal is to guide experiments and their analyses and reconcile results from spectroscopy and quantum chemistry calculations. T. Ichino, et al. J. Chem. Phys. 129, 084310 (2008) L. Yu, S. C. Foster, J. M. Williamson, M. C. Heaven and T. A. Miller J. Phys. Chem. 92, 4263 (1988) B. E. Applegate, A. J. Bezant and T. A. Miller J. Chem. Phys 114, 4869 (2001) D. Leicht, M. Kaufmann, G. Schwaab, and M. Havenith J. Chem. Phys. 145, 7 (2016), 074304.

VARIABILITY IN OPTICAL SPECTRA OF ε ORIONIS

International Nuclear Information System (INIS)

Thompson, Gregory B.; Morrison, Nancy D.

2013-01-01

We present the results of a time series analysis of 130 échelle spectra of ε Ori (B0 Ia), acquired over seven observing seasons between 1998 and 2006 at Ritter Observatory. The equivalent widths of Hα (net) and He I λ5876 were measured and radial velocities were obtained from the central absorption of He I λ5876. Temporal variance spectra (TVS) revealed significant wind variability in both Hα and He I λ5876. The He I TVS have a double-peaked profile consistent with radial velocity oscillations. A periodicity search was carried out on the equivalent width and radial velocity data, as well as on wavelength-binned spectra. This analysis has revealed several periods in the variability with timescales of two to seven days. Many of these periods exhibit sinusoidal modulation in the associated phase diagrams. Several of these periods were present in both Hα and He I, indicating a possible connection between the wind and the photosphere. Due to the harmonic nature of these periods, stellar pulsations may be the origin of some of the observed variability. Periods on the order of the rotational period were also detected in the He I line in the 1998-1999 season and in both lines during the 2004-2005 season. These periods may indicate rotational modulation due to structure in the wind.

Earthquake source scaling and self-similarity estimation from stacking P and S spectra

Science.gov (United States)

Prieto, GermáN. A.; Shearer, Peter M.; Vernon, Frank L.; Kilb, Debi

2004-08-01

We study the scaling relationships of source parameters and the self-similarity of earthquake spectra by analyzing a cluster of over 400 small earthquakes (ML = 0.5 to 3.4) recorded by the Anza seismic network in southern California. We compute P, S, and preevent noise spectra from each seismogram using a multitaper technique and approximate source and receiver terms by iteratively stacking the spectra. To estimate scaling relationships, we average the spectra in size bins based on their relative moment. We correct for attenuation by using the smallest moment bin as an empirical Green's function (EGF) for the stacked spectra in the larger moment bins. The shapes of the log spectra agree within their estimated uncertainties after shifting along the ω-3 line expected for self-similarity of the source spectra. We also estimate corner frequencies and radiated energy from the relative source spectra using a simple source model. The ratio between radiated seismic energy and seismic moment (proportional to apparent stress) is nearly constant with increasing moment over the magnitude range of our EGF-corrected data (ML = 1.8 to 3.4). Corner frequencies vary inversely as the cube root of moment, as expected from the observed self-similarity in the spectra. The ratio between P and S corner frequencies is observed to be 1.6 ± 0.2. We obtain values for absolute moment and energy by calibrating our results to local magnitudes for these earthquakes. This yields a S to P energy ratio of 9 ± 1.5 and a value of apparent stress of about 1 MPa.

Neutron and gamma-ray spectra of 239PuBe and 241AmBe

International Nuclear Information System (INIS)

Vega-Carrillo, H.R.; Manzanares-Acuna, Eduardo; Becerra-Ferreiro, A.M.; Carrillo-Nunez, Aureliano

2002-01-01

Neutron and gamma-ray spectra of 239 PuBe and 241 AmBe were measured and their dosimetric features were calculated. Neutron spectra were measured using a multisphere neutron spectrometer with a 6 LiI(Eu) scintillator. The 239 PuBe neutron spectrum was measured in an open environment, while the 241 AmBe neutron spectrum was measured in a closed environment. Gamma-ray spectra were measured using a NaI(Tl) scintillator using the same experimental conditions for both sources. The effect of measuring conditions for the 241 AmBe neutron spectrum indicates the presence of epithermal and thermal neutrons. The low-resolution neutron spectra obtained with the multisphere spectrometer allows one to calculate the dosimetric features of neutron sources. At 100 cm both sources produce approximately the same count rate as that of the 4.4 MeV gamma-ray per unit of alpha emitter activity

Long-term MST radar observations of vertical wave number spectra of gravity waves in the tropical troposphere over Gadanki (13.5° N, 79.2° E: comparison with model spectra

Directory of Open Access Journals (Sweden)

S. Vijaya Bhaskara Rao

2008-06-01

Full Text Available The potential utility of Mesosphere-Stratosphere-Troposphere (MST radar measurements of zonal, meridional and vertical winds for divulging the gravity wave vertical wave number spectra is discussed. The data collected during the years 1995–2004 are used to obtain the mean vertical wave number spectra of gravity wave kinetic energy in the tropical troposphere over Gadanki (13.5° N, 79.2° E. First, the climatology of 3-dimensional wind components is developed using ten years of radar observations, for the first time, over this latitude. This climatology brought out the salient features of background tropospheric winds over Gadanki. Further, using the second order polynomial fit as background, the day-to-day wind anomalies are estimated. These wind anomalies in the 4–14 km height regions are used to estimate the profiles of zonal, meridional and vertical kinetic energy per unit mass, which are then used to estimate the height profile of total kinetic energy. Finally, the height profiles of total kinetic energy are subjected to Fourier analysis to obtain the monthly mean vertical wave number spectra of gravity wave kinetic energy. The monthly mean vertical wave number spectra are then compared with a saturation spectrum predicted by gravity wave saturation theory. A slope of 5/3 is used for the model gravity wave spectrum estimation. In general, the agreement is good during all the months. However, it is noticed that the model spectrum overestimates the PSD at lower vertical wave numbers and underestimates it at higher vertical wave numbers, which is consistently observed during all the months. The observed discrepancies are attributed to the differences in the slopes of theoretical and observed gravity wave spectra. The slopes of the observed vertical wave number spectra are estimated and compared with the model spectrum slope, which are in good agreement. The estimated slopes of the observed monthly vertical wave number spectra are in the

Photons and photoneutrons spectra of a Linac of 15 MV

International Nuclear Information System (INIS)

Benites R, J. L.; Carrillo C, A.; Vega C, H. R.; Velazquez F, J. B.

2011-10-01

Using the Monte Carlo code MCNP-5, the photons and photoneutrons spectra generated in the head stock of the lineal accelerator (Linac) Varian of 15 MV of the Cancerology State of Nayarit were determined. For the calculations a heterogeneous head stock was modeled, more compatible with the work conditions. In the center of the head stock a tungsten target was located on a copper support, followed by the flattened filter. The photons and photoneutrons spectra were obtained accelerating electrons and making them collide against the target to produce photons by Bremsstrahlung, these photons were transported inside the head stock and the photons and photoneutrons spectra were calculated in a punctual detector located under the flattened filter and in the isocenter. The spectra were evaluated in punctual detectors that were located in the plane from the isocenter to the long of the X and Y axes each 20 cm, in an equidistant way, up to 2 m, so much in the longitudinal and transversal axes. In the calculations were used histories 5E(6) with the purpose of obtaining smaller uncertainties to 1%. It was found that the photons spectrum in the punctual detector inside the head stock presents a pick of 1.25 MeV in the energy interval of 0.5 and 1.5 MeV, later suffers a filtration and diminishes in asymptote form. This spectrum modifies when the beam reaches the isocenter, diminishing the low energy photons. Inside the head stock the photoneutrons spectrum shows a structure with two picks, one before 1 MeV and other after 1 MeV; this is for effect of the collimators geometry and the distance. Finally an increment of the total neutrons flow to 60 cm of distance of the isocenter on the Y axis was observed, due to the design geometry of the modeling heterogeneous head stock. (Author)

The application of n-γ discrimination in 252Cf spontaneous neutron TOF spectra measurement

International Nuclear Information System (INIS)

Zhou Haojun; Zhang Yi; Li Jiansheng; Jin Yu; Wang Jie; Li Chunyuan

2004-01-01

The BC501 scintillator is used as a fast neutron detector. The effect that the pulse rise time method was used to discriminate γ from 252 Cf spontaneous neutron TOF spectra is studied in the experiment. A pulse rise time separation spectra of γ and 252 Cf spontaneous neuron upon 1 MeV is obtained, the n-γ separation function reaches to 4.6. When the result of pulse rise time separation coincides with the time-of-flight spectra in which the neutron energy is upon 0.5 MeV, 0.8 MeV and 1.0 MeV, comparing with the anticoincidence, γ was eliminated 99.90% at least. (authors)

Influence of the initial guess spectrum in the unfolding of Bss data obtained inside a bunker of a PET cyclotron

Energy Technology Data Exchange (ETDEWEB)

Benavente C, J. A.; Lacerda, M. A. S.; Guimaraes, A. M.; Da Silva, T. A. [Universidade Federal de Minas Gerais, Departamento de Engenharia Nuclear, Programa de Pos-graduacao em Ciencias e Tecnicas Nucleares, Pte. Antonio Carlos 6627, Belo Horizonte 31270-901, Minas Gerais (Brazil); Vega C, H. R. [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Cipres No. 10, Fracc. La Penuela, 98060 Zacatecas, Zac. (Mexico)

2015-10-15

In a cyclotron facility is strongly advised the use of spectrometry techniques to support workplace neutron dosimetry. Bonner sphere spectrometer (Bss) is the most used for radiation protection applications. Bss data must be unfolded to determine the spectral particle fluence. Some computer codes have been utilized for this purpose. These codes allow unfolding the spectrum from the Bss count rates through different algorithms. Some iterative routines need an initial guess spectrum to start the unfolding. The adequate choice of this initial spectrum is a critical part of the process and can affect the final solution. In this work, we evaluate the influence of the initial guess spectrum in the unfolding of Bss data obtained in four points inside the bunker of a PET cyclotron. The measurements were done utilizing a modified Bss system with thermoluminescent detectors (TLDs). Codes BUNKIUT and NSDUAZ were utilized to unfold the Bss data. For the NSDUAZ the starting spectrum is automatically obtained from a library initial guess spectra. For the BUNKIUT code were utilized two different initial guess spectra: (a) a Maxwellian spectrum with temperature of 1.4 MeV and shape factor of 0.1, created with the MAXIET algorithm and; (b) the spectra obtained through simulation with the MCNPX code version 2.7. Spectra obtained with both unfold codes and with the different initial guess spectra presented epithermal and thermal neutrons due to room-return effects. However, the contribution of the fast neutron to the total fluence were quite different for the different cases studied. These differences highlight the importance of an appropriate choice of an initial guess spectra for the quality of the results. (Author)

Influence of the initial guess spectrum in the unfolding of Bss data obtained inside a bunker of a PET cyclotron

International Nuclear Information System (INIS)

Benavente C, J. A.; Lacerda, M. A. S.; Guimaraes, A. M.; Da Silva, T. A.; Vega C, H. R.

2015-10-01

In a cyclotron facility is strongly advised the use of spectrometry techniques to support workplace neutron dosimetry. Bonner sphere spectrometer (Bss) is the most used for radiation protection applications. Bss data must be unfolded to determine the spectral particle fluence. Some computer codes have been utilized for this purpose. These codes allow unfolding the spectrum from the Bss count rates through different algorithms. Some iterative routines need an initial guess spectrum to start the unfolding. The adequate choice of this initial spectrum is a critical part of the process and can affect the final solution. In this work, we evaluate the influence of the initial guess spectrum in the unfolding of Bss data obtained in four points inside the bunker of a PET cyclotron. The measurements were done utilizing a modified Bss system with thermoluminescent detectors (TLDs). Codes BUNKIUT and NSDUAZ were utilized to unfold the Bss data. For the NSDUAZ the starting spectrum is automatically obtained from a library initial guess spectra. For the BUNKIUT code were utilized two different initial guess spectra: (a) a Maxwellian spectrum with temperature of 1.4 MeV and shape factor of 0.1, created with the MAXIET algorithm and; (b) the spectra obtained through simulation with the MCNPX code version 2.7. Spectra obtained with both unfold codes and with the different initial guess spectra presented epithermal and thermal neutrons due to room-return effects. However, the contribution of the fast neutron to the total fluence were quite different for the different cases studied. These differences highlight the importance of an appropriate choice of an initial guess spectra for the quality of the results. (Author)

[Raman spectra of monkey cerebral cortex tissue].

Science.gov (United States)

Zhu, Ji-chun; Guo, Jian-yu; Cai, Wei-ying; Wang, Zu-geng; Sun, Zhen-rong

2010-01-01

Monkey cerebral cortex, an important part in the brain to control action and thought activities, is mainly composed of grey matter and nerve cell. In the present paper, the in situ Raman spectra of the cerebral cortex of the birth, teenage and aged monkeys were achieved for the first time. The results show that the Raman spectra for the different age monkey cerebral cortex exhibit most obvious changes in the regions of 1000-1400 and 2800-3000 cm(-1). With monkey growing up, the relative intensities of the Raman bands at 1313 and 2885 cm(-1) mainly assigned to CH2 chain vibrational mode of lipid become stronger and stronger whereas the relative intensities of the Raman bands at 1338 and 2932 cm(-1) mainly assigned to CH3 chain vibrational mode of protein become weaker and weaker. In addition, the two new Raman bands at 1296 and 2850 cm(-1) are only observed in the aged monkey cerebral cortex, therefore, the two bands can be considered as a character or "marker" to differentiate the caducity degree with monkey growth In order to further explore the changes, the relative intensity ratios of the Raman band at 1313 cm(-1) to that at 1338 cm(-1) and the Raman band at 2885 cm(-1) to that at 2 932 cm(-1), I1313/I1338 and I2885/I2932, which are the lipid-to-protein ratios, are introduced to denote the degree of the lipid content. The results show that the relative intensity ratios increase significantly with monkey growth, namely, the lipid content in the cerebral cortex increases greatly with monkey growth. So, the authors can deduce that the overmuch lipid is an important cause to induce the caducity. Therefore, the results will be a powerful assistance and valuable parameter to study the order of life growth and diagnose diseases.

Application of magnetic circular dichroism spectroscopy to the optical spectra of natural and irradiated diamonds

International Nuclear Information System (INIS)

Douglas, I.N.; Ruciman, W.A.; Australian National Univ., Canberra. Research School of Physical Sciences)

1977-01-01

The MCD spectra of natural type Ia and electron-irradiated type Ia and type IIa diamonds have been measured. The information obtained from MCD spectroscopy complements that obtained from absorption spectroscopy and can be helpful in the assignment of electronic transitions. (orig.) [de

New formalism for determining excitation spectra of many-body systems

International Nuclear Information System (INIS)

Saito, S.; Zhang, S.B.; Louie, S.G.; Cohen, M.L.

1990-01-01

We present a new general formalism for determining the excitation spectrum of interacting many-body systems. The basic assumption is that the number of the excitations is equal to the number of sites. Within this approximation, it is shown that the density-density response functions with two different pure-imaginary energies determine the excitation spectrum. The method is applied to the valence electrons of sodium clusters of differing sizes in the time-dependent local-density approximation (TDLDA). A jellium-sphere background model is used for the ion cores. The excitation spectra obtained in this way represent well the excitation spectra given by the full TDLDA calculation along the real energy axis. Important collective modes are reproduced very well

ZZ RECOIL/B, Heavy Charged Particle Recoil Spectra Library for Radiation Damage Calculation

International Nuclear Information System (INIS)

Gabriel, T.A.; Amburgey, J.D.; Greene, N.M.

1983-01-01

1 - Description of problem or function: Format: GAM-II group structure; Number of groups: 104 neutron and Recoil-energy groups; Nuclides: Elements Included in Charged-Particle Recoil Data Base: Al, W, Ti, Pb, V, Mg, Cr, Be, Mn, C, Fe, Au, Co, Si, Ni, B-10, Cu, B-11, Zr, N, Nb, Li-6, Mo, Li-7, Ta (Data for Ta-181,Ta-182), O, Origin: ENDF/B-IV cross-section data. A heavy charged-particle recoil data base (primary knock-on atom (PKA) spectra) and an analysis program have been created to assist experimentalists in studying, evaluating, and correlating radiation-damage effects in different neutron environments. Since experimentally obtained controlled thermo-nuclear-reactor-type neutron spectra are not presently available, the data base can be extremely useful in relating currently obtainable radiation damage to that which is anticipated in future fusion devices. However, the usefulness of the data base is not restricted to just CTR needs. Most of the elements of interest to the radiation-damage community and all neutron reactions of any significance for these elements have been processed, using available ENDF/B-IV cross-section data, and are included in the data base. Calculated data such as primary recoil spectra, displacement rates, and gas-production rates, obtained with the data base, for different radiation environments are presented and compared with previous calculations. Primary neutrons with energies up to 20 MeV have been considered. The elements included in the data base are listed in Table I. All neutron reactions of significance for these elements (i.e., elastic, inelastic, (n,2n), (n,3n), (n,p), (n,sigma), (n,gamma), etc.,) which have cross sections available from ENDF/B-IV have been processed and placed in the data base. Table I - Elements Included in Charged-Particle Recoil Data Base: Al, W, Ti, Pb, V, Mg, Cr, Be, Mn, C, Fe, Au, Co, Si, Ni, 10 B, Cu, 11 B, Zr, N, Nb, 6 Li, Mo, 7 Li, Ta (Data for Ta 181 ,Ta 182 ), O. 2 - Method of solution: The neutron

Development of edible films obtained from submicron emulsions based on whey protein concentrate, oil/beeswax and brea gum.

Science.gov (United States)

Cecchini, Juan Pablo; Spotti, María J; Piagentini, Andrea M; Milt, Viviana G; Carrara, Carlos R

2017-06-01

Edible films with whey protein concentrate (WPC) with a lipid component, sunflower oil (O) or beeswax (W), to enhance barrier to water vapor were obtained. Brea gum was used as emulsifier and also as matrix component. In order to achieve emulsion with small and homogeneous droplet size, an ultrasonicator equipment was used after obtaining a pre-emulsion using a blender. The films were made by casting. Effects of lipid fraction on droplet size, zeta potential, mechanical properties, water vapor permeability (WVP), solubility, and optical properties were determined. The droplet size of emulsions with BG decreased when decreasing the lipid content in the formulation. The zeta potential was negative for all the formulations, since the pH was close to 6 for all of them and pI of BG is close to 2.5, and pI of ß-lactoglobulin and α-lactalbumin (main proteins in WPC) are 5.2 and 4.1, respectively. Increasing W or SO content in blended films reduced the tensile strength and puncture resistance significantly. BG and WPC films without lipid presented better mechanical properties. The presence of lipids decreased the WVP, as expected, and those films having BG improved this property. BG films were slightly amber as a result of the natural color of the gum. BG has shown to be a good polysaccharide for emulsifying the lipid fraction and improving the homogeneity and mechanical properties of the films with WPC and beeswax or oil.