Mass Spectral Library Quality Assurance by Inter-Library Comparison

PubMed Central

Wallace, W.E.; Ji, W.; Tchekhovskoi, D.V.; Phinney, K.W.; Stein, S.E.

2017-01-01

A method to discover and correct errors in mass spectral libraries is described. Comparing across a set of highly curated reference libraries compounds that have the same chemical structure quickly identifies entries that are outliers. In cases where three or more entries for the same compound are compared the outlier as determined by visual inspection was almost always found to contain the error. These errors were either in the spectrum itself or in the chemical descriptors that accompanied it. The method is demonstrated on finding errors in compounds of forensic interest in the NIST/EPA/NIH Mass Spectral Library. The target list of compounds checked was the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) mass spectral library. Some examples of errors found are described. A checklist of errors that curators should look for when performing inter-library comparisons is provided. PMID:28127680

The development of retrosynthetic glycan libraries to profile and classify the human serum N-linked glycome.

PubMed

Kronewitter, Scott R; An, Hyun Joo; de Leoz, Maria Lorna; Lebrilla, Carlito B; Miyamoto, Suzanne; Leiserowitz, Gary S

2009-06-01

Annotation of the human serum N-linked glycome is a formidable challenge but is necessary for disease marker discovery. A new theoretical glycan library was constructed and proposed to provide all possible glycan compositions in serum. It was developed based on established glycobiology and retrosynthetic state-transition networks. We find that at least 331 compositions are possible in the serum N-linked glycome. By pairing the theoretical glycan mass library with a high mass accuracy and high-resolution MS, human serum glycans were effectively profiled. Correct isotopic envelope deconvolution to monoisotopic masses and the high mass accuracy instruments drastically reduced the amount of false composition assignments. The high throughput capacity enabled by this library permitted the rapid glycan profiling of large control populations. With the use of the library, a human serum glycan mass profile was developed from 46 healthy individuals. This paper presents a theoretical N-linked glycan mass library that was used for accurate high-throughput human serum glycan profiling. Rapid methods for evaluating a patient's glycome are instrumental for studying glycan-based markers.

RIPL - Reference Input Parameter Library for Calculation of Nuclear Reactions and Nuclear Data Evaluations

NASA Astrophysics Data System (ADS)

Capote, R.; Herman, M.; Obložinský, P.; Young, P. G.; Goriely, S.; Belgya, T.; Ignatyuk, A. V.; Koning, A. J.; Hilaire, S.; Plujko, V. A.; Avrigeanu, M.; Bersillon, O.; Chadwick, M. B.; Fukahori, T.; Ge, Zhigang; Han, Yinlu; Kailas, S.; Kopecky, J.; Maslov, V. M.; Reffo, G.; Sin, M.; Soukhovitskii, E. Sh.; Talou, P.

2009-12-01

We describe the physics and data included in the Reference Input Parameter Library, which is devoted to input parameters needed in calculations of nuclear reactions and nuclear data evaluations. Advanced modelling codes require substantial numerical input, therefore the International Atomic Energy Agency (IAEA) has worked extensively since 1993 on a library of validated nuclear-model input parameters, referred to as the Reference Input Parameter Library (RIPL). A final RIPL coordinated research project (RIPL-3) was brought to a successful conclusion in December 2008, after 15 years of challenging work carried out through three consecutive IAEA projects. The RIPL-3 library was released in January 2009, and is available on the Web through http://www-nds.iaea.org/RIPL-3/. This work and the resulting database are extremely important to theoreticians involved in the development and use of nuclear reaction modelling (ALICE, EMPIRE, GNASH, UNF, TALYS) both for theoretical research and nuclear data evaluations. The numerical data and computer codes included in RIPL-3 are arranged in seven segments: MASSES contains ground-state properties of nuclei for about 9000 nuclei, including three theoretical predictions of masses and the evaluated experimental masses of Audi et al. (2003). DISCRETE LEVELS contains 117 datasets (one for each element) with all known level schemes, electromagnetic and γ-ray decay probabilities available from ENSDF in October 2007. NEUTRON RESONANCES contains average resonance parameters prepared on the basis of the evaluations performed by Ignatyuk and Mughabghab. OPTICAL MODEL contains 495 sets of phenomenological optical model parameters defined in a wide energy range. When there are insufficient experimental data, the evaluator has to resort to either global parameterizations or microscopic approaches. Radial density distributions to be used as input for microscopic calculations are stored in the MASSES segment. LEVEL DENSITIES contains phenomenological parameterizations based on the modified Fermi gas and superfluid models and microscopic calculations which are based on a realistic microscopic single-particle level scheme. Partial level densities formulae are also recommended. All tabulated total level densities are consistent with both the recommended average neutron resonance parameters and discrete levels. GAMMA contains parameters that quantify giant resonances, experimental gamma-ray strength functions and methods for calculating gamma emission in statistical model codes. The experimental GDR parameters are represented by Lorentzian fits to the photo-absorption cross sections for 102 nuclides ranging from 51V to 239Pu. FISSION includes global prescriptions for fission barriers and nuclear level densities at fission saddle points based on microscopic HFB calculations constrained by experimental fission cross sections.

RIPL - Reference Input Parameter Library for Calculation of Nuclear Reactions and Nuclear Data Evaluations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Capote, R.; Herman, M.; Oblozinsky, P.

We describe the physics and data included in the Reference Input Parameter Library, which is devoted to input parameters needed in calculations of nuclear reactions and nuclear data evaluations. Advanced modelling codes require substantial numerical input, therefore the International Atomic Energy Agency (IAEA) has worked extensively since 1993 on a library of validated nuclear-model input parameters, referred to as the Reference Input Parameter Library (RIPL). A final RIPL coordinated research project (RIPL-3) was brought to a successful conclusion in December 2008, after 15 years of challenging work carried out through three consecutive IAEA projects. The RIPL-3 library was released inmore » January 2009, and is available on the Web through (http://www-nds.iaea.org/RIPL-3/). This work and the resulting database are extremely important to theoreticians involved in the development and use of nuclear reaction modelling (ALICE, EMPIRE, GNASH, UNF, TALYS) both for theoretical research and nuclear data evaluations. The numerical data and computer codes included in RIPL-3 are arranged in seven segments: MASSES contains ground-state properties of nuclei for about 9000 nuclei, including three theoretical predictions of masses and the evaluated experimental masses of Audi et al. (2003). DISCRETE LEVELS contains 117 datasets (one for each element) with all known level schemes, electromagnetic and {gamma}-ray decay probabilities available from ENSDF in October 2007. NEUTRON RESONANCES contains average resonance parameters prepared on the basis of the evaluations performed by Ignatyuk and Mughabghab. OPTICAL MODEL contains 495 sets of phenomenological optical model parameters defined in a wide energy range. When there are insufficient experimental data, the evaluator has to resort to either global parameterizations or microscopic approaches. Radial density distributions to be used as input for microscopic calculations are stored in the MASSES segment. LEVEL DENSITIES contains phenomenological parameterizations based on the modified Fermi gas and superfluid models and microscopic calculations which are based on a realistic microscopic single-particle level scheme. Partial level densities formulae are also recommended. All tabulated total level densities are consistent with both the recommended average neutron resonance parameters and discrete levels. GAMMA contains parameters that quantify giant resonances, experimental gamma-ray strength functions and methods for calculating gamma emission in statistical model codes. The experimental GDR parameters are represented by Lorentzian fits to the photo-absorption cross sections for 102 nuclides ranging from {sup 51}V to {sup 239}Pu. FISSION includes global prescriptions for fission barriers and nuclear level densities at fission saddle points based on microscopic HFB calculations constrained by experimental fission cross sections.« less

RIPL-Reference Input Parameter Library for Calculation of Nuclear Reactions and Nuclear Data Evaluations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Capote, R.; Herman, M.; Capote,R.

We describe the physics and data included in the Reference Input Parameter Library, which is devoted to input parameters needed in calculations of nuclear reactions and nuclear data evaluations. Advanced modelling codes require substantial numerical input, therefore the International Atomic Energy Agency (IAEA) has worked extensively since 1993 on a library of validated nuclear-model input parameters, referred to as the Reference Input Parameter Library (RIPL). A final RIPL coordinated research project (RIPL-3) was brought to a successful conclusion in December 2008, after 15 years of challenging work carried out through three consecutive IAEA projects. The RIPL-3 library was released inmore » January 2009, and is available on the Web through http://www-nds.iaea.org/RIPL-3/. This work and the resulting database are extremely important to theoreticians involved in the development and use of nuclear reaction modelling (ALICE, EMPIRE, GNASH, UNF, TALYS) both for theoretical research and nuclear data evaluations. The numerical data and computer codes included in RIPL-3 are arranged in seven segments: MASSES contains ground-state properties of nuclei for about 9000 nuclei, including three theoretical predictions of masses and the evaluated experimental masses of Audi et al. (2003). DISCRETE LEVELS contains 117 datasets (one for each element) with all known level schemes, electromagnetic and {gamma}-ray decay probabilities available from ENSDF in October 2007. NEUTRON RESONANCES contains average resonance parameters prepared on the basis of the evaluations performed by Ignatyuk and Mughabghab. OPTICAL MODEL contains 495 sets of phenomenological optical model parameters defined in a wide energy range. When there are insufficient experimental data, the evaluator has to resort to either global parameterizations or microscopic approaches. Radial density distributions to be used as input for microscopic calculations are stored in the MASSES segment. LEVEL DENSITIES contains phenomenological parameterizations based on the modified Fermi gas and superfluid models and microscopic calculations which are based on a realistic microscopic single-particle level scheme. Partial level densities formulae are also recommended. All tabulated total level densities are consistent with both the recommended average neutron resonance parameters and discrete levels. GAMMA contains parameters that quantify giant resonances, experimental gamma-ray strength functions and methods for calculating gamma emission in statistical model codes. The experimental GDR parameters are represented by Lorentzian fits to the photo-absorption cross sections for 102 nuclides ranging from {sup 51}V to {sup 239}Pu. FISSION includes global prescriptions for fission barriers and nuclear level densities at fission saddle points based on microscopic HFB calculations constrained by experimental fission cross sections.« less

Books on Atomic Energy for Adults and Children, Understanding the Atom Series.

ERIC Educational Resources Information Center

Atomic Energy Commission, Oak Ridge, TN. Div. of Technical Information.

This booklet in the "Understanding the Atom" series includes annotated bibliographies for children (grade level indicated) and adults. Over 100 basic books on atomic energy and closely related subjects are alphabetized by title and an author index. A list of publisher addresses are included. A brief introduction to library usage is given. The…

Study on Mass Conservation Techniques for Treatment of Library and Archives Material.

ERIC Educational Resources Information Center

Wachter, Wolfgang, Ed.

This document outlines the present state of development in mass restoration of library and archive materials and relates it to the economic, technical, and aesthetic aspects of various conservation and restoration methods, and discusses their implications for the formation of preservation policies in libraries. Ill effects to library materials…

ARC: An open-source library for calculating properties of alkali Rydberg atoms

NASA Astrophysics Data System (ADS)

Šibalić, N.; Pritchard, J. D.; Adams, C. S.; Weatherill, K. J.

2017-11-01

We present an object-oriented Python library for the computation of properties of highly-excited Rydberg states of alkali atoms. These include single-body effects such as dipole matrix elements, excited-state lifetimes (radiative and black-body limited) and Stark maps of atoms in external electric fields, as well as two-atom interaction potentials accounting for dipole and quadrupole coupling effects valid at both long and short range for arbitrary placement of the atomic dipoles. The package is cross-referenced to precise measurements of atomic energy levels and features extensive documentation to facilitate rapid upgrade or expansion by users. This library has direct application in the field of quantum information and quantum optics which exploit the strong Rydberg dipolar interactions for two-qubit gates, robust atom-light interfaces and simulating quantum many-body physics, as well as the field of metrology using Rydberg atoms as precise microwave electrometers. Program Files doi:http://dx.doi.org/10.17632/hm5n8w628c.1 Licensing provisions: BSD-3-Clause Programming language: Python 2.7 or 3.5, with C extension External Routines: NumPy [1], SciPy [1], Matplotlib [2] Nature of problem: Calculating atomic properties of alkali atoms including lifetimes, energies, Stark shifts and dipole-dipole interaction strengths using matrix elements evaluated from radial wavefunctions. Solution method: Numerical integration of radial Schrödinger equation to obtain atomic wavefunctions, which are then used to evaluate dipole matrix elements. Properties are calculated using second order perturbation theory or exact diagonalisation of the interaction Hamiltonian, yielding results valid even at large external fields or small interatomic separation. Restrictions: External electric field fixed to be parallel to quantisation axis. Supplementary material: Detailed documentation (.html), and Jupyter notebook with examples and benchmarking runs (.html and .ipynb). [1] T.E. Oliphant, Comput. Sci. Eng. 9, 10 (2007). http://www.scipy.org/. [2] J.D. Hunter, Comput. Sci. Eng. 9, 90 (2007). http://matplotlib.org/.

Block copolymer libraries: modular versatility of the macromolecular Lego system.

PubMed

Lohmeijer, Bas G G; Wouters, Daan; Yin, Zhihui; Schubert, Ulrich S

2004-12-21

The synthesis and characterization of a new 4 x 4 library of block copolymers based on polystyrene and poly(ethylene oxide) connected by an asymmetrical octahedral bis(terpyridine) ruthenium complex at the block junction are described, while initial studies on the thin film morphology of the components of the library are presented by the use of Atomic Force Microscopy, demonstrating the impact of a library approach to derive structure-property relationships.

Feed Me! Rethinking Traditional Modes of Library Access and Content Delivery

ERIC Educational Resources Information Center

Hutchens, Chad; Clark, Jason

2008-01-01

At their core, XML feeds are content-delivery vehicles. This fact has not always been highlighted in library conversations surrounding RSS and ATOM. The authors have looked to extend the conversation by offering a proof of concept application using RSS as a means to deliver all types of library data: PDFs, docs, images, video--to people where and…

[Progress in the spectral library based protein identification strategy].

PubMed

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.

DiffPy-CMI-Python libraries for Complex Modeling Initiative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

Atomic Mass and Nuclear Binding Energy for I-131 (Iodine)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope I-131 (Iodine, atomic number Z = 53, mass number A = 131).

Atomic Mass and Nuclear Binding Energy for F-22 (Fluorine)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope F-22 (Fluorine, atomic number Z = 9, mass number A = 22).

Evaluation of the sensitivity of the 'Wiley registry of tandem mass spectral data, MSforID' with MS/MS data of the 'NIST/NIH/EPA mass spectral library'.

PubMed

Oberacher, Herbert; Whitley, Graeme; Berger, Bernd

2013-04-01

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the 'Wiley Registry of Tandem Mass Spectral Data, MSforID' (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the 'NIST/NIH/EPA Mass Spectral Library' (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross-validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.

Mass Digitization of Books

ERIC Educational Resources Information Center

Coyle, Karen

2006-01-01

Mass digitization of the bound volumes that we generally call "books" has begun, and, thanks to the interest in Google and all that it does, it is getting widespread media attention. The Open Content Alliance (OCA), a library initiative formed after Google announced its library book digitization project, has brought library digitization projects…

ION COMPOSITION ELUCIDATION (ICE): A HIGH ...

EPA Pesticide Factsheets

Identifying compounds found in the environment without knowledge of their origin is a very difficult analytical problem. Comparison of the low resolution mass spectrum of a compound with those in the NIST or Wiley mass spectral libraries can provide a tentative identification when the mass spectrum is free of interferences, at least several prominent ions are observed in the mass spectrum, the mass spectrum is in the library, and only one plausible match is found. Because these libraries contain only 226,334 distinct compounds (1) compared to the 16 million compounds that have been synthesized or isolated from natural sources (2), most compounds are not found in the libraries. In addition, most compounds are ionic, too polar, too thermolabile, or too high in mass to traverse a GC column or to volatilize from a probe. For these compounds, liquid sample introduction with electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) provides few fragment ions for pattern matching, and adduct ions complicate the mass spectra. Commercial ESI and APCI mass spectral libraries are not available. Consequently, low resolution mass spectrometry cannot identify most compounds-. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support

Atomic Mass and Nuclear Binding Energy for U-287 (Uranium)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope U-287 (Uranium, atomic number Z = 92, mass number A = 287).

Atomic Mass and Nuclear Binding Energy for Ac-212 (Actinium)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Ac-212 (Actinium, atomic number Z = 89, mass number A = 212).

Combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for qualitative analysis of drugs.

PubMed

Pavlic, Marion; Libiseller, Kathrin; Oberacher, Herbert

2006-09-01

The potential of the combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for the identification of therapeutic and illicit drugs has been evaluated. Reserpine was used for standardizing experimental conditions and for characterization of the performance of the applied mass spectrometric system. Experiments revealed that because of the mass accuracy, the stability of calibration, and the reproducibility of fragmentation, the QqTOF mass spectrometer is an appropriate platform for establishment of a tandem-mass-spectral library. Three-hundred and nineteen substances were used as reference samples to build the spectral library. For each reference compound, product-ion spectra were acquired at ten different collision-energy values between 5 eV and 50 eV. For identification of unknown compounds, a library search algorithm was developed. The closeness of matching between a measured product-ion spectrum and a spectrum stored in the library was characterized by a value called "match probability", which took into account the number of matched fragment ions, the number of fragment ions observed in the two spectra, and the sum of the intensity differences calculated for matching fragments. A large value for the match probability indicated a close match between the measured and the reference spectrum. A unique feature of the library search algorithm-an implemented spectral purification option-enables characterization of multi-contributor fragment-ion spectra. With the aid of this software feature, substances comprising only 1.0% of the total amount of binary mixtures were unequivocally assigned, in addition to the isobaric main contributors. The spectral library was successfully applied to the characterization of 39 forensic casework samples.

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

PubMed Central

Dupradeau, François-Yves; Cézard, Christine; Lelong, Rodolphe; Stanislawiak, Élodie; Pêcher, Julien; Delepine, Jean Charles; Cieplak, Piotr

2008-01-01

The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications. PMID:17962302

Natural product-like virtual libraries: recursive atom-based enumeration.

PubMed

Yu, Melvin J

2011-03-28

A new molecular enumerator is described that allows chemically and architecturally diverse sets of natural product-like and drug-like structures to be generated from a core structure as simple as a single carbon atom or as complex as a polycyclic ring system. Integrated with a rudimentary machine-learning algorithm, the enumerator has the ability to assemble biased virtual libraries enriched in compounds predicted to meet target criteria. The ability to dynamically generate relatively small focused libraries in a recursive manner could reduce the computational time and infrastructure necessary to construct and manage extremely large static libraries. Depending on enumeration conditions, natural product-like structures can be produced with a wide range of heterocyclic and alicyclic ring assemblies. Because natural products represent a proven source of validated structures for identifying and designing new drug candidates, mimicking the structural and topological diversity found in nature with a dynamic set of virtual natural product-like compounds may facilitate the creation of new ideas for novel, biologically relevant lead structures in areas of uncharted chemical space.

Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: application to the Vps27 UIM-1-Ubiquitin complex.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2014-02-01

Reduced point charge models of amino acids are designed, (i) from local extrema positions in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions, and (ii) from local maxima positions in promolecular electron density distribution functions. Corresponding charge values are fitted versus all-atom Amber99 MEPs. To easily generate reduced point charge models for protein structures, libraries of amino acid templates are built. The program GROMACS is used to generate stable Molecular Dynamics trajectories of an Ubiquitin-ligand complex (PDB: 1Q0W), under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a nul mass and radius. The results illustrate how the intra- and inter-molecular H-bond interactions are affected by the degree of reduction of the point charge models and give directions for their implementation; a special attention to the atoms selected to locate the virtual sites and to the Coulomb-14 interactions is needed. Results obtained at various temperatures suggest that the use of reduced point charge models allows to probe local potential hyper-surface minima that are similar to the all-atom ones, but are characterized by lower energy barriers. It enables to generate various conformations of the protein complex more rapidly than the all-atom point charge representation. Copyright © 2013 Elsevier Inc. All rights reserved.

On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm.

PubMed

Oberacher, Herbert; Pavlic, Marion; Libiseller, Kathrin; Schubert, Birthe; Sulyok, Michael; Schuhmacher, Rainer; Csaszar, Edina; Köfeler, Harald C

2009-04-01

A sophisticated matching algorithm developed for highly efficient identity search within tandem mass spectral libraries is presented. For the optimization of the search procedure a collection of 410 tandem mass spectra corresponding to 22 compounds was used. The spectra were acquired in three different laboratories on four different instruments. The following types of tandem mass spectrometric instruments were used: quadrupole-quadrupole-time-of-flight (QqTOF), quadrupole-quadrupole-linear ion trap (QqLIT), quadrupole-quadrupole-quadrupole (QqQ), and linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer (LIT-FTICR). The obtained spectra were matched to an established MS/MS-spectral library that contained 3759 MS/MS-spectra corresponding to 402 different reference compounds. All 22 test compounds were part of the library. A dynamic intensity cut-off, the search for neutral losses, and optimization of the formula used to calculate the match probability were shown to significantly enhance the performance of the presented library search approach. With the aid of these features the average number of correct assignments was increased to 98%. For statistical evaluation of the match reliability the set of fragment ion spectra was extended with 300 spectra corresponding to 100 compounds not included in the reference library. Performance was checked with the aid of receiver operating characteristic (ROC) curves. Using the magnitude of the match probability as well as the precursor ion mass as benchmarks to rate the obtained top hit, overall correct classification of a compound being included or not included in the mass spectrometric library, was obtained in more than 95% of cases clearly indicating a high predictive accuracy of the established matching procedure. Copyright (c) 2009 John Wiley & Sons, Ltd.

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library.

PubMed

Lee, Hyeyoung; Cuthbertson, Daniel J; Otter, Don E; Barile, Daniela

2016-08-17

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching.

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library

PubMed Central

Lee, Hyeyoung; Cuthbertson, Daniel J.; Otter, Don E.; Barile, Daniela

2018-01-01

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching. PMID:27428379

The atomic simulation environment-a Python library for working with atoms.

PubMed

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The atomic simulation environment—a Python library for working with atoms

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

2017-07-01

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Atoms and Molecules. Physical Science in Action[TM]. Schlessinger Science Library. [Videotape].

ERIC Educational Resources Information Center

2000

There are more than 20 million known substances in the universe, and they are all made of the same basic ingredients--atoms and molecules. In this fun and engaging program, kids will learn about the three main subatomic particles--protons, neutrons and electrons--as well as the forces that keep atoms and molecules together. They'll discover how…

Library of Congress Mass Book Deacidification Facility. Hearing before the Committee on Rules and Administration, United States Senate, Ninety-Eighth Congress, Second Session, on S. 2418, Providing for the Library of Congress Mass Book Deacidification Facility.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Committee on Rules and Administration.

This document presents testimony heard on S. 2418, a bill to authorize the Librarian of Congress to construct the Library of Congress Mass Book Deacidification Facility at Fort Detrick, near Frederick, Maryland, subject to the supervision and construction authority of a federal, civilian, or military agency. The facility would be used to…

The Sun as a Library for High-Energy Astrophysics

NASA Astrophysics Data System (ADS)

Smith, David M.

2017-08-01

Our maternal G dwarf star gives us life, light, warmth, and a surprisingly well-stocked library of high-energy phenomena to study and compare to more distant, violent objects. I will give a survey of what we see from the Sun -- X-rays, gamma-rays, radio emission, energetic neutral atoms, neutrinos, and particles accelerated in the low and high corona -- and of the physical processes and emission mechanisms thought to be involved, including magnetic reconnection, Fermi acceleration, thermal and nonthermal bremsstrahlung, coherent and incoherent radio emission, and gamma-ray line mechanisms: nuclear de-excitation, pion decay, neutron capture, and positron annihilation. I will outline the range of transient coronal behaviors from hypothetical nanoflares below the limit of individual detection to coronal mass ejections and the largest flares, comparing the latter to what is observed from other stars. Throughout the presentation, I will look for parallels with a variety of cosmic objects and observations, with no guarantee that any particular comparison is quantitatively appropriate. Finally, I will advertise the recent contributions of focusing hard X-ray observations with NuSTAR and the FOXSI rockets.

Equilibrium vortex lattices of a binary rotating atomic Bose–Einstein condensate with unequal atomic masses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Biao; Wang, Lin-Xue; Chen, Guang-Ping

We perform a detailed numerical study of the equilibrium ground-state structures of a binary rotating Bose–Einstein condensate with unequal atomic masses. Our results show that the ground-state distribution and its related vortex configurations are complex events that differ markedly depending strongly on the strength of rotation frequency, as well as on the ratio of atomic masses. We also discuss the structures and radii of the clouds, the number and the size of the core region of the vortices, as a function of the rotation frequency, and of the ratio of atomic masses, and the analytical results agree well with ourmore » numerical simulations. This work may open an alternate way in the quantum control of the binary rotating quantum gases with unequal atomic masses. - Highlights: • A binary quantum gases with unequal atomic masses is considered. • Effects of the ratio of atomic masses and rotation frequency are discussed in full parameter space. • The detailed information about both the cloud and vortices are also discussed.« less

Evaluation of Three MALDI-TOF Mass Spectrometry Libraries for the Identification of Filamentous Fungi in Three Clinical Microbiology Laboratories in Manitoba, Canada.

PubMed

Stein, Markus; Tran, Vanessa; Nichol, Kimberly A; Lagacé-Wiens, Philippe; Pieroni, Peter; Adam, Heather J; Turenne, Christine; Walkty, Andrew J; Normand, Anne-Cécile; Hendrickx, Marijke; Piarroux, Renaud; Karlowsky, James A

2018-06-12

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify bacterial pathogens and yeasts, but not for the identification of moulds. Recent progress in extraction protocols and the composition of comparative libraries support potential application of MALDI-TOF MS for mould identification in clinical microbiology laboratories. We evaluated the performance of the Bruker Microflex ™ MALDI-TOF MS instrument (Billerica, MA, USA) to identify clinical isolates and reference strains of moulds using three libraries, the Bruker mould library, the National Institutes of Health (NIH) library, and the Mass Spectrometry Identification (MSI) online library, and compared those results to conventional (morphological) and molecular (18S/ITS; gold standard) identification methods. All three libraries demonstrated greater accuracy in genus identification (≥94.9%) than conventional methods (86.4%). MALDI-TOF MS identified 73.3% of isolates to species-level compared to only 31.7% by conventional methods. The MSI library demonstrated the highest rate of species-level identification (72.0%) compared to NIH (19.5%) and Bruker (13.6%) libraries. Greater than 20% of moulds remained unidentified to species-level by all three MALDI-TOF MS libraries primarily because of library limitations or imperfect spectra. The overall identification rate of each MALDI-TOF MS library depended on the number of species and the number of spectra representing each species in the library. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Atomic masses 1993. The 1993 atomic mass evaluation

NASA Astrophysics Data System (ADS)

Audi, G.; Wapstra, A. H.

1993-11-01

The 1993 atomic mass evaluation by G. Audi and A.H. Wapstra is documented. The resulting data files containing recommended values of atomic masses, obtained by experiment of systematics, and related data such as reaction and separation energies are described. The data files can be obtained through online services from several nuclear data centers or on magnetic tape, free of charge.

Mass Audience Circulation: Library Service in the U.S.S.R.

ERIC Educational Resources Information Center

Zhidkov, Grigory

1983-01-01

Presents overview of state of Soviet Union library service comprising 350,000 libraries, including national, governmental department, and public group (trade unions, professional associations) libraries. Training of Soviet librarians, library cooperation, national planning and funding, cultural exchange and cooperation, supporting international…

1986-87 atomic mass predictions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haustein, P.E.

A project to perform a comprehensive update of the atomic mass predictions has recently been concluded and will be published shortly in Atomic Data and Nuclear Data Tables. The project evolved from an ongoing comparison between available mass predictions and reports of newly measured masses of isotopes throughout the mass surface. These comparisons have highlighted a variety of features in current mass models which are responsible for predictions that diverge from masses determined experimentally. The need for a comprehensive update of the atomic mass predictions was therefore apparent and the project was organized and began at the last mass conferencemore » (AMCO-VII). Project participants included: Pape and Anthony; Dussel, Caurier and Zuker; Moeller and Nix; Moeller, Myers, Swiatecki and Treiner; Comay, Kelson, and Zidon; Satpathy and Nayak; Tachibana, Uno, Yamada and Yamada; Spanier and Johansson; Jaenecke and Masson; and Wapstra, Audi and Hoekstra. An overview of the new atomic mass predictions may be obtained by written request.« less

The 1986-87 atomic mass predictions

NASA Astrophysics Data System (ADS)

Haustein, P. E.

1987-12-01

A project to perform a comprehensive update of the atomic mass predictions has recently been concluded and will be published shortly in Atomic Data and Nuclear Data Tables. The project evolved from an ongoing comparison between available mass predictions and reports of newly measured masses of isotopes throughout the mass surface. These comparisons have highlighted a variety of features in current mass models which are responsible for predictions that diverge from masses determined experimentally. The need for a comprehensive update of the atomic mass predictions was therefore apparent and the project was organized and began at the last mass conference (AMCO-VII). Project participants included: Pape and Anthony; Dussel, Caurier and Zuker; Möller and Nix; Möller, Myers, Swiatecki and Treiner; Comay, Kelson, and Zidon; Satpathy and Nayak; Tachibana, Uno, Yamada and Yamada; Spanier and Johansson; Jänecke and Masson; and Wapstra, Audi and Hoekstra. An overview of the new atomic mass predictions may be obtained by written request.

Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

PubMed

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

INTRIGOSS: A new Library of High Resolution Synthetic Spectra

NASA Astrophysics Data System (ADS)

Franchini, Mariagrazia; Morossi, Carlo; Di Marcancantonio, Paolo; Chavez, Miguel; GES-Builders

2018-01-01

INTRIGOSS (INaf Trieste Grid Of Synthetic Spectra) is a new High Resolution (HiRes) synthetic spectral library designed for studying F, G, and K stars. The library is based on atmosphere models computed with specified individual element abundances via ATLAS12 code. Normalized SPectra (NSP) and surface Flux SPectra (FSP), in the 4800-5400 Å wavelength range, were computed by means of the SPECTRUM code. The synthetic spectra are computed with an atomic and bi-atomic molecular line list including "bona fide" Predicted Lines (PLs) built by tuning loggf to reproduce very high SNR Solar spectrum and the UVES-U580 spectra of five cool giants extracted from the Gaia-ESO survey (GES). The astrophysical gf-values were then assessed by using more than 2000 stars with homogenous and accurate atmosphere parameters and detailed chemical composition from GES. The validity and greater accuracy of INTRIGOSS NSPs and FSPs with respect to other available spectral libraries is discussed. INTRIGOSS will be available on the web and will be a valuable tool for both stellar atmospheric parameters and stellar population studies.

High impact technologies for natural products screening.

PubMed

Koehn, Frank E

2008-01-01

Natural products have historically been a rich source of lead molecules in drug discovery. However, natural products have been de-emphasized as high throughput screening resources in the recent past, in part because of difficulties in obtaining high quality natural products screening libraries, or in applying modern screening assays to these libraries. In addition, natural products programs based on screening of extract libraries, bioassay-guided isolation, structure elucidation and subsequent production scale-up are challenged to meet the rapid cycle times that are characteristic of the modern HTS approach. Fortunately, new technologies in mass spectrometry, NMR and other spectroscopic techniques can greatly facilitate the first components of the process - namely the efficient creation of high-quality natural products libraries, bimolecular target or cell-based screening, and early hit characterization. The success of any high throughput screening campaign is dependent on the quality of the chemical library. The construction and maintenance of a high quality natural products library, whether based on microbial, plant, marine or other sources is a costly endeavor. The library itself may be composed of samples that are themselves mixtures - such as crude extracts, semi-pure mixtures or single purified natural products. Each of these library designs carries with it distinctive advantages and disadvantages. Crude extract libraries have lower resource requirements for sample preparation, but high requirements for identification of the bioactive constituents. Pre-fractionated libraries can be an effective strategy to alleviate interferences encountered with crude libraries, and may shorten the time needed to identify the active principle. Purified natural product libraries require substantial resources for preparation, but offer the advantage that the hit detection process is reduced to that of synthetic single component libraries. Whether the natural products library consists of crude or partially fractionated mixtures, the library contents should be profiled to identify the known components present - a process known as dereplication. The use of mass spectrometry and HPLC-mass spectrometry together with spectral databases is a powerful tool in the chemometric profiling of bio-sources for natural product production. High throughput, high sensitivity flow NMR is an emerging tool in this area as well. Whether by cell based or biomolecular target based assays, screening of natural product extract libraries continues to furnish novel lead molecules for further drug development, despite challenges in the analysis and prioritization of natural products hits. Spectroscopic techniques are now being used to directly screen natural product and synthetic libraries. Mass spectrometry in the form of methods such as ESI-ICRFTMS, and FACS-MS as well as NMR methods such as SAR by NMR and STD-NMR have been utilized to effectively screen molecular libraries. Overall, emerging advances in mass spectrometry, NMR and other technologies are making it possible to overcome the challenges encountered in screening natural products libraries in today's drug discovery environment. As we apply these technologies and develop them even further, we can look forward to increased impact of natural products in the HTS based drug discovery.

PTools: an opensource molecular docking library

PubMed Central

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-01-01

Background Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. Results We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. Conclusion The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation. PMID:19409097

PTools: an opensource molecular docking library.

PubMed

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-05-01

Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.

MCNP6.1 simulations for low-energy atomic relaxation: Code-to-code comparison with GATEv7.2, PENELOPE2014, and EGSnrc

NASA Astrophysics Data System (ADS)

Jung, Seongmoon; Sung, Wonmo; Lee, Jaegi; Ye, Sung-Joon

2018-01-01

Emerging radiological applications of gold nanoparticles demand low-energy electron/photon transport calculations including details of an atomic relaxation process. Recently, MCNP® version 6.1 (MCNP6.1) has been released with extended cross-sections for low-energy electron/photon, subshell photoelectric cross-sections, and more detailed atomic relaxation data than the previous versions. With this new feature, the atomic relaxation process of MCNP6.1 has not been fully tested yet with its new physics library (eprdata12) that is based on the Evaluated Atomic Data Library (EADL). In this study, MCNP6.1 was compared with GATEv7.2, PENELOPE2014, and EGSnrc that have been often used to simulate low-energy atomic relaxation processes. The simulations were performed to acquire both photon and electron spectra produced by interactions of 15 keV electrons or photons with a 10-nm-thick gold nano-slab. The photon-induced fluorescence X-rays from MCNP6.1 fairly agreed with those from GATEv7.2 and PENELOPE2014, while the electron-induced fluorescence X-rays of the four codes showed more or less discrepancies. A coincidence was observed in the photon-induced Auger electrons simulated by MCNP6.1 and GATEv7.2. A recent release of MCNP6.1 with eprdata12 can be used to simulate the photon-induced atomic relaxation.

Broad screening and identification of β-agonists in feed and animal body fluid and tissues using ultra-high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry combined with spectra library search.

PubMed

Li, Tingting; Cao, Jingjing; Li, Zhen; Wang, Xian; He, Pingli

2016-02-01

Broad screening and identification of β-agonists in feed, serum, urine, muscle and liver samples was achieved in a quick and highly sensitive manner using ultra high performance liquid chromatography-quadrupole-orbitrap high resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) combined with a spectra library search. Solid-phase extraction technology was employed for sample purification and enrichment. After extraction and purification, the samples were analyzed using a Q-Orbitrap high-resolution mass spectrometer under full-scan and data-dependent MS/MS mode. The acquired mass spectra were compared with an in-house library (compound library and MS/MS mass spectral library) built with TraceFinder Software which contained the M/Z of the precursor ion, chemical formula, retention time, character fragment ions and the entire MS/MS spectra of 32 β-agonist standards. Screening was achieved by comparing 5 key mass spectral results and positive matches were marked. Using the developed method, the identification results from 10 spiked samples and 238 actual samples indicated that only 2% of acquired mass spectra produced false identities. The method validation results showed that the limit of detection ranged from 0.021-3.854 μg kg(-1)and 0.015-1.198 ng mL(-1) for solid and liquid samples, respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Building Mass Spectrometry Spectral Libraries of Human Cancer Cell Lines].

PubMed

Faktor, J; Bouchal, P

Cancer research often focuses on protein quantification in model cancer cell lines and cancer tissues. SWATH (sequential windowed acquisition of all theoretical fragment ion spectra), the state of the art method, enables the quantification of all proteins included in spectral library. Spectral library contains fragmentation patterns of each detectable protein in a sample. Thorough spectral library preparation will improve quantitation of low abundant proteins which usually play an important role in cancer. Our research is focused on the optimization of spectral library preparation aimed at maximizing the number of identified proteins in MCF-7 breast cancer cell line. First, we optimized the sample preparation prior entering the mass spectrometer. We examined the effects of lysis buffer composition, peptide dissolution protocol and the material of sample vial on the number of proteins identified in spectral library. Next, we optimized mass spectrometry (MS) method for spectral library data acquisition. Our thorough optimized protocol for spectral library building enabled the identification of 1,653 proteins (FDR < 1%) in 1 µg of MCF-7 lysate. This work contributed to the enhancement of protein coverage in SWATH digital biobanks which enable quantification of arbitrary protein from physically unavailable samples. In future, high quality spectral libraries could play a key role in preparing of patient proteome digital fingerprints.Key words: biomarker - mass spectrometry - proteomics - digital biobanking - SWATH - protein quantificationThis work was supported by the project MEYS - NPS I - LO1413.The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 7. 5. 2016Accepted: 9. 6. 2016.

Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition.

PubMed

Bruderer, Tobias; Varesio, Emmanuel; Hidasi, Anita O; Duchoslav, Eva; Burton, Lyle; Bonner, Ron; Hopfgartner, Gérard

2018-03-01

High-quality mass spectral libraries have become crucial in mass spectrometry-based metabolomics. Here, we investigate a workflow to generate accurate mass discrete and composite spectral libraries for metabolite identification and for SWATH mass spectrometry data processing. Discrete collision energy (5-100 eV) accurate mass spectra were collected for 532 metabolites from the human metabolome database (HMDB) by flow injection analysis and compiled into composite spectra over a large collision energy range (e.g., 10-70 eV). Full scan response factors were also calculated. Software tools based on accurate mass and predictive fragmentation were specially developed and found to be essential for construction and quality control of the spectral library. First, elemental compositions constrained by the elemental composition of the precursor ion were calculated for all fragments. Secondly, all possible fragments were generated from the compound structure and were filtered based on their elemental compositions. From the discrete spectra, it was possible to analyze the specific fragment form at each collision energy and it was found that a relatively large collision energy range (10-70 eV) gives informative MS/MS spectra for library searches. From the composite spectra, it was possible to characterize specific neutral losses as radical losses using in silico fragmentation. Radical losses (generating radical cations) were found to be more prominent than expected. From 532 metabolites, 489 provided a signal in positive mode [M+H] + and 483 in negative mode [M-H] - . MS/MS spectra were obtained for 399 compounds in positive mode and for 462 in negative mode; 329 metabolites generated suitable spectra in both modes. Using the spectral library, LC retention time, response factors to analyze data-independent LC-SWATH-MS data allowed the identification of 39 (positive mode) and 72 (negative mode) metabolites in a plasma pool sample (total 92 metabolites) where 81 previously were reported in HMDB to be found in plasma. Graphical abstract Library generation workflow for LC-SWATH MS, using collision energy spread, accurate mass, and fragment annotation.

Applying Tandem Mass Spectral Libraries for Solving the Critical Assessment of Small Molecule Identification (CASMI) LC/MS Challenge 2012

PubMed Central

Oberacher, Herbert

2013-01-01

The “Critical Assessment of Small Molecule Identification” (CASMI) contest was aimed in testing strategies for small molecule identification that are currently available in the experimental and computational mass spectrometry community. We have applied tandem mass spectral library search to solve Category 2 of the CASMI Challenge 2012 (best identification for high resolution LC/MS data). More than 230,000 tandem mass spectra part of four well established libraries (MassBank, the collection of tandem mass spectra of the “NIST/NIH/EPA Mass Spectral Library 2012”, METLIN, and the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’) were searched. The sample spectra acquired in positive ion mode were processed. Seven out of 12 challenges did not produce putative positive matches, simply because reference spectra were not available for the compounds searched. This suggests that to some extent the limited coverage of chemical space with high-quality reference spectra is still a problem encountered in tandem mass spectral library search. Solutions were submitted for five challenges. Three compounds were correctly identified (kanamycin A, benzyldiphenylphosphine oxide, and 1-isopropyl-5-methyl-1H-indole-2,3-dione). In the absence of any reference spectrum, a false positive identification was obtained for 1-aminoanthraquinone by matching the corresponding sample spectrum to the structurally related compounds N-phenylphthalimide and 2-aminoanthraquinone. Another false positive result was submitted for 1H-benz[g]indole; for the 1H-benz[g]indole-specific sample spectra provided, carbazole was listed as the best matching compound. In this case, the quality of the available 1H-benz[g]indole-specific reference spectra was found to hamper unequivocal identification. PMID:24957994

Method for quantitative determination and separation of trace amounts of chemical elements in the presence of large quantities of other elements having the same atomic mass

DOEpatents

Miller, C.M.; Nogar, N.S.

1982-09-02

Photoionization via autoionizing atomic levels combined with conventional mass spectroscopy provides a technique for quantitative analysis of trace quantities of chemical elements in the presence of much larger amounts of other elements with substantially the same atomic mass. Ytterbium samples smaller than 10 ng have been detected using an ArF* excimer laser which provides the atomic ions for a time-of-flight mass spectrometer. Elemental selectivity of greater than 5:1 with respect to lutetium impurity has been obtained. Autoionization via a single photon process permits greater photon utilization efficiency because of its greater absorption cross section than bound-free transitions, while maintaining sufficient spectroscopic structure to allow significant photoionization selectivity between different atomic species. Separation of atomic species from others of substantially the same atomic mass is also described.

Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

PubMed

Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

2017-11-13

A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

Mass Spectral Library with Search Program, Data Version: NIST v17

National Institute of Standards and Technology Data Gateway

SRD 1A NIST/EPA/NIH Mass Spectral Library with Search Program, Data Version: NIST v17 (PC database for purchase)   Available with full-featured NIST MS Search Program for Windows integrated tools, the NIST '98 is a fully evaluated collection of electron-ionization mass spectra. (147,198 Compounds with Spectra; 147,194 Chemical Structures; 174,948 Spectra )

Canadian Libraries and Mass Deacidification.

ERIC Educational Resources Information Center

Pacey, Antony

1992-01-01

Considers the advantages and disadvantages of six mass deacidification processes that libraries can use to salvage printed materials: the Wei T'o process, the Diethyl Zinc (DEZ) process, the FMC (Lithco) process, the Book Preservation Associates (BPA) process, the "Bookkeeper" process, and the "Lyophilization" process. The…

Overview of the 1986--1987 atomic mass predictions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haustein, P.E.

1988-07-01

The need for a comprehensive update of earlier sets of atomic mass predictions is documented. A project that grew from this need and which resulted in the preparation of the 1986--1987 Atomic Mass Predictions is summarized. Ten sets of new mass predictions and expository text from a variety of types of mass models are combined with the latest evaluation of experimentally determined atomic masses. The methodology employed in constructing these mass predictions is outlined. The models are compared with regard to their reproduction of the experimental mass surface and their use of varying numbers of adjustable parameters. Plots are presented,more » for each set of predictions, of differences between model calculations and the measured masses. These plots may be used to estimate the reliability of the new mass predictions in unmeasured regions that border the experimetally known mass surface. copyright 1988 Academic Press, Inc.« less

MRM-DIFF: data processing strategy for differential analysis in large scale MRM-based lipidomics studies.

PubMed

Tsugawa, Hiroshi; Ohta, Erika; Izumi, Yoshihiro; Ogiwara, Atsushi; Yukihira, Daichi; Bamba, Takeshi; Fukusaki, Eiichiro; Arita, Masanori

2014-01-01

Based on theoretically calculated comprehensive lipid libraries, in lipidomics as many as 1000 multiple reaction monitoring (MRM) transitions can be monitored for each single run. On the other hand, lipid analysis from each MRM chromatogram requires tremendous manual efforts to identify and quantify lipid species. Isotopic peaks differing by up to a few atomic masses further complicate analysis. To accelerate the identification and quantification process we developed novel software, MRM-DIFF, for the differential analysis of large-scale MRM assays. It supports a correlation optimized warping (COW) algorithm to align MRM chromatograms and utilizes quality control (QC) sample datasets to automatically adjust the alignment parameters. Moreover, user-defined reference libraries that include the molecular formula, retention time, and MRM transition can be used to identify target lipids and to correct peak abundances by considering isotopic peaks. Here, we demonstrate the software pipeline and introduce key points for MRM-based lipidomics research to reduce the mis-identification and overestimation of lipid profiles. The MRM-DIFF program, example data set and the tutorials are downloadable at the "Standalone software" section of the PRIMe (Platform for RIKEN Metabolomics, http://prime.psc.riken.jp/) database website.

MRM-DIFF: data processing strategy for differential analysis in large scale MRM-based lipidomics studies

PubMed Central

Tsugawa, Hiroshi; Ohta, Erika; Izumi, Yoshihiro; Ogiwara, Atsushi; Yukihira, Daichi; Bamba, Takeshi; Fukusaki, Eiichiro; Arita, Masanori

2015-01-01

Based on theoretically calculated comprehensive lipid libraries, in lipidomics as many as 1000 multiple reaction monitoring (MRM) transitions can be monitored for each single run. On the other hand, lipid analysis from each MRM chromatogram requires tremendous manual efforts to identify and quantify lipid species. Isotopic peaks differing by up to a few atomic masses further complicate analysis. To accelerate the identification and quantification process we developed novel software, MRM-DIFF, for the differential analysis of large-scale MRM assays. It supports a correlation optimized warping (COW) algorithm to align MRM chromatograms and utilizes quality control (QC) sample datasets to automatically adjust the alignment parameters. Moreover, user-defined reference libraries that include the molecular formula, retention time, and MRM transition can be used to identify target lipids and to correct peak abundances by considering isotopic peaks. Here, we demonstrate the software pipeline and introduce key points for MRM-based lipidomics research to reduce the mis-identification and overestimation of lipid profiles. The MRM-DIFF program, example data set and the tutorials are downloadable at the “Standalone software” section of the PRIMe (Platform for RIKEN Metabolomics, http://prime.psc.riken.jp/) database website. PMID:25688256

Rapid identification of fatty acid methyl esters using a multidimensional gas chromatography-mass spectrometry database.

PubMed

Härtig, Claus

2008-01-04

A multidimensional approach for the identification of fatty acid methyl esters (FAME) based on GC/MS analysis is described. Mass spectra and retention data of more than 130 FAME from various sources (chain lengths in the range from 4 to 24 carbon atoms) were collected in a database. Hints for the interpretation of FAME mass spectra are given and relevant diagnostic marker ions are deduced indicating specific groups of fatty acids. To verify the identity of single species and to ensure an optimized chromatographic resolution, the database was compiled with retention data libraries acquired on columns of different polarity (HP-5, DB-23, and HP-88). For a combined use of mass spectra and retention data standardized methods of measurement for each of these columns are required. Such master methods were developed and always applied under the conditions of retention time locking (RTL) which allowed an excellent reproducibility and comparability of absolute retention times. Moreover, as a relative retention index system, equivalent chain lengths (ECL) of FAME were determined by linear interpolation. To compare and to predict ECL values by means of structural features, fractional chain lengths (FCL) were calculated and fitted as well. As shown in an example, the use of retention data and mass spectral information together in a database search leads to an improved and reliable identification of FAME (including positional and geometrical isomers) without further derivatizations.

Storage and retrieval of mass spectral information

NASA Technical Reports Server (NTRS)

Hohn, M. E.; Humberston, M. J.; Eglinton, G.

1977-01-01

Computer handling of mass spectra serves two main purposes: the interpretation of the occasional, problematic mass spectrum, and the identification of the large number of spectra generated in the gas-chromatographic-mass spectrometric (GC-MS) analysis of complex natural and synthetic mixtures. Methods available fall into the three categories of library search, artificial intelligence, and learning machine. Optional procedures for coding, abbreviating and filtering a library of spectra minimize time and storage requirements. Newer techniques make increasing use of probability and information theory in accessing files of mass spectral information.

Planning for Preservation during Mass Digitization Projects

ERIC Educational Resources Information Center

Teper, Jennifer Hain; Shaw, Emily F.

2011-01-01

In anticipation of current and future mass digitization projects in which the University of Illinois at Urbana-Champaign's Library will participate, the Library's Conservation Unit began to gather data on the "scannability" of our general book collections to anticipate potential effects on conservation and preservation work flows. The…

An open library of relativistic core electron density function for the QTAIM analysis with pseudopotentials.

PubMed

Zou, Wenli; Cai, Ziyu; Wang, Jiankang; Xin, Kunyu

2018-04-29

Based on two-component relativistic atomic calculations, a free electron density function (EDF) library has been developed for nearly all the known ECPs of the elements Li (Z = 3) up to Ubn (Z = 120), which can be interfaced into modern quantum chemistry programs to save the .wfx wavefunction file. The applicability of this EDF library is demonstrated by the analyses of the quantum theory of atoms in molecules (QTAIM) and other real space functions on HeCuF, PtO42+, OgF 4 , and TlCl 3 (DMSO) 2 . When a large-core ECP is used, it shows that the corrections by EDF may significantly improve the properties of some density-derived real space functions, but they are invalid for the wavefunction-depending real space functions. To classify different chemical bonds and especially some nonclassical interactions, a list of universal criteria has also been proposed. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Extending a Tandem Mass Spectral Library to Include MS2 Spectra of Fragment Ions Produced In-Source and MSn Spectra.

PubMed

Yang, Xiaoyu; Neta, Pedatsur; Stein, Stephen E

2017-11-01

Tandem mass spectral library searching is finding increased use as an effective means of determining chemical identity in mass spectrometry-based omics studies. We previously reported on constructing a tandem mass spectral library that includes spectra for multiple precursor ions for each analyte. Here we report our method for expanding this library to include MS 2 spectra of fragment ions generated during the ionization process (in-source fragment ions) as well as MS 3 and MS 4 spectra. These can assist the chemical identification process. A simple density-based clustering algorithm was used to cluster all significant precursor ions from MS 1 scans for an analyte acquired during an infusion experiment. The MS 2 spectra associated with these precursor ions were grouped into the same precursor clusters. Subsequently, a new top-down hierarchical divisive clustering algorithm was developed for clustering the spectra from fragmentation of ions in each precursor cluster, including the MS 2 spectra of the original precursors and of the in-source fragments as well as the MS n spectra. This algorithm starts with all the spectra of one precursor in one cluster and then separates them into sub-clusters of similar spectra based on the fragment patterns. Herein, we describe the algorithms and spectral evaluation methods for extending the library. The new library features were demonstrated by searching the high resolution spectra of E. coli extracts against the extended library, allowing identification of compounds and their in-source fragment ions in a manner that was not possible before. Graphical Abstract ᅟ.

NIST Libraries of Peptide Fragmentation Mass Spectra Databass

National Institute of Standards and Technology Data Gateway

SRD 4 NIST Libraries of Peptide Fragmentation Mass Spectra Databass (PC database for purchase)   Interactive computer program for predicting thermodynamic and transport properties of pure fluids and fluid mixtures containing up to 20 components. The components are selected from a database of 196 components, mostly hydrocarbons.

RADIOACTIVE ELEMENTS IN THE STANDARD ATOMIC WEIGHTS TABLE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holden, N.E.; Holden, N.; Holden,N.E.

2011-07-27

In the 1949 Report of the Atomic Weights Commission, a series of new elements were added to the Atomic Weights Table. Since these elements had been produced in the laboratory and were not discovered in nature, the atomic weight value of these artificial products would depend upon the production method. Since atomic weight is a property of an element as it occurs in nature, it would be incorrect to assign an atomic weight value to that element. As a result of that discussion, the Commission decided to provide only the mass number of the most stable (or longest-lived) known isotopemore » as the number to be associated with these entries in the Atomic Weights Table. As a function of time, the mass number associated with various elements has changed as longer-lived isotopes of a particular element has been found in nature, or as improved half-life values of an element's isotopes might cause a shift in the longest-lived isotope from one mass to another. In the 1957 Report of the Atomic Weights Commission, it was decided to discontinue the listing of the mass number in the Atomic Weights Table on the grounds that the kind of information supplied by the mass number is inconsistent with the primary purpose of the Table, i.e., to provide accurate values of 'these constants' for use in various chemical calculations. In addition to the Table of Atomic Weights, the Commission included an auxiliary Table of Radioactive Elements for the first time, where the entry would be the isotope of that element which was the most stable, i.e., the one with the longest known half-life. In their 1973 Report, the Commission noted that the users of the main Table of Atomic Weights were dissatisfied with the omission of values for some elements in that Table and it was decided to reintroduce the mass number for the radioactive elements into the main Table. In their 1983 Report, the Commission decided that radioactive elements were considered to lack a characteristic terrestrial isotopic composition, from which an atomic weight value could be calculated to five or more figure accuracy, without prior knowledge of the sample involved. These elements were again listed in the Atomic Weights Table with no further information, i.e., with no mass number or atomic weight value. For the elements, which have no stable characteristic terrestrial isotopic composition, the data on the half-lives and the relative atomic masses for the nuclides of interest for those elements have been evaluated. The values of the half-lives with their uncertainties are listed in the table. The uncertainties are given for the last digit quoted of the half-life and are given in parentheses. A half-life entry for the Table having a value and an uncertainty of 7 {+-} 3 is listed in the half-life column as 7 (3). The criteria to include data in this Table, is to be the same as it has been for over sixty years. It is the same criteria, which are used for all data that are evaluated for inclusion in the Standard Table of Atomic Weights. If a report of data is published in a peer-reviewed journal, that data is evaluated and considered for inclusion in the appropriate table of the biennial report of the Atomic Weights Commission. As better data becomes available in the future, the information that is contained in either of the Tables of Standard Atomic Weights or in the Table of Radioactive Elements may be modified. It should be noted that the appearance of any datum in the Table of the Radioactive Elements is merely for the purposes of calculating an atomic mass value for any sample of a radioactive material, which might have a variety of isotopic compositions and it has no implication as to the priority for claiming discovery of a given element and is not intended to. The atomic mass values have been taken primarily from the 2003 Atomic Mass Table. Mass values for those radioisotopes that do not appear in the 2003 Atomic mass Table have been taken from preliminary data of the Atomic Mass Data Center. Most of the quoted half-lives.« less

Smoke Emission Tests on Series II and Series III Allison T56 Turboprop Engines

DTIC Science & Technology

1986-12-01

Buioary ■ (13) available to ARL of aromatic content of AVTUR from Australian sources. The US data was obtained from information contained in Sheldon...Library Flight Standards Division Statutory and State Authorities and Industry Australian Atomic Energy Commiasion, Director Australian Airlines...Ampol Petroleum (Vic) Pty Md, Lubricant Sales & Service Mgr Ansett Airlines of Australia, Library Australian Coal Industry Research Labs

Launch Vehicle Performance for Bipropellant Propulsion Using Atomic Propellants With Oxygen

NASA Technical Reports Server (NTRS)

Palaszewski, Bryan

2000-01-01

Atomic propellants for bipropellant launch vehicles using atomic boron, carbon, and hydrogen were analyzed. The gross liftoff weights (GLOW) and dry masses of the vehicles were estimated, and the 'best' design points for atomic propellants were identified. Engine performance was estimated for a wide range of oxidizer to fuel (O/F) ratios, atom loadings in the solid hydrogen particles, and amounts of helium carrier fluid. Rocket vehicle GLOW was minimized by operating at an O/F ratio of 1.0 to 3.0 for the atomic boron and carbon cases. For the atomic hydrogen cases, a minimum GLOW occurred when using the fuel as a monopropellant (O/F = 0.0). The atomic vehicle dry masses are also presented, and these data exhibit minimum values at the same or similar O/F ratios as those for the vehicle GLOW. A technology assessment of atomic propellants has shown that atomic boron and carbon rocket analyses are considered to be much more near term options than the atomic hydrogen rockets. The technology for storing atomic boron and carbon has shown significant progress, while atomic hydrogen is not able to be stored at the high densities needed for effective propulsion. The GLOW and dry mass data can be used to estimate the cost of future vehicles and their atomic propellant production facilities. The lower the propellant's mass, the lower the overall investment for the specially manufactured atomic propellants.

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ting, Ying S.; Egertson, Jarrett D.; Bollinger, James G.

Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based technique for unbiased and reproducible measurement of protein mixtures. DIA tandem mass spectrometry spectra are often highly multiplexed, containing product ions from multiple cofragmenting precursors. Detecting peptides directly from DIA data is therefore challenging; most DIA data analyses require spectral libraries. Here we present PECECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECECAN reports evidence of detection based on product ion scoring, which enables detection of low-abundance analytes with poor precursor ion signal. We demonstrate the chromatographic peak picking accuracy and peptide detectionmore » capability of PECECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECECAN to build a plasma proteome library from DIA data and to query known sequence variants.« less

IFLA General Conference, 1985. Division on Management and Technology. Section on Conservation. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations, The Hague (Netherlands).

Papers on conservation and preservation which were presented at the 1985 International Federation of Library Associations (IFLA) conference include: (1) "Mass Deacidification at the National Library of Canada" (Joyce M. Banks, National Library of Canada); (2) "The National Preservation Office in the British Library" (David W.…

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment

PubMed Central

Dasari, Surendra; Chambers, Matthew C.; Martinez, Misti A.; Carpenter, Kristin L.; Ham, Amy-Joan L.; Vega-Montoto, Lorenzo J.; Tabb, David L.

2012-01-01

Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measuring the quality of a spectrum-spectrum match (SSM). This scoring system does not offer a clear statistical interpretation and ignores fragment ion m/z discrepancies in the scoring. We developed a new spectral library search engine, Pepitome, which employs statistical systems for scoring SSMs. Pepitome outperformed the leading library search tool, SpectraST, when analyzing data sets acquired on three different mass spectrometry platforms. We characterized the reliability of spectral library searches by confirming shotgun proteomics identifications through RNA-Seq data. Applying spectral library and database searches on the same sample revealed their complementary nature. Pepitome identifications enabled the automation of quality analysis and quality control (QA/QC) for shotgun proteomics data acquisition pipelines. PMID:22217208

Evaluation of the performance of a tandem mass spectral library with mass spectral data extracted from literature.

PubMed

Würtinger, Philipp; Oberacher, Herbert

2012-01-01

MSforID represents a database of tandem mass spectral data obtained from (quasi-)molecular ions produced by atmospheric pressure ionization methods. At the current stage of development the library contains 12 122 spectra of 1208 small (bio-)organic molecules. The present work was aimed to evaluate the performance of the MSforID library in terms of accuracy and transferability with a collection of fragment ion mass spectra from various compounds acquired on multiple instruments. A literature survey was conducted to collect the set of sample spectra. A total number of 554 spectra covering 291 compounds were extracted from 109 publications. The majority of spectra originated from publications on applications of LC/MS/MS in drug monitoring, pharmacokinetics, environmental analysis, forensic analysis as well as food analysis. Almost all types of tandem mass spectrometric instruments distributed by the five most important instrument vendors were included in the study. The overall sensitivity of library search was found to be 96.4%, which clearly proves that the MSforID library can successfully handle data from a huge variety of mass spectrometric instruments to allow accurate compound identification. Only for spectra containing three or more fragment ions, however, the rate of classified matches (= matches with a relative average match probability (ramp) score > 40.0) was 95%. Ambiguous or unclassified results were mainly obtained for searches with single precursor-to-fragment ion transitions due to the insufficient specificity of such a low amount of structural information to unequivocally define a single compound. Copyright © 2011 John Wiley & Sons, Ltd.

Correlating the magic numbers of inorganic nanomolecular assemblies with a {Pd84} molecular-ring Rosetta Stone

PubMed Central

Xu, Feng; Miras, Haralampos N.; Scullion, Rachel A.; Long, De-Liang; Thiel, Johannes; Cronin, Leroy

2012-01-01

Molecular self-assembly has often been suggested as the ultimate route for the bottom-up construction of building blocks atom-by-atom for functional nanotechnology, yet structural design or prediction of nanomolecular assemblies is still far from reach. Whereas nature uses complex machinery such as the ribosome, chemists use painstakingly engineered step-by-step approaches to build complex molecules but the size and complexity of such molecules, not to mention the accessible yields, can be limited. Herein we present the discovery of a palladium oxometalate {Pd84}-ring cluster 3.3 nm in diameter; [Pd84O42(OAc)28(PO4)42]70- ({Pd84} ≡ {Pd12}7) that is formed in water just by mixing two reagents at room temperature, giving crystals of the compound in just a few days. The structure of the {Pd84}-ring has sevenfold symmetry, comprises 196 building blocks, and we also show, using mass spectrometry, that a large library of other related nanostructures is present in solution. Finally, by analysis of the symmetry and the building block library that construct the {Pd84} we show that the correlation of the symmetry, subunit number, and overall cluster nuclearity can be used as a “Rosetta Stone” to rationalize the “magic numbers” defining a number of other systems. This is because the discovery of {Pd84} allows the relationship between seemingly unrelated families of molecular inorganic nanosystems to be decoded from the overall cluster magic-number nuclearity, to the symmetry and building blocks that define such structures allowing the prediction of other members of these nanocluster families. PMID:22753516

Collisional Cooling of Light Ions by Cotrapped Heavy Atoms.

PubMed

Dutta, Sourav; Sawant, Rahul; Rangwala, S A

2017-03-17

We experimentally demonstrate cooling of trapped ions by collisions with cotrapped, higher-mass neutral atoms. It is shown that the lighter ^{39}K^{+} ions, created by ionizing ^{39}K atoms in a magneto-optical trap (MOT), when trapped in an ion trap and subsequently allowed to cool by collisions with ultracold, heavier ^{85}Rb atoms in a MOT, exhibit a longer trap lifetime than without the localized ^{85}Rb MOT atoms. A similar cooling of trapped ^{85}Rb^{+} ions by ultracold ^{133}Cs atoms in a MOT is also demonstrated in a different experimental configuration to validate this mechanism of ion cooling by localized and centered ultracold neutral atoms. Our results suggest that the cooling of ions by localized cold atoms holds for any mass ratio, thereby enabling studies on a wider class of atom-ion systems irrespective of their masses.

Simultaneous screening of targeted and non-targeted contaminants using an LC-QTOF-MS system and automated MS/MS library searching.

PubMed

Herrera-Lopez, S; Hernando, M D; García-Calvo, E; Fernández-Alba, A R; Ulaszewska, M M

2014-09-01

Simultaneous high-resolution full-scan and tandem mass spectrometry (MS/MS) analysis using time of flight mass spectrometry brings an answer for increasing demand of retrospective and non-targeted data analysis. Such analysis combined with spectral library searching is a promising tool for targeted and untargeted screening of small molecules. Despite considerable extension of the panel of compounds of tandem mass spectral libraries, the heterogeneity of spectral data poses a major challenge against the effective usage of spectral libraries. Performance evaluation of available LC-MS/MS libraries will significantly increase credibility in the search results. The present work was aimed to evaluate fluctuation of MS/MS pattern, in the peak intensities distribution together with mass accuracy measurements, and in consequence, performance compliant with ion ratio and mass error criteria as principles in identification processes for targeted and untargeted contaminants at trace levels. Matrix effect and ultra-trace levels of concentration (from 50 ng l(-1) to 1000 ng l(-1) were evaluated as potential source of inaccuracy in the performance of spectral matching. Matrix-matched samples and real samples were screened for proof of applicability. By manual review of data and application of ion ratio and ppm error criteria, false negatives were obtained; this number diminished when in-house library was used, while with on-line MS/MS databases 100% of positive samples were found. In our experience, intensity of peaks across spectra was highly correlated to the concentration effect and matrix complexity. In turn, analysis of spectra acquired at trace concentrations and in different matrices results in better performance in providing correct and reliable identification. Copyright © 2014 John Wiley & Sons, Ltd.

77 FR 71452 - Extension of Comment Period: Orphan Works and Mass Digitization

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-30

... Office hereby extends the time for filing comments to 5:00 p.m. EST on February 4, 2013. The due date for... LIBRARY OF CONGRESS Copyright Office [Docket No. 2012-10] Extension of Comment Period: Orphan Works and Mass Digitization AGENCY: Copyright Office, Library of Congress. ACTION: Extension of comment...

ION COMPOSITION ELUCIDATION (ICE): A HIGH RESOLUTION MASS SPECTROMETRIC TECHNIQUE FOR IDENTIFYING COMPOUNDS IN COMPLEX MIXTURES

EPA Science Inventory

When tentatively identifying compounds in complex mixtures using mass spectral libraries, multiple matches or no plausible matches due to a high level of chemical noise or interferences can occur. Worse yet, most analytes are not in the libraries. In each case, Ion Composition El...

Fast identification of dermatophytes by MALDI-TOF/MS using direct transfer of fungal cells on ground steel target plates.

PubMed

da Cunha, Keith C; Riat, Arnaud; Normand, Anne-Cecile; Bosshard, Philipp P; de Almeida, Margarete T G; Piarroux, Renaud; Schrenzel, Jacques; Fontao, Lionel

2018-05-15

Dermatophytes cause human infections limited to keratinized tissues. We showed that the direct transfer method allows reliable identification of non-dermatophytes mould and yeast by MALDI-TOF/MS. We aimed at assessing whether the direct transfer method can be used for dermatophytes and whether an own mass spectra library would be superior to the Bruker library. We used the Bruker Biotyper to build a dermatophyte mass spectra library and assessed its performance by 1/ testing a panel of mass spectrum produced with strains genotypically identified and, 2/ comparing MALDI-TOF/MS identification to morphology-based methods. Identification of dermatophytes using the Bruker library is poor. Our library provided 97% concordance between ITS sequencing and MALDI-TOF/MS analysis with a panel of 1104 spectra corresponding to 276 strains. Direct transfer method using unpolished target plates allowed proper identification of 85% of dermatophytes clinical isolates most of which were common dermatophytes. A homemade dermatophyte MSP library is a prerequisite for accurate identification of species absent in the Bruker library but it also improves identification of species already listed in the database. The direct deposit method can be used to identify the most commonly found dermatophytes such as T. rubrum and T. interdigitale/mentagrophytes by MALDI-TOF/MS. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Sources of Information on Atomic Energy, International Series of Monographs in Library and Information Science, Volume 2.

ERIC Educational Resources Information Center

Anthony, L. J.

This book provides a comprehensive survey of the principal national and international organizations which are sources of information on atomic and nuclear energy and of the published literature in this field. Organizations in all the major nuclear countries such as the United States, Britain, the Soviet Union, France, and Japan are described, and…

Comment on “Atomic mass compilation 2012” by B. Pfeiffer, K. Venkataramaniah, U. Czok, C. Scheidenberger

DOE Office of Scientific and Technical Information (OSTI.GOV)

Audi, G., E-mail: amdc.audi@gmail.com; Blaum, K.; Block, M.

In order to avoid errors and confusion that may arise from the recent publication of a paper entitled “Atomic Mass Compilation 2012”, we explain the important difference between a compilation and an evaluation; the former is a necessary but insufficient condition for the latter. The simple list of averaged mass values offered by the “Atomic Mass Compilation” uses none of the numerous links and correlations present in the large body of input data that are carefully maintained within the “Atomic Mass Evaluation”. As such, the mere compilation can only produce results of inferior accuracy. Illustrative examples are given.

Development and practical application of a library of CID accurate mass spectra of more than 2,500 toxic compounds for systematic toxicological analysis by LC-QTOF-MS with data-dependent acquisition.

PubMed

Broecker, Sebastian; Herre, Sieglinde; Wüst, Bernhard; Zweigenbaum, Jerry; Pragst, Fritz

2011-04-01

A library of collision-induced dissociation (CID) accurate mass spectra has been developed for efficient use of liquid chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) as a tool in systematic toxicological analysis. The mass spectra (Δm < 3 ppm) of more than 2,500 illegal and therapeutic drugs, pesticides, alkaloids, other toxic chemicals and metabolites were measured, by use of an Agilent 6530 instrument, by flow-injection of 1 ng of the pure substances in aqueous ammonium formate-formic acid-methanol, with positive and negative electrospray-ionization (ESI), selection of the protonated or deprotonated molecules [M+H](+) or [M-H](-) by the quadrupole, and collision induced dissociation (CID) with nitrogen as collision gas at CID energies of 10, 20, and 40 eV. The fragment mass spectra were controlled for structural plausibility, corrected by recalculation to the theoretical fragment masses and added to a database of accurate mass data and molecular formulas of more than 7,500 toxicologically relevant substances to form the "database and library of toxic compounds". For practical evaluation, blood and urine samples were spiked with a mixture of 33 drugs at seven concentrations between 0.5 and 500 ng mL(-1), prepared by dichloromethane extraction or protein precipitation, and analyzed by LC-QTOF-MS in data-dependent acquisition mode. Unambiguous identification by library search was possible for typical basic drugs down to 0.5-2 ng mL(-1) and for benzodiazepines down to 2-20 ng mL(-1). The efficiency of the method was also demonstrated by re-analysis of venous blood samples from 50 death cases and comparison with previous results. In conclusion, LC-QTOF-MS in data-dependent acquisition mode combined with an accurate mass database and CID spectra library seemed to be one of the most efficient tools for systematic toxicological analysis.

Ideas for the rapid development of the structural models in mechanical engineering

NASA Astrophysics Data System (ADS)

Oanta, E.; Raicu, A.; Panait, C.

2017-08-01

Conceiving computer based instruments is a long run concern of the authors. Some of the original solutions are: optimal processing of the large matrices, interfaces between the programming languages, approximation theory using spline functions, numerical programming increased accuracy based on the extended arbitrary precision libraries. For the rapid development of the models we identified the following directions: atomization, ‘librarization’, parameterization, automatization and integration. Each of these directions has some particular aspects if we approach mechanical design problems or software development. Atomization means a thorough top-down decomposition analysis which offers an insight regarding the basic features of the phenomenon. Creation of libraries of reusable mechanical parts and libraries of programs (data types, functions) save time, cost and effort when a new model must be conceived. Parameterization leads to flexible definition of the mechanical parts, the values of the parameters being changed either using a dimensioning program or in accord to other parts belonging to the same assembly. The resulting templates may be also included in libraries. Original software applications are useful for the model’s input data generation, to input the data into CAD/FEA commercial applications and for the data integration of the various types of studies included in the same project.

CSBB-ConeExclusion, adapting structure based solution virtual screening to libraries on solid support.

PubMed

Shave, Steven; Auer, Manfred

2013-12-23

Combinatorial chemical libraries produced on solid support offer fast and cost-effective access to a large number of unique compounds. If such libraries are screened directly on-bead, the speed at which chemical space can be explored by chemists is much greater than that addressable using solution based synthesis and screening methods. Solution based screening has a large supporting body of software such as structure-based virtual screening tools which enable the prediction of protein-ligand complexes. Use of these techniques to predict the protein bound complexes of compounds synthesized on solid support neglects to take into account the conjugation site on the small molecule ligand. This may invalidate predicted binding modes, the linker may be clashing with protein atoms. We present CSBB-ConeExclusion, a methodology and computer program which provides a measure of the applicability of solution dockings to solid support. Output is given in the form of statistics for each docking pose, a unique 2D visualization method which can be used to determine applicability at a glance, and automatically generated PyMol scripts allowing visualization of protein atom incursion into a defined exclusion volume. CSBB-ConeExclusion is then exemplarically used to determine the optimum attachment point for a purine library targeting cyclin-dependent kinase 2 CDK2.

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries.

PubMed

Wu, Jemma X; Song, Xiaomin; Pascovici, Dana; Zaw, Thiri; Care, Natasha; Krisp, Christoph; Molloy, Mark P

2016-07-01

The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at three different ratios to simulate protein abundance change comparisons. SWATH-MS performance was assessed using local and external assay libraries of varying complexities and proteome compositions. These experiments demonstrated that local seed libraries integrated with external assay libraries achieve better performance than local assay libraries alone, in terms of the number of identified peptides and proteins and the specificity to detect differentially abundant proteins. Our findings show that the performance of extended assay libraries is influenced by the MS/MS feature similarity of the seed and external libraries, while statistical analysis using multiple testing corrections increases the statistical rigor needed when searching against large extended assay libraries. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries*

PubMed Central

Wu, Jemma X.; Song, Xiaomin; Pascovici, Dana; Zaw, Thiri; Care, Natasha; Krisp, Christoph; Molloy, Mark P.

2016-01-01

The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at three different ratios to simulate protein abundance change comparisons. SWATH-MS performance was assessed using local and external assay libraries of varying complexities and proteome compositions. These experiments demonstrated that local seed libraries integrated with external assay libraries achieve better performance than local assay libraries alone, in terms of the number of identified peptides and proteins and the specificity to detect differentially abundant proteins. Our findings show that the performance of extended assay libraries is influenced by the MS/MS feature similarity of the seed and external libraries, while statistical analysis using multiple testing corrections increases the statistical rigor needed when searching against large extended assay libraries. PMID:27161445

Towards a full reference library of MS(n) spectra. Testing of a library containing 3126 MS2 spectra of 1743 compounds.

PubMed

Milman, Boris L

2005-01-01

A library consisting of 3766 MS(n) spectra of 1743 compounds, including 3126 MS2 spectra acquired mainly using ion trap (IT) and triple-quadrupole (QqQ) instruments, was composed of numerous collections/sources. Ionization techniques were mainly electrospray ionization and also atmospheric pressure chemical ionization and chemical ionization. The library was tested for the performance in identification of unknowns, and in this context this work is believed to be the largest of all known tests of product-ion mass spectral libraries. The MS2 spectra of the same compounds from different collections were in turn divided into spectra of 'unknown' and reference compounds. For each particular compound, library searches were performed resulting in selection by taking into account the best matches for each spectral collection/source. Within each collection/source, replicate MS2 spectra differed in the collision energy used. Overall, there were up to 950 search results giving the best match factors and their ranks in corresponding hit lists. In general, the correct answers were obtained as the 1st rank in up to 60% of the search results when retrieved with (on average) 2.2 'unknown' and 6.2 reference replicates per compound. With two or more replicates of both 'unknown' and reference spectra (the average numbers of replicates were 4.0 and 7.8, respectively), the fraction of correct answers in the 1st rank increased to 77%. This value is close to the performance of established electron ionization mass spectra libraries (up to 79%) found by other workers. The hypothesis that MS2 spectra better match reference spectra acquired using the same type of tandem mass spectrometer (IT or QqQ) was neither strongly proved nor rejected here. The present work shows that MS2 spectral libraries containing sufficiently numerous different entries for each compound are sufficiently efficient for identification of unknowns and suitable for use with different tandem mass spectrometers. 2005 John Wiley & Sons, Ltd.

Toward the Atomic-Level Mass Analysis of Biomolecules by the Scanning Atom Probe.

PubMed

Nishikawa, Osamu; Taniguchi, Masahiro

2017-04-01

In 1994, a new type of atom probe instrument, named the scanning atom probe (SAP), was proposed. The unique feature of the SAP is the introduction of a small extraction electrode, which scans over a specimen surface and confines the high field, required for field evaporation of surface atoms in a small space, between the specimen and the electrode. Thus, the SAP does not require a sharp specimen tip. This indicates that the SAP can mass analyze the specimens which are difficult to form in a sharp tip, such as organic materials and biomolecules. Clean single wall carbon nanotubes (CNT), made by high-pressure carbon monoxide process are found to be the best substrates for biomolecules. Various amino acids and dipeptide biomolecules were successfully mass analyzed, revealing characteristic clusters formed by strongly bound atoms in the specimens. The mass analysis indicates that SAP analysis of biomolecules is not only qualitative, but also quantitative.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Crx(Bi0.1Sb0.9)2-xTe3.

PubMed

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; Billinge, Simon J L; Zhong, Ruidan; Schneeloch, John A; Liu, Tiansheng; Valla, Tonica; Tranquada, John M; Gu, Genda; Davis, J C Séamus

2015-02-03

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a "Dirac-mass gap" in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in the ferromagnetic TI Cr0.08(Bi0.1Sb0.9)1.92Te3. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship [Formula: see text] is confirmed throughout and exhibits an electron-dopant interaction energy J* = 145 meV·nm(2). These observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Crx(Bi0.1Sb0.9)2-xTe3

PubMed Central

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; Billinge, Simon J. L.; Zhong, Ruidan; Schneeloch, John A.; Liu, Tiansheng; Valla, Tonica; Tranquada, John M.; Gu, Genda; Davis, J. C. Séamus

2015-01-01

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a “Dirac-mass gap” in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in the ferromagnetic TI Cr0.08(Bi0.1Sb0.9)1.92Te3. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship Δ(r)∝n(r) is confirmed throughout and exhibits an electron–dopant interaction energy J* = 145 meV·nm2. These observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential. PMID:25605947

Computational mass spectrometry for small molecules

PubMed Central

2013-01-01

The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline. PMID:23453222

β -decay Q values among the A = 50 Ti-V-Cr isobaric triplet and atomic masses of Ti 46 , 47 , 49 , 50 , V 50 , 51 , and Cr 50 , 52 – 54

DOE PAGES

Kandegedara, R. M. E. B.; Bollen, G.; Eibach, M.; ...

2017-10-20

This manuscript describes a measurement of the Q value for the highly forbidden beta-decays of 50V and the double electron capture decay of 50Cr. The Q value corresponds to the total energy released during the decay and is equivalent to the mass difference between parent and daughter atoms. This mass difference was measured using high precision Penning trap mass spectrometry with the Low Energy Beam and Ion Trap facility at the National Superconducting Cyclotron Laboratory. The Q value enters into theoretical calculations of the half-life and beta-decay spectrum for the decay, so improves these calculations. In addition the Q valuemore » corresponds to the end point energy of the beta-decay spectrum, which has been precisely measured for several highly-forbidden decays using modern low background detector techniques. Hence, our Q value measurements provide a test of systematics for these detectors. In addition, we have measured the absolute atomic masses of 46,47,49,50Ti, 50,51V, and 50,52-52Cr, providing improvements in precision by factors of up to 3. These atomic masses help to strengthen global evaluations of all atomic mass data, such as the Atomic Mass Evaluation.« less

β -decay Q values among the A = 50 Ti-V-Cr isobaric triplet and atomic masses of Ti 46 , 47 , 49 , 50 , V 50 , 51 , and Cr 50 , 52 – 54

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kandegedara, R. M. E. B.; Bollen, G.; Eibach, M.

This manuscript describes a measurement of the Q value for the highly forbidden beta-decays of 50V and the double electron capture decay of 50Cr. The Q value corresponds to the total energy released during the decay and is equivalent to the mass difference between parent and daughter atoms. This mass difference was measured using high precision Penning trap mass spectrometry with the Low Energy Beam and Ion Trap facility at the National Superconducting Cyclotron Laboratory. The Q value enters into theoretical calculations of the half-life and beta-decay spectrum for the decay, so improves these calculations. In addition the Q valuemore » corresponds to the end point energy of the beta-decay spectrum, which has been precisely measured for several highly-forbidden decays using modern low background detector techniques. Hence, our Q value measurements provide a test of systematics for these detectors. In addition, we have measured the absolute atomic masses of 46,47,49,50Ti, 50,51V, and 50,52-52Cr, providing improvements in precision by factors of up to 3. These atomic masses help to strengthen global evaluations of all atomic mass data, such as the Atomic Mass Evaluation.« less

Measuring and engineering the atomic mass density wave of a Gaussian mass-polariton pulse in optical fibers

NASA Astrophysics Data System (ADS)

Partanen, Mikko; Tulkki, Jukka

2018-02-01

Conventional theories of electromagnetic waves in a medium assume that only the energy of the field propagates inside the medium. Consequently, they neglect the transport of mass density by the medium atoms. We have recently presented foundations of a covariant theory of light propagation in a nondispersive medium by considering a light wave simultaneously with the dynamics of the medium atoms driven by optoelastic forces [Phys. Rev. A 95, 063850 (2017)]. In particular, we have shown that the mass is transferred by an atomic mass density wave (MDW), which gives rise to mass-polariton (MP) quasiparticles, i.e., covariant coupled states of the field and matter having a nonzero rest mass. Another key observation of the mass-polariton theory of light is that, in common semiconductors, most of the momentum of light is transferred by moving atoms, e.g., 92% in the case of silicon. In this work, we generalize the MP theory of light for dispersive media and consider experimental measurement of the mass transferred by the MDW atoms when an intense light pulse propagates in a silicon fiber. In particular, we consider optimal intensity and time dependence of a Gaussian pulse and account for the breakdown threshold irradiance of the material. The optical shock wave property of the MDW, which propagates with the velocity of light instead of the velocity of sound, prompts for engineering of novel device concepts like very high frequency mechanical oscillators not limited by the acoustic cutoff frequency.

Mass defect effects in atomic clocks

NASA Astrophysics Data System (ADS)

Yudin, Valeriy; Taichenachev, Alexey

2018-03-01

We consider some implications of the mass defect on the frequency of atomic transitions. We have found that some well-known frequency shifts (the gravitational shift and motion-induced shifts such as quadratic Doppler and micromotion shifts) can be interpreted as consequences of the mass defect in quantum atomic physics, i.e. without the need for the concept of time dilation used in special and general relativity theories. Moreover, we show that the inclusion of the mass defect leads to previously unknown shifts for clocks based on trapped ions.

Library Careers Project; Funded by L.S.C.A. through the State Library of Ohio to the Cuyahoga County Public Library. Annual Report, September 1967 to August 1968.

ERIC Educational Resources Information Center

Cuyahoga County Public Library, Cleveland, OH.

A report is given of a Northeast Ohio recruitment project to develop and test methods and material for use in sparking interest in library science among college upperclassmen and graduates looking for new careers. Two of the approaches utilized are: (1) counseling of individuals attracted to library careers and (2) mass publicity via direct mail,…

CHEMICAL EVOLUTION LIBRARY FOR GALAXY FORMATION SIMULATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saitoh, Takayuki R., E-mail: saitoh@elsi.jp

We have developed a software library for chemical evolution simulations of galaxy formation under the simple stellar population (SSP) approximation. In this library, all of the necessary components concerning chemical evolution, such as initial mass functions, stellar lifetimes, yields from Type II and Type Ia supernovae, asymptotic giant branch stars, and neutron star mergers, are compiled from the literature. Various models are pre-implemented in this library so that users can choose their favorite combination of models. Subroutines of this library return released energy and masses of individual elements depending on a given event type. Since the redistribution manner of thesemore » quantities depends on the implementation of users’ simulation codes, this library leaves it up to the simulation code. As demonstrations, we carry out both one-zone, closed-box simulations and 3D simulations of a collapsing gas and dark matter system using this library. In these simulations, we can easily compare the impact of individual models on the chemical evolution of galaxies, just by changing the control flags and parameters of the library. Since this library only deals with the part of chemical evolution under the SSP approximation, any simulation codes that use the SSP approximation—namely, particle-base and mesh codes, as well as semianalytical models—can use it. This library is named “CELib” after the term “Chemical Evolution Library” and is made available to the community.« less

The Use of Gas Chromatography and Mass Spectrometry to Introduce General Chemistry Students to Percent Mass and Atomic Mass Calculations

ERIC Educational Resources Information Center

Pfennig, Brian W.; Schaefer, Amy K.

2011-01-01

A general chemistry laboratory experiment is described that introduces students to instrumental analysis using gas chromatography-mass spectrometry (GC-MS), while simultaneously reinforcing the concepts of mass percent and the calculation of atomic mass. Working in small groups, students use the GC to separate and quantify the percent composition…

PCTDSE: A parallel Cartesian-grid-based TDSE solver for modeling laser-atom interactions

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Zeng, Jiaolong; Yuan, Jianmin

2017-01-01

We present a parallel Cartesian-grid-based time-dependent Schrödinger equation (TDSE) solver for modeling laser-atom interactions. It can simulate the single-electron dynamics of atoms in arbitrary time-dependent vector potentials. We use a split-operator method combined with fast Fourier transforms (FFT), on a three-dimensional (3D) Cartesian grid. Parallelization is realized using a 2D decomposition strategy based on the Message Passing Interface (MPI) library, which results in a good parallel scaling on modern supercomputers. We give simple applications for the hydrogen atom using the benchmark problems coming from the references and obtain repeatable results. The extensions to other laser-atom systems are straightforward with minimal modifications of the source code.

ITFITS model for vibration--translation energy partitioning in atom-- polyatomic molecule collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shobatake, K.; Rice, S.A.; Lee, Y.T.

1973-09-01

A model for vibration-translation energy partitioning in the collinear collision of an atom and an axially symmetric polyatonaic molecule is proposed. The model is based on an extension of the ideas of Mahan and Heidrich, Wilson, and Rapp. Comparison of energy transfers computed from classical trajesctory calculations and the model proposed indicate good agreement when the mass of the free atom is small relative to the mass of the bound atom it strikes. The agreement is less satisfactory when that mass ratio becomes large. (auth)

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Cr x(Bi 0.1Sb 0.9) 2-xTe 3

DOE PAGES

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; ...

2015-01-20

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a “Dirac-mass gap” in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in themore » ferromagnetic TI Cr₀.₀₈(Bi₀.₁Sb₀.₉)₁.₉₂Te₃. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship Δ(r)∝n(r) is confirmed throughout and exhibits an electron–dopant interaction energy J* = 145 meV·nm². In addition, these observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential.« less

Spontaneous emission and atomic line shift in causal perturbation theory

NASA Astrophysics Data System (ADS)

Marzlin, Karl-Peter; Fitzgerald, Bryce

2018-04-01

We derive a spontaneous emission rate and line shift for two-level atoms coupled to the radiation field using causal perturbation theory. In this approach, employing the theory of distribution splitting prevents the occurrence of divergent integrals. Our method confirms the result for an atomic decay rate but suggests that the cutoff frequency for the atomic line shift is determined by the atomic mass, rather than the Bohr radius or electron mass.

Curatr: a web application for creating, curating and sharing a mass spectral library.

PubMed

Palmer, Andrew; Phapale, Prasad; Fay, Dominik; Alexandrov, Theodore

2018-04-15

We have developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries from liquid-chromatography mass spectrometry datasets. Curatr handles datasets from single or multiplexed standards and extracts chromatographic profiles and potential fragmentation spectra for multiple adducts. An intuitive interface helps users to select high quality spectra that are stored along with searchable molecular information, the providence of each standard and experimental metadata. Curatr supports exports to several standard formats for use with third party software or submission to repositories. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library http://curatr.mcf.embl.de. Source code and example data are at http://github.com/alexandrovteam/curatr/. palmer@embl.de. Supplementary data are available at Bioinformatics online.

Atomic weights of the elements--Review 2000 (IUPAC Technical Report)

USGS Publications Warehouse

de Laeter, John R.; Böhlke, John Karl; De Bièvre, P.; Hidaka, H.; Peiser, H.S.; Rosman, K.J.R.; Taylor, P.D.P.

2003-01-01

A consistent set of internationally accepted atomic weights has long been an essential aim of the scientific community because of the relevance of these values to science and technology, as well as to trade and commerce subject to ethical, legal, and international standards. The standard atomic weights of the elements are regularly evaluated, recommended, and published in updated tables by the Commission on Atomic Weights and Isotopic Abundances (CAWIA) of the International Union of Pure and Applied Chemistry (IUPAC). These values are invariably associated with carefully evaluated uncertainties. Atomic weights were originally determined by mass ratio measurements coupled with an understanding of chemical stoichiometry, but are now based almost exclusively on knowledge of the isotopic composition (derived from isotope-abundance ratio measurements) and the atomic masses of the isotopes of the elements. Atomic weights and atomic masses are now scaled to a numerical value of exactly 12 for the mass of the carbon isotope of mass number 12. Technological advances in mass spectrometry and nuclear-reaction energies have enabled atomic masses to be determined with a relative uncertainty of better than 1 ×10−7 . Isotope abundances for an increasing number of elements can be measured to better than 1 ×10−3 . The excellent precision of such measurements led to the discovery that many elements, in different specimens, display significant variations in their isotope-abundance ratios, caused by a variety of natural and industrial physicochemical processes. While such variations increasingly place a constraint on the uncertainties with which some standard atomic weights can be stated, they provide numerous opportunities for investigating a range of important phenomena in physical, chemical, cosmological, biological, and industrial processes. This review reflects the current and increasing interest of science in the measured differences between source-specific and even sample-specific atomic weights. These relative comparisons can often be made with a smaller uncertainty than is achieved in the best calibrated “absolute ” (=SI-traceable) atomic-weight determinations. Accurate determinations of the atomic weights of certain elements also influence the values of fundamental constants such as the Avogadro, Faraday, and universal gas constants. This review is in two parts: the first summarizes the development of the science of atomic-weight determinations during the 20th century; the second summarizes the changes and variations that have been recognized in the values and uncertainties of atomic weights, on an element-by-element basis, in the latter part of the 20th century.

A retention index calculator simplifies identification of plant volatile organic compounds.

PubMed

Lucero, Mary; Estell, Rick; Tellez, María; Fredrickson, Ed

2009-01-01

Plant volatiles (PVOCs) are important targets for studies in natural products, chemotaxonomy and biochemical ecology. The complexity of PVOC profiles often limits research to studies targeting only easily identified compounds. With the availability of mass spectral libraries and recent growth of retention index (RI) libraries, PVOC identification can be achieved using only gas chromatography coupled to mass spectrometry (GCMS). However, RI library searching is not typically automated, and until recently, RI libraries were both limited in scope and costly to obtain. To automate RI calculation and lookup functions commonly utilised in PVOC analysis. Formulae required for calculating retention indices from retention time data were placed in a spreadsheet along with lookup functions and a retention index library. Retention times obtained from GCMS analysis of alkane standards and Koeberlinia spinosa essential oil were entered into the spreadsheet to determine retention indices. Indices were used in combination with mass spectral analysis to identify compounds contained in Koeberlinia spinosa essential oil. Eighteen compounds were positively identified. Total oil yield was low, with only 5 ppm in purple berries. The most abundant compounds were octen-3-ol and methyl salicylate. The spreadsheet accurately calculated RIs of the detected compounds. The downloadable spreadsheet tool developed for this study provides a calculator and RI library that works in conjuction with GCMS or other analytical techniques to identify PVOCs in plant extracts.

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library*

PubMed Central

Yen, Chia-Yu; Houel, Stephane; Ahn, Natalie G.; Old, William M.

2011-01-01

The unambiguous assignment of tandem mass spectra (MS/MS) to peptide sequences remains a key unsolved problem in proteomics. Spectral library search strategies have emerged as a promising alternative for peptide identification, in which MS/MS spectra are directly compared against a reference library of confidently assigned spectra. Two problems relate to library size. First, reference spectral libraries are limited to rediscovery of previously identified peptides and are not applicable to new peptides, because of their incomplete coverage of the human proteome. Second, problems arise when searching a spectral library the size of the entire human proteome. We observed that traditional dot product scoring methods do not scale well with spectral library size, showing reduction in sensitivity when library size is increased. We show that this problem can be addressed by optimizing scoring metrics for spectrum-to-spectrum searches with large spectral libraries. MS/MS spectra for the 1.3 million predicted tryptic peptides in the human proteome are simulated using a kinetic fragmentation model (MassAnalyzer version2.1) to create a proteome-wide simulated spectral library. Searches of the simulated library increase MS/MS assignments by 24% compared with Mascot, when using probabilistic and rank based scoring methods. The proteome-wide coverage of the simulated library leads to 11% increase in unique peptide assignments, compared with parallel searches of a reference spectral library. Further improvement is attained when reference spectra and simulated spectra are combined into a hybrid spectral library, yielding 52% increased MS/MS assignments compared with Mascot searches. Our study demonstrates the advantages of using probabilistic and rank based scores to improve performance of spectrum-to-spectrum search strategies. PMID:21532008

Characterization of Incidental Renal Mass With Dual-Energy CT: Diagnostic Accuracy of Effective Atomic Number Maps for Discriminating Nonenhancing Cysts From Enhancing Masses.

PubMed

Mileto, Achille; Allen, Brian C; Pietryga, Jason A; Farjat, Alfredo E; Zarzour, Jessica G; Bellini, Davide; Ebner, Lukas; Morgan, Desiree E

2017-10-01

The purpose of this study was to assess the diagnostic accuracy of effective atomic number maps reconstructed from dual-energy contrast-enhanced data for discriminating between nonenhancing renal cysts and enhancing masses. Two hundred six patients (128 men, 78 women; mean age, 64 years) underwent a CT renal mass protocol (single-energy unenhanced and dual-energy contrast-enhanced nephrographic imaging) at two different hospitals. For each set of patients, two blinded, independent observers performed measurements on effective atomic number maps from contrast-enhanced dual-energy data. Renal mass assessment on unenhanced and nephrographic images, corroborated by imaging and medical records, was the reference standard. The diagnostic accuracy of effective atomic number maps was assessed with ROC analysis. Significant differences in mean effective atomic numbers (Z eff ) were observed between nonenhancing and enhancing masses (set A, 8.19 vs 9.59 Z eff ; set B, 8.05 vs 9.19 Z eff ; sets combined, 8.13 vs 9.37 Z eff ) (p < 0.0001). An effective atomic number value of 8.36 Z eff was the optimal threshold, rendering an AUC of 0.92 (95% CI, 0.89-0.94), sensitivity of 90.8% (158/174 [95% CI, 85.5-94.7%]), specificity of 85.2% (445/522 [95% CI, 81.9-88.2%]), and overall diagnostic accuracy of 86.6% (603/696 [95% CI, 83.9-89.1%]). Nonenhancing renal cysts, including hyperattenuating cysts, can be discriminated from enhancing masses on effective atomic number maps generated from dual-energy contrast-enhanced CT data. This technique may be of clinical usefulness when a CT protocol for comprehensive assessment of renal masses is not available.

Fast Atom Bombardment Mass Spectrometry.

ERIC Educational Resources Information Center

Rinehart, Kenneth L., Jr.

1982-01-01

Discusses reactions and characteristics of fast atom bombardment (FAB) mass spectroscopy in which samples are ionized in a condensed state by bombardment with xenon or argon atoms, yielding positive/negative secondary ions. Includes applications of FAB to structural problems and considers future developments using the technique. (Author/JN)

Neutron radiation damage studies in the structural materials of a 500 MWe fast breeder reactor using DPA cross-sections from ENDF / B-VII.1

NASA Astrophysics Data System (ADS)

Saha, Uttiyoarnab; Devan, K.; Bachchan, Abhitab; Pandikumar, G.; Ganesan, S.

2018-04-01

The radiation damage in the structural materials of a 500 MWe Indian prototype fast breeder reactor (PFBR) is re-assessed by computing the neutron displacement per atom (dpa) cross-sections from the recent nuclear data library evaluated by the USA, ENDF / B-VII.1, wherein revisions were taken place in the new evaluations of basic nuclear data because of using the state-of-the-art neutron cross-section experiments, nuclear model-based predictions and modern data evaluation techniques. An indigenous computer code, computation of radiation damage (CRaD), is developed at our centre to compute primary-knock-on atom (PKA) spectra and displacement cross-sections of materials both in point-wise and any chosen group structure from the evaluated nuclear data libraries. The new radiation damage model, athermal recombination-corrected displacement per atom (arc-dpa), developed based on molecular dynamics simulations is also incorporated in our study. This work is the result of our earlier initiatives to overcome some of the limitations experienced while using codes like RECOIL, SPECTER and NJOY 2016, to estimate radiation damage. Agreement of CRaD results with other codes and ASTM standard for Fe dpa cross-section is found good. The present estimate of total dpa in D-9 steel of PFBR necessitates renormalisation of experimental correlations of dpa and radiation damage to ensure consistency of damage prediction with ENDF / B-VII.1 library.

Fragment-Based Screening of a Natural Product Library against 62 Potential Malaria Drug Targets Employing Native Mass Spectrometry

PubMed Central

2018-01-01

Natural products are well known for their biological relevance, high degree of three-dimensionality, and access to areas of largely unexplored chemical space. To shape our understanding of the interaction between natural products and protein targets in the postgenomic era, we have used native mass spectrometry to investigate 62 potential protein targets for malaria using a natural-product-based fragment library. We reveal here 96 low-molecular-weight natural products identified as binding partners of 32 of the putative malarial targets. Seventy-nine (79) fragments have direct growth inhibition on Plasmodium falciparum at concentrations that are promising for the development of fragment hits against these protein targets. This adds a fragment library to the published HTS active libraries in the public domain. PMID:29436819

Fragment-Based Screening of a Natural Product Library against 62 Potential Malaria Drug Targets Employing Native Mass Spectrometry.

PubMed

Vu, Hoan; Pedro, Liliana; Mak, Tin; McCormick, Brendan; Rowley, Jessica; Liu, Miaomiao; Di Capua, Angela; Williams-Noonan, Billy; Pham, Ngoc B; Pouwer, Rebecca; Nguyen, Bao; Andrews, Katherine T; Skinner-Adams, Tina; Kim, Jessica; Hol, Wim G J; Hui, Raymond; Crowther, Gregory J; Van Voorhis, Wesley C; Quinn, Ronald J

2018-04-13

Natural products are well known for their biological relevance, high degree of three-dimensionality, and access to areas of largely unexplored chemical space. To shape our understanding of the interaction between natural products and protein targets in the postgenomic era, we have used native mass spectrometry to investigate 62 potential protein targets for malaria using a natural-product-based fragment library. We reveal here 96 low-molecular-weight natural products identified as binding partners of 32 of the putative malarial targets. Seventy-nine (79) fragments have direct growth inhibition on Plasmodium falciparum at concentrations that are promising for the development of fragment hits against these protein targets. This adds a fragment library to the published HTS active libraries in the public domain.

The Scales of Time, Length, Mass, Energy, and Other Fundamental Physical Quantities in the Atomic World and the Use of Atomic Units in Quantum Mechanical Calculations

ERIC Educational Resources Information Center

Teo, Boon K.; Li, Wai-Kee

2011-01-01

This article is divided into two parts. In the first part, the atomic unit (au) system is introduced and the scales of time, space (length), and speed, as well as those of mass and energy, in the atomic world are discussed. In the second part, the utility of atomic units in quantum mechanical and spectroscopic calculations is illustrated with…

Mass Deacidification Procedures for Libraries and Archives: State of Development and Perspectives for Implementation in the Federal Republic of Germany.

ERIC Educational Resources Information Center

Schwerdt, Peter

Translated from its original German because of the great interest in mass deacidification in the United States, this report summarizes a substantial study of deacidification techniques conducted for the West German Library by the Battelle Institute. It begins with a summary of the findings of the study, which is followed by discussions of: (1) The…

A simple protocol for combinatorial cyclic depsipeptide libraries sequencing by matrix-assisted laser desorption/ionisation mass spectrometry.

PubMed

Gurevich-Messina, Juan M; Giudicessi, Silvana L; Martínez-Ceron, María C; Acosta, Gerardo; Erra-Balsells, Rosa; Cascone, Osvaldo; Albericio, Fernando; Camperi, Silvia A

2015-01-01

Short cyclic peptides have a great interest in therapeutic, diagnostic and affinity chromatography applications. The screening of 'one-bead-one-peptide' combinatorial libraries combined with mass spectrometry (MS) is an excellent tool to find peptides with affinity for any target protein. The fragmentation patterns of cyclic peptides are quite more complex than those of their linear counterparts, and the elucidation of the resulting tandem mass spectra is rather more difficult. Here, we propose a simple protocol for combinatorial cyclic libraries synthesis and ring opening before MS analysis. In this strategy, 4-hydroxymethylbenzoic acid, which forms a benzyl ester with the first amino acid, was used as the linker. A glycolamidic ester group was incorporated after the combinatorial positions by adding glycolic acid. The library synthesis protocol consisted in the following: (i) incorporation of Fmoc-Asp[2-phenylisopropyl (OPp)]-OH to Ala-Gly-oxymethylbenzamide-ChemMatrix, (ii) synthesis of the combinatorial library, (iii) assembly of a glycolic acid, (iv) couple of an Ala residue in the N-terminal, (v) removal of OPp, (vi) peptide cyclisation through side chain Asp and N-Ala amino terminus and (vii) removal of side chain protecting groups. In order to simultaneously open the ring and release each peptide, benzyl and glycolamidic esters were cleaved with ammonia. Peptide sequences could be deduced from the tandem mass spectra of each single bead evaluated. The strategy herein proposed is suitable for the preparation of one-bead-one-cyclic depsipeptide libraries that can be easily open for its sequencing by matrix-assisted laser desorption/ionisation MS. It employs techniques and reagents frequently used in a broad range of laboratories without special expertise in organic synthesis. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

Construction of Chinese adult male phantom library and its application in the virtual calibration of in vivo measurement.

PubMed

Chen, Yizheng; Qiu, Rui; Li, Chunyan; Wu, Zhen; Li, Junli

2016-03-07

In vivo measurement is a main method of internal contamination evaluation, particularly for large numbers of people after a nuclear accident. Before the practical application, it is necessary to obtain the counting efficiency of the detector by calibration. The virtual calibration based on Monte Carlo simulation usually uses the reference human computational phantom, and the morphological difference between the monitored personnel with the calibrated phantom may lead to the deviation of the counting efficiency. Therefore, a phantom library containing a wide range of heights and total body masses is needed. In this study, a Chinese reference adult male polygon surface (CRAM_S) phantom was constructed based on the CRAM voxel phantom, with the organ models adjusted to match the Chinese reference data. CRAM_S phantom was then transformed to sitting posture for convenience in practical monitoring. Referring to the mass and height distribution of the Chinese adult male, a phantom library containing 84 phantoms was constructed by deforming the reference surface phantom. Phantoms in the library have 7 different heights ranging from 155 cm to 185 cm, and there are 12 phantoms with different total body masses in each height. As an example of application, organ specific and total counting efficiencies of Ba-133 were calculated using the MCNPX code, with two series of phantoms selected from the library. The influence of morphological variation on the counting efficiency was analyzed. The results show only using the reference phantom in virtual calibration may lead to an error of 68.9% for total counting efficiency. Thus the influence of morphological difference on virtual calibration can be greatly reduced using the phantom library with a wide range of masses and heights instead of a single reference phantom.

Construction of Chinese adult male phantom library and its application in the virtual calibration of in vivo measurement

NASA Astrophysics Data System (ADS)

Chen, Yizheng; Qiu, Rui; Li, Chunyan; Wu, Zhen; Li, Junli

2016-03-01

In vivo measurement is a main method of internal contamination evaluation, particularly for large numbers of people after a nuclear accident. Before the practical application, it is necessary to obtain the counting efficiency of the detector by calibration. The virtual calibration based on Monte Carlo simulation usually uses the reference human computational phantom, and the morphological difference between the monitored personnel with the calibrated phantom may lead to the deviation of the counting efficiency. Therefore, a phantom library containing a wide range of heights and total body masses is needed. In this study, a Chinese reference adult male polygon surface (CRAM_S) phantom was constructed based on the CRAM voxel phantom, with the organ models adjusted to match the Chinese reference data. CRAMS phantom was then transformed to sitting posture for convenience in practical monitoring. Referring to the mass and height distribution of the Chinese adult male, a phantom library containing 84 phantoms was constructed by deforming the reference surface phantom. Phantoms in the library have 7 different heights ranging from 155 cm to 185 cm, and there are 12 phantoms with different total body masses in each height. As an example of application, organ specific and total counting efficiencies of Ba-133 were calculated using the MCNPX code, with two series of phantoms selected from the library. The influence of morphological variation on the counting efficiency was analyzed. The results show only using the reference phantom in virtual calibration may lead to an error of 68.9% for total counting efficiency. Thus the influence of morphological difference on virtual calibration can be greatly reduced using the phantom library with a wide range of masses and heights instead of a single reference phantom.

GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations.

PubMed

Maia, Julio Daniel Carvalho; Urquiza Carvalho, Gabriel Aires; Mangueira, Carlos Peixoto; Santana, Sidney Ramos; Cabral, Lucidio Anjos Formiga; Rocha, Gerd B

2012-09-11

In this study, we present some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size (up to 2500 atoms) molecular systems using GPU coprocessors and multithreaded shared-memory CPUs. Our modifications consisted of using a combination of highly optimized linear algebra libraries for both CPU (LAPACK and BLAS from Intel MKL) and GPU (MAGMA and CUBLAS) to hasten time-consuming parts of MOPAC such as the pseudodiagonalization, full diagonalization, and density matrix assembling. We have shown that it is possible to obtain large speedups just by using CPU serial linear algebra libraries in the MOPAC code. As a special case, we show a speedup of up to 14 times for a methanol simulation box containing 2400 atoms and 4800 basis functions, with even greater gains in performance when using multithreaded CPUs (2.1 times in relation to the single-threaded CPU code using linear algebra libraries) and GPUs (3.8 times). This degree of acceleration opens new perspectives for modeling larger structures which appear in inorganic chemistry (such as zeolites and MOFs), biochemistry (such as polysaccharides, small proteins, and DNA fragments), and materials science (such as nanotubes and fullerenes). In addition, we believe that this parallel (GPU-GPU) MOPAC code will make it feasible to use semiempirical methods in lengthy molecular simulations using both hybrid QM/MM and QM/QM potentials.

Techniques for Measuring Low Earth Orbital Atomic Oxygen Erosion of Polymers

NASA Technical Reports Server (NTRS)

deGroh, Kim K.; Banks, Bruce A.; Demko, Rikako

2002-01-01

Polymers such as polyimide Kapton and Teflon FEP (fluorinated ethylene propylene) are commonly used spacecraft materials due to their desirable properties such as flexibility, low density, and in the case of FEP, a low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low Earth orbit (LEO) environment are exposed to energetic atomic oxygen. Atomic oxygen reaction with polymers causes erosion, which is a threat to spacecraft durability. It is therefore important to understand the atomic oxygen erosion yield (E, the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. The most common technique for determining E is through mass loss measurements. For limited duration exposure experiments, such as shuttle experiments, where the atomic oxygen fluence is often so low that mass loss measurements can not produce acceptable uncertainties, recession measurements based on atomic force microscopy analyses can be used. Equally necessary to knowing the mass loss or recession depth for determining the erosion yield of polymers is the knowledge of the atomic oxygen fluence that the polymers were exposed to in space. This paper discusses the procedures and relevant issues for mass loss and recession depth measurements for passive atomic oxygen erosion yield characterization of polymers, along with techniques for active atomic oxygen fluence and erosion characterization. One active atomic oxygen erosion technique discussed is a new technique based on optical measurements. Details including the use of both semi-transparent and opaque polymers for active erosion measurement are reviewed.

Compound Identification Using Penalized Linear Regression on Metabolomics

PubMed Central

Liu, Ruiqi; Wu, Dongfeng; Zhang, Xiang; Kim, Seongho

2014-01-01

Compound identification is often achieved by matching the experimental mass spectra to the mass spectra stored in a reference library based on mass spectral similarity. Because the number of compounds in the reference library is much larger than the range of mass-to-charge ratio (m/z) values so that the data become high dimensional data suffering from singularity. For this reason, penalized linear regressions such as ridge regression and the lasso are used instead of the ordinary least squares regression. Furthermore, two-step approaches using the dot product and Pearson’s correlation along with the penalized linear regression are proposed in this study. PMID:27212894

Negative muon chemistry: the quantum muon effect and the finite nuclear mass effect.

PubMed

Posada, Edwin; Moncada, Félix; Reyes, Andrés

2014-10-09

The any-particle molecular orbital method at the full configuration interaction level has been employed to study atoms in which one electron has been replaced by a negative muon. In this approach electrons and muons are described as quantum waves. A scheme has been proposed to discriminate nuclear mass and quantum muon effects on chemical properties of muonic and regular atoms. This study reveals that the differences in the ionization potentials of isoelectronic muonic atoms and regular atoms are of the order of millielectronvolts. For the valence ionizations of muonic helium and muonic lithium the nuclear mass effects are more important. On the other hand, for 1s ionizations of muonic atoms heavier than beryllium, the quantum muon effects are more important. In addition, this study presents an assessment of the nuclear mass and quantum muon effects on the barrier of Heμ + H2 reaction.

Potential Interrelationships Between Library and Other Mass Media Systems.

ERIC Educational Resources Information Center

Parker, Edwin B.

The function of libraries is to make it easy for the people in their community to obtain information from other people or environments that may be distant is space, time or imagination. To perform this function libraries require communication media. Storage media are essential, but duplication and transmission media can improve the service of…

Characterizing Vaccinium berry Standard Reference Materials by GC-MS using NIST spectral libraries.

PubMed

Lowenthal, Mark S; Andriamaharavo, Nirina R; Stein, Stephen E; Phinney, Karen W

2013-05-01

A gas chromatography-mass spectrometry (GC-MS)-based method was developed for qualitative characterization of metabolites found in Vaccinium fruit (berry) dietary supplement Standard Reference Materials (SRMs). Definitive identifications are provided for 98 unique metabolites determined among six Vaccinium-related SRMs. Metabolites were enriched using an organic liquid/liquid extraction, and derivatized prior to GC-MS analysis. Electron ionization (EI) fragmentation spectra were searched against EI spectra of authentic standards compiled in the National Institute of Standards and Technology's mass spectral libraries, as well as spectra selected from the literature. Metabolite identifications were further validated using a retention index match along with prior probabilities and were compared with results obtained in a previous effort using collision-induced dissociation (CID) MS/MS datasets from liquid chromatography coupled to mass spectrometry experiments. This manuscript describes a nontargeted metabolite profile of Vaccinium materials, compares results among related materials and from orthogonal experimental platforms, and discusses the feasibility and development of using mass spectral library matching for nontargeted metabolite identification.

Measurements of Size Resolved Organic Particulate Mass Using An On-line Aerosol Mass Spectrometer (ams) Laboratory Validation; Analysis Tool Development; and Interpretation of Field Data

NASA Astrophysics Data System (ADS)

Alfarra, M. R.; Coe, H.; Allan, J. D.; Bower, K. N.; Garforth, A. A.; Canagaratna, M.; Worsnop, D.

The aerosol mass spectrometer (AMS) is a quantitative instrument designed to deliver real-time size resolved chemical composition of the volatile and semi volatile aerosol fractions. The AMS response to a wide range of organic compounds has been exper- imentally characterized, and has been shown to compare well with standard libraries of 70 eV electron impact ionization mass spectra. These results will be presented. Due to the scanning nature of the quadrupole mass spectrometer, the AMS provides averaged composition of ensemble of particles rather than single particle composi- tion. However, the mass spectra measured by AMS are reproducible and similar to those of standard libraries so analysis tools can be developed on large mass spectral libraries that can provide chemical composition information about the type of organic compounds in the aerosol. One such tool is presented and compared with laboratory measurements of single species and mixed component organic particles by the AMS. We will then discuss the applicability of these tools to interpreting field AMS data ob- tained in a range of experiments at different sites in the UK and Canada. The data will be combined with other measurements to show the behaviour of the organic aerosol fraction in urban and sub-urban environments.

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

PubMed

Wohlin, Åsa

2015-03-21

The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

PECAN: Library Free Peptide Detection for Data-Independent Acquisition Tandem Mass Spectrometry Data

PubMed Central

Ting, Ying S.; Egertson, Jarrett D.; Bollinger, James G.; Searle, Brian C.; Payne, Samuel H.; Noble, William Stafford; MacCoss, Michael J.

2017-01-01

In mass spectrometry-based shogun proteomics, data-independent acquisition (DIA) is an emerging technique for unbiased and reproducible measurement of protein mixtures. Without targeting a specific precursor ion, DIA MS/MS spectra are often highly multiplexed, containing product ions from multiple co-fragmenting precursors. Thus, detecting peptides directly from DIA data is challenging; most DIA data analyses require spectral libraries. Here we present a new library-free, peptide-centric tool PECAN that detects peptides directly from DIA data. PECAN reports evidence of detection based on product ion scoring, enabling detection of low abundance analytes with poor precursor ion signal. We benchmarked PECAN with chromatographic peak picking accuracy and peptide detection capability. We further validated PECAN detection with data-dependent acquisition and targeted analyses. Last, we used PECAN to build a library from DIA data and to query sequence variants. Together, these results show that PECAN detects peptides robustly and accurately from DIA data without using a library. PMID:28783153

Tailoring Thermal Conductivity of Single-stranded Carbon-chain Polymers through Atomic Mass Modification

PubMed Central

Liao, Quanwen; Zeng, Lingping; Liu, Zhichun; Liu, Wei

2016-01-01

Tailoring the thermal conductivity of polymers is central to enlarge their applications in the thermal management of flexible integrated circuits. Progress has been made over the past decade by fabricating materials with various nanostructures, but a clear relationship between various functional groups and thermal properties of polymers remains to be established. Here, we numerically study the thermal conductivity of single-stranded carbon-chain polymers with multiple substituents of hydrogen atoms through atomic mass modification. We find that their thermal conductivity can be tuned by atomic mass modifications as revealed through molecular dynamics simulations. The simulation results suggest that heavy homogeneous substituents do not assist heat transport and trace amounts of heavy substituents can in fact hinder heat transport substantially. Our analysis indicates that carbon chain has the biggest contribution (over 80%) to the thermal conduction in single-stranded carbon-chain polymers. We further demonstrate that atomic mass modifications influence the phonon bands of bonding carbon atoms, and the discrepancies of phonon bands between carbon atoms are responsible for the remarkable drops in thermal conductivity and large thermal resistances in carbon chains. Our study provides fundamental insight into how to tailor the thermal conductivity of polymers through variable substituents. PMID:27713563

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

An overview of the Evaluation of Oxygen Interactions with Materials 3 experiment: Space Shuttle Mission 46, July-August 1992

NASA Technical Reports Server (NTRS)

Koontz, Steven L.; Leger, Lubert J.; Visentine, James T.; Hunton, Don E.; Cross, Jon B.; Hakes, Charles L.

1995-01-01

The Evaluation of Oxygen Interactions with Materials 3 (EOIM-3) flight experiment was developed to obtain benchmark atomic oxygen reactivity data and was conducted during Space Transportation System Mission 46 (STS-46), July 31 to August 7, 1992. In this paper, we present an overview of EOIM-3 and the results of the Lyndon B. Johnson Space Center (JSC) materials reactivity and mass spectrometer/carousel experiments. Mass spectrometer calibration methods are discussed briefly, as a prelude to a detailed discussion of the mass spectrometric results produced during STS-46. Mass spectrometric measurements of ambient O-atom flux and fluence are in good agreement with the values calculated using the MSIS-86 model of the thermosphere as well as estimates based on the extent of O-atom reaction with Kapton polyimide. Mass spectrometric measurements of gaseous products formed by O-atom reaction with C(13) labeled Kapton revealed CO, CO2, H2O, NO, and NO2. Finally, by operating the mass spectrometer so as to detect naturally occurring ionospheric species, we characterized the ambient ionosphere at various times during EOIM-3 and detected the gaseous reaction products formed when ambient ions interacted with the C(13) Kapton carousel sector. By direct comparison of the results of on-orbit O-atom exposures with those conducted in ground-based laboratory systems, which provide known O-atom fluences and translational energies, we have demonstrated the strong translational energy dependence of O-atom reactions with a variety of polymers. A 'line-of-centers' reactive scattering model was shown to provide a reasonably accurate description of the translational energy dependence of polymer reactions with O atoms at high atom kinetic energies while a Beckerle-Ceyer model provided an accurate description of O-atom reactivity over a three order-of-magnitude range in translational energy and a four order-of-magnitude range in reaction efficiency. Postflight studies of the polymer samples by x-ray photoelectron spectroscopy and infrared spectroscopy demonstrate that O-atom attack is confined to the near-surface region of the sample, i.e. within 50 to 100 A of the surface.

Ultra-precise single-ion atomic mass measurements on deuterium and helium-3

NASA Astrophysics Data System (ADS)

Zafonte, S. L.; Van Dyck, R. S., Jr.

2015-04-01

The former University of Washington Penning Trap Mass Spectrometer (UW-PTMS), now located at the Max Planck Institute for Nuclear Physics in Heidelberg, Germany, was used in the decade before the move to determine new values for the deuteron atomic mass, M (2H+) = 2.013 553 212 745(40) u, and the deuterium atomic mass, M (2H) = 2.014 101 778 052(40) u, both of which are now more than an order-of-magnitude more accurate than the previous best 1994-MIT measurements of these quantities. The new value for the deuteron’s mass can then be used with the accepted 2010-CODATA proton mass and the most recent 1999-measurement of the 2.2 MeV gamma-ray binding energy of the deuteron to refine the neutron’s mass to mn = 1.008 664 916 018(435) u which has about half the uncertainty relative to the value computed using that previous 1994-MIT deuterium measurement. As a result, further improvements of mn must now come from a more accurate determination of the wavelength of this gamma ray. In this same period of time, this spectrometer has also been used to determine new values for the helion atomic mass, M (3He2+) = 3.014 932 246 668(43) u, and the neutral helium-3 atomic mass, M (3He) = 3.016 029 321 675(43) u, which are both about 60 times more accurate than the 2006-SMILETRAP measurements, but disagree with the 4.4-times less-accurate 2015-Florida-State measurements by 0.76 nu. It is expected that these helium-3 results will be used in the future 3H/3He mass ratio (to be determined by the Heidelberg, Germany version of the old UW-PTMS) in order to generate a more accurate value for the tritium atomic mass.

Mass Digitization at Yale University Library: Exposing the Treasures in Our Stacks

ERIC Educational Resources Information Center

Weintraub, Jennifer; Wisner, Melissa

2008-01-01

In September 2007, Yale University Library (YUL) and Microsoft agreed to partner in a large-scale project to digitize 100,000 books from the YUL collections--an ambitious effort that would substantially increase the library's digitized holdings, particularly in the area of its own text collections. YUL has been digitizing materials from its…

Transforming Libraries: Issues and Innovations in Electronic Scholarly Publishing. Transforming Libraries Series. SPEC Kit 223.

ERIC Educational Resources Information Center

Soete, George J.

This issue covers the broad topic of electronic scholarly publication. Some 25 professionals in 20 libraries, consortia, and publishing enterprises were interviewed for this issue. A section on issues and trends for managers discusses the proliferation of roles and models; assembling the critical mass; licensing, copyright and interlibrary loan;…

MARC and the Library Service Center: Automation at Bargain Rates.

ERIC Educational Resources Information Center

Pearson, Karl M.

Despite recent research and development in the field of library automation, libraries have been unable to reap the benefits promised by technology due to the high cost of building and maintaining their own computer-based systems. Time-sharing and disc mass storage devices will bring automation costs, if spread over a number of users, within the…

ATOMIC PHYSICS, AN AUTOINSTRUCTIONAL PROGRAM, VOLUME 2, SUPPLEMENT.

ERIC Educational Resources Information Center

DETERLINE, WILLIAM A.; KLAUS, DAVID J.

THE AUTOINSTRUCTIONAL MATERIALS IN THIS TEXT WERE PREPARED FOR USE IN AN EXPERIMENTAL STUDY, OFFERING SELF-TUTORING MATERIAL FOR LEARNING ATOMIC PHYSICS. THE TOPICS COVERED ARE (1) ISOTOPES AND MASS NUMBERS, (2) MEASURING ATOMIC MASS, (3) DISCOVERY OF THE NUCLEUS, (4) STRUCTURE OF THE NUCLEUS, (5) DISCOVERY OF THE NEUTRON, (6) NUCLEAR REACTIONS,…

Precise measurements of the atomic masses of silicon-28, phosphorus-31, sulfur-32, krypton-84,86, xenon-129,132,136, and the dipole moment of PH+ using single-ion and two-ion Penning trap techniques

NASA Astrophysics Data System (ADS)

Redshaw, Matthew

This dissertation describes high precision measurements of atomic masses by measuring the cyclotron frequency of ions trapped singly, or in pairs, in a precision, cryogenic Penning trap. By building on techniques developed at MIT for measuring the cyclotron frequency of single trapped ions, the atomic masses of 84,86Kr, and 129,132,136Xe have been measured to less than a part in 1010 fractional precision. By developing a new technique for measuring the cyclotron frequency ratio of a pair of simultaneously trapped ions, the atomic masses of 28Si, 31P and 32S have been measured to 2 or 3 parts in 10 11. This new technique has also been used to measure the dipole moment of PH+. During the course of these measurements, two significant, but previously unsuspected sources of systematic error were discovered, characterized and eliminated. Extensive tests for other sources of systematic error were performed and are described in detail. The mass measurements presented here provide a significant increase in precision over previous values for these masses, by factors of 3 to 700. The results have a broad range of physics applications: The mass of 136 Xe is important for searches for neutrinoless double-beta-decay; the mass of 28Si is relevant to the re-definition of the artifact kilogram in terms of an atomic mass standard; the masses of 84,86Kr, and 129,132,136Xe provide convenient reference masses for less precise mass spectrometers in diverse fields such as nuclear physics and chemistry; and the dipole moment of PH+ provides a test of molecular structure calculations.

Capturing Nature's Diversity

PubMed Central

Pascolutti, Mauro; Campitelli, Marc; Nguyen, Bao; Pham, Ngoc; Gorse, Alain-Dominique; Quinn, Ronald J.

2015-01-01

Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a high proportion of the individual molecular interaction motifs embedded within natural products using a fragment screening library spanning 422 structural clusters and comprised of approximately 2800 natural products. PMID:25902039

The 2012 Atomic Mass Evaluation and the Mass Tables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Audi, G., E-mail: amdc.audi@gmail.com; Wang, M.; MPI-K, D-69117 Heidelberg

The new evaluation of the Atomic Masses, Ame2012, has just been released. It represents a major step in the history of the 60 year old Atomic Mass Evaluation based on the method developed by Wapstra. This new publication includes all material available to date. Some of the policies and procedures used in our evaluation are reported, together with an illustration of one specially difficult case, the energy available for the {sup 102}Pd double-electron capture. The observation of the mass surface reveals many important new features. We illustrate this statement by the double magicity of {sup 270}Hs at N = 162more » and Z = 108.« less

Atom Interferometry in the Presence of an External Test Mass

DOE PAGES

Dubetsky, Boris; Libby, Stephen; Berman, Paul

2016-04-21

The influence of an external test mass on the phase of the signal of an atom interferometer is studied theoretically. Using traditional techniques in atom optics based on the density matrix equations in the Wigner representation, we are able to extract the various contributions to the phase of the signal associated with the classical motion of the atoms, the quantum correction to this motion resulting from atomic recoil that is produced when the atoms interact with Raman field pulses and quantum corrections to the atomic motion that occur in the time between the Raman field pulses. Thus, by increasing themore » effective wave vector associated with the Raman field pulses using modified field parameters, we can increase the sensitivity of the signal to the point where such quantum corrections can be measured. Furthermore, the expressions that are derived can be evaluated numerically to isolate the contribution to the signal from an external test mass. The regions of validity of the exact and approximate expressions are determined.« less

SLHAplus: A library for implementing extensions of the standard model

NASA Astrophysics Data System (ADS)

Bélanger, G.; Christensen, Neil D.; Pukhov, A.; Semenov, A.

2011-03-01

We provide a library to facilitate the implementation of new models in codes such as matrix element and event generators or codes for computing dark matter observables. The library contains an SLHA reader routine as well as diagonalisation routines. This library is available in CalcHEP and micrOMEGAs. The implementation of models based on this library is supported by LanHEP and FeynRules. Program summaryProgram title: SLHAplus_1.3 Catalogue identifier: AEHX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 6283 No. of bytes in distributed program, including test data, etc.: 52 119 Distribution format: tar.gz Programming language: C Computer: IBM PC, MAC Operating system: UNIX (Linux, Darwin, Cygwin) RAM: 2000 MB Classification: 11.1 Nature of problem: Implementation of extensions of the standard model in matrix element and event generators and codes for dark matter observables. Solution method: For generic extensions of the standard model we provide routines for reading files that adopt the standard format of the SUSY Les Houches Accord (SLHA) file. The procedure has been generalized to take into account an arbitrary number of blocks so that the reader can be used in generic models including non-supersymmetric ones. The library also contains routines to diagonalize real and complex mass matrices with either unitary or bi-unitary transformations as well as routines for evaluating the running strong coupling constant, running quark masses and effective quark masses. Running time: 0.001 sec

The Particle Adventure | What is fundamental? | Fundamental

Science.gov Websites

fundamental The atom Is the atom fundamental? Is the nucleus fundamental? Are protons and neutrons fundamental decay What is the Mechanism giving mass to fundamental particles? What is the Mechanism giving mass to fundamental particles? Part 2 How Does the Higgs Boson get its Mass? Finding the Mass of the Higgs Boson

Filtrates and Residues: Measuring the Atomic or Molecular Mass of a Gas with a Tire Gauge and a Butane Lighter Fluid Can.

ERIC Educational Resources Information Center

Bodner, George M.; Magginnis, Lenard J.

1985-01-01

Describes the use of an inexpensive apparatus (based on a butane lighter fluid can and a standard tire pressure gauge) in measuring the atomic/molecular mass of an unknown gas and in demonstrating the mass of air or the dependence of pressure on the mass of a gas. (JN)

Meta-atom cluster acoustic metamaterial with broadband negative effective mass density

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Huaijun; Zhai, Shilong; Ding, Changlin

2014-02-07

We design a resonant meta-atom cluster, via which a two-dimensional (2D) acoustic metamaterial (AM) with broadband negative effective mass density from 1560 Hz to 5580 Hz is fabricated. Experimental results confirm that there is only weak interaction among the meta-atoms in the cluster. And then the meta-atoms in the cluster independently resonate, resulting in the cluster becoming equivalent to a broadband resonance unit. Extracted effective refractive indices from reflection and transmission measurements of the 2D AM appear to be negative from 1500 Hz to 5480 Hz. The broadband negative refraction has also been demonstrated by our further experiments. We expectmore » that this meta-atom cluster AM will significantly contribute to the design of broadband negative effective mass density AM.« less

Interpretation of atomic mass systematics in terms of the valence shells and a simple scheme for predicting masses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haustein, P.E.; Brenner, D.S.; Casten, R.F.

1988-07-01

A new semiempirical method that significantly simplifies atomic mass systematics and which provides a method for making mass predictions by linear interpolation is discussed in the context of the nuclear valence space. In certain regions complicated patterns of mass systematics in traditional plots versus Z, N, or isospin are consolidated and transformed into linear ones extending over long isotopic and isotonic sequences.

Establishment of a search library about benzylisoquinoline alkaloids based on selective separation on the binaphthyl column and standard analysis on C18 column.

PubMed

Liu, Qiaoxia; Zhou, Binbin; Wang, Xinliang; Ke, Yanxiong; Jin, Yu; Yin, Lihui; Liang, Xinmiao

2012-12-01

A search library about benzylisoquinoline alkaloids was established based on preparation of alkaloid fractions from Rhizoma coptidis, Cortex phellodendri, and Rhizoma corydalis. In this work, two alkaloid fractions from each herbal medicine were first prepared based on selective separation on the "click" binaphthyl column. And then these alkaloid fractions were analyzed on C18 column by liquid chromatography coupled with tandem mass spectrometry. Many structure-related compounds were included in these alkaloids fractions, which led to easy separation and good MS response in further work. Therefore, a search library of 52 benzylisoquinoline alkaloids was established, which included eight aporphine, 19 tetrahydroprotoberberine, two protopine, two benzyltetrahydroisoquinoline, and 21 protoberberine alkaloids. The information of the search library contained compound names, structures, retention times, accurate masses, fragmentation pathways of benzylisoquionline alkaloids, and their sources from three herbal medicines. Using such a library, the alkaloids, especially those trace and unknown components in some herbal medicine could be accurately and quickly identified. In addition, the distribution of benzylisoquinoline alkaloids in the herbal medicines could be also summarized by searching the source samples in the library. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nuclear data libraries assessment for modelling a small fluoride salt-cooled, high-temperature reactor

NASA Astrophysics Data System (ADS)

Mohamed, Hassan; Lindley, Benjamin; Parks, Geoffrey

2017-01-01

Nuclear data consists of measured or evaluated probabilities of various fundamental physical interactions involving the nuclei of atoms and their properties. Most fluoride salt-cooled high-temperature reactor (FHR) studies that were reviewed do not give detailed information on the data libraries used in their assessments. Therefore, the main objective of this data libraries comparison study is to investigate whether there are any significant discrepancies between main data libraries, namely ENDF/B-VII, JEFF-3.1 and JEF-2.2. Knowing the discrepancies, especially its magnitude, is important and relevant for readers as to whether further cautions are necessary for any future verification or validation processes when modelling an FHR. The study is performed using AMEC's reactor physics software tool, WIMS. The WIMS calculation is simply a 2-D infinite lattice of fuel assembly calculation. The comparison between the data libraries in terms of infinite multiplication factor, kinf and pin power map are presented. Results show that the discrepancy between JEFF-3.1 and ENDF/B-VII libraries is reasonably small but increases as the fuel depletes due to the data libraries uncertainties that are accumulated at each burnup step. Additionally, there are large discrepancies between JEF-2.2 and ENDF/B-VII because of the inadequacy of the JEF-2.2 library.

Oxygen atom reaction with shuttle materials at orbital altitudes

NASA Technical Reports Server (NTRS)

Leger, L. J.

1982-01-01

Surfaces of materials used in the space shuttle orbiter payload bay and exposed during STS-1 through STS-3 were examined after flight. Paints and polymers, in particular Kapton used on the television camera thermal blanket, showed significant change. Generally, the change was a loss of surface gloss on the polymer with apparent aging on the paint surfaces. The Kapton surfaces showed the greatest change, and postflight analyses showed mass loss of 4.8 percent on STS-2 and 35 percent on STS-3 for most heavily affected surfaces. Strong shadow patterns were evident. The greatest mass loss was measured on surfaces which were exposed to solar radiation in conjunction with exposure in the vehicle velocity vector. A mechanism which involves the interaction of atomic oxygen with organic polymer surfaces is proposed. Atomic oxygen is the major ambient species at low orbital altitudes and presents a flux of 8 x 10 to the 14th power atoms/cu cm sec for reaction. Correlation of the expected mass loss based on ground-based oxygen atom/polymer reaction rates shows lower mass loss of the Kapton than measured. Consideration of solar heating effects on reaction rates as well as the high oxygen atom energy due to the orbiter's orbital velocity brings the predicted and measured mass loss in surprisingly good agreement. Flight sample surface morphology comparison with ground based Kapton/oxygen atom exposures provides additional support for the oxygen interaction mechanism.

Algorithm for quantum-mechanical finite-nuclear-mass variational calculations of atoms with two p electrons using all-electron explicitly correlated Gaussian basis functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharkey, Keeper L.; Pavanello, Michele; Bubin, Sergiy

2009-12-15

A new algorithm for calculating the Hamiltonian matrix elements with all-electron explicitly correlated Gaussian functions for quantum-mechanical calculations of atoms with two p electrons or a single d electron have been derived and implemented. The Hamiltonian used in the approach was obtained by rigorously separating the center-of-mass motion and it explicitly depends on the finite mass of the nucleus. The approach was employed to perform test calculations on the isotopes of the carbon atom in their ground electronic states and to determine the finite-nuclear-mass corrections for these states.

A method to improve visual similarity of breast masses for an interactive computer-aided diagnosis environment.

PubMed

Zheng, Bin; Lu, Amy; Hardesty, Lara A; Sumkin, Jules H; Hakim, Christiane M; Ganott, Marie A; Gur, David

2006-01-01

The purpose of this study was to develop and test a method for selecting "visually similar" regions of interest depicting breast masses from a reference library to be used in an interactive computer-aided diagnosis (CAD) environment. A reference library including 1000 malignant mass regions and 2000 benign and CAD-generated false-positive regions was established. When a suspicious mass region is identified, the scheme segments the region and searches for similar regions from the reference library using a multifeature based k-nearest neighbor (KNN) algorithm. To improve selection of reference images, we added an interactive step. All actual masses in the reference library were subjectively rated on a scale from 1 to 9 as to their "visual margins speculations". When an observer identifies a suspected mass region during a case interpretation he/she first rates the margins and the computerized search is then limited only to regions rated as having similar levels of spiculation (within +/-1 scale difference). In an observer preference study including 85 test regions, two sets of the six "similar" reference regions selected by the KNN with and without the interactive step were displayed side by side with each test region. Four radiologists and five nonclinician observers selected the more appropriate ("similar") reference set in a two alternative forced choice preference experiment. All four radiologists and five nonclinician observers preferred the sets of regions selected by the interactive method with an average frequency of 76.8% and 74.6%, respectively. The overall preference for the interactive method was highly significant (p < 0.001). The study demonstrated that a simple interactive approach that includes subjectively perceived ratings of one feature alone namely, a rating of margin "spiculation," could substantially improve the selection of "visually similar" reference images.

Clarifying atomic weights: A 2016 four-figure table of standard and conventional atomic weights

USGS Publications Warehouse

Coplen, Tyler B.; Meyers, Fabienne; Holden, Norman E.

2017-01-01

To indicate that atomic weights of many elements are not constants of nature, in 2009 and 2011 the Commission on Isotopic Abundances and Atomic Weights (CIAAW) of the International Union of Pure and Applied Chemistry (IUPAC) replaced single-value standard atomic weight values with atomic weight intervals for 12 elements (hydrogen, lithium, boron, carbon, nitrogen, oxygen, magnesium, silicon, sulfur, chlorine, bromine, and thallium); for example, the standard atomic weight of nitrogen became the interval [14.00643, 14.00728]. CIAAW recognized that some users of atomic weight data only need representative values for these 12 elements, such as for trade and commerce. For this purpose, CIAAW provided conventional atomic weight values, such as 14.007 for nitrogen, and these values can serve in education when a single representative value is needed, such as for molecular weight calculations. Because atomic weight values abridged to four figures are preferred by many educational users and are no longer provided by CIAAW as of 2015, we provide a table containing both standard atomic weight values and conventional atomic weight values abridged to four figures for the chemical elements. A retrospective review of changes in four-digit atomic weights since 1961 indicates that changes in these values are due to more accurate measurements over time or to the recognition of the impact of natural isotopic fractionation in normal terrestrial materials upon atomic weight values of many elements. Use of the unit “u” (unified atomic mass unit on the carbon mass scale) with atomic weight is incorrect because the quantity atomic weight is dimensionless, and the unit “amu” (atomic mass unit on the oxygen scale) is an obsolete term: Both should be avoided.

Determination of the Relative Atomic Masses of Metals by Liberation of Molecular Hydrogen

ERIC Educational Resources Information Center

Waghorne, W. Earle; Rous, Andrew J.

2009-01-01

Students determine the relative atomic masses of calcium, magnesium, and aluminum by reaction with hydrochloric acid and measurement of the volume of hydrogen gas liberated. The experiment demonstrates stoichiometry and illustrates clearly that mass of the reagent is not the determinant of the amounts in chemical reactions. The experiment is…

Topographical and Chemical Imaging of a Phase Separated Polymer Using a Combined Atomic Force Microscopy/Infrared Spectroscopy/Mass Spectrometry Platform

DOE PAGES

Tai, Tamin; Karácsony, Orsolya; Bocharova, Vera; ...

2016-02-18

This article describes how the use of a hybrid atomic force microscopy/infrared spectroscopy/mass spectrometry imaging platform was demonstrated for the acquisition and correlation of nanoscale sample surface topography and chemical images based on infrared spectroscopy and mass spectrometry.

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

PubMed Central

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23467006

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

PubMed

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013 Elsevier B.V. All rights reserved.

Suspected-target pesticide screening using gas chromatography-quadrupole time-of-flight mass spectrometry with high resolution deconvolution and retention index/mass spectrum library.

PubMed

Zhang, Fang; Wang, Haoyang; Zhang, Li; Zhang, Jing; Fan, Ruojing; Yu, Chongtian; Wang, Wenwen; Guo, Yinlong

2014-10-01

A strategy for suspected-target screening of pesticide residues in complicated matrices was exploited using gas chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS). The screening workflow followed three key steps of, initial detection, preliminary identification, and final confirmation. The initial detection of components in a matrix was done by a high resolution mass spectrum deconvolution; the preliminary identification of suspected pesticides was based on a special retention index/mass spectrum (RI/MS) library that contained both the first-stage mass spectra (MS(1) spectra) and retention indices; and the final confirmation was accomplished by accurate mass measurements of representative ions with their response ratios from the MS(1) spectra or representative product ions from the second-stage mass spectra (MS(2) spectra). To evaluate the applicability of the workflow in real samples, three matrices of apple, spinach, and scallion, each spiked with 165 test pesticides in a set of concentrations, were selected as the models. The results showed that the use of high-resolution TOF enabled effective extractions of spectra from noisy chromatograms, which was based on a narrow mass window (5 mDa) and suspected-target compounds identified by the similarity match of deconvoluted full mass spectra and filtering of linear RIs. On average, over 74% of pesticides at 50 ng/mL could be identified using deconvolution and the RI/MS library. Over 80% of pesticides at 5 ng/mL or lower concentrations could be confirmed in each matrix using at least two representative ions with their response ratios from the MS(1) spectra. In addition, the application of product ion spectra was capable of confirming suspected pesticides with specificity for some pesticides in complicated matrices. In conclusion, GC-QTOF MS combined with the RI/MS library seems to be one of the most efficient tools for the analysis of suspected-target pesticide residues in complicated matrices. Copyright © 2014 Elsevier B.V. All rights reserved.

40 CFR 65.83 - Performance requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... stream nonhalogenated by reducing the vent stream halogen atom mass emission rate to less than 0.45... requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms contained in...

40 CFR 63.994 - Halogen scrubbers and other halogen reduction devices.

Code of Federal Regulations, 2012 CFR

2012-07-01

... halogen scrubber or other halogen reduction technique used to reduce the vent stream halogen atom mass... subpart shall determine the halogen atom mass emission rate prior to the combustion device according to...

40 CFR 63.994 - Halogen scrubbers and other halogen reduction devices.

Code of Federal Regulations, 2014 CFR

2014-07-01

... halogen scrubber or other halogen reduction technique used to reduce the vent stream halogen atom mass... subpart shall determine the halogen atom mass emission rate prior to the combustion device according to...

40 CFR 65.83 - Performance requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... stream nonhalogenated by reducing the vent stream halogen atom mass emission rate to less than 0.45... requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms contained in...

40 CFR 63.994 - Halogen scrubbers and other halogen reduction devices.

Code of Federal Regulations, 2010 CFR

2010-07-01

... halogen scrubber or other halogen reduction technique used to reduce the vent stream halogen atom mass... subpart shall determine the halogen atom mass emission rate prior to the combustion device according to...

40 CFR 65.83 - Performance requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... stream nonhalogenated by reducing the vent stream halogen atom mass emission rate to less than 0.45... requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms contained in...

40 CFR 65.83 - Performance requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... stream nonhalogenated by reducing the vent stream halogen atom mass emission rate to less than 0.45... requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms contained in...

40 CFR 63.994 - Halogen scrubbers and other halogen reduction devices.

Code of Federal Regulations, 2013 CFR

2013-07-01

... halogen scrubber or other halogen reduction technique used to reduce the vent stream halogen atom mass... subpart shall determine the halogen atom mass emission rate prior to the combustion device according to...

40 CFR 63.994 - Halogen scrubbers and other halogen reduction devices.

Code of Federal Regulations, 2011 CFR

2011-07-01

... halogen scrubber or other halogen reduction technique used to reduce the vent stream halogen atom mass... subpart shall determine the halogen atom mass emission rate prior to the combustion device according to...

40 CFR 65.83 - Performance requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... stream nonhalogenated by reducing the vent stream halogen atom mass emission rate to less than 0.45... requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms contained in...

Precision mass measurements of magnesium isotopes and implications for the validity of the isobaric mass multiplet equation

DOE PAGES

Brodeur, M.; Kwiatkowski, A. A.; Drozdowski, O. M.; ...

2017-09-18

If the mass excess of neutron-deficient nuclei and their neutron-rich mirror partners are both known, it can be shown that deviations of the isobaric mass multiplet equation (IMME) in the form of a cubic term can be probed. Such a cubic term was probed by using the atomic mass of neutron-rich magnesium isotopes measured using the TITAN Penning trap and the recently measured proton-separation energies of 29Cl and 30Ar. The atomic mass of 27Mg was found to be within 1.6σ of the value stated in the Atomic Mass Evaluation. The atomic masses of 28,29Mg were measured to be both withinmore » 1σ, while being 7 and 33 times more precise, respectively. Using the 29Mg mass excess and previous measurements of 29Cl, we uncovered a cubic coefficient of d = 28(7)keV, which is the largest known cubic coefficient of the IMME. This departure, however, could also be caused by experimental data with unknown systematic errors. Hence there is a need to confirm the mass excess of 28S and the one-neutron separation energy of 29Cl, which have both come from a single measurement. Lastly, our results were compared with ab initio calculations from the valence-space in-medium similarity renormalization group, resulting in a good agreement.« less

Precision mass measurements of magnesium isotopes and implications for the validity of the isobaric mass multiplet equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brodeur, M.; Kwiatkowski, A. A.; Drozdowski, O. M.

If the mass excess of neutron-deficient nuclei and their neutron-rich mirror partners are both known, it can be shown that deviations of the isobaric mass multiplet equation (IMME) in the form of a cubic term can be probed. Such a cubic term was probed by using the atomic mass of neutron-rich magnesium isotopes measured using the TITAN Penning trap and the recently measured proton-separation energies of 29Cl and 30Ar. The atomic mass of 27Mg was found to be within 1.6σ of the value stated in the Atomic Mass Evaluation. The atomic masses of 28,29Mg were measured to be both withinmore » 1σ, while being 7 and 33 times more precise, respectively. Using the 29Mg mass excess and previous measurements of 29Cl, we uncovered a cubic coefficient of d = 28(7)keV, which is the largest known cubic coefficient of the IMME. This departure, however, could also be caused by experimental data with unknown systematic errors. Hence there is a need to confirm the mass excess of 28S and the one-neutron separation energy of 29Cl, which have both come from a single measurement. Lastly, our results were compared with ab initio calculations from the valence-space in-medium similarity renormalization group, resulting in a good agreement.« less

A DIRECT MEASUREMENT OF THE BARYONIC MASS FUNCTION OF GALAXIES AND IMPLICATIONS FOR THE GALACTIC BARYON FRACTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Papastergis, Emmanouil; Huang, Shan; Giovanelli, Riccardo

We use both an H I-selected and an optically selected galaxy sample to directly measure the abundance of galaxies as a function of their 'baryonic' mass (stars + atomic gas). Stellar masses are calculated based on optical data from the Sloan Digital Sky Survey and atomic gas masses are calculated using atomic hydrogen (H I) emission line data from the Arecibo Legacy Fast ALFA survey. By using the technique of abundance matching, we combine the measured baryonic function of galaxies with the dark matter halo mass function in a {Lambda}CDM universe, in order to determine the galactic baryon fraction asmore » a function of host halo mass. We find that the baryon fraction of low-mass halos is much smaller than the cosmic value, even when atomic gas is taken into account. We find that the galactic baryon deficit increases monotonically with decreasing halo mass, in contrast with previous studies which suggested an approximately constant baryon fraction at the low-mass end. We argue that the observed baryon fractions of low-mass halos cannot be explained by reionization heating alone, and that additional feedback mechanisms (e.g., supernova blowout) must be invoked. However, the outflow rates needed to reproduce our result are not easily accommodated in the standard picture of galaxy formation in a {Lambda}CDM universe.« less

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics.

PubMed

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations.

Faradaurate-940: Synthesis, Mass Spectrometry, STEM, PDF, and SAXS Study of Au~940(SR)~160 Nanocrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumara, Chanaka; Zuo, Xiaobing; Cullen, David A

2014-01-01

Obtaining monodisperse nanocrystals, and determining its composition to the atomic level and its atomic structure is highly desirable, but is generally lacking. Here, we report the discovery and comprehensive characterization of a 3-nm plasmonic nanocrystal with a composition of Au940 20(SCH2CH2Ph)160 4, which is, the largest mass spectrometrically characterized gold thiolate nanoparticle produced to date. The compositional assignment has been made using electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS). The MS results show an unprecedented size monodispersity, where the number of Au atoms vary by only 40 atoms (940 20). The mass spectrometrically-determined sizemore » and composition are supported by aberration-corrected scanning transmission electron microscopy (STEM) and synchrotron-based methods such as atomic pair distribution function (PDF) and small angle X-ray scattering (SAXS). Lower resolution STEM images show an ensemble of particles 1000 s per frame visually demonstrating monodispersity. Modelling of SAXS on statistically significant nanoparticle population approximately 1012 individual nanoparticles - shows that the diameter is 3.0 0.2nm, supporting mass spectrometry and electron microscopy results on monodispersity. Atomic PDF based on high energy X-ray diffraction experiments show decent match with either a Marks decahedral or truncated octrahedral structure. Atomic resolution STEM images of single particles and its FFT suggest face-centered cubic (fcc) arrangement. UV-visible spectroscopy data shows that the 940-atom size supports a surface plasmon resonance peak at 505 nm. These monodisperse plasmonic nanoparticles minimize averaging effects and has potential application in solar cells, nano-optical devices, catalysis and drug delivery.« less

xGASS: total cold gas scaling relations and molecular-to-atomic gas ratios of galaxies in the local Universe

NASA Astrophysics Data System (ADS)

Catinella, Barbara; Saintonge, Amélie; Janowiecki, Steven; Cortese, Luca; Davé, Romeel; Lemonias, Jenna J.; Cooper, Andrew P.; Schiminovich, David; Hummels, Cameron B.; Fabello, Silvia; Geréb, Katinka; Kilborn, Virginia; Wang, Jing

2018-05-01

We present the extended GALEX Arecibo SDSS Survey (xGASS), a gas fraction-limited census of the atomic hydrogen (H I) gas content of 1179 galaxies selected only by stellar mass (M⋆ = 109-1011.5 M⊙) and redshift (0.01 < z < 0.05). This includes new Arecibo observations of 208 galaxies, for which we release catalogues and H I spectra. In addition to extending the GASS H I scaling relations by one decade in stellar mass, we quantify total (atomic+molecular) cold gas fractions and molecular-to-atomic gas mass ratios, Rmol, for the subset of 477 galaxies observed with the IRAM 30 m telescope. We find that atomic gas fractions keep increasing with decreasing stellar mass, with no sign of a plateau down to log M⋆/M⊙ = 9. Total gas reservoirs remain H I-dominated across our full stellar mass range, hence total gas fraction scaling relations closely resemble atomic ones, but with a scatter that strongly correlates with Rmol, especially at fixed specific star formation rate. On average, Rmol weakly increases with stellar mass and stellar surface density μ⋆, but individual values vary by almost two orders of magnitude at fixed M⋆ or μ⋆. We show that, for galaxies on the star-forming sequence, variations of Rmol are mostly driven by changes of the H I reservoirs, with a clear dependence on μ⋆. Establishing if galaxy mass or structure plays the most important role in regulating the cold gas content of galaxies requires an accurate separation of bulge and disc components for the study of gas scaling relations.

DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis.

PubMed

MacConnell, Andrew B; McEnaney, Patrick J; Cavett, Valerie J; Paegel, Brian M

2015-09-14

The promise of exploiting combinatorial synthesis for small molecule discovery remains unfulfilled due primarily to the "structure elucidation problem": the back-end mass spectrometric analysis that significantly restricts one-bead-one-compound (OBOC) library complexity. The very molecular features that confer binding potency and specificity, such as stereochemistry, regiochemistry, and scaffold rigidity, are conspicuously absent from most libraries because isomerism introduces mass redundancy and diverse scaffolds yield uninterpretable MS fragmentation. Here we present DNA-encoded solid-phase synthesis (DESPS), comprising parallel compound synthesis in organic solvent and aqueous enzymatic ligation of unprotected encoding dsDNA oligonucleotides. Computational encoding language design yielded 148 thermodynamically optimized sequences with Hamming string distance ≥ 3 and total read length <100 bases for facile sequencing. Ligation is efficient (70% yield), specific, and directional over 6 encoding positions. A series of isomers served as a testbed for DESPS's utility in split-and-pool diversification. Single-bead quantitative PCR detected 9 × 10(4) molecules/bead and sequencing allowed for elucidation of each compound's synthetic history. We applied DESPS to the combinatorial synthesis of a 75,645-member OBOC library containing scaffold, stereochemical and regiochemical diversity using mixed-scale resin (160-μm quality control beads and 10-μm screening beads). Tandem DNA sequencing/MALDI-TOF MS analysis of 19 quality control beads showed excellent agreement (<1 ppt) between DNA sequence-predicted mass and the observed mass. DESPS synergistically unites the advantages of solid-phase synthesis and DNA encoding, enabling single-bead structural elucidation of complex compounds and synthesis using reactions normally considered incompatible with unprotected DNA. The widespread availability of inexpensive oligonucleotide synthesis, enzymes, DNA sequencing, and PCR make implementation of DESPS straightforward, and may prompt the chemistry community to revisit the synthesis of more complex and diverse libraries.

Recent developments in LIBXC - A comprehensive library of functionals for density functional theory

NASA Astrophysics Data System (ADS)

Lehtola, Susi; Steigemann, Conrad; Oliveira, Micael J. T.; Marques, Miguel A. L.

2018-01-01

LIBXC is a library of exchange-correlation functionals for density-functional theory. We are concerned with semi-local functionals (or the semi-local part of hybrid functionals), namely local-density approximations, generalized-gradient approximations, and meta-generalized-gradient approximations. Currently we include around 400 functionals for the exchange, correlation, and the kinetic energy, spanning more than 50 years of research. Moreover, LIBXC is by now used by more than 20 codes, not only from the atomic, molecular, and solid-state physics, but also from the quantum chemistry communities.

Broad screening of illicit ingredients in cosmetics using ultra-high-performance liquid chromatography-hybrid quadrupole-Orbitrap mass spectrometry with customized accurate-mass database and mass spectral library.

PubMed

Meng, Xianshuang; Bai, Hua; Guo, Teng; Niu, Zengyuan; Ma, Qiang

2017-12-15

Comprehensive identification and quantitation of 100 multi-class regulated ingredients in cosmetics was achieved using ultra-high-performance liquid chromatography (UHPLC) coupled with hybrid quadrupole-Orbitrap high-resolution mass spectrometry (Q-Orbitrap HRMS). A simple, efficient, and inexpensive sample pretreatment protocol was developed using ultrasound-assisted extraction (UAE), followed by dispersive solid-phase extraction (dSPE). The cosmetic samples were analyzed by UHPLC-Q-Orbitrap HRMS under synchronous full-scan MS and data-dependent MS/MS (full-scan MS 1 /dd-MS 2 ) acquisition mode. The mass resolution was set to 70,000 FWHM (full width at half maximum) for full-scan MS 1 and 17,500 FWHM for dd-MS 2 stage with the experimentally measured mass deviations of less than 2ppm (parts per million) for quasi-molecular ions and 5ppm for characteristic fragment ions for each individual analyte. An accurate-mass database and a mass spectral library were built in house for searching the 100 target compounds. Broad screening was conducted by comparing the experimentally measured exact mass of precursor and fragment ions, retention time, isotopic pattern, and ionic ratio with the accurate-mass database and by matching the acquired MS/MS spectra against the mass spectral library. The developed methodology was evaluated and validated in terms of limits of detection (LODs), limits of quantitation (LOQs), linearity, stability, accuracy, and matrix effect. The UHPLC-Q-Orbitrap HRMS approach was applied for the analysis of 100 target illicit ingredients in 123 genuine cosmetic samples, and exhibited great potential for high-throughput, sensitive, and reliable screening of multi-class illicit compounds in cosmetics. Copyright © 2017 Elsevier B.V. All rights reserved.

40 CFR 63.128 - Transfer operations provisions-test methods and procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... using a scrubber or other halogen reduction device to reduce the vent stream halogen atom mass emission...)(2) shall determine the halogen atom mass emission rate prior to the combustor according to the...

40 CFR 63.128 - Transfer operations provisions-test methods and procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... using a scrubber or other halogen reduction device to reduce the vent stream halogen atom mass emission...)(2) shall determine the halogen atom mass emission rate prior to the combustor according to the...

40 CFR 63.128 - Transfer operations provisions-test methods and procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... using a scrubber or other halogen reduction device to reduce the vent stream halogen atom mass emission...)(2) shall determine the halogen atom mass emission rate prior to the combustor according to the...

40 CFR 63.128 - Transfer operations provisions-test methods and procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... using a scrubber or other halogen reduction device to reduce the vent stream halogen atom mass emission...)(2) shall determine the halogen atom mass emission rate prior to the combustor according to the...

40 CFR 63.128 - Transfer operations provisions-test methods and procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... using a scrubber or other halogen reduction device to reduce the vent stream halogen atom mass emission...)(2) shall determine the halogen atom mass emission rate prior to the combustor according to the...

USING AN ACCURATE MASS, TRIPLE QUADRUPOLE MASS SPECTROMETER AND AN ION CORRELATION PROGRAM TO IDENTIFY COMPOUNDS

EPA Science Inventory

Most compounds are not found in mass spectral libraries and must be identified by other means. Often, compound identities can be deduced from the compositions of the ions in their mass spectra and review of the chemical literature. Confirmation is provided by mass spectra and r...

Progress towards a space-borne quantum gravity gradiometer

NASA Technical Reports Server (NTRS)

Yu, Nan; Kohel, James M.; Ramerez-Serrano, Jaime; Kellogg, James R.; Lim, Lawrence; Maleki, Lute

2004-01-01

Quantum interferometer gravity gradiometer for 3D mapping is a project for developing the technology of atom interferometer-based gravity sensor in space. The atom interferometer utilizes atomic particles as free fall test masses to measure inertial forces with unprecedented sensitivity and precision. It also allows measurements of the gravity gradient tensor components for 3D mapping of subsurface mass distribution. The overall approach is based on recent advances of laser cooling and manipulation of atoms in atomic and optical physics. Atom interferometers have been demonstrated in research laboratories for gravity and gravity gradient measurements. In this approach, atoms are first laser cooled to micro-kelvin temperatures. Then they are allowed to freefall in vacuum as true drag-free test masses. During the free fall, a sequence of laser pulses is used to split and recombine the atom waves to realize the interferometric measurements. We have demonstrated atom interferometer operation in the Phase I period, and we are implementing the second generation for a complete gradiometer demonstration unit in the laboratory. Along with this development, we are developing technologies at component levels that will be more suited for realization of a space instrument. We will present an update of these developments and discuss the future directions of the quantum gravity gradiometer project.

Nanoscale mass conveyors

DOEpatents

Regan, Brian C [Oakland, CA; Aloni, Shaul [Albany, CA; Zettl, Alexander K [Kensington, CA

2008-03-11

A mass transport method and device for individually delivering chargeable atoms or molecules from source particles is disclosed. It comprises a channel; at least one source particle of chargeable material fixed to the surface of the channel at a position along its length; a means of heating the channel; and a means for applying an controllable electric field along the channel, whereby the device transports the atoms or molecules along the channel in response to applied electric field. In a preferred embodiment, the mass transport device will comprise a multiwalled carbon nanotube (MWNT), although other one dimensional structures may also be used. The MWNT or other structure acts as a channel for individual or small collections of atoms due to the atomic smoothness of the material. Also preferred is a source particle of a metal such as indium. The particles move by dissociation into small units, in some cases, individual atoms. The particles are preferably less than 100 nm in size.

Establishment of reliable mass spectra and retention indices library: identification of fatty acids in human plasma without authentic standards.

PubMed

Zhang, Liangxiao; Tan, Binbin; Zeng, Maomao; Lu, Hongmei; Liang, Yizeng

2012-01-15

Gas chromatography mass spectrometry (GC-MS) is routinely employed to analyze small molecules in various samples. The more challenge of GC-MS data processing is to identify the unknown compounds in samples. Mass spectra and retention indices library searching are commonly used method. However, the current libraries are often built through collecting data from different groups. To unknown compounds with similar mass spectra and retention indices (e.g. geometric (cis/trans) isomers), the inaccurate results sometime are supplied. In this case, the costly standard compounds have to be used in every analysis. In this report, taking identification of fatty acids as an example, we proposed a strategy of establishment of special database constructed by equivalent chain length (ECL) values in uniform conditions and mass spectra of fatty acid methyl esters (FAMEs). The mass spectral characteristics were firstly used to identify all expected straight saturated fatty acids, and subsequently calculate the ECL for fatty acids in the sample. Finally, the ECL values of fatty acids in the sample were compared with those of fatty acids in the customized database to identify their structures. The results showed that the method developed in this report could effectively identify similar unknown compounds (FAMEs in the human plasma) after validated by the authentic standards. Copyright © 2011 Elsevier B.V. All rights reserved.

Amber Plug-In for Protein Shop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliva, Ricardo

2004-05-10

The Amber Plug-in for ProteinShop has two main components: an AmberEngine library to compute the protein energy models, and a module to solve the energy minimization problem using an optimization algorithm in the OPTI-+ library. Together, these components allow the visualization of the protein folding process in ProteinShop. AmberEngine is a object-oriented library to compute molecular energies based on the Amber model. The main class is called ProteinEnergy. Its main interface methods are (1) "init" to initialize internal variables needed to compute the energy. (2) "eval" to evaluate the total energy given a vector of coordinates. Additional methods allow themore » user to evaluate the individual components of the energy model (bond, angle, dihedral, non-bonded-1-4, and non-bonded energies) and to obtain the energy of each individual atom. The Amber Engine library source code includes examples and test routines that illustrate the use of the library in stand alone programs. The energy minimization module uses the AmberEngine library and the nonlinear optimization library OPT++. OPT++ is open source software available under the GNU Lesser General Public License. The minimization module currently makes use of the LBFGS optimization algorithm in OPT++ to perform the energy minimization. Future releases may give the user a choice of other algorithms available in OPT++.« less

A broad-group cross-section library based on ENDF/B-VII.0 for fast neutron dosimetry Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alpan, F.A.

2011-07-01

A new ENDF/B-VII.0-based coupled 44-neutron, 20-gamma-ray-group cross-section library was developed to investigate the latest evaluated nuclear data file (ENDF) ,in comparison to ENDF/B-VI.3 used in BUGLE-96, as well as to generate an objective-specific library. The objectives selected for this work consisted of dosimetry calculations for in-vessel and ex-vessel reactor locations, iron atom displacement calculations for reactor internals and pressure vessel, and {sup 58}Ni(n,{gamma}) calculation that is important for gas generation in the baffle plate. The new library was generated based on the contribution and point-wise cross-section-driven (CPXSD) methodology and was applied to one of the most widely used benchmarks, themore » Oak Ridge National Laboratory Pool Critical Assembly benchmark problem. In addition to the new library, BUGLE-96 and an ENDF/B-VII.0-based coupled 47-neutron, 20-gamma-ray-group cross-section library was generated and used with both SNLRML and IRDF dosimetry cross sections to compute reaction rates. All reaction rates computed by the multigroup libraries are within {+-} 20 % of measurement data and meet the U. S. Nuclear Regulatory Commission acceptance criterion for reactor vessel neutron exposure evaluations specified in Regulatory Guide 1.190. (authors)« less

Atom Interferometry for Fundamental Physics and Gravity Measurements in Space

NASA Technical Reports Server (NTRS)

Kohel, James M.

2012-01-01

Laser-cooled atoms are used as freefall test masses. The gravitational acceleration on atoms is measured by atom-wave interferometry. The fundamental concept behind atom interferometry is the quantum mechanical particle-wave duality. One can exploit the wave-like nature of atoms to construct an atom interferometer based on matter waves analogous to laser interferometers.

A NEW MASS SPECTROMETRIC TECHNIQUE FOR IDENTIFYING TRACE-LEVEL ORGANIC COMPOUNDS IN COMPLEX MIXTURES

EPA Science Inventory

Most organic compounds are not found in mass spectral libraries and cannot be easily identified from low resolution mass spectra. Ion Composition Elucidation (ICE) utilizes selected ion recording with a double focusing mass spectrometer in a new way to determine exact mas...

Enriching screening libraries with bioactive fragment space.

PubMed

Zhang, Na; Zhao, Hongtao

2016-08-01

By deconvoluting 238,073 bioactive molecules in the ChEMBL library into extended Murcko ring systems, we identified a set of 2245 ring systems present in at least 10 molecules. These ring systems belong to 2221 clusters by ECFP4 fingerprints with a minimum intracluster similarity of 0.8. Their overlap with ring systems in commercial libraries was further quantified. Our findings suggest that success of a small fragment library is driven by the convergence of effective coverage of bioactive ring systems (e.g., 10% coverage by 1000 fragments vs. 40% by 2million HTS compounds), high enrichment of bioactive ring systems, and low molecular complexity enhancing the probability of a match with the protein targets. Reconciling with the previous studies, bioactive ring systems are underrepresented in screening libraries. As such, we propose a library of virtual fragments with key functionalities via fragmentation of bioactive molecules. Its utility is exemplified by a prospective application on protein kinase CK2, resulting in the discovery of a series of novel inhibitors with the most potent compound having an IC50 of 0.5μM and a ligand efficiency of 0.41kcal/mol per heavy atom. Copyright © 2016 Elsevier Ltd. All rights reserved.

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

PubMed

Beisken, Stephan; Earll, Mark; Portwood, David; Seymour, Mark; Steinbeck, Christoph

2014-04-01

Liquid chromatography coupled to mass spectrometry (LC-MS) is commonly applied to investigate the small molecule complement of organisms. Several software tools are typically joined in custom pipelines to semi-automatically process and analyse the resulting data. General workflow environments like the Konstanz Information Miner (KNIME) offer the potential of an all-in-one solution to process LC-MS data by allowing easy integration of different tools and scripts. We describe MassCascade and its workflow plug-in for processing LC-MS data. The Java library integrates frequently used algorithms in a modular fashion, thus enabling it to serve as back-end for graphical front-ends. The functions available in MassCascade have been encapsulated in a plug-in for the workflow environment KNIME, allowing combined use with e.g. statistical workflow nodes from other providers and making the tool intuitive to use without knowledge of programming. The design of the software guarantees a high level of modularity where processing functions can be quickly replaced or concatenated. MassCascade is an open-source library for LC-MS data processing in metabolomics. It embraces the concept of visual programming through its KNIME plug-in, simplifying the process of building complex workflows. The library was validated using open data.

Performance and properties of atomic oxygen protective coatings for polymeric materials

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Lamoreaux, Cynthia

1992-01-01

Such large LEO spacecraft as the Space Station Freedom will encounter high atomic oxygen fluences which entail the use of protective coatings for their polymeric structural materials. Such coatings have demonstrated polymer mass losses due to oxidation that are much smaller than those of unprotected materials. Attention is here given to protective and/or electrically conductive coatings of SiO(x), Ge, and indium-tin oxide which have been exposed to atomic oxygen in order to ascertain mass loss, electrical conductivity, and optical property dependence on atomic oxygen exposure.

Separation and characterization of metallosupramolecular libraries by ion mobility mass spectrometry.

PubMed

Li, Xiaopeng; Chan, Yi-Tsu; Casiano-Maldonado, Madalis; Yu, Jing; Carri, Gustavo A; Newkome, George R; Wesdemiotis, Chrys

2011-09-01

The self-assembly of Zn(II) ions and bis(terpyridine) (tpy) ligands carrying 120° or 180° angles between their metal binding sites was utilized to prepare metallosupramolecular libraries with the connectivity. These combinatorial libraries were separated and characterized by ion mobility mass spectrometry (IM MS) and tandem mass spectrometry (MS(2)). The 180°-angle building blocks generate exclusively linear complexes, which were used as standards to determine the architectures of the assemblies resulting from the 120°-angle ligands. The latter ligand geometry promotes the formation of macrocyclic hexamers, but other n-mers with smaller (n = 5) or larger ring sizes (n = 7-9) were identified as minor products, indicating that the angles in the bis(terpyridine) ligand and within the coordinative tpy-Zn(II)-tpy bonds are not as rigid, as previously believed. Macrocyclic and linear isomers were detected in penta- and heptameric assemblies; in the larger octa- and nonameric assemblies, ring-opened conformers with compact and folded geometries were observed in addition to linear extended and cyclic architectures. IM MS(2) experiments provided strong evidence that the macrocycles present in the libraries were already formed in solution, during the self-assembly process, not by dissociation of larger complexes in the gas phase. The IM MS/MS(2) methods provide a means to analyze, based on size and shape (architecture), supramolecular libraries that are not amenable to liquid chromatography, LC-MS, NMR, and/or X-ray techniques.

40 CFR 65.63 - Performance and group status change requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... halogen atom mass emission rate to less than 0.45 kilogram per hour (0.99 pound per hour) prior to any... the requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms...

40 CFR 65.63 - Performance and group status change requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... halogen atom mass emission rate to less than 0.45 kilogram per hour (0.99 pound per hour) prior to any... the requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms...

40 CFR 65.63 - Performance and group status change requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... halogen atom mass emission rate to less than 0.45 kilogram per hour (0.99 pound per hour) prior to any... the requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms...

40 CFR 65.63 - Performance and group status change requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... halogen atom mass emission rate to less than 0.45 kilogram per hour (0.99 pound per hour) prior to any... the requirements of paragraph (a)(1) or (2) of this section. The mass emission rate of halogen atoms...

The effect of center-of-mass motion on photon statistics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yang; Zhang, Jun; Wu, Shao-xiong

2015-10-15

We analyze the photon statistics of a weakly driven cavity quantum electrodynamics system and discuss the effects of photon blockade and photon-induced tunneling by effectively utilizing instead of avoiding the center-of-mass motion of a two-level atom trapped in the cavity. With the resonant interaction between atom, photon and phonon, it is shown that the bunching and anti-bunching of photons can occur with properly driving frequency. Our study shows the influence of the imperfect cooling of atom on the blockade and provides an attempt to take advantage of the center-of-mass motion.

Vector dark matter detection using the quantum jump of atoms

NASA Astrophysics Data System (ADS)

Yang, Qiaoli; Di, Haoran

2018-05-01

The hidden sector U(1) vector bosons created from inflationary fluctuations can be a substantial fraction of dark matter if their mass is around 10-5 eV. The creation mechanism makes the vector bosons' energy spectral density ρcdm / ΔE very high. Therefore, the dark electric dipole transition rate in atoms is boosted if the energy gap between atomic states equals the mass of the vector bosons. By using the Zeeman effect, the energy gap between the 2S state and the 2P state in hydrogen atoms or hydrogen like ions can be tuned. The 2S state can be populated with electrons due to its relatively long life, which is about 1/7 s. When the energy gap between the semi-ground 2S state and the 2P state matches the mass of the cosmic vector bosons, induced transitions occur and the 2P state subsequently decays into the 1S state. The 2 P → 1 S decay emitted Lyman-α photons can then be registered. The choices of target atoms depend on the experimental facilities and the mass ranges of the vector bosons. Because the mass of the vector boson is connected to the inflation scale, the proposed experiment may provide a probe to inflation.

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization.

PubMed

Dong, Qian; Liang, Yuxue; Yan, Xinjian; Markey, Sanford P; Mirokhin, Yuri A; Tchekhovskoi, Dmitrii V; Bukhari, Tallat H; Stein, Stephen E

2018-04-01

We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1κ. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins.

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization

PubMed Central

Dong, Qian; Liang, Yuxue; Yan, Xinjian; Markey, Sanford P.; Mirokhin, Yuri A.; Tchekhovskoi, Dmitrii V.; Bukhari, Tallat H.; Stein, Stephen E.

2018-01-01

ABSTRACT We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1κ. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins. PMID:29425077

Mutations of Electrons as Constituents of Hadrons

NASA Astrophysics Data System (ADS)

Driscoll, R. B.

1997-04-01

Conjecture (C) 1: Coulomb-charged constituents of electron (e) are attracted to its barycentre by lepto-strong force F=K/r^2+f; f is stably perturbative for r < the "radius" of e. An exterior magnetic field (MF) with gradient (G) secularly perturbs the eccentricities but not the energies of the constituents' orbits, changing the spin (s) and magnetic moment (μ) of e. (C) 2: F coheres two or more e's dynamically with r approximately equal to the "radius" of e. The resulting MF and G at each e oscillate. Stable values of s and μ result for each e which differs from the atomic values. Binding energies change the masses of the e's. A hadron results. (C) 3: An e similarly may bind to a proton to form a Rutherford- Santilli neutron. The proton is negligibly mutated.(References: H. Dehmelt, Science 247, 539 (1990); T.E. Phipps, Jr., Heretical Verities (Classic Non-fiction Library, Urbana, 1986); R.M. Santilli, Hadronic Mechanics (Ukrainian Academy of Sciences, Kiev, 1995 and 1996), 3 volumes.)

A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics.

PubMed

Marx, Harald; Lemeer, Simone; Schliep, Jan Erik; Matheron, Lucrece; Mohammed, Shabaz; Cox, Jürgen; Mann, Matthias; Heck, Albert J R; Kuster, Bernhard

2013-06-01

We present a peptide library and data resource of >100,000 synthetic, unmodified peptides and their phosphorylated counterparts with known sequences and phosphorylation sites. Analysis of the library by mass spectrometry yielded a data set that we used to evaluate the merits of different search engines (Mascot and Andromeda) and fragmentation methods (beam-type collision-induced dissociation (HCD) and electron transfer dissociation (ETD)) for peptide identification. We also compared the sensitivities and accuracies of phosphorylation-site localization tools (Mascot Delta Score, PTM score and phosphoRS), and we characterized the chromatographic behavior of peptides in the library. We found that HCD identified more peptides and phosphopeptides than did ETD, that phosphopeptides generally eluted later from reversed-phase columns and were easier to identify than unmodified peptides and that current computational tools for proteomics can still be substantially improved. These peptides and spectra will facilitate the development, evaluation and improvement of experimental and computational proteomic strategies, such as separation techniques and the prediction of retention times and fragmentation patterns.

TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits.

PubMed

Farabella, Irene; Vasishtan, Daven; Joseph, Agnel Praveen; Pandurangan, Arun Prasad; Sahota, Harpal; Topf, Maya

2015-08-01

Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.

Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

PubMed

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K; Martin, Daniel B

2011-06-03

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.

Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.

PubMed

Chen, Gengbo; Walmsley, Scott; Cheung, Gemmy C M; Chen, Liyan; Cheng, Ching-Yu; Beuerman, Roger W; Wong, Tien Yin; Zhou, Lei; Choi, Hyungwon

2017-05-02

Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups. Here we developed a bioinformatics workflow called MetaboDIA to build customized MS/MS spectral libraries using a user's own data dependent acquisition (DDA) data and to perform MS/MS-based quantification with DIA data, thus complementing conventional MS1-based quantification. MetaboDIA also allows users to build a spectral library directly from DIA data in studies of a large sample size. Using a marine algae data set, we show that quantification of fragment ions extracted with a customized MS/MS library can provide as reliable quantitative data as the direct quantification of precursor ions based on MS1 data. To test its applicability in complex samples, we applied MetaboDIA to a clinical serum metabolomics data set, where we built a DDA-based spectral library containing consensus spectra for 1829 compounds. We performed fragment ion quantification using DIA data using this library, yielding sensitive differential expression analysis.

Fast flexible modeling of RNA structure using internal coordinates.

PubMed

Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ Biagio

2011-01-01

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.

Mass spectrometric screening of ligands with lower off-rate from a clicked-based pooled library.

PubMed

Arai, Satoshi; Hirosawa, Shota; Oguchi, Yusuke; Suzuki, Madoka; Murata, Atsushi; Ishiwata, Shin'ichi; Takeoka, Shinji

2012-08-13

This paper describes a convenient screening method using ion trap electrospray ionization mass spectrometry to classify ligands to a target molecule in terms of kinetic parameters. We demonstrate this method in the screening of ligands to a hexahistidine tag from a pooled library synthesized by click chemistry. The ion trap mass spectrometry analysis revealed that higher stabilities of ligand-target complexes in the gas phase were related to lower dissociation rate constants, i.e., off-rates in solution. Finally, we prepared a fluorescent probe utilizing the ligand with lowest off-rate and succeeded in performing single molecule observations of hexahistidine-tagged myosin V walking on actin filaments.

QCDLoop: A comprehensive framework for one-loop scalar integrals

NASA Astrophysics Data System (ADS)

Carrazza, Stefano; Ellis, R. Keith; Zanderighi, Giulia

2016-12-01

We present a new release of the QCDLoop library based on a modern object-oriented framework. We discuss the available new features such as the extension to the complex masses, the possibility to perform computations in double and quadruple precision simultaneously, and useful caching mechanisms to improve the computational speed. We benchmark the performance of the new library, and provide practical examples of phenomenological implementations by interfacing this new library to Monte Carlo programs.

POWERFUL NEW TOOLS FOR ANALYZING ENVIRONMENTAL CONTAMINATION: MASS PEAK PROFILING FROM SELECTED-ION RECORDING DATA AND A PROFILE GENERATION MODEL

EPA Science Inventory

Capillary gas chromatography with mass spectrometric detection is the most commonly used technique for analyzing samples from Superfund sites. While the U.S. EPA has developed target lists of compounds for which library mass spectra are available on most mass spectrometer data s...

Dielectric barrier discharge ionization for liquid chromatography/mass spectrometry.

PubMed

Hayen, Heiko; Michels, Antje; Franzke, Joachim

2009-12-15

An atmospheric pressure microplasma ionization source based on a dielectric barrier discharge with a helium plasma cone outside the electrode region has been developed for liquid chromatography/mass spectrometry (LC/MS). For this purpose, the plasma was realized in a commercial atmospheric pressure ionization source. Dielectric barrier discharge ionization (DBDI) was compared to conventional electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), and atmospheric pressure photoionization (APPI) in the positive ionization mode. Therefore, a heterogeneous compound library was investigated that covered polar compounds such as amino acids, water-soluble vitamins, and nonpolar compounds like polycyclic aromatic hydrocarbons and functionalized hydrocarbons. It turned out that DBDI can be regarded as a soft ionization technique characterized by only minor fragmentation similar to APCI. Mainly protonated molecules were detected. Additionally, molecular ions were observed for polycyclic aromatic hydrocarbons and derivatives thereof. During DBDI, adduct formation with acetonitrile occurred. For aromatic compounds, addition of one to four oxygen atoms and to a smaller extend one nitrogen and oxygen was observed which delivered insight into the complexity of the ionization processes. In general, compounds covering a wider range of polarities can be ionized by DBDI than by ESI. Furthermore, limits of detection compared to APCI are in most cases equal or even better.

Electrostatic interaction energy and factor 1.23

NASA Astrophysics Data System (ADS)

Rubčić, A.; Arp, H.; Rubčić, J.

The factor F≫1.23 has originally been found in the redshift of quasars. Recently, it has been found in very different physical phenomena: the life-time of muonium, the masses of elementary particles (leptons, quarks,...), the correlation of atomic weight (A) and atomic number (Z) and the correlation of the sum of masses of all orbiting bodies with the mass of the central body in gravitational systems.

23. Photocopy of plan. Original in library of Lehmann Building, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

23. Photocopy of plan. Original in library of Lehmann Building, Missouri Botanical Garden. GENERAL PLAN OF 1905 BY OLMSTED BROTHERS, BROOKLINE, MASS., SHOWING NORTH AMERICAN TRACT AND PROPOSED HENRY SHAW TOWN HOUSE - Missouri Botanical Garden, 2345 Tower Grove Avenue, Saint Louis, Independent City, MO

Experimental study of the spray characteristics of a research airblast atomizer

NASA Technical Reports Server (NTRS)

Acosta, W. A.

1985-01-01

Airblast atomization was studied using a especially designed atomizer in which the liquid first impinges on a splash plate, then is directed radially outward and is atomized by the air passing through two concentric, vaned swirlers that swirl the air in opposite directions. The effect of flow conditions, air mass velocity (mass flow rate per unit area) and liquid to air ratio on the mean drop size was studied. Seven different ethanol solutions were used to simulate changes in fuel physical properties. The range of atomizing air velocities was from 30 to 80 m/s. The mean drop diameter was measured at ambient temperature (295 K) and atmospheric pressure.

Experimental study of the spray characteristics of a research airblast atomizer

NASA Technical Reports Server (NTRS)

Acosta, W. A.

1985-01-01

Airblast atomization was studied using a especially designed atomizer in which the liquid first impinges on a splash plate, then is directed radically outward and is atomized by the air passing through two concentric, vaned swirlers that swirl the air in opposite directions. The effect of flow conditions, air mass velocity (mass flow rate per unit area) and liquid to air ratio on the mean drop size was studied. Seven different ethanol solutions were used to simulate changes in fuel physical properties. The range of atomizing air velocities was from 30 to 80 m/s. The mean drop diameter was measured at ambient temperature (295 K) and atmospheric pressure.

Tandem mass spectrometry spectral libraries and library searching.

PubMed

Deutsch, Eric W

2011-01-01

Spectral library searching in the field of proteomics has been gaining visibility and use in the last few years, primarily due to the expansion of public proteomics data repositories and the large spectral libraries that can be generated from them. Spectral library searching has several advantages over conventional sequence searching: it is generally much faster, and has higher specificity and sensitivity. The speed increase is primarily, due to having a smaller, fully indexable search space of real spectra that are known to be observable. The increase in specificity and sensitivity is primarily due to the ability of a search engine to utilize the known intensities of the fragment ions, rather than just comparing with theoretical spectra as is done with sequence searching. The main disadvantage of spectral library searching is that one can only identify peptide ions that have been seen before and are stored in the spectral library. In this chapter, an overview of spectral library searching and the libraries currently available are presented.

Testing atomic mass models with radioactive beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haustein, P.E.

1989-01-01

Significantly increased yields of new or poorly characterized exotic isotopes that lie far from beta-decay stability can be expected when radioactive beams are used to produce these nuclides. Measurements of the masses of these new species are very important. Such measurements are motivated by the general tendency of mass models to diverge from one another upon excursions from the line of beta-stability. Therefore in these regions (where atomic mass data are presently nonexistent or sparse) the models can be tested rigorously to highlight the features that affect the quality of their short-range and long-range extrapolation properties. Selection of systems tomore » study can be guided, in part, by a desire to probe those mass regions where distinctions among mass models are most apparent and where yields of exotic isotopes, produced via radioactive beams, can be optimized. Identification of models in such regions that have good predictive properties will aid materially in guiding the selection of additional experiments which ultimately will provide expansion of the atomic mass database for further refinement of the mass models. 6 refs., 5 figs.« less

Ion optical design of a collinear laser-negative ion beam apparatus.

PubMed

Diehl, C; Wendt, K; Lindahl, A O; Andersson, P; Hanstorp, D

2011-05-01

An apparatus for photodetachment studies on atomic and molecular negative ions of medium up to heavy mass (M ≃ 500) has been designed and constructed. Laser and ion beams are merged in the apparatus in a collinear geometry and atoms, neutral molecules and negative ions are detected in the forward direction. The ion optical design and the components used to optimize the mass resolution and the transmission through the extended field-free interaction region are described. A 90° sector field magnet with 50 cm bending radius in combination with two slits is used for mass dispersion providing a resolution of M∕ΔM≅800 for molecular ions and M∕ΔM≅400 for atomic ions. The difference in mass resolution for atomic and molecular ions is attributed to different energy distributions of the sputtered ions. With 1 mm slits, transmission from the source through the interaction region to the final ion detector was determined to be about 0.14%.

Performance of Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry for Identification of Aspergillus, Scedosporium, and Fusarium spp. in the Australian Clinical Setting

PubMed Central

Sleiman, Sue; Halliday, Catriona L.; Chapman, Belinda; Brown, Mitchell; Nitschke, Joanne; Lau, Anna F.

2016-01-01

We developed an Australian database for the identification of Aspergillus, Scedosporium, and Fusarium species (n = 28) by matrix-assisted laser desorption ionization−time of flight mass spectrometry (MALDI-TOF MS). In a challenge against 117 isolates, species identification significantly improved when the in-house-built database was combined with the Bruker Filamentous Fungi Library compared with that for the Bruker library alone (Aspergillus, 93% versus 69%; Fusarium, 84% versus 42%; and Scedosporium, 94% versus 18%, respectively). PMID:27252460

An Electron/Photon/Relaxation Data Library for MCNP6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, III, H. Grady

The capabilities of the MCNP6 Monte Carlo code in simulation of electron transport, photon transport, and atomic relaxation have recently been significantly expanded. The enhancements include not only the extension of existing data and methods to lower energies, but also the introduction of new categories of data and methods. Support of these new capabilities has required major additions to and redesign of the associated data tables. In this paper we present the first complete documentation of the contents and format of the new electron-photon-relaxation data library now available with the initial production release of MCNP6.

Profiling and characterizing skin ceramides using reversed-phase liquid chromatography-quadrupole time-of-flight mass spectrometry.

PubMed

t'Kindt, Ruben; Jorge, Lucie; Dumont, Emmie; Couturon, Pauline; David, Frank; Sandra, Pat; Sandra, Koen

2012-01-03

An LC-MS based method for the profiling and characterization of ceramide species in the upper layer of human skin is described. Ceramide samples, collected by tape stripping of human skin, were analyzed by reversed-phase liquid chromatography coupled to high-resolution quadrupole time-of-flight mass spectrometry operated in both positive and negative electrospray ionization mode. All known classes of ceramides could be measured in a repeatable manner. Furthermore, the data set showed several undiscovered ceramides, including a class with four hydroxyl functionalities in its sphingoid base. High-resolution MS/MS fragmentation spectra revealed that each identified ceramide species is composed of several skeletal isomers due to variation in carbon length of the respective sphingoid bases and fatty acyl building blocks. The resulting variety in skeletal isomers has not been previously demonstrated. It is estimated that over 1000 unique ceramide structures could be elucidated in human stratum corneum. Ceramide species with an even and odd number of carbon atoms in both chains were detected in all ceramide classes. Acid hydrolysis of the ceramides, followed by LC-MS analysis of the end-products, confirmed the observed distribution of both sphingoid bases and fatty acyl groups in skin ceramides. The study resulted in an accurate mass retention time library for targeted profiling of skin ceramides. It is furthermore demonstrated that targeted data processing results in an improved repeatability versus untargeted data processing (72.92% versus 62.12% of species display an RSD < 15%). © 2011 American Chemical Society

Characterization of Volatile Nylon 6.6 Thermal-Oxidative Degradation Products by Selective Isotopic Labeling and Cryo-GC/MS

NASA Astrophysics Data System (ADS)

Smith, Jonell N.; V. White, Gregory; White, Michael I.; Bernstein, Robert; Hochrein, James M.

2012-09-01

Aged materials, such as polymers, can exhibit modifications to their chemical structure and physical properties, which may render the material ineffective for its intended purpose. Isotopic labeling was used to characterize low-molecular weight volatile thermal-oxidative degradation products of nylon 6.6 in an effort to better understand and predict changes in the aged polymer. Headspace gas from aged (up to 243 d at 138 °C) nylon 6.6 monomers (adipic acid and 1,6-hexanediamine) and polymer were preconcentrated, separated, and detected using cryofocusing gas chromatography mass spectrometry (cryo-GC/MS). Observations regarding the relative concentrations observed in each chromatographic peak with respect to aging time were used in conjunction with mass spectra for samples aged under ambient air to determine the presence and identity of 18 degradation products. A comparison of the National Institute of Standards and Technology (NIST) library, unlabeled, and isotopically labeled mass spectra (C-13 or N-15) and expected fragmentation pathways of each degradation product were used to identify the location of isotopically labeled atoms within the product's chemical structure, which can later be used to determine the exact origin of the species. In addition, observations for unlabeled nylon 6.6 aged in an O-18 enriched atmosphere were used to determine if the source of oxygen in the applicable degradation products was from the gaseous environment or the polymer. Approximations for relative isotopic ratios of unlabeled to labeled products are reported, where appropriate.

Ion implantation of solar cell junctions without mass analysis

NASA Technical Reports Server (NTRS)

Fitzgerald, D.; Tonn, D. G.

1981-01-01

This paper is a summary of an investigation to determine the feasibility of producing solar cells by means of ion implantation without the use of mass analysis. Ion implants were performed using molecular and atomic phosphorus produced by the vaporization of solid red phosphorus and ionized in an electron bombardment source. Solar cell junctions were ion implanted by mass analysis of individual molecular species and by direct unanalyzed implants from the ion source. The implant dose ranged from 10 to the 14th to 10 to the 16th atoms/sq cm and the energy per implanted atom ranged from 5 KeV to 40 KeV in this study.

The nuclear size and mass effects on muonic hydrogen-like atoms embedded in Debye plasma

NASA Astrophysics Data System (ADS)

Poszwa, A.; Bahar, M. K.; Soylu, A.

2016-10-01

Effects of finite nuclear size and finite nuclear mass are investigated for muonic atoms and muonic ions embedded in the Debye plasma. Both nuclear charge radii and nuclear masses are taken into account with experimentally determined values. In particular, isotope shifts of bound state energies, radial probability densities, transition energies, and binding energies for several atoms are studied as functions of Debye length. The theoretical model based on semianalytical calculations, the Sturmian expansion method, and the perturbative approach has been constructed, in the nonrelativistic frame. For some limiting cases, the comparison with previous most accurate literature results has been made.

LOOS: an extensible platform for the structural analysis of simulations.

PubMed

Romo, Tod D; Grossfield, Alan

2009-01-01

We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.

Preparing for ENDF/B-VIII

NASA Astrophysics Data System (ADS)

Brown, David

2017-09-01

Although the next major release of the ENDF/B library is not due until the 2017-2018 time frame, ENDF/B-VIII is already positioned to become the most important release of the library in some time. ENDF/B-VIII will be built around the Neutron Reaction Standards as well as the 1H, 16O, 56Fe, 235U, 238U and 239Pu evaluations developed as part of the Coordinated International Evaluation Library Organization (CIELO) pilot project. In this contribution, we summarize these improvements as well as the many other improvements to ENDF that have already been made or are scheduled to be made in the next year. Improvements already included in the ENDF/B-VIII beta releases: • Aggressive use of the flexible and physically correct LRF=7 resolved resonance format in 12 updated evaluations (35,37Cl, 40Ca, 54,56,57Fe, 63,65Cu and 182,183,184,186W) • Thermal capture gammas from the EGAF project (6,7Li, 11B, 19F, 23Na, 27Al, 28Si, 35,37Cl) • Thermal Scattering Law evaluations from NCSU (α and β phase SiO2, SiC, lucite, BeO, and polyethylene) and from the CAB-CNL collaboration (heavy and light water) • Many new evaluations in the neutron sublibrary (n, 12,13C, 40Ar, 54,57,58Fe, 58,59,60,61,62,64Ni, 63,65Cu, 73As, 120Sn, 236m1Np) Inclusion of Red Cullen's EPICS2014 library, updating the photo-atomic, electron and atomic-relaxation sublibraries. Many improvements are planned in the next year including new evaluations such as charged particle evaluations translated from LLNL's ECPL. In addition to these major changes, ENDF/B-VIII will be the first official library released simultaneously in the legacy ENDF-6 and the newly developed Generalized Nuclear Data (GND) formats.

The Documentation of Current Affairs in Public Libraries

ERIC Educational Resources Information Center

Smith, Gerry M.

1971-01-01

Current affairs phenomena are inadequately treated by the mass media. Primary materials produced by pressure groups is a valuable complement. Larger public libraries could perform a useful service in making some of the material more widely available. This article explains why and how it should be done. (2 references) (Author/NH)

mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data.

PubMed

Strohalm, Martin; Kavan, Daniel; Novák, Petr; Volný, Michael; Havlícek, Vladimír

2010-06-01

While tools for the automated analysis of MS and LC-MS/MS data are continuously improving, it is still often the case that at the end of an experiment, the mass spectrometrist will spend time carefully examining individual spectra. Current software support is mostly provided only by the instrument vendors, and the available software tools are often instrument-dependent. Here we present a new generation of mMass, a cross-platform environment for the precise analysis of individual mass spectra. The software covers a wide range of processing tasks such as import from various data formats, smoothing, baseline correction, peak picking, deisotoping, charge determination, and recalibration. Functions presented in the earlier versions such as in silico digestion and fragmentation were redesigned and improved. In addition to Mascot, an interface for ProFound has been implemented. A specific tool is available for isotopic pattern modeling to enable precise data validation. The largest available lipid database (from the LIPID MAPS Consortium) has been incorporated and together with the new compound search tool lipids can be rapidly identified. In addition, the user can define custom libraries of compounds and use them analogously. The new version of mMass is based on a stand-alone Python library, which provides the basic functionality for data processing and interpretation. This library can serve as a good starting point for other developers in their projects. Binary distributions of mMass, its source code, a detailed user's guide, and video tutorials are freely available from www.mmass.org .

New version: GRASP2K relativistic atomic structure package

NASA Astrophysics Data System (ADS)

Jönsson, P.; Gaigalas, G.; Bieroń, J.; Fischer, C. Froese; Grant, I. P.

2013-09-01

A revised version of GRASP2K [P. Jönsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597] is presented. It supports earlier non-block and block versions of codes as well as a new block version in which the njgraf library module [A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375] has been replaced by the librang angular package developed by Gaigalas based on the theory of [G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747, G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263]. Tests have shown that errors encountered by njgraf do not occur with the new angular package. The three versions are denoted v1, v2, and v3, respectively. In addition, in v3, the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Changes in v2 include minor improvements. For example, the new version of rci2 may be used to compute quantum electrodynamic (QED) corrections only from selected orbitals. In v3, a new program, jj2lsj, reports the percentage composition of the wave function in LSJ and the program rlevels has been modified to report the configuration state function (CSF) with the largest coefficient of an LSJ expansion. The bioscl2 and bioscl3 application programs have been modified to produce a file of transition data with one record for each transition in the same format as in ATSP2K [C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. All versions of the codes have been adapted for 64-bit computer architecture. Program SummaryProgram title: GRASP2K, version 1_1 Catalogue identifier: ADZL_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 730252 No. of bytes in distributed program, including test data, etc.: 14808872 Distribution format: tar.gz Programming language: Fortran. Computer: Intel Xeon, 2.66 GHz. Operating system: Suse, Ubuntu, and Debian Linux 64-bit. RAM: 500 MB or more Classification: 2.1. Catalogue identifier of previous version: ADZL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 597 Does the new version supersede the previous version?: Yes Nature of problem: Prediction of atomic properties — atomic energy levels, oscillator strengths, radiative decay rates, hyperfine structure parameters, Landé gJ-factors, and specific mass shift parameters — using a multiconfiguration Dirac-Hartree-Fock approach. Solution method: The computational method is the same as in the previous GRASP2K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j=9/2, making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A comprehensive user manual in pdf format for the program package has been added. Restrictions: The packing algorithm restricts the maximum number of orbitals to be ≤214. The tables of reduced coefficients of fractional parentage used in this version are limited to subshells with j≤9/2 [5]; occupied subshells with j>9/2 are, therefore, restricted to a maximum of two electrons. Some other parameters, such as the maximum number of subshells of a CSF outside a common set of closed shells are determined by a parameter.def file that can be modified prior to compile time. Unusual features: The bioscl3 program reports transition data in the same format as in Atsp2K [6], and the data processing program tables of the latter package can be used. The tables program takes a name.lsj file, usually a concatenated file of all the .lsj transition files for a given atom or ion, and finds the energy structure of the levels and the multiplet transition arrays. The tables posted at the website http://atoms.vuse.vanderbilt.edu are examples of tables produced by the tables program. With the extension of coefficients of fractional parentage to j=9/2, calculations for the lanthanides and actinides become possible. Running time: CPU time required to execute test cases: 70.5 s.

IDENTIFICATION OF POLLUTANTS IN A MUNICIPAL WELL USING HIGH RESOLUTION MASS SPECTROMETRY

EPA Science Inventory

An elevated incidence of childhood cancer was observed near a contaminated site. Trace amounts of several isomeric compounds were detected by gas chromatography/mass spectrometry (GC/MS) in a concentrated extract of municipal well water. No matching library mass spectra were foun...

Composition measurements of the topside ionosphere.

PubMed

Hoffman, J H

1967-01-20

Data from a magnetic mass spectrometer flown on the Explorer 31 satellite show that the ionosphere above 1000 kilometers usually consists of hydrogen ions as the predominant species. Between this altitude and perigee (500 kilometers) the dominant ion species shifts to atomic oxygen, with a significant amount of atomic nitrogen ions also present. Helium ions are present in small quantities at all altitudes. Other minor ions observed are those of 2, 7, 8, 15, 18, and 20 atomic mass units.

Polymeric spatial resolution test patterns for mass spectrometry imaging using nano-thermal analysis with atomic force microscopy

DOE PAGES

Tai, Tamin; Kertesz, Vilmos; Lin, Ming -Wei; ...

2017-05-11

As the spatial resolution of mass spectrometry imaging technologies has begun to reach into the nanometer regime, finding readily available or easily made resolution reference materials has become particularly challenging for molecular imaging purposes. This study describes the fabrication, characterization and use of vertical line array polymeric spatial resolution test patterns for nano-thermal analysis/atomic force microscopy/mass spectrometry chemical imaging.

Polymeric spatial resolution test patterns for mass spectrometry imaging using nano-thermal analysis with atomic force microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, Tamin; Kertesz, Vilmos; Lin, Ming -Wei

As the spatial resolution of mass spectrometry imaging technologies has begun to reach into the nanometer regime, finding readily available or easily made resolution reference materials has become particularly challenging for molecular imaging purposes. This study describes the fabrication, characterization and use of vertical line array polymeric spatial resolution test patterns for nano-thermal analysis/atomic force microscopy/mass spectrometry chemical imaging.

On the emergence of molecular structure from atomic shape in the 1/r2 harmonium model.

PubMed

Müller-Herold, Ulrich

2006-01-07

The formal similarity of the three-body Hamiltonians for helium and the hydrogen molecule ion is used to demonstrate the unfolding of a rotating dumbbell-like proton distribution from a (1s)2-type electron distribution by smooth variation of the particles' masses in the 1/r2 harmonium model. The 1/r2 harmonium is an exactly solvable modification of the harmonium model (also known as Hooke's law atom) where the attraction between different particles is harmonic and the repulsion between the two equal particles is given by a 1/r2 potential. The dumbbell-like molecular structure appears as an expression of increasing spatial correlation due to increasing mass. It gradually appears in the one-density distribution of the two equal particles if their mass exceeds a critical value depending on the mass of the third particle. For large mass of the equal particles, their one-density distribution approaches an asymptotic form derived from the Born-Oppenheimer treatment of H2+ in the 1/r2 harmonium model. Below the critical value, the one density is a spherical, Gaussian-type atomic density distribution with a maximum at the center of mass. The topological transition at the critical value separates molecular structure and atomic shape as two qualitatively different manifestations of spatial structure.

High-precision Penning trap mass measurements of 9,10Be and the one-neutron halo nuclide 11Be

NASA Astrophysics Data System (ADS)

Ringle, R.; Brodeur, M.; Brunner, T.; Ettenauer, S.; Smith, M.; Lapierre, A.; Ryjkov, V. L.; Delheij, P.; Drake, G. W. F.; Lassen, J.; Lunney, D.; Dilling, J.

2009-05-01

Penning trap mass measurements of 9Be, 10Be (t1 / 2 = 1.51 My), and the one-neutron halo nuclide 11Be (t1 / 2 = 13.8 s) have been performed using TITAN at TRIUMF. The resulting 11Be mass excess (ME = 20 177.60 (58) keV) is in agreement with the current Atomic Mass Evaluation (AME03) [G. Audi, et al., Nucl. Phys. A 729 (2003) 337] value, but is over an order of magnitude more precise. The precision of the mass values of 9,10Be have been improved by about a factor of four and reveal a ≈ 2 σ deviation from the AME mass values. Results of new atomic physics calculations are presented for the isotope shift of 11Be relative to 9Be, and it is shown that the new mass values essentially remove atomic mass uncertainties as a contributing factor in determining the relative nuclear charge radius from the isotope shift. The new mass values of 10,11Be also allow for a more precise determination of the single-neutron binding energy of the halo neutron in 11Be.

God particles in the perspective of The AlQuran Surah Yunus: 61 and modern science

NASA Astrophysics Data System (ADS)

Jumini, Sri

2017-01-01

The Qur'an is the book of Allah revealed to guide human beings, settting the rules of life to enable them to achieve happiness in this world and hereafter. The Qur'an has mentioned various scientific nature detailly and accurately so we are able to find new knowledge which is previously unknown by human being. One was about the God particle (Higgs Boson). This article aims to provide a deeper understanding of the concept of the Higgs Boson, the Higgs Boson explained this concept in detail relatated to 1) Perspective of science 2) Perspective of Al-Qur'an 3) Development of technology or science and technology. This study is a qualitative research using library research (library research) that examines and analyzes the books relating directly or indirectly. The results of the analysis states that 1) The concept of the Higgs Boson particle in terms of basic science is also the reason why almost all elementary particles have a greater mass, 2) The concept of the Higgs Boson in the Qur'an is implied from the results of the comparison interpretation of the commentators in Surah Yunus paragraph 61 related to Atom concepts and smaller particles theory of (Higgs Boson), interpretation of Al-Maraghi, and Al-Misbah. 3) The concept of the Higgs Boson in science and technology provide the most advance technology and it is the greatest achievement in the world of science and technology.

Library Staff operate a Microfilm Reader at the Lewis Research Center

NASA Image and Video Library

1961-04-21

Jean Neidengard and George Mandel operate a Kodak Recordak microfilm reader in the library at the National Aeronautics and Space Administration (NASA) Lewis Research Center. The library was located in the Administration Building until the mid-1960s. It was then moved to the Propulsion Systems Laboratory Office Building. In 2008 the library was moved once again, to the Research Analysis Center. At the time of this photograph, the Lewis library claimed to possess “One of the most complete aero-technical collections in the world.” It was doing a brisk business in the early 1960s. During 1960 alone the library acquired 19,000 new documents and provided 100,000 documents to customers. The library’s eleven-person staff provided reference services, archived technical reports, and supplied periodicals. The staff also included Sam Reiss, a full-time translator who could read 30 languages. He translated technical reports from all over the world for the Lewis research staff. Jean Neidengard oversaw the secret Atomic Energy Commission (AEC) documents in the collection. NASA was partnering with the AEC at the time on Nuclear Engine for Rocket Vehicle Application (NERVA) program. NASA Lewis was the agency’s lead center in the NERVA program. Neidengard’s husband Bill was the head mechanic in the Propulsion Systems Laboratory. George Mandel led the library staff from 1955 to 1968.

Surface Geometry and Chemistry of Hydrothermally Synthesized Single Crystal Thorium Dioxide

DTIC Science & Technology

2015-03-01

meeting the larger goals. I appreciate Dr. McClory’s skeptical views and critical thinking that kept me from straying into scientific error. I...Secondary Ion Mass Spectrometry .....................20 UPS ......................Ultraviolet Photoemission Spectrometry...19 M1/M2 ................... Mass of atom 1 and atom 2 ..........................................................18 Mm ........................Molar

NNDC Tools and Publications

Science.gov Websites

Site Index NNDC Tools and Publications Nuclear Structure and Decay Tools Nuclear Reaction Tools Nuclear Structure and Decay Tools 2016 Atomic Mass Evaluation Atomic mass evaluation, by Wang, Audi values as a function of gamma energy and multipolarity. Calculations based on I.M. Band and S. Raman

Protocol for an electrospray ionization tandem mass spectral product ion library: development and application for identification of 240 pesticides in foods.

PubMed

Zhang, Kai; Wong, Jon W; Yang, Paul; Hayward, Douglas G; Sakuma, Takeo; Zou, Yunyun; Schreiber, André; Borton, Christopher; Nguyen, Tung-Vi; Kaushik, Banerjee; Oulkar, Dasharath

2012-07-03

Modern determination techniques for pesticides must yield identification quickly with high confidence for timely enforcement of tolerances. A protocol for the collection of liquid chromatography (LC) electrospray ionization (ESI)-quadruple linear ion trap (Q-LIT) mass spectrometry (MS) library spectra was developed. Following the protocol, an enhanced product ion (EPI) library of 240 pesticides was developed by use of spectra collected from two laboratories. A LC-Q-LIT-MS workflow using scheduled multiple reaction monitoring (sMRM) survey scan, information-dependent acquisition (IDA) triggered collection of EPI spectra, and library search was developed and tested to identify the 240 target pesticides in one single LC-Q-LIT MS analysis. By use of LC retention time, one sMRM survey scan transition, and a library search, 75-87% of the 240 pesticides were identified in a single LC/MS analysis at fortified concentrations of 10 ng/g in 18 different foods. A conventional approach with LC-MS/MS using two MRM transitions produced the same identifications and comparable quantitative results with the same incurred foods as the LC-Q-LIT using EPI library search, finding 1.2-49 ng/g of either carbaryl, carbendazim, fenbuconazole, propiconazole, or pyridaben in peaches; carbendazim, imazalil, terbutryn, and thiabendazole in oranges; terbutryn in salmon; and azoxystrobin in ginseng. Incurred broccoli, cabbage, and kale were screened with the same EPI library using three LC-Q-LIT and a LC-quadruple time-of-flight (Q-TOF) instruments. The library search identified azoxystrobin, cyprodinil, fludioxinil, imidacloprid, metalaxyl, spinosyn A, D, and J, amd spirotetramat with each instrument. The approach has a broad application in LC-MS/MS type targeted screening in food analysis.

Learning-assisted theorem proving with millions of lemmas☆

PubMed Central

Kaliszyk, Cezary; Urban, Josef

2015-01-01

Large formal mathematical libraries consist of millions of atomic inference steps that give rise to a corresponding number of proved statements (lemmas). Analogously to the informal mathematical practice, only a tiny fraction of such statements is named and re-used in later proofs by formal mathematicians. In this work, we suggest and implement criteria defining the estimated usefulness of the HOL Light lemmas for proving further theorems. We use these criteria to mine the large inference graph of the lemmas in the HOL Light and Flyspeck libraries, adding up to millions of the best lemmas to the pool of statements that can be re-used in later proofs. We show that in combination with learning-based relevance filtering, such methods significantly strengthen automated theorem proving of new conjectures over large formal mathematical libraries such as Flyspeck. PMID:26525678

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

Mass Deacidification Systems: Planning and Managerial Decision Making.

ERIC Educational Resources Information Center

Turko, Karen

Library administrators, faced with the problems of acid-paper deterioration, are examining mass deacidification procedures. Mass deacidification of acidic books while they are still physically sound and not yet brittle is the most cost-effective corrective action to extend the life of the paper. There are currently at least five mass…

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

PubMed

Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

2010-07-28

Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

The AME2016 atomic mass evaluation (I). Evaluation of input data; and adjustment procedures

NASA Astrophysics Data System (ADS)

Huang, W. J.; Audi, G.; Wang, Meng; Kondev, F. G.; Naimi, S.; Xu, Xing

2017-03-01

This paper is the first of two articles (Part I and Part II) that presents the results of the new atomic mass evaluation, AME2016. It includes complete information on the experimental input data (also including unused and rejected ones), as well as details on the evaluation procedures used to derive the tables of recommended values given in the second part. This article describes the evaluation philosophy and procedures that were implemented in the selection of specific nuclear reaction, decay and mass-spectrometric results. These input values were entered in the least-squares adjustment for determining the best values for the atomic masses and their uncertainties. Details of the calculation and particularities of the AME are then described. All accepted and rejected data, including outweighted ones, are presented in a tabular format and compared with the adjusted values obtained using the least-squares fit analysis. Differences with the previous AME2012 evaluation are discussed and specific information is presented for several cases that may be of interest to AME users. The second AME2016 article gives a table with the recommended values of atomic masses, as well as tables and graphs of derived quantities, along with the list of references used in both the AME2016 and the NUBASE2016 evaluations (the first paper in this issue). AMDC: http://amdc.impcas.ac.cn/ Contents The AME2016 atomic mass evaluation (I). Evaluation of input data; and adjustment proceduresAcrobat PDF (1.2 MB) Table I. Input data compared with adjusted valuesAcrobat PDF (1.3 MB)

L1 Korean and L1 Mandarin L2 English Learners' Acquisition of the Count/Mass Distinction in English

ERIC Educational Resources Information Center

Choi, Sea Hee; Ionin, Tania; Zhu, Yeqiu

2018-01-01

This study investigates the second language (L2) acquisition of the English count/mass distinction by speakers of Korean and Mandarin Chinese, with a focus on the semantics of atomicity. It is hypothesized that L1-Korean and L1-Mandarin L2-English learners are influenced by atomicity in the use of the count/mass morphosyntax in English. This…

Fast parallel tandem mass spectral library searching using GPU hardware acceleration

PubMed Central

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K.; Martin, Daniel B.

2011-01-01

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching) is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment. PMID:21545112

Reaction Mechanism of Oxygen Atoms with Unsaturated Hydrocarbons by the Crossed-Molecular-Beams Method

DOE R&D Accomplishments Database

Buss, R. J.; Baseman, R. J.; Guozhong, H.; Lee, Y. T.

1982-04-01

From a series of studies of the reaction of oxygen atoms with unsaturated hydrocarbons using the crossed molecular beam method, the dominant reaction mechanisms were found to be the simple substitution reactions with oxygen atoms replacing H, Cl, Br atom or alkyl groups. Complication due to secondary reaction was avoided by carrying out experiments under single collisions and observing primary products directly. Primary products were identified by measuring the angular and velocity distributions of products at all the mass numbers which could be detected by the mass spectrometer, and from comparison of these distributions, applying the requirement of energy and momentum conservation.

The NIST Step Class Library (Step Into the Future)

DTIC Science & Technology

1990-09-01

Figure 6. Excerpt from a STEP exclange file based on the Geometry model 1be NIST STEP Class Libary Page 13 An issue of concern in this...Scheifler, R., Gettys, J., and Newman, P., X Window System: C Library and Protocol Reference. Digital Press, Bedford, Mass, 1988. [Schenck90] Schenck, D

Mass Deacidification in the Harvard University Library. A Report on the 1991/92 Pilot Operational Program.

ERIC Educational Resources Information Center

Harvard Univ., Cambridge, MA. Univ. Library.

This report examines the institutional level deacidification program that was formalized and instituted at Harvard University (Cambridge, Massachusetts)) for its research libraries. The report is organized into six sections. The first section, which describes the project's background, discusses the acidic paper problem, available mass…

One-Shot Library Instruction and Cambourne's Theory of Learning

ERIC Educational Resources Information Center

Masuchika, Glenn Norio; Boldt, Gail

2012-01-01

Librarians who teach one-shot library instruction classes (one-time, one- to three-hour classes to students who are assumed to be novice researchers) are often torn between two pedagogic approaches: a "critical mass" pedagogy emphasizing a minimum amount of databases that must be introduced with little time for student searching, and a…

Template-based combinatorial enumeration of virtual compound libraries for lipids

PubMed Central

2012-01-01

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license. PMID:23006594

Template-based combinatorial enumeration of virtual compound libraries for lipids.

PubMed

Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

2012-09-25

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.

Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Aspergillus, Scedosporium, and Fusarium spp. in the Australian Clinical Setting.

PubMed

Sleiman, Sue; Halliday, Catriona L; Chapman, Belinda; Brown, Mitchell; Nitschke, Joanne; Lau, Anna F; Chen, Sharon C-A

2016-08-01

We developed an Australian database for the identification of Aspergillus, Scedosporium, and Fusarium species (n = 28) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a challenge against 117 isolates, species identification significantly improved when the in-house-built database was combined with the Bruker Filamentous Fungi Library compared with that for the Bruker library alone (Aspergillus, 93% versus 69%; Fusarium, 84% versus 42%; and Scedosporium, 94% versus 18%, respectively). Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Fission fragment yield distribution in the heavy-mass region from the 239Pu (nth,f ) reaction

NASA Astrophysics Data System (ADS)

Gupta, Y. K.; Biswas, D. C.; Serot, O.; Bernard, D.; Litaize, O.; Julien-Laferrière, S.; Chebboubi, A.; Kessedjian, G.; Sage, C.; Blanc, A.; Faust, H.; Köster, U.; Ebran, A.; Mathieu, L.; Letourneau, A.; Materna, T.; Panebianco, S.

2017-07-01

The fission fragment yield distribution has been measured in the 239Pu(nth,f ) reaction in the mass region of A =126 to 150 using the Lohengrin recoil-mass spectrometer. Three independent experimental campaigns were performed, allowing a significant reduction of the uncertainties compared to evaluated nuclear data libraries. The long-standing discrepancy of around 10% for the relative yield of A =134 reported in JEF-2.2 and JEFF-3.1.1 data libraries is finally solved. Moreover, the measured mass distribution in thermal neutron-induced fission does not show any significant dip around the shell closure (A =136 ) as seen in heavy-ion fission data of 208Pb(18O, f ) and 238U(18O, f ) reactions. Lastly, comparisons between our experimental data and the predictions from Monte Carlo codes (gef and fifrelin) are presented and discussed.

A novel spectral library workflow to enhance protein identifications.

PubMed

Li, Haomin; Zong, Nobel C; Liang, Xiangbo; Kim, Allen K; Choi, Jeong Ho; Deng, Ning; Zelaya, Ivette; Lam, Maggie; Duan, Huilong; Ping, Peipei

2013-04-09

The innovations in mass spectrometry-based investigations in proteome biology enable systematic characterization of molecular details in pathophysiological phenotypes. However, the process of delineating large-scale raw proteomic datasets into a biological context requires high-throughput data acquisition and processing. A spectral library search engine makes use of previously annotated experimental spectra as references for subsequent spectral analyses. This workflow delivers many advantages, including elevated analytical efficiency and specificity as well as reduced demands in computational capacity. In this study, we created a spectral matching engine to address challenges commonly associated with a library search workflow. Particularly, an improved sliding dot product algorithm, that is robust to systematic drifts of mass measurement in spectra, is introduced. Furthermore, a noise management protocol distinguishes spectra correlation attributed from noise and peptide fragments. It enables elevated separation between target spectral matches and false matches, thereby suppressing the possibility of propagating inaccurate peptide annotations from library spectra to query spectra. Moreover, preservation of original spectra also accommodates user contributions to further enhance the quality of the library. Collectively, this search engine supports reproducible data analyses using curated references, thereby broadening the accessibility of proteomics resources to biomedical investigators. This article is part of a Special Issue entitled: From protein structures to clinical applications. Copyright © 2013 Elsevier B.V. All rights reserved.

Fast atom bombardment mass spectrometry of condensed tannin sulfonate derivatives

Treesearch

J.J. Karchesy; L.Y. Foo; Richard W. Hemingway; E. Barofsky; D.F. Barofsky

1989-01-01

Condensed tannin sulfonate derivatives were studied by fast atom bombardment mass spectrometry (FAB-MS) to assess the feasibility of using this technique for determining molecular weight and structural information about these compounds. Both positive- and negative-ion spectra provided useful data with regard to molecular weight, cation species present, and presence of...

Effective atomic numbers and electron density of dosimetric material

PubMed Central

Kaginelli, S. B.; Rajeshwari, T.; Sharanabasappa; Kerur, B. R.; Kumar, Anil S.

2009-01-01

A novel method for determination of mass attenuation coefficient of x-rays employing NaI (Tl) detector system and radioactive sources is described.in this paper. A rigid geometry arrangement and gating of the spectrometer at FWHM position and selection of absorber foils are all done following detailed investigation, to minimize the effect of small angle scattering and multiple scattering on the mass attenuation coefficient, μ/ρ, value. Firstly, for standardization purposes the mass attenuation coefficients of elemental foils such as Aluminum, Copper, Molybdenum, Tantalum and Lead are measured and then, this method is utilized for dosimetric interested material (sulfates). The experimental mass attenuation coefficient values are compared with the theoretical values to find good agreement between the theory and experiment within one to two per cent. The effective atomic numbers of the biological substitute material are calculated by sum rule and from the graph. The electron density of dosimetric material is calculated using the effective atomic number. The study has discussed in detail the attenuation coefficient, effective atomic number and electron density of dosimetric material/biological substitutes. PMID:20098566

An introduction to mass cytometry: fundamentals and applications.

PubMed

Tanner, Scott D; Baranov, Vladimir I; Ornatsky, Olga I; Bandura, Dmitry R; George, Thaddeus C

2013-05-01

Mass cytometry addresses the analytical challenges of polychromatic flow cytometry by using metal atoms as tags rather than fluorophores and atomic mass spectrometry as the detector rather than photon optics. The many available enriched stable isotopes of the transition elements can provide up to 100 distinguishable reporting tags, which can be measured simultaneously because of the essential independence of detection provided by the mass spectrometer. We discuss the adaptation of traditional inductively coupled plasma mass spectrometry to cytometry applications. We focus on the generation of cytometry-compatible data and on approaches to unsupervised multivariate clustering analysis. Finally, we provide a high-level review of some recent benchmark reports that highlight the potential for massively multi-parameter mass cytometry.

Stable-isotope-labeled Histone Peptide Library for Histone Post-translational Modification and Variant Quantification by Mass Spectrometry *

PubMed Central

Lin, Shu; Wein, Samuel; Gonzales-Cope, Michelle; Otte, Gabriel L.; Yuan, Zuo-Fei; Afjehi-Sadat, Leila; Maile, Tobias; Berger, Shelley L.; Rush, John; Lill, Jennie R.; Arnott, David; Garcia, Benjamin A.

2014-01-01

To facilitate accurate histone variant and post-translational modification (PTM) quantification via mass spectrometry, we present a library of 93 synthetic peptides using Protein-Aqua™ technology. The library contains 55 peptides representing different modified forms from histone H3 peptides, 23 peptides representing H4 peptides, 5 peptides representing canonical H2A peptides, 8 peptides representing H2A.Z peptides, and peptides for both macroH2A and H2A.X. The PTMs on these peptides include lysine mono- (me1), di- (me2), and tri-methylation (me3); lysine acetylation; arginine me1; serine/threonine phosphorylation; and N-terminal acetylation. The library was subjected to chemical derivatization with propionic anhydride, a widely employed protocol for histone peptide quantification. Subsequently, the detection efficiencies were quantified using mass spectrometry extracted ion chromatograms. The library yields a wide spectrum of detection efficiencies, with more than 1700-fold difference between the peptides with the lowest and highest efficiencies. In this paper, we describe the impact of different modifications on peptide detection efficiencies and provide a resource to correct for detection biases among the 93 histone peptides. In brief, there is no correlation between detection efficiency and molecular weight, hydrophobicity, basicity, or modification type. The same types of modifications may have very different effects on detection efficiencies depending on their positions within a peptide. We also observed antagonistic effects between modifications. In a study of mouse trophoblast stem cells, we utilized the detection efficiencies of the peptide library to correct for histone PTM/variant quantification. For most histone peptides examined, the corrected data did not change the biological conclusions but did alter the relative abundance of these peptides. For a low-abundant histone H2A variant, macroH2A, the corrected data led to a different conclusion than the uncorrected data. The peptide library and detection efficiencies presented here may serve as a resource to facilitate studies in the epigenetics and proteomics fields. PMID:25000943

Did the Allies Know in 1942 About Nazi Germany's Poor Prospects for an Atomic Bomb?

NASA Astrophysics Data System (ADS)

Lustig, Harry

2008-04-01

According to official accounts, the U.S. knew nothing about Nazi Germany's efforts to get an atomic bomb until the end of the World War II, but had feared the worst. As it turned out, the Germans had made little progress. But did someone in the Allied camp know in 1942? In his 1986 book, The Griffin, Arnold Kramish relates how Paul Rosbaud, a spy for MI6, the British secret intelligence service, kept his handlers informed during the War about the German atomic project and reported the decision to give up on a bomb. Kramish's revelations are, understandably, thinly documented and Rosbaud's name can hardly be found independenly anywhere else. But as Samuel Goudsmit's papers in the Bohr Library show, he knew and communicated with Rosbaud from August 1945 on. In 1986, 15 letters exchanged by Goudsmit and Rosbaud were removed by the Government from the Library and eventually placed in the National Archives under classification review. Renewed interest in the Rosbaud story was engendered last year when his family sued MI6 in an English court for the release of the Rosbaud file. So far the spy agency has refused to reveal even that there is such a file. Discovering authoritatively what Rosbaud told the British and what they did with the information is clearly of historical interest.

Single-Atom Catalyst of Platinum Supported on Titanium Nitride for Selective Electrochemical Reactions.

PubMed

Yang, Sungeun; Kim, Jiwhan; Tak, Young Joo; Soon, Aloysius; Lee, Hyunjoo

2016-02-05

As a catalyst, single-atom platinum may provide an ideal structure for platinum minimization. Herein, a single-atom catalyst of platinum supported on titanium nitride nanoparticles were successfully prepared with the aid of chlorine ligands. Unlike platinum nanoparticles, the single-atom active sites predominantly produced hydrogen peroxide in the electrochemical oxygen reduction with the highest mass activity reported so far. The electrocatalytic oxidation of small organic molecules, such as formic acid and methanol, also exhibited unique selectivity on the single-atom platinum catalyst. A lack of platinum ensemble sites changed the reaction pathway for the oxygen-reduction reaction toward a two-electron pathway and formic acid oxidation toward direct dehydrogenation, and also induced no activity for the methanol oxidation. This work demonstrates that single-atom platinum can be an efficient electrocatalyst with high mass activity and unique selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Effects of Rare Earth Doping on Gallium Nitride Thin Films

DTIC Science & Technology

2011-09-01

MAW Molar mass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Microscopic nuclear cross...container) is ∼ 770 nm−2 s−1 [8]. When compared to an unmoderated, unshielded hypothetical mass of 5 kg of 94% enriched 239Pu (weapons grade) at a...emission of a doubly-ionized helium atom ( 4 2He 2+ ) , or alpha particle, as A ZX −→ A-4Z-2Y + 42He2+ + Q , (4) where A represents the atomic mass or the

Determination of the direct double- β -decay Q value of Zr 96 and atomic masses of Zr 90 - 92 , 94 , 96 and Mo 92 , 94 - 98 , 100

DOE PAGES

Gulyuz, K.; Ariche, J.; Bollen, G.; ...

2015-05-06

Experimental searches for neutrinoless double-β decay offer one of the best opportunities to look for physics beyond the standard model. Detecting this decay would confirm the Majorana nature of the neutrino, and a measurement of its half-life can be used to determine the absolute neutrino mass scale. Important to both tasks is an accurate knowledge of the Q value of the double-β decay. The LEBIT Penning trap mass spectrometer was used for the first direct experimental determination of the ⁹⁶Zr double-β decay Q value: Q ββ=3355.85(15) keV. This value is nearly 7 keV larger than the 2012 Atomic Mass Evaluationmore » [M. Wang et al., Chin. Phys. C 36, 1603 (2012)] value and one order of magnitude more precise. The 3-σ shift is primarily due to a more accurate measurement of the ⁹⁶Zr atomic mass: m(⁹⁶Zr)=95.90827735(17) u. Using the new Q value, the 2νββ-decay matrix element, |M 2ν|, is calculated. Improved determinations of the atomic masses of all other zirconium ( 90-92,94,96Zr) and molybdenum ( 92,94-98,100Mo) isotopes using both ¹²C₈ and ⁸⁷Rb as references are also reported.« less

IDENTIFICATION OF POLLUTANTS IN A MUNICIPAL WELL USING MASS PEAK PROFILING OF THE MOLECULAR ION AND FRAGMENT IONS

EPA Science Inventory

An elevated incidence of childhood cancer was observed near a contaminated site. Trace amounts of several isomeric compounds were detected by gas chromatography/mass spectrometry (GC/MS) in a concentrated extract of municipal well water. No matching library mass spectra wer...

ION COMPOSITION ELUCIDATION (ICE): A HIGH RESOLUTION MASS SPECTROMETRIC TECHNIQUE FOR CHARACTERIZATION AND IDENTIFICATION OF ORGANIC COMPOUNDS

EPA Science Inventory

Identifying compounds found in the environment without knowledge of their origin is a very difficult analytical problem. Comparison of the low resolution mass spectrum of a compound with those in the NIST or Wiley mass spectral libraries can provide a tentative identification whe...

The interaction of excited He, Ar and Ne metastable atoms with the CF2Cl2 molecule

NASA Astrophysics Data System (ADS)

Cherid, M.; Ben Arfa, M.; Driss Khodja, M.

2004-02-01

We studied Penning ionization of the CF2Cl2 molecule by neon and helium metastable atoms. In the case of the neon ionizing particle, we measured the electron kinetic energy as well as mass spectra; for helium metastable atoms, only the mass spectrum was recorded. We, therefore, obtained the branching ratios for the heavy charged particles produced in both interactions. In this report we will discuss the mechanism involved in the production of metastable halogen atoms in the dielectric barrier discharge further to the use of rare gases/CF2Cl2 mixtures. We show that this process needs a two-stage reaction. Ground state free halogen atoms are formed over the first stage by Penning ionization, charge transfer, dissociate excitation and ionization. Therefore, metastable halogen atoms can be produced by excitation transfer process in the second stage through interaction with metastable rare gas atoms. This paper is dedicated to Professor F M E Tuffin on the occasion of his retirement.

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching.

PubMed

Pai, Pei-Jing; Hu, Yingwei; Lam, Henry

2016-08-31

Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Determination of atomic hydrogen in non-thermal hydrogen plasmas by means of molecular beam threshold ionization mass spectrometry.

PubMed

Wang, Wei-Guo; Xu, Yong; Yang, Xue-Feng; Wang, Wen-Chun; Zhu, Ai-Min

2005-01-01

Atomic hydrogen plays important roles in chemical vapor deposition of functional materials, plasma etching and new approaches to chemical synthesis of hydrogen-containing compounds. The present work reports experimental determinations of atomic hydrogen near the grounded electrode in medium-pressure dielectric barrier discharge hydrogen plasmas by means of molecular beam threshold ionization mass spectrometry (MB-TIMS). At certain discharge conditions (a.c. frequency of 24 kHz, 28 kV of peak-to-peak voltage), the measured hydrogen dissociation fraction is decreased from approximately 0.83% to approximately 0.14% as the hydrogen pressure increases from 2.0 to 14.0 Torr. A simulation method for extraction of the approximate electron beam energy distribution function in the mass spectrometer ionizer and a semi-quantitative approach to calibrate the mass discrimination effect caused by the supersonic beam formation and the mass spectrometer measurement are reported. Copyright 2005 John Wiley & Sons, Ltd.

The Atomic Mass Evaluation (AME2012): Status and Perspectives

NASA Astrophysics Data System (ADS)

Kondev, F. G.; Audi, G.; Wang, M.; Xu, X.; Wapstra, A. H.; MacCormick, M.; Pfeiffer, B.

2013-10-01

The atomic mass is a fundamental property of the nucleus that has wide applications in natural sciences and technology. The new evaluated mass table, AME2012, has been recently published as a collaborative effort between scientists from China, Europe and USA, under the leadership of G. Audi. It represents a significant update of the previous AME2003 evaluation by considering a large number of precise experimental results obtained at existing Penning Trap and Storage Ring facilities, thus expending the region of experimentally known masses towards exotic neutron- and proton-rich nuclei. Since the presence of isomers plays an important role in determining the masses of many nuclei, a complementary database, NUBASE2012, that contains the isomer-level properties for all nuclei was also developed. This presentation will briefly review recent achievements of the collaboration, present on-going activities, and reflect on ideas for future developments and challenges in the field of evaluation of atomic masses. The work at ANL was supported by the U.S. Department of Energy, Office of Nuclear Physics, under Contract No. DE-AC02-06CH11357.

An open-source library for the numerical modeling of mass-transfer in solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Novaresio, Valerio; García-Camprubí, María; Izquierdo, Salvador; Asinari, Pietro; Fueyo, Norberto

2012-01-01

The generation of direct current electricity using solid oxide fuel cells (SOFCs) involves several interplaying transport phenomena. Their simulation is crucial for the design and optimization of reliable and competitive equipment, and for the eventual market deployment of this technology. An open-source library for the computational modeling of mass-transport phenomena in SOFCs is presented in this article. It includes several multicomponent mass-transport models ( i.e. Fickian, Stefan-Maxwell and Dusty Gas Model), which can be applied both within porous media and in porosity-free domains, and several diffusivity models for gases. The library has been developed for its use with OpenFOAM ®, a widespread open-source code for fluid and continuum mechanics. The library can be used to model any fluid flow configuration involving multicomponent transport phenomena and it is validated in this paper against the analytical solution of one-dimensional test cases. In addition, it is applied for the simulation of a real SOFC and further validated using experimental data. Program summaryProgram title: multiSpeciesTransportModels Catalogue identifier: AEKB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 18 140 No. of bytes in distributed program, including test data, etc.: 64 285 Distribution format: tar.gz Programming language:: C++ Computer: Any x86 (the instructions reported in the paper consider only the 64 bit case for the sake of simplicity) Operating system: Generic Linux (the instructions reported in the paper consider only the open-source Ubuntu distribution for the sake of simplicity) Classification: 12 External routines: OpenFOAM® (version 1.6-ext) ( http://www.extend-project.de) Nature of problem: This software provides a library of models for the simulation of the steady state mass and momentum transport in a multi-species gas mixture, possibly in a porous medium. The software is particularly designed to be used as the mass-transport library for the modeling of solid oxide fuel cells (SOFC). When supplemented with other sub-models, such as thermal and charge-transport ones, it allows the prediction of the cell polarization curve and hence the cell performance. Solution method: Standard finite volume method (FVM) is used for solving all the conservation equations. The pressure-velocity coupling is solved using the SIMPLE algorithm (possibly adding a porous drag term if required). The mass transport can be calculated using different alternative models, namely Fick, Maxwell-Stefan or dusty gas model. The code adopts a segregated method to solve the resulting linear system of equations. The different regions of the SOFC, namely gas channels, electrodes and electrolyte, are solved independently, and coupled through boundary conditions. Restrictions: When extremely large species fluxes are considered, current implementation of the Neumann and Robin boundary conditions do not avoid negative values of molar and/or mass fractions, which finally end up with numerical instability. However this never happened in the documented runs. Eventually these boundary conditions could be reformulated to become more robust. Running time: From seconds to hours depending on the mesh size and number of species. For example, on a 64 bit machine with Intel Core Duo T8300 and 3 GBytes of RAM, the provided test run requires less than 1 second.

AtomPy: an open atomic-data curation environment

NASA Astrophysics Data System (ADS)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

A high flux source of swift oxygen atoms

NASA Technical Reports Server (NTRS)

Fink, M.; Kohl, D. A.; Keto, J. W.; Antoniewicz, P.

1987-01-01

A source of swift oxygen atoms is described which has several unique features. A high current ion beam is produced by a microwave discharge, accelerated to 10 keV and the mass selected by a modified Du Pont 21-110 mass spectrometer. The O(+) beam exciting the mass spectrometer is focused into a rectangular shape with an energy spread of less than 1 eV. The next section of the machine decelerates the ion beam into a counterpropagating electron beam in order to minimize space charge effects. After deceleration, the ion beam intersects at 90 deg, a neutral oxygen atom beam, which via resonant charge exchange produces a mixture of O(+) and O. Any remaining O(+) are swept out of the beam by an electric field and differentially pumped away while the desired O beam, collimated by slits, impinges on the target. In situ monitoring of the target surface is done by X-ray photoelectron or Auger spectroscopy. Faraday cups provide flux measurements in the ion sections while the neutral flux is determined by a special torsion balance or by a quadrupole mass spectrometer specially adapted for swift atoms. While the vacuum from the source through the mass spectrometer is maintained by diffusion pumps, the rest of the machine is UHV.

Sympathetic cooling of a membrane oscillator in a hybrid mechanical-atomic system

NASA Astrophysics Data System (ADS)

Jöckel, Andreas; Faber, Aline; Kampschulte, Tobias; Korppi, Maria; Rakher, Matthew T.; Treutlein, Philipp

2015-01-01

Sympathetic cooling with ultracold atoms and atomic ions enables ultralow temperatures in systems where direct laser or evaporative cooling is not possible. It has so far been limited to the cooling of other microscopic particles, with masses up to 90 times larger than that of the coolant atom. Here, we use ultracold atoms to sympathetically cool the vibrations of a Si3N4 nanomembrane, the mass of which exceeds that of the atomic ensemble by a factor of 1010. The coupling of atomic and membrane vibrations is mediated by laser light over a macroscopic distance and is enhanced by placing the membrane in an optical cavity. We observe cooling of the membrane vibrations from room temperature to 650 ± 230 mK, exploiting the large atom-membrane cooperativity of our hybrid optomechanical system. With technical improvements, our scheme could provide ground-state cooling and quantum control of low-frequency oscillators such as nanomembranes or levitated nanoparticles, in a regime where purely optomechanical techniques cannot reach the ground state.

To Bind or Not To Bind: Pros & Cons of Maintaining Paper Periodicals in the Library's Collection.

ERIC Educational Resources Information Center

Anderson, Iris W.

1999-01-01

Explores controversial questions related to libraries' decision-making on paper journals and electronic journals. Notes that the critical mass of scholarly publishing is still in print. Discusses benefits and drawbacks of electronic journals and paper journals. Presents comments on the pros and cons to binding paper periodicals gathered from an…

Historical Work in Mass Communication Studies: Literacy, Libraries, and Popular Reading.

ERIC Educational Resources Information Center

Inglesby, Pamela

Recent work in both the history of education and the influence of popular culture suggests that libraries can be studied as sites where the public is taught--through a variety of mechanisms--important lessons about communication, knowledge and society. Researchers have addressed the interpretive question of whether literacy is tied to progress and…

A Paper Chase: Technology Helps Library Save Its Collections on Paper.

ERIC Educational Resources Information Center

Dalrymple, Will

1997-01-01

Bookkeeper, a liquid-based mass deacidification technology, may help the Library of Congress win its war against acid damage in its paper collection. The process impregnates books with magnesium oxide particles that both neutralize the acid in paper and leave an alkaline buffer behind. Describes the problem of acidic degradation and the Bookkeeper…

Teaching Avogadro's Hypothesis and Helping Students to See the World Differently

ERIC Educational Resources Information Center

Criswell, Brett

2008-01-01

Within the historical context of the development of chemistry, Avogadro's hypothesis represents a fundamental concept: It allowed Avogadro to explain Gay-Lussac's law of combining volumes and it allowed Cannizzaro to establish a more accurate set of atomic mass values. If students are going to understand the concept of relative atomic masses and…

The Atomic Mass Unit, the Avogadro Constant, and the Mole: A Way to Understanding

ERIC Educational Resources Information Center

Baranski, Andrzej

2012-01-01

Numerous articles have been published that address problems encountered in teaching basic concepts of chemistry such as the atomic mass unit, Avogadro's number, and the mole. The origin of these problems is found in the concept definitions. If these definitions are adjusted for teaching purposes, understanding could be improved. In the present…

A Fifth Force: Generalized through Superconductors

NASA Technical Reports Server (NTRS)

Robertson, Glen A.

1999-01-01

The connection between the Biefield-Brown Effect, the recent repeat of the 1902 Trouton-Noble (TN) experiments, and the gravity shielding experiments was explored. This connection is visualized through high capacitive electron concentrations. From this connection, a theory is proposed that connects mass energy to gravity and a fifth force. The theory called the Gravi-Atomic Energy theory presents two new terms: Gravi-atomic energy and quantum vacuum pressure (QVP). Gravi-atomic energy is defined as the radiated mass energy, which acts on vacuum energy to create a QVP about a mass, resulting in gravity and the fifth force. The QVP emission from a superconductor was discussed followed by the description of a test for QVP from a superconductor using a Cavendish balance.

Screening of Small Molecule Interactor Library by Using In-Cell NMR Spectroscopy (SMILI-NMR)

PubMed Central

Xie, Jingjing; Thapa, Rajiv; Reverdatto, Sergey; Burz, David S.; Shekhtman, Alexander

2011-01-01

We developed an in-cell NMR assay for screening small molecule interactor libraries (SMILI-NMR) for compounds capable of disrupting or enhancing specific interactions between two or more components of a biomolecular complex. The method relies on the formation of a well-defined biocomplex and utilizes in-cell NMR spectroscopy to identify the molecular surfaces involved in the interaction at atomic scale resolution. Changes in the interaction surface caused by a small molecule interfering with complex formation are used as a read-out of the assay. The in-cell nature of the experimental protocol insures that the small molecule is capable of penetrating the cell membrane and specifically engaging the target molecule(s). Utility of the method was demonstrated by screening a small dipeptide library against the FKBP–FRB protein complex involved in cell cycle arrest. The dipeptide identified by SMILI-NMR showed biological activity in a functional assay in yeast. PMID:19422228

Advances in structure elucidation of small molecules using mass spectrometry

PubMed Central

Fiehn, Oliver

2010-01-01

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855

Linear electric field time-of-flight ion mass spectrometer

DOEpatents

Funsten, Herbert O [Los Alamos, NM; Feldman, William C [Los Alamos, NM

2008-06-10

A linear electric field ion mass spectrometer having an evacuated enclosure with means for generating a linear electric field located in the evacuated enclosure and means for injecting a sample material into the linear electric field. A source of pulsed ionizing radiation injects ionizing radiation into the linear electric field to ionize atoms or molecules of the sample material, and timing means determine the time elapsed between ionization of atoms or molecules and arrival of an ion out of the ionized atoms or molecules at a predetermined position.

Ergodic properties of the multidimensional rayleigh gas with a semipermeable barrier

NASA Astrophysics Data System (ADS)

Erdős, L.; Tuyen, D. Q.

1990-06-01

We consider a multidimensional system consisting of a particle of mass M and radius r (molecule), surrounded by an infinite ideal gas of point particles of mass m (atoms). The molecule is confined to the unit ball and interacts with its boundary ( barrier) via elastic collision, while the atoms are not affected by the boundary. We obtain convergence to equilibrium for the molecule from almost every initial distribution on its position and velocity. Furthermore, we prove that the infinite composite system of the molecule and the atoms is Bernoulli.

Mass spectrometric identification of Au68(SR)34 molecular gold nanoclusters with 34-electron shell closing.

PubMed

Dass, Amala

2009-08-26

The molecular formula Au(68)(SCH(2)CH(2)Ph)(34) has been assigned to the 14 kDa nanocluster using MALDI-TOF mass spectrometry. The 34-electron shell closing in a macroscopically obtained thiolated gold nanocluster is demonstrated. The Au(68) nanocluster is predicted to have a 49 atom Marks decahedral core with 19 inner core atoms and 30 outer atoms chelating with the staple motifs. The nanoclusters' predicted formulation is [Au](19+30) [Au(SR)(2)](11) [Au(2)(SR)(3)](4).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mount, Brianna J.; Redshaw, Matthew; Myers, Edmund G.

By fitting the Dunham-Watson model to extensive rotational and vibrational spectroscopic data of isotopic variants of CO, and by using existing precise masses of {sup 13}C,{sup 16}O, and {sup 18}O from Penning-trap mass spectrometry, we determine the atomic mass of {sup 17}O to be M[{sup 17}O]=16.999 131 644(30) u, where the uncertainty is purely statistical. Using Penning-trap mass spectrometry, we have also directly determined the atomic mass of {sup 17}O with the more precise result M[{sup 17}O]=16.999 131 756 6(9) u. The Dunham-Watson model applied to the molecular spectroscopic data hence predicts the mass of {sup 17}O to better thanmore » 1 part in 10{sup 8}.« less

Species Identification and Delineation of Pathogenic Mucorales by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Shao, Jin; Wan, Zhe; Li, Ruoyu; Yu, Jin

2018-04-01

This study aimed to validate the effectiveness of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification of filamentous fungi of the order Mucorales. A total of 111 isolates covering six genera preserved at the Research Center for Medical Mycology of Peking University were selected for MALDI-TOF MS analysis. We emphasized the study of 23 strains of Mucor irregularis predominantly isolated from patients in China. We first used the Bruker Filamentous Fungi library (v1.0) to identify all 111 isolates. To increase the identification rate, we created a compensatory in-house database, the Beijing Medical University (BMU) database, using 13 reference strains covering 6 species, including M. irregularis , Mucor hiemalis , Mucor racemosus , Cunninghamella bertholletiae , Cunninghamella phaeospora , and Cunninghamella echinulata All 111 isolates were then identified by MALDI-TOF MS using a combination of the Bruker library and BMU database. MALDI-TOF MS identified 55 (49.5%) and 74 (66.7%) isolates at the species and genus levels, respectively, using the Bruker Filamentous Fungi library v1.0 alone. A combination of the Bruker library and BMU database allowed MALDI-TOF MS to identify 90 (81.1%) and 111 (100%) isolates at the species and genus levels, respectively, with a significantly increased accuracy rate. MALDI-TOF MS poorly identified Mucorales when the Bruker library was used alone due to its lack of some fungal species. In contrast, this technique perfectly identified M. irregularis after main spectrum profiles (MSPs) of relevant reference strains were added to the Bruker library. With an expanded Bruker library, MALDI-TOF MS is an effective tool for the identification of pathogenic Mucorales. Copyright © 2018 American Society for Microbiology.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

Detection and identification of 700 drugs by multi-target screening with a 3200 Q TRAP LC-MS/MS system and library searching.

PubMed

Dresen, S; Ferreirós, N; Gnann, H; Zimmermann, R; Weinmann, W

2010-04-01

The multi-target screening method described in this work allows the simultaneous detection and identification of 700 drugs and metabolites in biological fluids using a hybrid triple-quadrupole linear ion trap mass spectrometer in a single analytical run. After standardization of the method, the retention times of 700 compounds were determined and transitions for each compound were selected by a "scheduled" survey MRM scan, followed by an information-dependent acquisition using the sensitive enhanced product ion scan of a Q TRAP hybrid instrument. The identification of the compounds in the samples analyzed was accomplished by searching the tandem mass spectrometry (MS/MS) spectra against the library we developed, which contains electrospray ionization-MS/MS spectra of over 1,250 compounds. The multi-target screening method together with the library was included in a software program for routine screening and quantitation to achieve automated acquisition and library searching. With the help of this software application, the time for evaluation and interpretation of the results could be drastically reduced. This new multi-target screening method has been successfully applied for the analysis of postmortem and traffic offense samples as well as proficiency testing, and complements screening with immunoassays, gas chromatography-mass spectrometry, and liquid chromatography-diode-array detection. Other possible applications are analysis in clinical toxicology (for intoxication cases), in psychiatry (antidepressants and other psychoactive drugs), and in forensic toxicology (drugs and driving, workplace drug testing, oral fluid analysis, drug-facilitated sexual assault).

COMPARISON OF TIME-OF-FLIGHT AND DOUBLE FOCUSING MASS SPECTROMETRY FOR REACHING TENTATIVE IDENTIFICATIONS FOR UNANTICIPATED COMPOUNDS ADDED TO DRINKING WATER BY TERRORISTS

EPA Science Inventory

Local monitoring of post-treatment drinking water using bench-top mass spectrometers could identify target compounds in a mass spectral library. However, a terrorist might seek to incite greater hysteria by injecting or infusing a mixture of unanticipated compounds of unknown tox...

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

PubMed

Collins, Andrew; Jones, Andrew R

2018-03-02

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .

Nuclear Matter Properties with the Re-evaluated Coefficients of Liquid Drop Model

NASA Astrophysics Data System (ADS)

Chowdhury, P. Roy; Basu, D. N.

2006-06-01

The coefficients of the volume, surface, Coulomb, asymmetry and pairing energy terms of the semiempirical liquid drop model mass formula have been determined by furnishing best fit to the observed mass excesses. Slightly different sets of the weighting parameters for liquid drop model mass formula have been obtained from minimizations of \\chi 2 and mean square deviation. The most recent experimental and estimated mass excesses from Audi-Wapstra-Thibault atomic mass table have been used for the least square fitting procedure. Equation of state, nuclear incompressibility, nuclear mean free path and the most stable nuclei for corresponding atomic numbers, all are in good agreement with the experimental results.

Compact hydrogen/helium isotope mass spectrometer

DOEpatents

Funsten, Herbert O.; McComas, David J.; Scime, Earl E.

1996-01-01

The compact hydrogen and helium isotope mass spectrometer of the present invention combines low mass-resolution ion mass spectrometry and beam-foil interaction technology to unambiguously detect and quantify deuterium (D), tritium (T), hydrogen molecule (H.sub.2, HD, D.sub.2, HT, DT, and T.sub.2), .sup.3 He, and .sup.4 He concentrations and concentration variations. The spectrometer provides real-time, high sensitivity, and high accuracy measurements. Currently, no fieldable D or molecular speciation detectors exist. Furthermore, the present spectrometer has a significant advantage over traditional T detectors: no confusion of the measurements by other beta-emitters, and complete separation of atomic and molecular species of equivalent atomic mass (e.g., HD and .sup.3 He).

Control of atomic transition rates via laser-light shaping

NASA Astrophysics Data System (ADS)

Jáuregui, R.

2015-04-01

A modular systematic analysis of the feasibility of modifying atomic transition rates by tailoring the electromagnetic field of an external coherent light source is presented. The formalism considers both the center of mass and internal degrees of freedom of the atom, and all properties of the field: frequency, angular spectrum, and polarization. General features of recoil effects for internal forbidden transitions are discussed. A comparative analysis of different structured light sources is explicitly worked out. It includes spherical waves, Gaussian beams, Laguerre-Gaussian beams, and propagation invariant beams with closed analytical expressions. It is shown that increments in the order of magnitude of the transition rates for Gaussian and Laguerre-Gaussian beams, with respect to those obtained in the paraxial limit, require waists of the order of the wavelength, while propagation invariant modes may considerably enhance transition rates under more favorable conditions. For transitions that can be naturally described as modifications of the atomic angular momentum, this enhancement is maximal (within propagation invariant beams) for Bessel modes, Mathieu modes can be used to entangle the internal and center-of-mass involved states, and Weber beams suppress this kind of transition unless they have a significant component of odd modes. However, if a recoil effect of the transition with an adequate symmetry is allowed, the global transition rate (center of mass and internal motion) can also be enhanced using Weber modes. The global analysis presented reinforces the idea that a better control of the transitions between internal atomic states requires both a proper control of the available states of the atomic center of mass, and shaping of the background electromagnetic field.

The DTIC Review: Volume 2, Number 4, Surviving Chemical and Biological Warfare

DTIC Science & Technology

1996-12-01

CHROMATOGRAPHIC ANALYSIS, NUCLEAR MAGNETIC RESONANCE, INFRARED SPECTROSCOPY , ARMY RESEARCH, DEGRADATION, VERIFICATION, MASS SPECTROSCOPY , LIQUID... mycotoxins . Such materials are not attractive as weapons of mass destruction however, as large amounts are required to produce lethal effects. In...VERIFICATION, ATOMIC ABSORPTION SPECTROSCOPY , ATOMIC ABSORPTION. AL The DTIC Review Defense Technical Information Center AD-A285 242 AD-A283 754 EDGEWOOO

Precise Measurements of the Masses of Cs, Rb and Na A New Route to the Fine Structure Constant

NASA Astrophysics Data System (ADS)

Rainville, Simon; Bradley, Michael P.; Porto, James V.; Thompson, James K.; Pritchard, David E.

2001-01-01

We report new values for the atomic masses of the alkali 133Cs, 87Rb, 85Rb, and 23Na with uncertainties ≤ 0.2 ppb. These results, obtained using Penning trap single ion mass spectrometry, are typically two orders of magnitude more accurate than previously measured values. Combined with values of h/m atom from atom interferometry measurements and accurate wavelength measurements for different atoms, these values will lead to new ppb-level determinations of the molar Planck constant N A h and the fine structure constant α. This route to α is based on simple physics. It can potentially achieve the several ppb level of accuracy needed to test the QED determination of α extracted from measurements of the electron g factor. We also demonstrate an electronic cooling technique that cools our detector and ion below the 4 K ambient temperature. This technique improves by about a factor of three our ability to measure the ion's axial motion.

Discrimination of ionic species from broad-beam ion sources

NASA Technical Reports Server (NTRS)

Anderson, J. R.

1993-01-01

The performance of a broad-beam, three-grid, ion extraction system incorporating radio frequency (RF) mass discrimination was investigated experimentally. This testing demonstrated that the system, based on a modified single-stage Bennett mass spectrometer, can discriminate between ionic species having about a 2-to-1 mass ratio while producing a broad-beam of ions with low kinetic energy (less than 15 eV). Testing was conducted using either argon and krypton ions or atomic and diatomic oxygen ions. A simple one-dimensional model, which ignores magnetic field and space-charge effects, was developed to predict the species separation capabilities as well as the kinetic energies of the extracted ions. The experimental results correlated well with the model predictions. This RF mass discrimination system can be used in applications where both atomic and diatomic ions are produced, but a beam of only one of the species is desired. An example of such an application is a 5 eV atomic oxygen source. This source would produce a beam of atomic oxygen with 5 eV kinetic energy, which would be directed onto a material specimen, to simulate the interaction between the surface of a satellite and the rarefied atmosphere encountered in low-Earth orbit.

Determination of the direct double-β -decay Q value of 96Zr and atomic masses of Zr 90 -92 ,94 ,96 and Mo 92 ,94 -98 ,100

NASA Astrophysics Data System (ADS)

Gulyuz, K.; Ariche, J.; Bollen, G.; Bustabad, S.; Eibach, M.; Izzo, C.; Novario, S. J.; Redshaw, M.; Ringle, R.; Sandler, R.; Schwarz, S.; Valverde, A. A.

2015-05-01

Experimental searches for neutrinoless double-β decay offer one of the best opportunities to look for physics beyond the standard model. Detecting this decay would confirm the Majorana nature of the neutrino, and a measurement of its half-life can be used to determine the absolute neutrino mass scale. Important to both tasks is an accurate knowledge of the Q value of the double-β decay. The LEBIT Penning trap mass spectrometer was used for the first direct experimental determination of the 96Zr double-β decay Q value: Qβ β=3355.85 (15 ) keV. This value is nearly 7 keV larger than the 2012 Atomic Mass Evaluation [M. Wang et al., Chin. Phys. C 36, 1603 (2012), 10.1088/1674-1137/36/12/003] value and one order of magnitude more precise. The 3-σ shift is primarily due to a more accurate measurement of the 96Zr atomic mass: m (96Zr ) =95.908 277 35 (17 ) u. Using the new Q value, the 2 ν β β -decay matrix element, | M2 ν| , is calculated. Improved determinations of the atomic masses of all other zirconium (Zr 90 -92 ,94 ,96 ) and molybdenum (92 ,94 -98 ,100Mo ) isotopes using both 12C8 and 87Rb as references are also reported.

Self Organization in Compensated Semiconductors

NASA Astrophysics Data System (ADS)

Berezin, Alexander A.

2004-03-01

In partially compensated semiconductor (PCS) Fermi level is pinned to donor sub-band. Due to positional randomness and almost isoenergetic hoppings, donor-spanned electronic subsystem in PCS forms fluid-like highly mobile collective state. This makes PCS playground for pattern formation, self-organization, complexity emergence, electronic neural networks, and perhaps even for origins of life, bioevolution and consciousness. Through effects of impact and/or Auger ionization of donor sites, whole PCS may collapse (spinodal decomposition) into microblocks potentially capable of replication and protobiological activity (DNA analogue). Electronic screening effects may act in RNA fashion by introducing additional length scale(s) to system. Spontaneous quantum computing on charged/neutral sites becomes potential generator of informationally loaded microstructures akin to "Carl Sagan Effect" (hidden messages in Pi in his "Contact") or informational self-organization of "Library of Babel" of J.L. Borges. Even general relativity effects at Planck scale (R.Penrose) may affect the dynamics through (e.g.) isotopic variations of atomic mass and local density (A.A.Berezin, 1992). Thus, PCS can serve as toy model (experimental and computational) at interface of physics and life sciences.

Searching for microbial protein over-expression in a complex matrix using automated high throughput MS-based proteomics tools.

PubMed

Akeroyd, Michiel; Olsthoorn, Maurien; Gerritsma, Jort; Gutker-Vermaas, Diana; Ekkelkamp, Laurens; van Rij, Tjeerd; Klaassen, Paul; Plugge, Wim; Smit, Ed; Strupat, Kerstin; Wenzel, Thibaut; van Tilborg, Marcel; van der Hoeven, Rob

2013-03-10

In the discovery of new enzymes genomic and cDNA expression libraries containing thousands of differential clones are generated to obtain biodiversity. These libraries need to be screened for the activity of interest. Removing so-called empty and redundant clones significantly reduces the size of these expression libraries and therefore speeds up new enzyme discovery. Here, we present a sensitive, generic workflow for high throughput screening of successful microbial protein over-expression in microtiter plates containing a complex matrix based on mass spectrometry techniques. MALDI-LTQ-Orbitrap screening followed by principal component analysis and peptide mass fingerprinting was developed to obtain a throughput of ∼12,000 samples per week. Alternatively, a UHPLC-MS(2) approach including MS(2) protein identification was developed for microorganisms with a complex protein secretome with a throughput of ∼2000 samples per week. TCA-induced protein precipitation enhanced by addition of bovine serum albumin is used for protein purification prior to MS detection. We show that this generic workflow can effectively reduce large expression libraries from fungi and bacteria to their minimal size by detection of successful protein over-expression using MS. Copyright © 2012 Elsevier B.V. All rights reserved.

Development of a dedicated peptide tandem mass spectral library for conservation science.

PubMed

Fremout, Wim; Dhaenens, Maarten; Saverwyns, Steven; Sanyova, Jana; Vandenabeele, Peter; Deforce, Dieter; Moens, Luc

2012-05-30

In recent years, the use of liquid chromatography tandem mass spectrometry (LC-MS/MS) on tryptic digests of cultural heritage objects has attracted much attention. It allows for unambiguous identification of peptides and proteins, and even in complex mixtures species-specific identification becomes feasible with minimal sample consumption. Determination of the peptides is commonly based on theoretical cleavage of known protein sequences and on comparison of the expected peptide fragments with those found in the MS/MS spectra. In this approach, complex computer programs, such as Mascot, perform well identifying known proteins, but fail when protein sequences are unknown or incomplete. Often, when trying to distinguish evolutionarily well preserved collagens of different species, Mascot lacks the required specificity. Complementary and often more accurate information on the proteins can be obtained using a reference library of MS/MS spectra of species-specific peptides. Therefore, a library dedicated to various sources of proteins in works of art was set up, with an initial focus on collagen rich materials. This paper discusses the construction and the advantages of this spectral library for conservation science, and its application on a number of samples from historical works of art. Copyright © 2012 Elsevier B.V. All rights reserved.

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

PubMed

Griss, Johannes; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan Antonio

2012-03-01

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

78 FR 31988 - Atomic Safety and Licensing Board; In the Matter of Charlissa C. Smith (Denial of Senior Reactor...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-28

... hearing will be held in Room A of the Augusta Public Library, 823 Telfair Street, Augusta, GA 30901. It... Regulatory Commission's Agencywide Documents Access and Management System (ADAMS), which can be accessed through http://www.nrc.gov/reading-rm/adams.html#web-based-adams . General information regarding...

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

PubMed Central

Röst, Hannes L.; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

Motivation In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Results Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Availability Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS. PMID:25927999

Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures.

PubMed

Telu, Kelly H; Yan, Xinjian; Wallace, William E; Stein, Stephen E; Simón-Manso, Yamil

2016-03-15

The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different liquid chromatography/mass spectrometry (LC/MS) platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC/MS platforms using reversed-phase chromatography and different chromatographic scales (conventional HPLC, UHPLC and nanoLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (relative standard deviation (RSD) <2%); however, substantial differences were found in the LC/MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.

Rapid Assessment of Contaminants and Interferences in Mass Spectrometry Data Using Skyline

NASA Astrophysics Data System (ADS)

Rardin, Matthew J.

2018-04-01

Proper sample preparation in proteomic workflows is essential to the success of modern mass spectrometry experiments. Complex workflows often require reagents which are incompatible with MS analysis (e.g., detergents) necessitating a variety of sample cleanup procedures. Efforts to understand and mitigate sample contamination are a continual source of disruption with respect to both time and resources. To improve the ability to rapidly assess sample contamination from a diverse array of sources, I developed a molecular library in Skyline for rapid extraction of contaminant precursor signals using MS1 filtering. This contaminant template library is easily managed and can be modified for a diverse array of mass spectrometry sample preparation workflows. Utilization of this template allows rapid assessment of sample integrity and indicates potential sources of contamination. [Figure not available: see fulltext.

The AME2016 atomic mass evaluation (II). Tables, graphs and references

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Meng; Audi, G.; Kondev, F. G.

This paper is the second part of the new evaluation of atomic masses, Ame2016. Using least-squares adjustments to all evaluated and accepted experimental data, described in Part I, we derive tables with numerical values and graphs to replace those given in Ame2012. The first table lists the recommended atomic mass values and their uncertainties. It is followed by a table of the influences of data on primary nuclides, a table of various reaction and decay energies, and finally, a series of graphs of separation and decay energies. The last section of this paper lists all references of the input datamore » used in the Ame2016 and the Nubase2016 evaluations (first paper in this issue). Amdc: http://amdc.impcas.ac.cn/« less

Silver/oxygen depth profile in coins by using laser ablation, mass quadrupole spectrometer and X-rays fluorescence

NASA Astrophysics Data System (ADS)

Cutroneo, M.; Torrisi, L.; Caridi, F.; Sayed, R.; Gentile, C.; Mondio, G.; Serafino, T.; Castrizio, E. D.

2013-05-01

Silver coins belonging to different historical periods were investigated to determine the Ag/O atomic ratio depth profiles. Laser ablation has been employed to remove, in high vacuum, the first superficial layers of the coins. Mass quadrupole spectrometry has been used to detect the Ag and the O atomic elements vaporized from the coin surface. The depth profile allowed to determine the thickness of the oxidation layer indicating that, in general, it is high in old coins. A complementary technique, using scanning electron microscope and the associated XRF microprobe, have been devoted to confirm the measurements of Ag/O atomic ratio measured with the laser-coupled mass spectrometry. The oxidation layer thicknesses range between about 25 and 250 microns.

X-ray Reflected Spectra from Accretion Disk Models. III. A Complete Grid of Ionized Reflection Calculations

NASA Technical Reports Server (NTRS)

Garcia, J.; Dauser, T.; Reynolds, C. S.; Kallman, T. R.; McClintock, J. E.; Wilms, J.; Ekmann, W.

2013-01-01

We present a new and complete library of synthetic spectra for modeling the component of emission that is reflected from an illuminated accretion disk. The spectra were computed using an updated version of our code xillver that incorporates new routines and a richer atomic data base. We offer in the form of a table model an extensive grid of reflection models that cover a wide range of parameters. Each individual model is characterized by the photon index Gamma of the illuminating radiation, the ionization parameter zeta at the surface of the disk (i.e., the ratio of the X-ray flux to the gas density), and the iron abundance A(sub Fe) relative to the solar value. The ranges of the parameters covered are: 1.2 <= Gamma <= 3.4, 1 <= zeta <= 104, and 0.5 <= A(sub Fe) <= 10. These ranges capture the physical conditions typically inferred from observations of active galactic nuclei, and also stellar-mass black holes in the hard state. This library is intended for use when the thermal disk flux is faint compared to the incident power-law flux. The models are expected to provide an accurate description of the Fe K emission line, which is the crucial spectral feature used to measure black hole spin. A total of 720 reflection spectra are provided in a single FITS file suitable for the analysis of X-ray observations via the atable model in xspec. Detailed comparisons with previous reflection models illustrate the improvements incorporated in this version of xillver.

Effective Atomic Number, Mass Attenuation Coefficient Parameterization, and Implications for High-Energy X-Ray Cargo Inspection Systems

NASA Astrophysics Data System (ADS)

Langeveld, Willem G. J.

The most widely used technology for the non-intrusive active inspection of cargo containers and trucks is x-ray radiography at high energies (4-9 MeV). Technologies such as dual-energy imaging, spectroscopy, and statistical waveform analysis can be used to estimate the effective atomic number (Zeff) of the cargo from the x-ray transmission data, because the mass attenuation coefficient depends on energy as well as atomic number Z. The estimated effective atomic number, Zeff, of the cargo then leads to improved detection capability of contraband and threats, including special nuclear materials (SNM) and shielding. In this context, the exact meaning of effective atomic number (for mixtures and compounds) is generally not well-defined. Physics-based parameterizations of the mass attenuation coefficient have been given in the past, but usually for a limited low-energy range. Definitions of Zeff have been based, in part, on such parameterizations. Here, we give an improved parameterization at low energies (20-1000 keV) which leads to a well-defined Zeff. We then extend this parameterization up to energies relevant for cargo inspection (10 MeV), and examine what happens to the Zeff definition at these higher energies.

Monte Carlo Computational Modeling of the Energy Dependence of Atomic Oxygen Undercutting of Protected Polymers

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Stueber, Thomas J.; Norris, Mary Jo

1998-01-01

A Monte Carlo computational model has been developed which simulates atomic oxygen attack of protected polymers at defect sites in the protective coatings. The parameters defining how atomic oxygen interacts with polymers and protective coatings as well as the scattering processes which occur have been optimized to replicate experimental results observed from protected polyimide Kapton on the Long Duration Exposure Facility (LDEF) mission. Computational prediction of atomic oxygen undercutting at defect sites in protective coatings for various arrival energies was investigated. The atomic oxygen undercutting energy dependence predictions enable one to predict mass loss that would occur in low Earth orbit, based on lower energy ground laboratory atomic oxygen beam systems. Results of computational model prediction of undercut cavity size as a function of energy and defect size will be presented to provide insight into expected in-space mass loss of protected polymers with protective coating defects based on lower energy ground laboratory testing.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubetsky, Boris; Libby, Stephen; Berman, Paul

The influence of an external test mass on the phase of the signal of an atom interferometer is studied theoretically. Using traditional techniques in atom optics based on the density matrix equations in the Wigner representation, we are able to extract the various contributions to the phase of the signal associated with the classical motion of the atoms, the quantum correction to this motion resulting from atomic recoil that is produced when the atoms interact with Raman field pulses and quantum corrections to the atomic motion that occur in the time between the Raman field pulses. Thus, by increasing themore » effective wave vector associated with the Raman field pulses using modified field parameters, we can increase the sensitivity of the signal to the point where such quantum corrections can be measured. Furthermore, the expressions that are derived can be evaluated numerically to isolate the contribution to the signal from an external test mass. The regions of validity of the exact and approximate expressions are determined.« less

Improved Limits on Axionlike-Particle-Mediated P, T-Violating Interactions between Electrons and Nucleons from Electric Dipole Moments of Atoms and Molecules.

PubMed

Stadnik, Y V; Dzuba, V A; Flambaum, V V

2018-01-05

In the presence of P, T-violating interactions, the exchange of axionlike particles between electrons and nucleons in atoms and molecules induces electric dipole moments (EDMs) of atoms and molecules. We perform calculations of such axion-exchange-induced atomic EDMs using the relativistic Hartree-Fock-Dirac method including electron core polarization corrections. We present analytical estimates to explain the dependence of these induced atomic EDMs on the axion mass and atomic parameters. From the experimental bounds on the EDMs of atoms and molecules, including ^{133}Cs, ^{205}Tl, ^{129}Xe, ^{199}Hg, ^{171}Yb^{19}F, ^{180}Hf^{19}F^{+}, and ^{232}Th^{16}O, we constrain the P, T-violating scalar-pseudoscalar nucleon-electron and electron-electron interactions mediated by a generic axionlike particle of arbitrary mass. Our limits improve on existing laboratory bounds from other experiments by many orders of magnitude for m_{a}≳10^{-2}  eV. We also place constraints on CP violation in certain types of relaxion models.

Search for light scalar dark matter with atomic gravitational wave detectors

NASA Astrophysics Data System (ADS)

Arvanitaki, Asimina; Graham, Peter W.; Hogan, Jason M.; Rajendran, Surjeet; Van Tilburg, Ken

2018-04-01

We show that gravitational wave detectors based on a type of atom interferometry are sensitive to ultralight scalar dark matter. Such dark matter can cause temporal oscillations in fundamental constants with a frequency set by the dark matter mass and amplitude determined by the local dark matter density. The result is a modulation of atomic transition energies. We point out a new time-domain signature of this effect in a type of gravitational wave detector that compares two spatially separated atom interferometers referenced by a common laser. Such a detector can improve on current searches for electron-mass or electric-charge modulus dark matter by up to 10 orders of magnitude in coupling, in a frequency band complementary to that of other proposals. It demonstrates that this class of atomic sensors is qualitatively different from other gravitational wave detectors, including those based on laser interferometry. By using atomic-clock-like interferometers, laser noise is mitigated with only a single baseline. These atomic sensors can thus detect scalar signals in addition to tensor signals.

Gravitational Wave Detection with Single-Laser Atom Interferometers

NASA Technical Reports Server (NTRS)

Yu, Nan; Tinto, Massimo

2011-01-01

A new design for a broadband detector of gravitational radiation relies on two atom interferometers separated by a distance L. In this scheme, only one arm and one laser are used for operating the two atom interferometers. The innovation here involves the fact that the atoms in the atom interferometers are not only considered as perfect test masses, but also as highly stable clocks. Atomic coherence is intrinsically stable, and can be many orders of magnitude more stable than a laser.

Lurking systematics in dust-based estimates of galaxy ISM masses

NASA Astrophysics Data System (ADS)

Janowiecki, Steven; Cortese, Luca; Catinella, Barbara; Goodwin, Adelle

2018-01-01

We use galaxies from the Herschel Reference Survey to evaluate commonly used indirect predictors of cold gas masses. With observations of cold neutral atomic and molecular gas, we calibrate predictive relationships using infrared dust emission and gas depletion time methods. We derive a set of self-consistent predictions of cold gas masses with ~20% scatter, and the greatest accuracy for total cold gas mass. However, significant systematic residuals are found in all calibrations which depend strongly on the molecular-to-atomic hydrogen mass ratio, and they can over/under-predict gas masses by >0.5 dex. Extending these types of indirect predictions to high-z galaxies (e.g., using ALMA observations of dust continuum to determine gas masses) requires implicit assumptions about the conditions in their interstellar medium. Any scaling relations derived using predicted gas masses may be more closely related to the calibrations used than to the actual galaxies observed.

libvdwxc: a library for exchange-correlation functionals in the vdW-DF family

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Kuisma, Mikael; Löfgren, Joakim; Pouillon, Yann; Erhart, Paul; Hyldgaard, Per

2017-09-01

We present libvdwxc, a general library for evaluating the energy and potential for the family of vdW-DF exchange-correlation functionals. libvdwxc is written in C and provides an efficient implementation of the vdW-DF method and can be interfaced with various general-purpose DFT codes. Currently, the Gpaw and Octopus codes implement interfaces to libvdwxc. The present implementation emphasizes scalability and parallel performance, and thereby enables ab initio calculations of nanometer-scale complexes. The numerical accuracy is benchmarked on the S22 test set whereas parallel performance is benchmarked on ligand-protected gold nanoparticles ({{Au}}144{({{SC}}11{{NH}}25)}60) up to 9696 atoms.

Rotational Energy as Mass in H3 + and Lower Limits on the Atomic Masses of D and 3He

NASA Astrophysics Data System (ADS)

Smith, J. A.; Hamzeloui, S.; Fink, D. J.; Myers, E. G.

2018-04-01

We have made precise measurements of the cyclotron frequency ratios H3 +/HD+ and H3 +/ 3He+ and observe that different H3+ ions result in different cyclotron frequency ratios. We interpret these differences as due to the molecular rotational energy of H3 + changing its inertial mass. We also confirm that certain high J , K rotational levels of H3+ have mean lifetimes exceeding several weeks. From measurements with the lightest H3+ ion we obtain lower limits on the atomic masses of deuterium and helium-3 with respect to the proton.

Continuous time-of-flight ion mass spectrometer

DOEpatents

Funsten, Herbert O.; Feldman, William C.

2004-10-19

A continuous time-of-flight mass spectrometer having an evacuated enclosure with means for generating an electric field located in the evacuated enclosure and means for injecting a sample material into the electric field. A source of continuous ionizing radiation injects ionizing radiation into the electric field to ionize atoms or molecules of the sample material, and timing means determine the time elapsed between arrival of a secondary electron out of said ionized atoms or molecules at a first predetermined location and arrival of a sample ion out of said ionized atoms or molecules at a second predetermined location.

Supersonic N-Crowdions in a Two-Dimensional Morse Crystal

NASA Astrophysics Data System (ADS)

Dmitriev, S. V.; Korznikova, E. A.; Chetverikov, A. P.

2018-03-01

An interstitial atom placed in a close-packed atomic row of a crystal is called crowdion. Such defects are highly mobile; they can move along the row, transferring mass and energy. We generalize the concept of a classical supersonic crowdion to an N-crowdion in which not one but N atoms move simultaneously with a high velocity. Using molecular dynamics simulations for a close-packed two-dimensional Morse crystal, we show that N-crowdions transfer mass much more efficiently, because they are capable of covering large distances while having a lower total energy than that of a classical 1-crowdion.

Atomic selectivity in dissociative electron attachment to dihalobenzenes.

PubMed

Kim, Namdoo; Sohn, Taeil; Lee, Sang Hak; Nandi, Dhananjay; Kim, Seong Keun

2013-10-21

We investigated electron attachment to three dihalobenzene molecules, bromochlorobenzene (BCB), bromoiodobenzene (BIB) and chloroiodobenzene (CIB), by molecular beam photoelectron spectroscopy. The most prominent product of electron attachment in the anion mass spectra was the atomic fragment of the less electronegative halogen of the two, i.e., Br(-) for BCB and I(-) for BIB and CIB. Photoelectron spectroscopy and ab initio calculations suggested that the approaching electron prefers to attack the less electronegative atom, a seemingly counterintuitive finding but consistent with the mass spectrometric result. For the iodine-containing species BIB and CIB, the photoelectron spectrum consists of bands from both the molecular anion and atomic I(-), the latter of which is produced by photodissociation of the former. Molecular orbital analysis revealed that a large degree of orbital energy reordering takes place upon electron attachment. These phenomena were shown to be readily explained by simple molecular orbital theory and the electronegativity of the halogen atoms.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Analysis of Human Plasma Metabolites across Different Liquid Chromatography - Mass Spectrometry Platforms: Cross-platform Transferable Chemical Signatures

PubMed Central

Telu, Kelly H.; Yan, Xinjian; Wallace, William E.; Stein, Stephen E.; Simón-Manso, Yamil

2016-01-01

RATIONALE The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different LC-MS platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. METHODS Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC-MS platforms using reversed phase chromatography and different chromatographic scales (nano, conventional and UHPLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). RESULTS Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (RSD < 2%); however, substantial differences were found in the LC-MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. CONLUSIONS Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. PMID:26842580

Extreme red shifted SERS nanotags† †Electronic supplementary information (ESI) available: General experimental details for the synthesis and characterization of dyes 1–14, intermediates 15–17, and HGNs; general description of the chemometrics used for principal component analysis; figures of SERS spectra of dye/HGN nanotags with 1280 nm excitation; extinction spectrum for HGNs; SERS spectra of Au and Ag nanoparticles and dye 13 aggregated with KCl; SERS spectra of dyes 13 and 14 on HGN not aggregated with KCl; details of mean plane angle calculations, tables of crystallographic data, atomic coordinates and equivalent isotropic displacement parameters, anisotropic placement parameters, bond lengths, bond angles, and hydrogen atom coordinates and isotropic displacement parameters for dye 14. CCDC 1040064. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03917c Click here for additional data file. Click here for additional data file.

PubMed Central

Bedics, Matthew A.; Kearns, Hayleigh; Cox, Jordan M.; Mabbott, Sam; Ali, Fatima; Shand, Neil C.; Faulds, Karen; Benedict, Jason B.

2015-01-01

Surfaced enhanced Raman scattering (SERS) nanotags operating with 1280 nm excitation were constructed from reporter molecules selected from a library of 14 chalcogenopyrylium dyes containing phenyl, 2-thienyl, and 2-selenophenyl substituents and a surface of hollow gold nanoshells (HGNs). These 1280 SERS nanotags are unique as they have multiple chalcogen atoms available which allow them to adsorb strongly onto the gold surface of the HGN thus producing exceptional SERS signals at this long excitation wavelength. Picomolar limits of detection (LOD) were observed and individual reporters of the library were identified by principal component analysis and classified according to their unique structure and SERS spectra. PMID:29308144

In situ calibration of inductively coupled plasma-atomic emission and mass spectroscopy

DOEpatents

Braymen, Steven D.

1996-06-11

A method and apparatus for in situ addition calibration of an inductively coupled plasma atomic emission spectrometer or mass spectrometer using a precision gas metering valve to introduce a volatile calibration gas of an element of interest directly into an aerosol particle stream. The present situ calibration technique is suitable for various remote, on-site sampling systems such as laser ablation or nebulization.

Sensitive Technique Developed Using Atomic Force Microscopy to Measure the Low-Earth-Orbit Atomic Oxygen Erosion of Polymers

NASA Technical Reports Server (NTRS)

deGroh, Kim D.; Banks, Bruce A.; Clark, Gregory W.; Hammerstrom, Anne; Youngstrom, Erica; Kaminski, Carolyn; Fine, Elizabeth; Marx, Laura

2001-01-01

A recession measurement technique has been developed at the NASA Glenn Research Center to determine the atomic oxygen durability of polymers exposed to the space environment for short durations. Polymers such as polyimide Kapton and Teflon FEP (fluorinated ethylene propylene, DuPont) are commonly used in spacecraft because of their desirable properties, such as flexibility, low density, and in the case of FEP, low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low- Earth-orbit environment are exposed to energetic atomic oxygen, resulting in erosion and potential structural loss. It is, therefore, important to understand the atomic oxygen erosion yield (E, the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. Because long-term space exposure data are rare and very costly, short-term exposures, such as on the space shuttles, are often relied on for atomic oxygen erosion determination. The most common technique for determining E is through mass-loss measurements. For limited-duration exposure experiments, such as shuttle flight experiments, the atomic oxygen fluence is often so small that mass-loss measurements are not sensitive enough. Therefore, a recession measurement technique has been developed at Glenn to obtain accurate erosion yields of polymers exposed to low atomic oxygen fluences.

A NEW MASS SPECTROMETRIC TECHNIQUE FOR ...

EPA Pesticide Factsheets

Most organic compounds are not found in mass spectral libraries and cannot be easily identified from low resolution mass spectra. Ion Composition Elucidation (ICE) utilizes selected ion recording with a double focusing mass spectrometer in a new way to determine exact masses and relative abundances of ions more rapidly and with greater accuracy than by full scanning. These measurements are made as analytes from a complex mixture elute from a GC column into the ion source. The exact masses and relative abundances establish the elemental compositions of the ions in a mass spectrum, which limits the possible identify of the compound sufficiently to make searches of the chemical and commercial literature feasible. ICE has two facets: Mass Peak Profiling from Selected Ion Recording Data (MPPSIRD) for data acquisition and a Profile Generation Model (PGM) for automated data interpretation. NTPSIRD and the PGM will be described and several applications of ICE will be shown: tentative identification of a compound that provided a mass spectrum with I I plausible NIST library matches; confirmation of the presence of temazepam, a sedative and one of the 200 most prescribed drugs in 1999. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this T

Building high-quality assay libraries for targeted analysis of SWATH MS data.

PubMed

Schubert, Olga T; Gillet, Ludovic C; Collins, Ben C; Navarro, Pedro; Rosenberger, George; Wolski, Witold E; Lam, Henry; Amodei, Dario; Mallick, Parag; MacLean, Brendan; Aebersold, Ruedi

2015-03-01

Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches (PSMs), generation of consensus spectra and compilation of MS coordinates that uniquely define each targeted peptide. Crucial steps such as false discovery rate (FDR) control, retention time normalization and handling of post-translationally modified peptides are detailed. Finally, we show how to use the library to extract SWATH data with the open-source software Skyline. The protocol takes 2-3 d to complete, depending on the extent of the library and the computational resources available.

VizieR Online Data Catalog: Brussels nuclear reaction rate library (Aikawa+, 2005)

NASA Astrophysics Data System (ADS)

Aikawa, M.; Arnould, M.; Goriely, S.; Jorissen, A.; Takahashi, K.

2005-07-01

The present data is part of the Brussels nuclear reaction rate library (BRUSLIB) for astrophysics applications and concerns nuclear reaction rate predictions calculated within the statistical Hauser-Feshbach approximation and making use of global and coherent microscopic nuclear models for the quantities (nuclear masses, nuclear structure properties, nuclear level densities, gamma-ray strength functions, optical potentials) entering the rate calculations. (4 data files).

Building phytochemical mass spec identification protocols and database libraries

USDA-ARS?s Scientific Manuscript database

An optimized single LC-MS evaluation that would accurately determine the elemental composition of as many compounds present in an extract would greatly aid in the evaluation of plant tissues. For phytochemicals, we have used accurate mass analysis to quickly characterize the potential chemical formu...

Method and apparatus for noble gas atom detection with isotopic selectivity

DOEpatents

Hurst, G. Samuel; Payne, Marvin G.; Chen, Chung-Hsuan; Parks, James E.

1984-01-01

Apparatus and methods of operation are described for determining, with isotopic selectivity, the number of noble gas atoms in a sample. The analysis is conducted within an evacuated chamber which can be isolated by a valve from a vacuum pumping system capable of producing a pressure of 10.sup.-8 Torr. Provision is made to pass pulses of laser beams through the chamber, these pulses having wavelengths appropriate for the resonance ionization of atoms of the noble gas under analysis. A mass filter within the chamber selects ions of a specific isotope of the noble gas, and means are provided to accelerate these selected ions sufficiently for implantation into a target. Specific types of targets are discussed. An electron measuring device produces a signal relatable to the number of ions implanted into the target and thus to the number of atoms of the selected isotope of the noble gas removed from the gas sample. The measurement can be continued until a substantial fraction, or all, of the atoms in the sample have been counted. Furthermore, additional embodiments of the apparatus are described for bunching the atoms of a noble gas for more rapid analysis, and for changing the target for repetitive cycling of the gas in the chamber. The number of repetitions of the cyclic steps depend upon the concentration of the isotope of interest, the separative efficiency of the mass filter, etc. The cycles are continued until a desired selectivity is achieved. Also described are components and a method of operation for a pre-enrichment operation for use when an introduction of a total sample would elevate the pressure within the chamber to levels in excess of those for operation of the mass filter, specifically a quadrupole mass filter. Specific examples of three noble gas isotope analyses are described.

Project Physics Tests 5, Models of the Atom.

ERIC Educational Resources Information Center

Harvard Univ., Cambridge, MA. Harvard Project Physics.

Test items relating to Project Physics Unit 5 are presented in this booklet. Included are 70 multiple-choice and 23 problem-and-essay questions. Concepts of atomic model are examined on aspects of relativistic corrections, electron emission, photoelectric effects, Compton effect, quantum theories, electrolysis experiments, atomic number and mass,…

MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

PubMed Central

2015-01-01

Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae. PMID:25263576

Bacterial Community Composition Associated with Chironomid Egg Masses

PubMed Central

Senderovich, Yigal; Halpern, Malka

2012-01-01

Chironomids (Diptera: Chironomidae) are the most widely distributed and often the most abundant insect in freshwater. They undergo a complete metamorphosis of four life stages, of which the egg, larva, and pupae are aquatic and the adult is terrestrial. Chironomid egg masses were found to be natural reservoirs of Vibrio cholerae and Aeromonas species. To expand the knowledge of the endogenous bacterial community associated with chironomid egg masses, denaturing gradient gel electrophoresis and clone analysis of 16S rRNA gene libraries were used in this study. Bacterial community composition associated with chironomid egg masses was found to be stable among different sampling periods. Cloned libraries of egg masses revealed that about 40% of the clones were related to bacteria known to degrade various toxicants. These findings were further supported when bacterial species that showed resistance to different toxic metals were isolated from egg masses and larval samples. Chironomids are found under a wide range of water conditions and are able to survive pollutants. However, little is known about their protective mechanisms under these conditions. Chironomid egg masses are inhabited by a stable endogenous bacterial community, which may potentially play a role in protecting chironomids from toxicants in polluted environments. Further study is needed to support this hypothesis. PMID:23461272

Low earth orbit durability evaluation of Haynes 188 solar receiver material

NASA Technical Reports Server (NTRS)

De Groh, Kim K.; Rutledge, Sharon K.; Burke, Christopher A.; Dever, Therese M.; Olle, Raymond M.; Terlep, Judith A.

1992-01-01

The effects of elevated-temperature vacuum and elevated-temperature atomic oxygen exposure on the mass, surface chemistry, surface morphology, and optical properties of Haynes 188, a possible heat receiver material for space-based solar dynamic power systems, have been studied. Pristine and surface modified Haynes 188 were exposed to vacuum less than or equal to 10 exp -6 torr at 820 C for 5215.5 h, and to atomic oxygen in an air plasma asher at 34 and 827 C for fluences up to 5.6 x 10 exp 21 atoms/sq cm. Results obtained indicate that vacuum heat treatment caused surface morphology and chemistry changes with corresponding optical property changes. Atomic oxygen exposure caused optical property changes which diminished with time. Mass changes are considered to be negligible for both exposures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pang, Yuan-Ping, E-mail: pang@mayo.edu

Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its nativemore » conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.« less

Magnetism. Physical Science in Action[TM]. Schlessinger Science Library. [Videotape].

ERIC Educational Resources Information Center

2000

Most people know what magnets do. Sometimes they stick together, sometimes they push apart and sometimes they don't do anything at all. But why do magnets act the way they do? Students will learn about the role of atoms in magnetism and why certain substances are magnetic while others are not. They will also discover some of the many ways…

Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination.

PubMed

Woods, Lucy A; Dolezal, Olan; Ren, Bin; Ryan, John H; Peat, Thomas S; Poulsen, Sally-Ann

2016-03-10

Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.

Authentication of Closely Related Fish and Derived Fish Products Using Tandem Mass Spectrometry and Spectral Library Matching.

PubMed

Nessen, Merel A; van der Zwaan, Dennis J; Grevers, Sander; Dalebout, Hans; Staats, Martijn; Kok, Esther; Palmblad, Magnus

2016-05-11

Proteomics methodology has seen increased application in food authentication, including tandem mass spectrometry of targeted species-specific peptides in raw, processed, or mixed food products. We have previously described an alternative principle that uses untargeted data acquisition and spectral library matching, essentially spectral counting, to compare and identify samples without the need for genomic sequence information in food species populations. Here, we present an interlaboratory comparison demonstrating how a method based on this principle performs in a realistic context. We also increasingly challenge the method by using data from different types of mass spectrometers, by trying to distinguish closely related and commercially important flatfish, and by analyzing heavily contaminated samples. The method was found to be robust in different laboratories, and 94-97% of the analyzed samples were correctly identified, including all processed and contaminated samples.

Advanced Spectral Library (ASTRAL): Atomic Fluorescence in Cool, Evolved Stars

NASA Astrophysics Data System (ADS)

Carpenter, Ken G.; Nielsen, Krister E.; Kober, Gladys V.; Rau, Gioia

2018-01-01

The "Advanced Spectral Library (ASTRAL) Project: Cool Stars" (PI = T. Ayres) collected a definitive set of representative, high-resolution (R~46,000 in the FUV up to ~1700 Å, R~30,000 for 1700-2150 Å, and R~114,000 >2150 Å) and high signal/noise (S/N>100) UV spectra of eight F-M evolved cool stars. These extremely high-quality STIS UV echelle spectra are available from the HST archive and from the Univ. of Colorado (http://casa.colorado.edu/~ayres/ASTRAL/) and will enable investigations of a broad range of problems -- stellar, interstellar, and beyond -- for many years. In this paper, we extend our study of the very rich emission-line spectra of the four evolved K-M stars in the sample, Beta Gem (K0 IIIb), Gamma Dra (K5 III), Gamma Cru (M3.4 III), and Alpha Ori (M2 Iab), to study the atomic fluorescence processes operating in their outer atmospheres. We summarize the pumping transitions and fluorescent line products known on the basis of previous work (e.g. Carpenter 1988, etc.) and newly identified in our current, on-going analysis of these extraordinary ASTRAL STIS spectra.

Melting point of high-purity germanium stable isotopes

NASA Astrophysics Data System (ADS)

Gavva, V. A.; Bulanov, A. D.; Kut'in, A. M.; Plekhovich, A. D.; Churbanov, M. F.

2018-05-01

The melting point (Tm) of germanium stable isotopes 72Ge, 73Ge, 74Ge, 76Ge was determined by differential scanning calorimetry. With the increase in atomic mass of isotope the decrease in Tm is observed. The decrease was equal to 0.15 °C per the unit of atomic mass which qualitatively agrees with the value calculated by Lindemann formula accounting for the effect of "isotopic compression" of elementary cell.

Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data

NASA Astrophysics Data System (ADS)

Ting, Ying S.; Shaffer, Scott A.; Jones, Jace W.; Ng, Wailap V.; Ernst, Robert K.; Goodlett, David R.

2011-05-01

Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS n ) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS n spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS n spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS n data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS n spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS n spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.

Mass Communication: A Guide to Reference Sources.

ERIC Educational Resources Information Center

McGill Univ., Montreal (Quebec). McLennan Library.

For the study of mass communication in social, cultural and political contexts, this annotated resource guide presents a list of materials available in the McGill University Libraries in Montreal, Canada. As a select bibliography, the guide concentrates on current sources, although some historical coverage of newspaper and journalism is included.…

ION COMPOSITION ELUCIDATION (ICE): AN INVESTIGATIVE TOOL FOR CHARACTERIZATION AND IDENTIFICATION OF COMPOUNDS OF REGULATORY IMPORTANCE

EPA Science Inventory

Ion Composition Elucidation (ICE) often leads to identification of compounds and provides high quality evidence for tracking compounds to their sources. Mass spectra for most organic compounds are not found in mass spectral libraries used to tentatively identify analytes. In addi...

Influence of Geometry on a High Surface Area-Solid Phase Microextraction Sampler for Chemical Vapor Collection

DTIC Science & Technology

2007-06-04

LCDR Greg Cook , PhD Date...Science Research Unit • Dr. Robert Mustacich of RVM Scientific • My thesis advisory committee: LtCol Peter LaPuma, LCDR Greg Cook , and Dr. Brian...which constitutes a mass spectrum. A computer compares the mass spectrum to a mass spectral library like a fingerprint. (McMaster and McMaster, 1997

A Hartree-Fock Application Using UPC++ and the New DArray Library

DOE PAGES

Ozog, David; Kamil, Amir; Zheng, Yili; ...

2016-07-21

The Hartree-Fock (HF) method is the fundamental first step for incorporating quantum mechanics into many-electron simulations of atoms and molecules, and it is an important component of computational chemistry toolkits like NWChem. The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front static partitioning of tasks, followed by work stealing whenever necessary. To enable innovations in algorithms and exploit next generation exascale systems, it is crucial to support quantum chemistry codes using expressive and convenient programming modelsmore » and runtime systems that are also efficient and scalable. Here, this paper presents an HF implementation similar to GTFock using UPC++, a partitioned global address space model that includes flexible communication, asynchronous remote computation, and a powerful multidimensional array library. UPC++ offers runtime features that are useful for HF such as active messages, a rich calculus for array operations, hardware-supported fetch-and-add, and functions for ensuring asynchronous runtime progress. We present a new distributed array abstraction, DArray, that is convenient for the kinds of random-access array updates and linear algebra operations on block-distributed arrays with irregular data ownership. Finally, we analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. Our optimized implementation of HF using UPC++ and the DArrays library shows up to 20% improvement over GTFock with Global Arrays at scales up to 24,000 cores.« less

A Hartree-Fock Application Using UPC++ and the New DArray Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozog, David; Kamil, Amir; Zheng, Yili

The Hartree-Fock (HF) method is the fundamental first step for incorporating quantum mechanics into many-electron simulations of atoms and molecules, and it is an important component of computational chemistry toolkits like NWChem. The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front static partitioning of tasks, followed by work stealing whenever necessary. To enable innovations in algorithms and exploit next generation exascale systems, it is crucial to support quantum chemistry codes using expressive and convenient programming modelsmore » and runtime systems that are also efficient and scalable. Here, this paper presents an HF implementation similar to GTFock using UPC++, a partitioned global address space model that includes flexible communication, asynchronous remote computation, and a powerful multidimensional array library. UPC++ offers runtime features that are useful for HF such as active messages, a rich calculus for array operations, hardware-supported fetch-and-add, and functions for ensuring asynchronous runtime progress. We present a new distributed array abstraction, DArray, that is convenient for the kinds of random-access array updates and linear algebra operations on block-distributed arrays with irregular data ownership. Finally, we analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. Our optimized implementation of HF using UPC++ and the DArrays library shows up to 20% improvement over GTFock with Global Arrays at scales up to 24,000 cores.« less

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

PubMed

Willighagen, Egon L; Mayfield, John W; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomáš; Rojas-Chertó, Miquel; Spjuth, Ola; Torrance, Gilleain; Evelo, Chris T; Guha, Rajarshi; Steinbeck, Christoph

2017-06-06

The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software. Graphical abstract CDK 2.0 provides new features and improved performance.

The discrimination of automotive clear coats by pyrolysis-gas chromatography/mass spectrometry and comparison of samples by a chromatogram library software.

PubMed

Plage, Bernd; Berg, Anna-Dolores; Luhn, Steven

2008-05-20

The differentiation of 25 automotive clear coats was evaluated using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). The samples were selected from eight different groups of samples which slightly differ in their infrared spectra. Most of the samples could be differentiated by visual inspection of the pyrograms. As an objective mean for evaluation a new software based on the comparison of chromatograms was tested for automatic classification considering retention times as well as mass spectra. The database was formed by the triplicate results of the set of the 25 samples. Normally a replicate measurement of a sample yields the best fit by library search. In addition, for most groups classification with moderate fits are obtained for samples belonging to the same group. Some samples are completely rearranged forming a new group of similar samples containing five samples from three different IR groups and four samples of three other groups, respectively. Furthermore detailed visual recognition of individual pyrolysis products allows subgrouping. Therefore, most samples can be differentiated from each other by Py-GC/MS. The exception were three sample groups containing two samples each, which could not be differentiated from each other neither by library search nor by recognition of minor individual pyrolysis products.

DETERMINING ION COMPOSITIONS USING AN ACCURATE MASS, TRIPLE QUADRUPOLE MASS SPECTROMETER

EPA Science Inventory

For the past decade, we have used double focusing mass spectrometers to determine
compositions of ions observed in mass spectra produced from compounds introduced by GC
based on measured exact masses of the ions and their +1 and +2 isotopic profiles arising from atoms of ...

Hydrogen rearrangements in the fragmentation of anthracene by low-energy electron impact

NASA Astrophysics Data System (ADS)

van der Burgt, Peter J. M.; Dunne, Melissa; Gradziel, Marcin L.

2018-02-01

We have measured mass spectra for positive ions produced by low-energy electron impact on anthracene using a reflectron time-of-flight mass spectrometer. The electron impact energy has been varied from 0 to 100 eV in steps of 0.5 eV. Ion yield curves of most of the fragment ions have been determined by fitting groups of adjacent peaks in the mass spectra with sequences of normalized Gaussians. Appearance energies for all these ions have been determined, and we report the first direct measurement of the triple ionization energy of anthracene at 45.5±0.5 eV. The groups of fragments containing 8-13 carbon atoms provide evidence for hydrogen rearrangements during the fragmentation, involving retention or loss of one or two additional hydrogen atoms. Groups of fragments with 6 and 7 carbon atoms clearly show the presence of doubly-charged fragments. The smaller fragments with 1-4 carbon atoms all show broadened peaks, and these fragments may be partly or mostly due to energetic charge-separation fragmentations of doubly-charged anthracene.

Anomaly of the composition of the F-2 equatorial region of the ionosphere during the hours after sunset according to data from the mass-spectrometer experiment on the Cosmos-274

NASA Technical Reports Server (NTRS)

Gaydukov, V. Y.; Istomin, V. G.; Romanovskiy, Y. A.

1979-01-01

A mass spectrometer on board Cosmos-274 measured concentrations of light atoms and ions. While traversing the geomagnetic equator during the evening hours it recorded on anomalous drop in ionized molecular oxygen and ionized atomic oxygen and nitrogen. A similar, less dramatic, decline was observed in the concentration of neutral atomic oxygen. A possible explanation for this and previously observed behavior is an ascent in altitude of the F layer in the hours after sunset, a possibility which is supported by calculations.

Atomic mass and double-β-decay Q value of 48Ca

NASA Astrophysics Data System (ADS)

Redshaw, Matthew; Bollen, Georg; Brodeur, Maxime; Bustabad, Scott; Lincoln, David L.; Novario, Samuel J.; Ringle, Ryan; Schwarz, Stefan

2012-10-01

The possibility of detecting neutrinoless double-β-decay (0νββ-decay) in experiments that are currently in operation or under development provides the exciting opportunity to determine the Dirac or Majorana nature of the neutrino and its absolute mass scale. An important datum for interpreting 0νββ-decay experimental results is the Q value of the decay. Using Penning trap mass spectrometry we have measured the atomic mass of 48Ca to be M[48Ca] = 47.952 522 76(21) u which, combined with the mass of 48Ti evaluated by Audi [Nucl. Phys. ANUPABL0375-947410.1016/j.nuclphysa.2003.11.003 729, 337 (2003)], provides a new determination of the 48Ca ββ-decay Q value: Qββ = 4262.96(84) keV.

Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

PubMed

Koes, David R; Vries, John K

2017-01-01

Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these coordinates are correct and the sample size is adequate, the ensemble average of these chemical shifts should be equal to the chemical shifts obtained from NMR spectroscopy. If this is not the case, the coordinates must be incorrect. We have utilized this fact to quantify the errors associated with the backbone atoms in MD simulations of proteins. A library of regional conformers containing 169,499 members was constructed from 6 model proteins. The chemical shifts associated with the backbone atoms in each of these conformers was obtained from QM calculations using density functional theory at the B3LYP level with a 6-311+G(2d,p) basis set. Chemical shifts were assigned to each backbone atom in each MD simulation frame using a template matching approach. The ensemble average of these chemical shifts was compared to chemical shifts from NMR spectroscopy. A large systematic error was identified that affected the 1 H atoms of the peptide bonds involved in hydrogen bonding with water molecules or peptide backbone atoms. This error was highly sensitive to changes in electrostatic parameters. Smaller errors affecting the 13 C a and 15 N atoms were also detected. We believe these errors could be useful as metrics for comparing the force-fields and parameter sets used in MD simulation because they are directly tied to errors in atomic coordinates.

High intensity 5 eV atomic oxygen source and Low Earth Orbit (LEO) simulation facility

NASA Technical Reports Server (NTRS)

Cross, J. B.; Spangler, L. H.; Hoffbauer, M. A.; Archuleta, F. A.; Leger, Lubert; Visentine, James

1987-01-01

An atomic oxygen exposure facility has been developed for studies of material degradation. The goal of these studies is to provide design criteria and information for the manufacture of long life (20 to 30 years) construction materials for use in LEO. The studies that are being undertaken using the facility will provide: absolute reaction cross sections for use in engineering design problems; formulations of reaction mechanisms; and calibration of flight hardware (mass spectrometers, etc.) in order to directly relate experiments performed in LEO to ground based investigations. The facility consists of: (1) a CW laser sustained discharge source of O atoms having a variable energy up to 5 eV and an intensity between 10(15) and 10(17) O atoms s(-1) cm(-2); (2) an atomic beam formation and diagnostics system consisting of various stages of differential pumping, a mass spectrometer detector, and a time of flight analyzer; (3) a spinning rotor viscometer for absolute O atom flux measurements; and (4) provision for using the system for calibration of actual flight instruments. Surface analysis equipment is available for the characterization of material surfaces before and after exposure to O atoms.

Laser-Assisted Atom Probe Tomography of Deformed Minerals: A Zircon Case Study.

PubMed

La Fontaine, Alexandre; Piazolo, Sandra; Trimby, Patrick; Yang, Limei; Cairney, Julie M

2017-04-01

The application of atom probe tomography to the study of minerals is a rapidly growing area. Picosecond-pulsed, ultraviolet laser (UV-355 nm) assisted atom probe tomography has been used to analyze trace element mobility within dislocations and low-angle boundaries in plastically deformed specimens of the nonconductive mineral zircon (ZrSiO4), a key material to date the earth's geological events. Here we discuss important experimental aspects inherent in the atom probe tomography investigation of this important mineral, providing insights into the challenges in atom probe tomography characterization of minerals as a whole. We studied the influence of atom probe tomography analysis parameters on features of the mass spectra, such as the thermal tail, as well as the overall data quality. Three zircon samples with different uranium and lead content were analyzed, and particular attention was paid to ion identification in the mass spectra and detection limits of the key trace elements, lead and uranium. We also discuss the correlative use of electron backscattered diffraction in a scanning electron microscope to map the deformation in the zircon grains, and the combined use of transmission Kikuchi diffraction and focused ion beam sample preparation to assist preparation of the final atom probe tip.

Use of immobilized exopeptidases and volatile buffers for analysis of peptides by fast atom bombardment mass spectrometry.

PubMed

Wagner, R M; Fraser, B A

1987-05-01

beta-Lipotrophin (62-77) or Ac-gastrin releasing peptide was incubated with immobilized carboxypeptidase Y or aminopeptidase M. Subsequent aliquots of each incubation mixture were analysed by fast atom bombardment mass spectrometry using a dithiothreitol/dithioerythritol liquid matrix. The use of immobilized enzymes and volatile buffers for exopeptidase digestions enabled rapid and facile separation of enzyme from digestion products. This approach to mass spectral peptide analysis reduced spectral background arising from a glycerol matrix, buffer salts, or enzyme proteins and contaminants, enabling analysis of as little as 200 picomoles of a suitable peptide.

Studies of the chemistry of the nightside ionosphere of Venus

NASA Technical Reports Server (NTRS)

Fox, J. L.

1991-01-01

A combination of numerical modeling and analysis of the Pioneer Venus UADS data base is studied, specifically data from the orbiter ion mass spectrometer (OIMS), orbiter neutral mass spectrometer (ONMS), and orbiter electron temperature probe (OETP). A one dimensional model of the Venus nightside ionosphere was set up in which downward fluxes of atomic ions are introduced at the upper boundary to simulate transport of ions from the dayside. The model shows that the densities of mass-28 ions, CO(+) + N(2+), resulting from an influx of atomic ions from the dayside are quite small, due to the high ionization potentials of CO and N2 that make chemical production difficult. A look at the data reveals that the actual densities of mass-28 ions are quite variable, from values near 10 to more than 10(exp 4) cm(exp -3). The excess mass-28 ions are assumed to be produced by electron precipitation and that the presence of high densities of mass-28 ions is a signature of auroral precipitation. A discussion of the atomic oxygen green line in the nightglow of Venus, which is produced mainly by dissociative recombination of O(2+), is presented. Original calculations of production rates of excited states for models based on Pioneer Venus data are also presented.

Atomic hydrogen propellants: Historical perspectives and future possibilities

NASA Technical Reports Server (NTRS)

Palaszewski, Bryan

1993-01-01

Atomic hydrogen, a very high density free-radical propellant, is anticipated to generate a specific impulse of 600-1500 lb-f sec/lb-mass performance; this may facilitate the development of unique launch vehicles. A development status evaluation is presently given for atomic hydrogen investigations. It is noted that breakthroughs are required in the production, storage, and transfer of atomic hydrogen, before this fuel can become a viable rocket propellant.

Quantization of Differences Between Atomic and Nuclear Rest Masses and Self-organization of Atoms and Nuclei

NASA Astrophysics Data System (ADS)

Gareev, F. A.; Zhidkova, I. E.

2007-03-01

We come to the conclusion that all atomic models based on either the Newton equation and the Kepler laws, or the Maxwell equations, or the Schrodinger and Dirac equations are in reasonable agreement with experimental data. We can only suspect that these equations are grounded on the same fundamental principle(s) which is (are) not known or these equations can be transformed into each other. We proposed a new mechanism of LENR: cooperative processes in the whole system nuclei + atoms + condensed matter - nuclear reactions in plasma - can occur at smaller threshold energies than the corresponding ones on free constituents. We were able to quantize phenomenologically the first time the differences between atomic and nuclear rest masses by the formula: δδM =n1/n2 X 0.0076294 (in MeV/ c^2), ni=1,2,3,.... Note that this quantization rule is justified for atoms and nuclei with different A, N and Z and the nuclei and atoms represent a coherent synchronized systems - a complex of coupled oscillators (resonators). The cooperative resonance synchronization mechanisms can explain how electron volt (atomic-) scale processes can induce and control nuclear MeV (nuclear-) scale processes and reactions., F.A. Gareev, I.E. Zhidkova, E-print arXiv Nucl-th/ 0610002 2006.

Impact-induced concerted mass transport on W surfaces by a voidion mechanism

NASA Astrophysics Data System (ADS)

Mazilova, T. I.; Sadanov, E. V.; Voyevodin, V. N.; Ksenofontov, V. A.; Mikhailovskij, I. M.

2018-03-01

Using low-temperature field ion microscope techniques, we studied at the atomic level morphological evolution of the W surface through bombardment by a beam of several keV He atoms. This technique allows the direct observation of the results of the high energy He atom impact on the elementary damage stages. The formation of the 〈110〉 and 〈100〉 linear vacancy chains and the high relaxation of the near-neighbors of the surface vacancy clusters were revealed. Performed molecular dynamics simulations shows that a single He atom impact triggers the relaxation process of the linear vacancy chain by a substantial decrease of the distance between atoms at both sides of the chain. The observed inward relaxations in W and Mo are an order of magnitude more than that for a single vacancy. It was revealed a novel highly cooperative impact-induced mass transport mechanism on the stepped surface: the formation and motion of a surface spatially delocalized vacancies (voidions). Surface voidions are extremely mobile: the mean velocity of atoms in voidions equals to a substantial portion of the sound velocity. Successive collective translations of the 〈111〉 lines of atoms in adjacent voidions give rise to a concerted gliding motion of great atomic clusters.

Quantitation of the phosphoproteome using the library-assisted extracted ion chromatogram (LAXIC) strategy.

PubMed

Arrington, Justine V; Xue, Liang; Tao, W Andy

2014-01-01

Phosphorylation is a key posttranslational modification that regulates many signaling pathways, but quantifying changes in phosphorylation between samples can be challenging due to its low stoichiometry within cells. We have introduced a mass spectrometry-based label-free quantitation strategy termed LAXIC for the analysis of the phosphoproteome. This method uses a spiked-in synthetic peptide library designed to elute across the entire chromatogram for local normalization of phosphopeptides within complex samples. Normalization of phosphopeptides by library peptides that co-elute within a small time frame accounts for fluctuating ion suppression effects, allowing more accurate quantitation even when LC-MS performance varies. Here we explain the premise of LAXIC, the design of a suitable peptide library, and how the LAXIC algorithm can be implemented with software developed in-house.

IAEA Nuclear Data Section: provision of atomic and nuclear databases for user applications.

PubMed

Humbert, Denis P; Nichols, Alan L; Schwerer, Otto

2004-01-01

The Nuclear Data Section (NDS) of the International Atomic Energy Agency (IAEA) provides a wide range of atomic and nuclear data services to scientists worldwide, with particular emphasis placed on the needs of developing countries. Highly focused Co-ordinated Research Projects and multinational data networks are sponsored under the auspices of the IAEA for the development and assembly of databases through the organised participation of specialists from Member States. More than 100 data libraries are readily available cost-free through the Internet, CD-ROM and other media. These databases are used in a wide range of applications, including fission- and fusion-energy, non-energy applications and basic research studies. Further information concerning the various services can be found through the web address of the IAEA Nuclear Data Section: and a mirror site at IPEN, Brazil that is maintained by NDS staff:.

Generating "fragment-based virtual library" using pocket similarity search of ligand-receptor complexes.

PubMed

Khashan, Raed S

2015-01-01

As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand's fragment(s) corresponding to that binding pocket are extracted, thus forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.

Effects of Mass Fluctuation on Thermal Transport Properties in Bulk Bi2Te3

NASA Astrophysics Data System (ADS)

Huang, Ben; Zhai, Pengcheng; Yang, Xuqiu; Li, Guodong

2017-05-01

In this paper, we applied large-scale molecular dynamics and lattice dynamics to study the influence of mass fluctuation on thermal transport properties in bulk Bi2Te3, namely thermal conductivity ( K), phonon density of state (PDOS), group velocity ( v g), and mean free path ( l). The results show that total atomic mass change can affect the relevant vibrational frequency on the micro level and heat transfer rate in the macro statistic, hence leading to the strength variation of the anharmonic phonon processes (Umklapp scattering) in the defect-free Bi2Te3 bulk. Moreover, it is interesting to find that the anharmonicity of Bi2Te3 can be also influenced by atomic differences of the structure such as the mass distribution in the primitive cell. Considering the asymmetry of the crystal structure and interatomic forces, it can be concluded by phonon frequency, lifetime, and velocity calculation that acoustic-optical phonon scattering shows the structure-sensitivity to the mass distribution and complicates the heat transfer mechanism, hence resulting in the low lattice thermal conductivity of Bi2Te3. This study is helpful for designing the material with tailored thermal conductivity via atomic substitution.

Direct Measurement of the Mass Difference of 163Ho and 163Dy Solves the Q -Value Puzzle for the Neutrino Mass Determination

NASA Astrophysics Data System (ADS)

Eliseev, S.; Blaum, K.; Block, M.; Chenmarev, S.; Dorrer, H.; Düllmann, Ch. E.; Enss, C.; Filianin, P. E.; Gastaldo, L.; Goncharov, M.; Köster, U.; Lautenschläger, F.; Novikov, Yu. N.; Rischka, A.; Schüssler, R. X.; Schweikhard, L.; Türler, A.

2015-08-01

The atomic mass difference of 163 and 163Dy has been directly measured with the Penning-trap mass spectrometer SHIPTRAP applying the novel phase-imaging ion-cyclotron-resonance technique. Our measurement has solved the long-standing problem of large discrepancies in the Q value of the electron capture in 163Ho determined by different techniques. Our measured mass difference shifts the current Q value of 2555(16) eV evaluated in the Atomic Mass Evaluation 2012 [G. Audi et al., Chin. Phys. C 36, 1157 (2012)] by more than 7 σ to 2833 (30stat)(15sys) eV /c2 . With the new mass difference it will be possible, e.g., to reach in the first phase of the ECHo experiment a statistical sensitivity to the neutrino mass below 10 eV, which will reduce its present upper limit by more than an order of magnitude.

In situ calibration of inductively coupled plasma-atomic emission and mass spectroscopy

DOEpatents

Braymen, S.D.

1996-06-11

A method and apparatus are disclosed for in situ addition calibration of an inductively coupled plasma atomic emission spectrometer or mass spectrometer using a precision gas metering valve to introduce a volatile calibration gas of an element of interest directly into an aerosol particle stream. The present in situ calibration technique is suitable for various remote, on-site sampling systems such as laser ablation or nebulization. 5 figs.

Jet atomization and cavitation induced by interactions between focused ultrasound and a water surfacea)

NASA Astrophysics Data System (ADS)

Tomita, Y.

2014-09-01

Atomization of a jet produced by the interaction of 1 MHz focused ultrasound with a water surface was investigated using high-speed photography. Viewing various aspects of jet behavior, threshold conditions were obtained necessary for water surface elevation and jet breakup, including drop separation and spray formation. In addition, the position of drop atomization, where a single drop separates from the tip of a jet without spraying, showed good correlation with the jet Weber number. For a set of specified conditions, multiple beaded water masses were formed, moving upwards to produce a vigorous jet. Cavitation phenomena occurred near the center of the primary drop-shaped water mass produced at the leading part of the jet; this was accompanied by fine droplets at the neck between the primary and secondary drop-shaped water masses, due to the collapse of capillary waves.

Characterization of dilute species within CVD-grown silicon nanowires doped using trimethylboron: protected lift-out specimen preparation for atom probe tomography.

PubMed

Prosa, T J; Alvis, R; Tsakalakos, L; Smentkowski, V S

2010-08-01

Three-dimensional quantitative compositional analysis of nanowires is a challenge for standard techniques such as secondary ion mass spectrometry because of specimen size and geometry considerations; however, it is precisely the size and geometry of nanowires that makes them attractive candidates for analysis via atom probe tomography. The resulting boron composition of various trimethylboron vapour-liquid-solid grown silicon nanowires were measured both with time-of-flight secondary ion mass spectrometry and pulsed-laser atom probe tomography. Both characterization techniques yielded similar results for relative composition. Specialized specimen preparation for pulsed-laser atom probe tomography was utilized and is described in detail whereby individual silicon nanowires are first protected, then lifted out, trimmed, and finally wet etched to remove the protective layer for subsequent three-dimensional analysis.

Production of pulsed atomic oxygen beams via laser vaporization methods

NASA Technical Reports Server (NTRS)

Brinza, David E.; Coulter, Daniel R.; Liang, Ranty H.; Gupta, Amitava

1987-01-01

Energetic pulsed atomic oxygen beams were generated by laser-driven evaporation of cryogenically frozen ozone/oxygen films and thin films of indium-tin oxide (ITO). Mass and energy characterization of beams from the ozone/oxygen films were carried out by mass spectrometry. The peak flux, found to occur at 10 eV, is estimated from this data to be 3 x 10(20) m(-2) s(-1). Analysis of the time-of-flight data indicates a number of processes contribute to the formation of the atomic oxygen beam. The absence of metastable states such as the 2p(3) 3s(1) (5S) level of atomic oxygen blown off from ITO films is supported by the failure to observe emission at 777.3 nm from the 2p(3) 3p(1) (5P sub J) levels. Reactive scattering experiments with polymer film targets for atomic oxygen bombardment are planned using a universal crossed molecular beam apparatus.

Electrochemical hydrogen storage alloys and batteries fabricated from Mg containing base alloys

DOEpatents

Ovshinsky, Stanford R.; Fetcenko, Michael A.

1996-01-01

An electrochemical hydrogen storage material comprising: (Base Alloy).sub.a M.sub.b where, Base Alloy is an alloy of Mg and Ni in a ratio of from about 1:2 to about 2:1, preferably 1:1; M represents at least one modifier element chosen from the group consisting of Co, Mn, Al, Fe, Cu, Mo, W, Cr, V, Ti, Zr, Sn, Th, Si, Zn, Li, Cd, Na, Pb, La, Mm, and Ca; b is greater than 0.5, preferably 2.5, atomic percent and less than 30 atomic percent; and a+b=100 atomic percent. Preferably, the at least one modifier is chosen from the group consisting of Co, Mn, Al, Fe, and Cu and the total mass of the at least one modifier element is less than 25 atomic percent of the final composition. Most preferably, the total mass of said at least one modifier element is less than 20 atomic percent of the final composition.

LC-MS-Based Lipidomics and Automated Identification of Lipids Using the LipidBlast In-Silico MS/MS Library.

PubMed

Cajka, Tomas; Fiehn, Oliver

2017-01-01

This protocol describes the analysis, specifically the identification, of blood plasma lipids. Plasma lipids are extracted using methyl tert-butyl ether (MTBE), methanol, and water followed by separation and data acquisition of isolated lipids using reversed-phase liquid chromatography coupled to quadrupole/time-of-flight mass spectrometry (RPLC-QTOFMS) operated in MS/MS mode. For lipid identification, acquired MS/MS spectra are converted to the mascot generic format (MGF) followed by library search using the in-silico MS/MS library LipidBlast. Using this approach, lipid classes, carbon-chain lengths, and degree of unsaturation of fatty-acid components are annotated.

Application of visual basic in high-throughput mass spectrometry-directed purification of combinatorial libraries.

PubMed

Li, B; Chan, E C Y

2003-01-01

We present an approach to customize the sample submission process for high-throughput purification (HTP) of combinatorial parallel libraries using preparative liquid chromatography electrospray ionization mass spectrometry. In this study, Visual Basic and Visual Basic for Applications programs were developed using Microsoft Visual Basic 6 and Microsoft Excel 2000, respectively. These programs are subsequently applied for the seamless electronic submission and handling of data for HTP. Functions were incorporated into these programs where medicinal chemists can perform on-line verification of the purification status and on-line retrieval of postpurification data. The application of these user friendly and cost effective programs in our HTP technology has greatly increased our work efficiency by reducing paper work and manual manipulation of data.

Performance measurements and operational characteristics of the Storage Tek ACS 4400 tape library with the Cray Y-MP EL

NASA Technical Reports Server (NTRS)

Hull, Gary; Ranade, Sanjay

1993-01-01

With over 5000 units sold, the Storage Tek Automated Cartridge System (ACS) 4400 tape library is currently the most popular large automated tape library. Based on 3480/90 tape technology, the library is used as the migration device ('nearline' storage) in high-performance mass storage systems. In its maximum configuration, one ACS 4400 tape library houses sixteen 3480/3490 tape drives and is capable of holding approximately 6000 cartridge tapes. The maximum storage capacity of one library using 3480 tapes is 1.2 TB and the advertised aggregate I/O rate is about 24 MB/s. This paper reports on an extensive set of tests designed to accurately assess the performance capabilities and operational characteristics of one STK ACS 4400 tape library holding approximately 5200 cartridge tapes and configured with eight 3480 tape drives. A Cray Y-MP EL2-256 was configured as its host machine. More than 40,000 tape jobs were run in a variety of conditions to gather data in the areas of channel speed characteristics, robotics motion, time taped mounts, and timed tape reads and writes.

Flight. Physical Science in Action[TM]. Schlessinger Science Library. [Videotape].

ERIC Educational Resources Information Center

2000

For thousands of years, humans dreamed of flying--but it isn't as easy as birds make it look. Students will learn about lift, gravity, thrust and drag--the forces that are used to get tons of steel off the ground and carry people thousands of miles before landing safely. They will also discover the role atoms and air pressure play in this amazing…

All about Solids, Liquids & Gases. Physical Science for Children[TM]. Schlessinger Science Library. [Videotape].

ERIC Educational Resources Information Center

2000

In All About Solids, Liquids and Gases, young students will be introduced to the three common forms of matter. They'll learn that all things are made up of tiny particles called atoms and that the movement of these particles determines the form that matter takes. In solids, the particles are packed tightly together and move very little. The…

CHARACTERIZATION OR IDENTIFICATION OF ORGANIC COMPOUNDS BY ION COMPOSITION ELUCIDATION (ICE) USING GAS CHROMATOGRAPHY/HIGH RESOLUTION MASS SPECTROMETRY

EPA Science Inventory

Only a small fraction of the compounds found in contaminated sites and water supplies is found in mass spectral libraries or has known toxicological effects. The EPA lists 2800 high production volume chemicals. These compounds, byproducts, and degradation products might be found ...

UTILITY OF THREE TYPES OF MASS SPECTROMETERS FOR DETERMINING ELEMENTAL COMPOSITIONS OF IONS FORMED FROM CHROMATOGRAPHICALLY SEPARATED COMPOUNDS

EPA Science Inventory

Sponsor Referee: Douglas F. Barofsky, Oregon State University Concentration factors of 1000 and more reveal dozens of compounds in extracts of water supplies. Library mass spectra for most of these compounds are not available, and alternative means of identification are needed. D...

Quantification of 60Fe atoms by MC-ICP-MS for the redetermination of the half-life.

PubMed

Kivel, Niko; Schumann, Dorothea; Günther-Leopold, Ines

2013-03-01

In many scientific fields, the half-life of radionuclides plays an important role. The accurate knowledge of this parameter has direct impact on, e.g., age determination of archeological artifacts and of the elemental synthesis in the universe. In order to derive the half-life of a long-lived radionuclide, the activity and the absolute number of atoms have to be analyzed. Whereas conventional radiation measurement methods are typically applied for activity determinations, the latter can be determined with high accuracy by mass spectrometric techniques. Over the past years, the half-lives of several radionuclides have been specified by means of multiple-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) complementary to the earlier reported values mainly derived by accelerator mass spectrometry. The present paper discusses all critical aspects (amount of material, radiochemical sample preparation, interference correction, isotope dilution mass spectrometry, calculation of measurement uncertainty) for a precise analysis of the number of atoms by MC-ICP-MS exemplified for the recently published half-life determination of 60Fe (Rugel et al, Phys Rev Lett 103:072502, 2009).

A molecular dynamics study of thermal transport in nanoparticle doped Argon like solid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shahadat, Muhammad Rubayat Bin, E-mail: rubayat37@gmail.com; Ahmed, Shafkat; Morshed, A. K. M. M.

2016-07-12

Interfacial phenomena such as mass and type of the interstitial atom, nano scale material defect influence heat transfer and the effect become very significant with the reduction of the material size. Non Equilibrium Molecular Dynamics (NEMD) simulation was carried out in this study to investigate the effect of the interfacial phenomena on solid. Argon like solid was considered in this study and LJ potential was used for atomic interaction. Nanoparticles of different masses and different molecular defects were inserted inside the solid. From the molecular simulation, it was observed that a large interfacial mismatch due to change in mass inmore » the homogenous solid causes distortion of the phonon frequency causing increase in thermal resistance. Position of the doped nanoparticles have more profound effect on the thermal conductivity of the solid whereas influence of the mass ratio is not very significant. Interstitial atom positioned perpendicular to the heat flow causes sharp reduction in thermal conductivity. Structural defect caused by the molecular defect (void) also observed to significantly affect the thermal conductivity of the solid.« less

Energy levels for Ac-212 (Actinium-212)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of Subvolume C `Tables of Excitations of Proton- and Neutron-rich Unstable Nuclei' of Volume 19 `Nuclear States from Charged Particle Reactions' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides energy levels for atomic nuclei of the isotope Ac-212 (actinium, atomic number Z = 89, mass number A = 212).

Empirical mass formula with proton-neutron interaction

NASA Astrophysics Data System (ADS)

Tachibana, Takahiro; Uno, Masahiro; Yamada, So; Yamada, Masami

1987-12-01

An atomic mass formula consisting of a gross part, and averge even-odd part and an empirical shell part is studied. The gross part is, apart from a small atomic term, taken to be the sum of nucleon rest masses. Coulomb energies and a polynomial in A1/3 and ‖N-Z‖/A. The shell part includes, in addition to proton and neutron support of nuclear magicities and the cooperative deformation effect. After the first construction of such a formula, refinements have been made in two respects. One is a separate treatment of Z=N odd-odd nuclei suggested by a quartet model, and the other is an improvement of the proton neutron interaction term. By these refinements the root-mean-square deviation of calculated masses from the 1986 Audi-Wapstra masses has been reduced from 538 keV to 460 keV.

X-RAY REFLECTED SPECTRA FROM ACCRETION DISK MODELS. III. A COMPLETE GRID OF IONIZED REFLECTION CALCULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia, J.; McClintock, J. E.; Dauser, T.

2013-05-10

We present a new and complete library of synthetic spectra for modeling the component of emission that is reflected from an illuminated accretion disk. The spectra were computed using an updated version of our code XILLVER that incorporates new routines and a richer atomic database. We offer in the form of a table model an extensive grid of reflection models that cover a wide range of parameters. Each individual model is characterized by the photon index {Gamma} of the illuminating radiation, the ionization parameter {xi} at the surface of the disk (i.e., the ratio of the X-ray flux to themore » gas density), and the iron abundance A{sub Fe} relative to the solar value. The ranges of the parameters covered are 1.2 {<=} {Gamma} {<=} 3.4, 1 {<=} {xi} {<=} 10{sup 4}, and 0.5 {<=} A{sub Fe} {<=} 10. These ranges capture the physical conditions typically inferred from observations of active galactic nuclei, and also stellar-mass black holes in the hard state. This library is intended for use when the thermal disk flux is faint compared to the incident power-law flux. The models are expected to provide an accurate description of the Fe K emission line, which is the crucial spectral feature used to measure black hole spin. A total of 720 reflection spectra are provided in a single FITS file (http://hea-www.cfa.harvard.edu/{approx}javier/xillver/) suitable for the analysis of X-ray observations via the atable model in XSPEC. Detailed comparisons with previous reflection models illustrate the improvements incorporated in this version of XILLVER.« less

Combination of atomic force microscopy and mass spectrometry for the detection of target protein in the serum samples of children with autism spectrum disorders

NASA Astrophysics Data System (ADS)

Kaysheva, A. L.; Pleshakova, T. O.; Kopylov, A. T.; Shumov, I. D.; Iourov, I. Y.; Vorsanova, S. G.; Yurov, Y. B.; Ziborov, V. S.; Archakov, A. I.; Ivanov, Y. D.

2017-10-01

Possibility of detection of target proteins associated with development of autistic disorders in children with use of combined atomic force microscopy and mass spectrometry (AFM/MS) method is demonstrated. The proposed method is based on the combination of affine enrichment of proteins from biological samples and visualization of these proteins by AFM and MS analysis with quantitative detection of target proteins.

The AME2016 atomic mass evaluation (I). Evaluation of input data; and adjustment procedures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, W. J.; Audi, G.; Wang, Meng

This paper is the first of two articles (Part I and Part II) that presents the results of the new atomic mass evaluation, Ame2016. It includes complete information on the experimental input data (also including unused and rejected ones), as well as details on the evaluation procedures used to derive the tables of recommended values given in the second part. This article describes the evaluation philosophy and procedures that were implemented in the selection of specific nuclear reaction, decay and mass-spectrometric results. These input values were entered in the least-squares adjustment for determining the best values for the atomic massesmore » and their uncertainties. Details of the calculation and particularities of the Ame are then described. All accepted and rejected data, including outweighted ones, are presented in a tabular format and compared with the adjusted values obtained using the least-squares fit analysis. Differences with the previous Ame2012 evaluation are discussed and specific information is presented for several cases that may be of interest to Ame users. The second Ame2016 article gives a table with the recommended values of atomic masses, as well as tables and graphs of derived quantities, along with the list of references used in both the Ame2016 and the Nubase2016 evaluations (the first paper in this issue). Amdc: http://amdc.impcas.ac.cn/« less

Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

PubMed

Pang, Yuan-Ping

2016-09-01

Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å 2 for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å 2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

Highly sensitive solids mass spectrometer uses inert-gas ion source

NASA Technical Reports Server (NTRS)

1966-01-01

Mass spectrometer provides a recorded analysis of solid material surfaces and bulk. A beam of high-energy inert-gas ions bombards the surface atoms of a sample and converts a percentage into an ionized vapor. The mass spectrum analyzer separates the vapor ionic constituents by mass-to-charge ratio.

Sensitive electrospray mass spectrometry analysis of one-bead-one-compound peptide libraries labeled by quaternary ammonium salts.

PubMed

Bąchor, Remigiusz; Cydzik, Marzena; Rudowska, Magdalena; Kluczyk, Alicja; Stefanowicz, Piotr; Szewczuk, Zbigniew

2012-08-01

A rapid and straightforward method for high-throughput analysis of single resin beads from one-bead-one-compound combinatorial libraries with high resolution electrospray ionization tandem mass spectrometry (HR ESI-MS/MS) is presented. The application of an efficient method of peptide derivatization by quaternary ammonium salts (QAS) formation increases ionization efficiency and reduces the detection limit, allowing analysis of trace amounts of compounds by ESI-MS. Peptides, synthesized on solid support, contain a new cleavable linker composed of a Peg spacer (9-aza-3,6,12,15-tetraoxa-10-on-heptadecanoic acid), lysine with ɛ-amino group marked by the N,N,N-triethylglycine salt, and methionine, which makes possible the selective cleavage by cyanogen bromide. Even a small portion of peptides derivatized by QAS cleaved from a single resin bead is sufficient for sequencing by HR ESI-MS/MS experiments. The developed strategy was applied to a small training library of α chymotrypsin substrates. The obtained results confirm the applicability of the proposed method in combinatorial chemistry.

Identification of Highly Pathogenic Microorganisms by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Results of an Interlaboratory Ring Trial

PubMed Central

Lasch, Peter; Wahab, Tara; Weil, Sandra; Pályi, Bernadett; Tomaso, Herbert; Zange, Sabine; Kiland Granerud, Beathe; Drevinek, Michal; Kokotovic, Branko; Wittwer, Matthias; Pflüger, Valentin; Di Caro, Antonino; Stämmler, Maren; Grunow, Roland

2015-01-01

In the case of a release of highly pathogenic bacteria (HPB), there is an urgent need for rapid, accurate, and reliable diagnostics. MALDI-TOF mass spectrometry is a rapid, accurate, and relatively inexpensive technique that is becoming increasingly important in microbiological diagnostics to complement classical microbiology, PCR, and genotyping of HPB. In the present study, the results of a joint exercise with 11 partner institutions from nine European countries are presented. In this exercise, 10 distinct microbial samples, among them five HPB, Bacillus anthracis, Brucella canis, Burkholderia mallei, Burkholderia pseudomallei, and Yersinia pestis, were characterized under blinded conditions. Microbial strains were inactivated by high-dose gamma irradiation before shipment. Preparatory investigations ensured that this type of inactivation induced only subtle spectral changes with negligible influence on the quality of the diagnosis. Furthermore, pilot tests on nonpathogenic strains were systematically conducted to ensure the suitability of sample preparation and to optimize and standardize the workflow for microbial identification. The analysis of the microbial mass spectra was carried out by the individual laboratories on the basis of spectral libraries available on site. All mass spectra were also tested against an in-house HPB library at the Robert Koch Institute (RKI). The averaged identification accuracy was 77% in the first case and improved to >93% when the spectral diagnoses were obtained on the basis of the RKI library. The compilation of complete and comprehensive databases with spectra from a broad strain collection is therefore considered of paramount importance for accurate microbial identification. PMID:26063856

MzJava: An open source library for mass spectrometry data processing.

PubMed

Horlacher, Oliver; Nikitin, Frederic; Alocci, Davide; Mariethoz, Julien; Müller, Markus; Lisacek, Frederique

2015-11-03

Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library's API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Probing the dynamic reversibility and generation of dynamic combinatorial libraries in the presence of bacterial model oligopeptides as templating guests of tetra-carbohydrazide macrocycles using electrospray mass spectrometry.

PubMed

Nour, Hany F; Islam, Tuhidul; Fernández-Lahore, Marcelo; Kuhnert, Nikolai

2012-12-30

Over the past few decades, bacterial resistance to antibiotics has emerged as a real threat to human health. Accordingly, there is an urgent demand for the development of innovative strategies for discovering new antibiotics. We present the first use of tetra-carbohydrazide cyclophane macrocycles in dynamic combinatorial chemistry (DCC) and molecular recognition as chiral hosts binding oligopeptides, which mimic bacterial cell wall. This study introduces an innovative application of electrospray ionisation time-of-flight mass spectrometry (ESI-TOF MS) to oligopeptides recognition using DCC. A small dynamic library composed of eight functionalised macrocycles has been generated in solution and all members were characterised by ESI-TOF MS. We also probed the dynamic reversibility and mechanism of formation of tetra-carbohydrazide cyclophanes in real-time using ESI-TOF MS. Dynamic reversibility of tetra-carbohydrazide cyclophanes is favored under thermodynamic control. The mechanism of formation of tetra-carbohydrazide cyclophanes involves key dialdehyde intermediates, which have been detected and assigned according to their high-resolution m/z values. Three members of the dynamic library bind efficiently in the gas phase to a selection of oligopeptides, unique to bacteria, allowing observation of host/guest complex ions in the gas phase. We probed the mechanism of the [2+2]-cyclocondensation reaction forming library members, proved dynamic reversibility of tetra-carbohydrazide cyclophanes and showed that complex ions formed between library members and hosts can be observed in the gas phase, allowing the solution of an important problem of biological interest. Copyright © 2012 John Wiley & Sons, Ltd.

Modelica buildings library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wetter, Michael; Zuo, Wangda; Nouidui, Thierry S.

This paper describes the Buildings library, a free open-source library that is implemented in Modelica, an equation-based object-oriented modeling language. The library supports rapid prototyping, as well as design and operation of building energy and control systems. First, we describe the scope of the library, which covers HVAC systems, multi-zone heat transfer and multi-zone airflow and contaminant transport. Next, we describe differentiability requirements and address how we implemented them. We describe the class hierarchy that allows implementing component models by extending partial implementations of base models of heat and mass exchangers, and by instantiating basic models for conservation equations andmore » flow resistances. We also describe associated tools for pre- and post-processing, regression tests, co-simulation and real-time data exchange with building automation systems. Furthermore, the paper closes with an example of a chilled water plant, with and without water-side economizer, in which we analyzed the system-level efficiency for different control setpoints.« less

Modelica buildings library

DOE PAGES

Wetter, Michael; Zuo, Wangda; Nouidui, Thierry S.; ...

2013-03-13

This paper describes the Buildings library, a free open-source library that is implemented in Modelica, an equation-based object-oriented modeling language. The library supports rapid prototyping, as well as design and operation of building energy and control systems. First, we describe the scope of the library, which covers HVAC systems, multi-zone heat transfer and multi-zone airflow and contaminant transport. Next, we describe differentiability requirements and address how we implemented them. We describe the class hierarchy that allows implementing component models by extending partial implementations of base models of heat and mass exchangers, and by instantiating basic models for conservation equations andmore » flow resistances. We also describe associated tools for pre- and post-processing, regression tests, co-simulation and real-time data exchange with building automation systems. Furthermore, the paper closes with an example of a chilled water plant, with and without water-side economizer, in which we analyzed the system-level efficiency for different control setpoints.« less

Screening Carbohydrate Libraries for Protein Interactions Using the Direct ESI-MS Assay. Applications to Libraries of Unknown Concentration

NASA Astrophysics Data System (ADS)

Kitova, Elena N.; El-Hawiet, Amr; Klassen, John S.

2014-08-01

A semiquantitative electrospray ionization mass spectrometry (ESI-MS) binding assay suitable for analyzing mixtures of oligosaccharides, at unknown concentrations, for interactions with target proteins is described. The assay relies on the differences in the ratio of the relative abundances of the ligand-bound and free protein ions measured by ESI-MS at two or more initial protein concentrations to distinguish low affinity (≤103 M-1) ligands from moderate and high affinity (>105 M-1) ligands present in the library and to rank their affinities. Control experiments were performed on solutions of a single chain antibody and a mixture of synthetic oligosaccharides, with known affinities, in the absence and presence of a 40-component carbohydrate library to demonstrate the implementation and reliability of the assay. The application of the assay for screening natural libraries of carbohydrates against proteins is also demonstrated using mixtures of human milk oligosaccharides, isolated from breast milk, and fragments of a bacterial toxin and human galectin 3.

SSmiles.

ERIC Educational Resources Information Center

Sunal, Dennis W., Ed.; Tracy, Dyanne M., Ed.

1992-01-01

Presents activities to supplement lessons on length and mass measurement or as part of a unit on atoms or orders of magnitude. Provides a lesson plan using aluminum foil to estimate unit measures, calculate the foil's thickness, and do an atom count. (MDH)

Development of a Plutonium Ceramic Target for the MASHA Separator

NASA Astrophysics Data System (ADS)

Shaughnessy, D. A.; Moody, K. J.; Kenneally, J. M.; Wild, J. F.; Stoyer, M. A.; Lougheed, R. W.; Yeremin, A. V.; Oganessian, Yu. Ts.

2004-04-01

We are participating in the development of the target for the MASHA (Mass Analyzer of Super Heavy Atoms) on-line mass separator in Dubna. Along with recent upgrades of the U400 cyclotron, MASHA will provide for at least a ten-fold increase in the production- and-detection rate for element 114 atoms, and will allow us to measure their atomic masses precisely. The MASHA separator will employ a thick Pu ceramic target capa- ble of tolerating temperatures in the vicinity of 2000 C without vaporizing the actinide compound. Reaction products will diffuse out of the target and will drift to an ECR ion source after which they will be transported through the separator and will impinge on a position-sensitive focal-plane detector array. Furthermore, operation of the MASHA hot target/ion source combination will provide chemical volatility information that will support our assignment of an atomic number of 114 to these nuclei. Taken together, these experiments on MASHA will allow us to make measurements that will cement our identification of element 114 and provide for future experiments in which the chemical properties of the heaviest elements are studied.

Improved Limits on Axionlike-Particle-Mediated P , T -Violating Interactions between Electrons and Nucleons from Electric Dipole Moments of Atoms and Molecules

NASA Astrophysics Data System (ADS)

Stadnik, Y. V.; Dzuba, V. A.; Flambaum, V. V.

2018-01-01

In the presence of P , T -violating interactions, the exchange of axionlike particles between electrons and nucleons in atoms and molecules induces electric dipole moments (EDMs) of atoms and molecules. We perform calculations of such axion-exchange-induced atomic EDMs using the relativistic Hartree-Fock-Dirac method including electron core polarization corrections. We present analytical estimates to explain the dependence of these induced atomic EDMs on the axion mass and atomic parameters. From the experimental bounds on the EDMs of atoms and molecules, including Cs 133 , Tl 205 , Xe 129 , Hg 199 , Yb 171 F 19 , Hf 180 F+ 19 , and Th 232 O 16 , we constrain the P , T -violating scalar-pseudoscalar nucleon-electron and electron-electron interactions mediated by a generic axionlike particle of arbitrary mass. Our limits improve on existing laboratory bounds from other experiments by many orders of magnitude for ma≳10-2 eV . We also place constraints on C P violation in certain types of relaxion models.

Atomic Oxygen Erosion Yield Prediction for Spacecraft Polymers in Low Earth Orbit

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Backus, Jane A.; Manno, Michael V.; Waters, Deborah L.; Cameron, Kevin C.; deGroh, Kim K.

2009-01-01

The ability to predict the atomic oxygen erosion yield of polymers based on their chemistry and physical properties has been only partially successful because of a lack of reliable low Earth orbit (LEO) erosion yield data. Unfortunately, many of the early experiments did not utilize dehydrated mass loss measurements for erosion yield determination, and the resulting mass loss due to atomic oxygen exposure may have been compromised because samples were often not in consistent states of dehydration during the pre-flight and post-flight mass measurements. This is a particular problem for short duration mission exposures or low erosion yield materials. However, as a result of the retrieval of the Polymer Erosion and Contamination Experiment (PEACE) flown as part of the Materials International Space Station Experiment 2 (MISSE 2), the erosion yields of 38 polymers and pyrolytic graphite were accurately measured. The experiment was exposed to the LEO environment for 3.95 years from August 16, 2001 to July 30, 2005 and was successfully retrieved during a space walk on July 30, 2005 during Discovery s STS-114 Return to Flight mission. The 40 different materials tested (including Kapton H fluence witness samples) were selected specifically to represent a variety of polymers used in space as well as a wide variety of polymer chemical structures. The MISSE 2 PEACE Polymers experiment used carefully dehydrated mass measurements, as well as accurate density measurements to obtain accurate erosion yield data for high-fluence (8.43 1021 atoms/sq cm). The resulting data was used to develop an erosion yield predictive tool with a correlation coefficient of 0.895 and uncertainty of +/-6.3 10(exp -25)cu cm/atom. The predictive tool utilizes the chemical structures and physical properties of polymers to predict in-space atomic oxygen erosion yields. A predictive tool concept (September 2009 version) is presented which represents an improvement over an earlier (December 2008) version.

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

PubMed Central

Ma, Jian; Casey, Cameron P.; Zheng, Xueyun; Ibrahim, Yehia M.; Wilkins, Christopher S.; Renslow, Ryan S.; Thomas, Dennis G.; Payne, Samuel H.; Monroe, Matthew E.; Smith, Richard D.; Teeguarden, Justin G.; Baker, Erin S.; Metz, Thomas O.

2017-01-01

Abstract Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results: We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation: PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Contact: erin.baker@pnnl.gov or thomas.metz@pnnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28505286

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association.

PubMed

Ma, Jian; Casey, Cameron P; Zheng, Xueyun; Ibrahim, Yehia M; Wilkins, Christopher S; Renslow, Ryan S; Thomas, Dennis G; Payne, Samuel H; Monroe, Matthew E; Smith, Richard D; Teeguarden, Justin G; Baker, Erin S; Metz, Thomas O

2017-09-01

Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library . erin.baker@pnnl.gov or thomas.metz@pnnl.gov. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Time-of-flight mass spectrographs—From ions to neutral atoms

NASA Astrophysics Data System (ADS)

Möbius, E.; Galvin, A. B.; Kistler, L. M.; Kucharek, H.; Popecki, M. A.

2016-12-01

After their introduction to space physics in the mid 1980s time-of-flight (TOF) spectrographs have become a main staple in spaceborne mass spectrometry. They have largely replaced magnetic spectrometers, except when extremely high mass resolution is required to identify complex molecules, for example, in the vicinity of comets or in planetary atmospheres. In combination with electrostatic analyzers and often solid state detectors, TOF spectrographs have become key instruments to diagnose space plasma velocity distributions, mass, and ionic charge composition. With a variety of implementation schemes that also include isochronous electric field configurations, TOF spectrographs can respond to diverse science requirements. This includes a wide range in mass resolution to allow the separation of medium heavy isotopes or to simply provide distributions of the major species, such as H, He, and O, to obtain information on source tracers or mass fluxes. With a top-hat analyzer at the front end, or in combination with deflectors for three-axis stabilized spacecraft, the distribution function of ions can be obtained with good time resolution. Most recently, the reach of TOF ion mass spectrographs has been extended to include energetic neutral atoms. After selecting the arrival direction with mechanical collimation, followed by conversion to ions, adapted TOF sensors form a new branch of the spectrograph family tree. We review the requirements, challenges, and implementation schemes for ion and neutral atom spectrographs, including potential directions for the future, while largely avoiding overlap with complementary contributions in this special issue.

QuBiLS-MIDAS: a parallel free-software for molecular descriptors computation based on multilinear algebraic maps.

PubMed

García-Jacas, César R; Marrero-Ponce, Yovani; Acevedo-Martínez, Liesner; Barigye, Stephen J; Valdés-Martiní, José R; Contreras-Torres, Ernesto

2014-07-05

The present report introduces the QuBiLS-MIDAS software belonging to the ToMoCoMD-CARDD suite for the calculation of three-dimensional molecular descriptors (MDs) based on the two-linear (bilinear), three-linear, and four-linear (multilinear or N-linear) algebraic forms. Thus, it is unique software that computes these tensor-based indices. These descriptors, establish relations for two, three, and four atoms by using several (dis-)similarity metrics or multimetrics, matrix transformations, cutoffs, local calculations and aggregation operators. The theoretical background of these N-linear indices is also presented. The QuBiLS-MIDAS software was developed in the Java programming language and employs the Chemical Development Kit library for the manipulation of the chemical structures and the calculation of the atomic properties. This software is composed by a desktop user-friendly interface and an Abstract Programming Interface library. The former was created to simplify the configuration of the different options of the MDs, whereas the library was designed to allow its easy integration to other software for chemoinformatics applications. This program provides functionalities for data cleaning tasks and for batch processing of the molecular indices. In addition, it offers parallel calculation of the MDs through the use of all available processors in current computers. The studies of complexity of the main algorithms demonstrate that these were efficiently implemented with respect to their trivial implementation. Lastly, the performance tests reveal that this software has a suitable behavior when the amount of processors is increased. Therefore, the QuBiLS-MIDAS software constitutes a useful application for the computation of the molecular indices based on N-linear algebraic maps and it can be used freely to perform chemoinformatics studies. Copyright © 2014 Wiley Periodicals, Inc.

Interpreting the Atomic Age: Scientific News Coverage of the Atomic Bomb in Representative Newspapers and Magazines.

ERIC Educational Resources Information Center

Barwis, Gail L.

A study examined the coverage of the scientific aspects of the atomic bomb in four representative newspapers (New York "Times," New York "Herald Tribune," Chicago "Daily Tribune," and Boston "Daily Globe") and in 14 general mass circulation magazines in the time period immediately following the dropping of the bomb. Among the conclusions of the…

Fast, low-level detection of strontium-90 and strontium-89 in environmental samples by collinear resonance ionization spectroscopy

NASA Astrophysics Data System (ADS)

Monz, L.; Hohmann, R.; Kluge, H.-J.; Kunze, S.; Lantzsch, J.; Otten, E. W.; Passler, G.; Senne, P.; Stenner, J.; Stratmann, K.; Swendt, K.; Zimmer, K.; Herrmann, G.; Trautmann, N.; Walter, K.

1993-12-01

Environmental assessment in the wake of a nuclear accident requires the rapid determination of the radiotoxic isotopes 89Sr and 90Sr. Useful measurements must be able to detect 10 8 atoms in the presence of about 10 18 atoms of the stable, naturally occurring isotopes. This paper describes a new approach to this problem using resonance ionization spectroscopy in collinear geometry, combined with classical mass separation. After collection and chemical separation, the strontium from a sample is surface-ionized and the ions are accelerated to an energy of about 30 keV. Initially, a magnetic mass separator provides an isotopic selectivity of about 10 6. The ions are then neutralized by charge exchange and the resulting fast strontium atoms are selectively excited into high-lying atomic Rydberg states by narrow-band cw laser light in collinear geometry. The Rydberg atoms are then field-ionized and detected. Thus far, a total isotopic selectivity of S > 10 10 and an overall efficiency of ξ = 5 × 10 -6 have been achieved. The desired detection limit of 10 8 atoms 90Sr has been demonstrated with synthetic samples.

Variation in the terrestrial isotopic composition and atomic weight of argon

USGS Publications Warehouse

Böhlke, John Karl

2014-01-01

The isotopic composition and atomic weight of argon (Ar) are variable in terrestrial materials. Those variations are a source of uncertainty in the assignment of standard properties for Ar, but they provide useful information in many areas of science. Variations in the stable isotopic composition and atomic weight of Ar are caused by several different processes, including (1) isotope production from other elements by radioactive decay (radiogenic isotopes) or other nuclear transformations (e.g., nucleogenic isotopes), and (2) isotopic fractionation by physical-chemical processes such as diffusion or phase equilibria. Physical-chemical processes cause correlated mass-dependent variations in the Ar isotope-amount ratios (40Ar/36Ar, 38Ar/36Ar), whereas nuclear transformation processes cause non-mass-dependent variations. While atmospheric Ar can serve as an abundant and homogeneous isotopic reference, deviations from the atmospheric isotopic ratios in other Ar occurrences limit the precision with which a standard atomic weight can be given for Ar. Published data indicate variation of Ar atomic weights in normal terrestrial materials between about 39.7931 and 39.9624. The upper bound of this interval is given by the atomic mass of 40Ar, as some samples contain almost pure radiogenic 40Ar. The lower bound is derived from analyses of pitchblende (uranium mineral) containing large amounts of nucleogenic 36Ar and 38Ar. Within this interval, measurements of different isotope ratios (40Ar/36Ar or 38Ar/36Ar) at various levels of precision are widely used for studies in geochronology, water–rock interaction, atmospheric evolution, and other fields.

Evaluation of methods for trace-element determination with emphasis on their usability in the clinical routine laboratory.

PubMed

Bolann, B J; Rahil-Khazen, R; Henriksen, H; Isrenn, R; Ulvik, R J

2007-01-01

Commonly used techniques for trace-element analysis in human biological material are flame atomic absorption spectrometry (FAAS), graphite furnace atomic absorption spectrometry (GFAAS), inductively coupled plasma atomic emission spectrometry (ICP-AES) and inductively coupled plasma mass spectrometry (ICP-MS). Elements that form volatile hydrides, first of all mercury, are analysed by hydride generation techniques. In the absorption techniques the samples are vaporized into free, neutral atoms and illuminated by a light source that emits the atomic spectrum of the element under analysis. The absorbance gives a quantitative measure of the concentration of the element. ICP-AES and ICP-MS are multi-element techniques. In ICP-AES the atoms of the sample are excited by, for example, argon plasma at very high temperatures. The emitted light is directed to a detector, and the optical signals are processed to values for the concentrations of the elements. In ICP-MS a mass spectrometer separates and detects ions produced by the ICP, according to their mass-to-charge ratio. Dilution of biological fluids is commonly needed to reduce the effect of the matrix. Digestion using acids and microwave energy in closed vessels at elevated pressure is often used. Matrix and spectral interferences may cause problems. Precautions should be taken against trace-element contamination during collection, storage and processing of samples. For clinical problems requiring the analysis of only one or a few elements, the use of FAAS may be sufficient, unless the higher sensitivity of GFAAS is required. For screening of multiple elements, however, the ICP techniques are preferable.

On the size and structure of helium snowballs formed around charged atoms and clusters of noble gases.

PubMed

Bartl, Peter; Leidlmair, Christian; Denifl, Stephan; Scheier, Paul; Echt, Olof

2014-09-18

Helium nanodroplets doped with argon, krypton, or xenon are ionized by electrons and analyzed in a mass spectrometer. HenNgx(+) ions containing up to seven noble gas (Ng) atoms and dozens of helium atoms are identified; the high resolution of the mass spectrometer combined with advanced data analysis make it possible to unscramble contributions from isotopologues that have the same nominal mass but different numbers of helium or Ng atoms, such as the magic He20(84)Kr2(+) and the isobaric, nonmagic He41(84)Kr(+). Anomalies in these ion abundances reveal particularly stable ions; several intriguing patterns emerge. Perhaps most astounding are the results for HenAr(+), which show evidence for three distinct, solid-like solvation shells containing 12, 20, and 12 helium atoms. This observation runs counter to the common notion that only the first solvation shell is solid-like but agrees with calculations by Galli et al. for HenNa(+) [J. Phys. Chem. A 2011, 115, 7300] that reveal three shells of icosahedral symmetry. HenArx(+) (2 ≤ x ≤ 7) ions appear to be especially stable if they contain a total of n + x = 19 atoms. A sequence of anomalies in the abundance distribution of HenKrx(+) suggests that rings of six helium atoms are inserted into the solvation shell each time a krypton atom is added to the ionic core, from Kr(+) to Kr3(+). Previously reported strong anomalies at He12Kr2(+) and He12Kr3(+) [Kim , J. H.; et al. J. Chem. Phys. 2006, 124, 214301] are attributed to a contamination. Only minor local anomalies appear in the distributions of HenXex(+) (x ≤ 3). The distributions of HenKr(+) and HenXe(+) show strikingly similar, broad features that are absent from the distribution of HenAr(+); differences are tentatively ascribed to the very different fragmentation dynamics of these ions.

On the Size and Structure of Helium Snowballs Formed around Charged Atoms and Clusters of Noble Gases

PubMed Central

2013-01-01

Helium nanodroplets doped with argon, krypton, or xenon are ionized by electrons and analyzed in a mass spectrometer. HenNgx+ ions containing up to seven noble gas (Ng) atoms and dozens of helium atoms are identified; the high resolution of the mass spectrometer combined with advanced data analysis make it possible to unscramble contributions from isotopologues that have the same nominal mass but different numbers of helium or Ng atoms, such as the magic He2084Kr2+ and the isobaric, nonmagic He4184Kr+. Anomalies in these ion abundances reveal particularly stable ions; several intriguing patterns emerge. Perhaps most astounding are the results for HenAr+, which show evidence for three distinct, solid-like solvation shells containing 12, 20, and 12 helium atoms. This observation runs counter to the common notion that only the first solvation shell is solid-like but agrees with calculations by Galli et al. for HenNa+ [J. Phys. Chem. A2011, 115, 730021568337] that reveal three shells of icosahedral symmetry. HenArx+ (2 ≤ x ≤ 7) ions appear to be especially stable if they contain a total of n + x = 19 atoms. A sequence of anomalies in the abundance distribution of HenKrx+ suggests that rings of six helium atoms are inserted into the solvation shell each time a krypton atom is added to the ionic core, from Kr+ to Kr3+. Previously reported strong anomalies at He12Kr2+ and He12Kr3+ [KimJ. H.; et al. J. Chem. Phys.2006, 124, 21430116774401] are attributed to a contamination. Only minor local anomalies appear in the distributions of HenXex+ (x ≤ 3). The distributions of HenKr+ and HenXe+ show strikingly similar, broad features that are absent from the distribution of HenAr+; differences are tentatively ascribed to the very different fragmentation dynamics of these ions. PMID:24128371

The Mass Media: A Student's Guide to Reference Sources.

ERIC Educational Resources Information Center

McGill Univ., Montreal (Quebec). McLennan Library.

This guide to materials available in the McLennan Library is intended to assist students in locating information and literature necessary for sociological studies of the mass media (excluding film). It does not deal with the more technical aspects of the media or the "how to" literature. The annotations are arranged under the following headings:…

Polymers Erosion and Contamination Experiment Being Developed

NASA Technical Reports Server (NTRS)

deGroh, Kim K.; Banks, Bruce A.; Barney-Barton, Elyse A.; Sechkar, Edward; Hunt, Patricia

1999-01-01

The Polymers Erosion and Contamination Experiment (PEACE) is currently being developed at the NASA Lewis Research Center by the Electro-Physics Branch in conjunction with students and faculty from Hathaway Brown School in Cleveland. The experiment is a Get Away Special Canister shuttle flight experiment sponsored by the American Chemical Society. The two goals of this experiment are (1) to measure ram atomic oxygen erosion rates of approximately 40 polymers that have potential use in space applications and (2) to validate a method for identifying sources of silicone contamination that occur in the shuttle bay. Equipment to be used in this flight experiment is shown in the schematic diagram. Spacecraft materials subjected to attack by atomic oxygen in the space environment experience significant degradation over the span of a typical mission. Therefore, learning the rates of atomic oxygen erosion of a wide variety of polymers would be of great benefit to future missions. PEACE will use two independent techniques to determine the atomic oxygen erosion rates of polymers. Large (1-in.-diameter) samples will be used for obtaining mass loss. Preflight and postflight dehydrated masses will be obtained, and the mass lost during flight will be determined. Small (0.5-in.-diameter) samples will be protected with isolated particles (such as NaCl crystals) and then exposed to the space environment. After flight, the protective particles will be removed (washed off) and atomic force microscopy (AFM) will be used to measure the erosion depth from protected mesas. Erosion depth measurements are more sensitive than traditional mass measurements and are very useful for materials with low erosion yields or with very low fluence missions.

Carbon atom and cluster sputtering under low-energy noble gas plasma bombardment

NASA Astrophysics Data System (ADS)

Oyarzabal, E.; Doerner, R. P.; Shimada, M.; Tynan, G. R.

2008-08-01

Exit-angle resolved carbon atom and cluster (C2 and C3) sputtering yields are measured during different noble gas (Xe, Kr, Ar, Ne, and He) ion bombardments from a plasma, for low incident energies (75-225 eV). A quadrupole mass spectrometer (QMS) is used to detect the fraction of sputtered neutrals that is ionized in the plasma and to obtain the angular distribution by changing the angle between the target normal and the QMS aperture. A one-dimensional Monte Carlo code is used to simulate the interaction of the plasma and the sputtered particles in the region between the sample and the QMS. The effective elastic scattering cross sections of C, C2, and C3 with the different bombarding gas neutrals are obtained by varying the distance between the sample and the QMS and by performing a best fit of the simulation results to the experimental results. The total sputtering yield (C+C2+C3) for each bombarding gas is obtained from weight-loss measurements and the sputtering yield for C, C2, and C3 is then calculated from the integration of the measured angular distribution, taking into account the scattering and ionization of the sputtered particles between the sample and the QMS. We observe undercosine angular distributions of the sputtered atoms and clusters for all the studied bombarding gases and a clear decrease of the atom to cluster (C2 and C3) sputtering ratio as the incident ion mass increases, changing from a carbon atom preferential erosion for the lower incident ion masses (He, Ne, and Ar) to a cluster preferential erosion for the higher incident ion masses (Kr and Xe).

Peptides for functionalization of InP semiconductors.

PubMed

Estephan, Elias; Saab, Marie-belle; Larroque, Christian; Martin, Marta; Olsson, Fredrik; Lourdudoss, Sebastian; Gergely, Csilla

2009-09-15

The challenge is to achieve high specificity in molecular sensing by proper functionalization of micro/nano-structured semiconductors by peptides that reveal specific recognition for these structures. Here we report on surface modification of the InP semiconductors by adhesion peptides produced by the phage display technique. An M13 bacteriophage library has been used to screen 10(10) different peptides against the InP(001) and the InP(111) surfaces to finally isolate specific peptides for each orientation of the InP. MALDI-TOF/TOF mass spectrometry has been employed to study real affinity of the peptide towards the InP surfaces. The peptides serve for controlled placement of biotin onto InP to bind then streptavidin. Our Atomic Force Microscopy study revealed a total surface coverage of molecules when the InP surface was functionalized by its specific biotinylated peptide (YAIKGPSHFRPS). Finally, fluorescence microscopy has been employed to demonstrate the preferential attachment of the peptide onto a micro-patterned InP surface. Use of substrate specific peptides could present an alternative solution for the problems encountered in the actually existing sensing methods and molecular self-assembly due to the unwanted unspecific interactions.

Comprehensive gas chromatography coupled to mass spectrometry for the separation of pesticides in a very complex matrix.

PubMed

Mondello, Luigi; Casilli, Alessandro; Tranchida, Peter Quinto; Lo Presti, Maria; Dugo, Paola; Dugo, Giovanni

2007-11-01

The present research is focused on the development of a comprehensive two-dimensional gas chromatography-rapid scanning quadrupole mass spectrometric (GC x GC-qMS) methodology for the analysis of trace-amount pesticides contained in a complex real-world sample. Reliable peak assignment was carried out by using a recently developed, dedicated pesticide MS library (for comprehensive GC analysis), characterized by a twin-filter search procedure, the first based on a minimum degree of spectral similarity and the second on the interactive use of linear retention indices (LRI). The library was constructed by subjecting mixtures of commonly used pesticides to GC x GC-qMS analysis and then deriving their pure mass spectra and LRI values. In order to verify the effectiveness of the approach, a pesticide-contaminated red grapefruit extract was analysed. The certainty of peak assignment was attained by exploiting both the enhanced separation power of dual-oven GC x GC and the highly effective search procedure.

Resolving mass spectral overlaps in atom probe tomography by isotopic substitutions - case of TiSi15N.

PubMed

Engberg, David L J; Johnson, Lars J S; Jensen, Jens; Thuvander, Mattias; Hultman, Lars

2018-01-01

Mass spectral overlaps in atom probe tomography (APT) analyses of complex compounds typically limit the identification of elements and microstructural analysis of a material. This study concerns the TiSiN system, chosen because of severe mass-to-charge-state ratio overlaps of the 14 N + and 28 Si 2+ peaks as well as the 14 N 2 + and 28 Si + peaks. By substituting 14 N with 15 N, mass spectrum peaks generated by ions composed of one or more N atoms will be shifted toward higher mass-to-charge-state ratios, thereby enabling the separation of N from the predominant Si isotope. We thus resolve thermodynamically driven Si segregation on the nanometer scale in cubic phase Ti 1- x Si x 15 N thin films for Si contents 0.08 ≤ x ≤ 0.19 by APT, as corroborated by transmission electron microscopy. The APT analysis yields a composition determination that is in good agreement with energy dispersive X-ray spectroscopy and elastic recoil detection analyses. Additionally, a method for determining good voxel sizes for visualizing small-scale fluctuations is presented and demonstrated for the TiSiN system. Copyright © 2017 Elsevier B.V. All rights reserved.

Adaptive detection of missed text areas in OCR outputs: application to the automatic assessment of OCR quality in mass digitization projects

NASA Astrophysics Data System (ADS)

Ben Salah, Ahmed; Ragot, Nicolas; Paquet, Thierry

2013-01-01

The French National Library (BnF*) has launched many mass digitization projects in order to give access to its collection. The indexation of digital documents on Gallica (digital library of the BnF) is done through their textual content obtained thanks to service providers that use Optical Character Recognition softwares (OCR). OCR softwares have become increasingly complex systems composed of several subsystems dedicated to the analysis and the recognition of the elements in a page. However, the reliability of these systems is always an issue at stake. Indeed, in some cases, we can find errors in OCR outputs that occur because of an accumulation of several errors at different levels in the OCR process. One of the frequent errors in OCR outputs is the missed text components. The presence of such errors may lead to severe defects in digital libraries. In this paper, we investigate the detection of missed text components to control the OCR results from the collections of the French National Library. Our verification approach uses local information inside the pages based on Radon transform descriptors and Local Binary Patterns descriptors (LBP) coupled with OCR results to control their consistency. The experimental results show that our method detects 84.15% of the missed textual components, by comparing the OCR ALTO files outputs (produced by the service providers) to the images of the document.

Molybdenum and carbon atom and carbon cluster sputtering under low-energy noble gas plasma bombardment

NASA Astrophysics Data System (ADS)

Oyarzabal, Eider

Exit-angle resolved Mo atom sputtering yield under Xe ion bombardment and carbon atom and cluster (C2 and C3) sputtering yields under Xe, Kr, Ar, Ne and He ion bombardment from a plasma are measured for low incident energies (75--225 eV). An energy-resolved quadrupole mass spectrometer (QMS) is used to detect the fraction of un-scattered sputtered neutrals that become ionized in the plasma; the angular distribution is obtained by changing the angle between the target and the QMS aperture. A one-dimensional Monte Carlo code is used to simulate the interaction of the plasma and the sputtered particles between the sample and the QMS. The elastic scattering cross-sections of C, C2 and C3 with the different bombarding gas neutrals is obtained by varying the distance between the sample and the QMS and by performing a best fit of the simulation results to the experimental results. Because the results obtained with the QMS are relative, the Mo atom sputtering results are normalized to the existing data in the literature and the total sputtering yield for carbon (C+C 2+C3) for each bombarding gas is obtained from weight loss measurements. The absolute sputtering yield for C, C2 and C 3 is then calculated from the integration of the measured angular distribution, taking into account the scattering and ionization of the sputtered particles between the sample and the QMS. The angular sputtering distribution for Mo has a maximum at theta=60°, and this maximum becomes less pronounced as the incident ion energy increases. The results of the Monte Carlo TRIDYN code simulation for the angular distribution of Mo atoms sputtered by Xe bombardment are in agreement with the experiments. For carbon sputtering under-cosine angular distributions of the sputtered atoms and clusters for all the studied bombarding gases are also observed. The C, C2 and C3 sputtering yield data shows a clear decrease of the atom to cluster (C/C2 and C/C3) sputtering ratio as the incident ion mass increases, changing from a carbon atom preferential erosion for the lower incident ion masses (He, Ne and Ar) to a cluster preferential erosion for the higher incident ion masses (Kr and Xe).

First Measurement of the Atomic Electric Dipole Moment of (225)Ra.

PubMed

Parker, R H; Dietrich, M R; Kalita, M R; Lemke, N D; Bailey, K G; Bishof, M; Greene, J P; Holt, R J; Korsch, W; Lu, Z-T; Mueller, P; O'Connor, T P; Singh, J T

2015-06-12

The radioactive radium-225 ((225)Ra) atom is a favorable case to search for a permanent electric dipole moment. Because of its strong nuclear octupole deformation and large atomic mass, (225)Ra is particularly sensitive to interactions in the nuclear medium that violate both time-reversal symmetry and parity. We have developed a cold-atom technique to study the spin precession of (225)Ra atoms held in an optical dipole trap, and demonstrated the principle of this method by completing the first measurement of its atomic electric dipole moment, reaching an upper limit of |d((225)Ra)|<5.0×10(-22)  e cm (95% confidence).

Negative-Mass Instability of the Spin and Motion of an Atomic Gas Driven by Optical Cavity Backaction

NASA Astrophysics Data System (ADS)

Kohler, Jonathan; Gerber, Justin A.; Dowd, Emma; Stamper-Kurn, Dan M.

2018-01-01

We realize a spin-orbit interaction between the collective spin precession and center-of-mass motion of a trapped ultracold atomic gas, mediated by spin- and position-dependent dispersive coupling to a driven optical cavity. The collective spin, precessing near its highest-energy state in an applied magnetic field, can be approximated as a negative-mass harmonic oscillator. When the Larmor precession and mechanical motion are nearly resonant, cavity mediated coupling leads to a negative-mass instability, driving exponential growth of a correlated mode of the hybrid system. We observe this growth imprinted on modulations of the cavity field and estimate the full covariance of the resulting two-mode state by observing its transient decay during subsequent free evolution.

NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary.

PubMed

Yilmaz, Emel Maden; Güntert, Peter

2015-09-01

An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

Health information-seeking behavior and older African American women.

PubMed Central

Gollop, C J

1997-01-01

This study explored the ways in which urban, older, African American women obtain health information and some of the factors that influence such activity. Among the possible determinants examined were self-perceived literacy, access to health information, and mobility. The findings suggest that respondents receive health information from their physicians, the mass media, and members of their social networks. The results of this research also indicated that members of this population have a highly positive perception of the public library, although only a small segment use the library regularly, and that it may be in the interest of the library to investigate the role it could play in providing health information to older adults. PMID:9160150

Generation of Dynamic Combinatorial Libraries Using Hydrazone‐Functionalized Surface Mimetics

PubMed Central

Hewitt, Sarah H.

2018-01-01

Dynamic combinatorial chemistry (DCC) represents an approach, whereby traditional supramolecular scaffolds used for protein surface recognition might be exploited to achieve selective high affinity target recognition. Synthesis, in situ screening and amplification under selection pressure allows the generation of ligands, which bear different moieties capable of making multivalent non‐covalent interactions with target proteins. Generic tetracarboxyphenyl porphyrin scaffolds bearing four hydrazide moieties have been used to form dynamic combinatorial libraries (DCLs) using aniline‐catalyzed reversible hydrazone exchange reactions, in 10 % DMSO, 5 mm NH4OAc, at pH 6.75. High resolution mass spectrometry (HRMS) was used to monitor library composition and establish conditions under which equilibria were established.

Health information-seeking behavior and older African American women.

PubMed

Gollop, C J

1997-04-01

This study explored the ways in which urban, older, African American women obtain health information and some of the factors that influence such activity. Among the possible determinants examined were self-perceived literacy, access to health information, and mobility. The findings suggest that respondents receive health information from their physicians, the mass media, and members of their social networks. The results of this research also indicated that members of this population have a highly positive perception of the public library, although only a small segment use the library regularly, and that it may be in the interest of the library to investigate the role it could play in providing health information to older adults.

Empirical mass formula with proton-neutron interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tachibana, T.; Uno, M.; Yamada, S.

An atomic mass formula consisting of a gross part, and averge even-odd part and an empirical shell part is studied. The gross part is, apart from a small atomic term, taken to be the sum of nucleon rest masses. Coulomb energies and a polynomial in A/sup 1/3/ and chemically bondN-Zchemically bond/A. The shell part includes, in addition to proton and neutron support of nuclear magicities and the cooperative deformation effect. After the first construction of such a formula, refinements have been made in two respects. One is a separate treatment of Z = N odd-odd nuclei suggested by a quartetmore » model, and the other is an improvement of the proton neutron interaction term. By these refinements the root-mean-square deviation of calculated masses from the 1986 Audi-Wapstra masses has been reduced from 538 keV to 460 keV.« less

A tandem mass spectrometer for crossed-beam irradiation of mass-selected molecular systems by keV atomic ions

NASA Astrophysics Data System (ADS)

Schwob, Lucas; Lalande, Mathieu; Chesnel, Jean-Yves; Domaracka, Alicja; Huber, Bernd A.; Maclot, Sylvain; Poully, Jean-Christophe; Rangama, Jimmy; Rousseau, Patrick; Vizcaino, Violaine; Adoui, Lamri; Méry, Alain

2018-04-01

In the present paper, we describe a new home-built crossed-beam apparatus devoted to ion-induced ionization and fragmentation of isolated biologically relevant molecular systems. The biomolecular ions are produced by an electrospray ionization source, mass-over-charge selected, accumulated in a 3D ion trap, and then guided to the extraction region of an orthogonal time-of-flight mass spectrometer. Here, the target molecular ions interact with a keV atomic ion beam produced by an electron cyclotron resonance ion source. Cationic products from the collision are detected on a position sensitive detector and analyzed by time-of-flight mass spectrometry. A detailed description of the operation of the setup is given, and early results from irradiation of a protonated pentapeptide (leucine-enkephalin) by a 7 keV He+ ion beam are presented as a proof-of-principle.

[Recent Development of Atomic Spectrometry in China].

PubMed

Xiao, Yuan-fang; Wang, Xiao-hua; Hang, Wei

2015-09-01

As an important part of modern analytical techniques, atomic spectrometry occupies a decisive status in the whole analytical field. The development of atomic spectrometry also reflects the continuous reform and innovation of analytical techniques. In the past fifteen years, atomic spectrometry has experienced rapid development and been applied widely in many fields in China. This review has witnessed its development and remarkable achievements. It contains several directions of atomic spectrometry, including atomic emission spectrometry (AES), atomic absorption spectrometry (AAS), atomic fluorescence spectrometry (AFS), X-ray fluorescence spectrometry (XRF), and atomic mass spectrometry (AMS). Emphasis is put on the innovation of the detection methods and their applications in related fields, including environmental samples, biological samples, food and beverage, and geological materials, etc. There is also a brief introduction to the hyphenated techniques utilized in atomic spectrometry. Finally, the prospects of atomic spectrometry in China have been forecasted.

Affordable and accurate large-scale hybrid-functional calculations on GPU-accelerated supercomputers

NASA Astrophysics Data System (ADS)

Ratcliff, Laura E.; Degomme, A.; Flores-Livas, José A.; Goedecker, Stefan; Genovese, Luigi

2018-03-01

Performing high accuracy hybrid functional calculations for condensed matter systems containing a large number of atoms is at present computationally very demanding or even out of reach if high quality basis sets are used. We present a highly optimized multiple graphics processing unit implementation of the exact exchange operator which allows one to perform fast hybrid functional density-functional theory (DFT) calculations with systematic basis sets without additional approximations for up to a thousand atoms. With this method hybrid DFT calculations of high quality become accessible on state-of-the-art supercomputers within a time-to-solution that is of the same order of magnitude as traditional semilocal-GGA functionals. The method is implemented in a portable open-source library.

Production and reactions of silicon atoms in hot wire deposition of amorphous silicon

NASA Astrophysics Data System (ADS)

Zheng, Wengang; Gallagher, Alan

2003-10-01

Decomposing silane and hydrogen molecules on a hot tungsten filament is an alternative method of depositing hydrogenated microcrystal and amorphous Si for thin-film semmiconductor devices. This "hot-wire" method can have significant advantages, such as high film deposition rates. The deposition chemistry involves Si and H atoms released from the filament, followed by their reactions with the vapor and surfaces. To establish these deposition pathways, we measure radicals at the substrate with a home built, threshold ionization mass spectrometer. The design and operation of this mass spectrometer for radical detection, and the behavior of Si atom production and reactions, will be presented. This work is supported by the National Renewable Energy Laboratory, Golden, CO 80401

Measurement of leakage neutron spectra from graphite cylinders irradiated with D-T neutrons for validation of evaluated nuclear data.

PubMed

Luo, F; Han, R; Chen, Z; Nie, Y; Shi, F; Zhang, S; Lin, W; Ren, P; Tian, G; Sun, Q; Gou, B; Ruan, X; Ren, J; Ye, M

2016-10-01

A benchmark experiment for validation of graphite data evaluated from nuclear data libraries was conducted for 14MeV neutrons irradiated on graphite cylinder samples. The experiments were performed using the benchmark experimental facility at the China Institute of Atomic Energy (CIAE). The leakage neutron spectra from the surface of graphite (Φ13cm×20cm) at 60° and 120° and graphite (Φ13cm×2cm) at 60° were measured by the time-of-flight (TOF) method. The obtained results were compared with the measurements made by the Monte Carlo neutron transport code MCNP-4C with the ENDF/B-VII.1, CENDL-3.1 and JENDL-4.0 libraries. The results obtained from a 20cm-thick sample revealed that the calculation results with CENDL-3.1 and JENDL-4.0 libraries showed good agreements with the experiments conducted in the whole energy region. However, a large discrepancy of approximately 40% was observed below the 3MeV energy region with the ENDF/B-VII.1 library. For the 2cm-thick sample, the calculated results obtained from the abovementioned three libraries could not reproduce the experimental data in the energy range of 5-7MeV. The graphite data in CENDL-3.1 were verified for the first time and were proved to be reliable. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complementary Characterization of Cu(In,Ga)Se₂ Thin-Film Photovoltaic Cells Using Secondary Ion Mass Spectrometry, Auger Electron Spectroscopy, and Atom Probe Tomography.

PubMed

Jang, Yun Jung; Lee, Jihye; Jeong, Jeung-Hyun; Lee, Kang-Bong; Kim, Donghwan; Lee, Yeonhee

2018-05-01

To enhance the conversion performance of solar cells, a quantitative and depth-resolved elemental analysis of photovoltaic thin films is required. In this study, we determined the average concentration of the major elements (Cu, In, Ga, and Se) in fabricated Cu(In,Ga)Se2 (CIGS) thin films, using inductively coupled plasma atomic emission spectroscopy, X-ray fluorescence, and wavelengthdispersive electron probe microanalysis. Depth profiling results for CIGS thin films with different cell efficiencies were obtained using secondary ion mass spectrometry and Auger electron spectroscopy to compare the atomic concentrations. Atom probe tomography, a characterization technique with sub-nanometer resolution, was used to obtain three-dimensional elemental mapping and the compositional distribution at the grain boundaries (GBs). GBs are identified by Na increment accompanied by Cu depletion and In enrichment. Segregation of Na atoms along the GB had a beneficial effect on cell performance. Comparative analyses of different CIGS absorber layers using various analytical techniques provide us with understanding of the compositional distributions and structures of high efficiency CIGS thin films in solar cells.

Effective Inertial Frame in an Atom Interferometric Test of the Equivalence Principle

NASA Astrophysics Data System (ADS)

Overstreet, Chris; Asenbaum, Peter; Kovachy, Tim; Notermans, Remy; Hogan, Jason M.; Kasevich, Mark A.

2018-05-01

In an ideal test of the equivalence principle, the test masses fall in a common inertial frame. A real experiment is affected by gravity gradients, which introduce systematic errors by coupling to initial kinematic differences between the test masses. Here we demonstrate a method that reduces the sensitivity of a dual-species atom interferometer to initial kinematics by using a frequency shift of the mirror pulse to create an effective inertial frame for both atomic species. Using this method, we suppress the gravity-gradient-induced dependence of the differential phase on initial kinematic differences by 2 orders of magnitude and precisely measure these differences. We realize a relative precision of Δ g /g ≈6 ×10-11 per shot, which improves on the best previous result for a dual-species atom interferometer by more than 3 orders of magnitude. By reducing gravity gradient systematic errors to one part in 1 013 , these results pave the way for an atomic test of the equivalence principle at an accuracy comparable with state-of-the-art classical tests.

Backscattering spectrometry device for identifying unknown elements present in a workpiece

DOEpatents

Doyle, Barney L.; Knapp, James A.

1991-01-01

A backscattering spectrometry method and device for identifying and quantifying impurities in a workpiece during processing and manufacturing of that workpiece. While the workpiece is implanted with an ion beam, that same ion beam backscatters resulting from collisions with known atoms and with impurities within the workpiece. Those ions backscatter along a predetermined scattering angle and are filtered using a self-supporting filter to stop the ions with a lower energy because they collided with the known atoms of the workpiece of a smaller mass. Those ions which pass through the filter have a greater energy resulting from impact with impurities having a greater mass than the known atoms of the workpiece. A detector counts the number and measures the energy of the ions which pass through the filter. From the energy determination and knowledge of the scattering angle, a mass calculation determines the identity, and from the number and solid angle of the scattering angle, a relative concentration of the impurity is obtained.

Analysis of the effects of atomic mass, jet velocity, and radiative cooling on the dimensionless parameters of counter-propagating, weakly collisional plasma flows

NASA Astrophysics Data System (ADS)

Collins, Gilbert; Valenzuela, Julio; Beg, Farhat

2016-10-01

We have studied the collision of counter-propagating plasma flows using opposing conical wire arrays driven by the 200kA, 150ns rise-time `GenASIS' driver. These plasma flows produced weakly collisional, well-defined bow-shock structures. Varying initial parameters such as the opening angle of the array and the atomic mass of the wires allowed us to modify quantities such as the density contrast between jets, intra-jet mean free path (λmfp, scales with v, atomic mass A, and ionization state Zi-4) , Reynolds number (Re, scales with AZ), and the Peclet number (Pe, scales with Z). We calculate these dimensionless quantities using schlieren imagery, interferometry, and emission data, and determine whether they meet the scaling criteria necessary for the comparison to and subsequent study of astrophysical plasmas. This work was partially supported by the Department of Energy Grant Number DE-SC0014493.

Phage display peptide libraries: deviations from randomness and correctives

PubMed Central

Ryvkin, Arie; Ashkenazy, Haim; Weiss-Ottolenghi, Yael; Piller, Chen; Pupko, Tal; Gershoni, Jonathan M

2018-01-01

Abstract Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study, we demonstrate that the UAG over-representation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by mass spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications. PMID:29420788

Reaction profiling by ultra high-pressure liquid chromatography/time-of-flight mass spectrometry in support of the synthesis of DNA-encoded libraries.

PubMed

Hargiss, Leonard O; Zipp, G Greg; Jessop, Theodore C; Sun, Xuejun; Keyes, Philip; Rawlins, David B; Liang, Zhi; Park, Kum Joo; Gu, Huizhong

2014-11-15

An ultra high-pressure liquid chromatography/mass spectrometry (UHPLC/MS) separation and analysis method has been devised for open access analysis of synthetic reactions used in the production of DNA-encoded chemical libraries. The aqueous mobile phase is 100mM hexafluoroisopropanol and 8.6mM triethylamine; the organic mobile phase is methanol. The UHPLC separation uses a C18 OST column (50mm×2.1mm×1.7μm) at 60°C, with a flow rate of 0.6mL/min. Gradient concentration is from 10 to 40% B in 1.0min, increasing to 95% B at 1.2min. Cycle time was about 5min. This method provides a detection limit of a 20-mer oligonucleotide by mass spectrometry of better than 1pmol on-column. Linear UV response for 20-mer extends from 2 to 200pmol/μL in concentration, same-day relative average deviations are less than 5% and bias (observed minus expected) is less than 10%. Deconvoluted mass spectra are generated for components in the predicted mass range using a maximum entropy algorithm. Mass accuracy of deconvoluted spectra is typically 20ppm or better for isotopomers of oligonucleotides up to 7000Da. Copyright © 2014 Elsevier B.V. All rights reserved.

MoleCoolQt – a molecule viewer for charge-density research

PubMed Central

Hübschle, Christian B.; Dittrich, Birger

2011-01-01

MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS. PMID:22477783

Identification of arsenobetaine in sole, lemon sole, flounder, dab, crab and shrimps by field desorption and fast atom bombardment mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luten, J.B.; Riekwel-Booy, G.; Greef, M.C.

1983-01-01

Organo-arsenic has been isolated from sole, lemon sole, flounder, dab, crab and shrimps by extraction or ion-exchange in combination with thin-layer chromatography. An alkaline digestion of the samples, followed by a reduction with sodiumborohydride leads to the formation of trimethylarsine. Field desorption mass spectrometry (FDMS) can be used to identify arsenobetaine in the isolates. Sufficient purification by thin-layer chromatography is found to be a prerequisite for the detection of a protonated molecular ion of arsenobetaine. If this situation is not met acid enchanced FDMS or Fast Atom Bombardment mass spectrometry in high resolution can be used successfully.

Decoupling of Solid 4He Layers under the Superfluid Overlayer

NASA Astrophysics Data System (ADS)

Ishibashi, Kenji; Hiraide, Jo; Taniguchi, Junko; Suzuki, Masaru

2018-03-01

It has been reported that in a large oscillation amplitude, the mass decoupling of multilayer 4He films adsorbed on graphite results from the depinning of the second solid atomic layer. This decoupling suddenly vanishes below a certain low temperature TD due to the cancellation of mass decoupling by the superfluid counterflow of the the overylayer. We studied the relaxation of the depinned state at various temperatures, after reduction of oscillation amplitude below TD . It was found that above the superfluid transition temperature the mass decoupling revives with a relaxation time of several 100 s. It strongly supports that the depinned state of the second solid atomic layer remains underneath the superfluid overlayer.

Manifold and method of batch measurement of Hg-196 concentration using a mass spectrometer

DOEpatents

Grossman, Mark W.; Evans, Roger

1991-01-01

A sample manifold and method of its use has been developed so that milligram quantities of mercury can be analyzed mass spectroscopically to determine the .sup.196 Hg concentration to less than 0.02 atomic percent. Using natural mercury as a standard, accuracy of .+-.0.002 atomic percent can be obtained. The mass spectrometer preferably used is a commercially available GC/MS manufactured by Hewlett Packard. A novel sample manifold is contained within an oven allowing flow rate control of Hg into the MS. Another part of the manifold connects to an auxiliary pumping system which facilitates rapid clean up of residual Hg in the manifold. Sample cycle time is about 1 hour.

A comparison of different functions for predicted protein model quality assessment.

PubMed

Li, Juan; Fang, Huisheng

2016-07-01

In protein structure prediction, a considerable number of models are usually produced by either the Template-Based Method (TBM) or the ab initio prediction. The purpose of this study is to find the critical parameter in assessing the quality of the predicted models. A non-redundant template library was developed and 138 target sequences were modeled. The target sequences were all distant from the proteins in the template library and were aligned with template library proteins on the basis of the transformation matrix. The quality of each model was first assessed with QMEAN and its six parameters, which are C_β interaction energy (C_beta), all-atom pairwise energy (PE), solvation energy (SE), torsion angle energy (TAE), secondary structure agreement (SSA), and solvent accessibility agreement (SAE). Finally, the alignment score (score) was also used to assess the quality of model. Hence, a total of eight parameters (i.e., QMEAN, C_beta, PE, SE, TAE, SSA, SAE, score) were independently used to assess the quality of each model. The results indicate that SSA is the best parameter to estimate the quality of the model.

Mass loss of shuttle space suit orthofabric under simulated ionospheric atomic oxygen bombardment

NASA Technical Reports Server (NTRS)

Miller, W. L.

1985-01-01

Many polymeric materials used for thermal protection and insulation on spacecraft degrade significantly under prolonged bombardment by ionospheric atomic oxygen. The covering fabric of the multilayered shuttle space suit is composed of a loose weave of GORE-TEX fibers, Nomex and Kevlar-29, which are all polymeric materials. The complete evaluation of suit fabric degradation from ionospheric atomic oxygen is of importance in reevaluating suit lifetime and inspection procedures. The mass loss and visible physical changes of each test sample was determined. Kapton control samples and data from previous asher and flight tests were used to scale the results to reflect ionospheric conditions at about 220 km altitude. It is predicted that the orthofabric loses mass in the ionosphere at a rate of about 66% of the original orthofabric mass/yr. The outer layer of the two-layer orthofabric test samples shows few easily visible signs of degradation, even when observed at 440X. It is concluded that the orthofabric could suffer significant loss of performance after much less than a year of total exposure time, while the degradation might be undetectable in post flight visual examinations of space suits.

Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs.

PubMed

Yan, Yan; Zhang, Kaizhong

2016-12-23

De novo peptide sequencing via tandem mass spectrometry (MS/MS) has been developed rapidly in recent years. With the use of spectra pairs from the same peptide under different fragmentation modes, performance of de novo sequencing is greatly improved. Currently, with large amount of spectra sequenced everyday, spectra libraries containing tens of thousands of annotated experimental MS/MS spectra become available. These libraries provide information of the spectra properties, thus have the potential to be used with de novo sequencing to improve its performance. In this study, an improved de novo sequencing method assisted with spectra library is proposed. It uses spectra libraries as training datasets and introduces significant scores of the features used in our previous de novo sequencing method for HCD and ETD spectra pairs. Two pairs of HCD and ETD spectral datasets were used to test the performance of the proposed method and our previous method. The results show that this proposed method achieves better sequencing accuracy with higher ranked correct sequences and less computational time. This paper proposed an advanced de novo sequencing method for HCD and ETD spectra pair and used information from spectra libraries and significant improved previous similar methods.

A REMF's View of Viet Nam War Literature Bibliography.

ERIC Educational Resources Information Center

Willson, David A.

An academic librarian who is a Vietnam War veteran was inspired by the exemplary collection of Vietnam War literature at the Colorado State University Library to begin his own personal collection of mass market paperbacks dealing with the Vietnam War. Although Vietnam War fiction was common on the mass market racks in the mid 1980s, it has been…

Cloud parallel processing of tandem mass spectrometry based proteomics data.

PubMed

Mohammed, Yassene; Mostovenko, Ekaterina; Henneman, Alex A; Marissen, Rob J; Deelder, André M; Palmblad, Magnus

2012-10-05

Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

A program to compute the two-step excitation of mesospheric sodium atoms for the Polychromatic Laser Guide Star Project

NASA Astrophysics Data System (ADS)

Bellanger, Véronique; Courcelle, Arnaud; Petit, Alain

2004-09-01

A program to compute the two-step excitation of sodium atoms ( 3S→3P→4D) using the density-matrix formalism is presented. The BEACON program calculates population evolution and the number of photons emitted by fluorescence from the 3P, 4D, 4P, 4S levels. Program summaryTitle of program: BEACON Catalogue identifier:ADSX Program Summary URL:http://cpc.cs.qub.ac.uk/cpc/summaries/ADSX Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: none Operating systems under which the program has been tested: Win; Unix Programming language used: FORTRAN 77 Memory required to execute with typical data: 1 Mw Number of bits in a word: 32 Number of processors used: 1 (a parallel version of this code is also available and can be obtained on request) Number of lines in distributed program, including test data, etc.: 29 287 Number of bytes in distributed program, including test data, etc.: 830 331 Distribution format: tar.gz CPC Program Library subprograms used: none Nature of physical problem: Resolution of the Bloch equations in the case of the two-step laser excitation of sodium atoms. Method of solution: The program BEACON calculates the evolution of level population versus time using the density-matrix formalism. The number of photons emitted from the 3P, 4D and 4P levels is calculated using the branching ratios and the level lifetimes. Restriction on the complexity of the problem: Since the backscatter emission is calculated after the excitation process, excitation with laser pulse duration longer than the 4D level lifetime cannot be rigorously treated. Particularly, cw laser excitation cannot be calculated with this code. Typical running time:12 h

The project of the mass separator of atomic nuclei produced in heavy ion induced reactions

NASA Astrophysics Data System (ADS)

Oganessian, Yu. Ts.; Shchepunov, V. A.; Dmitriev, S. N.; Itkis, M. G.; Gulbekyan, G. G.; Khabarov, M. V.; Bekhterev, V. V.; Bogomolov, S. L.; Efremov, A. A.; Pashenko, S. V.; Stepantsov, S. V.; Yeremin, A. V.; Yavor, M. I.; Kalimov, A. G.

2003-05-01

A new separator and mass analyzer, named MASHA (mass analyzer of super heavy atoms), has been designed at the Flerov Laboratory JINR Dubna to separate and measure masses of nuclei and molecules with precision better than 10 -3. The set up can work in the wide mass range from A≈20 to A≈500, its mass acceptance is as large as ±2.8%. In particular, it allows unambiguous mass identification of super heavy nuclei with a resolution better than 1 amu at the level of 300 amu. Synthesized in nuclear reactions nuclides are emitted from an ECR ion source at energy E=40 kV and charge state Q=+1. Then they pass the following steps of separation and analysis: the first section of rough separation, the second section of separation and mass analysis and the final section of separation with a 90° electrostatic deflector. In the focal plane of the device, a focal plane detector determines positions (masses) of studied nuclei. Ion optics of the analyzer, optimized up to the second order, is considered. Description of its elements and subsystems is given.

40 CFR 63.11496 - What are the standards and compliance requirements for process vents?

Code of Federal Regulations, 2014 CFR

2014-07-01

... of halogen atoms in accordance with § 63.115(d)(2)(v). Alternatively, you may elect to designate the... 20 parts per million by volume (ppmv). (2) Reduce the halogen atom mass emission rate before the...

40 CFR 63.2450 - What are my general requirements for complying with this subpart?

Code of Federal Regulations, 2012 CFR

2012-07-01

..., as defined in § 63.2550, by calculating the mass emission rate of halogen atoms in accordance with... determine the halogen atom emission rate prior to the combustion device according to the procedures in § 63...

40 CFR 63.11496 - What are the standards and compliance requirements for process vents?

Code of Federal Regulations, 2013 CFR

2013-07-01

... of halogen atoms in accordance with § 63.115(d)(2)(v). Alternatively, you may elect to designate the... 20 parts per million by volume (ppmv). (2) Reduce the halogen atom mass emission rate before the...

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

PubMed

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Paik, Young-Ki

2017-12-01

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

Microorganism Identification Based On MALDI-TOF-MS Fingerprints

NASA Astrophysics Data System (ADS)

Elssner, Thomas; Kostrzewa, Markus; Maier, Thomas; Kruppa, Gary

Advances in MALDI-TOF mass spectrometry have enabled the ­development of a rapid, accurate and specific method for the identification of bacteria directly from colonies picked from culture plates, which we have named the MALDI Biotyper. The picked colonies are placed on a target plate, a drop of matrix solution is added, and a pattern of protein molecular weights and intensities, "the protein fingerprint" of the bacteria, is produced by the MALDI-TOF mass spectrometer. The obtained protein mass fingerprint representing a molecular signature of the microorganism is then matched against a database containing a library of previously measured protein mass fingerprints, and scores for the match to every library entry are produced. An ID is obtained if a score is returned over a pre-set threshold. The sensitivity of the techniques is such that only approximately 104 bacterial cells are needed, meaning that an overnight culture is sufficient, and the results are obtained in minutes after culture. The improvement in time to result over biochemical methods, and the capability to perform a non-targeted identification of bacteria and spores, potentially makes this method suitable for use in the detect-to-treat timeframe in a bioterrorism event. In the case of white-powder samples, the infectious spore is present in sufficient quantity in the powder so that the MALDI Biotyper result can be obtained directly from the white powder, without the need for culture. While spores produce very different patterns from the vegetative colonies of the corresponding bacteria, this problem is overcome by simply including protein fingerprints of the spores in the library. Results on spores can be returned within minutes, making the method suitable for use in the "detect-to-protect" timeframe.

Tiny Grains Give Huge Gains: Nanocrystal–Based Signal Amplification for Biomolecule Detection

PubMed Central

Tong, Sheng; Ren, Binbin; Zheng, Zhilan; Shen, Han; Bao, Gang

2013-01-01

Nanocrystals, despite their tiny sizes, contain thousands to millions of atoms. Here we show that the large number of atoms packed in each metallic nanocrystal can provide a huge gain in signal amplification for biomolecule detection. We have devised a highly sensitive, linear amplification scheme by integrating the dissolution of bound nanocrystals and metal-induced stoichiometric chromogenesis, and demonstrated that signal amplification is fully defined by the size and atom density of nanocrystals, which can be optimized through well-controlled nanocrystal synthesis. Further, the rich library of chromogenic reactions allows implementation of this scheme in various assay formats, as demonstrated by the iron oxide nanoparticle linked immunosorbent assay (ILISA) and blotting assay developed in this study. Our results indicate that, owing to the inherent simplicity, high sensitivity and repeatability, the nanocrystal based amplification scheme can significantly improve biomolecule quantification in both laboratory research and clinical diagnostics. This novel method adds a new dimension to current nanoparticle-based bioassays. PMID:23659350

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

PubMed

Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L

2016-05-10

Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme.

Identification of phases, symmetries and defects through local crystallography

DOE PAGES

Belianinov, Alex; He, Qian; Kravchenko, Mikhail; ...

2015-07-20

Here we report that advances in electron and probe microscopies allow 10 pm or higher precision in measurements of atomic positions. This level of fidelity is sufficient to correlate the length (and hence energy) of bonds, as well as bond angles to functional properties of materials. Traditionally, this relied on mapping locally measured parameters to macroscopic variables, for example, average unit cell. This description effectively ignores the information contained in the microscopic degrees of freedom available in a high-resolution image. Here we introduce an approach for local analysis of material structure based on statistical analysis of individual atomic neighbourhoods. Clusteringmore » and multivariate algorithms such as principal component analysis explore the connectivity of lattice and bond structure, as well as identify minute structural distortions, thus allowing for chemical description and identification of phases. This analysis lays the framework for building image genomes and structure–property libraries, based on conjoining structural and spectral realms through local atomic behaviour.« less

Lurking systematics in predicting galaxy cold gas masses using dust luminosities and star formation rates

NASA Astrophysics Data System (ADS)

Janowiecki, Steven; Cortese, Luca; Catinella, Barbara; Goodwin, Adelle J.

2018-05-01

We use galaxies from the Herschel Reference Survey to evaluate commonly used indirect predictors of cold gas masses. We calibrate predictions for cold neutral atomic and molecular gas using infrared dust emission and gas depletion time methods that are self-consistent and have ˜20 per cent accuracy (with the highest accuracy in the prediction of total cold gas mass). However, modest systematic residual dependences are found in all calibrations that depend on the partition between molecular and atomic gas, and can over/underpredict gas masses by up to 0.3 dex. As expected, dust-based estimates are best at predicting the total gas mass while depletion time-based estimates are only able to predict the (star-forming) molecular gas mass. Additionally, we advise caution when applying these predictions to high-z galaxies, as significant (0.5 dex or more) errors can arise when incorrect assumptions are made about the dominant gas phase. Any scaling relations derived using predicted gas masses may be more closely related to the calibrations used than to the actual galaxies observed.

First Measurement of the Atomic Electric Dipole Moment of Ra 225

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parker, R. H.; Dietrich, M. R.; Kalita, M. R.

The radioactive radium-225 (Ra-225) atom is a favorable case to search for a permanent electric dipole moment. Because of its strong nuclear octupole deformation and large atomic mass, Ra-225 is particularly sensitive to interactions in the nuclear medium that violate both time-reversal symmetry and parity. We have developed a cold-atom technique to study the spin precession of Ra-225 atoms held in an optical dipole trap, and demonstrated the principle of this method by completing the first measurement of its atomic electric dipole moment, reaching an upper limit of vertical bar d(Ra-225)vertical bar < 5.0 x 10(-22) e cm (95% confidence).

The neutral mass spectrometer on Dynamics Explorer B

NASA Technical Reports Server (NTRS)

Carignan, G. R.; Block, B. P.; Maurer, J. C.; Hedin, A. E.; Reber, C. A.; Spencer, N. W.

1981-01-01

A neutral gas mass spectrometer has been developed to satisfy the measurement requirements of the Dynamics Explorer mission. The mass spectrometer, a quadrupole, will measure the abundances of neutral species in the region 300-500 km in the earth's atmosphere. These measurements will be used in concert with other simultaneous observations on Dynamics Explorer to study the physical processes involved in the interactions of the magnetosphere-ionosphere-atmosphere system. The instrument, which is similar to that flown on Atmosphere Explorer, employs an electron beam ion source operating in the closed mode and a discrete dynode multiplier as a detector. The mass range is 22 to 50 amu. The abundances of atomic oxygen, molecular nitrogen, helium, argon, and possibly atomic nitrogen will be measured to an accuracy of about + or - 15% over the specified altitude range, with a temporal resolution of one second.

Characterisation of zinc-binding domains of peroxisomal RING finger proteins using size exclusion chromatography/inductively coupled plasma-mass spectrometry.

PubMed

Koellensperger, Gunda; Daubert, Simon; Erdmann, Ralf; Hann, Stephan; Rottensteiner, Hanspeter

2007-11-01

We determined the zinc binding stoichiometry of peroxisomal RING finger proteins by measuring sulfur/metal ratios using inductively coupled plasma-mass spectrometry coupled to size exclusion chromatography, a strategy that provides a fast and quantitative overview on the binding of metals in proteins. As a quality control, liquid chromatography-electrospray ionisation-time of flight-mass spectrometry was used to measure the molar masses of the intact proteins. The RING fingers of Pex2p, Pex10p, and Pex12p showed a stoichiometry of 2.0, 2.1, and 1.2 mol zinc/mol protein, respectively. Thus, Pex2p and Pex10p possess a typical RING domain with two coordinated zinc atoms, whereas that of Pex12p coordinates only a single zinc atom.

Impurity coupled to an artificial magnetic field in a Fermi gas in a ring trap

NASA Astrophysics Data System (ADS)

Ünal, F. Nur; Hetényi, B.; Oktel, M. Ã.-.

2015-05-01

The dynamics of a single impurity interacting with a many-particle background is one of the central problems of condensed-matter physics. Recent progress in ultracold-atom experiments makes it possible to control this dynamics by coupling an artificial gauge field specifically to the impurity. In this paper, we consider a narrow toroidal trap in which a Fermi gas is interacting with a single atom. We show that an external magnetic field coupled to the impurity is a versatile tool to probe the impurity dynamics. Using a Bethe ansatz, we calculate the eigenstates and corresponding energies exactly as a function of the flux through the trap. Adiabatic change of flux connects the ground state to excited states due to flux quantization. For repulsive interactions, the impurity disturbs the Fermi sea by dragging the fermions whose momentum matches the flux. This drag transfers momentum from the impurity to the background and increases the effective mass. The effective mass saturates to the total mass of the system for infinitely repulsive interactions. For attractive interactions, the drag again increases the effective mass which quickly saturates to twice the mass of a single particle as a dimer of the impurity and one fermion is formed. For excited states with momentum comparable to number of particles, effective mass shows a resonant behavior. We argue that standard tools in cold-atom experiments can be used to test these predictions.

Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification.

PubMed

Cao, Mingshu; Fraser, Karl; Rasmussen, Susanne

2013-10-31

Mass spectrometry coupled with chromatography has become the major technical platform in metabolomics. Aided by peak detection algorithms, the detected signals are characterized by mass-over-charge ratio (m/z) and retention time. Chemical identities often remain elusive for the majority of the signals. Multi-stage mass spectrometry based on electrospray ionization (ESI) allows collision-induced dissociation (CID) fragmentation of selected precursor ions. These fragment ions can assist in structural inference for metabolites of low molecular weight. Computational investigations of fragmentation spectra have increasingly received attention in metabolomics and various public databases house such data. We have developed an R package "iontree" that can capture, store and analyze MS2 and MS3 mass spectral data from high throughput metabolomics experiments. The package includes functions for ion tree construction, an algorithm (distMS2) for MS2 spectral comparison, and tools for building platform-independent ion tree (MS2/MS3) libraries. We have demonstrated the utilization of the package for the systematic analysis and annotation of fragmentation spectra collected in various metabolomics platforms, including direct infusion mass spectrometry, and liquid chromatography coupled with either low resolution or high resolution mass spectrometry. Assisted by the developed computational tools, we have demonstrated that spectral trees can provide informative evidence complementary to retention time and accurate mass to aid with annotating unknown peaks. These experimental spectral trees once subjected to a quality control process, can be used for querying public MS2 databases or de novo interpretation. The putatively annotated spectral trees can be readily incorporated into reference libraries for routine identification of metabolites.

Au 329–xAg x(SR) 84 Nanomolecules: Plasmonic Alloy Faradaurate-329

DOE PAGES

Kumara, Chanaka; Zuo, Xiaobing; Cullen, David A.; ...

2015-08-10

Though significant progress has been made to improve the monodispersity of larger (>10 nm) alloy metal nanoparticles, there still exists a significant variation in nanoparticle composition, ranging from ±1000s of atoms. Here in this paper, for the first time, we report the synthesis of atomically precise (±0 metal atom variation) Au 329–xAg x(SCH 2CH 2Ph) 84 alloy nanomolecules. The composition was determined using high resolution electrospray ionization mass spectrometry. In contrast to larger (>10 nm) Au–Ag nanoparticles, the surface plasmon resonance (SPR) peak does not show a major shift, but a minor ~10 nm red-shift, upon increasing silver content. Themore » intensity of the SPR peak also varies in an intriguing manner, where a dampening is observed with medium silver incorporation, and a significant sharpening is observed upon higher Ag content. The report outlines (a) an unprecedented advance in nanoparticle mass spectrometry of high mass at atomic precision; and (b) the unexpected optical behavior of Au–Ag alloys in the region where nascent SPR emerges; specifically, in this work, the SPR-like peak does not show a major ~100 nm blue-shift with Ag alloying of Au 329 nanomolecules, as shown to be common in larger nanoparticles.« less

Interactive content-based image retrieval (CBIR) computer-aided diagnosis (CADx) system for ultrasound breast masses using relevance feedback

NASA Astrophysics Data System (ADS)

Cho, Hyun-chong; Hadjiiski, Lubomir; Sahiner, Berkman; Chan, Heang-Ping; Paramagul, Chintana; Helvie, Mark; Nees, Alexis V.

2012-03-01

We designed a Content-Based Image Retrieval (CBIR) Computer-Aided Diagnosis (CADx) system to assist radiologists in characterizing masses on ultrasound images. The CADx system retrieves masses that are similar to a query mass from a reference library based on computer-extracted features that describe texture, width-to-height ratio, and posterior shadowing of a mass. Retrieval is performed with k nearest neighbor (k-NN) method using Euclidean distance similarity measure and Rocchio relevance feedback algorithm (RRF). In this study, we evaluated the similarity between the query and the retrieved masses with relevance feedback using our interactive CBIR CADx system. The similarity assessment and feedback were provided by experienced radiologists' visual judgment. For training the RRF parameters, similarities of 1891 image pairs obtained from 62 masses were rated by 3 MQSA radiologists using a 9-point scale (9=most similar). A leave-one-out method was used in training. For each query mass, 5 most similar masses were retrieved from the reference library using radiologists' similarity ratings, which were then used by RRF to retrieve another 5 masses for the same query. The best RRF parameters were chosen based on three simulated observer experiments, each of which used one of the radiologists' ratings for retrieval and relevance feedback. For testing, 100 independent query masses on 100 images and 121 reference masses on 230 images were collected. Three radiologists rated the similarity between the query and the computer-retrieved masses. Average similarity ratings without and with RRF were 5.39 and 5.64 on the training set and 5.78 and 6.02 on the test set, respectively. The average Az values without and with RRF were 0.86+/-0.03 and 0.87+/-0.03 on the training set and 0.91+/-0.03 and 0.90+/-0.03 on the test set, respectively. This study demonstrated that RRF improved the similarity of the retrieved masses.

A Sensitive Technique Using Atomic Force Microscopy to Measure the Low Earth Orbit Atomic Oxygen Erosion of Polymers

NASA Technical Reports Server (NTRS)

deGroh, Kim K.; Banks, Bruce A.; Clark, Gregory W.; Hammerstrom, Anne M.; Youngstrom, Erica E.; Kaminski, Carolyn; Fine, Elizabeth S.; Marx, Laura M.

2001-01-01

Polymers such as polyimide Kapton and Teflon FEP (fluorinated ethylene propylene) are commonly used spacecraft materials due to their desirable properties such as flexibility, low density, and in the case of FEP low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low Earth orbit (LEO) environment are exposed to energetic atomic oxygen. Atomic oxygen erosion of polymers occurs in LEO and is a threat to spacecraft durability. It is therefore important to understand the atomic oxygen erosion yield (E, the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. Because long-term space exposure data is rare and very costly, short-term exposures such as on the shuttle are often relied upon for atomic oxygen erosion determination. The most common technique for determining E is through mass loss measurements. For limited duration exposure experiments, such as shuttle experiments, the atomic oxygen fluence is often so small that mass loss measurements can not produce acceptable uncertainties. Therefore, a recession measurement technique has been developed using selective protection of polymer samples, combined with postflight atomic force microscopy (AFM) analysis, to obtain accurate erosion yields of polymers exposed to low atomic oxygen fluences. This paper discusses the procedures used for this recession depth technique along with relevant characterization issues. In particular, a polymer is salt-sprayed prior to flight, then the salt is washed off postflight and AFM is used to determine the erosion depth from the protected plateau. A small sample was salt-sprayed for AFM erosion depth analysis and flown as part of the Limited Duration Candidate Exposure (LDCE-4,-5) shuttle flight experiment on STS-51. This sample was used to study issues such as use of contact versus non-contact mode imaging for determining recession depth measurements. Error analyses were conducted and the percent probable error in the erosion yield when obtained by the mass loss and recession depth techniques has been compared. The recession depth technique is planned to be used to determine the erosion yield of 42 different polymers in the shuttle flight experiment PEACE (Polymer Erosion And Contamination Experiment) planned to fly in 2002 or 2003.

Dissociative excitation of H2, HD, and D2 by electron impact

NASA Technical Reports Server (NTRS)

Carnahan, B. L.; Zipf, E. C.

1977-01-01

Time-of-flight techniques have been used to investigate the electron-impact dissociation of H2, HD, and D2 in order to determine the effect of isotopic mass variation in the target molecule on the dissociative excitation process. At incident electron energies near 100 eV, the time-of-flight spectrum produced from each molecule consists of atoms in the metastable 2s state and in high-lying long-lived Rydberg levels. The individual time-of-flight distributions, kinetic-energy spectra, and relative differential cross sections for these two species resulting from each molecule have been measured. The kinetic-energy spectrum of the Rydberg atoms produced from dissociative excitation of H2 was notably dissimilar in shape from the corresponding distributions produced from HD and D2. Also the 2s and Rydberg production cross sections differed between the three molecules. In the dissociation of the heteronuclear HD molecule, the ratio of fast H(2s) atoms to D(2s) atoms was about 1 to 1, while the same ratio comparing the Rydberg atoms was nearly 2 to 1. These differences indicate the influence of the mass variation on the position of the Franck-Condon region in the production of 2s atoms and on the competition between autoionization and dissociation in the formation of Rydberg fragments.

How can we probe the atom mass currents induced by synthetic gauge fields?

NASA Astrophysics Data System (ADS)

Paramekanti, Arun; Killi, Matthew; Trotzky, Stefan

2013-05-01

Ultracold atomic fermions and bosons in an optical lattice can have quantum ground states which support equilibrium currents in the presence of synthetic magnetic fields or spin orbit coupling. As a tool to uncover these mass currents, we propose using an anisotropic quantum quench of the optical lattice which dynamically converts the current patterns into measurable density patterns. Using analytical calculations and numerical simulations, we show that this scheme can probe diverse equilibrium bulk current patterns in Bose superfluids and Fermi fluids induced by synthetic magnetic fields, as well as detect the chiral edge currents in topological states of atomic matter such as quantum Hall and quantum spin Hall insulators. This work is supported by NSERC of Canada and the Canadian Institute for Advanced Research.

Production of pulsed atomic oxygen beams via laser vaporization methods

NASA Technical Reports Server (NTRS)

Brinza, David E.; Coulter, Daniel R.; Liang, Ranty H.; Gupta, Amitava

1986-01-01

The generation of energetic pulsed atomic oxygen beams by laser-driven evaporation of cryogenically frozen ozone/oxygen films and thin indium-tin oxide (ITO) films is reported. Mass spectroscopy is used in the mass and energy characterization of beams from the ozone/oxygen films, and a peak flux of 3 x 10 to the 20th/sq m per sec at 10 eV is found. Analysis of the time-of-flight data suggests that several processes contribute to the formation of the oxygen beam. Results show the absence of metastable states such as the 2p(3)3s(1)(5S) level of atomic oxygen blown-off from the ITO films. The present process has application to the study of the oxygen degradation problem of LEO materials.

The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN compiler

NASA Technical Reports Server (NTRS)

Stewart, J. M.; Kruger, G. J.; Ammon, H. L.; Dickinson, C.; Hall, S. R.

1972-01-01

A manual is presented for the use of a library of crystallographic programs. This library, called the X-ray system, is designed to carry out the calculations required to solve the structure of crystals by diffraction techniques. It has been implemented at the University of Maryland on the Univac 1108. It has, however, been developed and run on a variety of machines under various operating systems. It is considered to be an essentially machine independent library of applications programs. The report includes definition of crystallographic computing terms, program descriptions, with some text to show their application to specific crystal problems, detailed card input descriptions, mass storage file structure and some example run streams.

TRIM.FaTE Public Reference Library Documentation

EPA Pesticide Factsheets

TRIM.FaTE is a spatially explicit, compartmental mass balance model that describes the movement and transformation of pollutants over time, through a user-defined, bounded system that includes both biotic and abiotic compartments.

Drop size distribution and air velocity measurements in air assist swirl atomizer sprays

NASA Technical Reports Server (NTRS)

Mao, C.-P.; Oechsle, V.; Chigier, N.

1987-01-01

Detailed measurements of mean drop size (SMD) and size distribution parameters have been made using a Fraunhofer diffraction particle sizing instrument in a series of sprays generated by an air assist swirl atomizer. Thirty-six different combinations of fuel and air mass flow rates were examined with liquid flow rates up to 14 lbm/hr and atomizing air flow rates up to 10 lbm/hr. Linear relationships were found between SMD and liquid to air mass flow rate ratios. SMD increased with distance downstream along the center line and also with radial distance from the axis. Increase in obscuration with distance downstream was due to an increase in number density of particles as the result of deceleration of drops and an increase in the exposed path length of the laser beam. Velocity components of the atomizing air flow field measured by a laser anemometer show swirling jet air flow fields with solid body rotation in the core and free vortex flow in the outer regions.

99Tc atom counting by quadrupole ICP-MS. Optimisation of the instrumental response

NASA Astrophysics Data System (ADS)

Más, José L.; Garcia-León, Manuel; Bolívar, Juan P.

2002-05-01

In this paper, an extensive work is done on the specific tune of a conventional ICP-MS for 99Tc atom counting. For this, two methods have been used and compared: the partial variable control method and the 5D Simplex method. Instrumental limits of detection of 0.2 and 0.8 ppt, respectively, were obtained. They are noticeably lower than that found with the automatic tune method of the spectrometer, 47 ppt, which shows the need of a specific tune when very low levels of 99Tc have to be determined. A study is presented on the mass interferences for 99Tc. Our experiments show that the formation of polyatomic atoms or refractory oxides as well as 98Mo hydrides seem to be irrelevant for 99Tc atom counting. The opposite occurs with the presence of isobaric interferences, i.e. 99Ru, and the effect of abundance sensitivity, or low-mass resolution, which can modify the response at m/ z=99 to a non-negligible extent.

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

DOE PAGES

Payne, Samuel H.; Monroe, Matthew E.; Overall, Christopher C.; ...

2015-08-18

This dataset deposition announces the submission to public repositories of the PNNL Biodiversity Library, a large collection of global proteomics data for 112 bacterial and archaeal organisms. The data comprises 35,162 tandem mass spectrometry (MS/MS) datasets from ~10 years of research. All data has been searched, annotated and organized in a consistent manner to promote reuse by the community. Protein identifications were cross-referenced with KEGG functional annotations which allows for pathway oriented investigation. We present the data as a freely available community resource. A variety of data re-use options are described for computational modeling, proteomics assay design and bioengineering. Instrumentmore » data and analysis files are available at ProteomeXchange via the MassIVE partner repository under the identifiers PXD001860 and MSV000079053.« less

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Payne, Samuel H.; Monroe, Matthew E.; Overall, Christopher C.

This dataset deposition announces the submission to public repositories of the PNNL Biodiversity Library, a large collection of global proteomics data for 112 bacterial and archaeal organisms. The data comprises 35,162 tandem mass spectrometry (MS/MS) datasets from ~10 years of research. All data has been searched, annotated and organized in a consistent manner to promote reuse by the community. Protein identifications were cross-referenced with KEGG functional annotations which allows for pathway oriented investigation. We present the data as a freely available community resource. A variety of data re-use options are described for computational modeling, proteomics assay design and bioengineering. Instrumentmore » data and analysis files are available at ProteomeXchange via the MassIVE partner repository under the identifiers PXD001860 and MSV000079053.« less

Identifying Carbohydrate Ligands of a Norovirus P Particle using a Catch and Release Electrospray Ionization Mass Spectrometry Assay

NASA Astrophysics Data System (ADS)

Han, Ling; Kitova, Elena N.; Tan, Ming; Jiang, Xi; Klassen, John S.

2014-01-01

Noroviruses (NoVs), the major cause of epidemic acute gastroenteritis, recognize human histo-blood group antigens (HBGAs), which are present as free oligosaccharides in bodily fluid or glycolipids and glycoproteins on the surfaces of cells. The subviral P particle formed by the protruding (P) domain of the NoV capsid protein serves as a useful model for the study NoV-HBGA interactions. Here, we demonstrate the application of a catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay for screening carbohydrate libraries against the P particle to rapidly identify NoV ligands and potential inhibitors. Carbohydrate libraries of 50 and 146 compounds, which included 18 and 24 analogs of HBGA receptors, respectively, were screened against the P particle of VA387, a member of the predominant GII.4 NoVs. Deprotonated ions corresponding to the P particle bound to carbohydrates were isolated and subjected to collision-induced dissociation to release the ligands in their deprotonated forms. The released ligands were identified by ion mobility separation followed by mass analysis. All 13 and 16 HBGA ligands with intrinsic affinities >500 M-1 were identified in the 50 and the 146 compound libraries, respectively. Furthermore, screening revealed interactions with a series of oligosaccharides with structures found in the cell wall of mycobacteria and human milk. The affinities of these newly discovered ligands are comparable to those of the HBGA receptors, as estimated from the relative abundance of released ligand ions.

Brachytherapy dosimetry of 125I and 103Pd sources using an updated cross section library for the MCNP Monte Carlo transport code.

PubMed

Bohm, Tim D; DeLuca, Paul M; DeWerd, Larry A

2003-04-01

Permanent implantation of low energy (20-40 keV) photon emitting radioactive seeds to treat prostate cancer is an important treatment option for patients. In order to produce accurate implant brachytherapy treatment plans, the dosimetry of a single source must be well characterized. Monte Carlo based transport calculations can be used for source characterization, but must have up to date cross section libraries to produce accurate dosimetry results. This work benchmarks the MCNP code and its photon cross section library for low energy photon brachytherapy applications. In particular, we calculate the emitted photon spectrum, air kerma, depth dose in water, and radial dose function for both 125I and 103Pd based seeds and compare to other published results. Our results show that MCNP's cross section library differs from recent data primarily in the photoelectric cross section for low energies and low atomic number materials. In water, differences as large as 10% in the photoelectric cross section and 6% in the total cross section occur at 125I and 103Pd photon energies. This leads to differences in the dose rate constant of 3% and 5%, and differences as large as 18% and 20% in the radial dose function for the 125I and 103Pd based seeds, respectively. Using a partially updated photon library, calculations of the dose rate constant and radial dose function agree with other published results. Further, the use of the updated photon library allows us to verify air kerma and depth dose in water calculations performed using MCNP's perturbation feature to simulate updated cross sections. We conclude that in order to most effectively use MCNP for low energy photon brachytherapy applications, we must update its cross section library. Following this update, the MCNP code system will be a very effective tool for low energy photon brachytherapy dosimetry applications.

High-Throughput Synthesis and Characterization of Eu Doped Ba xSr2- xSiO4 Thin Film Phosphors.

PubMed

Frost, Sara; Guérin, Samuel; Hayden, Brian E; Soulié, Jean-Philippe; Vian, Chris

2018-06-20

High-throughput techniques have been employed for the synthesis and characterization of thin film phosphors of Eu-doped Ba x Sr 2- x SiO 4 . Direct synthesis from evaporation of the constituent elements under a flux of atomic oxygen on a sapphire substrate at 850 °C was used to directly produce thin film libraries (415 nm thickness) of the crystalline orthosilicate phase with the desired compositional variation (0.24 > x > 1.86). The orthosilicate phase could be synthesized as a pure, or predominantly pure, phase. Annealing the as synthesized library in a reducing atmosphere resulted in the reduction of the Eu while retaining the orthosilicate phase, and resulted in a materials thin film library where fluorescence excited by blue light (450 nm) was observable by the naked eye. Parallel screening of the fluorescence from the combinatorial libraries of Eu doped Ba x Sr 2- x SiO 4 has been implemented by imaging the fluorescent radiation over the library using a monochrome digital camera using a series of color filters. Informatics tools have been developed to allow the 1931 CIE color coordinates and the relative quantum efficiencies of the materials library to be rapidly assessed and mapped against composition, crystal structure and phase purity. The range of compositions gave values of CIE x between 0.17 and 0.52 and CIE y between 0.48 and 0.69 with relative efficiencies in the range 2.0 × 10 -4 -7.6 × 10 -4 . Good agreement was obtained between the thin film phosphors and the fluorescence characteristics of a number of corresponding bulk phosphor powders. The thermal quenching of fluorescence in the thin film libraries was also measured in the temperature range 25-130 °C: The phase purity of the thin film was found to significantly influence both the relative quantum efficiency and the thermal quenching of the fluorescence.

The Mendeleev-Meyer force project.

PubMed

Santos, Sergio; Lai, Chia-Yun; Amadei, Carlo A; Gadelrab, Karim R; Tang, Tzu-Chieh; Verdaguer, Albert; Barcons, Victor; Font, Josep; Colchero, Jaime; Chiesa, Matteo

2016-10-14

Here we present the Mendeleev-Meyer Force Project which aims at tabulating all materials and substances in a fashion similar to the periodic table. The goal is to group and tabulate substances using nanoscale force footprints rather than atomic number or electronic configuration as in the periodic table. The process is divided into: (1) acquiring nanoscale force data from materials, (2) parameterizing the raw data into standardized input features to generate a library, (3) feeding the standardized library into an algorithm to generate, enhance or exploit a model to identify a material or property. We propose producing databases mimicking the Materials Genome Initiative, the Medical Literature Analysis and Retrieval System Online (MEDLARS) or the PRoteomics IDEntifications database (PRIDE) and making these searchable online via search engines mimicking Pubmed or the PRIDE web interface. A prototype exploiting deep learning algorithms, i.e. multilayer neural networks, is presented.

The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

PubMed Central

Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M.; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R.

2015-01-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML‐based format, capable of representing data about two‐dimensional features from LC‐MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java‐based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)‐level quantification values from peptide‐level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC‐MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in‐built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq‐lib/. PMID:26037908

The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

PubMed

Qi, Da; Zhang, Huaizhong; Fan, Jun; Perkins, Simon; Pisconti, Addolorata; Simpson, Deborah M; Bessant, Conrad; Hubbard, Simon; Jones, Andrew R

2015-09-01

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mass, radius and composition of the outer crust of nonaccreting cold neutron stars

NASA Astrophysics Data System (ADS)

Hempel, Matthias; Schaffner-Bielich, Jürgen

2008-01-01

The properties and composition of the outer crust of nonaccreting cold neutron stars are studied by applying the model of Baym, Pethick and Sutherland, which was extended by including higher order corrections of the atomic binding, screening, exchange and zero-point energy. The most recent experimental nuclear data from the atomic mass table of Audi, Wapstra and Thibault from 2003 are used. Extrapolation to the drip line is utilized by various state-of-the-art theoretical nuclear models (finite range droplet, relativistic nuclear field and non-relativistic Skyrme Hartree Fock parameterizations). The different nuclear models are compared with respect to the mass and radius of the outer crust for different neutron star configurations and the nuclear compositions of the outer crust.

Manifold and method of batch measurement of Hg-196 concentration using a mass spectrometer

DOEpatents

Grossman, M.W.; Evans, R.

1991-11-26

A sample manifold and method of its use has been developed so that milligram quantities of mercury can be analyzed mass spectroscopically to determine the [sup 196]Hg concentration to less than 0.02 atomic percent. Using natural mercury as a standard, accuracy of [+-]0.002 atomic percent can be obtained. The mass spectrometer preferably used is a commercially available GC/MS manufactured by Hewlett Packard. A novel sample manifold is contained within an oven allowing flow rate control of Hg into the MS. Another part of the manifold connects to an auxiliary pumping system which facilitates rapid clean up of residual Hg in the manifold. Sample cycle time is about 1 hour. 8 figures.

Mass energy-absorption coefficients and average atomic energy-absorption cross-sections for amino acids in the energy range 0.122-1.330 MeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

More, Chaitali V., E-mail: chaitalimore89@gmail.com; Lokhande, Rajkumar M.; Pawar, Pravina P., E-mail: pravinapawar4@gmail.com

Mass attenuation coefficients of amino acids such as n-acetyl-l-tryptophan, n-acetyl-l-tyrosine and d-tryptophan were measured in the energy range 0.122-1.330 MeV. NaI (Tl) scintillation detection system was used to detect gamma rays with a resolution of 8.2% at 0.662 MeV. The measured attenuation coefficient values were then used to determine the mass energy-absorption coefficients (σ{sub a,en}) and average atomic energy-absorption cross sections (μ{sub en}/ρ) of the amino acids. Theoretical values were calculated based on XCOM data. Theoretical and experimental values are found to be in good agreement.

Rapid Identification of Cryptococcus neoformans and Cryptococcus gattii by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry ▿

PubMed Central

McTaggart, Lisa R.; Lei, Eric; Richardson, Susan E.; Hoang, Linda; Fothergill, Annette; Zhang, Sean X.

2011-01-01

Compared to DNA sequence analysis, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) correctly identified 100% of Cryptococcus species, distinguishing the notable pathogens Cryptococcus neoformans and C. gattii. Identification was greatly enhanced by supplementing a commercial spectral library with additional entries to account for subspecies variability. PMID:21653762

Systematic toxicological analysis: computer-assisted identification of poisons in biological materials.

PubMed

Stimpfl, Th; Demuth, W; Varmuza, K; Vycudilik, W

2003-06-05

A new software was developed to improve the chances for identification of a "general unknown" in complex biological materials. To achieve this goal, the total ion current chromatogram was simplified by filtering the acquired mass spectra via an automated subtraction procedure, which removed mass spectra originating from the sample matrix, as well as interfering substances from the extraction procedure. It could be shown that this tool emphasizes mass spectra of exceptional compounds, and therefore provides the forensic toxicologist with further evidence-even in cases where mass spectral data of the unknown compound are not available in "standard" spectral libraries.

Mass spectrometry of aerospace materials

NASA Technical Reports Server (NTRS)

Colony, J. A.

1976-01-01

Mass spectrometry is used for chemical analysis of aerospace materials and contaminants. Years of analytical aerospace experience have resulted in the development of specialized techniques of sampling and analysis which are required in order to optimize results. This work has resulted in the evolution of a hybrid method of indexing mass spectra which include both the largest peaks and the structurally significant peaks in a concise format. With this system, a library of mass spectra of aerospace materials was assembled, including the materials responsible for 80 to 90 percent of the contamination problems at Goddard Space Flight Center during the past several years.

Use of a single trajectory to study product energy partitioning in unimolecular dissociation: mass effects for halogenated alkanes.

PubMed

Sun, Lipeng; Park, Kyoyeon; Song, Kihyung; Setser, Donald W; Hase, William L

2006-02-14

A single trajectory (ST) direct dynamics approach is compared with quasiclassical trajectory (QCT) direct dynamics calculations for determining product energy partitioning in unimolecular dissociation. Three comparisons are made by simulating C(2)H(5)F-->HF + C(2)H(4) product energy partitioning for the MP26-31G(*) and MP26-311 + + G(**) potential energy surfaces (PESs) and using the MP26-31G(*) PES for C(2)H(5)F dissociation as a model to simulate CHCl(2)CCl(3)-->HCl + C(2)Cl(4) dissociation and its product energy partitioning. The trajectories are initiated at the transition state with fixed energy in reaction-coordinate translation E(t) (double dagger). The QCT simulations have zero-point energy (ZPE) in the vibrational modes orthogonal to the reaction coordinate, while there is no ZPE for the STs. A semiquantitative agreement is obtained between the ST and QCT average percent product energy partitionings. The ST approach is used to study mass effects for product energy partitioning in HX(X = F or Cl) elimination from halogenated alkanes by using the MP26-31G(*) PES for C(2)H(5)F dissociation and varying the masses of the C, H, and F atoms. There is, at most, only a small mass effect for partitioning of energy to HX vibration and rotation. In contrast, there are substantial mass effects for partitioning to relative translation and the polyatomic product's vibration and rotation. If the center of mass of the polyatomic product is located away from the C atom from which HX recoils, the polyatomic has substantial rotation energy. Polyatomic products, with heavy atoms such as Cl atoms replacing the H atoms, receive substantial vibration energy that is primarily transferred to the wag-bend motions. For E(t) (double dagger) of 1.0 kcalmol, the ST calculations give average percent partitionings to relative translation, polyatomic vibration, polyatomic rotation, HX vibration, and HX rotation of 74.9%, 6.8%, 1.5%, 14.4%, and 2.4% for C(2)H(5)F dissociation and 39.7%, 38.1%, 0.2%, 16.1%, and 5.9% for a model of CHCl(2)CCl(3) dissociation.

New Active Optical Technique Developed for Measuring Low-Earth-Orbit Atomic Oxygen Erosion of Polymers

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; deGroh, Kim K.; Demko, Rikako

2003-01-01

Polymers such as polyimide Kapton (DuPont) and Teflon FEP (DuPont, fluorinated ethylene propylene) are commonly used spacecraft materials because of desirable properties such as flexibility, low density, and in the case of FEP, a low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low-Earth-orbit (LEO) environment are exposed to energetic atomic oxygen. Atomic oxygen reaction with polymers causes erosion, which is a threat to spacecraft performance and durability. It is, therefore, important to understand the atomic oxygen erosion yield E (the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. The most common technique for determining E is a passive technique based on mass-loss measurements of samples exposed to LEO atomic oxygen during a space flight experiment. There are certain disadvantages to this technique. First, because it is passive, data are not obtained until after the flight is completed. Also, obtaining the preflight and postflight mass measurements is complicated by the fact that many polymers absorb water and, therefore, the mass change due to water absorption can affect the E data. This is particularly true for experiments that receive low atomic oxygen exposures or for samples that have a very low E. An active atomic oxygen erosion technique based on optical measurements has been developed that has certain advantages over the mass-loss technique. This in situ technique can simultaneously provide the erosion yield data on orbit and the atomic oxygen exposure fluence, which is needed for erosion yield determination. In the optical technique, either sunlight or artificial light can be used to measure the erosion of semitransparent or opaque polymers as a result of atomic oxygen attack. The technique is simple and adaptable to a rather wide range of polymers, providing that they have a sufficiently high optical absorption coefficient. If one covers a photodiode with a uniformly thick sheet of semitransparent polymer such as Kapton H polyimide, then as atomic oxygen erodes the polymer, the short-circuit current from the photodiode will increase in an exponential manner with fluence. This nonlinear response with fluence results in a lack of sensitivity for measuring low atomic oxygen fluences. However, if one uses a variable-thickness polymer or carbon sample, which is configured as shown in the preceding figure, then a linear response can be achieved for opaque materials using a parabolic well for a circular geometry detector or a V-shaped well for a rectangular-geometry detector. Variable-thickness samples can be fabricated using many thin polymer layers. For semitransparent polymers such as Kapton H polyimide, there is an initial short-circuit current that is greater than zero. This current has a slightly nonlinear dependence on atomic oxygen fluence in comparison to opaque materials such as black Kapton as shown in the graph. For this graph figure, the total thickness of Kapton H was assumed to be 0.03 cm. The photodiode short-circuit current shown in the graph was generated on the basis of preliminary measurements-a total reflectance rho of 0.0424 and an optical absorption coefficient a of 146.5 cm(sup -1). In addition to obtaining on-orbit data, the advantage of this active erosion and erosion yield measurement technique is its simplicity and reliance upon well-characterized fluence witness materials as well as a nearly linear photodiode short-circuit current dependence upon atomic oxygen fluence. The optical technique is useful for measuring either atomic oxygen fluence or erosion, depending on the information desired. To measure the atomic oxygen erosion yield of a test material, one would need to have two photodiode sensors, one for the test material and one that uses a known erosion yield material (such as Kapton) to measure the atomic oxygen fluence.

Measurement of the intensity ratio of Auger and conversion electrons for the electron capture decay of 125I.

PubMed

Alotiby, M; Greguric, I; Kibédi, T; Lee, B Q; Roberts, M; Stuchbery, A E; Tee, Pi; Tornyi, T; Vos, M

2018-03-21

Auger electrons emitted after nuclear decay have potential application in targeted cancer therapy. For this purpose it is important to know the Auger electron yield per nuclear decay. In this work we describe a measurement of the ratio of the number of conversion electrons (emitted as part of the nuclear decay process) to the number of Auger electrons (emitted as part of the atomic relaxation process after the nuclear decay) for the case of 125 I. Results are compared with Monte-Carlo type simulations of the relaxation cascade using the BrIccEmis code. Our results indicate that for 125 I the calculations based on rates from the Evaluated Atomic Data Library underestimate the K Auger yields by 20%.

Atomic physics modeling of transmission spectra of Sc-doped aerogel foams to support OMEGA experiments

DOE PAGES

Johns, Heather Marie; Lanier, Nicholas Edward; Kline, John L.; ...

2016-09-07

Here, we present synthetic transmission spectra generated with PrismSPECT utilizing both the ATBASE model and the Los Alamos opacity library (OPLIB) to evaluate whether an alternative choice in atomic data will impact modeling of experimental data from radiation transport experiments using Sc-doped aerogel foams (ScSi 6O 12 at 75 mg/cm 3 density). We have determined that in the 50-200 eV T e range there is a significant difference in the 1s-3p spectra, especially below 100 eV, and for T e = 200 eV above 5000 eV in photon energy. Examining synthetic spectra generated using OPLIB with 300 resolving power revealsmore » spectral sensitivity to T e changes of ~3 eV.« less

Atomic physics modeling of transmission spectra of Sc-doped aerogel foams to support OMEGA experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johns, Heather Marie; Lanier, Nicholas Edward; Kline, John L.

Here, we present synthetic transmission spectra generated with PrismSPECT utilizing both the ATBASE model and the Los Alamos opacity library (OPLIB) to evaluate whether an alternative choice in atomic data will impact modeling of experimental data from radiation transport experiments using Sc-doped aerogel foams (ScSi 6O 12 at 75 mg/cm 3 density). We have determined that in the 50-200 eV T e range there is a significant difference in the 1s-3p spectra, especially below 100 eV, and for T e = 200 eV above 5000 eV in photon energy. Examining synthetic spectra generated using OPLIB with 300 resolving power revealsmore » spectral sensitivity to T e changes of ~3 eV.« less