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Sample records for al angew chem

  1. Electrical properties of medium field, chem-prep varistors. [ZnO doped with Co, Mn, or Al

    SciTech Connect

    Tuttle, B.A.; Voigt, J.A.; Binasiewicz, E.J.; Kimball, K.M.

    1988-01-01

    Medium field, chem-prep, ZnO varistors were synthesized and electrically tested. Eight formulations were used with three dopants: (1) Co (0, 0.25, 0.5 mol %), (2) Mn (0, 0.25, 0.5 mol %) and (3) Al (0, 125, and 150 ppM by weight). Al doping produced two dramatic effects: (1) an increase in the electric switching field by factors of 5 to 10, and (2) a significant enhancement of the high current density nonlinearity coefficient. Firing temperatures of 800, 900 and 1000/sup 0/C were used to densify materials and produce varistors with electrical switching fields in the 3 to 10 kV/cm range. Current density vs electric field measurements were made from 1 ..mu..A/cm/sup 2/ to 10 A/cm/sup 2/ using dc and pulse techniques. The varistor with the largest nonlinearity coefficient over this extended current density range was fired at 1000/sup 0/C and contained 0.25 Co, 0.25 Mn, 0.56 Bi (mol %) and 150 ppM Al (by weight). The nonlinearity coefficient was 14 at low current densities (0.1 mA/cm/sup 2/ to 5 mA/cm/sup 2/) and 28 for high current densities (0.1 to 10 A/cm/sup 2/). Because of the large nonlinearity coefficient, this varistor is the best candidate for Sandia applications of all varistors we synthesized. Further, the varistor had an electrical switch field of 5 kV/cm at 10 A/cm/sup 2/ and was greater than 96% of theoretical density. Low field dielectric properties and J vs. E characteristics as a function of temperature were measured for this varistor. 7 tabs.

  2. A Decade of ChemMedChem.

    PubMed

    Williams, Scott D; Ortúzar, Natalia

    2016-01-05

    Happy birthday! Issue 01/2016 marks the 10th anniversary of ChemMedChem. With a complete set of 10 volumes, the Editorial Team takes a look back at how the journal, and indeed the field of medicinal chemistry, have evolved and changed over the past decade.

  3. Turning the digital page at ChemBioChem.

    PubMed

    Gölitz, Peter; Campbell, Meghan

    2014-01-03

    Chemical biology has been in the spotlight for numerous reasons lately. ChemBioChem has had a productive year at the forefront of these advances and is looking forward to many changes in 2014. Advances in digital publishing promise to increase the visibility and functionality of ChemBioChem for our worldwide readership.

  4. Readying ChemCam

    NASA Image and Video Library

    2012-08-17

    This image shows the calibration target for the Chemistry and Camera ChemCam instrument on NASA Curiosity rover. The calibration target is one square and a group of nine circles that look dark in the black-and-white image.

  5. AdapChem

    NASA Technical Reports Server (NTRS)

    Oluwole, Oluwayemisi O.; Wong, Hsi-Wu; Green, William

    2012-01-01

    AdapChem software enables high efficiency, low computational cost, and enhanced accuracy on computational fluid dynamics (CFD) numerical simulations used for combustion studies. The software dynamically allocates smaller, reduced chemical models instead of the larger, full chemistry models to evolve the calculation while ensuring the same accuracy to be obtained for steady-state CFD reacting flow simulations. The software enables detailed chemical kinetic modeling in combustion CFD simulations. AdapChem adapts the reaction mechanism used in the CFD to the local reaction conditions. Instead of a single, comprehensive reaction mechanism throughout the computation, a dynamic distribution of smaller, reduced models is used to capture accurately the chemical kinetics at a fraction of the cost of the traditional single-mechanism approach.

  6. AutoChem

    NASA Technical Reports Server (NTRS)

    Lary, David John

    2005-01-01

    AutoChem is a suite of Fortran 90 computer programs for the modeling of kinetic reaction systems. AutoChem performs automatic code generation, symbolic differentiation, analysis, and documentation. It produces a documented stand-alone system for the modeling and assimilation of atmospheric chemistry. Given databases of chemical reactions and a list of constituents defined by the user, AutoChem automatically does the following: 1. Selects the subset of reactions that involve a user-defined list of constituents and automatically prepares a document listing the reactions; 2. Constructs the ordinary differential equations (ODEs) that describe the reactions as functions of time and prepares a document containing the ODEs; 3. Symbolically differentiates the time derivatives to obtain the Jacobian and prepares a document containing the Jacobian; 4. Symbolically differentiates the Jacobian to obtain the Hessian and prepares a document containing the Hessian; and 5. Writes all the required Fortran 90 code and datafiles for a stand-alone chemical modeling and assimilation system (implementation of steps 1 through 5). Typically, the time taken for steps 1 through 5 is about 3 seconds. The modeling system includes diagnostic components that automatically analyze each ODE at run time, the relative importance of each term, time scales, and other attributes of the model.

  7. ChemCam video footage

    NASA Image and Video Library

    ChemCam is a rock-zapping laser instrument that can hit rocks with a laser then observes the flash through a telescope and analyzes the spectrum of light to identify the chemical elements in the ta...

  8. Chem-E-Car Downunder.

    ERIC Educational Resources Information Center

    Rhodes, Martin

    2002-01-01

    Presents the Chem-E-Car competition in which students build a small car powered by a chemical reaction. Focuses on a controlled chemical reaction in which the car travels a required specific distance and stops. Requires participants to prepare poster presentations. (YDS)

  9. Depth Profiles Using ChemCam

    NASA Astrophysics Data System (ADS)

    Cousin, A.; Maurice, S.; Berger, G.; Forni, O.; Gasnault, O.; Wiens, R.

    2011-03-01

    ChemCam, which is in part of the MSL payload, uses the LIBS technique to investigate the martian surface. The capabilities of ChemCam for the depth profile have to be understood, as ChemCam will shoot several targets which can have alteration coating.

  10. Comment on the article ;Cation-π interaction of Ag+ with [6]helicene: An experimental and theoretical study; by E. Makrlík et al. [Chem. Phys. Lett. 633 (2015) 105-108

    NASA Astrophysics Data System (ADS)

    Gal, Jean-François

    2017-07-01

    In an article dedicated to the structure and energetics of the adduct Ag+/[6]helicene (Chem. Phys. Letters 633 (2015) 105-108), the authors measured an energy threshold for the dissociation into Ag0 and ([ 6 ]helicene) +rad , using collision induced dissociation in an ion trap mass spectrometer. The result is incorrectly interpreted in term of a bond dissociation energy (BDE) related to the formation of Ag+ and neutral [6]helicene. In this Comment, the initial experimental result is converted into the true BDE using ionization energies of Ag0 and [6]helicene. The experimental method, accuracy and significance of this BDE in term of cation/π interaction, are discussed.

  11. PubChem atom environments.

    PubMed

    Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

    2015-01-01

    Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many

  12. Comment on 'Enhancement in the production of nucleating clusters due to dimethylamine and large uncertainties in the thermochemistry of amine-enhanced nucleation' by Nadykto et al., Chem. Phys. Lett. 609 (2014) 42-49

    NASA Astrophysics Data System (ADS)

    Kupiainen-Määttä, Oona; Henschel, Henning; Kurtén, Theo; Loukonen, Ville; Olenius, Tinja; Paasonen, Pauli; Vehkamäki, Hanna

    2015-03-01

    We comment on a study by Nadykto et al. recently published in this journal. Earlier work from our group has been misrepresented in this study, and we feel that the claims made need to be amended. Also the analysis of Nadykto et al. concerning the implications of their own density functional calculations is incomplete. We present cluster formation simulations allowing more conclusions to be drawn from their data, and also compare them to recent experimental results not cited in their work.

  13. Checking out ChemCam View

    NASA Image and Video Library

    2012-08-17

    This mosaic shows the calibration target for the Chemistry and Camera ChemCam instrument on NASA Curiosity rover, as seen by the ChemCam remote micro-imager. The 10 images incorporated in this mosaic were taken on Aug. 15.

  14. A History of ChemMatters Magazine

    NASA Astrophysics Data System (ADS)

    Tinnesand, Michael J.

    2007-04-01

    First published by the ACS Education Division in 1983, ChemMatters is a magazine for high school chemistry students and their teachers. ChemMatters has strong links to past publications in the same genre. This history of the magazine presents not only the development of ChemMatters , but also the development of ACS education activities over the past 25 years. ChemMatters has the editorial goal of helping high school students understand how chemistry works in their everyday lives and as a result, to see the relevance of what they are learning in school. After more than two decades of production, ChemMatters continues to be a popular and useful resource for learning and understanding chemistry.

  15. ChemRad Sample Form Instructions

    EPA Pesticide Factsheets

    These instructons are intended to assist registered users of the EPA Region 8 Drinking Water Watch website who would like to create ChemRad Sample Forms for monitoring that is required during the current year.

  16. Exploiting PubChem for Virtual Screening

    PubMed Central

    Xie, Xiang-Qun

    2011-01-01

    Importance of the field PubChem is a public molecular information repository, a scientific showcase of the NIH Roadmap Initiative. The PubChem database holds over 27 million records of unique chemical structures of compounds (CID) derived from nearly 70 million substance depositions (SID), and contains more than 449,000 bioassay records with over thousands of in vitro biochemical and cell-based screening bioassays established, with targeting more than 7000 proteins and genes linking to over 1.8 million of substances. Areas covered in this review This review builds on recent PubChem-related computational chemistry research reported by other authors while providing readers with an overview of the PubChem database, focusing on its increasing role in cheminformatics, virtual screening and toxicity prediction modeling. What the reader will gain These publicly available datasets in PubChem provide great opportunities for scientists to perform cheminformatics and virtual screening research for computer-aided drug design. However, the high volume and complexity of the datasets, in particular the bioassay-associated false positives/negatives and highly imbalanced datasets in PubChem, also creates major challenges. Several approaches regarding the modeling of PubChem datasets and development of virtual screening models for bioactivity and toxicity predictions are also reviewed. Take home message Novel data-mining cheminformatics tools and virtual screening algorithms are being developed and used to retrieve, annotate and analyze the large-scale and highly complex PubChem biological screening data for drug design. PMID:21691435

  17. The Best of Chem 13 News

    NASA Astrophysics Data System (ADS)

    Thorsen, Kathy

    1999-07-01

    This column is designed to give JCE readers a few highlights from Chem 13 News, a monthly publication for chemistry educators from the University of Waterloo in Ontario, Canada, and provides annotations describing a particular activity or a variety of sources from which new and creative ideas can be extracted.

  18. "CHEM"opera for Chemistry Education

    ERIC Educational Resources Information Center

    Chung, Yong Hee

    2013-01-01

    "CHEM"opera is an opera blended with demonstrations of chemical reactions. It has been produced and performed twice by chemistry undergraduate students at Hallym University in South Korea. It aims to demonstrate interesting chemical reactions to chemistry students, children and the public and to facilitate their understanding of the role…

  19. A History of ChemMatters Magazine

    ERIC Educational Resources Information Center

    Tinnesand, Michael J.

    2007-01-01

    ChemMatters, the chemistry magazine published since 1983, has always provided interesting topics for chemistry students. The American Chemical Society publishes the magazine and many well-known authors like Isaac Asimov, Glen Seaborg and Derek Davenport have contributed to the magazine and the magazine has succeeded in its goal of demystifying…

  20. "CHEM"opera for Chemistry Education

    ERIC Educational Resources Information Center

    Chung, Yong Hee

    2013-01-01

    "CHEM"opera is an opera blended with demonstrations of chemical reactions. It has been produced and performed twice by chemistry undergraduate students at Hallym University in South Korea. It aims to demonstrate interesting chemical reactions to chemistry students, children and the public and to facilitate their understanding of the role…

  1. Dust Detection by Curiosity ChemCam

    NASA Image and Video Library

    2013-04-08

    The ChemCam instrument on NASA Curiosity Mars rover fired its laser 50 times at its onboard graphite target showing spectral measurements from the first shot, which hit dust on the target, compared to spectral measurements of from the 50th shot.

  2. Curiosity ChemCam Removes Dust

    NASA Image and Video Library

    2013-04-08

    This pair of images taken a few minutes apart show how laser firing by NASA Mars rover Curiosity removes dust from the surface of a rock. The images were taken by the remote micro-imager camera in the laser-firing Chemistry and Camera ChemCam.

  3. A History of ChemMatters Magazine

    ERIC Educational Resources Information Center

    Tinnesand, Michael J.

    2007-01-01

    ChemMatters, the chemistry magazine published since 1983, has always provided interesting topics for chemistry students. The American Chemical Society publishes the magazine and many well-known authors like Isaac Asimov, Glen Seaborg and Derek Davenport have contributed to the magazine and the magazine has succeeded in its goal of demystifying…

  4. [Al

    PubMed

    Purath; Köppe; Schnöckel

    1999-10-04

    A "naked" aluminum atom links two aluminum tetrahedra in the [Al(7){N(SiMe(3))(2)}(6)](-) ion (see picture), which results from the reaction of a metastable AlCl solution with LiN(SiMe(3))(2) and crystallizes with [Li(OEt(2))(3)](+) as cation. This unique structure among molecular metal atom clusters represents a small but characteristic section of cubic close-packed aluminum.

  5. ChemCam Targeted Science at Gale Crater

    NASA Astrophysics Data System (ADS)

    Wiens, R. C.; Blaney, D. L.; Clark, B. C.; Bridges, N. T.; Clegg, S. M.; Maurice, S.; Newsom, H. E.; Vaniman, D. T.; Herkenhoff, K. E.; Ollila, A. M.; Gasnault, O.; Pinet, P. C.; Dromart, G.; Barraclough, B. L.; Lasue, J.

    2011-12-01

    The MSL rover, Curiosity, uses a novel remote-sensing instrument, ChemCam, which combines laser-induced breakdown spectroscopy (LIBS) with a high resolution remote micro-imager (RMI). ChemCam uses a focused, pulsed laser beam at targets up to 7 m away to excite a light-emitting plasma. Spectral analysis identifies elements present and provides rapid semi-quantitative analyses. Repeated laser pulses remove dust and weathering coatings from rock samples to depths >0.5 mm and ~0.4 mm in diameter. The RMI, with ~20x20 mrad field of view, provides a broad-band image with 100 μm resolution. LIBS yields abundances of H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, Cl, K, Ca, Ti, V, Cr, Fe, Ni, Zr, Rb, Sr, As, Ba, and Pb. Interference from atmospheric constituents raises the detection limits of C, N, and O (e.g., >2% wt for C). LIBS is very sensitive to alkali and alkali earth elements, with some detection limits to ~1 ppm at close range. Conversely, LIBS is insensitive to F, Cl, S, P, and N, with detection limits of several wt. %. Pointing accuracy is ~3 mrad, however relative pointing accuracy is better, so line scans and rasters will enable analyses of targeted features to ~1 mm. At Gale Crater, determination of elements not previously analyzed in-situ, i.e., H, Li, Rb, Sr, and Ba, along with other elements will constrain aqueous, hydrothermal and vapor geochemical transport processes. Initial analyses after landing will characterize air fall dust and weathering coatings on local rocks, and profile the soil and surfacial materials including bedforms to investigate compositional differences in near-surface layers. Targets within the landing ellipse include fan and inverted channel deposits derived from the crater rim, which may contain alteration minerals produced by impact hydrothermal processes. Enigmatic deposits with bright fracture fill could represent lake sediments modified by injection of deposits from groundwater. During the drive to the Gale mound, ChemCam will

  6. ChemMatCARS Data Archive

    DOE Data Explorer

    ChemMatCARS is a high-brilliance national synchrotron x-ray facility dedicated primarily to static and dynamic condensed matter chemistry and materials science. The scientific focus of the facility includes the study of surface and interfacial properties of liquids and solids as well as their bulk structure at atomic, molecular and mesoscopic length scales with high spatial and energy resolution. Experimental techniques supported by the facility include: 1) Liquid Surface X-ray Scattering; 2) Solid Surface X-ray Scattering; 3) Time-Resolved Crystallography; 4) Micro-Crystal Diffraction; 5) Small and Wide-angle X-ray Scattering. The data archive referenced here contains data for various components along the beamline within the First Optics Enclosure and is intended to be input or parameter data. See the Science Nuggets at http://cars9.uchicago.edu/chemmat/pages/nuggets.html for leads to some of the research conducted at the ChemMatCARS beamline.

  7. Restoration of AMPTE/CHEM Data

    NASA Astrophysics Data System (ADS)

    Vandegriff, J.

    2006-12-01

    The highest time resolution digital data for the Charge-Energy-Mass (CHEM) Spectrometer instrument on the Active Magnetospheric Particle Explorers (AMPTE) mission has been restored and made available online at http://sd-www.jhuapl.edu/AMPTE. During the period 1984 to the beginning of 1989, CHEM measured the mass and charge-state compositions as well as the energy spectra and pitch-angle distributions of all major ions from H through Fe with energies from 0.3 to 300 keV/charge. The data cadence is less than one minute. With the spacecraft in a low inclination orbit passing through the magnetopause and well into the magnetosphere, many samplings of the ring-current were made. The data itself consist of so-called PHA (pulse height analysis) events, in which the energy per charge, time of flight, and total energy are measured for each particle. The original Fortran software for calculating fluxes from the PHA events has been ported from VMS to modern Unix Fortran compilers. The CHEM data will be very useful in conjunction with the upcoming Radiation Belt Storm Probe (RBSP) mission, which is part of NASA's Living With a Star (LWS) initiative, and this restoration effort was funded through the LWS Targeted Research and Technology (TR&T) program.

  8. ChemDemos II Videodisc: Abstract of Special Issue 14

    NASA Astrophysics Data System (ADS)

    Moore, John W.; Jacobsen, Jerrold J.; Houston Jetzer, Kelly; Gilbert, George; Mattes, Fred; Phillips, David; Lisensky, George; Zweerink, Gerald

    1996-09-01

    Literature Cited Moore, J. W., Jacobsen, J. J., Hunsberger, L. R., Gammon, S. D., Jetzer, K. H., Zimmerman, J. ChemDemos Videodisc, J. Chem. Educ.: Software, 1995, Special Issue 8. Jacobsen, J. J. Videodisc Browser 2.0, J. Chem. Educ.: Software, 1995, 7C, No. 2. Jacobsen, J. J. Videodisc Browser 2.0, J. Chem. Educ.: Software, 1996, 3D, No. 2. HyperCard, Apple Computer, Cupertino, CA 65014-2084. ToolBook, Asymetrics Corp., Bellevue, WA 98004.

  9. Building the EarthChem System for Advanced Data Management in Igneous Geochemistry

    NASA Astrophysics Data System (ADS)

    Lehnert, K.; Walker, J. D.; Carlson, R. W.; Hofmann, A. W.; Sarbas, B.

    2004-12-01

    Several mature databases of geochemical analyses for igneous rocks are now available over the Internet. The existence of these databases has revolutionized access to data for researchers and students allowing them to extract data sets customized to their specific problem from global data compilations with their desktop computer within a few minutes. Three of the database efforts - PetDB, GEOROC, and NAVDAT - have initiated a collaborative effort called EarthChem to create better and more advanced and integrated data management for igneous geochemistry. The EarthChem web site (http://www.earthchem.org/) serves as a portal to the three databases and information related to EarthChem activities. EarthChem participants agreed to establish a dialog to minimize duplication of effort and share useful tools and approaches. To initiate this dialog, a workshop was run by EarthChem in October, 2003 to discuss cyberinfrastructure needs in igneous geochemistry (workshop report available at the EarthChem site). EarthChem ran an information booth with database and visualization demonstrations at the Fall 2003 AGU meeting (and will have one in 2004) and participated in the May 2003 GERM meeting in Lyon, France where we provided the newly established Publishers' Round Table a list of minimum standards of data reporting to ease the assimilation of data into the databases. Aspects of these suggestions already have been incorporated into new data policies at Geochimica et Cosmochimica Acta and Chemical Geology (Goldstein et al. 2004), and are under study by the Geological Society of America. EarthChem presented its objectives and activities to the Solid Earth Sciences community at the Annual GSA Meeting 2003 (Lehnert et al, 2003). Future plans for EarthChem include expanding the types and amounts of data available from a single portal, giving researchers, faculty, students, and the general public the ability to search, visualize, and download geochemical and geochronological data for a

  10. ChemCam Science Objectives for the Mars Science Laboratory (MSL) Rover

    NASA Technical Reports Server (NTRS)

    Wiens, R.; Maurice, S.; Bridges, N.; Clark, B.; Cremers, D.; Herkenhoff, K.; Kirkland, L.; Mangold, N.; Manhes, G.; Mauchien, P.

    2005-01-01

    ChemCam consists of two remote sensing instruments. One, a Laser-Induced Breakdown Spectroscopy (LIBS) instrument provides rapid elemental composition data on rocks and soils within 13 m of the rover. By using laser pulses, it can remove dust or profile through weathering layers remotely. The other instrument, the Remote Micro-Imager (RMI), provides the highest resolution images between 2 m and infinity. At approximately 80 Rad field of view, its resolution exceeds that of MER Pancam by at least a factor of four. The ChemCam instruments are described in a companion paper by Maurice et al. Here we present the science objectives for the ChemCam instrument package.

  11. ChemCam Science Objectives for the Mars Science Laboratory (MSL) Rover

    NASA Technical Reports Server (NTRS)

    Wiens, R.; Maurice, S.; Bridges, N.; Clark, B.; Cremers, D.; Herkenhoff, K.; Kirkland, L.; Mangold, N.; Manhes, G.; Mauchien, P.

    2005-01-01

    ChemCam consists of two remote sensing instruments. One, a Laser-Induced Breakdown Spectroscopy (LIBS) instrument provides rapid elemental composition data on rocks and soils within 13 m of the rover. By using laser pulses, it can remove dust or profile through weathering layers remotely. The other instrument, the Remote Micro-Imager (RMI), provides the highest resolution images between 2 m and infinity. At approximately 80 Rad field of view, its resolution exceeds that of MER Pancam by at least a factor of four. The ChemCam instruments are described in a companion paper by Maurice et al. [1]. Here we present the science objectives for the ChemCam instrument package.

  12. ChemCam Science Objectives for the Mars Science Laboratory (MSL) Rover

    NASA Technical Reports Server (NTRS)

    Wiens, R.; Maurice, S.; Bridges, N.; Clark, B.; Cremers, D.; Herkenhoff, K.; Kirkland, L.; Mangold, N.; Manhes, G.; Mauchien, P.

    2005-01-01

    ChemCam consists of two remote sensing instruments. One, a Laser-Induced Breakdown Spectroscopy (LIBS) instrument provides rapid elemental composition data on rocks and soils within 13 m of the rover. By using laser pulses, it can remove dust or profile through weathering layers remotely. The other instrument, the Remote Micro-Imager (RMI), provides the highest resolution images between 2 m and infinity. At approximately 80 Rad field of view, its resolution exceeds that of MER Pancam by at least a factor of four. The ChemCam instruments are described in a companion paper by Maurice et al. [1]. Here we present the science objectives for the ChemCam instrument package.

  13. The PubChem chemical structure sketcher

    PubMed Central

    2009-01-01

    PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

  14. The PubChem chemical structure sketcher.

    PubMed

    Ihlenfeldt, Wolf D; Bolton, Evan E; Bryant, Stephen H

    2009-12-17

    PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.

  15. Chem-2-Chem: A One-to-One Supportive Learning Environment for Chemistry

    NASA Astrophysics Data System (ADS)

    Báez-Galib, Rosita; Colón-Cruz, Héctor; Resto, Wilfredo; Rubin, Michael R.

    2005-12-01

    The Chem-2-Chem (C2C) tutoring mentoring program was developed at the University of Puerto Rico at Cayey, an undergraduate institution serving Hispanic students, to increase student retention and help students achieve successful general chemistry course outcomes. This program provides a supportive learning environment designed to address students' academic and emotional needs in a holistic way. Advanced chemistry students offered peer-led, personalized, and individualized learning experiences through tutoring and mentoring to approximately 21% of students enrolled in the general chemistry course. Final grades from official class lists of all general chemistry course sections were analyzed using Student's t -test, paired t -test, and χ 2 analysis. Results during the seven semesters studied show an increase of 29% in successful course outcomes defined as final letter grades of A, B, and C obtained by Chem-2-Chem participants. For each final grade, highly statistically significant differences between participants and nonparticipants were detected. There were also statistically significant differences between successful course outcomes obtained by participants and nonparticipants for each of the semesters studied. This research supports recent trends in chemical education to provide a social context for learning experiences. This peer-led learning strategy can serve as an effective model to achieve excellence in science courses at a wide range of educational institutions.

  16. ConfChem Conference on Flipped Classroom: Spring 2014 ConfChem Virtual Poster Session

    ERIC Educational Resources Information Center

    Belford, Robert E.; Stoltzfus, Matthew; Houseknecht, Justin B.

    2015-01-01

    This communication describes the virtual poster session of the Flipped Classroom online ConfChem conference that was hosted by the ACS CHED Committee on Computers in Chemical Education (CCCE) from May 9 to June 12, 2014. During the conference's online discussions, it became evident that multiple participants who were not presenting papers had been…

  17. ConfChem Conference on Flipped Classroom: Spring 2014 ConfChem Virtual Poster Session

    ERIC Educational Resources Information Center

    Belford, Robert E.; Stoltzfus, Matthew; Houseknecht, Justin B.

    2015-01-01

    This communication describes the virtual poster session of the Flipped Classroom online ConfChem conference that was hosted by the ACS CHED Committee on Computers in Chemical Education (CCCE) from May 9 to June 12, 2014. During the conference's online discussions, it became evident that multiple participants who were not presenting papers had been…

  18. Air Quality Modeling and Forecasting over the United States Using WRF-Chem

    NASA Astrophysics Data System (ADS)

    Boxe, C.; Hafsa, U.; Blue, S.; Emmanuel, S.; Griffith, E.; Moore, J.; Tam, J.; Khan, I.; Cai, Z.; Bocolod, B.; Zhao, J.; Ahsan, S.; Gurung, D.; Tang, N.; Bartholomew, J.; Rafi, R.; Caltenco, K.; Rivas, M.; Ditta, H.; Alawlaqi, H.; Rowley, N.; Khatim, F.; Ketema, N.; Strothers, J.; Diallo, I.; Owens, C.; Radosavljevic, J.; Austin, S. A.; Johnson, L. P.; Zavala-Gutierrez, R.; Breary, N.; Saint-Hilaire, D.; Skeete, D.; Stock, J.; Salako, O.

    2016-12-01

    WRF-Chem is the Weather Research and Forecasting (WRF) model coupled with Chemistry. The model simulates the emission, transport, mixing, and chemical transformation of trace gases and aerosols simultaneously with the meteorology. The model is used for investigation of regional-scale air quality, field program analysis, and cloud-scale interactions between clouds and chemistry. The development of WRF-Chem is a collaborative effort among the community led by NOAA/ESRL scientists. The Official WRF-Chem web page is located at the NOAA web site. Our model development is closely linked with both NOAA/ESRL and DOE/PNNL efforts. Description of PNNL WRF-Chem model development is located at the PNNL web site as well as the PNNL Aerosol Modeling Testbed. High school and undergraduate students, representative of academic institutions throughout USA's Tri-State Area (New York, New Jersey, Connecticut), set up WRF-Chem on CUNY CSI's High Performance Computing Center. Students learned the back-end coding that governs WRF-Chems structure and the front-end coding that displays visually specified weather simulations and forecasts. Students also investigated the impact, to select baseline simulations/forecasts, due to the reaction, NO2 + OH + M → HOONO + M (k = 9.2 × 10-12 cm3 molecule-1 s-1, Mollner et al. 2010). The reaction of OH and NO2 to form gaseous nitric acid (HONO2) is among the most influential and in atmospheric chemistry. Till a few years prior, its rate coefficient remained poorly determined under tropospheric conditions because of difficulties in making laboratory measurements at 760 torr. These activities fosters student coding competencies and deep insights into weather forecast and air quality.

  19. LANL Researcher Roger Wiens Discusses ChemCam

    SciTech Connect

    Wiens, Roger

    2012-02-15

    Discussion of the ChemCam instrument on the Curiosity Rover that occurred during the NASA press conference prior to launch of the Mars Science Laboratory. The ChemCam instrument was developed by Los Alamos National Laboratory and the French Space Institute. Los Alamos National Laboratory researcher Roger Wiens discusses the instrument on this video. ChemCam uses a laser to "zap" features of the Martian landscape and then uses a spectrometer to gather information about the composition of the sample. ChemCam will help the Curiosity Rover determine whether Mars is or was habitable. The Rover is expected to touch down on the Red Planet on August 5, 2012.

  20. LANL Researcher Roger Wiens Discusses ChemCam

    ScienceCinema

    Wiens, Roger

    2016-07-12

    Discussion of the ChemCam instrument on the Curiosity Rover that occurred during the NASA press conference prior to launch of the Mars Science Laboratory. The ChemCam instrument was developed by Los Alamos National Laboratory and the French Space Institute. Los Alamos National Laboratory researcher Roger Wiens discusses the instrument on this video. ChemCam uses a laser to "zap" features of the Martian landscape and then uses a spectrometer to gather information about the composition of the sample. ChemCam will help the Curiosity Rover determine whether Mars is or was habitable. The Rover is expected to touch down on the Red Planet on August 5, 2012.

  1. Drosophila chem mutations disrupt epithelial polarity in Drosophila embryos

    PubMed Central

    Zamudio-Arroyo, José M.

    2016-01-01

    Drosophila embryogenesis has proven to be an extremely powerful system for developmental gene discovery and characterization. We isolated five new EMS-induced alleles that do not complement the l(3R)5G83 lethal line isolated in the Nüsslein-Volhard and Wieschaus screens. We have named this locus chem. Lethality of the new alleles as homozygous zygotic mutants is not completely penetrant, and they have an extended phenocritical period. Like the original allele, a fraction of mutant embryos die with cuticular defects, notably head involution and dorsal closure defects. Embryonic defects are much more extreme in germline clones, where the majority of mutant embryos die during embryogenesis and do not form cuticle, implying a strong chem maternal contribution. chem mutations genetically interact with mutations in cytoskeletal genes (arm) and with mutations in the epithelial polarity genes coracle, crumbs, and yurt. chem mutants dorsal open defects are similar to those present in yurt mutants, and, likewise, they have epithelial polarity defects. chem1 and chem3 mutations suppress yurt3, and chem3 mutants suppress crumbs1 mutations. In contrast, chem1 and coracle2 mutations enhance each other. Compared to controls, in chem mutants in embryonic lateral epithelia Crumbs expression is mislocalized and reduced, Coracle is increased and mislocalized basally at embryonic stages 13–14, then reduced at stage 16. Arm expression has a similar pattern but levels are reduced. PMID:27920954

  2. Legal issues for chem-bioinformatics models.

    PubMed

    Duardo-Sanchez, Aliuska; Gonzalez-Diaz, Humberto

    2013-01-01

    Chem-Bioinformatic models connect the chemical structure of drugs and/or targets (protein, gen, RNA, microorganism, tissue, disease...) with drug biological activity over this target. On the other hand, a systematic judicial framework is needed to provide appropriate and relevant guidance for addressing various computing techniques as applied to scientific research in biosciences frontiers. This article reviews both: the use of the predictions made with models for regulatory purposes and how to protect (in legal terms) the models of molecular systems per se, and the software used to seek them. First we review: i) models as a tool for regulatory purposes, ii) Organizations Involved with Validation of models, iii) Regulatory Guidelines and Documents for models, iv) Models for Human Health and Environmental Endpoint, and v) Difficulties to Validation of models, and other issues. Next, we focused on the legal protection of models and software; including: a short summary of topics, and methods for legal protection of computer software. We close the review with a section that treats the taxes in software use.

  3. Tagged Ozone Mechanisms for WRF-Chem

    NASA Astrophysics Data System (ADS)

    Lupascu, A.; Coates, J.; Mar, K. A.; Butler, T. M.

    2016-12-01

    Surface ozone is a secondary air pollutant that affects human health and vegetation, and is a key ingredient of smog. It has been shown that the background O3 concentrations have increased during the last several decades due to the increase of overall global anthropogenic emissions of O3 precursors (NOx and VOCs). Cities are facing serious challenges in surface ozone pollution due to increased urbanization and vehicle use. Attribution of ozone concentration to local, regional, and remote sources is an important component of the design of mitigation strategies. These strategies rely on accurate predictions of O3 and the impact of source emissions of NOx and VOC from surface anthropogenic sources, fires, soil, lightning, and the stratosphere on total O3 production. Thus, a chemical model in which emissions of NO or VOCs and corresponding resulting products are "tagged" and followed to the production of ozone could be very helpful for these strategies. Here we present a system for attribution of surface ozone separately to each of these precursors, as well as transport from the lateral boundary and the stratosphere in WRF-Chem. This technique adds tracers to the chemical mechanism, with the possibility of specifying an arbitrary number of tags per model run.

  4. NARSTO EPA SS ST LOUIS AIR CHEM PM MET DATA

    Atmospheric Science Data Center

    2014-05-07

    NARSTO EPA SS ST LOUIS AIR CHEM PM MET DATA Project Title:  NARSTO ... Amount Surface Pressure Solar Radiation Surface Air Temperature Particulates Trace Metals Order Data:  ... Data Guide Documents:  St Louis Air Chem Guide St Louis Final Report  (PDF) St Louis QA ...

  5. Engineering Analysis in the Chem-E-Car Competition

    ERIC Educational Resources Information Center

    Lewis, Randy S.; Moshfeghian, Aliakbar; Madihally, Sundararajan V.

    2006-01-01

    The AIChE Chem-E-Car competition provides students an opportunity to demonstrate their design and teamwork skills. Engineering analysis is not required at the national competition and is often not applied. This work describes an engineering analysis of a Chem-E-Car to predict the distance traveled by the car. Engineering analysis is advantageous…

  6. CHEM Study in an English School--A Personal View

    ERIC Educational Resources Information Center

    Shayer, M.

    1970-01-01

    Critiques the content and structure of the CHEM Study course as it is used in English schools. RElates student achievement and criticisms of the course over a three year period. Compares CHEM Study with the English A-level chemistry. Author offers his assessment of the course in terms of Skinner's learning theory and American cultural influences.…

  7. ChemOkey: A Game to Reinforce Nomenclature

    ERIC Educational Resources Information Center

    Kavak, Nusret

    2012-01-01

    Learning the symbolic language of chemistry is a difficult task that can be frustrating for students. This article introduces a game, ChemOkey, that can help students learn the names and symbols of common ions and their compounds in a fun environment. ChemOkey, a game similar to Rummikub, is played with a set of 106 plastic or wooden tiles. The…

  8. ChemOkey: A Game to Reinforce Nomenclature

    ERIC Educational Resources Information Center

    Kavak, Nusret

    2012-01-01

    Learning the symbolic language of chemistry is a difficult task that can be frustrating for students. This article introduces a game, ChemOkey, that can help students learn the names and symbols of common ions and their compounds in a fun environment. ChemOkey, a game similar to Rummikub, is played with a set of 106 plastic or wooden tiles. The…

  9. Mars Rock Rocknest 3 Imaged by Curiosity ChemCam

    NASA Image and Video Library

    2012-11-26

    This view of a rock called Rocknest 3 combines two images taken by the Chemistry and Camera ChemCam instrument on the NASA Mars rover Curiosity and indicates five spots where ChemCam had hit the rock with laser pulses to check its composition.

  10. A Java API for working with PubChem datasets.

    PubMed

    Southern, Mark R; Griffin, Patrick R

    2011-03-01

    PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose-response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. http://code.google.com/p/pubchemdb.

  11. Engineering Analysis in the Chem-E-Car Competition

    ERIC Educational Resources Information Center

    Lewis, Randy S.; Moshfeghian, Aliakbar; Madihally, Sundararajan V.

    2006-01-01

    The AIChE Chem-E-Car competition provides students an opportunity to demonstrate their design and teamwork skills. Engineering analysis is not required at the national competition and is often not applied. This work describes an engineering analysis of a Chem-E-Car to predict the distance traveled by the car. Engineering analysis is advantageous…

  12. PubChem applications in drug discovery: a bibliometric analysis.

    PubMed

    Cheng, Tiejun; Pan, Yongmei; Hao, Ming; Wang, Yanli; Bryant, Stephen H

    2014-11-01

    A bibliometric analysis of PubChem applications is presented by reviewing 1132 research articles. The massive volume of chemical structure and bioactivity data in PubChem and its online services have been used globally in various fields including chemical biology, medicinal chemistry and informatics research. PubChem supports drug discovery in many aspects such as lead identification and optimization, compound-target profiling, polypharmacology studies and unknown chemical identity elucidation. PubChem has also become a valuable resource for developing secondary databases, informatics tools and web services. The growing PubChem resource with its public availability offers support and great opportunities for the interrogation of pharmacological mechanisms and the genetic basis of diseases, which are vital for drug innovation and repurposing.

  13. PubChem applications in drug discovery: a bibliometric analysis

    PubMed Central

    Cheng, Tiejun; Pan, Yongmei; Hao, Ming; Wang, Yanli; Bryant, Stephen H.

    2014-01-01

    A bibliometric analysis of PubChem applications is presented by reviewing 1132 research articles. The massive volume of chemical structure and bioactivity data in PubChem and its online services has been used globally in various fields including chemical biology, medicinal chemistry and informatics research. PubChem supports drug discovery in many aspects such as lead identification and optimization, compound–target profiling, polypharmacology studies and unknown chemical identity elucidation. PubChem has also become a valuable resource for developing secondary databases, informatics tools and web services. The growing PubChem resource with its public availability offers support and great opportunities for the interrogation of pharmacological mechanisms and the genetic basis of diseases, which are vital for drug innovation and repurposing. PMID:25168772

  14. PubChem BioAssay: 2017 update

    PubMed Central

    Wang, Yanli; Bryant, Stephen H.; Cheng, Tiejun; Wang, Jiyao; Gindulyte, Asta; Shoemaker, Benjamin A.; Thiessen, Paul A.; He, Siqian; Zhang, Jian

    2017-01-01

    PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing. PMID:27899599

  15. Evaluation of the Chem 1 analyzer.

    PubMed

    Biosca, C; Antoja, F; Sierra, C; Aluma, A; Farre, J; Alsina, M J; Galimany, R

    1991-01-01

    The selective multitest Technicon Chem 1 analyser was evaluated according to the guidelines of the 'Comisión de Instrumentación de la Sociedad Española de Química Clínica', and the protocols of the 'European Committee for Clinical Laboratory Standards' and 'Commission de validation de techniques' of the 'Société Française de Biologie Clinique'. The evaluation was performed in three steps: evaluation in routine conditions, assessment of the interferences and study of practicability. Under routine working conditions, eighteen constituents were studied. Within-run imprecision ranged from 0.6% (CV) for gamma-GT to 4.7% (CV) for AST. Between-run imprecision ranged from 1.6% (CV) for ion sodium to 5.5% (CV) for creatinine. Specimen related carry-over was not within the samples; specimen independent carry-over was found in some of the constituents studied. The relative inaccuracy is good for all the constituents assayed. Haemoglobin (290 mumol.l1) showed a positive interference with urate at three concentration levels (low, medium and high). Bilirubin (up to 300 mumol.l-1) caused a negative interference with creatinine at three concentration levels. Turbidity (trigliceride up to 4 mumol.l-1) stated a positive interference with creatinine at three concentration levels and with AST at two concentration levels (low and medium). Turbidity also caused a negative interference with urate at three concentration levels and with urea at two concentration levels (low and medium).

  16. One year of chemical diversity seen by ChemCam at Gale crater, Mars

    NASA Astrophysics Data System (ADS)

    Gasnault, Olivier; Wiens, Roger; Maurice, Sylvestre; Meslin, Pierre-Yves; Forni, Olivier; Leveillé, Richard; Bridges, Nathan; Lasue, Jérémie; Le Mouélic, Stéphane; Mangold, Nicolas; Sautter, Violaine

    2014-05-01

    evidences are provided by the discovery with ChemCam of three rocks with Mn-enriched coatings [11]. There are also some indications through the measurement of lithium abundance for a low level aqueous alteration pulling the alkalis out to the surface [12]. The influx of subsurface water must have been limited though otherwise the Li concentration in the soils should be higher than what ChemCam measured (first detection on Mars [12]). References: [1] Meslin et al. (2013) Science, 341, doi:10.1126/science.1238670 ; [2] Schröder et al. (2013) Europ. Planet. Sci. Congress, 120 ; [3] Cousin et al. (2014) Lunar Planet. Conf., 1278; [4] Sautter et al. (2014) J. Geophys. Res., doi:10.1002/2013JE004472; [5] Grotzinger et al. (2013) Science, doi:10.1126/science.1242777; [6] McLennan et al. (2013) Science, doi:10.1126/science.1244734; [7] Vaniman et al. (2013) Science, doi:10.1126/science.1243480; [8] Siebach et al. (2013) Am. Geophys. Union Assembly, P13D-07; [9] Leveillé et al. (2013) Am. Geophys. Union Assembly, P13D-08; [10] Nachon et al. (2014) Lunar Planet. Conf.; [11] Lanza et al. (2014) Lunar Planet. Conf.; [12] Ollila et al. (2013) J. Geophys. Res., doi:10.1002/2013JE004517.

  17. RESRAD-CHEM: A computer code for chemical risk assessment

    SciTech Connect

    Cheng, J.J.; Yu, C.; Hartmann, H.M.; Jones, L.G.; Biwer, B.M.; Dovel, E.S.

    1993-10-01

    RESRAD-CHEM is a computer code developed at Argonne National Laboratory for the U.S. Department of Energy to evaluate chemically contaminated sites. The code is designed to predict human health risks from multipathway exposure to hazardous chemicals and to derive cleanup criteria for chemically contaminated soils. The method used in RESRAD-CHEM is based on the pathway analysis method in the RESRAD code and follows the U.S. Environmental Protection Agency`s (EPA`s) guidance on chemical risk assessment. RESRAD-CHEM can be used to evaluate a chemically contaminated site and, in conjunction with the use of the RESRAD code, a mixed waste site.

  18. Comment on ``The application of the thermodynamic perturbation theory to study the hydrophobic hydration'' [J. Chem. Phys. 139, 024101 (2013)

    NASA Astrophysics Data System (ADS)

    Graziano, Giuseppe

    2013-09-01

    It is shown that the behaviour of the hydration thermodynamic functions obtained in the 3D Mercedes-Benz model of water by Mohoric et al. [J. Chem. Phys. 139, 024101 (2013)] is not qualitatively correct with respect to experimental data for a solute whose diameter is 1.5-fold larger than that of a water molecule. It is also pointed out that the failure is due to the fact that the used 3D Mercedes-Benz model of water [A. Bizjak, T. Urbic, V. Vlachy, and K. A. Dill, J. Chem. Phys. 131, 194504 (2009)] does not reproduce in a quantitatively correct manner the peculiar temperature dependence of water density.

  19. ChemEx: information extraction system for chemical data curation.

    PubMed

    Tharatipyakul, Atima; Numnark, Somrak; Wichadakul, Duangdao; Ingsriswang, Supawadee

    2012-01-01

    Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure image recognition and text mining together. We have developed ChemEx, a chemical information extraction system. ChemEx processes both text and images in publications. Text annotator is able to extract compound, organism, and assay entities from text content while structure image recognition enables translation of chemical raster images to machine readable format. A user can view annotated text along with summarized information of compounds, organism that produces those compounds, and assay tests. ChemEx facilitates and speeds up chemical data curation by extracting compounds, organisms, and assays from a large collection of publications. The software and corpus can be downloaded from http://www.biotec.or.th/isl/ChemEx.

  20. ChemPreview: an augmented reality-based molecular interface.

    PubMed

    Zheng, Min; Waller, Mark P

    2017-05-01

    Human computer interfaces make computational science more comprehensible and impactful. Complex 3D structures such as proteins or DNA are magnified by digital representations and displayed on two-dimensional monitors. Augmented reality has recently opened another door to access the virtual three-dimensional world. Herein, we present an augmented reality application called ChemPreview with the potential to manipulate bio-molecular structures at an atomistic level. ChemPreview is available at https://github.com/wallerlab/chem-preview/releases, and is built on top of the Meta 1 platform https://www.metavision.com/. ChemPreview can be used to interact with a protein in an intuitive way using natural hand gestures, thereby making it appealing to computational chemists or structural biologists. The ability to manipulate atoms in real world could eventually provide new and more efficient ways of extracting structural knowledge, or designing new molecules in silico. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Comparing UCLALES-SALSA and WRF-Chem LES

    NASA Astrophysics Data System (ADS)

    Tonttila, Juha; Dunne, Eimear; Ahola, Jaakko; Korhonen, Hannele; Kokkola, Harri; Romakkaniemi, Sami

    2016-04-01

    The new UCLALES-SALSA model, which uses a sectional representation of aerosols and cloud droplets, is compared against the LES configuration of the established WRF-Chem model. Two configurations of WRF-Chem are compared: the first using the sectional MOSAIC aerosol representation, and the second using the modal MADE/SORGAM representation. Both sets of WRF-Chem simulations use the two-moment Morrisson bulk cloud scheme. Wherever possible, the three sets of simulations have identical processes and initial conditions. By comparing UCLALES-SALSA against an established model in an ideal scenario, we demonstrate that the new model provides a realistic representation of warm cloud processes. The two configurations of WRF-Chem make it possible (to an extent) to isolate whether differences in model outputs are due to meteorological or microphysical effects.

  2. Curiosity ChemCam Analyzes Rocks, Soils and Dust

    NASA Image and Video Library

    2013-04-08

    This diagram shows how materials analyzed by the ChemCam instrument on NASA Curiosity Mars rover during the first 100 Martian days of the mission differed with regard to hydrogen content horizontal axis and alkali vertical axis.

  3. Drilled Hole and ChemCam Marks at Cumberland

    NASA Image and Video Library

    2013-06-05

    The Chemistry and Camera ChemCam instrument on NASA Mars rover Curiosity was used to check the composition of gray tailings from the hole in rock target Cumberland that the rover drilled on May 19, 2013.

  4. ChemCam Mast Unit Being Prepared for Laser Firing

    NASA Image and Video Library

    2010-12-23

    Researchers prepare for a test of the Chemistry and Camera ChemCam instrument that will fly on NASA Mars Science Laboratory mission; researchers are preparing the instrument mast unit for a laser firing test.

  5. Comment on "Fe2: As simple as a Herculean labour. Neutral (Fe2), cationic (Fe2+), and anionic (Fe2-) species" [J. Chem. Phys. 142, 244304 (2015)

    NASA Astrophysics Data System (ADS)

    Hoyer, Chad E.; Li Manni, Giovanni; Truhlar, Donald G.; Gagliardi, Laura

    2016-01-01

    A recent paper on Fe2 [A. Kalemos, J. Chem. Phys. 142, 244304 (2015)] critiqued our previous work on the system [Hoyer et al., J. Chem. Phys. 141, 204309 (2014)]. In this comment, we explain the nature of our previously reported potential energy curve for Fe2 and we discuss our computed properties for Fe2. Additionally, we fix a labeling error that was present in our previous work, although this error is unrelated to the main point of discussion.

  6. Chemerin-ChemR23 Signaling in Tooth Development

    PubMed Central

    Ohira, T.; Spear, D.; Azimi, N.; Andreeva, V.; Yelick, P.C.

    2012-01-01

    Our long-term goal is to identify and characterize molecular mechanisms regulating tooth development, including those mediating the critical dental epithelial-dental mesenchymal (DE-DM) cell interactions required for normal tooth development. The goal of this study was to investigate Chemerin (Rarres2)/ChemR23(Cmklr1) signaling in DE-DM cell interactions in normal tooth development. Here we present, for the first time, tissue-specific expression patterns of Chemerin and ChemR23 in mouse tooth development. We show that Chemerin is expressed in cultured DE progenitor cells, while ChemR23 is expressed in cultured DM cells. Moreover, we demonstrate that ribosomal protein S6 (rS6) and Akt, downstream targets of Chemerin/ChemR23 signaling, are phosphorylated in response to Chemerin/ChemR23 signaling in vitro and are expressed in mouse tooth development. Together, these results suggest roles for Chemerin/ChemR23-mediated DE-DM cell signaling during tooth morphogenesis. PMID:23053848

  7. ChromPlot for MicroChemLab

    SciTech Connect

    Lewis, Patrick R.

    2001-12-19

    The software entitled "ChromPlot for MicroChemLab" is used to collect, display, and save data from the Sandia National Laboratories chemical analysis system dubbed MicroChemLab. Sensor data is streamed from a MicroChemLab unit into a computer thru RS-232 in a manner that is not amenable to plotting. Also, there is no direct way to start and stop the unit as is. This software rearranges the data into something that can be easily plotted in real-time then save the data into a text file. In addition, this software provides the users a means to start and stop the hardware. This software was written specifically for MicroChemLab. MicroChemLab data is delivered at 6- 7 pts/sec/channel in a two-channel system for 1-2 min. This code is written around that premise. It is written for Pentium or higher machines running Windows 9x/Me/NT/2000/XP. This software was not developed under the BMS CRADA; it is software we use in the lab for our own testing. Bristol Meyers Squibb (BMS) will use this software for testing an online process monitor based on MicroChemLab. They have not indicated their interest in marketing our device or the software.

  8. AEGIS Automated Targeting for the MSL ChemCam Instrument

    NASA Astrophysics Data System (ADS)

    Estlin, T.; Anderson, R. C.; Blaney, D. L.; Bornstein, B.; Burl, M. C.; Castano, R.; Gaines, D.; Judd, M.; Thompson, D. R.; Wiens, R. C.

    2013-12-01

    The Autonomous Exploration for Gathering Increased Science (AEGIS) system enables automated science data collection by a planetary rover. AEGIS has been in use on the Mars Exploration Rover (MER) mission Opportunity rover since 2010 to provide onboard targeting of the MER Panoramic Camera based on scientist-specified objectives. AEGIS is now being applied for use with the Mars Science Laboratory (MSL) mission ChemCam spectrometer. ChemCam uses a Laser Induced Breakdown Spectrometer (LIBS) to analyze the elemental composition of rocks and soil from up to seven meters away. ChemCam's tightly-focused laser beam (350-550 um) enables targeting of very fine-scale terrain features. AEGIS is being applied in two ways to help ChemCam collect valuable science data. The first application is to enable automated targeting of ChemCam during or after or in the middle of long drives. The majority of ChemCam measurements are collected by allowing the science team to select specific targets in rover images. However this requires the rover to stay in the same area while images are downlinked, analyzed for targets, and new commands uplinked. The only data that can be acquired without this communication cycle is via blind targeting, where measurements are often of soil patches vs. instead of more valuable targets such as rocks with specific properties. AEGIS is being applied to automatically analyze images onboard and select targets for ChemCam analysis. This approach allows the rover to autonomously select and sequence targeted measurements in an opportunistic fashion at different points along the rover's drive path. Rock targets can be prioritized for measurement based on various geologically relevant features, including size, shape and albedo. A second application is to enable intelligent pointing refinement of ChemCam when acquiring data of small targets, such as veins or concretions that are only a few millimeters wide. Due to backlash and other pointing challenges, it can often

  9. Alkali trace elements in Gale crater, Mars, with ChemCam: Calibration update and geological implications

    NASA Astrophysics Data System (ADS)

    Payré, V.; Fabre, C.; Cousin, A.; Sautter, V.; Wiens, R. C.; Forni, O.; Gasnault, O.; Mangold, N.; Meslin, P.-Y.; Lasue, J.; Ollila, A.; Rapin, W.; Maurice, S.; Nachon, M.; Le Deit, L.; Lanza, N.; Clegg, S.

    2017-03-01

    The Chemistry Camera (ChemCam) instrument onboard Curiosity can detect minor and trace elements such as lithium, strontium, rubidium, and barium. Their abundances can provide some insights about Mars' magmatic history and sedimentary processes. We focus on developing new quantitative models for these elements by using a new laboratory database (more than 400 samples) that displays diverse compositions that are more relevant for Gale crater than the previous ChemCam database. These models are based on univariate calibration curves. For each element, the best model is selected depending on the results obtained by using the ChemCam calibration targets onboard Curiosity. New quantifications of Li, Sr, Rb, and Ba in Gale samples have been obtained for the first 1000 Martian days. Comparing these data in alkaline and magnesian rocks with the felsic and mafic clasts from the Martian meteorite NWA7533—from approximately the same geologic period—we observe a similar behavior: Sr, Rb, and Ba are more concentrated in soluble- and incompatible-element-rich mineral phases (Si, Al, and alkali-rich). Correlations between these trace elements and potassium in materials analyzed by ChemCam reveal a strong affinity with K-bearing phases such as feldspars, K-phyllosilicates, and potentially micas in igneous and sedimentary rocks. However, lithium is found in comparable abundances in alkali-rich and magnesium-rich Gale rocks. This very soluble element can be associated with both alkali and Mg-Fe phases such as pyroxene and feldspar. These observations of Li, Sr, Rb, and Ba mineralogical associations highlight their substitution with potassium and their incompatibility in magmatic melts.

  10. PubChem BioAssay: 2014 update

    PubMed Central

    Wang, Yanli; Suzek, Tugba; Zhang, Jian; Wang, Jiyao; He, Siqian; Cheng, Tiejun; Shoemaker, Benjamin A.; Gindulyte, Asta; Bryant, Stephen H.

    2014-01-01

    PubChem’s BioAssay database (http://pubchem.ncbi.nlm.nih.gov) is a public repository for archiving biological tests of small molecules generated through high-throughput screening experiments, medicinal chemistry studies, chemical biology research and drug discovery programs. In addition, the BioAssay database contains data from high-throughput RNA interference screening aimed at identifying critical genes responsible for a biological process or disease condition. The mission of PubChem is to serve the community by providing free and easy access to all deposited data. To this end, PubChem BioAssay is integrated into the National Center for Biotechnology Information retrieval system, making them searchable by Entrez queries and cross-linked to other biomedical information archived at National Center for Biotechnology Information. Moreover, PubChem BioAssay provides web-based and programmatic tools allowing users to search, access and analyze bioassay test results and metadata. In this work, we provide an update for the PubChem BioAssay resource, such as information content growth, new developments supporting data integration and search, and the recently deployed PubChem Upload to streamline chemical structure and bioassay submissions. PMID:24198245

  11. PubChem as a public resource for drug discovery.

    PubMed

    Li, Qingliang; Cheng, Tiejun; Wang, Yanli; Bryant, Stephen H

    2010-12-01

    PubChem is a public repository of small molecules and their biological properties. Currently, it contains more than 25 million unique chemical structures and 90 million bioactivity outcomes associated with several thousand macromolecular targets. To address the potential utility of this public resource for drug discovery, we systematically summarized the protein targets in PubChem by function, 3D structure and biological pathway. Moreover, we analyzed the potency, selectivity and promiscuity of the bioactive compounds identified for these biological targets, including the chemical probes generated by the NIH Molecular Libraries Program. As a public resource, PubChem lowers the barrier for researchers to advance the development of chemical tools for modulating biological processes and drug candidates for disease treatments. Published by Elsevier Ltd.

  12. Applying RESRAD-CHEM for chemical risk assessment

    SciTech Connect

    Cheng, J.J.; Yu, C.

    1995-07-01

    RESRAD-CHEM is a multiple pathway analysis computer code to evaluate chemically contaminated sites; it was developed at Argonne National Laboratory for the US Department of Energy. The code is designed to predict human health risks from exposure to hazardous chemicals and to derive cleanup criteria for chemically contaminated soils. It consists of environmental fate and transport models and is capable of predicting chemical concentrations over time in different environmental media. The methodology used in RESRAD-CHEM for exposure assessment and risk characterization follows the US Environmental Protection Agency`s guidance on Human Health Evaluation for Superfund. A user-friendly interface is incorporated for entering data, operating the code, and displaying results. RESRAD-CHEM is easy to use and is a powerful tool to assess chemical risk from environmental exposure.

  13. Understanding chemical and facies variability in the Murray Formation, Gale crater, from ChemCam data

    NASA Astrophysics Data System (ADS)

    Rivera-Hernandez, Frances; Mangold, Nicolas; Sumner, Dawn Y.; Nachon, Marion; Wiens, Roger C.; Maurice, Sylvestre; Forni, Olivier; Frydenvang, Jens; Newsom, Horton; Dehouck, Erwin; Payre, Valerie

    2017-04-01

    The primary goal of the Mars Science Laboratory (MSL) mission is to determine if habitable environments existed on Mars [1]. To evaluate the potential for habitability, reconstructing the transport and depositional history of the sedimentary rocks at Gale Crater relies on the accurate interpretation of changes in depositional facies. This study uses ChemCam data to identify and characterize chemical variations that may be due to grain size and possibly facies changes within the Murray formation, a fluvio-lacustrine unit in Gale Crater dominated by interbedded mudstones and fine-grained sandstones [1]. These analyses compliment current efforts by APXS and ChemCam in reconstructing a chemostratigraphic record for the Curiosity rover traverse [e.g.,2,3]. Textural analyses from images taken by the Mars Hand Lens Imager (MAHLI), and the ChemCam Remote Micro Imager (RMI), and ChemCam chemical data were used to exclude targets with resolvable diagenetic features. Remaining targets were analyzed for chemical heterogeneity using the Gini Index (G), where G=0 indicates no point-to-point chemical variation and G=1 for a completely heterogeneous target [4]. Sandstones with grains larger than the laser beam diameter ( 0.3-0.5 mm; medium sand) typically have G>0.25 [4]. Hence, heterogeneity in composition among closely spaced points on a single target may reflect variations in mineralogy among individual sand grains or concentrations of grains. In contrast, homogeneous rocks may have homogeneous grain compositions or only contain grains smaller than sand. Thus, even when the presence of sand grains cannot be demonstrated from images, their presence can be inferred using the Gini Index. Preliminary analyses from sols 1400-1500 suggest that the abundances of FeOT, SiO2, Al2O3, and TiO2 do not vary significantly in individual rock targets (G<0.1) or between targets. In contrast, CaO, MgO, K2O, and Na2O vary more from target to target (G>0.1). Most variations between targets are

  14. BioCom? Is that Like ChemCom?

    ERIC Educational Resources Information Center

    Leonard, William H.; And Others

    1996-01-01

    Describes the philosophy, development, content structure, and general instructional strategy of BioCom, an introductory biology curriculum for the heterogeneously mixed high school science classroom. Discusses recent recommendations by national commissions and science education research and similarities and differences between BioCom and ChemCom.…

  15. Spark Generated by ChemCam Laser During Tests

    NASA Image and Video Library

    2010-09-21

    The ChemCam instrument for NASA Mars Science Laboratory mission uses a pulsed laser beam to vaporize a pinhead-size target, producing a flash of light from the ionized material plasma that can be analyzed to identify chemical elements in the target.

  16. AutoClickChem: Click Chemistry in Silico

    PubMed Central

    Durrant, Jacob D.; McCammon, J. Andrew

    2012-01-01

    Academic researchers and many in industry often lack the financial resources available to scientists working in “big pharma.” High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu. PMID:22438795

  17. ChemEx: information extraction system for chemical data curation

    PubMed Central

    2012-01-01

    Background Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure image recognition and text mining together. Results We have developed ChemEx, a chemical information extraction system. ChemEx processes both text and images in publications. Text annotator is able to extract compound, organism, and assay entities from text content while structure image recognition enables translation of chemical raster images to machine readable format. A user can view annotated text along with summarized information of compounds, organism that produces those compounds, and assay tests. Conclusions ChemEx facilitates and speeds up chemical data curation by extracting compounds, organisms, and assays from a large collection of publications. The software and corpus can be downloaded from http://www.biotec.or.th/isl/ChemEx. PMID:23282330

  18. ChemGPS-NPWeb: chemical space navigation online

    NASA Astrophysics Data System (ADS)

    Rosén, Josefin; Lövgren, Anders; Kogej, Thierry; Muresan, Sorel; Gottfries, Johan; Backlund, Anders

    2009-04-01

    Internet has become a central source for information, tools, and services facilitating the work for medicinal chemists and drug discoverers worldwide. In this paper we introduce a web-based public tool, ChemGPS-NPWeb (http://chemgps.bmc.uu.se), for comprehensive chemical space navigation and exploration in terms of global mapping onto a consistent, eight dimensional map over structure derived physico-chemical characteristics. ChemGPS-NPWeb can assist in compound selection and prioritization; property description and interpretation; cluster analysis and neighbourhood mapping; as well as comparison and characterization of large compound datasets. By using ChemGPS-NPWeb, researchers can analyze and compare chemical libraries in a consistent manner. In this study it is demonstrated how ChemGPS-NPWeb can assist in interpreting results from two large datasets tested for activity in biological assays for pyruvate kinase and Bcl-2 family related protein interactions, respectively. Furthermore, a more than 30-year-old suggestion of "chemical similarity" between the natural pigments betalains and muscaflavins is tested.

  19. ChemCam Depth Profiles at Gale Crater to Assess Coating and Alteration Distribution and Chemistry

    NASA Astrophysics Data System (ADS)

    Blaney, D. L.; Clegg, S. M.; Wiens, R. C.; Maurice, S.; Lanza, N.; Bridges, N.

    2014-12-01

    Coating and rock alteration formation on Mars is constrained by both the availability of water and rock composition. Detection of these materials depends on the both formation rate and the rate of abrasion that these alteration products and coatings experience. ChemCam on the Curiosity rover can investigate coating/alteration formation and preservation by looking at chemical composition as a function of depth into the rock. ChemCam LIBS works by firing a laser focused to a 350 - 550 mm diameter spot that produces plasma from the rock. Spectra of elemental emission lines are recorded from 240-850 nm and used to determine the elemental composition of the rock. A chemical composition is generated from each individual spectrum. Each laser firing penetrates deeper into the rock allowing for a composition as a function of depth to be determined. By comparing geochemical trends from the beginning and end of the observations evidence for coatings and alteration can be assessed by geologic setting and rock type. Previous ChemCam work has identified Li variations (Ollila et al 2014) and MnO coatings (Lanza et al 2014) on a few rocks with high abundances of these elements. However this work is the first systematic assessment of alteration and coatings in the entire data set. From landing until Sol 583 there were 2,610 good quality ChemCam rock and outcrop observations. These measurements were assessed for internal elemental composition variability by the calculation of heterogeneity index. Only 7% (178) had positive internal heterogeneity. However, internal heterogeneity can be due to other factors besides coatings and alteration. Thick soil coverage and differential sampling of materials in coarse-grained rocks also produce positive heterogeneity indexes. The actual number of potential coatings at Gale is significantly lower. For most of Gale, current geochemical alteration rates are slower the rate of abrasion. This result is consistent with limited availability of water in

  20. Characterising Biomass Burning Aerosol in WRF-Chem using the Volatility Basis Set, with Evaluation against SAMBBA Flight Data

    NASA Astrophysics Data System (ADS)

    Lowe, D.; Topping, D. O.; Archer-Nicholls, S.; Darbyshire, E.; Morgan, W.; Liu, D.; Allan, J. D.; Coe, H.; McFiggans, G.

    2015-12-01

    The burning of forests in the Amazonia region is a globally significant source of carbonaceous aerosol, containing both absorbing and scattering components [1]. In addition biomass burning aerosol (BBA) are also efficient cloud condensation nuclei (CCN), modifying cloud properties and influencing atmospheric circulation and precipitation tendencies [2]. The impacts of BBA are highly dependent on their size distribution and composition. A bottom-up emissions inventory, the Brazilian Biomass Burning Emissions Model (3BEM) [3], utilising satellite products to generate daily fire emission maps is used. Injection of flaming emissions within the atmospheric column is simulated using both a sub-grid plume-rise parameterisation [4], and simpler schemes, within the Weather Research and Forecasting Model with Chemistry (WRF-Chem, v3.4.1) [5]. Aerosol dynamics are simulated using the sectional MOSAIC scheme [6], incorporating a volatility basis set (VBS) treatment of organic aerosol [7]. For this work we have modified the 9-bin VBS to use the biomass burning specific scheme developed by May et al. [8]. The model has been run for September 2012 over South America (at a 25km resolution). We will present model results evaluating the modelled aerosol vertical distribution, size distribution, and composition against measurements taken by the FAAM BAe-146 research aircraft during the SAMBBA campaign. The main focus will be on investigating the factors controlling the vertical gradient of the organic mass to black carbon ratio of the measured aerosol. This work is supported by the Nature Environment Research Council (NERC) as part of the SAMBBA project under grant NE/J010073/1. [1] D. G. Streets et al., 2004, J. Geophys. Res., 109, D24212. [2] M. O. Andreae et al., 2004, Science, 303, 1337-1342. [3] K. Longo et al., 2010, Atmos. Chem. Phys., 10, 5,785-5,795. [4] S. Freitas et al., 2007, Atmos. Chem. Phys., 7, 3,385-3,398. [5] S. Archer-Nicholls et al., 2015, Geosci. Model Dev., 8

  1. Application of distance correction to ChemCam laser-induced breakdown spectroscopy measurements

    DOE PAGES

    Mezzacappa, A.; Melikechi, N.; Cousin, A.; ...

    2016-04-04

    Laser-induced breakdown spectroscopy (LIBS) provides chemical information from atomic, ionic, and molecular emissions from which geochemical composition can be deciphered. Analysis of LIBS spectra in cases where targets are observed at different distances, as is the case for the ChemCam instrument on the Mars rover Curiosity, which performs analyses at distances between 2 and 7.4 m is not a simple task. Previously, we showed that spectral distance correction based on a proxy spectroscopic standard created from first-shot dust observations on Mars targets ameliorates the distance bias in multivariate-based elemental-composition predictions of laboratory data. In this work, we correct an expandedmore » set of neutral and ionic spectral emissions for distance bias in the ChemCam data set. By using and testing different selection criteria to generate multiple proxy standards, we find a correction that minimizes the difference in spectral intensity measured at two different distances and increases spectral reproducibility. When the quantitative performance of distance correction is assessed, there is improvement for SiO2, Al2O3, CaO, FeOT, Na2O, K2O, that is, for most of the major rock forming elements, and for the total major-element weight percent predicted. But, for MgO the method does not provide improvements while for TiO2, it yields inconsistent results. Additionally, we observed that many emission lines do not behave consistently with distance, evidenced from laboratory analogue measurements and ChemCam data. This limits the effectiveness of the method.« less

  2. Application of distance correction to ChemCam laser-induced breakdown spectroscopy measurements

    SciTech Connect

    Mezzacappa, A.; Melikechi, N.; Cousin, A.; Wiens, R. C.; Lasue, J.; Clegg, S. M.; Tokar, R.; Bender, S.; Lanza, N. L.; Maurice, S.; Berger, G.; Forni, O.; Gasnault, O.; Dyar, M. D.; Boucher, T.; Lewin, E.; Fabre, C.

    2016-04-04

    Laser-induced breakdown spectroscopy (LIBS) provides chemical information from atomic, ionic, and molecular emissions from which geochemical composition can be deciphered. Analysis of LIBS spectra in cases where targets are observed at different distances, as is the case for the ChemCam instrument on the Mars rover Curiosity, which performs analyses at distances between 2 and 7.4 m is not a simple task. Previously, we showed that spectral distance correction based on a proxy spectroscopic standard created from first-shot dust observations on Mars targets ameliorates the distance bias in multivariate-based elemental-composition predictions of laboratory data. In this work, we correct an expanded set of neutral and ionic spectral emissions for distance bias in the ChemCam data set. By using and testing different selection criteria to generate multiple proxy standards, we find a correction that minimizes the difference in spectral intensity measured at two different distances and increases spectral reproducibility. When the quantitative performance of distance correction is assessed, there is improvement for SiO2, Al2O3, CaO, FeOT, Na2O, K2O, that is, for most of the major rock forming elements, and for the total major-element weight percent predicted. But, for MgO the method does not provide improvements while for TiO2, it yields inconsistent results. Additionally, we observed that many emission lines do not behave consistently with distance, evidenced from laboratory analogue measurements and ChemCam data. This limits the effectiveness of the method.

  3. Application of distance correction to ChemCam laser-induced breakdown spectroscopy measurements

    NASA Astrophysics Data System (ADS)

    Mezzacappa, A.; Melikechi, N.; Cousin, A.; Wiens, R. C.; Lasue, J.; Clegg, S. M.; Tokar, R.; Bender, S.; Lanza, N. L.; Maurice, S.; Berger, G.; Forni, O.; Gasnault, O.; Dyar, M. D.; Boucher, T.; Lewin, E.; Fabre, C.

    2016-06-01

    Laser-induced breakdown spectroscopy (LIBS) provides chemical information from atomic, ionic, and molecular emissions from which geochemical composition can be deciphered. Analysis of LIBS spectra in cases where targets are observed at different distances, as is the case for the ChemCam instrument on the Mars rover Curiosity, which performs analyses at distances between 2 and 7.4 m is not a simple task. In our previous work we showed that spectral distance correction based on a proxy spectroscopic standard created from first-shot dust observations on Mars targets ameliorates the distance bias in multivariate-based elemental-composition predictions of laboratory data. In this work, we correct an expanded set of neutral and ionic spectral emissions for distance bias in the ChemCam data set. By using and testing different selection criteria to generate multiple proxy standards, we find a correction that minimizes the difference in spectral intensity measured at two different distances and increases spectral reproducibility. When the quantitative performance of distance correction is assessed, there is improvement for SiO2, Al2O3, CaO, FeOT, Na2O, K2O, that is, for most of the major rock forming elements, and for the total major-element weight percent predicted. However, for MgO the method does not provide improvements while for TiO2, it yields inconsistent results. In addition, we have observed that many emission lines do not behave consistently with distance, evidenced from laboratory analogue measurements and ChemCam data. This limits the effectiveness of the method.

  4. Waveguide-enhanced mid-infrared chem/bio sensors.

    PubMed

    Mizaikoff, Boris

    2013-11-21

    Despite providing the opportunity for directly sensing molecular constituents with inherent fingerprint specificity in the 2.5-20 μm spectral regime, mid-infrared optical sensing technologies have not yet achieved the same penetration in waveguide-based chem/bio sensing compared to related sensing schemes operating at visible and near-infrared frequencies. In this review, current advances in mid-infrared chem/bio sensor technology will be highlighted and contrasted with the prevalent bottlenecks that have to date limited a more widespread adoption of mid-infrared sensing devices. However, with the increasing availability of advanced light sources such as quantum cascade lasers and the advent of on-chip semiconductor waveguide technologies, a prosperous future of this sensing concept for label-free detection in environmental analysis, process monitoring, and bioanalytics is perceived.

  5. ChemCalc: a building block for tomorrow's chemical infrastructure.

    PubMed

    Patiny, Luc; Borel, Alain

    2013-05-24

    Web services, as an aspect of cloud computing, are becoming an important part of the general IT infrastructure, and scientific computing is no exception to this trend. We propose a simple approach to develop chemical Web services, through which servers could expose the essential data manipulation functionality that students and researchers need for chemical calculations. These services return their results as JSON (JavaScript Object Notation) objects, which facilitates their use for Web applications. The ChemCalc project http://www.chemcalc.org demonstrates this approach: we present three Web services related with mass spectrometry, namely isotopic distribution simulation, peptide fragmentation simulation, and molecular formula determination. We also developed a complete Web application based on these three Web services, taking advantage of modern HTML5 and JavaScript libraries (ChemDoodle and jQuery).

  6. ChemCam Passive Reflectance Spectroscopy at Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Johnson, J. R.; Bell, J. F.; Cloutis, E.; Bender, S.; Blaney, D. L.; Ehlmann, B. L.; Gasnault, O.; Kinch, K. M.; Le Mouelic, S.; Rice, M. S.; Wiens, R. C.; DeFlores, L.; Team, M.

    2013-12-01

    The Laser-Induced Breakdown Spectrometer (LIBS) portion of the ChemCam instrument on the Mars Science Laboratory Curiosity rover uses 3 dispersive spectrometers to cover the ultraviolet (240-342 nm), visible (382-469 nm) and visible/near-infrared (474-906 nm) spectral regions at high spectral (<0.5nm) and spatial (0.65mrad) resolution. In active LIBS mode, light emitted from a laser-generated plasma is dispersed onto these spectrometers and used to detect elemental emission lines. Typical observations include 3 msec-exposure 'dark' spectra (acquired with the LIBS laser off) used to remove the background signal from the LIBS measurement. Similar 'passive' observations of the ChemCam calibration target holder can be made at similar times of day and at identical exposure times (to minimize variations from dark current). Because this target exhibits ~95% flat reflectance in the ~400-900 nm region, radiance spectra ratios (surface/calibration target) can be normalized to known calibration target lab spectra to produce relative reflectance spectra (400-900 nm) with an estimated accuracy of 10-20%. Initial results replicated the known spectral shape and overall reflectance values of the ChemCam calibration targets and green color chip on the Mastcam calibration target. Dust contamination was evident, although dust on the ChemCam calibration targets is minimized by their tilted placement on the rover deck. All ChemCam targets that were sunlit during LIBS acquisition (~80% of all measurements) provide 'dark' spectra for which relative reflectance spectra can be obtained. Owing to the dusty nature of the Gale landing sites, passive spectra observed to date exhibit spectral shapes indicative of ferric phases, similar to spectra of palagonitic soils. Most spectra are bracketed in reflectance by typical 'bright' and 'dark' spectra from the OMEGA and CRISM orbital spectrometers. Preliminary Mastcam reflectance spectra are similar, providing additional confidence regarding the

  7. Atmospheric Chemistry of Volcanic Plumes in WRF-Chem

    NASA Astrophysics Data System (ADS)

    Surl, L.; Donohoue, D.; von Glasow, R.

    2014-12-01

    Volcanic eruptions are known to be a strong and concentrated source of reactive halogen species. The chemistry that these species are known to take part in include ozone-destruction cycles. Despite the potentially large perturbation to the chemistry of the troposphere that eruptions may cause the magnitude of such impacts on global and regional scales is largely unknown. We used WRF-Chem to investigate the influence of Mount Etna on the tropospheric chemistry of the Mediterranean region. The chemistry of bromine, chlorine and mercury has been added to the chemical mechanism CBMZ and we have coupled WRF-Chem with the emissions program PrepChem. We developed a simple parameterisation of the key multiphase reaction cycles involving halogens. Comparison with published field data shows that the model is able to reproduce the bromine explosion phenomenon seen in spectroscopic investigations of volcanic plumes. From the model results we are able to determine a detailed picture of the chemistry of a volcanic plume; results are presented which show how the character of the volcanic plume evolves as it is advected downwind. We determine the magnitude of Mt. Etna's regional influence under typical conditions. We also present results which show how the variation in volcanic output, as well as meteorological variation within the region, can influence the extent of Mt. Etna's regional impact. As WRF-Chem is very flexible, we also performed model runs fir other volcanoes.. The model results are compared to satellite measurements of BrO and SO2 to improve our understanding of chemical processes in tropospheric volcanic plumes.

  8. PubChem structure-activity relationship (SAR) clusters.

    PubMed

    Kim, Sunghwan; Han, Lianyi; Yu, Bo; Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

    2015-01-01

    Developing structure-activity relationships (SARs) of molecules is an important approach in facilitating hit exploration in the early stage of drug discovery. Although information on millions of compounds and their bioactivities is freely available to the public, it is very challenging to infer a meaningful and novel SAR from that information. Research discussed in the present paper employed a bioactivity-centered clustering approach to group 843,845 non-inactive compounds stored in PubChem according to both structural similarity and bioactivity similarity, with the aim of mining bioactivity data in PubChem for useful SAR information. The compounds were clustered in three bioactivity similarity contexts: (1) non-inactive in a given bioassay, (2) non-inactive against a given protein, and (3) non-inactive against proteins involved in a given pathway. In each context, these small molecules were clustered according to their two-dimensional (2-D) and three-dimensional (3-D) structural similarities. The resulting 18 million clusters, named "PubChem SAR clusters", were delivered in such a way that each cluster contains a group of small molecules similar to each other in both structure and bioactivity. The PubChem SAR clusters, pre-computed using publicly available bioactivity information, make it possible to quickly navigate and narrow down the compounds of interest. Each SAR cluster can be a useful resource in developing a meaningful SAR or enable one to design or expand compound libraries from the cluster. It can also help to predict the potential therapeutic effects and pharmacological actions of less-known compounds from those of well-known compounds (i.e., drugs) in the same cluster.

  9. ChemCam rock laser for Mars Science Laboratory "Curiosity"

    SciTech Connect

    Wiens, Roger

    2010-09-03

    Los Alamos has a long history of space-related instruments, tied primarily to its role in defense-related treaty verification. Space-based detectors have helped determine the differences between signals from lightning bolts and potential nuclear explosions. LANL-developed gamma-ray detection instruments first revealed the existence of what we now know as gamma-ray bursts, an exciting area of astrophysical research. And the use of LANL instruments on varied space missions continues with such products as the ChemCam rock laser for NASA, shown here. The Engineering Model of the ChemCam Mars Science Laboratory rover instrument arrived at NASA's Jet Propulsion Laboratory on February 6, 2008. The Flight Model was shipped in August, 2010 for installation on the rover at JPL. ChemCam will use imaging and laser-induced breakdown spectroscopy (LIBS) to determine rock and soil compositions on Mars, up to 9 meters from the rover. The engineering model is being integrated into the rover test bed for the development and testing of the rover software. The actual flight model components were concurrently assembled at Los Alamos and in Toulouse, France. The Mars Science Laboratory is scheduled to launch in 2011. Animations courtesy of JPL/NASA.

  10. ChemCam Rock Laser for the Mars Science Laboratory

    SciTech Connect

    LANL

    2008-03-24

    Los Alamos has a long history of space-related instr... Los Alamos has a long history of space-related instruments, tied primarily to its role in defense-related treaty verification. Space-based detectors have helped determine the differences between signals from lightning bolts and potential nuclear explosions. LANL-developed gamma-ray detection instruments first revealed the existence of what we now know as gamma-ray bursts, an exciting area of astrophysical research. And the use of LANL instruments on varied space missions continues with such products as the ChemCam rock laser for NASA, shown here. The Engineering Model of the ChemCam Mars Science Laboratory rover instrument arrived at NASA's Jet Propulsion Laboratory on February 6, 2008. ChemCam will use imaging and laser-induced breakdown spectroscopy (LIBS) to determine rock and soil compositions on Mars, up to 9 meters from the rover. The engineering model is being integrated into the rover test bed for the development and testing of the rover software. The actual flight model components are concurrently being assembled at Los Alamos and in Toulouse, France, and will be delivered to JPL in July. The Mars Science Laboratory is scheduled to launch in 2009. Animations courtesy of JPL/NASA.

  11. ChemCam rock laser for Mars Science Laboratory "Curiosity"

    ScienceCinema

    Wiens, Roger

    2016-07-12

    Los Alamos has a long history of space-related instruments, tied primarily to its role in defense-related treaty verification. Space-based detectors have helped determine the differences between signals from lightning bolts and potential nuclear explosions. LANL-developed gamma-ray detection instruments first revealed the existence of what we now know as gamma-ray bursts, an exciting area of astrophysical research. And the use of LANL instruments on varied space missions continues with such products as the ChemCam rock laser for NASA, shown here. The Engineering Model of the ChemCam Mars Science Laboratory rover instrument arrived at NASA's Jet Propulsion Laboratory on February 6, 2008. The Flight Model was shipped in August, 2010 for installation on the rover at JPL. ChemCam will use imaging and laser-induced breakdown spectroscopy (LIBS) to determine rock and soil compositions on Mars, up to 9 meters from the rover. The engineering model is being integrated into the rover test bed for the development and testing of the rover software. The actual flight model components were concurrently assembled at Los Alamos and in Toulouse, France. The Mars Science Laboratory is scheduled to launch in 2011. Animations courtesy of JPL/NASA.

  12. ChemCam Rock Laser for the Mars Science Laboratory

    ScienceCinema

    LANL

    2016-07-12

    Los Alamos has a long history of space-related instr... Los Alamos has a long history of space-related instruments, tied primarily to its role in defense-related treaty verification. Space-based detectors have helped determine the differences between signals from lightning bolts and potential nuclear explosions. LANL-developed gamma-ray detection instruments first revealed the existence of what we now know as gamma-ray bursts, an exciting area of astrophysical research. And the use of LANL instruments on varied space missions continues with such products as the ChemCam rock laser for NASA, shown here. The Engineering Model of the ChemCam Mars Science Laboratory rover instrument arrived at NASA's Jet Propulsion Laboratory on February 6, 2008. ChemCam will use imaging and laser-induced breakdown spectroscopy (LIBS) to determine rock and soil compositions on Mars, up to 9 meters from the rover. The engineering model is being integrated into the rover test bed for the development and testing of the rover software. The actual flight model components are concurrently being assembled at Los Alamos and in Toulouse, France, and will be delivered to JPL in July. The Mars Science Laboratory is scheduled to launch in 2009. Animations courtesy of JPL/NASA.

  13. CHEM-Based Self-Deploying Spacecraft Radar Antennas

    NASA Technical Reports Server (NTRS)

    Sokolowski, Witold; Huang, John; Ghaffarian, Reza

    2004-01-01

    A document proposes self-deploying spacecraft radar antennas based on cold hibernated elastic memory (CHEM) structures. Described in a number of prior NASA Tech Briefs articles, the CHEM concept is one of utilizing open-cell shape-memory-polymer (SMP) foams to make lightweight structures that can be compressed for storage and can later be expanded, then rigidified for use. A CHEM-based antenna according to the proposal would comprise three layers of microstrip patches and transmission lines interspersed with two flat layers of SMP foam, which would serve as both dielectric spacers and as means of deployment. The SMP foam layers would be fabricated at full size at a temperature below the SMP glass-transition temperature (Tg). The layers would be assembled into a unitary structure, which, at temperature above Tg, would be compacted to much smaller thickness, then rolled up for storage. Next, the structure would be cooled to below Tg and kept there during launch. Upon reaching the assigned position in outer space, the structure would be heated above Tg to make it rebound to its original size and shape. The structure as thus deployed would then be rigidified by natural cooling to below Tg

  14. Atmospheric Halogen Chemistry of Volcanic Plumes in WRF-Chem

    NASA Astrophysics Data System (ADS)

    Surl, Luke; Donohoue, Deanna; von Glasow, Roland

    2015-04-01

    Volcanic eruptions are known to be a strong and concentrated source of reactive halogen species. The chemistry that these species are known to take part in include ozone-destruction cycles. Despite the potentially large perturbation to the chemistry of the troposphere that eruptions may cause, the magnitude of such impacts on global and regional scales is largely unknown. We used WRF-Chem to investigate the influence of Mount Etna on the tropospheric chemistry of the Mediterranean region. The chemistry of bromine, chlorine and mercury has been added to the chemical mechanism CBMZ and we have coupled WRF-Chem with the emissions program PrepChem. We developed a simple parameterisation of the key multiphase reaction cycles involving halogens. Comparison with published field data shows that the model is able to reproduce the bromine explosion phenomenon seen in spectroscopic investigations of volcanic plumes. From the model results we are able to determine a detailed picture of the chemistry of a volcanic plume; results are presented which show in detail how the character of the volcanic plume evolves as it is advected downwind and we identify which parts of the chemical cycle are most likely to be the limiting factors for the speed of the processing. Additionally, these modelled results are supplemented with, and compared against, measurements of ozone depletion that we made within the plume at the summit of Mount Etna.

  15. Prediction of particle formation and number concentration over the United States with WRF-Chem + APM model

    NASA Astrophysics Data System (ADS)

    Luo, G.; Yu, F.

    2010-12-01

    Aerosol nucleation events have been widely observed at various locations around the world and well recognized to dominate the particle number abundance and cloud condensation nuclei concentrations in many parts of the troposphere. An advanced particle microphysics model (APM), which has been previously incorporated into a global chemistry transport model (GEOS-Chem) and validated against a large set of aerosol measurements (Yu and Luo, 2009; Yu et al., 2010), has been successfully integrated into the Weather Research and Forecast model coupled with Chemistry (WRF-Chem). The size-resolved (sectional) APM model, which distinguishes secondary and primary particles and keeps track of the amount of secondary species coated on each type of primary particles (black carbon, primary organic carbon, dust, and sea salt), is designed to capture key particle properties important for their health and climatic effects while keep the computing cost at a reasonable level. WRF-Chem has 53 tracers for CBM-Z mechanism, and it took 2.2 hours for one day simulations covering a region of 3780×2916 km2 with 27 km horizontal resolutions and 34 layers on an 8-CPU Linux workstation (2.2 Ghz Dual Quad-Core AMD Opteron Processor 2354). The coupled WRF-Chem-APM model has 138 tracers (85 additional tracers associated with APM), and it took 5.02 hours on the same machine for same day simulation with full size-resolved microphysics (nucleation, condensation, coagulation, deposition, and scavenging) and CBM-Z chemistry. The WRF-Chem + APM has been employed to study the formation and growth of particles over the United States, using relevant outputs from GEOS-Chem + APM as initial conditions and boundary conditions. We show that ion-mediated nucleation of sulfuric acid and water can lead to significant new particle formation over the United States and nucleation rates have strongly spatial and temporal variations. The simulated spatial (both horizontal and vertical) distribution of particle

  16. Response to ``Comment on `Slow Debye-type peak observed in the dielectric response of polyalcohols' '' [J. Chem. Phys. 134, 037101 (2011)

    NASA Astrophysics Data System (ADS)

    Bergman, R.; Jansson, H.; Swenson, J.

    2011-01-01

    In our recent article [R. Bergman et al., J. Chem. Phys. 132, 044504 (2010)] we investigated some polyalcohols, i.e., glycerol, xylitol, and sorbitol by dielectric spectroscopy. In the study, a low-frequency peak of Debye character that normally is hidden by the large low-frequency dispersion due to conductivity was revealed by analyzing the real part of the permittivity and by using a thin Teflon film to suppress the low-frequency dispersion. We agree with the comment by Paluch et al. [J. Chem. Phys. 134, 037101 (2011)] that the Teflon film setup will indeed create a peak due to the dc conductivity. However, due to the fact that the location of the peak was almost identical in measurement with and without Teflon, we unfortunately mainly showed the data measured with Teflon, despite that it could also be observed in the real part of the permittivity without using the Teflon setup, as shown in our original article [R. Bergman et al., J. Chem. Phys. 132, 044504 (2010)]. Here, we show that the low-frequency peak of Debye character can also be observed by subtracting the dc conductivity. Furthermore, we show that the modulus representation used in Paluch et al. [J. Chem. Phys. 134, 037101 (2011).] is also not suitable for detecting processes hidden by the conductivity.

  17. ChemCam analysis of Martian fine dust

    NASA Astrophysics Data System (ADS)

    Lasue, Jeremie; Mangold, Nicolas; Cousin, Agnes; Meslin, Pierre-Yves; Wiens, Roger; Gasnault, Olivier; Rapin, William; Schroder, Susanne; Ollila, Ann; Fabre, Cécile; Berger, Gilles; Le Mouélic, Stéphane; Dehouck, Erwin; Forni, Olivier; Maurice, Sylvestre; Anderson, Ryan; Bridges, Nathan; Clark, Benton; Clegg, Samuel; d'Uston, Claude; Goetz, Walter; Johnson, Jeffrey R.; Lanza, Nina; Madsen, Morten; Melikechi, Noureddine; Newsom, Horton; Sautter, Violaine; Martin-Torres, Javier; Zorzano, Maria-Paz; MSL Science Team

    2016-10-01

    In this work, we examine the chemical composition of dust observed by the Chemistry Camera (ChemCam) instrument onboard the Mars Science Laboratory (MSL) rover at Gale Crater. The Laser Induced Breakdown Spectroscopy technique analyses samples without preparation, which allows detection of the elemental composition of surface deposits. Mars aeolian fine dust (<2-3 microns) composition is analyzed on the first shot of each Mars target. It is reproducible over time and present a composition characteristic of the global martian fine dust, which covers the entire planet and contributes to the local geology analyzed by MSL. Its composition can also be retrieved on the ChemCam Calibration Targets (CCCT) by subtraction of the well characterized CCCT spectra. The CCCT include eight glasses and ceramics that have been generated to simulate Martian rocks of interest and two targets of a single element (graphite for carbon and an alloy of titanium). ChemCam passive spectroscopy also indicates varying deposition of the dust cover on the CCCT.Major elements are quantified and shown to be very similar to the fine soils encountered at Gale crater. The composition is also similar to the soils and fine dust measured by APXS for the elements common to both instruments. The minor elements quantified by ChemCam (Ba, Sr, Rb, Li, Mn, Cr) are within the range of soil surveys, but we see a higher concentration of Li than in other types of remotely characterized targets. Sulfur is possibly detected at the ChemCam limit of detection. Hydrogen is clearly identified, indicating that this fine dust is a contributor to the H content of the martian soils, as also detected by the SAM and CheMin instruments, and provides constraints as to which fraction of the Martian surface is hydrated and altered. In conclusion, the finest fraction of dust particles on the surface of Mars contains hydrated components mixed intimately within the fine aeolian dust fraction, suggesting that this dust likely

  18. Dust modeling over Saudi Arabia using WRF-Chem: March 2009 severe dust case

    NASA Astrophysics Data System (ADS)

    Zhang, Yongxin; Liu, Yubao; Kucera, Paul A.; Alharbi, Badr H.; Pan, Linlin; Ghulam, Ayman

    2015-10-01

    This paper documents the performance of the fully coupled WRF-Chem model at 21.6 km and 7.2 km resolution over Saudi Arabia in simulating a severe dust storm event that occurred in March 2009. The comparisons between the model simulations and the observed AOD at the Solar Village AERONET site and the MODIS measurements show that WRF-Chem satisfactorily resolves the arrival, evolution and spatial distributions of the dust storm over Saudi Arabia especially for the fine domain at 7.2 km resolution. The model simulated surface meteorological variables at Riyadh Airport, Hafr Al-Batin Airport, Dammam Airport and Gassim Airport follow the observations in terms of magnitude and temporal evolution although model biases such as deficiencies in simulating the amplitude of diurnal cycles are noted. Higher resolution and shorter initialization time improve the model performance in aerosol optical depth but for surface variables shorter initialization time improves correlation while higher horizontal resolution improves mean biases to some extent. The simulated dust plume is mainly confined between the surface and the 5-km height, with the peak concentrations located in the lowest 500 m. The vertical extent of the dust plume shows gradual decreases during the simulation period when averaged over the entire fine domain and an area centered around Solar Village, and also varies in accordance with the development and decay of the boundary layer.

  19. Engaging Organic Chemistry Students Using ChemDraw for iPad

    ERIC Educational Resources Information Center

    Morsch, Layne A.; Lewis, Michael

    2015-01-01

    Drawing structures, mechanisms, and syntheses is a vital part of success in organic chemistry courses. ChemDraw for iPad has been used to increase classroom experiences in the preparation of high quality chemical drawings. The embedded Flick-to-Share allows for simple, real-time exchange of ChemDraw documents. ChemDraw for iPad also allows…

  20. Engaging Organic Chemistry Students Using ChemDraw for iPad

    ERIC Educational Resources Information Center

    Morsch, Layne A.; Lewis, Michael

    2015-01-01

    Drawing structures, mechanisms, and syntheses is a vital part of success in organic chemistry courses. ChemDraw for iPad has been used to increase classroom experiences in the preparation of high quality chemical drawings. The embedded Flick-to-Share allows for simple, real-time exchange of ChemDraw documents. ChemDraw for iPad also allows…

  1. Formation Conditions of Basalts at Gale Crater, Mars from ChemCam Analyses

    NASA Astrophysics Data System (ADS)

    Filiberto, J.; Bridges, J.; Dasgupta, R.; Edwards, P.; Schwenzer, S. P.; Wiens, R. C.

    2015-12-01

    Surface igneous rocks shed light onto the chemistry, tectonic, and thermal state of planetary interiors. For the purpose of comparative planetology, therefore, it is critical to fully utilize the compositional diversity of igneous rocks for different terrestrial planets. For Mars, igneous float rocks and conglomerate clasts at Gale Crater, as analyzed by ChemCam [1] using a new calibration [2], have a larger range in chemistry than have been analyzed at any other landing site or within the Martian meteorite collection [3, 4]. These rocks may reflect different conditions of melting within the Martian interior than any previously analyzed basalts. Here we present new formation conditions for basaltic and trachybasalt/dioritic rocks at Gale Crater from ChemCam analyses following previous procedures [5, 6]. We then compare these estimates of basalt formation with previous estimates for rocks from the Noachian (Gusev Crater, Meridiani Planum, and a clast in the NWA 7034 meteorite [5, 6]), Hesperian (surface volcanics [7]), and Amazonian (surface volcanics and shergottites [7-8]), to calculate an average mantle potential temperature for different Martian epochs and investigate how the interior of Mars has changed through time. Finally, we will compare Martian mantle potential temperatures with petrologic estimate of cooling for the Earth. Our calculated estimate for the mantle potential temperature (TP) of rocks at Gale Crater is 1450 ± 45 °C which is within error of previous estimates for Noachian aged rocks [5, 6]. The TP estimates for the Hesperian and Amazonian, based on orbital analyses of the crust [7], are lower in temperature than the estimates for the Noachian. Our results are consistent with simple convective cooling of the Martian interior. [1] Wiens R. et al. (2012) Space Sci Rev 170. 167-227. [2] Anderson R. et al. (2015) LPSC. Abstract #7031. [3] Schmidt M.E. et al. (2014) JGRP 2013JE004481. [4] Sautter V. et al. (2014) JGRP 2013JE004472. [5] Filiberto J

  2. EOS CHEM: A Mission to Study Ozone and Climate

    NASA Technical Reports Server (NTRS)

    Schoeberl, Mark

    1998-01-01

    The Earth's stratosphere contains the ozone layer, which shields us from the Sun@ harmful ultraviolet (UV) radiation. Ozone is destroyed through chemical reactions involving natural and man-made nitrogen, hydrogen, bromine, and chlorine compounds. The release of chlorofluoro-carbons CFCs) has caused a dramatic decrease in the protective stratospheric ozone layer during the last two decades. Detection of stratospheric ozone depletion led to regulation and phase-out of CFC production worldwide. As a result, man-made chlorine levels in the atmosphere are slowly beginning to decrease. CHEM will be able to determine whether the stratospheric ozone layer is now recovering, as predicted by scientific models.

  3. EOS CHEM: A Mission to Study Ozone and Climate

    NASA Technical Reports Server (NTRS)

    Schoeberl, Mark

    1998-01-01

    The Earth's stratosphere contains the ozone layer, which shields us from the Sun@ harmful ultraviolet (UV) radiation. Ozone is destroyed through chemical reactions involving natural and man-made nitrogen, hydrogen, bromine, and chlorine compounds. The release of chlorofluoro-carbons CFCs) has caused a dramatic decrease in the protective stratospheric ozone layer during the last two decades. Detection of stratospheric ozone depletion led to regulation and phase-out of CFC production worldwide. As a result, man-made chlorine levels in the atmosphere are slowly beginning to decrease. CHEM will be able to determine whether the stratospheric ozone layer is now recovering, as predicted by scientific models.

  4. Biophotonic imaging: lighting the way for chem/bio detection

    NASA Astrophysics Data System (ADS)

    Ripp, Steven; Jegier, Patricia; Lopes, Nicholas

    2009-05-01

    Biophotonic imaging is a versatile and powerful tool, that when combined with living microbial bioreporters, can be applied in diagnostic technologies for sensitive, nondestructive, real-time monitoring of chemical and biological targets. Bioreporters, consisting of bacteria as well as the viruses (bacteriophage) that infect them, can be genetically engineered to emit visible light upon interaction with a specific chemical or biological entity. By interfacing these bioreporters with imaging cameras or miniaturized integrated circuit microluminometers, fully standalone detection units are formed that can be deployed for intelligent distributed multi-target chem/bio monitoring.

  5. [Determination of iron with CentrifiChem System].

    PubMed

    Eisenwiener, H G

    1975-01-01

    The determination of iron was adapted to the CentrifiChem System. The iron bound to transferrin is freed with a detergent, reduced to Fe++ with sodium dithionite, and determined with bathophenanthroline disulphonate. The operation consists of one run for the blank value and one analytical run. Although the actual reaction time is extremely short, a reaction time of 8--10 min is recommended for both the blank value and the analysis. This ensures adequate clearing during centrifugation under the influence of Teepol. 2 times 100 mul serum are required, and 80 determinations per hour are possible.

  6. Curiosity ChemCam Finds High-Silica Mars Rocks

    SciTech Connect

    Frydenvang, Jens

    2015-12-17

    A team of scientists, including one from Los Alamos National Laboratory, has found much higher concentrations of silica at some sites the Curiosity rover has investigated in the past seven months than anywhere else it has visited since landing on Mars 40 months ago. The first discovery was as Curiosity approached the area “Marias Pass,” where a lower geological unit contacts an overlying one. ChemCam, the rover’s laser-firing instrument for checking rock composition from a distance, detected bountiful silica in some targets the rover passed along the way to the contact zone. The ChemCam instrument was developed at Los Alamos in partnership with the French IRAP laboratory in Toulouse and the French Space Agency. “The high silica was a surprise,” said Jens Frydenvang of Los Alamos National Laboratory and the University of Copenhagen, also a Curiosity science team member. “While we’re still working with multiple hypotheses on how the silica got so enriched, these hypotheses all require considerable water activity, and on Earth high silica deposits are often associated with environments that provide excellent support for microbial life. Because of this, the science team agreed to make a rare backtrack to investigate it more.”

  7. Implementing marine organic aerosols into the GEOS-Chem model

    DOE PAGES

    Gantt, B.; Johnson, M. S.; Crippa, M.; ...

    2015-03-17

    Marine-sourced organic aerosols (MOAs) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem (Global Earth Observing System Chemistry) model. The implemented emission scheme improved the large underprediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Modelmore » predictions were also in good agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOAs observed during the summertime at an inland site near Paris, France. Our study shows that MOAs have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having >10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.« less

  8. Implementing marine organic aerosols into the GEOS-Chem model

    NASA Astrophysics Data System (ADS)

    Gantt, B.; Johnson, M. S.; Crippa, M.; Prévôt, A. S. H.; Meskhidze, N.

    2015-03-01

    Marine-sourced organic aerosols (MOAs) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem (Global Earth Observing System Chemistry) model. The implemented emission scheme improved the large underprediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Model predictions were also in good agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOAs observed during the summertime at an inland site near Paris, France. Our study shows that MOAs have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having >10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.

  9. Curiosity ChemCam Finds High-Silica Mars Rocks

    ScienceCinema

    Frydenvang, Jens

    2016-07-12

    A team of scientists, including one from Los Alamos National Laboratory, has found much higher concentrations of silica at some sites the Curiosity rover has investigated in the past seven months than anywhere else it has visited since landing on Mars 40 months ago. The first discovery was as Curiosity approached the area “Marias Pass,” where a lower geological unit contacts an overlying one. ChemCam, the rover’s laser-firing instrument for checking rock composition from a distance, detected bountiful silica in some targets the rover passed along the way to the contact zone. The ChemCam instrument was developed at Los Alamos in partnership with the French IRAP laboratory in Toulouse and the French Space Agency. “The high silica was a surprise,” said Jens Frydenvang of Los Alamos National Laboratory and the University of Copenhagen, also a Curiosity science team member. “While we’re still working with multiple hypotheses on how the silica got so enriched, these hypotheses all require considerable water activity, and on Earth high silica deposits are often associated with environments that provide excellent support for microbial life. Because of this, the science team agreed to make a rare backtrack to investigate it more.”

  10. Implementing marine organic aerosols into the GEOS-Chem model

    NASA Astrophysics Data System (ADS)

    Gantt, B.; Johnson, M. S.; Crippa, M.; Prévôt, A. S. H.; Meskhidze, N.

    2014-09-01

    Marine organic aerosols (MOA) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem model. The implemented emission scheme improved the large underprediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Model predictions were also in good agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOA observed during the summertime at an inland site near Paris, France. Our study shows that MOA have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having > 10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly-emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.

  11. Implementing Marine Organic Aerosols Into the GEOS-Chem Model

    NASA Technical Reports Server (NTRS)

    Johnson, Matthew S.

    2015-01-01

    Marine-sourced organic aerosols (MOA) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem model. The implemented emission scheme improved the large under-prediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Model predictions were also in good agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOA observed during the summertime at an inland site near Paris, France. Our study shows that MOA have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having > 10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly-emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.

  12. CHEM-Based Self-Deploying Planetary Storage Tanks

    NASA Technical Reports Server (NTRS)

    Sokolowski, Witold; Bhattacharya, Kaushik

    2007-01-01

    A document proposes self-deploying storage tanks, based on the cold elastic hibernated memory (CHEM) concept, to be used on remote planets. The CHEM concept, described in previous NASA Tech Briefs articles, involves the use of open-cell shape-memory-polymer (SMP) foam sandwich structures to make lightweight, space-deployable structures that can be compressed for storage and can later be expanded, then rigidified for use. A tank according to the proposal would be made of multiple SMP layers (of which at least one could be an SMP foam). The tank would be fabricated at full size in the rigid, deployed condition at ambient temperature, the SMP material(s) having been chosen so that ambient temperature would be below the SMP glass-transition temperature (T(sub g)). The tank would then be warmed to a temperature above T(sub g), where it would be compacted and packaged, then cooled to below T(sub g) and kept there during launch and transport to a distant planet. At the assigned position on the planet, the compacted tank would be heated above T(sub g) by the solar radiation making it rebound to its original size and shape. Finally, the tank would be rigidified through natural cooling to below T(sub g) in the planetary ambient environment.

  13. Development of the EarthChem Geochronology and Thermochronology database: Collaboration of the EarthChem and EARTHTIME efforts

    NASA Astrophysics Data System (ADS)

    Walker, J. D.; Ash, J. M.; Bowring, J.; Bowring, S. A.; Deino, A. L.; Kislitsyn, R.; Koppers, A. A.

    2009-12-01

    One of the most onerous tasks in rigorous development of data reporting and databases for geochronological and thermochronological studies is to fully capture all of the metadata needed to completely document both the analytical work as well as the interpretation effort. This information is available in the data reduction programs used by researchers, but has proven difficult to harvest into either publications or databases. For this reason, the EarthChem and EARTHTIME efforts are collaborating to foster the next generation of data management and discovery for age information by integrating data reporting with data reduction. EarthChem is a community-driven effort to facilitate the discovery, access, and preservation of geochemical data of all types and to support research and enable new and better science. EARTHTIME is also a community-initiated project whose aim is to foster the next generation of high-precision geochronology and thermochoronology. In addition, collaboration with the CRONUS effort for cosmogenic radionuclides is in progress. EarthChem workers have met with groups working on the Ar-Ar, U-Pb, and (U-Th)/He systems to establish data reporting requirements as well as XML schemas to be used for transferring data from reduction programs to database. At present, we have prototype systems working for the U-Pb_Redux, ArArCalc, MassSpec, and Helios programs. In each program, the user can select to upload data and metadata to the GEOCHRON system hosted at EarthChem. There are two additional requirements for upload. The first is having a unique identifier (IGSN) obtained either manually or via web services contained within the reduction program from the SESAR system. The second is that the user selects whether the sample is to be available for discovery (public) or remain hidden (private). Search for data at the GEOCHRON portal can be done using age, method, mineral, or location parameters. Data can be downloaded in the full XML format for ingestion back

  14. Evaluation of Meso-NH and WRF/CHEM simulated gas and aerosol chemistry over Europe based on hourly observations

    NASA Astrophysics Data System (ADS)

    Berger, A.; Barbet, C.; Leriche, M.; Deguillaume, L.; Mari, C.; Chaumerliac, N.; Bègue, N.; Tulet, P.; Gazen, D.; Escobar, J.

    2016-07-01

    Gas chemistry and aerosol chemistry of 10 km-resolution mesoscale models Meso-NH and WRF/CHEM were evaluated on three cases over Europe. These one-day duration cases were selected from Freney et al. (2011) and occurred on contrasted meteorological conditions and at different seasons: a cyclonic circulation with a well-marked frontal zone on winter, an anti-cyclonic situation with local storm precipitations on summer and a cold front in the northwest of Europe associated to a convergence of air masses over eastern Europe and conflicting air masses over Spain and France on autumn. To assess the performance of the two models, surface hourly databases from observation stations over Europe were used, together with airborne measurements. For both models, the meteorological fields were in good agreement with the measurements for the three days. Winds presented the largest normalised mean bias integrated over all European stations for both models. Daily gas chemistry was reproduced with normalised mean biases between - 14 and 11%, a level of accuracy that is acceptable for policy support. The two models' performances were degraded during night-time quite likely due to the constant primary species emissions. The PM2.5 bulk mass concentration was overestimated by Meso-NH over Europe and slightly underestimated by WRF/CHEM. The absence of wet deposition in the models partly explains the local discrepancies with the observations. More locally, the systematic low mixing ratio of volatile organic compounds in the gas phase simulated by WRF/CHEM at three stations was correlated with the underestimation of OM (organic matter) mass in the aerosol phase. Moreover, this mass of OM was mainly composed of anthropogenic POAs (primary organic aerosols) in WRF/CHEM, suggesting a missing source for SOAs (secondary organic aerosols) mass in WRF/CHEM aerosol parameterisation. The contribution of OM was well simulated by Meso-NH, with a higher contribution for the summer case. For Meso

  15. Getting the most out of PubChem for virtual screening.

    PubMed

    Kim, Sunghwan

    2016-09-01

    With the emergence of the 'big data' era, the biomedical research community has great interest in exploiting publicly available chemical information for drug discovery. PubChem is an example of public databases that provide a large amount of chemical information free of charge. This article provides an overview of how PubChem's data, tools, and services can be used for virtual screening and reviews recent publications that discuss important aspects of exploiting PubChem for drug discovery. PubChem offers comprehensive chemical information useful for drug discovery. It also provides multiple programmatic access routes, which are essential to build automated virtual screening pipelines that exploit PubChem data. In addition, PubChemRDF allows users to download PubChem data and load them into a local computing facility, facilitating data integration between PubChem and other resources. PubChem resources have been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). These studies demonstrate the usefulness of PubChem as a key resource for computer-aided drug discovery and related area.

  16. Triumphs and Tribulations of WRF-Chem Development and Use

    SciTech Connect

    Gustafson, William I.; Fast, Jerome D.; Easter, Richard C.; Ghan, Steven J.

    2005-06-27

    In order to address scientific questions related to aerosol chemistry and meteorological-aerosol-radiation-cloud feedbacks at the urban to regional scale, scientists at the Pacific Northwest National Laboratory (PNNL) have made substantial contributions to the chemistry version of the Weather Research and Forecasting model (WRF-Chem) during the past one and a half years. These contributions include an additional gas-phase chemistry mechanism, a sectional aerosol module, an additional photolysis module, feedbacks between aerosols and radiation, and extending the nesting capability of WRF to include the chemistry scalars. During the development process, a number of limitations in WRF have been identified that complicate adding all the desired chemistry capabilities as originally planned. These issues will be discussed along with changes that have been made to help mitigate some of them. Mechanisms currently in development will also be discussed including a secondary organic aerosol (SOA) mechanism for the sectional aerosol module, aqueous chemistry, and the aerosol indirect effect.

  17. Hydrogen isotope MicroChemLab FY15.

    SciTech Connect

    Robinson, David; Luo, Weifang; Stewart, Kenneth D.

    2015-09-01

    We have developed a new method to measure the composition of gaseous mixtures of any two hydrogen isotopes, as well as an inert gas component. When tritium is one of those hydrogen isotopes, there is usually some helium present, because the tritium decays to form helium at a rate of about 1% every 2 months. The usual way of measuring composition of these mixtures involves mass spectrometry, which involves bulky, energy-intensive, expensive instruments, including vacuum pumps that can quite undesirably disperse tritium. Our approach uses calorimetry of a small quantity of hydrogen-absorbing material to determine gas composition without consuming or dispersing the analytes. Our work was a proof of principle using a rather large and slow benchtop calorimeter. Incorporation of microfabricated calorimeters, such as those that have been developed in Sandia’s MicroChemLab program or that are now commercially available, would allow for faster measurements and a smaller instrument footprint.

  18. Hydrogen detection with ChemCam at Gale crater

    NASA Astrophysics Data System (ADS)

    Schröder, S.; Meslin, P.-Y.; Gasnault, O.; Maurice, S.; Cousin, A.; Wiens, R. C.; Rapin, W.; Dyar, M. D.; Mangold, N.; Forni, O.; Nachon, M.; Clegg, S.; Johnson, J. R.; Lasue, J.; Le Mouélic, S.; Ollila, A.; Pinet, P.; Sautter, V.; Vaniman, D.

    2015-03-01

    One of the main advantages of ChemCam's LIBS (Laser-Induced Breakdown Spectroscopy) instrument onboard the Curiosity rover is its potential to detect light elements such as hydrogen at fine scales, which has never been achieved on Mars. Hydrogen lines are detected in most of the data obtained within the first 320 sols of the mission at Gale crater, Mars. This work is a description of the hydrogen signal and its variability in the ChemCam LIBS spectra; it discusses the challenges of qualitative and quantitative analysis. Data acquisition and processing steps are investigated and optimized for the detection of hydrogen on Mars. Subtraction of an appropriate dark spectrum and the deconvolution of the superimposed emission of carbon from the low-pressure CO2-dominated atmosphere are particularly important. Because the intensities of hydrogen are also affected by matrix effects, the hydrogen signal was investigated within groups of targets sharing common chemical features and similar matrices. The different groups cover a variety of rock and soil compositions encountered along the traverse (calcium sulfate veins, mafic soils, felsic, Mg-rich and Fe-rich rocks) including data from both drill holes and their tailings. Almost all these targets were found to be hydrated to variable extents. Soils have systematically higher hydrogen signals than rocks and pebbles, probably as a result of their alteration. The results from rocks suggest that various alteration processes leading to their hydration have taken place, which is consistent with the fluvial lacustrine context, the diagenetic features, and the mineralogy observed by Curiosity in Yellowknife Bay.

  19. Development and application of the WRFPLUS-Chem online chemistry adjoint and WRFDA-Chem assimilation system

    NASA Astrophysics Data System (ADS)

    Guerrette, J. J.; Henze, D. K.

    2015-06-01

    Here we present the online meteorology and chemistry adjoint and tangent linear model, WRFPLUS-Chem (Weather Research and Forecasting plus chemistry), which incorporates modules to treat boundary layer mixing, emission, aging, dry deposition, and advection of black carbon aerosol. We also develop land surface and surface layer adjoints to account for coupling between radiation and vertical mixing. Model performance is verified against finite difference derivative approximations. A second-order checkpointing scheme is created to reduce computational costs and enable simulations longer than 6 h. The adjoint is coupled to WRFDA-Chem, in order to conduct a sensitivity study of anthropogenic and biomass burning sources throughout California during the 2008 Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) field campaign. A cost-function weighting scheme was devised to reduce the impact of statistically insignificant residual errors in future inverse modeling studies. Results of the sensitivity study show that, for this domain and time period, anthropogenic emissions are overpredicted, while wildfire emission error signs vary spatially. We consider the diurnal variation in emission sensitivities to determine at what time sources should be scaled up or down. Also, adjoint sensitivities for two choices of land surface model (LSM) indicate that emission inversion results would be sensitive to forward model configuration. The tools described here are the first step in conducting four-dimensional variational data assimilation in a coupled meteorology-chemistry model, which will potentially provide new constraints on aerosol precursor emissions and their distributions. Such analyses will be invaluable to assessments of particulate matter health and climate impacts.

  20. Major-Element Compositional Diversity Observed by ChemCam Along the MSL Traverse: The First Three Years

    NASA Astrophysics Data System (ADS)

    Wiens, R. C.; Mangold, N.; Maurice, S.; Blaney, D. L.; Clegg, S. M.; Gasda, P. J.; Frydenvang, J.; Gasnault, O.; Forni, O.; Cousin, A.; Lasue, J.; Lanza, N.; Anderson, R. B.; Sautter, V.; Bridges, J.; Le Deit, L.; Nachon, M.; Rapin, W.; Meslin, P. Y.; Newsom, H. E.; Clark, B. C.; Vaniman, D. T.; Bridges, N.; Herkenhoff, K. E.; Ehlmann, B. L.; Dyar, M. D.; Fisk, M. R.; Francis, R.; Leveille, R. J.; Johnson, J. R.; Melikechi, N.; Jackson, R.; Fabre, C.; Payré, V.; Grotzinger, J. P.; Vasavada, A. R.; Crisp, J. A.

    2015-12-01

    ChemCam on Curiosity has used LIBS to obtain elemental compositions of >6000 target points at distances to 7.4 m from the rover. Observations include igneous clasts, sediments, diagenetic features, and other details often not accessible by the rover arm. A major re-calibration was recently completed using >350 standards. This significantly improved the accuracies of mineral end-members including plag-feldspars, hi-Si compositions, oxide grains, Mg-rich end-members (presumably Mg saponites; not yet confirmed by CheMin), and Mg and Ca sulfates. Here we draw conclusions from the overall compositional distributions observed in Gale crater from landing until the present using the new calibration. Observations from Bradbury Rise (sols 0-53, 326-520) show a scattering of compositions toward mineral end-members from igneous clasts and pebbles transported from the crater rim. In contrast, Sheepbed mudstones (first drill location; sols 126-300) form a tight cluster close to average Mars composition. The nearby Shaler fluvial sandstone outcrop (sols 306-325)--the first outcrop of potential deltaic foreset beds--shows K enrichment. This enrichment reaches a peak of 6 wt % K2O (sol 625) in the Mt. Remarkable member of the Kimberley formation, Kimberley being a drill location flanked by foreset beds 7 km SW of Shaler. The Pahrump outcrop (sols 753-919)—first observed material of the Murray formation at Mt. Sharp's base—shows lower Mg, higher Si, and much higher Al, consistent with stronger alteration. Further along the traverse ChemCam discovered an outcrop of light-toned Murray formation rock (sols 992 on) of nearly pure SiO2+TiO2. Overall, the ChemCam database points to a very strong diversity of inputs and alteration processes within a relatively short distance within Gale. Igneous compositions: while Jake Matijevic, a float analyzed early by APXS, appeared nepheline normative, no clear nepheline has been found by ChemCam. Additionally, despite the significant number of

  1. ChemCam Education and Public Outreach: Zapping the Public into Awareness of ChemCam, the Mars Science Laboratory, and Mars Science and Exploration

    NASA Astrophysics Data System (ADS)

    Shaner, A. J.; Shipp, S. S.; Wiens, R. C.; Maurice, S.; Gasnault, O.; Newsom, H.; Anderson, R.

    2012-03-01

    The Chemistry and Camera (ChemCam) instrument EPO program utilizes a public website and educator professional development to capture the public’s interest and imagination in Mars science and exploration.

  2. Operational forecast products and applications based on WRF/Chem

    NASA Astrophysics Data System (ADS)

    Hirtl, Marcus; Flandorfer, Claudia; Langer, Matthias; Mantovani, Simone; Olefs, Marc; Schellander-Gorgas, Theresa

    2015-04-01

    The responsibilities of the national weather service of Austria (ZAMG) include the support of the federal states and the public in questions connected to the protection of the environment in the frame of advisory and counseling services as well as expert opinions. The ZAMG conducts daily Air-Quality forecasts using the on-line coupled model WRF/Chem. The mother domain expands over Europe, North Africa and parts of Russia. The nested domain includes the alpine region and has a horizontal resolution of 4 km. Local emissions (Austria) are used in combination with European inventories (TNO and EMEP) for the simulations. The modeling system is presented and the results from the evaluation of the assimilation of pollutants using the 3D-VAR software GSI is shown. Currently observational data (PM10 and O3) from the Austrian Air-Quality network and from European stations (EEA) are assimilated into the model on an operational basis. In addition PM maps are produced using Aerosol Optical Thickness (AOT) observations from MODIS in combination with model data using machine learning techniques. The modeling system is operationally evaluated with different data sets. The emphasis of the application is on the forecast of pollutants which are compared to the hourly values (PM10, O3 and NO2) of the Austrian Air-Quality network. As the meteorological conditions are important for transport and chemical processes, some parameters like wind and precipitation are automatically evaluated (SAL diagrams, maps, …) with other models (e.g. ECMWF, AROME, …) and ground stations via web interface. The prediction of the AOT is also important for operators of solar power plants. In the past Numerical Weather Prediction (NWP) models were used to predict the AOT based on cloud forecasts at the ZAMG. These models do not consider the spatial and temporal variation of the aerosol distribution in the atmosphere with a consequent impact on the accuracy of forecasts especially during clear-sky days

  3. ChemCam on MSL: Status and Initial Calibrations

    NASA Astrophysics Data System (ADS)

    Wiens, R. C.; Maurice, S.; Clegg, S. M.

    2009-12-01

    The ChemCam instrument suite is being built for remote sensing analyses on the “Curiosity” Mars Science Laboratory rover to be launched in 2011. ChemCam consists of the first flight laser-induced breakdown spectrometer (LIBS) and a remote micro-imager (RMI) to provide context images of the LIBS analysis locations. The LIBS instrument focuses ~15 mJ laser pulses onto analysis spots < 0.5 mm in diameter within 7 m of the rover to produce light-emitting plasma consisting primarily of characteristic emission lines from the materials ablated from the surface, providing elemental compositions of the samples. Multiple laser pulses can remove surface dust and probe weathering layers as well as obtain the composition of the underlying rock. The analyses are rapid, low power, and provide light element compositions including hydrogen and carbon as well as the heavier elements. The RMI imager can resolve 200 µm details at a distance of 2 m, or 1 mm at 10 m. The instrument suite is due to be delivered to JPL in 2010. Activities in the fall of 2009 include replacement of the original flight detectors, which were found to be non-linear at low count rates. Re-assembly of the optical demultiplexer is also taking place to fix a problem with optical transmission found during a shock test. The spectrometers will be mated with the thermal-electric cooler prior to final thermal and vibration tests. Initial calibrations in the fall of 2008 were done with LIBS standards in a Mars chamber at 1.5, 3.5, 5.5, and 7 m distance. The analysis set consisted of more than sixty pressed rock powder standards of basalt, andesite, rhyolite, dacite, sulfate, carbonate, and stream and marine sediment compositions. In spite of the detector nonlinearity the resulting data set has been used to develop and test the LIBS ground data software. Multivariate analysis techniques including independent component analysis (ICA) and partial least squares (PLS) are being used, the former for qualitative rock

  4. Comment on ``Study of dielectric relaxations of anhydrous trehalose and maltose glasses'' [J. Chem. Phys. 134, 014508 (2011)

    NASA Astrophysics Data System (ADS)

    Kaminski, K.; Wlodarczyk, P.; Paluch, M.

    2011-10-01

    Very recently Kwon et al. [H.-J. Kwon, J.-A. Seo, H. K. Kim, and Y. H. Hwang, J. Chem. Phys. 134, 014508 (2011)] published an article on the study of dielectric relaxation in trehalose and maltose glasses. They carried out broadband dielectric measurements at very wide range of temperatures covering supercooled liquid as well as glassy state of both saccharides. It is worth to mention that authors have also applied a new method for obtaining anhydrous glasses of trehalose and maltose that enables avoiding their caramelization. Four relaxation processes were identified in dielectric spectra of both saccharides. The slower one was identified as structural relaxation process the next one, not observed by the others, was assigned as Johari-Goldstein (JG) β-relaxation, while the last two secondary modes were of the same nature as found by Kaminski et al. [K. Kaminski, E. Kaminska, P. Wlodarczyk, S. Pawlus, D. Kimla, A. Kasprzycka, M. Paluch, J. Ziolo, W. Szeja, and K. L. Ngai, J. Phys. Chem. B 112, 12816 (2008)]. In this comment we show that the authors mistakenly assigned the slowest relaxation process as structural mode of disaccharides. We have proven that this relaxation process is an effect of formation of thin layer of air or water between plate of capacitor and sample. The same effect can be observed if plates of capacitor are oxidized. Thus, we concluded that their slowest mode is connected to the dc conduction process while their β JG process is primary relaxation of trehalose and maltose.

  5. Comment on "Scaling properties of information-theoretic quantities in density functional reactivity theory" by C. Rong, T. Lu, P. W. Ayers, P. K. Chattaraj and S. Liu, Phys. Chem. Chem. Phys., 2015, 17, 4977-4988.

    PubMed

    Bohórquez, Hugo J

    2015-12-21

    The scaling properties of density functionals are key for fundamentally understanding density functional theory. Accordingly, the dependence of density functionals on the number of particles is of paramount relevance. The numerical exploration by Rong et al. addressed N-scaling for a set of quantum information quantities; they found linear relationships between each one of them and the electronic population for atoms, molecules, and atoms in molecules. The main motivation for their computational work was that the theoretical scaling of these quantities is unknown; however, these scaling properties can be analytically determined. Here I reveal the derivation of the N-scaling rules for the quantities studied by Rong et al. by following the procedure introduced in Comput. Theor. Chem., 2015, 1053, 38. In addition, a new atomic scaling rule explains the linear relationship between atomic populations and atomic values of the same quantum information quantities.

  6. CdSe nanocrystal based chem-/bio- sensors.

    PubMed

    Somers, Rebecca C; Bawendi, Moungi G; Nocera, Daniel G

    2007-04-01

    Semiconductor nanocrystals (NCs) have found application in biology mostly as optical imaging agents where the photophysical properties of the NCs are insensitive to species in their environment. This tutorial review examines the application of CdSe NCs as optical sensing agents where the NC's photophysical properties are sensitive to species in their environment. For this case, the NC is modified at the surface with a conjugate, which interacts with an external agent by physical (i.e. recognition) or chemical means. Signal transduction in these chem-bio (CB) sensitive NCs is derived primarily from energy transfer between the NC and the external agent, which functions as the energy transfer acceptor or donor. Signaling may be obtained by directly detecting luminescence from the NC and/or the conjugate. New developments for the use of NCs as gain materials in micro-lasing cavities (distributed feedback gratings and spherical resonators) opens the way to designing CB-sensitive NCs for high-gain sensing applications.

  7. Ceramic ChemCam Calibration Targets on Mars Science Laboratory

    NASA Astrophysics Data System (ADS)

    Vaniman, D.; Dyar, M. D.; Wiens, R.; Ollila, A.; Lanza, N.; Lasue, J.; Rhodes, J. M.; Clegg, S.; Newsom, H.

    2012-09-01

    The ChemCam instrument on the Mars Science Laboratory rover Curiosity will use laser-induced breakdown spectroscopy (LIBS) to analyze major and minor element chemistry from sub-millimeter spot sizes, at ranges of ˜1.5-7 m. To interpret the emission spectra obtained, ten calibration standards will be carried on the rover deck. Graphite, Ti metal, and four glasses of igneous composition provide primary, homogeneous calibration targets for the laser. Four granular ceramic targets have been added to provide compositions closer to soils and sedimentary materials like those expected at the Gale Crater field site on Mars. Components used in making these ceramics include basalt, evaporite, and phyllosilicate materials that approximate the chemical compositions of detrital and authigenic constituents of clastic and evaporite sediments, including the elevated sulfate contents present in many Mars sediments and soils. Powdered components were sintered at low temperature (800 °C) with a small amount (9 wt.%) of lithium tetraborate flux to produce ceramics that retain volatile sulfur yet are durable enough for the mission. The ceramic targets are more heterogeneous than the pure element and homogenous glass standards but they provide standards with compositions more similar to the sedimentary rocks that will be Curiosity's prime targets at Gale Crater.

  8. ChemLabBox for SnifferStars

    SciTech Connect

    Lewis, Patrick R.

    2002-01-24

    The software entitled "ChemLabBox for SnifferStars" is used to collect, display, and save data from the Sandia National Laboratories chemical analysis system dubbed SnifferStar. Sensor data is streamed from a SnifferStar unit into a computer thru RS-232 in a manner that is not amendable to plotting. Also, there is no direct way to start and stop the unit as is. This software rearranges the data into something that can be easily plotted in real-time then saves the data into a text fild. In addition, this software provides the users a means to start and stop the hardware. This software was written specifically for SnifferStar. SnifferStar data is delivered at a very fast rate but for a short period of time. This software is written around that premise. It is written for Pentium or higher machines running Windows 95/98/ME/NT/2000/XP. Lockheed Martin is interested in using it for testing SnifferStar units before deployment. To date they have not indicated their intent to deliver the code either in part or whole as part of their product.

  9. Microfabricated thermal conductivity detector for the micro-ChemLab.

    SciTech Connect

    Chang, Jane P.; Cruz, Dolores Y.; Blain, Matthew Glenn; Manginell, Ronald Paul; Showalter, Steven Kedrick; Gelbard, Fred

    2005-08-01

    This work describes the design, computational prototyping, fabrication, and characterization of a microfabricated thermal conductivity detector ({mu}TCD) to analyze the effluent from a micro-gas chromatograph column ({mu}GC) and to complement the detection efficacy of a surface acoustic wave detector in the micro-ChemLab{trademark} system. To maximize the detection sensitivity, we designed a four-filament Wheatstone bridge circuit where the resistors are suspended by a thin silicon nitride membrane in pyramidal or trapezoidal shaped flow cells. The geometry optimization was carried out by simulation of the heat transfer in the devices, utilizing a boundary element algorithm. Within microfabrication constraints, we determined and fabricated nine sensitivity-optimized geometries of the {mu}TCD. The nine optimal geometries were tested with two different flow patterns. We demonstrated that the perpendicular flow, where the gas directly impinged upon the membrane, yielded a sensitivity that is three times greater than the parallel flow, where the gas passed over the membrane. The functionality of the {mu}TCD was validated with the theoretical prediction and showed a consistent linear response to effluent concentrations, with a detection sensitivity of 1 ppm, utilizing less than 1 W of power.

  10. Development of a New Spatial and Temporal resizing Tool of Natural and Anthropogenic Emissions for use in WRF/Chem Regional Modeling

    NASA Astrophysics Data System (ADS)

    Fernandez, Rafael Pedro; Schiavone, Juan Franco; Cremades, Pablo Gabriel; Ruben Santos, Jorge; Lopez Noreña, Ana Isabel; Puliafito, Salvador Enrique

    2017-04-01

    Atmospheric physical and chemical processes can be simulated with different degrees of complexity using global (CAM-Chem) and regional (WRF-Chem) chemical transport models. The proper representation of such processes strongly depends on the quality and temporal resolution of the initial and boundary conditions (IC/BC), as well as on the spatial resolution of the static fields used to represent the land/ocean - atmosphere interaction (e.g., emission sources). This work presents the development on a new spatial and temporal resizing tool of natural and anthropogenic emissions oriented to adapt the global emission inventories used in CAM-Chem to the technical requirements of the regional WRF/Chem model. The new resizing tool, which is based on the anthro_emiss NCAR pre-processor, allows to i) spatially interpolate and extrapolate any local or global emissions inventory to a given user-defined WRF/Chem domain (including nested domains); while at the same time it ii) imposes an hourly variation of the surface emission flux based on the superposition of the time-dependent Solar Zenith Angle (SZA) with high-resolution political maps (for anthropogenic sources) or geophysical land/ocean fields (for natural sources). Here we present results for the adaptation of two different emission inventories into a three-nested regional domain located in South America (with 36 x 36, 12 x 12 and 4 x 4 km2 spatial resolution, respectively): the global halogenated Very Short-Lived (VSLs) emissions inventory used in CAM-Chem (Ordoñez et al., 2012; with a spatial resolution of 100 x 250 km2 and a monthly seasonality); and a local vehicular emissions inventory of GHG for Argentina (Puliafito et al., 2015; which posses national annual means with a local resolution of 2.5 x 2.5 km2). Different diurnal profiles are analyzed for both natural and anthropogenic sources, assuring an identical total surface flux independently of the spatial resolution and temporal variation imposed to each source

  11. Online-coupled modeling of volcanic ash and SO2 dispersion with WRF-Chem

    NASA Astrophysics Data System (ADS)

    Stuefer, Martin; Egan, Sean; Webley, Peter; Grell, Georg; Freitas, Saulo; Pavolonis, Mike; Dehn, Jonathan

    2014-05-01

    We included a volcanic emission and plume model into the Weather Research Forecast Model with inline Chemistry (WRF-Chem). The volcanic emission model with WRF-Chem has been tested and evaluated with historic eruptions, and the volcanic application was included into the official release of WRF-Chem beginning with WRF version 3.3 in 2011. Operational volcanic WRF-Chem runs have been developed using different domains centered on main volcanoes of the Aleutian chain and Popocatépetl Volcano, Mexico. The Global Forecast System (GFS) is used for the meteorological initialization of WRF-Chem, and default eruption source parameters serve as initial source data for the runs. We report on the model setup, and the advantages to treat the volcanic ash and sulphur dioxide emissions inline within the numerical weather prediction model. In addition we outline possibilities to initialize WRF-Chem with a fully automated algorithm to retrieve volcanic ash cloud properties from satellite data. WRF-Chem runs from recent volcanic eruptions resulted in atmospheric ash loadings, which compared well with the satellite data taking into account that satellite retrieval data represent only a limited amount of the actually emitted source due to detection thresholds. In addition particle aggregative effects are not included in the WRF-Chem model to date.

  12. Outreach within the Bristol ChemLabS CETL (Centre for Excellence in Teaching and Learning)

    ERIC Educational Resources Information Center

    Shallcross, Dudley E.; Harrison, Tim G.; Obey, Tim M.; Croker, Steve J.; Norman, Nick C.

    2013-01-01

    This paper presents an overview of the Bristol ChemLabS project. In particular, it describes the development and impacts of the outreach project within Bristol ChemLabS, the UK's Centre for Excellence in Teaching and Learning (CETL) in practical chemistry, and its continuation beyond the funded project. The major elements of working with both…

  13. Overview of ChemCam Activities and Discoveries During 4 Years at Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Schröder, S.; Wiens, R. C.; Maurice, S.; Gasnault, O.; Cousin, A.

    2016-08-01

    The ChemCam instrument on NASA’s MSL rover has been successfully analyzing materials on the martian surface since the rover’s landing in August 2012. Since then, the rover drove more than 13km and over 330.000 ChemCam LIBS spectra were recorded.

  14. TREC Blog and TREC Chem: A View from the Corn Fields

    DTIC Science & Technology

    2009-11-01

    TREC Blog and TREC Chem: A View from the Corn Fields Yelena Mejovac, Viet Ha Thucc, Steven Fosterd, Christopher Harrisa, Bob Arensc, Padmini...TREC Blog and TREC Chem: A View from the Corn Fields 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER

  15. Life after "ChemCom": Do They Succeed in University-Level Chemistry Courses?

    ERIC Educational Resources Information Center

    Mason, Diana

    Chemistry in the Community ("ChemCom") is a high-school level chemistry text developed by the American Chemical Society (ACS) designed for the college-bound student. The purpose of this study was to identify students enrolled in a university-level chemistry course designed for the nonscience major who had experienced the ChemCom…

  16. Lightning NOx Parameterization for Synoptic Meteorological-scale Prediction with Convective Parameterization in WRF-Chem

    NASA Astrophysics Data System (ADS)

    Wong, J.; Noone, D. C.; Barth, M. C.

    2011-12-01

    Lightning NOx (LNOx) is an important precursor to tropospheric ozone production and monsoonal upper tropospheric ozone enhancement. A parameterization for LNOx emission is designed for convective-parameterized synoptic meteorological-scale predictions in the NCAR Weather Research and Forecasting Model with Chemistry (WRF-Chem). The implementation uses the Price and Rind (1992) flash rate equation to produce a flash density as a function of cloud height. A fixed emission rate of 500 moles NO per flash and Gaussian vertical distributions are then used to produce the predicted LNOx emission. Comparison of the results from a month long simulation over continental United States against a multiyear climatology based on Optical Transient Detector (OTD) computed by Boccippio et al (2000) shows confidence in reproducing the proper geographical distribution. Regional comparison against National Lightning Detection Network (NLDN) data also shows confidence of using a constant tuning parameter to produce a flash density within the order of magnitude of that observed with consideration of model bias in convection. The produced tropospheric NO2 column also matches well (reduced χ2=0.88) with SCHIAMACHY NO2 vertical column density. Several sensitivity simulations are also performed to evaluate the model's response to the parameterization in ozone and related species such as isoprene and formaldehyde. Results show that the species-specific sensitivities to LNOx emission are significantly altered by convective detrainment as well as the variability of NOx residence time throughout the troposphere from the prescribed vertical distribution.

  17. Recalibration of the Mars Science Laboratory ChemCam instrument with an expanded geochemical database

    NASA Astrophysics Data System (ADS)

    Clegg, Samuel M.; Wiens, Roger C.; Anderson, Ryan; Forni, Olivier; Frydenvang, Jens; Lasue, Jeremie; Cousin, Agnes; Payré, Valérie; Boucher, Tommy; Dyar, M. Darby; McLennan, Scott M.; Morris, Richard V.; Graff, Trevor G.; Mertzman, Stanley A.; Ehlmann, Bethany L.; Belgacem, Ines; Newsom, Horton; Clark, Ben C.; Melikechi, Noureddine; Mezzacappa, Alissa; McInroy, Rhonda E.; Martinez, Ronald; Gasda, Patrick; Gasnault, Olivier; Maurice, Sylvestre

    2017-03-01

    The ChemCam Laser-Induced Breakdown Spectroscopy (LIBS) instrument onboard the Mars Science Laboratory (MSL) rover Curiosity has obtained > 300,000 spectra of rock and soil analysis targets since landing at Gale Crater in 2012, and the spectra represent perhaps the largest publicly-available LIBS datasets. The compositions of the major elements, reported as oxides (SiO2, TiO2, Al2O3, FeOT, MgO, CaO, Na2O, K2O), have been re-calibrated using a laboratory LIBS instrument, Mars-like atmospheric conditions, and a much larger set of standards (408) that span a wider compositional range than previously employed. The new calibration uses a combination of partial least squares (PLS1) and Independent Component Analysis (ICA) algorithms, together with a calibration transfer matrix to minimize differences between the conditions under which the standards were analyzed in the laboratory and the conditions on Mars. While the previous model provided good results in the compositional range near the average Mars surface composition, the new model fits the extreme compositions far better. Examples are given for plagioclase feldspars, where silicon was significantly over-estimated by the previous model, and for calcium-sulfate veins, where silicon compositions near zero were inaccurate. The uncertainties of major element abundances are described as a function of the abundances, and are overall significantly lower than the previous model, enabling important new geochemical interpretations of the data.

  18. Importance of reactive halogens in the tropical marine atmosphere using WRF-chem

    NASA Astrophysics Data System (ADS)

    Badia, Alba; Reeves, Claire E.; Baker, Alex; Volkamer, Rainer; Apel, Eric; Saiz-Lopez, Alfonso; von Glasow, Roland

    2017-04-01

    Halogen species (chlorine, bromine and iodine) are known to play an important role in the chemistry and oxidizing capacity of the troposphere, particularly in the marine boundary layer (MBL). Reactive halogens participate in catalytic reaction cycles that efficiently destroy O3, change the HOX and NOX partitioning, affect the oxidation of volatile organic compounds (VOCs) and mercury, reduce the lifetime of methane, and take part in new particle formation. Numerical models predicted that reactive halogen compounds account for 30% of O3 destruction in the MBL and 5-20% globally. Up to 34% of O3 loss in the tropical East Pacific is due to I and Br combined. Recent studies have highlighted the key role that heterogeneous chemistry plays in explaining observations of BrO and IO abundances in the tropical troposphere. The main objective of this study is to investigate the atmospheric chemistry in the tropical East Pacific with a focus on reactive halogens using the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) and field data from the TORERO campaign. Our reaction mechanism in WRF-Chem is based on the MOZART mechanism and has been extended to include bromine, chlorine and iodine chemistry. Heterogeneous recycling reactions involving sea-salt aerosol and other particles have been included into the model, along with oceanic emissions of important OVOCs and halocarbons. Sea surface emissions of inorganic iodine are calculated using the parameterisation of Carpenter et al., 2013. Focusing on TORERO observations from the ships and a selected number of flights we present the tropospheric impacts of halogens (BrO, IO) in the tropospheric chemistry of relevant species (O3, OH and OVOCS). Sensitivity runs are made in order to study the impact of heterogeneous chemistry in the iodine and bromine species partitioning. A comparison between the online calculation of Very Short Lived Halocarbons (VSLH) oceanic emissions with prescribed oceanic emissions is

  19. Comment on “Frequency-domain stimulated and spontaneous light emission signals at molecular junctions” [J. Chem. Phys. 141, 074107 (2014)

    SciTech Connect

    Galperin, Michael; Ratner, Mark A.; Nitzan, Abraham

    2015-04-07

    We discuss the derivation of the optical response in molecular junctions presented by U. Harbola et al. [J. Chem. Phys. 141, 074107 (2014)], which questions some terms in the theory of Raman scattering in molecular junctions developed in our earlier publications. We show that the terms considered in our theory represent the correct contribution to calculated Raman scattering and are in fact identical to those considered by Harbola et al. We also indicate drawbacks of the presented approach in treating the quantum transport part of the problem.

  20. An overview of the PubChem BioAssay resource.

    PubMed

    Wang, Yanli; Bolton, Evan; Dracheva, Svetlana; Karapetyan, Karen; Shoemaker, Benjamin A; Suzek, Tugba O; Wang, Jiyao; Xiao, Jewen; Zhang, Jian; Bryant, Stephen H

    2010-01-01

    The PubChem BioAssay database (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activities of small molecules and small interfering RNAs (siRNAs) hosted by the US National Institutes of Health (NIH). It archives experimental descriptions of assays and biological test results and makes the information freely accessible to the public. A PubChem BioAssay data entry includes an assay description, a summary and detailed test results. Each assay record is linked to the molecular target, whenever possible, and is cross-referenced to other National Center for Biotechnology Information (NCBI) database records. 'Related BioAssays' are identified by examining the assay target relationship and activity profile of commonly tested compounds. A key goal of PubChem BioAssay is to make the biological activity information easily accessible through the NCBI information retrieval system-Entrez, and various web-based PubChem services. An integrated suite of data analysis tools are available to optimize the utility of the chemical structure and biological activity information within PubChem, enabling researchers to aggregate, compare and analyze biological test results contributed by multiple organizations. In this work, we describe the PubChem BioAssay database, including data model, bioassay deposition and utilities that PubChem provides for searching, downloading and analyzing the biological activity information contained therein.

  1. ChemT, an open-source software for building template-based chemical libraries.

    PubMed

    Abreu, R M V; Froufe, H J C; Daniel, P O M; Queiroz, M J R P; Ferreira, I C F R

    2011-01-01

    In computational chemistry, vast quantities of compounds are generated, and there is a need for cheminformatic tools to efficiently build chemical compound libraries. Several software tools for drawing and editing compound structures are available, but they lack options for automatic generation of chemical libraries. We have implemented ChemT, an easy-to-use open-source software tool that automates the process of preparing custom-made template-based chemical libraries. ChemT automatically generates three-dimensional chemical libraries by inputting a chemical template and the functional groups of interest. The graphical user interface of ChemT is self-explanatory, and a complete tutorial is provided. Several file formats are accepted by ChemT, and it is possible to filter the generated compounds according to different physicochemical properties. The compounds can be subject to force field minimization, and the resulting three-dimensional structures recorded on commonly used file formats. ChemT may be a valuable tool for investigators interested in using in silico virtual screening tools, such as quantitative structure-activity relationship modelling or molecular docking, in order to prioritize compounds for further chemical synthesis. To demonstrate the usefulness of ChemT, we describe an example based on a thieno[3,2-b]pyridine template. ChemT is available free of charge from our website at http://www.esa.ipb.pt/~ruiabreu/chemt .

  2. Ultrafine particles from power plants: Evaluation of WRF-Chem simulations with airborne measurements

    NASA Astrophysics Data System (ADS)

    Forkel, Renate; Junkermann, Wolfgang

    2017-04-01

    Ultrafine particles (UFP, particles with a diameter < 100 nm) are an acknowledged risk to human health and have a potential effect on climate as their presence affects the number concentration of cloud condensation nuclei. Despite of the possibly hazardous effects no regulations exist for this size class of ambient air pollution particles. While ground based continuous measurements of UFP are performed in Germany at several sites (e.g. the German Ultrafine Aerosol Network GUAN, Birmili et al. 2016, doi:10.5194/essd-8-355-2016) information about the vertical distribution of UFP within the atmospheric boundary layer is only scarce. This gap has been closed during the last years by regional-scale airborne surveys for UFP concentrations and size distributions over Germany (Junkermann et al., 2016, doi: 10.3402/tellusb.v68.29250) and Australia (Junkermann and Hacker, 2015, doi: 10.3402/tellusb.v67.25308). Power stations and refineries have been identified as a major source of UFP in Germany with observed particle concentrations > 50000 particles cm-3 downwind of these elevated point sources. Nested WRF-Chem simulations with 2 km grid width for the innermost domain are performed with UFP emission source strengths derived from the measurements in order to study the advection and vertical exchange of UFP from power plants near the Czech and Polish border and their impact on planetary boundary layer particle patterns. The simulations are evaluated against the airborne observations and the downward mixing of the UFP from the elevated sources is studied.

  3. Reply to the 'Comment on "trans-1,2-Disiloxybenzocyclobutene, an adequate partner for the auto-oxidation: EPR/spin trapping and theoretical studies"' by H.-G. Korth, P. Mulder and T. Paul, Phys. Chem. Chem. Phys., 2017, 19, C6CP04187F.

    PubMed

    Carissan, Yannick; Nava, Paola; Tuccio, Béatrice; Commeiras, Laurent; Parrain, Jean-Luc

    2017-01-25

    The proposal and the comments made by Korth et al. on a biradical intermediate along the isomerization path of the reaction of trans-1,2-tert-butyldimethyldisilyloxybenzocyclobutene 1 with dioxygen are unsuitable in our case. The mechanism scenario that we proposed is in agreement with our experimental observations. Moreover, new calculations were able to give an answer to the crucial question, "is the biradical an intermediate or a transition state?" together with the localization of the two radicals. This full article is a response to the "Comment on "trans-1,2-Disiloxybenzocyclobutene, an adequate partner for the auto-oxidation: EPR/spin trapping and theoretical studies" by J. Drujon et al., Phys. Chem. Chem. Phys. 2014, 16, 7513".

  4. Self-Cleaning Coatings

    DTIC Science & Technology

    2014-06-01

    treated ACNT (aligned carbon nanotube ) films formed on quartz surface by using hydrolyzed heptadecafluorodecyltrimethoxysilane. The fabricated surfaces...al., Super-"Amphiphobic" Aligned Carbon Nanotube Films, Angew, Chem. Int. Ed., 40(9), 1743, 2001 [4] Deng X., Mammen L., et al., Candle Soot as a...with a mechanical grease worker for 15 minutes. What we have done Hydraulic liquid soil was prepared by blending 1:10 (weight ratio) carbon black and

  5. Updated dust-iron dissolution mechanism in GEOS-Chem

    NASA Astrophysics Data System (ADS)

    Johnson, M. S.; Meskhidze, N.

    2012-12-01

    Aeolian dust deposition has been suggested to be a critical source of the micronutrient iron (Fe) to high nitrate-low-chlorophyll (HNLC) oceanic regions where marine primary productivity can be limited by the supply of bioavailable Fe. In general, for Fe to be utilized by phytoplankton (i.e., bioavailable Fe), it must be in an aqueous/soluble, colloidal, or nanoparticulate form. The soluble/bioavailable fraction of Fe-containing minerals commonly found in freshly-emitted dust particles are typically small (<< 1%). However, in situ measurements downwind from the dust source regions show increased (> 10%) and spatially variable fraction of soluble iron (sol-Fe), suggesting that chemical processes occurring during the atmospheric transport of mineral dust can increase the amount of bioavailable Fe. The objective of this study is to estimate the supply of bioavailable Fe to different regions of the global oceans through atmospheric pathways. In this study, a comprehensive dust-Fe dissolution scheme has been implemented in the global 3-D chemical transport model GEOS-Chem to calculate sol-Fe deposition rates to the oceans. The acid-based mobilization scheme has been updated to explicitly simulate organic (oxalate) ligand-promoted Fe dissolution processes, Fe(II)/Fe(III) photochemical redox cycling, and dust mineralogy. During the yearlong simulation ~0.17 Tg of sol-Fe was deposited to global oceanic regions. The oxalate-promoted Fe dissolution increased global annual model-predicted sol-Fe deposition rates by ~20% and displayed distinct spatiotemporal differences compared to acid-based dust-Fe mobilization. The explicit calculations of Fe(II)/Fe(III) photochemical cycling showed that during daylight hours the majority of model-predicted sol-Fe is expected to be in a more soluble ferrous iron (Fe(II)) form, while at night virtually all sol-Fe was oxidized into the ferric, Fe(III) form. As Fe(II) species have been shown to be more soluble than Fe(III), ferrous iron

  6. PubChem: a public information system for analyzing bioactivities of small molecules.

    PubMed

    Wang, Yanli; Xiao, Jewen; Suzek, Tugba O; Zhang, Jian; Wang, Jiyao; Bryant, Stephen H

    2009-07-01

    PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). PubChem BioAssay database currently contains biological test results for more than 700 000 compounds. The goal of PubChem is to make this information easily accessible to biomedical researchers. In this work, we present a set of web servers to facilitate and optimize the utility of biological activity information within PubChem. These web-based services provide tools for rapid data retrieval, integration and comparison of biological screening results, exploratory structure-activity analysis, and target selectivity examination. This article reviews these bioactivity analysis tools and discusses their uses. Most of the tools described in this work can be directly accessed at http://pubchem.ncbi.nlm.nih.gov/assay/. URLs for accessing other tools described in this work are specified individually.

  7. ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

    PubMed

    Burger, Melanie C

    2015-01-01

    ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

  8. MinChem: A Prototype Petrologic Database for Hanford Site Sediments

    SciTech Connect

    Mackley, Rob D.; Last, George V.; Serkowski, John A.; Middleton, Lisa A.; Cantrell, Kirk J.

    2010-09-01

    A prototype petrologic database (MinChem) has been under continual development for several years. MinChem contains petrologic, mineralogical, and bulk-rock geochemical data for Hanford Site sediments collected over multiple decades. The database is in relational form and consists of a series of related tables modeled after the Hanford Environmental Information System HEIS (BHI 2002) structures. The HEIS-compatible tables were created in anticipation of eventual migration into HEIS, or some future form of HEIS (e.g. HEIS-GEO). There are currently a total of 13,129 results in MinChem from 521 samples collected at 381 different sampling sites. These data come from 19 different original source documents published and unpublished (e.g. letter reports) between 1976 and 2009. The data in MinChem consist of results from analytical methods such as optical and electron microscopy, x-ray diffraction, x-ray fluorescence, and electron probe microanalysis.

  9. Tropospheric Emission Spectrometer (TES) for the Earth Observing System (EOS) CHEM Satellite

    NASA Technical Reports Server (NTRS)

    Beer, R.; Glavich, T.; Rider, D.

    2000-01-01

    The Tropospheric Emission Spectrometer (TES) is an imaging infrared Fourier transform spectrometer scheduled to be launched into polar sun-synchronous orbit on the Earth Observing System (EOS) CHEM satellite in December 2002.

  10. ChemView: EPA’s Web Tool for TSCA Chemicals

    EPA Pesticide Factsheets

    Overview of the development and features of ChemView, a new Web-based EPA system that significantly enhances public access to chemical information regulated under the Toxic Substances Control Act (TSCA).

  11. First Fluorine and Chlorine Detections on Mars with ChemCam On-Board MSL

    NASA Astrophysics Data System (ADS)

    Forni, O.; Gaft, M.; Toplis, M.; Clegg, S. M.; Maurice, S.; Wiens, R. C.; Mangold, N.; Sautter, V.; Gasnault, O.; Berger, G.; Nachon, M.; Meslin, P.-Y.; Blaney, D.; Cousin, A.

    2014-07-01

    We report the first detection of fluorine on Mars and the first detection of chlorine with ChemCam onboard MSL/Curiosity. We discuss the plausible mineralogies for these two halogens and their possible origin.

  12. Microsampling homogeneous immunoassay with Cedia digoxin reagents on the Technicon CHEM 1 chemistry analyzer.

    PubMed

    Lua, A C; Chu, D K; Vlastelica, D

    1994-10-01

    We report the determination of digoxin concentration in serum with Microgenics Cedia digoxin reagents on the Technicon CHEM 1. The Technicon CHEM 1 clinical chemistry analyzer has a throughput of 720 tests per hour and uses only 7 microliters each of two reagents. A 100 test kit can perform 2,640 tests. The within-run coefficient of variation (CV) range is 2.3-0.9% and the total CV is 6.3-2.9% at concentrations tested ranging from 1.10 to 2.94 ng/ml. The results of the Technicon CHEM 1 (y) assay correlated well with those by the Technicon RA 1000 system (x) with 31 clinical serum samples (y = -0.03 + 1.11x, r = 0.96). We concluded that the Cedia digoxin assay on the Technicon CHEM 1 provides a very cost-effective, precise, rapid, and accurate means to determine digoxin concentration in serum.

  13. ChemCom: A Software Program for Searching and Comparing Chemical Libraries.

    PubMed

    Saeedipour, Sirus; Tai, David; Fang, Jianwen

    2015-07-27

    An efficient chemical comparator, a computer application facilitating searching and comparing chemical libraries, is useful in drug discovery and other relevant areas. The need for an efficient and user-friendly chemical comparator prompted us to develop ChemCom (Chemical Comparator) based on Java Web Start (JavaWS) technology. ChemCom provides a user-friendly graphical interface to a number of fast algorithms including a novel algorithm termed UnionBit Tree Algorithm. It utilizes an intuitive stepwise mechanism for selecting chemical comparison parameters before starting the comparison process. UnionBit has shown approximately an 165% speedup on average compared to its closest competitive algorithm implemented in ChemCom over real data. It is approximately 11 times faster than the Open Babel FastSearch algorithm in our tests. ChemCom can be accessed free-of-charge via a user-friendly website at http://bioinformatics.org/chemcom/.

  14. Real-time Aerosol Forecasting over North America using RAP-Chem and the GSI.

    NASA Astrophysics Data System (ADS)

    Pagowski, M.

    2015-12-01

    RAP-Chem is an implementation of WRF-Chem meteorology-chemistry model that is run daily at NOAA/ESRL over continental domain for air-quality forecasting. The chemical forecasts are combined with observations of species using three-dimensional variational data assimilation procedure implemented in the Gridpoint Statistical Interpolation (GSI). In the presentation we detail the method of the assimilation and show verification statistics of the model performance.

  15. Comment on 'The diatomic dication CuZn{sup 2+} in the gas phase' [J. Chem. Phys. 135, 034306 (2011)

    SciTech Connect

    Fiser, Jiri; Diez, Reinaldo Pis; Franzreb, Klaus; Alonso, Julio A.

    2013-02-21

    In this Comment, the density functional theory (DFT) calculations carried out by Diez et al. [J. Chem. Phys. 135, 034306 (2011)] are revised within the framework of the coupled-cluster single double triple method. These more sophisticated calculations allow us to show that the {sup 2}{Sigma}{sup +} electronic ground state of CuZn{sup 2+}, characterized as the metastable ground state by DFT calculations, is a repulsive state instead. The {sup 2}{Delta} and {sup 2}{Pi} metastable states of CuZn{sup 2+}, on the other hand, should be responsible for the formation mechanism of the dication through the near-resonant electron transfer CuZn{sup +}+ Ar{sup +}{yields} CuZn{sup 2+}+ Ar reaction.

  16. Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

    PubMed

    Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

    2008-04-01

    We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

  17. radEq Add-On Module for CFD Solver Loci-CHEM

    NASA Technical Reports Server (NTRS)

    McCloud, Peter

    2013-01-01

    Loci-CHEM to be applied to flow velocities where surface radiation due to heating from compression and friction becomes significant. The module adds a radiation equilibrium boundary condition to the computational fluid dynamics (CFD) code to produce accurate results. The module expanded the upper limit for accurate CFD solutions of Loci-CHEM from Mach 4 to Mach 10 based on Space Shuttle Orbiter Re-Entry trajectories. Loci-CHEM already has a very promising architecture and performance, but absence of radiation equilibrium boundary condition limited the application of Loci-CHEM to below Mach 4. The immediate advantage of the add-on module is that it allows Loci-CHEM to work with supersonic flows up to Mach 10. This transformed Loci-CHEM from a rocket engine- heritage CFD code with general subsonic and low-supersonic applications, to an aeroheating code with hypersonic applications. The follow-on advantage of the module is that it is a building block for additional add-on modules that will solve for the heating generated at Mach numbers higher than 10.

  18. Global impacts of tropospheric halogens (Cl, Br, I) on oxidants and composition in GEOS-Chem

    NASA Astrophysics Data System (ADS)

    Sherwen, Tomás; Schmidt, Johan A.; Evans, Mat J.; Carpenter, Lucy J.; Großmann, Katja; Eastham, Sebastian D.; Jacob, Daniel J.; Dix, Barbara; Koenig, Theodore K.; Sinreich, Roman; Ortega, Ivan; Volkamer, Rainer; Saiz-Lopez, Alfonso; Prados-Roman, Cristina; Mahajan, Anoop S.; Ordóñez, Carlos

    2016-09-01

    We present a simulation of the global present-day composition of the troposphere which includes the chemistry of halogens (Cl, Br, I). Building on previous work within the GEOS-Chem model we include emissions of inorganic iodine from the oceans, anthropogenic and biogenic sources of halogenated gases, gas phase chemistry, and a parameterised approach to heterogeneous halogen chemistry. Consistent with Schmidt et al. (2016) we do not include sea-salt debromination. Observations of halogen radicals (BrO, IO) are sparse but the model has some skill in reproducing these. Modelled IO shows both high and low biases when compared to different datasets, but BrO concentrations appear to be modelled low. Comparisons to the very sparse observations dataset of reactive Cl species suggest the model represents a lower limit of the impacts of these species, likely due to underestimates in emissions and therefore burdens. Inclusion of Cl, Br, and I results in a general improvement in simulation of ozone (O3) concentrations, except in polar regions where the model now underestimates O3 concentrations. Halogen chemistry reduces the global tropospheric O3 burden by 18.6 %, with the O3 lifetime reducing from 26 to 22 days. Global mean OH concentrations of 1.28 × 106 molecules cm-3 are 8.2 % lower than in a simulation without halogens, leading to an increase in the CH4 lifetime (10.8 %) due to OH oxidation from 7.47 to 8.28 years. Oxidation of CH4 by Cl is small (˜ 2 %) but Cl oxidation of other VOCs (ethane, acetone, and propane) can be significant (˜ 15-27 %). Oxidation of VOCs by Br is smaller, representing 3.9 % of the loss of acetaldehyde and 0.9 % of the loss of formaldehyde.

  19. Comparison of Laser Induced Breakdown Spectroscopy (LIBS) on Martian Meteorite NWA 7034 to ChemCam Observations at Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Gordon, S.; Newsom, H. E.; Agee, C. B.; Santos, A. R.; Clegg, S. M.; Wiens, R. C.; Lasue, J.; Sautter, V.

    2014-12-01

    The ChemCam instrument on board the Mars Science Laboratory (MSL) Curiosity rover uses laser-induced breakdown spectroscopy (LIBS) to analyze rock and soil targets on Mars from up to 7 m away. The Nd:KGW laser can shoot up to 1000 shots at one location and profile up to 1 mm depth into a rock. Identical LIBS instrumentation is located at Los Alamos National Laboratory and was used to analyze martian meteorite NWA 7034, a non-SNC basaltic breccia whose bulk composition matches the martian surface. Initial LIBS analysis of NWA 7034 included observations on two basaltic clasts in the meteorite. Electron microprobe analysis (EPMA) was performed on the two clasts for comparison with elemental compositions measured using LIBS. The two instruments give similar compositions of major oxides within the error of both techniques. EPMA analysis was also completed on three light-toned clasts and a dark-toned clast in the meteorite. The light-toned clasts have Al/Si vs. (Fe+Mg)/Si compositions ranging from felsic to mafic, and the dark-toned clast shows a mafic composition. A Sammon's map was created to compare LIBS data for NWA 7034 and ChemCam targets Stark, Crestaurum, Link, Portage, Jake_M, Mara, Thor_Lake, Coronation, Pearson, and Prebble. This nonlinear statistical mapping technique is used for clustering assessment of LIBS data in two dimensions. The map shows NWA 7034 clustering in its own location, and the closest similar ChemCam rock targets are La_Reine and Ashuamipi, which are both coarse grained targets that have a mafic component consistent with augite. The most similar ChemCam soil targets are the Crestaurum and Portage. Creation of maps with a greater number of targets will show more of the similarities between NWA 7034 and ChemCam target rocks and soils. Further analysis will compare NWA 7034 LIBS data, data from the paired meteorite NWA 7533, and a variety of ChemCam targets that are similar in morphology and texture.

  20. tmChem: a high performance approach for chemical named entity recognition and normalization

    PubMed Central

    2015-01-01

    Chemical compounds and drugs are an important class of entities in biomedical research with great potential in a wide range of applications, including clinical medicine. Locating chemical named entities in the literature is a useful step in chemical text mining pipelines for identifying the chemical mentions, their properties, and their relationships as discussed in the literature. We introduce the tmChem system, a chemical named entity recognizer created by combining two independent machine learning models in an ensemble. We use the corpus released as part of the recent CHEMDNER task to develop and evaluate tmChem, achieving a micro-averaged f-measure of 0.8739 on the CEM subtask (mention-level evaluation) and 0.8745 f-measure on the CDI subtask (abstract-level evaluation). We also report a high-recall combination (0.9212 for CEM and 0.9224 for CDI). tmChem achieved the highest f-measure reported in the CHEMDNER task for the CEM subtask, and the high recall variant achieved the highest recall on both the CEM and CDI tasks. We report that tmChem is a state-of-the-art tool for chemical named entity recognition and that performance for chemical named entity recognition has now tied (or exceeded) the performance previously reported for genes and diseases. Future research should focus on tighter integration between the named entity recognition and normalization steps for improved performance. The source code and a trained model for both models of tmChem is available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmChem. The results of running tmChem (Model 2) on PubMed are available in PubTator: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator PMID:25810774

  1. Overview of 3 years of ChemCam' chemical compositions along the Curiosity's traverse at Gale Crater.

    NASA Astrophysics Data System (ADS)

    Cousin, Agnès; Wiens, Roger; Maurice, Sylvestre; Gasnault, Olivier

    2016-04-01

    Curiosity rover has been in Gale crater for more than3 years now. It drove ~12 km from its landing point up to the Bagnold Dunes. The ChemCam instrument is widely used to assess the chemistry of rocks and soils at the submillimeter scale. As of sol 1200, ChemCam sampled >1000 targets, corresponding to >300000 laser shots, >6000 images, and many passive spectra. The Bradbury landing site, a plain located at a distal portion of the alluvial fan from Peace Vallis, exposed several float rocks presenting igneous compositions ranging from mafic up to a trachytic end-member. These observations provided an important clue concerning the diversity of early Mars magmatism that was not previously recognized. More igneous float rocks have been observed all along the traverse, being more felsic closer to the landing site, and more mafic near the cratered unit, after the Kimberley formation. The Sheepbed area is essentially composed of mudstones that show a very homogeneous composition, close to the average Martian crust, providing evidence of aqueous episodes with little alteration in this area. ChemCam showed that the bedrock host experienced other diagenetic events with Mg- and Fe-rich clays in erosion-resistant raised ridges on one hand, and calcium sulfate veins on the other hand. The nearby Shaler fluvial sandstone outcrop, the first outcrop of potential deltaic foreset beds, shows K enrichment. This enrichment is also observed at the Kimberley formation (another drill site flanked by foreset beds), located 7 km SW of Shaler, with up to 5.3 wt % at the Mount Remarkable member. Conglomerates have been analyzed in detail all along the traverse as they represent a link between the source rocks and the finer-grained sediments such as the sandstones and mudstones. They have shown an average composition that is enriched in alkalis, Al, and Si compared to the average Martian crust, with a clear enrichment in K2O in the vicinity of the Kimberley formation. Enrichment in K2O at

  2. Chemo-stratigraphy in the Murray Formation Using ChemCam

    NASA Astrophysics Data System (ADS)

    Blaney, D. L.; Anderson, R. B.; Bridges, N.; Bridges, J.; Calef, F. J., III; Clegg, S. M.; Le Deit, L.; Fisk, M. R.; Forni, O.; Gasnault, O.; Kah, L. C.; Kronyak, R. E.; Lanza, N.; Lasue, J.; Mangold, N.; Maurice, S.; Milliken, R.; Ming, D. W.; Nachon, M.; Newsom, H. E.; Rapin, W.; Stack, K.; Sumner, D. Y.; Wiens, R. C.

    2015-12-01

    Curiosity has completed a detailed chemo-stratigraphy analysis at the Pahrump exposure of the Murray formation. In total >570 chemical measurements and supporting remote micro images to classify texturally were collected. Chemical trends with both stratigraphic position and with texture were evaluated. From these data emerges a complex aqueous history where sediments have interacted with fluids with variable chemistry in distinct episodes. The ChemCam data collected at the nearby "Garden City" (GC) vein complex provides constraints on the chemical evolution of the Pahrump. GC is thought be stratigraphically above the Pahrump outcrop. Fluids producing the veins likely also migrated through the Pahrump sediments. Multiple episodes of fluids are evident at GC, forming distinct Ca sulfate, F-rich, enhanced MgO, and FeO-rich veins. These different fluid chemistries could be the result of distinct fluids migrating through the section from a distance with a pre-established chemical signature, fluids locally evolved from water rock interactions, or both. Texturally rocks have been classified into two distinct categories: fine grained or as cross-bedded sandstones. The sandstones have significantly lower SiO2, Al2O3, and K2O and higher FeO, and CaO. Fine grained rocks have further been sub-classified as resistant and recessive with other textural features such as laminations and pits noted.The strongest chemical trend in the fine-grained sandstones shows enhancements in MgO and FeO in erosion-resistant materials compared to fine grained recessive units, suggesting that increased abundance of Mg- and/or iron-rich cements may provide additional strength. The MgO and FeO variations with texture are independent of stratigraphic locations (e.g resistant material at both the bottom and top of the outcrop both are enhanced in MgO and FeO). The presence of the GC MgO and FeO rich veins provides additional evidence for fluids rich in these elements were present in the outcrop. Other

  3. ChemDIS: a chemical-disease inference system based on chemical-protein interactions.

    PubMed

    Tung, Chun-Wei

    2015-01-01

    The characterization of toxicities associated with environmental and industrial chemicals is required for risk assessment. However, we lack the toxicological data for a large portion of chemicals due to the high cost of experiments for a huge number of chemicals. The development of computational methods for identifying potential risks associated with chemicals is desirable for generating testable hypothesis to accelerate the hazard identification process. A chemical-disease inference system named ChemDIS was developed to facilitate hazard identification for chemicals. The chemical-protein interactions from a large database STITCH and protein-disease relationship from disease ontology and disease ontology lite were utilized for chemical-protein-disease inferences. Tools with user-friendly interfaces for enrichment analysis of functions, pathways and diseases were implemented and integrated into ChemDIS. An analysis on maleic acid and sibutramine showed that ChemDIS could be a useful tool for the identification of potential functions, pathways and diseases affected by poorly characterized chemicals. ChemDIS is an integrated chemical-disease inference system for poorly characterized chemicals with potentially affected functions and pathways for experimental validation. ChemDIS server is freely accessible at http://cwtung.kmu.edu.tw/chemdis.

  4. The first synthesis of chem-prep varistor LAC (lightning arrestor connector) granules

    SciTech Connect

    Tuttle, B.A.; Voigt, J.A.; Andrews, L.A.

    1988-03-01

    ZnO variestor granules are the active medis for many lightning arrestor connectors (LACs). The 150 to 200 micron diameter granules provide a controlled electrical breakdown in the 400 micron gap between the electrically conductive pin and web of the connector. Tradiationally, the varistor granules are made from commercially available, reagent grade, mixed oxide powders that range in particle size from 1 to 20 microns. For the first time, we have synthesized varistor granules from chemically prepared powders developed at Sandia. These chem-prep varistor powders are more homogeneous and much finer than the mixed oxide powders; the mean particle size of the chem-prep powders is approximately 0.06 microns. LAC granules were formed from chemically prepared powders by traditional ceramic processing techniques. Although the chem-prep granules were not as spherical as the mixed oxide granules, the chem-prep granules did meet present LAC component requirements for fast-rise breakdown voltage and insulation resistance. The insulation resistance of chem-prep granules for a 200 volt pin-to-web voltage was 100 times less than for mixed oxide granules; however, both types of granules had similar insulation resistance for a 250 volt pin-to-web voltage.

  5. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    PubMed

    McGuire, Ross; Verhoeven, Stefan; Vass, Márton; Vriend, Gerrit; de Esch, Iwan J P; Lusher, Scott J; Leurs, Rob; Ridder, Lars; Kooistra, Albert J; Ritschel, Tina; de Graaf, Chris

    2017-02-27

    3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

  6. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    PubMed Central

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine (http://3d-e-chem.github.io/3D-e-Chem-VM/) that integrates cheminformatics and bioinformatics tools for the analysis of protein–ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein–ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb). PMID:28125221

  7. ChemBank: a small-molecule screening and cheminformatics resource database

    PubMed Central

    Seiler, Kathleen Petri; George, Gregory A.; Happ, Mary Pat; Bodycombe, Nicole E.; Carrinski, Hyman A.; Norton, Stephanie; Brudz, Steve; Sullivan, John P.; Muhlich, Jeremy; Serrano, Martin; Ferraiolo, Paul; Tolliday, Nicola J.; Schreiber, Stuart L.; Clemons, Paul A.

    2008-01-01

    ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector. PMID:17947324

  8. Comment on ``Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics'' [J. Chem. Phys. 134, 204904 (2011)

    NASA Astrophysics Data System (ADS)

    Wittmer, J. P.; Meyer, H.; Johner, A.; Obukhov, S.; Baschnagel, J.

    2013-12-01

    Recent computational studies on melts of nonconcatenated rings suggest compact configurations of fractal dimension df = 3. This begs the question of whether the irregular surfaces of these compact rings may be characterized by a fractal surface dimension ds < 3. We revisit the scaling analysis of the form factor by Halverson et al. [J. Chem. Phys. 134, 204904 (2011)] implying ds ≈ 2.8. Our analysis suggests that this conclusion might be due to the application of the Generalized Porod Law at large wavevectors where length scales other than the total chain size do matter. We present an alternative "decorated Gaussian loop" model which does not require ds < 3.

  9. Interactions between volatile organic compounds and reactive halogen in the tropical marine atmosphere using WRF-Chem

    NASA Astrophysics Data System (ADS)

    Badia, Alba; Reeves, Claire E.; Baker, Alex; Volkamer, Rainer; von Glasow, Roland

    2016-04-01

    Halogen species (chlorine, bromine and iodine) are known to play an important role in the chemistry and oxidizing capacity of the troposphere, particularly in the marine boundary layer (MBL). Reactive halogens cause ozone (O3) destruction, change the HOx and NOX partitioning, affect the oxidation of volatile organic compounds (VOCs) and mercury, reduce the lifetime of methane, and take part in new particle formation. Numerical models predicted that reactive halogen compounds account for 30% of O3 destruction in the MBL and 5-20% globally. There are indications that the chemistry of reactive halogens and oxygenated VOCs (OVOCs) in the tropics are inter-related. Moreover, the presence of aldehydes, such as glyoxal (CHOCHO), has a potential impact on radical cycling and secondary organic aerosol (SOA) formation in the MBL and free troposphere (FT). Model calculations suggest aldehydes to be an important sink for bromine atoms and hence competition for their reaction with O3 forming BrO and so illustrating a link between the cycles of halogens and OVOCs in the marine atmosphere. The main objective of this contribution is to investigate the atmospheric chemistry in the tropical East Pacific with a focus on reactive halogens and OVOCs and their links using the latest version of the Weather Research and Forecasting (WRF) model coupled with Chemistry (WRF-Chem) and field data from the TORERO campaign. WRF-Chem is a highly flexible community model for atmospheric research where aerosol-radiation-cloud feedback processes are taken into account. Our current reaction mechanism in WRF-Chem is based on the MOZART mechanism and has been extended to include bromine, chlorine and iodine chemistry. The MOZART mechanism includes detailed gas-phase chemistry of CHOCHO formation as well as state-of-the-science pathways to form SOA. Oceanic emissions of aldehydes, including CHOCHO, and of organic halogens based on measurements from the TORERO campaign have been added into the model. Sea

  10. The ChemCam Instrument Suite on the Mars Science Laboratory (MSL) Rover: Science Objectives and Mast Unit Description

    USGS Publications Warehouse

    Maurice, S.; Wiens, R.C.; Saccoccio, M.; Barraclough, B.; Gasnault, O.; Forni, O.; Mangold, N.; Baratoux, D.; Bender, S.; Berger, G.; Bernardin, J.; Berthé, M.; Bridges, N.; Blaney, D.; Bouyé, M.; Caïs, P.; Clark, B.; Clegg, S.; Cousin, A.; Cremers, D.; Cros, A.; DeFlores, L.; Derycke, C.; Dingler, B.; Dromart, G.; Dubois, B.; Dupieux, M.; Durand, E.; d'Uston, L.; Fabre, C.; Faure, B.; Gaboriaud, A.; Gharsa, T.; Herkenhoff, K.; Kan, E.; Kirkland, L.; Kouach, D.; Lacour, J.-L.; Langevin, Y.; Lasue, J.; Le Mouélic, S.; Lescure, M.; Lewin, E.; Limonadi, D.; Manhès, G.; Mauchien, P.; McKay, C.; Meslin, P.-Y.; Michel, Y.; Miller, E.; Newsom, Horton E.; Orttner, G.; Paillet, A.; Parès, L.; Parot, Y.; Pérez, R.; Pinet, P.; Poitrasson, F.; Quertier, B.; Sallé, B.; Sotin, Christophe; Sautter, V.; Séran, H.; Simmonds, J.J.; Sirven, J.-B.; Stiglich, R.; Striebig, N.; Thocaven, J.-J.; Toplis, M.J.; Vaniman, D.

    2012-01-01

    ChemCam is a remote sensing instrument suite on board the "Curiosity" rover (NASA) that uses Laser-Induced Breakdown Spectroscopy (LIBS) to provide the elemental composition of soils and rocks at the surface of Mars from a distance of 1.3 to 7 m, and a telescopic imager to return high resolution context and micro-images at distances greater than 1.16 m. We describe five analytical capabilities: rock classification, quantitative composition, depth profiling, context imaging, and passive spectroscopy. They serve as a toolbox to address most of the science questions at Gale crater. ChemCam consists of a Mast-Unit (laser, telescope, camera, and electronics) and a Body-Unit (spectrometers, digital processing unit, and optical demultiplexer), which are connected by an optical fiber and an electrical interface. We then report on the development, integration, and testing of the Mast-Unit, and summarize some key characteristics of ChemCam. This confirmed that nominal or better than nominal performances were achieved for critical parameters, in particular power density (>1 GW/cm2). The analysis spot diameter varies from 350 μm at 2 m to 550 μm at 7 m distance. For remote imaging, the camera field of view is 20 mrad for 1024×1024 pixels. Field tests demonstrated that the resolution (˜90 μrad) made it possible to identify laser shots on a wide variety of images. This is sufficient for visualizing laser shot pits and textures of rocks and soils. An auto-exposure capability optimizes the dynamical range of the images. Dedicated hardware and software focus the telescope, with precision that is appropriate for the LIBS and imaging depths-of-field. The light emitted by the plasma is collected and sent to the Body-Unit via a 6 m optical fiber. The companion to this paper (Wiens et al. this issue) reports on the development of the Body-Unit, on the analysis of the emitted light, and on the good match between instrument performance and science specifications.

  11. The ChemCam Instrument Suite on the Mars Science Laboratory (MSL) Rover: Science Objectives and Mast Unit Description

    NASA Astrophysics Data System (ADS)

    Maurice, S.; Wiens, R. C.; Saccoccio, M.; Barraclough, B.; Gasnault, O.; Forni, O.; Mangold, N.; Baratoux, D.; Bender, S.; Berger, G.; Bernardin, J.; Berthé, M.; Bridges, N.; Blaney, D.; Bouyé, M.; Caïs, P.; Clark, B.; Clegg, S.; Cousin, A.; Cremers, D.; Cros, A.; DeFlores, L.; Derycke, C.; Dingler, B.; Dromart, G.; Dubois, B.; Dupieux, M.; Durand, E.; d'Uston, L.; Fabre, C.; Faure, B.; Gaboriaud, A.; Gharsa, T.; Herkenhoff, K.; Kan, E.; Kirkland, L.; Kouach, D.; Lacour, J.-L.; Langevin, Y.; Lasue, J.; Le Mouélic, S.; Lescure, M.; Lewin, E.; Limonadi, D.; Manhès, G.; Mauchien, P.; McKay, C.; Meslin, P.-Y.; Michel, Y.; Miller, E.; Newsom, H. E.; Orttner, G.; Paillet, A.; Parès, L.; Parot, Y.; Pérez, R.; Pinet, P.; Poitrasson, F.; Quertier, B.; Sallé, B.; Sotin, C.; Sautter, V.; Séran, H.; Simmonds, J. J.; Sirven, J.-B.; Stiglich, R.; Striebig, N.; Thocaven, J.-J.; Toplis, M. J.; Vaniman, D.

    2012-09-01

    ChemCam is a remote sensing instrument suite on board the "Curiosity" rover (NASA) that uses Laser-Induced Breakdown Spectroscopy (LIBS) to provide the elemental composition of soils and rocks at the surface of Mars from a distance of 1.3 to 7 m, and a telescopic imager to return high resolution context and micro-images at distances greater than 1.16 m. We describe five analytical capabilities: rock classification, quantitative composition, depth profiling, context imaging, and passive spectroscopy. They serve as a toolbox to address most of the science questions at Gale crater. ChemCam consists of a Mast-Unit (laser, telescope, camera, and electronics) and a Body-Unit (spectrometers, digital processing unit, and optical demultiplexer), which are connected by an optical fiber and an electrical interface. We then report on the development, integration, and testing of the Mast-Unit, and summarize some key characteristics of ChemCam. This confirmed that nominal or better than nominal performances were achieved for critical parameters, in particular power density (>1 GW/cm2). The analysis spot diameter varies from 350 μm at 2 m to 550 μm at 7 m distance. For remote imaging, the camera field of view is 20 mrad for 1024×1024 pixels. Field tests demonstrated that the resolution (˜90 μrad) made it possible to identify laser shots on a wide variety of images. This is sufficient for visualizing laser shot pits and textures of rocks and soils. An auto-exposure capability optimizes the dynamical range of the images. Dedicated hardware and software focus the telescope, with precision that is appropriate for the LIBS and imaging depths-of-field. The light emitted by the plasma is collected and sent to the Body-Unit via a 6 m optical fiber. The companion to this paper (Wiens et al. this issue) reports on the development of the Body-Unit, on the analysis of the emitted light, and on the good match between instrument performance and science specifications.

  12. Soil diversity and hydration as observed by ChemCam at Gale crater, Mars

    USGS Publications Warehouse

    Meslin, P.-Y.; Gasnault, O.; Forni, O.; Schroder, S.; Cousin, A.; Berger, G.; Clegg, S.M.; Lasue, J.; Maurice, S.; Sautter, V.; Le Mouélic, S.; Wiens, R.C.; Fabre, C.; Goetz, W.; Bish, D.L.; Mangold, N.; Ehlmann, B.; Lanza, N.; Harri, A.-M.; Anderson, Ryan Bradley; Rampe, E.; McConnochie, T.H.; Pinet, P.; Blaney, D.; ,; Archer, D.; Barraclough, B.; Bender, S.; Blake, D.; Blank, J.G.; Bridges, N.; Clark, B. C.; DeFlores, L.; Delapp, D.; Dromart, G.; Dyar, M.D.; Fisk, M. R.; Gondet, B.; Grotzinger, J.; Herkenhoff, K.; Johnson, J.; Lacour, J.-L.; Langevin, Y.; Leshin, L.; Lewin, E.; Madsen, M.B.; Melikechi, N.; Mezzacappa, Alissa; Mischna, M.A.; Moores, J.E.; Newsom, H.; Ollila, A.; ,; Renno, N.; Sirven, J.B.; Tokar, R.; de la Torre, M.; d'Uston, L.; Vaniman, D.; Yingst, A.

    2013-01-01

    The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

  13. A algorithm benchmark data suite for chemical and biological (chem/bio) defense applications

    NASA Astrophysics Data System (ADS)

    Slamani, Mohamed-Adel; Fisk, Brian; Chyba, Thomas; Emge, Darren; Waugh, Steve

    2008-04-01

    A Chem/Bio Defense Algorithm Benchmark is proposed as a way to leverage algorithm expertise and apply it to high fidelity Chem/Bio challenge problems in a high fidelity simulation environment. Initially intended to provide risk mitigation to the DTRA-sponsored US Army CUGR ACTD, its intent is to enable the assessment and transition of algorithms to support P3I of future spiral updates. The key chemical sensor in the CUGR ACTD is the Joint Contaminated Surface Detector (JCSD), a short-range stand-off Raman spectroscopy sensor for tactical in-the-field applications. The significant challenges in discriminating chemical signatures in such a system include, but are not limited to, complex background clutter and low signal to noise ratios (SNR). This paper will present an overview of the Chem-Bio Defense Algorithm Benchmark, and the JCSD Challenge Problem specifically.

  14. MTCI/ThermoChem steam reforming process for solid fuels for combined cycle power generation

    SciTech Connect

    Mansour, M.N.; Voelker, G.; Dural-Swamy, K.

    1995-12-31

    Manufacturing and Technology Conversion International, Inc. (MTCI) has developed a novel technology to convert solid fuels including biomass, coal, municipal solid waste (MSW) and wastewater sludges into usable syngas by steam reforming in an indirectly heated, fluid-bed reactor. MTCI has licensed and patented the technology to ThermoChem, Inc. Both MTCI and ThermoChem have built two modular commercial-scale demonstration units: one for recycle paper mill rejects (similar to refuse-derived fuel [RDF]), and another for chemical recovery of black liquor. ThermoChem has entered into an agreement with Ajinkyatara Cooperative Sugar Factory, India, for building a 10 MW combined cycle power generation facility based on bagasse and agro-residue gasification.

  15. Soil diversity and hydration as observed by ChemCam at Gale crater, Mars.

    PubMed

    Meslin, P-Y; Gasnault, O; Forni, O; Schröder, S; Cousin, A; Berger, G; Clegg, S M; Lasue, J; Maurice, S; Sautter, V; Le Mouélic, S; Wiens, R C; Fabre, C; Goetz, W; Bish, D; Mangold, N; Ehlmann, B; Lanza, N; Harri, A-M; Anderson, R; Rampe, E; McConnochie, T H; Pinet, P; Blaney, D; Léveillé, R; Archer, D; Barraclough, B; Bender, S; Blake, D; Blank, J G; Bridges, N; Clark, B C; DeFlores, L; Delapp, D; Dromart, G; Dyar, M D; Fisk, M; Gondet, B; Grotzinger, J; Herkenhoff, K; Johnson, J; Lacour, J-L; Langevin, Y; Leshin, L; Lewin, E; Madsen, M B; Melikechi, N; Mezzacappa, A; Mischna, M A; Moores, J E; Newsom, H; Ollila, A; Perez, R; Renno, N; Sirven, J-B; Tokar, R; de la Torre, M; d'Uston, L; Vaniman, D; Yingst, A

    2013-09-27

    The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

  16. Soil Diversity and Hydration as Observed by ChemCam at Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Meslin, P.-Y.; Gasnault, O.; Forni, O.; Schröder, S.; Cousin, A.; Berger, G.; Clegg, S. M.; Lasue, J.; Maurice, S.; Sautter, V.; Le Mouélic, S.; Wiens, R. C.; Fabre, C.; Goetz, W.; Bish, D.; Mangold, N.; Ehlmann, B.; Lanza, N.; Harri, A.-M.; Anderson, R.; Rampe, E.; McConnochie, T. H.; Pinet, P.; Blaney, D.; Léveillé, R.; Archer, D.; Barraclough, B.; Bender, S.; Blake, D.; Blank, J. G.; Bridges, N.; Clark, B. C.; DeFlores, L.; Delapp, D.; Dromart, G.; Dyar, M. D.; Fisk, M.; Gondet, B.; Grotzinger, J.; Herkenhoff, K.; Johnson, J.; Lacour, J.-L.; Langevin, Y.; Leshin, L.; Lewin, E.; Madsen, M. B.; Melikechi, N.; Mezzacappa, A.; Mischna, M. A.; Moores, J. E.; Newsom, H.; Ollila, A.; Perez, R.; Renno, N.; Sirven, J.-B.; Tokar, R.; de la Torre, M.; d'Uston, L.; Vaniman, D.; Yingst, A.; Kemppinen, Osku; Minitti, Michelle; Cremers, David; Bell, James F.; Edgar, Lauren; Farmer, Jack; Godber, Austin; Wadhwa, Meenakshi; Wellington, Danika; McEwan, Ian; Newman, Claire; Richardson, Mark; Charpentier, Antoine; Peret, Laurent; King, Penelope; Weigle, Gerald; Schmidt, Mariek; Li, Shuai; Milliken, Ralph; Robertson, Kevin; Sun, Vivian; Baker, Michael; Edwards, Christopher; Farley, Kenneth; Griffes, Jennifer; Miller, Hayden; Newcombe, Megan; Pilorget, Cedric; Rice, Melissa; Siebach, Kirsten; Stack, Katie; Stolper, Edward; Brunet, Claude; Hipkin, Victoria; Marchand, Geneviève; Sánchez, Pablo Sobrón; Favot, Laurent; Cody, George; Steele, Andrew; Flückiger, Lorenzo; Lees, David; Nefian, Ara; Martin, Mildred; Gailhanou, Marc; Westall, Frances; Israël, Guy; Agard, Christophe; Baroukh, Julien; Donny, Christophe; Gaboriaud, Alain; Guillemot, Philippe; Lafaille, Vivian; Lorigny, Eric; Paillet, Alexis; Pérez, René; Saccoccio, Muriel; Yana, Charles; Armiens-Aparicio, Carlos; Rodríguez, Javier Caride; Blázquez, Isaías Carrasco; Gómez, Felipe Gómez; Gómez-Elvira, Javier; Hettrich, Sebastian; Malvitte, Alain Lepinette; Jiménez, Mercedes Marín; Martínez-Frías, Jesús; Martín-Soler, Javier; Martín-Torres, F. Javier; Jurado, Antonio Molina; Mora-Sotomayor, Luis; Caro, Guillermo Muñoz; López, Sara Navarro; Peinado-González, Verónica; Pla-García, Jorge; Manfredi, José Antonio Rodriguez; Romeral-Planelló, Julio José; Fuentes, Sara Alejandra Sans; Martinez, Eduardo Sebastian; Redondo, Josefina Torres; Urqui-O'Callaghan, Roser; Mier, María-Paz Zorzano; Chipera, Steve; Mauchien, Patrick; Manning, Heidi; Fairén, Alberto; Hayes, Alexander; Joseph, Jonathan; Squyres, Steven; Sullivan, Robert; Thomas, Peter; Dupont, Audrey; Lundberg, Angela; DeMarines, Julia; Grinspoon, David; Reitz, Günther; Prats, Benito; Atlaskin, Evgeny; Genzer, Maria; Haukka, Harri; Kahanpää, Henrik; Kauhanen, Janne; Kemppinen, Osku; Paton, Mark; Polkko, Jouni; Schmidt, Walter; Siili, Tero; Wray, James; Wilhelm, Mary Beth; Poitrasson, Franck; Patel, Kiran; Gorevan, Stephen; Indyk, Stephen; Paulsen, Gale; Gupta, Sanjeev; Schieber, Juergen; Geffroy, Claude; Baratoux, David; Cros, Alain; Lee, Qiu-Mei; Pallier, Etienne; Parot, Yann; Toplis, Mike; Brunner, Will; Heydari, Ezat; Achilles, Cherie; Oehler, Dorothy; Sutter, Brad; Cabane, Michel; Coscia, David; Israël, Guy; Szopa, Cyril; Robert, François; Nachon, Marion; Buch, Arnaud; Stalport, Fabien; Coll, Patrice; François, Pascaline; Raulin, François; Teinturier, Samuel; Cameron, James; Dingler, Robert; Jackson, Ryan Steele; Johnstone, Stephen; Little, Cynthia; Nelson, Tony; Williams, Richard B.; Jones, Andrea; Kirkland, Laurel; Treiman, Allan; Baker, Burt; Cantor, Bruce; Caplinger, Michael; Davis, Scott; Duston, Brian; Edgett, Kenneth; Fay, Donald; Hardgrove, Craig; Harker, David; Herrera, Paul; Jensen, Elsa; Kennedy, Megan R.; Krezoski, Gillian; Krysak, Daniel; Lipkaman, Leslie; Malin, Michael; McCartney, Elaina; McNair, Sean; Nixon, Brian; Posiolova, Liliya; Ravine, Michael; Salamon, Andrew; Saper, Lee; Stoiber, Kevin; Supulver, Kimberley; Van Beek, Jason; Van Beek, Tessa; Zimdar, Robert; French, Katherine Louise; Iagnemma, Karl; Miller, Kristen; Summons, Roger; Goesmann, Fred; Hviid, Stubbe; Johnson, Micah; Lefavor, Matthew; Lyness, Eric; Breves, Elly; Fassett, Caleb; Bristow, Thomas; DesMarais, David; Edwards, Laurence; Haberle, Robert; Hoehler, Tori; Hollingsworth, Jeff; Kahre, Melinda; Keely, Leslie; McKay, Christopher; Wilhelm, Mary Beth; Bleacher, Lora; Brinckerhoff, William; Choi, David; Conrad, Pamela; Dworkin, Jason P.; Eigenbrode, Jennifer; Floyd, Melissa; Freissinet, Caroline; Garvin, James; Glavin, Daniel; Harpold, Daniel; Jones, Andrea; Mahaffy, Paul; Martin, David K.; McAdam, Amy; Pavlov, Alexander; Raaen, Eric; Smith, Michael D.; Stern, Jennifer; Tan, Florence; Trainer, Melissa; Meyer, Michael; Posner, Arik; Voytek, Mary; Anderson, Robert C.; Aubrey, Andrew; Beegle, Luther W.; Behar, Alberto; Brinza, David; Calef, Fred; Christensen, Lance; Crisp, Joy A.; Feldman, Jason; Feldman, Sabrina; Flesch, Gregory; Hurowitz, Joel; Jun, Insoo; Keymeulen, Didier; Maki, Justin; Morookian, John Michael; Parker, Timothy; Pavri, Betina; Schoppers, Marcel; Sengstacken, Aaron; Simmonds, John J.; Spanovich, Nicole; Vasavada, Ashwin R.; Webster, Christopher R.; Yen, Albert; Cucinotta, Francis; Jones, John H.; Ming, Douglas; Morris, Richard V.; Niles, Paul; Nolan, Thomas; Radziemski, Leon; Berman, Daniel; Dobrea, Eldar Noe; Williams, Rebecca M. E.; Lewis, Kevin; Cleghorn, Timothy; Huntress, Wesley; Manhès, Gérard; Hudgins, Judy; Olson, Timothy; Stewart, Noel; Sarrazin, Philippe; Grant, John; Vicenzi, Edward; Wilson, Sharon A.; Bullock, Mark; Ehresmann, Bent; Hamilton, Victoria; Hassler, Donald; Peterson, Joseph; Rafkin, Scot; Zeitlin, Cary; Fedosov, Fedor; Golovin, Dmitry; Karpushkina, Natalya; Kozyrev, Alexander; Litvak, Maxim; Malakhov, Alexey; Mitrofanov, Igor; Mokrousov, Maxim; Nikiforov, Sergey; Prokhorov, Vasily; Sanin, Anton; Tretyakov, Vladislav; Varenikov, Alexey; Vostrukhin, Andrey; Kuzmin, Ruslan; Wolff, Michael; McLennan, Scott; Botta, Oliver; Drake, Darrell; Bean, Keri; Lemmon, Mark; Schwenzer, Susanne P.; Lee, Ella Mae; Sucharski, Robert; Hernández, Miguel Ángel de Pablo; Ávalos, Juan José Blanco; Ramos, Miguel; Kim, Myung-Hee; Malespin, Charles; Plante, Ianik; Muller, Jan-Peter; Navarro-González, Rafael; Ewing, Ryan; Boynton, William; Downs, Robert; Fitzgibbon, Mike; Harshman, Karl; Morrison, Shaunna; Dietrich, William; Kortmann, Onno; Palucis, Marisa; Sumner, Dawn Y.; Williams, Amy; Lugmair, Günter; Wilson, Michael A.; Rubin, David; Jakosky, Bruce; Balic-Zunic, Tonci; Frydenvang, Jens; Jensen, Jaqueline Kløvgaard; Kinch, Kjartan; Koefoed, Asmus; Stipp, Susan Louise Svane; Boyd, Nick; Campbell, John L.; Gellert, Ralf; Perrett, Glynis; Pradler, Irina; VanBommel, Scott; Jacob, Samantha; Owen, Tobias; Rowland, Scott; Atlaskin, Evgeny; Savijärvi, Hannu; Boehm, Eckart; Böttcher, Stephan; Burmeister, Sönke; Guo, Jingnan; Köhler, Jan; García, César Martín; Mueller-Mellin, Reinhold; Wimmer-Schweingruber, Robert; Bridges, John C.; Benna, Mehdi; Franz, Heather; Bower, Hannah; Brunner, Anna; Blau, Hannah; Boucher, Thomas; Carmosino, Marco; Atreya, Sushil; Elliott, Harvey; Halleaux, Douglas; Rennó, Nilton; Wong, Michael; Pepin, Robert; Elliott, Beverley; Spray, John; Thompson, Lucy; Gordon, Suzanne; Williams, Joshua; Vasconcelos, Paulo; Bentz, Jennifer; Nealson, Kenneth; Popa, Radu; Kah, Linda C.; Moersch, Jeffrey; Tate, Christopher; Day, Mackenzie; Kocurek, Gary; Hallet, Bernard; Sletten, Ronald; Francis, Raymond; McCullough, Emily; Cloutis, Ed; ten Kate, Inge Loes; Kuzmin, Ruslan; Arvidson, Raymond; Fraeman, Abigail; Scholes, Daniel; Slavney, Susan; Stein, Thomas; Ward, Jennifer; Berger, Jeffrey

    2013-09-01

    The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

  17. ChemCam on MSL 2009: first laser induced breakdown spectrometer for space science

    SciTech Connect

    Wiens, Roger C

    2008-01-01

    ChemCam is one of the 10 instrument suites on the Mars Science Laboratory, a martian rover being built by Jet Propulsion Laboratory, for the next NASA mission to Mars (MSL 2009). ChemCam is an instrument package consisting of two remote sensing instruments: a Laser-Induced Breakdown Spectrometer (LIBS) and a Remote Micro-Imager (RMI). LIBS provides elemental compositions of rocks and soils, while the RMI places the LIBS analyses in their geomorphologic context. Both instruments rely on an autofocus capability to precisely focus on the chosen target, located at distances from the rover comprised between 1 and 9 m for LIBS, and 2 m and infinity for RMI. ChemCam will help determine which samples, within the vicinity of the MSL rover, are of sufficient interest to use the contact and in-situ instruments for further characterization. It will provide valuable analyses of samples that are inaccessible to contact and in-situ instruments, and of a much larger number of samples than can be done with this kind of instrument. ChemCam also has a capability to provide passive spectroscopy data of rocks and soils on Mars. ChemCam hardware consists of a Mast Unit (MU), provided by France, and a Body Unit (BU) built and tested in the USA. The Flight Model of the MU is assembled, tested and now available in the USA, while the BU is currently being assembled and tested. Both will be connected by the end of year '08 for end-to-end functional and performance tests, before delivery to JPL and assembly on the MSL rover. Launch is scheduled for October 09. After describing the concept of ChemCam, this presentation focuses on its French part, Mast Unit. The results presented show that Mast Unit is able to generate a plasma and collect its light, over the full applicable ranges of distances and temperatures on Mars.

  18. Calibrating the ChemCam LIBS for carbonate minerals on Mars

    SciTech Connect

    Wiens, Roger C; Clegg, Samuel M; Ollila, Ann M; Barefield, James E; Lanza, Nina; Newsom, Horton E

    2009-01-01

    The ChemCam instrument suite on board the NASA Mars Science Laboratory (MSL) rover includes the first LIBS instrument for extraterrestrial applications. Here we examine carbonate minerals in a simulated martian environment using the LIDS technique in order to better understand the in situ signature of these materials on Mars. Both chemical composition and rock type are determined using multivariate analysis (MVA) techniques. Composition is confirmed using scanning electron microscopy (SEM) techniques. Our initial results suggest that ChemCam can recognize and differentiate between carbonate materials on Mars.

  19. Calibrating the ChemCam laser-induced breakdown spectroscopy instrument for carbonate minerals on Mars

    SciTech Connect

    Lanza, Nina L.; Wiens, Roger C.; Clegg, Samuel M.; Ollila, Ann M.; Humphries, Seth D.; Newsom, Horton E.; Barefield, James E.

    2010-05-01

    The ChemCam instrument suite onboard the NASA Mars Science Laboratory rover includes the first laser-induced breakdown spectroscopy (LIBS) instrument for extraterrestrial applications. Here we examine carbonate minerals in a simulated martian environment to better understand the LIBS signature of these materials on Mars. Both chemical composition and rock type are determined using multivariate analysis techniques. Composition is confirmed using scanning electron microscopy. Our results show that ChemCam can recognize and differentiate between different types of carbonate materials on Mars.

  20. Calibrating the ChemCam LIBS for Carbonate Minerals on Mars

    DOE R&D Accomplishments Database

    Wiens, Roger C.; Clegg, Samuel M.; Ollila, Ann M.; Barefield, James E.; Lanza, Nina; Newsom, Horton E.

    2009-01-01

    The ChemCam instrument suite on board the NASA Mars Science Laboratory (MSL) rover includes the first LIBS instrument for extraterrestrial applications. Here we examine carbonate minerals in a simulated martian environment using the LIDS technique in order to better understand the in situ signature of these materials on Mars. Both chemical composition and rock type are determined using multivariate analysis (MVA) techniques. Composition is confirmed using scanning electron microscopy (SEM) techniques. Our initial results suggest that ChemCam can recognize and differentiate between carbonate materials on Mars.

  1. EarthChem: International Collaboration for Solid Earth Geochemistry in Geoinformatics

    NASA Astrophysics Data System (ADS)

    Walker, J. D.; Lehnert, K. A.; Hofmann, A. W.; Sarbas, B.; Carlson, R. W.

    2005-12-01

    The current on-line information systems for igneous rock geochemistry - PetDB, GEOROC, and NAVDAT - convincingly demonstrate the value of rigorous scientific data management of geochemical data for research and education. The next generation of hypothesis formulation and testing can be vastly facilitated by enhancing these electronic resources through integration of available datasets, expansion of data coverage in location, time, and tectonic setting, timely updates with new data, and through intuitive and efficient access and data analysis tools for the broader geosciences community. PetDB, GEOROC, and NAVDAT have therefore formed the EarthChem consortium (www.earthchem.org) as a international collaborative effort to address these needs and serve the larger earth science community by facilitating the compilation, communication, serving, and visualization of geochemical data, and their integration with other geological, geochronological, geophysical, and geodetic information to maximize their scientific application. We report on the status of and future plans for EarthChem activities. EarthChem's development plan includes: (1) expanding the functionality of the web portal to become a `one-stop shop for geochemical data' with search capability across databases, standardized and integrated data output, generally applicable tools for data quality assessment, and data analysis/visualization including plotting methods and an information-rich map interface; and (2) expanding data holdings by generating new datasets as identified and prioritized through community outreach, and facilitating data contributions from the community by offering web-based data submission capability and technical assistance for design, implementation, and population of new databases and their integration with all EarthChem data holdings. Such federated databases and datasets will retain their identity within the EarthChem system. We also plan on working with publishers to ease the assimilation

  2. Calcium Sulfate Characterized by ChemCam/Curiosity at Gale Crater, Mars

    NASA Technical Reports Server (NTRS)

    Nachon, M.; Clegg, S. N.; Mangold, N.; Schroeder, S.; Kah, L. C.; Dromart, G.; Ollila, A.; Johnson, J. R.; Oehler, D. Z.; Bridges, J. C.; hide

    2014-01-01

    Onboard the Mars Science Laboratory (MSL) Curiosity rover, the ChemCam instrument consists of :(1) a Laser-Induced Breakdown Spectrometer (LIBS) for elemental analysis of the targets [1;2] and (2) a Remote Micro Imager (RMI), for the imaging context of laser analysis [3]. Within the Gale crater, Curiosity traveled from Bradbury Landing through the Rocknest region and into Yellowknife Bay (YB). In the latter, abundant light-toned fracture-fill material were seen [4;5]. ChemCam analysis demonstrate that those fracture fills consist of calcium sulfates [6].

  3. 2005 Science and Technology for Chem-Bio Information Systems (S and T CBIS) volume 3 Thursday

    DTIC Science & Technology

    2005-10-28

    Protection Without Chem-Bio Sensors: Low Cost, Dual Use, Alternative Sensor and Information Architectures, Mr. Steven S. Streetman, ENSCO, Inc. Working...Steven Streetman Chem-Bio Protection Without Chem-Bio Sensors: Low Cost, Dual Use Alternative Sensor and Information Architectures...Concentration 100 – 40000 PPM Moisture Mixing ratio X Air Quality [NOX], VOC, O3, … Land Use Urban, ocean, forest, … X Methodology: Surrogate for Air

  4. Fluorine observations by ChemCam: A tracer of magmatic and hydrothermal processes in the martian crust

    NASA Astrophysics Data System (ADS)

    Clegg, S. M.; Forni, O.; Toplis, M. J.; Wiens, R. C.; Gasnault, O.; Sautter, V.; Mangold, N.; Maurice, S.

    2014-12-01

    The ChemCam LIBS instrument on the Curiosity rover has observed fluorine in more than 60 locations along the traverse. These are the first fluorine detections on Mars, although the SNC meteorites contain moderate amounts of F, suggesting that is present in the Mars crust. The detection limit is < 0.4 wt % but requires the simultaneous presence of Ca in the LIBS plasma (Gaft et al., 2014). Approximately one fourth of the observations were made on conglomerate clasts in the Bradbury Rise area near the landing site, and another third were made in sediments in the Kimberley area (around sol 550). In these targets F was correlated with K, Al, and Si enrichments; in the Kimberley area they were also correlated with Li enrichments in the 10s of ppm. The most likely mineral host in these settings is muscovite and potentially also biotite. In other observations the fluorine is correlated with high Ca; P was observed above the relatively high LIBS detection limit in some targets, suggesting the presence of fluorapatites. Chlorine was not found in association with fluorine. A number of these observations were made in the rocks around the aeolian drift (around sol 60). The presence of the implied apatites and mica minerals has strong implications for the petrologic environment in which these phases were formed. We will discuss the origin and possible processes that led to the presence of these fluorine-bearing targets.

  5. Comment on ``Unified explanation of the anomalous dynamic properties of highly asymmetric polymer blends'' [J. Chem. Phys. 138, 054903 (2013)

    NASA Astrophysics Data System (ADS)

    Colmenero, J.

    2013-05-01

    In a recent paper by Ngai and Capaccioli ["Unified explanation of the anomalous dynamic properties of highly asymmetric polymer blends," J. Chem. Phys. 138, 054903 (2013), 10.1063/1.4789585] the authors claimed that the so-called coupling model (CM) provides a unified explanation of all dynamical anomalies that have been reported for dynamically asymmetric blends over last ten years. Approximately half of the paper is devoted to chain-dynamic properties involving un-entangled polymers. According to the authors, the application of the CM to these results is based on the existence of a crossover at a time tc ≈ 1-2 ns of the magnitudes describing chain-dynamics. Ngai and Capaccioli claimed that the existence of such a crossover is supported by the neutron scattering and MD-simulation results, corresponding to the blend poly(methyl methacrylate)/poly(ethylene oxide), by Niedzwiedz et al. [Phys. Rev. Lett. 98, 168301 (2007), 10.1103/PhysRevLett.98.168301] and Brodeck et al. [Macromolecules 43, 3036 (2010), 10.1021/ma902820a], respectively. Being one of the authors of these two papers, I will demonstrate here that there is no evidence supporting such a crossover in the data reported in these papers.

  6. 2005 Science and Technology for Chem-Bio Information Systems (S and T CBIS). Volume 1 - Tuesday

    DTIC Science & Technology

    2005-10-28

    Untitled Document 2005 Science and Technology for Chem-Bio Information Systems.html[9/7/ 2016 3:43:54 PM] Science and Technology for Chem-Bio...Persistence and Prediction Modeling: Untitled Document 2005 Science and Technology for Chem-Bio Information Systems.html[9/7/ 2016 3:43:54 PM] Session A-II...NMSU and Sundara Vadlamudi and Markus Binder, Monterey Untitled Document 2005 Science and Technology for Chem-Bio Information Systems.html[9/7/ 2016 3

  7. Classification of igneous rocks analyzed by ChemCam at Gale crater, Mars

    NASA Astrophysics Data System (ADS)

    Cousin, Agnes; Sautter, Violaine; Payré, Valérie; Forni, Olivier; Mangold, Nicolas; Gasnault, Olivier; Le Deit, Laetitia; Johnson, Jeff; Maurice, Sylvestre; Salvatore, Mark; Wiens, Roger C.; Gasda, Patrick; Rapin, William

    2017-05-01

    Several recent studies have revealed that Mars is not a simple basalt-covered planet, but has a more complex geological history. In Gale crater on Mars, the Curiosity rover discovered 59 igneous rocks. This paper focuses on their textures (acquired from the cameras such as MAHLI and MastCam) and their geochemical compositions that have been obtained using the ChemCam instrument. Light-toned crystals have been observed in most of the rocks. They correspond to feldspars ranging from andesines/oligoclases to anorthoclases and sanidines in the leucocratic vesiculated rocks. Darker crystals observed in all igneous rocks (except the leucocratic vesiculated ones) were analyzed by LIBS and mainly identified as Fe-rich pigeonites and Fe-augites. Iron oxides have been observed in all groups whereas F-bearing minerals have been detected only in few of them. From their textural analysis and their whole-rock compositions, all these 59 igneous rocks have been classified in five different groups; from primitive rocks i.e. dark aphanitic basalts/basanites, trachybasalts, tephrites and fine/coarse-grained gabbros/norites to more evolved materials i.e. porphyritic trachyandesites, leucocratic trachytes and quartz-diorites. The basalts and gabbros are found all along the traverse of the rover, whereas the felsic rocks are located before the Kimberley formation, i.e. close to the Peace Vallis alluvial fan deposits. This suggests that these alkali rocks have been transported by fluvial activity and could come from the Northern rim of the crater, and may correspond to deeper strata buried under basaltic regolith (Sautter et al., 2015). Some of the basaltic igneous rocks are surprisingly enriched in iron, presenting low Mg# similar to the nakhlite parental melt that cannot be produced by direct melting of the Dreibus and Wanke (1986) martian primitive mantle. The basaltic rocks at Gale are thus different from Gusev basalts. They could originate from different mantle reservoirs, or they

  8. MicroChemLab, A Novel Approach for Handheld Chemical Sensing

    NASA Astrophysics Data System (ADS)

    Lewis, Patrick

    2003-03-01

    In 1996, Sandia National Laboratories began development of a chemical sensing platform based on microfabricated components. The goal of the project was to develop a handheld system for the detection of chemical warfare (CW) agent vapors in air. The components developed for this project are analogous to devices used in analytical laboratories. The benefit of microfabrication is that the resulting components are small and require little power to operate. The key elements of MicroChemLab are a sample collector - preconcentrator, a GC column and a surface acoustic wave (SAW) array detector. The preconcentrator is a thermally isolated silicon nitride membrane with a resistive heater patterned on one side and a sorptive sol gel film deposited on the other. Since the membrane has a very small mass, the resistive heater can ballistically elevate the temperature of the sorptive film to 200° C in approximately 10 ms. The sol gel film collects target compounds efficiently, but rejects volatile industrial solvents like alcohols, ketones, etc. The GC column is a one-meter high aspect ratio spiral channel etched in silicon with an anodically bonded pyrex lid completing the channel. A heater patterned on the silicon allows the column to be temperature ramped. Analytes injected from the preconcentrator are separated in this stage. The SAW array detector contains 3 delay lines used for sensing and 1 reference delay line. Each delay line is driven by an application specific integrated circuit (ASIC) at 500 MHz. Instead of counting frequency, additional ASICs incorporate a phase comparator that delivers a DC signal proportional to the amount of phase change. The three sensing elements of the detector provide a pattern that is indicative of the class of compound detected i.e. nerve agents or blister agents. Combined, these components provide a selective and sensitive handheld solution for the detection of chemical warfare agents. We will present lab data showing the performance of

  9. Compositions of Sub-Millimeter-Size Clasts seen by ChemCam in Martian Soils at Gale : A Window Into the Production processes of Soils

    NASA Astrophysics Data System (ADS)

    Cousin, A.; Meslin, P.; Forni, O.; Rapin, W.; Tokar, R. L.; Fabre, C.; Wiens, R. C.; Gasnault, O.; Ollila, A.; Maurice, S.; Lasue, J.; Sautter, V.; Clegg, S. M.; Le Mouélic, S.; Dromart, G.; Mangold, N.; Berger, G.; Team, M.

    2013-12-01

    Curiosity landed the August 6, 2012 in Gale Crater, Mars. With its 80 kg payload, this rover possesses unique analytical capabilities to investigate the chemistry and mineralogy of the Martian soil. In particular, the ChemCam laser-induced breakdown spectroscopy (LIBS) instrument allows shallow (mm to cm) soil depth profile analysis, thanks to shot-to-shot spectra acquisition (usually 30 laser shots are performed, but many more can be done). This instrument gives for the first time a good opportunity to carry out large numbers of analyses on soil chemistry and its homogeneity at fine spatial scales (from 360 to 550 μm [Maurice et al, 2012]). This study is focused on the geochemical diversity observed between different soil separates, in particular between fine sand and coarse sand particles, whose mobility and geographical origin are likely to be different. Previous missions have shown that the soils have a uniform composition planet-wide [Yen et al., 2005]. Analyses performed by the APXS and by ChemCam in an aeolian sand shadow and in its vicinity extend this result to the fine-grained soils encountered in Gale Crater [Blake et al., 2013; Meslin et al., 2013]. However, ChemCam has sampled more than 170 soils during the first 250 sols, and has revealed the presence of three kinds of soils in Gale: i) mm-sized grains of felsic composition, usually encountered in the hummocky unit, ii) mafic, fine-grained soils found at Rocknest and throughout the rover traverse, and iii) soils with an intermediate composition, possibly as a result of mechanical mixing between the two former categories, or possibly chemically distinct [Meslin et al, 2013]. To follow up with this analysis, the composition of coarse sand grains was investigated using the spectra acquired shot by shot. Independent Component Analysis (ICA) [Forni et al., 2013] shows that there are two principal groups of clasts. Spectral analysis confirms that a first group is enriched in Na, Si, Ca and Al, whereas the

  10. A statistical downscaling approach for roadside NO2 concentrations: Application to a WRF-Chem study for Berlin

    NASA Astrophysics Data System (ADS)

    Kuik, Friderike; Lauer, Axel; von Schneidemesser, Erika; Butler, Tim

    2017-04-01

    Many European cities continue to struggle with meeting the European air quality limits for NO2. In Berlin, Germany, most of the exceedances in NO2 recorded at monitoring sites near busy roads can be largely attributed to emissions from traffic. In order to assess the impact of changes in traffic emissions on air quality at policy relevant scales, we combine the regional atmosphere-chemistry transport model WRF-Chem at a resolution of 1kmx1km with a statistical downscaling approach. Here, we build on the recently published study evaluating the performance of a WRF-Chem setup in representing observed urban background NO2 concentrations from Kuik et al. (2016) and extend this setup by developing and testing an approach to statistically downscale simulated urban background NO2 concentrations to street level. The approach uses a multilinear regression model to relate roadside NO2 concentrations observed with the municipal monitoring network with observed NO2 concentrations at urban background sites and observed traffic counts. For this, the urban background NO2 concentrations are decomposed into a long term, a synoptic and a diurnal component using the Kolmogorov-Zurbenko filtering method. We estimate the coefficients of the regression model for five different roadside stations in Berlin representing different street types. In a next step we combine the coefficients with simulated urban background concentrations and observed traffic counts, in order to estimate roadside NO2 concentrations based on the results obtained with WRF-Chem at the five selected stations. In a third step, we extrapolate the NO2 concentrations to all major roads in Berlin. The latter is based on available data for Berlin of daily mean traffic counts, diurnal and weekly cycles of traffic as well as simulated urban background NO2 concentrations. We evaluate the NO2 concentrations estimated with this method at street level for Berlin with additional observational data from stationary measurements and

  11. Introduction to the Spring 2014 ConfChem on the Flipped Classroom

    ERIC Educational Resources Information Center

    Luker, Chris; Muzyka, Jennifer; Belford, Robert

    2015-01-01

    Students' active engagement is one of the most critical challenges to any successful learning environment. The blending of active engagement along with rich, meaningful content is necessary for chemical educators to re-examine the purpose of the chemistry classroom. The Spring 2014 ConfChem conference, Flipped Classroom, was held from May 9 to…

  12. The ChemViz Project: Using a Supercomputer To Illustrate Abstract Concepts in Chemistry.

    ERIC Educational Resources Information Center

    Beckwith, E. Kenneth; Nelson, Christopher

    1998-01-01

    Describes the Chemistry Visualization (ChemViz) Project, a Web venture maintained by the University of Illinois National Center for Supercomputing Applications (NCSA) that enables high school students to use computational chemistry as a technique for understanding abstract concepts. Discusses the evolution of computational chemistry and provides a…

  13. Rocknest, Bradbury Plateau, and Kimberly: Iron Cemented Sediments Observed in Gale Crater with ChemCam

    NASA Astrophysics Data System (ADS)

    Blaney, D. L.; Wiens, R. C.; Maurice, S.; Clegg, S. M.; Anderson, R. B.; Kahn, L. C.; Le Mouélic, S.; Ollila, A.; Gerger, G.; Bridges, J. C.; Cousin, A.; Clark, B.; Dyar, M. D.; King, P. L.; Mangold, N.; Meslin, P. Y.; Newsom, H.; Schröder, S.; Rowland, S.; Johnson, J.; Edgar, L.; Forni, O.; Schmidt, M.; Goetz, W.; Stack, K.; Sumner, D.; Fisk, M.; Maden, M. B.; Tokar, R.; MSL Science Team

    2014-07-01

    Numerous locations with Fe-rich cements were identified at Gale Crater with ChemCam. This indicates that Fe-rich waters were widespread in the area explored. Rocks also experienced different diagenetic histories involving Mg loss, sulfates, and CaF.

  14. Chemistry Provision for Primary Pupils: The Experiences of 10 Years of Bristol ChemLabs Outreach

    ERIC Educational Resources Information Center

    Harrison, Timothy G.; Shallcross, Dudley E.

    2016-01-01

    Bristol ChemLabS, the UK's Centre for Excellence in Teaching and Learning in practical chemistry, delivers numerous outreach activity days per year for thousands of primary school pupils annually. These mainly comprise demonstration assemblies and hands on workshops for pupils in the main. The activities support the UK's Key Stage 2 science…

  15. ConfChem Conference on Flipped Classroom: Using a Blog to Flip a Classroom

    ERIC Educational Resources Information Center

    Haile, January D.

    2015-01-01

    This communication summarizes one of the invited papers to the Flipped Classroom ACS Division of Chemical Education Committee on Computers in Chemical Education online ConfChem held from May 18 to June 24, 2014. Just in Time Teaching is a technique in which students read the material before class and respond to a few questions. In a first-year…

  16. Industrial capability to chem-mill aluminum alloy 2219 in T-37 and T-87

    NASA Technical Reports Server (NTRS)

    Milewski, C., Jr.; Chen, K. C. S.

    1979-01-01

    Procedures and chemical baths were developed for chem-milling aluminum alloy 2219. Using a series of sample etchings, it was found that good etching results could be obtained by using 'white plastic for porcelain repair (toluol, xylol, and petroleum distillates)' on top of cellosolve acetate as resist coatings and ferric chloride as on etchant.

  17. ChemSource SourceBook, Version 2.0: Volume 1.

    ERIC Educational Resources Information Center

    Orna, Mary Virginia, Ed.; And Others

    ChemSource is designed as a strategy to help preservice and inservice high school chemistry teachers promote student learning more effectively. Its major premise is that well-designed laboratory investigations are an important avenue for cultivating student interest, engagement, and meaningful learning in chemistry. The SourceBook component of…

  18. ChemSource SourceBook, Version 2.0: Volume 4.

    ERIC Educational Resources Information Center

    Orna, Mary Virginia, Ed.; And Others

    ChemSource is designed as a strategy to help preservice and inservice high school chemistry teachers promote student learning more effectively. Its major premise is that well-designed laboratory investigations are an important avenue for cultivating student interest, engagement, and meaningful learning in chemistry. The SourceBook component of…

  19. Guide for Teaching Chemistry-Physics Combined 1-2, 3-4 (PSSC - CHEMS).

    ERIC Educational Resources Information Center

    Millstone, H. George

    This guide is written for a combined physics-chemistry course taught over a two-year period. The subject matter contains the major ideas in Chemical Education Materials Study (CHEMS) Chemistry and Physical Science Study Committee (PSSC) Physics. The guide includes discussion of text references, laboratory experiments, films, testing and evaluation…

  20. ConfChem Conference on Flipped Classroom: Using a Blog to Flip a Classroom

    ERIC Educational Resources Information Center

    Haile, January D.

    2015-01-01

    This communication summarizes one of the invited papers to the Flipped Classroom ACS Division of Chemical Education Committee on Computers in Chemical Education online ConfChem held from May 18 to June 24, 2014. Just in Time Teaching is a technique in which students read the material before class and respond to a few questions. In a first-year…

  1. ChemSource SourceBook, Version 2.0: Volume 1.

    ERIC Educational Resources Information Center

    Orna, Mary Virginia, Ed.; And Others

    ChemSource is designed as a strategy to help preservice and inservice high school chemistry teachers promote student learning more effectively. Its major premise is that well-designed laboratory investigations are an important avenue for cultivating student interest, engagement, and meaningful learning in chemistry. The SourceBook component of…

  2. ChemSource SourceBook, Version 2.0: Volume 4.

    ERIC Educational Resources Information Center

    Orna, Mary Virginia, Ed.; And Others

    ChemSource is designed as a strategy to help preservice and inservice high school chemistry teachers promote student learning more effectively. Its major premise is that well-designed laboratory investigations are an important avenue for cultivating student interest, engagement, and meaningful learning in chemistry. The SourceBook component of…

  3. Web search and data mining of natural products and their bioactivities in PubChem.

    PubMed

    Ming, Hao; Tiejun, Cheng; Yanli, Wang; Stephen, Bryant H

    2013-10-01

    Natural products, as major resources for drug discovery historically, are gaining more attentions recently due to the advancement in genomic sequencing and other technologies, which makes them attractive and amenable to drug candidate screening. Collecting and mining the bioactivity information of natural products are extremely important for accelerating drug development process by reducing cost. Lately, a number of publicly accessible databases have been established to facilitate the access to the chemical biology data for small molecules including natural products. Thus, it is imperative for scientists in related fields to exploit these resources in order to expedite their researches on natural products as drug leads/candidates for disease treatment. PubChem, as a public database, contains large amounts of natural products associated with bioactivity data. In this review, we introduce the information system provided at PubChem, and systematically describe the applications for a set of PubChem web services for rapid data retrieval, analysis, and downloading of natural products. We hope this work can serve as a starting point for the researchers to perform data mining on natural products using PubChem.

  4. The ChemViz Project: Using a Supercomputer To Illustrate Abstract Concepts in Chemistry.

    ERIC Educational Resources Information Center

    Beckwith, E. Kenneth; Nelson, Christopher

    1998-01-01

    Describes the Chemistry Visualization (ChemViz) Project, a Web venture maintained by the University of Illinois National Center for Supercomputing Applications (NCSA) that enables high school students to use computational chemistry as a technique for understanding abstract concepts. Discusses the evolution of computational chemistry and provides a…

  5. Viewing Spark Generated by ChemCam Laser for Mars Rover

    NASA Image and Video Library

    2010-09-21

    The ChemCam instrument for NASA Mars Science Laboratory mission uses a pulsed laser beam to vaporize a pinhead-size target, producing a flash of light from the ionized material plasma that can be analyzed to identify chemical elements in the target.

  6. ChemSource SourceBook, Version 2.0: Volume 3.

    ERIC Educational Resources Information Center

    Orna, Mary Virginia, Ed.; And Others

    ChemSource is designed as a strategy to help preservice and inservice high school chemistry teachers promote student learning more effectively. Its major premise is that well-designed laboratory investigations are an important avenue for cultivating student interest, engagement, and meaningful learning in chemistry. The SourceBook component of…

  7. ChemSource SourceBook, Version 2.0: Volume 3.

    ERIC Educational Resources Information Center

    Orna, Mary Virginia, Ed.; And Others

    ChemSource is designed as a strategy to help preservice and inservice high school chemistry teachers promote student learning more effectively. Its major premise is that well-designed laboratory investigations are an important avenue for cultivating student interest, engagement, and meaningful learning in chemistry. The SourceBook component of…

  8. ChemSource SourceBook, Version 2.0: Volume 2.

    ERIC Educational Resources Information Center

    Orna, Mary Virginia, Ed.; And Others

    ChemSource is designed as a strategy to help preservice and inservice high school chemistry teachers promote student learning more effectively. Its major premise is that well-designed laboratory investigations are an important avenue for cultivating student interest, engagement, and meaningful learning in chemistry. The SourceBook component of…

  9. WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

    PubMed Central

    2014-01-01

    Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360

  10. ChemSource SourceBook, Version 2.0: Volume 2.

    ERIC Educational Resources Information Center

    Orna, Mary Virginia, Ed.; And Others

    ChemSource is designed as a strategy to help preservice and inservice high school chemistry teachers promote student learning more effectively. Its major premise is that well-designed laboratory investigations are an important avenue for cultivating student interest, engagement, and meaningful learning in chemistry. The SourceBook component of…

  11. The Chem-E-Car as a Vehicle for Service Learning through K-12 Outreach

    ERIC Educational Resources Information Center

    Chirdon, William

    2017-01-01

    This article presents the results of combining the American Institute of Chemical Engineers' (AIChE) Chem-E-Car competition activities with engineering outreach to K-12 students in a service-learning course. Survey results are presented to show how the program develops technical skills as well as leadership, teamwork, and communication skills in…

  12. a Spectroscopy Based P-Chem Lab, Including a Detailed Text and Lab Manual

    NASA Astrophysics Data System (ADS)

    Muenter, John

    2015-06-01

    Rochester's second semester physical chemistry lab course is based on spectroscopy experiments and follows a full semester of quantum mechanics lectures. The laboratory course is fully separate from the traditional physical chemistry course and has its own lectures. The lab course is constructed to achieve three major goals: provide a detailed knowledge of the instrumentation that acquires data, establish a good understanding of how that data is analyzed, and give students a familiarity with spectroscopic techniques and quantum mechanical models. Instrumentation is emphasized by using common components to construct different experiments. Microwave, modulation and detection components are used for both OCS pure rotation and ESR experiments. Optical components, a monochromator, and PMT detectors are used in a HeNe laser induced fluorescence experiment on I2 {(J. Chem. Ed. 73, 576 (1996)) and a photoluminescence experiment on pyrene {(J. Chem. Ed. 73, 580 (1996)). OCS is studied in both the microwave and infrared regions, and the C=S stretching vibration is identified through microwave intensity measurements. Lecture notes and laboratory instructions are combined in an exhaustive text of more than 400 pages, containing 325 figures, 285 equations and numerous MathCad data analysis programs. This text can be downloaded as a 10 Mbyte pdf file at chem.rochester.edu/˜muenter/CHEM232Manual.

  13. CHEM2D: a two-dimensional, three-phase, nine-component chemical flood simulator. Volume I. CHEM2D technical description and FORTRAN code

    SciTech Connect

    Fanchi, J.R.

    1985-04-01

    Under the sponsorship of the US Department of Energy, a publicly available chemical simulator has been evaluated and substantially enhanced to serve as a useful tool for projecting polymer or chemical flood performance. The program, CHEM2D, is a two-dimensional, three-phase, nine-component finite-difference numerical simulator. It can model primary depletion, waterfloods, polymer floods, and micellar/polymer floods using heterogeneous linear, areal, or cross-sectional reservoir descriptions. The user may specify well performance as either pressure or rate constrained. Both a constant time step size and a variable time step size based on extrapolation of concentration changes are available as options. A solution technique which is implicit in pressure and explicit in saturations and concentrations is used. The major physical mechanisms that are modeled include adsorption, capillary trapping, cation exchange, dilution, dispersion, interfacial tension, binary or ternary phase behavior, non-Newtonian polymer rheology, and two-phase or three-phase relative permeability. Typical components include water, oil, surfactant, polymer, and three ions (chloride, calcium, and sodium). Components may partition amongst the aqueous, oleic, and microemulsion phases. Volume I of this report provides a discussion of the formulation and algorithms used within CHEM2D. Included in Volume I are a number of validation and illustrative examples, as well as the FORTRAN code. The CHEM2D user's manual, Volume II, contains both the input data sets for the examples presented in Volume I and an example output. All appendices and a phase behavior calculation program are collected in Volume III. 20 references.

  14. iNuc-PhysChem: A Sequence-Based Predictor for Identifying Nucleosomes via Physicochemical Properties

    PubMed Central

    Feng, Peng-Mian; Ding, Chen; Zuo, Yong-Chun; Chou, Kuo-Chen

    2012-01-01

    Nucleosome positioning has important roles in key cellular processes. Although intensive efforts have been made in this area, the rules defining nucleosome positioning is still elusive and debated. In this study, we carried out a systematic comparison among the profiles of twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces cerevisiae genome. We found that nucleosomal sequences have some position-specific physicochemical features, which can be used for in-depth studying nucleosomes. Meanwhile, a new predictor, called iNuc-PhysChem, was developed for identification of nucleosomal sequences by incorporating these physicochemical properties into a 1788-D (dimensional) feature vector, which was further reduced to a 884-D vector via the IFS (incremental feature selection) procedure to optimize the feature set. It was observed by a cross-validation test on a benchmark dataset that the overall success rate achieved by iNuc-PhysChem was over 96% in identifying nucleosomal or linker sequences. As a web-server, iNuc-PhysChem is freely accessible to the public at http://lin.uestc.edu.cn/server/iNuc-PhysChem. For the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented just for the integrity in developing the predictor. Meanwhile, for those who prefer to run predictions in their own computers, the predictor's code can be easily downloaded from the web-server. It is anticipated that iNuc-PhysChem may become a useful high throughput tool for both basic research and drug design. PMID:23144709

  15. Data mining a small molecule drug screening representative subset from NIH PubChem.

    PubMed

    Xie, Xiang-Qun; Chen, Jian-Zhong

    2008-03-01

    PubChem is a scientific showcase of the NIH Roadmap Initiatives. It is a compound repository created to facilitate information exchange and data sharing among the NIH Roadmap-funded Molecular Library Screening Center Network (MLSCN) and the scientific community. However, PubChem has more than 10 million records of compound information. It will be challenging to conduct a drug screening of the whole database of millions of compounds. Thus, the purpose of the present study was to develop a data mining cheminformatics approach in order to construct a representative and structure-diverse sublibrary from the large PubChem database. In this study, a new chemical diverse representative subset, rePubChem, was selected by whole-molecule chemistry-space matrix calculation using the cell-based partition algorithm. The representative subset was generated and was then subjected to evaluations by compound property analyses based on 1D and 2D molecular descriptors. The new subset was also examined and assessed for self-similarity analysis based on 2D molecular fingerprints in comparing with the source compound library. The new subset has a much smaller library size (540K compounds) with minimum similarity and redundancy without loss of the structural diversity and basic molecular properties of its parent library (5.3 million compounds). The new representative subset library generated could be a valuable structure-diverse compound resource for in silico virtual screening and in vitro HTS drug screening. In addition, the established subset generation method of using the combined cell-based chemistry-space partition metrics with pairwised 2D fingerprint-based similarity search approaches will also be important to a broad scientific community interested in acquiring structurally diverse compounds for efficient drug screening, building representative virtual combinatorial chemistry libraries for syntheses, and data mining large compound databases like the PubChem library in general.

  16. Regional and global crustal context of soil and rock chemistry from ChemCam and APXS at Gale crater

    NASA Astrophysics Data System (ADS)

    Newsom, H. E.; Gordon, S.; Jackson, R.; Agee, C. B.; Wiens, R. C.; Clegg, S. M.; Lanza, N.; Cousin, A.; Gasnault, O.; Meslin, P. Y.; Maurice, S.; Forni, O.; McLennan, S. M.; Mangold, N.; Sautter, V.; Clark, B. C.; Anderson, R. B.; Gellert, R.; Schmidt, M. E.; Ollila, A.; Boynton, W. V.; Martín-Torres, J.; Zorzano, M. P.

    2014-12-01

    The chemistry of rocks and soils analyzed by Curiosity represent a diverse population including mafic and felsic compositions. The data from Gale Crater can be compared with the accumulated data for martian materials from other landing sites, the Gamma Ray Spectrometer (GRS) experiment on the Mars Odyssey Spacecraft, and the data for martian meteorites. Variations in the CaO/Al2O3 ratio in primitive igneous rocks can provide a fundamental signature of crustal formation on Mars. Abundances of other elements like Fe in the surface rocks can reflect later differentiation effects. Comparing the chemistry of Gale samples with other martian data must take into account the different geochemical components in the samples. The most important distinction is between the volatile elements including H, C, Cl, S, and the lithophile elements including Al, Si, Fe, Mn, Ca, Na, Mg, etc. The large enrichments of the volatile elements SO3, Cl, and H2O in the soils may represent contributions from volcanic aerosols or other local sources of volatiles. Alteration and transport of fluid mobile major elements by aqueous or hydrothermal processes could complicate the estimation of crustal abundances of elements such as Ca but early results suggest little or no chemical fractionation attributable to alteration. Other clues to the role of fluids can come from the ChemCam data for the highly fluid mobile elements lithium and manganese. Regional comparisons of chemistry only make sense when considering the absolute abundances and elemental ratios within the different component classes. The use of elemental ratios avoids the problem of the correction required to get volatile-free abundance data for comparison of GRS data with meteorites and landing site rocks measured by the ChemCam Laser Induced Breakdown Spectroscopy (LIBS) experiment and Alpha Particle X-ray Spectrometer (APXS). The huge size of the GRS footprint makes it especially difficult to make the required corrections. Eventually data

  17. Diagnosing ALS

    MedlinePlus

    ... that a person diagnosed with ALS seek a second opinion from an ALS "expert" - someone who diagnoses and treats many ALS patients and has training in this medical specialty. The ALS Association maintains a list of recognized experts in the field of ALS. See ALS Association Certified Centers of ...

  18. Comment on ‘To stack or not to stack: Performance of a new density functional for the uracil and thymine dimers’ [Chem. Phys. Lett. 459 (2008) 164

    NASA Astrophysics Data System (ADS)

    van Mourik, Tanja

    2009-04-01

    A Letter by Gu et al. [J. Gu, J. Wang, J. Leszczynski, Y. Xie, H.F. Schaefer III, Chem. Phys. Lett. 459 (2008) 164] presented MP2/6-31+G(d) and MP2/TZVPP stacking energies for the uracil and thymine dimers, with the aim to assess the performance of the new M06-2X density functional. However, the stacking energies were not corrected for the basis set superposition error (BSSE). Here we show that correction for this error dramatically changes the results. BSSE correction severely reduces the stacking energy of the thymine dimer, whereas the stacked uracil dimer structure considered by Gu et al. is not even a minimum on the MP2/6-31+G(d) potential energy surface.

  19. Synergy of SAM and ChemCam instruments (Curiosity Rover) to Search for Organic Matter at Mars

    NASA Astrophysics Data System (ADS)

    Dequaire, T.; Coll, P.; Szopa, C.; Maurice, S.; Mangold, N.

    2014-07-01

    This work proposes to determine ChemCam capabilities to detect organic molecules in the martian rocks, by coupling LIBS and passive spectroscopy using the ChemCam testbed (IRAP) in order to select at best the samples analyzed by the SAM instrument.

  20. Calcium Sulfate Vein Observations at Yellowknife Bay using ChemCam on the Curiosity Rover

    NASA Astrophysics Data System (ADS)

    Clegg, S. M.; Mangold, N.; Nachon, M.; Le Mouelic, S.; Ollila, A.; Vaniman, D. T.; Kah, L. C.; Dromart, G.; Bridges, J.; Rice, M. S.; Wellington, D. F.; Bell, J. F.; Anderson, R. B.; Clark, B. C.; Cousin, A.; Forni, O.; Lasue, J.; Schröder, S.; Meslin, P.; Dyar, M. D.; Blaney, D. L.; Maurice, S.; Wiens, R. C.; Team, M.

    2013-12-01

    The Mars Science Laboratory Curiosity rover completed its traverse from the Bradbury landing site into Yellowknife Bay (YKB) on sol 125, where it spent ~175 sols. The YKB region is characterized as a fluvio-lacustrine depositional environment. The entire Curiosity payload was used to thoroughly investigate parts of YKB from which significant geochemical observations were made, including the identification of anhydrite and hydrated calcium sulfate. The Curiosity ChemCam package consists of a remote Laser-Induced Breakdown Spectrometer (LIBS) and a Remote Micro-Imager (RMI). LIBS is essentially an elemental analysis micro-probe capable of 300 - 550 μm spatial resolution from 1.5 - 7.0 m standoff distance from the Curiosity mast. The RMI records context images that have a resolution of 40 μrad, which corresponds to 120 μm at 3 meters. The ChemCam instrument recorded many calcium rich geochemical features as it descended ~18 m into YKB. Many light-toned veins became apparent with the ChemCam RMI and Mastcam once Curiosity entered YKB. The ChemCam LIBS instrument is uniquely capable of distinctly probing the elemental composition of these vein structures separately from the host rock. LIBS demonstrated that the white vein material was dominated by CaSO4, while the host rock had relatively low SO3 compositions. The ChemCam instrument can also qualitatively detect H, presumably due to H2O, in many samples. While some of these veins contained no H signature beyond the ubiquitous small amount of H on rock surfaces and in soils, some of the veins contained various amounts of H as a function of depth indicating that some of the samples were either bassanite or gypsum. Mastcam spectral hydration surveys detect evidence of hydration that is consistent with (but not a unique indicator of) the presence of gypsum in some, but not all, of the veins. The CheMin X-ray diffraction instrument identified both anhydrite and bassanite in the matrix of a mudstone unit but did not detect

  1. Studies of stratospheric and mesospheric chemistry in polar regions with the Berlin Climate Middle Atmosphere Model (CMAM CHEM)

    NASA Astrophysics Data System (ADS)

    Grenfell, J. L.; Mieth, P.; Kruger, K.; Langematz, U.; Labitzke, K.; Steil, B.

    2001-12-01

    The Berlin Climate Middle Atmosphere model (CMAM) with resolution T21 and lid at 84km (Langematz and Pawson, 1997) has been interactively coupled with the chemistry module of Steil et al., (1998). Chemical tracer fields from a test run which used the Palmer gravity wave drag (GWD) scheme have been found to compare well both with observations and other models (e.g. MA-ECHAM4-CHEM). However, in this run the model pole has a warm bias and dynamical variability is not well reproduced. Therefore we are currently testing a suite of orographic and non-orographic GWD schemes in the model. Preliminary results from these latter runs are presented here and focus on stratospheric and mesospheric chemical processes during polar winter, particularly those affecting ozone. The contrast between hemispheres, the springtime 'recovery' of polar stratospheric ozone and relevant chemical diurnal cycles are explored. Bibliography U. Langematz, and Pawson S., The Berlin troposphere-stratosphere-mesosphere GCM: Climatology and forcing mechanisms, Q. J. R. Meteorol. Soc., 123, 1075-1096, 1997 B. Steil, Dameris M., Brühl C., Crutzen P. J., Grewe V., Ponater M., and Sausen R., Development of a chemistry module for GCMs: first results of a multiannual integration, Ann. Geophys., 16, 205-228, 1998

  2. Diagenetic Features Analyzed by ChemCam/Curiosity at Pahrump Hills, Gale Crater, Mars

    NASA Technical Reports Server (NTRS)

    Nachon, M.; Mangold, N.; Cousin, A.; Forni, O.; Anderson, R. B.; Blank, J. G.; Calef, F.; Clegg, S.; Fabre, C.; Fisk, M.; Gasnault, O.; Kah, L. C.; Kronyak, R.; Lasue, J.; Meslin, P.-Y.; Le Mouelic, S.; Maurice, S.; Oehler, D. Z.; Payre, V.; Rapin, W.; Sumner, D.; Stack, K.; Schroeder, S.; Wiens, R. C.

    2015-01-01

    Onboard the Mars Science Laboratory (MSL) Curiosity rover, the ChemCam instrument consists of : (1) a Laser-Induced Breakdown Spectrometer (LIBS) for elemental analysis of targets and (2) a Remote Micro Imager (RMI), which provides imaging context for the LIBS. The LIBS/ChemCam performs analysis typically of spot sizes 350-550 micrometers in diameter, up to 7 meters from the rover. Within Gale crater, Curiosity traveled from Bradbury Landing toward the base of Mount Sharp, reaching Pahrump Hills outcrop circa sol 750. This region, as seen from orbit, represents the first exposures of lower Mount Sharp. In this abstract we focus on two types of features present within the Pahrump Hills outcrop: concretion features and light-toned veins.

  3. The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

    PubMed Central

    2012-01-01

    This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications. PMID:22870956

  4. Managing the computational chemistry big data problem: the ioChem-BD platform.

    PubMed

    Álvarez-Moreno, M; de Graaf, C; López, N; Maseras, F; Poblet, J M; Bo, C

    2015-01-26

    We present the ioChem-BD platform ( www.iochem-bd.org ) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers' needs in the form of HTML5 reports, supporting information, and other research media.

  5. The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

    PubMed

    Phadungsukanan, Weerapong; Kraft, Markus; Townsend, Joe A; Murray-Rust, Peter

    2012-08-07

    : This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

  6. Characterising Brazilian biomass burning emissions using WRF-Chem with MOSAIC sectional aerosol

    NASA Astrophysics Data System (ADS)

    Archer-Nicholls, S.; Lowe, D.; Darbyshire, E.; Morgan, W. T.; Bela, M. M.; Pereira, G.; Trembath, J.; Kaiser, J. W.; Longo, K. M.; Freitas, S. R.; Coe, H.; McFiggans, G.

    2015-03-01

    The South American Biomass Burning Analysis (SAMBBA) field campaign took detailed in situ flight measurements of aerosol during the 2012 dry season to characterise biomass burning aerosol and improve understanding of its impacts on weather and climate. Developments have been made to the Weather Research and Forecast model with chemistry (WRF-Chem) model to improve the representation of biomass burning aerosol in the region, by coupling a sectional aerosol scheme to the plume-rise parameterisation. Brazilian Biomass Burning Emissions Model (3BEM) fire emissions are used, prepared using PREP-CHEM-SRC, and mapped to CBM-Z and MOSAIC species. Model results have been evaluated against remote sensing products, AERONET sites, and four case studies of flight measurements from the SAMBBA campaign. WRF-Chem predicted layers of elevated aerosol loadings (5-20 μg sm-3) of particulate organic matter at high altitude (6-8 km) over tropical forest regions, while flight measurements showed a sharp decrease above 2-4 km altitude. This difference was attributed to the plume-rise parameterisation overestimating injection height. The 3BEM emissions product was modified using estimates of active fire size and burned area for the 2012 fire season, which reduced the fire size. The enhancement factor for fire emissions was increased from 1.3 to 5 to retain reasonable aerosol optical depths (AODs). The smaller fire size lowered the injection height of the emissions, but WRF-Chem still showed elevated aerosol loadings between 4-5 km altitude. Over eastern cerrado (savannah-like) regions, both modelled and measured aerosol loadings decreased above approximately 4 km altitude. Compared with MODIS satellite data and AERONET sites, WRF-Chem represented AOD magnitude well (between 0.3-1.5) over western tropical forest fire regions in the first half of the campaign, but tended to over-predict them in the second half, when precipitation was more significant. Over eastern cerrado regions, WRF-Chem

  7. Characterising Brazilian biomass burning emissions using WRF-Chem with MOSAIC sectional aerosol

    NASA Astrophysics Data System (ADS)

    Archer-Nicholls, S.; Lowe, D.; Darbyshire, E.; Morgan, W. T.; Bela, M. M.; Pereira, G.; Trembath, J.; Kaiser, J. W.; Longo, K. M.; Freitas, S. R.; Coe, H.; McFiggans, G.

    2014-09-01

    The South American Biomass Burning Analysis (SAMBBA) field campaign took detailed in-situ flight measurements of aerosol during the 2012 dry season to characterise biomass burning aerosol and improve understanding of its impacts on weather and climate. Developments have been made to the Weather research and Forecast model with chemistry (WRF-Chem) model to improve the representation of biomass burning aerosol in the region by coupling a sectional aerosol scheme to the plume rise parameterisation. Brazilian Biomass Burning Emissions Model (3BEM) fire emissions are used, prepared using PREP-CHEM-SRC, and mapped to CBM-Z and MOSAIC species. Model results have been evaluated against remote sensing products, AERONET sites, and four case studies of flight measurements from the SAMBBA campaign. WRF-Chem predicted layers of elevated aerosol loadings (5-20 μg sm-3) of particulate organic matter at high altitude (6-8 km) over tropical forest regions, while flight measurements showed a sharp decrease above 2-4 km altitude. This difference was attributed to the plume-rise parameterisation overestimating injection height. The 3BEM emissions product was modified using estimates of active fire size and burned area for the 2012 fire season, which reduced the fire size. The enhancement factor for fire emissions was increased from 1.3 to 5 to retain reasonable aerosol optical depths (AOD). The smaller fire size lowered the injection height of the emissions, but WRF-Chem still showed elevated aerosol loadings between 4-5 km altitude. Over eastern Cerrado (savannah-like) regions, both modelled and measured aerosol loadings decreased above approximately 4 km altitude. Compared with MODIS satellite data and AERONET sites, WRF-Chem represented AOD magnitude well (between 0.3-1.5) over western tropical forest fire regions in the first half of the campaign, but tended to over-predict them in the second half, when precipitation was more significant. Over eastern Cerrado regions, WRF-Chem

  8. ChemCam for Mars Science Laboratory rover, undergoing pre-flight testing

    SciTech Connect

    2011-10-20

    Los Alamos National Laboratory and partners developed a laser instrument, ChemCam, that will ride on the elevated mast of the Mars Science Laboratory rover Curiosity. The system allows Curiosity to "zap" rocks from a distance, reading their chemical composition through spectroscopic analysis. In this video, laboratory shaker-table testing of the instrument ensures that all of its components are solidly attached and resistant to damage from the rigors of launch, travel and landing.

  9. ChemCam for Mars Science Laboratory rover, undergoing pre-flight testing

    ScienceCinema

    None

    2016-07-12

    Los Alamos National Laboratory and partners developed a laser instrument, ChemCam, that will ride on the elevated mast of the Mars Science Laboratory rover Curiosity. The system allows Curiosity to "zap" rocks from a distance, reading their chemical composition through spectroscopic analysis. In this video, laboratory shaker-table testing of the instrument ensures that all of its components are solidly attached and resistant to damage from the rigors of launch, travel and landing.

  10. HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors

    National Institute of Standards and Technology Data Gateway

    SRD 155 HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors (Web, free access)   The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data Bank (PDB).

  11. Mixed waste treatment using the ChemChar thermolytic detoxification technique

    SciTech Connect

    Kuchynka, D.

    1995-10-01

    The diversity of mixed waste matrices contained at Department of Energy sites that require treatment preclude a single, universal treatment technology capable of handling sludges, solids, heterogeneous debris, aqueous and organic liquids and soils. This report describes the ChemChar thermolytic detoxification process. The process is a thermal, chemically reductive technology that converts the organic portion of mixed wastes to a synthesis gas, while simultaneously absorbing volatile inorganics on a carbon-based char.

  12. Comment on ``Multireference configuration-interaction calculations for positronium halides'' [J. Chem. Phys. 122, 054302 (2005)

    NASA Astrophysics Data System (ADS)

    Mitroy, J.; Bromley, M. W. J.

    2005-07-01

    Large-scale configuration-interaction calculations of the binding energies and annihilation rates of the positronium halides, PsF, PsCl, PsBr, and PsI [S. L. Saito, J. Chem. Phys. 122 054302 (2005)], have made erroneous predictions about the structures of these atoms. The predictions were based on small annihilation rates, which result from using a small basis and additionally invalid estimates of the contributions from single-particle orbitals with ℓ >8 .

  13. Sensitivity of WRF-chem predictions to dust source function specification in West Asia

    NASA Astrophysics Data System (ADS)

    Nabavi, Seyed Omid; Haimberger, Leopold; Samimi, Cyrus

    2017-02-01

    Dust storms tend to form in sparsely populated areas covered by only few observations. Dust source maps, known as source functions, are used in dust models to allocate a certain potential of dust release to each place. Recent research showed that the well known Ginoux source function (GSF), currently used in Weather Research and Forecasting Model coupled with Chemistry (WRF-chem), exhibits large errors over some regions in West Asia, particularly near the IRAQ/Syrian border. This study aims to improve the specification of this critical part of dust forecasts. A new source function based on multi-year analysis of satellite observations, called West Asia source function (WASF), is therefore proposed to raise the quality of WRF-chem predictions in the region. WASF has been implemented in three dust schemes of WRF-chem. Remotely sensed and ground-based observations have been used to verify the horizontal and vertical extent and location of simulated dust clouds. Results indicate that WRF-chem performance is significantly improved in many areas after the implementation of WASF. The modified runs (long term simulations over the summers 2008-2012, using nudging) have yielded an average increase of Spearman correlation between observed and forecast aerosol optical thickness by 12-16 percent points compared to control runs with standard source functions. They even outperform MACC and DREAM dust simulations over many dust source regions. However, the quality of the forecasts decreased with distance from sources, probably due to deficiencies in the transport and deposition characteristics of the forecast model in these areas.

  14. Developing ChemFin(Trademark), a Miniature Biogeochemical Sensor Payload for Gliders, Profilers, and Other AUVs

    DTIC Science & Technology

    2009-09-30

    single domain antibodies (sdA) isolated from llamas . Work also continued on MarChem sensor prototype testing, including incorporation of a next...conjugates were prepared and tested using polyclonal antibodies and initial antibodies produced in llamas , which are single domain antibodies rather than the...The limit of detection for Saxition in this assay is in the low ng/mL range. Llama Anti-saxitoxin Production - Two llamas were immunized with

  15. ChemDB update--full-text search and virtual chemical space.

    PubMed

    Chen, Jonathan H; Linstead, Erik; Swamidass, S Joshua; Wang, Dennis; Baldi, Pierre

    2007-09-01

    ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. The data is publicly available over the web for download and for targeted searches using a variety of powerful methods. The chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. Recent developments include optimization of chemical structure (and substructure) retrieval algorithms, enabling full database searches in less than a second. A text-based search engine allows efficient searching of compounds based on over 65M annotations from over 150 vendors. When searching for chemicals by name, fuzzy text matching capabilities yield productive results even when the correct spelling of a chemical name is unknown, taking advantage of both systematic and common names. Finally, built in reaction models enable searches through virtual chemical space, consisting of hypothetical products readily synthesizable from the building blocks in ChemDB. ChemDB and Supplementary Materials are available at http://cdb.ics.uci.edu. Supplementary data are available at Bioinformatics online.

  16. A CNES remote operations center for the MSL ChemCam instrument

    SciTech Connect

    Wiens, Roger C; Lafaille, Vivian; Lorgny, Eric; Baroukh, Julien; Gaboriaud, Alain; Saccoccio, Muriel; Perez, Rene; Gasnault, Olivier

    2010-01-01

    For the first time, a CNES remote operations center in Toulouse will be involved in the tactical operations of a Martian rover in order to operate the ChemCam science instrument in the framework of the NASA MSL (Mars Science Laboratory) mission in 2012. CNES/CESR and LANL have developed and delivered to JPL the ChemCam (Chemistry Camera) instrument located on the top of mast and in the body of the rover. This instrument incorporates a Laser-Induced Breakdown Spectrometer (LIBS) and a Remote Micro-Imager (RMI) for determining elemental compositions of rock targets or soil samples at remote distances from the rover (2-7 m). An agreement has been achieved for operating ChemCam, alternatively, from Toulouse (FR) and Los Alamos (NM, USA), through the JPL ground data system in Pasadena (CA, USA) for a complete Martian year (2 years on Earth). After a brief overview of the MSL mission, this paper presents the instrument, the mission operational system and JPL organization requirements for the scientific investigators (PI and Co-Is). This paper emphasizes innovations applied on the ground segment components and on the operational approach to satisfy the requirements and constraints due to these shared and distributed operations over the world.

  17. OrChem - An open source chemistry search engine for Oracle(R).

    PubMed

    Rijnbeek, Mark; Steinbeck, Christoph

    2009-10-22

    Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

  18. ChemSpot: a hybrid system for chemical named entity recognition.

    PubMed

    Rocktäschel, Tim; Weidlich, Michael; Leser, Ulf

    2012-06-15

    The accurate identification of chemicals in text is important for many applications, including computer-assisted reconstruction of metabolic networks or retrieval of information about substances in drug development. But due to the diversity of naming conventions and traditions for such molecules, this task is highly complex and should be supported by computational tools. We present ChemSpot, a named entity recognition (NER) tool for identifying mentions of chemicals in natural language texts, including trivial names, drugs, abbreviations, molecular formulas and International Union of Pure and Applied Chemistry entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a hybrid approach combining a Conditional Random Field with a dictionary. It achieves an F(1) measure of 68.1% on the SCAI corpus, outperforming the only other freely available chemical NER tool, OSCAR4, by 10.8 percentage points. ChemSpot is freely available at: http://www.informatik.hu-berlin.de/wbi/resources.

  19. WRF-Chem simulation of aerosol seasonal variability in the San Joaquin Valley

    NASA Astrophysics Data System (ADS)

    Wu, Longtao; Su, Hui; Kalashnikova, Olga V.; Jiang, Jonathan H.; Zhao, Chun; Garay, Michael J.; Campbell, James R.; Yu, Nanpeng

    2017-06-01

    WRF-Chem simulations of aerosol seasonal variability in the San Joaquin Valley (SJV), California, are evaluated by satellite and in situ observations. Results show that the WRF-Chem model successfully captures the distribution and magnitude of and variation in SJV aerosols during the cold season. However, aerosols are not well represented in the warm season. Aerosol simulations in urban areas during the cold season are sensitive to model horizontal resolution, with better simulations at 4 km resolution than at 20 km resolution, mainly due to inhomogeneous distribution of anthropogenic emissions and precipitation that is represented better in the 4 km simulation. In rural areas, the model sensitivity to grid size is rather small. Our observational analysis reveals that dust is a primary contributor to aerosols in the SJV, especially during the warm season. Aerosol simulations in the warm season are sensitive to the parameterization of dust emission in WRF-Chem. The GOCART (Goddard Global Ozone Chemistry Aerosol Radiation and Transport) dust scheme produces very little dust in the SJV, while the DUSTRAN (DUST TRANsport model) scheme overestimates dust emission. Vertical mixing of aerosols is not adequately represented in the model based on CALIPSO (Cloud-Aerosol Lidar and Infrared pathfinder Satellite Observation) aerosol extinction profiles. Improved representation of dust emission and vertical mixing in the boundary layer is needed for better simulations of aerosols during the warm season in the SJV.

  20. ChemProt-3.0: a global chemical biology diseases mapping

    PubMed Central

    Kringelum, Jens; Kjaerulff, Sonny Kim; Brunak, Søren; Lund, Ole; Oprea, Tudor I.; Taboureau, Olivier

    2016-01-01

    ChemProt is a publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity from molecular to clinical levels. In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19 504 proteins. Here, we report the implementation of global pharmacological heatmap, supporting a user-friendly navigation of chemogenomics space. This facilitates the visualization and selection of chemicals that share similar structural properties. In addition, the user has the possibility to search by compound, target, pathway, disease and clinical effect. Genetic variations associated to target proteins were integrated, making it possible to plan pharmacogenetic studies and to suggest human response variability to drug. Finally, Quantitative Structure–Activity Relationship models for 850 proteins having sufficient data were implemented, enabling secondary pharmacological profiling predictions from molecular structure. Database URL: http://potentia.cbs.dtu.dk/ChemProt/ PMID:26876982

  1. Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database

    PubMed Central

    Butkiewicz, Mariusz; Lowe, Edward W.; Mueller, Ralf; Mendenhall, Jeffrey L.; Teixeira, Pedro L.; Weaver, C. David; Meiler, Jens

    2013-01-01

    With the rapidly increasing availability of High-Throughput Screening (HTS) data in the public domain, such as the PubChem database, methods for ligand-based computer-aided drug discovery (LB-CADD) have the potential to accelerate and reduce the cost of probe development and drug discovery efforts in academia. We assemble nine data sets from realistic HTS campaigns representing major families of drug target proteins for benchmarking LB-CADD methods. Each data set is public domain through PubChem and carefully collated through confirmation screens validating active compounds. These data sets provide the foundation for benchmarking a new cheminformatics framework BCL::ChemInfo, which is freely available for non-commercial use. Quantitative structure activity relationship (QSAR) models are built using Artificial Neural Networks (ANNs), Support Vector Machines (SVMs), Decision Trees (DTs), and Kohonen networks (KNs). Problem-specific descriptor optimization protocols are assessed including Sequential Feature Forward Selection (SFFS) and various information content measures. Measures of predictive power and confidence are evaluated through cross-validation, and a consensus prediction scheme is tested that combines orthogonal machine learning algorithms into a single predictor. Enrichments ranging from 15 to 101 for a TPR cutoff of 25% are observed. PMID:23299552

  2. ChemScreener: A Distributed Computing Tool for Scaffold based Virtual Screening.

    PubMed

    Karthikeyan, Muthukumarasamy; Pandit, Deepak; Vyas, Renu

    2015-01-01

    In this work we present ChemScreener, a Java-based application to perform virtual library generation combined with virtual screening in a platform-independent distributed computing environment. ChemScreener comprises a scaffold identifier, a distinct scaffold extractor, an interactive virtual library generator as well as a virtual screening module for subsequently selecting putative bioactive molecules. The virtual libraries are annotated with chemophore-, pharmacophore- and toxicophore-based information for compound prioritization. The hits selected can then be further processed using QSAR, docking and other in silico approaches which can all be interfaced within the ChemScreener framework. As a sample application, in this work scaffold selectivity, diversity, connectivity and promiscuity towards six important therapeutic classes have been studied. In order to illustrate the computational power of the application, 55 scaffolds extracted from 161 anti-psychotic compounds were enumerated to produce a virtual library comprising 118 million compounds (17 GB) and annotated with chemophore, pharmacophore and toxicophore based features in a single step which would be non-trivial to perform with many standard software tools today on libraries of this size.

  3. ChemProt-2.0: visual navigation in a disease chemical biology database.

    PubMed

    Kim Kjærulff, Sonny; Wich, Louis; Kringelum, Jens; Jacobsen, Ulrik P; Kouskoumvekaki, Irene; Audouze, Karine; Lund, Ole; Brunak, Søren; Oprea, Tudor I; Taboureau, Olivier

    2013-01-01

    ChemProt-2.0 (http://www.cbs.dtu.dk/services/ChemProt-2.0) is a public available compilation of multiple chemical-protein annotation resources integrated with diseases and clinical outcomes information. The database has been updated to >1.15 million compounds with 5.32 millions bioactivity measurements for 15 290 proteins. Each protein is linked to quality-scored human protein-protein interactions data based on more than half a million interactions, for studying diseases and biological outcomes (diseases, pathways and GO terms) through protein complexes. In ChemProt-2.0, therapeutic effects as well as adverse drug reactions have been integrated allowing for suggesting proteins associated to clinical outcomes. New chemical structure fingerprints were computed based on the similarity ensemble approach. Protein sequence similarity search was also integrated to evaluate the promiscuity of proteins, which can help in the prediction of off-target effects. Finally, the database was integrated into a visual interface that enables navigation of the pharmacological space for small molecules. Filtering options were included in order to facilitate and to guide dynamic search of specific queries.

  4. OrChem - An open source chemistry search engine for Oracle®

    PubMed Central

    2009-01-01

    Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

  5. ALS Association

    MedlinePlus

    ... toward a world without ALS! Walk to Defeat ALS® Walk to Defeat ALS® draws people of all ... We need your help. I Will Advocate National ALS Registry The National ALS Registry is a congressionally ...

  6. ODM2 (Observation Data Model): The EarthChem Use Case

    NASA Astrophysics Data System (ADS)

    Lehnert, Kerstin; Song, Lulin; Hsu, Leslie; Horsburgh, Jeffrey S.; Aufdenkampe, Anthony K.; Mayorga, Emilio; Tarboton, David; Zaslavsky, Ilya

    2014-05-01

    PetDB is an online data system that was created in the late 1990's to serve online a synthesis of published geochemical and petrological data of igneous and metamorphic rocks. PetDB has today reached a volume of 2.5 million analytical values for nearly 70,000 rock samples. PetDB's data model (Lehnert et al., G-Cubed 2000) was designed to store sample-based observational data generated by the analysis of rocks, together with a wide range of metadata documenting provenance of the samples, analytical procedures, data quality, and data source. Attempts to store additional types of geochemical data such as time-series data of seafloor hydrothermal springs and volcanic gases, depth-series data for marine sediments and soils, and mineral or mineral inclusion data revealed the limitations of the schema: the inability to properly record sample hierarchies (for example, a garnet that is included in a diamond that is included in a xenolith that is included in a kimberlite rock sample), inability to properly store time-series data, inability to accommodate classification schemes other than rock lithologies, deficiencies of identifying and documenting datasets that are not part of publications. In order to overcome these deficiencies, PetDB has been developing a new data schema using the ODM2 information model (ODM=Observation Data Model). The development of ODM2 is a collaborative project that leverages the experience of several existing information representations, including PetDB and EarthChem, and the CUAHSI HIS Observations Data Model (ODM), as well as the general specification for encoding observational data called Observations and Measurements (O&M) to develop a uniform information model that seamlessly manages spatially discrete, feature-based earth observations from environmental samples and sample fractions as well as in-situ sensors, and to test its initial implementation in a variety of user scenarios. The O&M model, adopted as an international standard by the Open

  7. EarthChem and SESAR: Data Resources and Interoperability for EarthScope Cyberinfrastructure

    NASA Astrophysics Data System (ADS)

    Lehnert, K. A.; Walker, D.; Block, K.; Vinay, S.; Ash, J.

    2008-12-01

    Data management within the EarthScope Cyberinfrastructure needs to pursue two goals in order to advance and maximize the broad scientific application and impact of the large volumes of observational data acquired by EarthScope facilities: (a) to provide access to all data acquired by EarthScope facilities, and to promote their use by broad audiences, and (b) to facilitate discovery of, access to, and integration of multi-disciplinary data sets that complement EarthScope data in support of EarthScope science. EarthChem and SESAR, the System for Earth Sample Registration, are two projects within the Geoinformatics for Geochemistry program that offer resources for EarthScope CI. EarthChem operates a data portal that currently provides access to >13 million analytical values for >600,000 samples, more than half of which are from North America, including data from the USGS and all data from the NAVDAT database, a web-accessible repository for age, chemical and isotopic data from Mesozoic and younger igneous rocks in western North America. The new EarthChem GEOCHRON database will house data collected in association with GeoEarthScope, storing and serving geochronological data submitted by participating facilities. The EarthChem Deep Lithosphere Dataset is a compilation of petrological data for mantle xenoliths, initiated in collaboration with GeoFrame to complement geophysical endeavors within EarthScope science. The EarthChem Geochemical Resource Library provides a home for geochemical and petrological data products and data sets. Parts of the digital data in EarthScope CI refer to physical samples such as drill cores, igneous rocks, or water and gas samples, collected, for example, by SAFOD or by EarthScope science projects and acquired through lab-based analysis. Management of sample-based data requires the use of global unique identifiers for samples, so that distributed data for individual samples generated in different labs and published in different papers can be

  8. Impact of improved soil climatology and intialization on WRF-chem dust simulations over West Asia

    NASA Astrophysics Data System (ADS)

    Omid Nabavi, Seyed; Haimberger, Leopold; Samimi, Cyrus

    2016-04-01

    Meteorological forecast models such as WRF-chem are designed to forecast not only standard atmospheric parameters but also aerosol, particularly mineral dust concentrations. It has therefore become an important tool for the prediction of dust storms in West Asia where dust storms have the considerable impact on living conditions. However, verification of forecasts against satellite data indicates only moderate skill in prediction of such events. Earlier studies have already indicated that the erosion factor, land use classification, soil moisture, and temperature initializations play a critical role in the accuracy of WRF-chem dust simulations. In the standard setting the erosion factor and land use classification are based on topographic variations and post-processed images of the advanced very high-resolution radiometer (AVHRR) during the period April 1992-March 1993. Furthermore, WRF-chem is normally initialized by the soil moisture and temperature of Final Analysis (FNL) model on 1.0x1.0 degree grids. In this study, we have changed boundary initial conditions so that they better represent current changing environmental conditions. To do so, land use (only bare soil class) and the erosion factor were both modified using information from MODIS deep blue AOD (Aerosol Optical Depth). In this method, bare soils are where the relative frequency of dust occurrence (deep blue AOD > 0.5) is more than one-third of a given month. Subsequently, the erosion factor, limited within the bare soil class, is determined by the monthly frequency of dust occurrence ranging from 0.3 to 1. It is worth to mention, that 50 percent of calculated erosion factor is afterward assigned to sand class while silt and clay classes each gain 25 percent of it. Soil moisture and temperature from the Global Land Data Assimilation System (GLDAS) were utilized to provide these initializations in higher resolution of 0.25 degree than in the standard setting. Modified and control simulations were

  9. Chemerin15 inhibits neutrophil-mediated vascular inflammation and myocardial ischemia-reperfusion injury through ChemR23

    PubMed Central

    Cash, Jenna L; Bena, Stefania; Headland, Sarah E; McArthur, Simon; Brancaleone, Vincenzo; Perretti, Mauro

    2013-01-01

    Neutrophil activation and adhesion must be tightly controlled to prevent complications associated with excessive inflammatory responses. The role of the anti-inflammatory peptide chemerin15 (C15) and the receptor ChemR23 in neutrophil physiology is unknown. Here, we report that ChemR23 is expressed in neutrophil granules and rapidly upregulated upon neutrophil activation. C15 inhibits integrin activation and clustering, reducing neutrophil adhesion and chemotaxis in vitro. In the inflamed microvasculature, C15 rapidly modulates neutrophil physiology inducing adherent cell detachment from the inflamed endothelium, while reducing neutrophil recruitment and heart damage in a murine myocardial infarction model. These effects are mediated through ChemR23. We identify the C15/ChemR23 pathway as a new regulator and thus therapeutic target in neutrophil-driven pathologies. PMID:23999103

  10. Science-Technology-Society (STS) and ChemCom Courses versus College Chemistry Courses: Is There a Mismatch?

    ERIC Educational Resources Information Center

    Sanger, Michael J.; Greenbowe, Thomas J.

    1996-01-01

    This opinion paper discusses several issues surrounding questions of ChemCom and STS courses taken by science majors. Explores the basis for a potential mismatch students having an STS-based course may experience. Discusses objectivism and constructivism. (MKR)

  11. Comment on ``Glass transition in pure and doped amorphous solid water: An ultrafast microcalorimetry study'' [J. Chem. Phys. 125, 094501 (2006)

    NASA Astrophysics Data System (ADS)

    Johari, G. P.

    2007-10-01

    On investigating the data of Chonde et al. [J. Chem. Phys.125, 094501 (2006)], we find that (i) the relaxation time of the test liquid toluene used for determining the ultrafast scans' reliability was mistaken by several decades and incorrectly plotted, (ii) extrinsic effects had led to an exceptionally broad endotherm showing an enthalpy relaxation occurring implausibly at 500ps time scale, (iii) enthalpy relaxation times at structural unfreezing and at crystallization temperatures were assumed to be the same, equal to the reciprocal of the heating rate, and (iv) the data for water were incorrectly analyzed. An appropriate analysis would alter their conclusion and would be useful for discussing other ultrafast scans and nanocalorimetry data.

  12. Igneous mineralogy at Bradbury Rise: The first ChemCam campaign at Gale crater

    NASA Astrophysics Data System (ADS)

    Sautter, V.; Fabre, C.; Forni, O.; Toplis, M. J.; Cousin, A.; Ollila, A. M.; Meslin, P. Y.; Maurice, S.; Wiens, R. C.; Baratoux, D.; Mangold, N.; Le Mouélic, S.; Gasnault, O.; Berger, G.; Lasue, J.; Anderson, R. A.; Lewin, E.; Schmidt, M.; Dyar, D.; Ehlmann, B. L.; Bridges, J.; Clark, B.; Pinet, P.

    2014-01-01

    and compositional analyses using Chemistry Camera (ChemCam) remote microimager and laser-induced breakdown spectroscopy (LIBS) have been performed on five float rocks and coarse gravels along the first 100 m of the Curiosity traverse at Bradbury Rise. ChemCam, the first LIBS instrument sent to another planet, offers the opportunity to assess mineralogic diversity at grain-size scales (~ 100 µm) and, from this, lithologic diversity. Depth profiling indicates that targets are relatively free of surface coatings. One type of igneous rock is volcanic and includes both aphanitic (Coronation) and porphyritic (Mara) samples. The porphyritic sample shows dark grains that are likely pyroxene megacrysts in a fine-grained mesostasis containing andesine needles. Both types have magnesium-poor basaltic compositions and in this respect are similar to the evolved Jake Matijevic rock analyzed further along the Curiosity traverse both with Alpha-Particle X-ray Spectrometer and ChemCam instruments. The second rock type encountered is a coarse-grained intrusive rock (Thor Lake) showing equigranular texture with millimeter size crystals of feldspars and Fe-Ti oxides. Such a rock is not unique at Gale as the surrounding coarse gravels (such as Beaulieu) and the conglomerate Link are dominated by feldspathic (andesine-bytownite) clasts. Finally, alkali feldspar compositions associated with a silica polymorph have been analyzed in fractured filling material of Preble rock and in Stark, a putative pumice or an impact melt. These observations document magmatic diversity at Gale and describe the first fragments of feldspar-rich lithologies (possibly an anorthosite) that may be ancient crust transported from the crater rim and now forming float rocks, coarse gravel, or conglomerate clasts.

  13. Incorporation of a Chemical Equilibrium Equation of State into LOCI-Chem

    NASA Technical Reports Server (NTRS)

    Cox, Carey F.

    2005-01-01

    Renewed interest in development of advanced high-speed transport, reentry vehicles and propulsion systems has led to a resurgence of research into high speed aerodynamics. As this flow regime is typically dominated by hot reacting gaseous flow, efficient models for the characteristic chemical activity are necessary for accurate and cost effective analysis and design of aerodynamic vehicles that transit this regime. The LOCI-Chem code recently developed by Ed Luke at Mississippi State University for NASA/MSFC and used by NASA/MSFC and SSC represents an important step in providing an accurate, efficient computational tool for the simulation of reacting flows through the use of finite-rate kinetics [3]. Finite rate chemistry however, requires the solution of an additional N-1 species mass conservation equations with source terms involving reaction kinetics that are not fully understood. In the equilibrium limit, where the reaction rates approach infinity, these equations become very stiff. Through the use of the assumption of local chemical equilibrium the set of governing equations is reduced back to the usual gas dynamic equations, and thus requires less computation, while still allowing for the inclusion of reacting flow phenomenology. The incorporation of a chemical equilibrium equation of state module into the LOCI-Chem code was the primary objective of the current research. The major goals of the project were: (1) the development of a chemical equilibrium composition solver, and (2) the incorporation of chemical equilibrium solver into LOCI-Chem. Due to time and resource constraints, code optimization was not considered unless it was important to the proper functioning of the code.

  14. Toward Regional Fossil Fuel CO2 Emissions Verification Using WRF-CHEM

    NASA Astrophysics Data System (ADS)

    Delle Monache, L.; Kosoviæ, B.; Cameron-Smith, P.; Bergmann, D.; Grant, K.; Guilderson, T.

    2008-12-01

    As efforts to reduce emissions of green house gases take shape it is becoming obvious that an essential component of a viable solution will involve emission verification. While detailed inventories of green house gas sources will represent important component of the solution additional verification methodologies will be necessary to reduce uncertainties in emission estimates especially for distributed sources and CO2 offsets. We developed tools for solving inverse dispersion problem for distributed emissions of green house gases. For that purpose we combine probabilistic inverse methodology based on Bayesian inversion with stochastic sampling and weather forecasting and air quality model WRF-CHEM. We demonstrate estimation of CO2 emissions associated with fossil fuel burning in California over two one-week periods in 2006. We use WRF- CHEM in tracer simulation mode to solve forward dispersion problem for emissions over eleven air basins. We first use direct inversion approach to determine optimal location for a limited number of CO2 - C14 isotope sensors. We then use Bayesian inference with stochastic sampling to determine probability distributions for emissions from California air basins. Moreover, we vary the number of sensors and frequency of measurements to study their effect on the accuracy and uncertainty level of the emission estimation. Finally, to take into account uncertainties associated with forward modeling, we combine Bayesian inference and stochastic sampling with ensemble modeling. The ensemble is created by running WRF-CHEM with different initial and boundary conditions as well as different boundary layer and surface model options. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory (LLNL) under Contract DE-AC52-07NA27344 (LLNL-ABS-406901-DRAFT). The project 07-ERD- 064 was funded by the Laboratory Directed Research and Development Program at LLNL.

  15. New Development of the Online Integrated Climate-Chemistry model framwork (RegCM-CHEM4)

    NASA Astrophysics Data System (ADS)

    Zakey, A. S.; Shalaby, A. K.; Solmon, F.; Giorgi, F.; Tawfik, A. B.; Steiner, A. L.; Baklanov, A.

    2012-04-01

    The RegCM-CHEM4 is a new online integrated climate-chemistry model based on the regional climate model (RegCM4). The RegCM4 developed at the Abdus Salam International Centre for Theoretical Physics (ICTP), is a hydrostatic, sigma coordinate model. Tropospheric gas-phase chemistry is integrated into the climate model using the condensed version of the Carbon Bond Mechanism CBM-Z with lumped species that represent broad categories of organics based on carbon bond structure. The computationally rapid radical balance method RBM is coupled as a chemical solver to the gas-phase mechanism. Photolysis rates are determined as a function of meteorological and chemical inputs and interpolated from an array of pre-determined values based on the Tropospheric Ultraviolet-Visible Model (TUV) with cloud cover corrections. Cloud optical depths and cloud altitudes from RegCM-CHEM4 are used in the photolysis calculations, thereby directly coupling the photolysis rates and chemical reactions to meteorological conditions at each model time step. In this study, we evaluate the model over Europe for two different time scales: (1) an event-based analysis of the ozone episode associated with the heat wave of August 2003 and (2) a climatological analysis of a six-year simulation (2000-2005). For the episode analysis, model simulations show a good agreement with the European Monitoring and Evaluation Program (EMEP) observations of hourly ozone over different regions in Europe and capture ozone concentrations during and after the summer 2003 heat wave event. Analysis of the full six years of simulation indicates that the coupled chemistry-climate model can reproduce the seasonal cycle of ozone, with an overestimation of ozone in the non-event years of 5-15 ppb depending on the geographic region. Overall, the ozone and ozone precursor evaluation shows the feasibility of using RegCM-CHEM4 for decadal-length simulations of chemistry-climate interactions.

  16. Evaluating WRF-Chem aerosol indirect effects in Southeast Pacific marine stratocumulus during VOCALS-REx

    SciTech Connect

    Saide, Pablo; Spak, S. N.; Carmichael, Gregory; Mena-Carrasco, M. A.; Yang, Qing; Howell, S. G.; Leon, Dolislager; Snider, Jefferson R.; Bandy, Alan R.; Collett, Jeffrey L.; Benedict, K. B.; de Szoeke, S.; Hawkins, Lisa; Allen, Grant; Crawford, I.; Crosier, J.; Springston, S. R.

    2012-03-30

    We evaluate a regional-scale simulation with the WRF-Chem model for the VAMOS (Variability of the American Monsoon Systems) Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx), which sampled the Southeast Pacific's persistent stratocumulus deck. Evaluation of VOCALS-REx ship-based and aircraft observations focuses on analyzing how aerosol loading affects marine boundary layer (MBL) dynamics and cloud microphysics. We compare local time series and campaign averaged longitudinal gradients, and highlight differences in model simulations with (W) and without wet (NW) deposition processes. The higher aerosol loadings in the NW case produce considerable changes in MBL dynamics and cloud microphysics, in accordance with the established conceptual model of aerosol indirect effects. These include increase in cloud albedo, increase in MBL and cloud heights, drizzle suppression, increase in liquid water content, and increase in cloud lifetime. Moreover, better statistical representation of aerosol mass and number concentration improves model fidelity in reproducing observed spatial and temporal variability in cloud properties, including top and base height, droplet concentration, water content, rain rate, optical depth (COD) and liquid water path (LWP). Together, these help to quantify confidence in WRF-Chem's modeled aerosol-cloud interactions, while identifying structural and parametric uncertainties including: irreversibility in rain wet removal; overestimation of marine DMS and sea salt emissions and accelerated aqueous sulfate conversion. Our findings suggest that WRF-Chem simulates marine cloud-aerosol interactions at a level sufficient for applications in forecasting weather and air quality and studying aerosol climate forcing, including the reliability required for policy analysis and geo-engineering applications.

  17. Evaluating WRF-Chem aerosol indirect effects in Southeast Pacific marine stratocumulus during VOCALS-REx

    SciTech Connect

    Saide P. E.; Springston S.; Spak, S. N.; Carmichael, G. R.; Mena-Carrasco, M. A.; Yang, Q.; Howell, S.; Leon, D. C.; Snider, J. R.; Bandy, A. R.; Collett, J. L.; Benedict, K. B.; de Szoeke, S. P.; Hawkins, L. N.; Allen, G.; Crawford, I.; Crosier, J.

    2012-03-29

    We evaluate a regional-scale simulation with the WRF-Chem model for the VAMOS (Variability of the American Monsoon Systems) Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx), which sampled the Southeast Pacific's persistent stratocumulus deck. Evaluation of VOCALS-REx ship-based and three aircraft observations focuses on analyzing how aerosol loading affects marine boundary layer (MBL) dynamics and cloud microphysics. We compare local time series and campaign-averaged longitudinal gradients, and highlight differences in model simulations with (W) and without (NW) wet deposition processes. The higher aerosol loadings in the NW case produce considerable changes in MBL dynamics and cloud microphysics, in accordance with the established conceptual model of aerosol indirect effects. These include increase in cloud albedo, increase in MBL and cloud heights, drizzle suppression, increase in liquid water content, and increase in cloud lifetime. Moreover, better statistical representation of aerosol mass and number concentration improves model fidelity in reproducing observed spatial and temporal variability in cloud properties, including top and base height, droplet concentration, water content, rain rate, optical depth (COD) and liquid water path (LWP). Together, these help to quantify confidence in WRF-Chem's modeled aerosol-cloud interactions, especially in the activation parameterization, while identifying structural and parametric uncertainties including: irreversibility in rain wet removal; overestimation of marine DMS and sea salt emissions, and accelerated aqueous sulfate conversion. Our findings suggest that WRF-Chem simulates marine cloud-aerosol interactions at a level sufficient for applications in forecasting weather and air quality and studying aerosol climate forcing, and may do so with the reliability required for policy analysis.

  18. Regional Modeling of Dust Mass Balance and Radiative Forcing over East Asia using WRF-Chem

    SciTech Connect

    Chen, Siyu; Zhao, Chun; Qian, Yun; Leung, Lai-Yung R.; Huang, J.; Huang, Zhongwei; Bi, Jianrong; Zhang, Wu; Shi, Jinsen; Yang, Lei; Li, Deshuai; Li, Jinxin

    2014-12-01

    The Weather Research and Forecasting model with Chemistry (WRF-Chem) is used to investigate the seasonal and annual variations of mineral dust over East Asia during 2007-2011, with a focus on the dust mass balance and radiative forcing. A variety of measurements from in-stu and satellite observations have been used to evaluate simulation results. Generally, WRF-Chem reproduces not only the column variability but also the vertical profile and size distribution of mineral dust over and near the dust source regions of East Asia. We investigate the dust lifecycle and the factors that control the seasonal and spatial variations of dust mass balance and radiative forcing over the seven sub-regions of East Asia, i.e. source regions, the Tibetan Plateau, Northern China, Southern China, the ocean outflow region, and Korea-Japan regions. Results show that, over the source regions, transport and dry deposition are the two dominant sinks. Transport contributes to ~30% of the dust sink over the source regions. Dust results in a surface cooling of up to -14 and -10 W m-2, atmospheric warming of up to 20 and 15 W m-2, and TOA cooling of -5 and -8 W m-2 over the two major dust source regions of East Asia, respectively. Over the Tibetan Plateau, transport is the dominant source with a peak in summer. Over identified outflow regions, maximum dust mass loading in spring is contributed by the transport. Dry and wet depositions are the comparably dominant sinks, but wet deposition is larger than dry deposition over the Korea-Japan region, particularly in spring (70% versus 30%). The WRF-Chem simulations can generally capture the measured features of dust aerosols and its radaitve properties and dust mass balance over East Asia, which provides confidence for use in further investigation of dust impact on climate over East Asia.

  19. Development of the Grid-Independent GEOS-Chem Module and its deployment in the GEOS-5 General Circulation Model

    NASA Astrophysics Data System (ADS)

    Long, M. S.; Yantosca, R. M.; Nielsen, J. E.; da Silva, A.; Pawson, S.; Keller, C. A.; Sulprizio, M.; Jacob, D. J.

    2013-12-01

    The Harvard University GEOS-Chem 3-D chemical transport model simulates atmospheric composition - including tropospheric oxidants, primary and secondary aerosols, carbon gases, mercury, and others - driven by NASA's Goddard Earth Observing System (GEOS) assimilated meteorological data. A collaborative project between Harvard University and NASA's Global Modeling and Assimilation Office (GMAO) is focused on redesigning GEOS-Chem's core program structure to meet requirements of the Earth System Modeling Framework (ESMF). This new module, the Grid-Independent GEOS-Chem (GIGC), is capable of operating on an arbitrary horizontal geophysical grid, and has been embedded as the tropospheric chemistry component in GEOS-5, which is an HPC-capable Earth System Model. The primary goals of the GIGC are (1) the use of the GEOS-Chem inside the GEOS-5 Data Assimilation System, for multi-constituent chemical data assimilation of satellite observations (including tropospheric ozone, CO, and NO2); and (2) studies of fully-coupled atmospheric chemistry-climate feedbacks. Both of these goals are enhanced by the ease-of-implementation of new science within GEOS-Chem, which permits model development by GEOS-Chem's wide user community to be quickly integrated within both the stand-alone and the GCM-embedded model versions. Here, we present the first results of the GIGC-coupled GEOS-5 GCM, run at multiple grid resolutions and both rectilinear and cubed-sphere grids. Case studies are used to illustrate model performance at a variety of spatial resolutions.

  20. School absentee data modeling for possible detection of chem-bio attacks

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger M.; Handley, James W.; Jaenisch, Kristina L.; Faucheux, Jeffrey P.

    2005-05-01

    A baseline mathematical Data Model for rapid detection of events affecting school attendance was established using measured absenteeism. We derived a process model in the form of a differential equation of baseline or nominal behavior of sufficient fidelity to enable predictive what-if excursions to be done. Also, we derived a change detector equation enabling aberrant absenteeism to be flagged on the first day of detection. Used together, both mathematical models provide a powerful tool set for analysis and examining what unusual absenteeism patterns might be like due to chem-bio attack. A convenient single page lookup table is provided to give predictive analysis capability without resorting to cumbersome calculations.

  1. Photothermal nano-cavities for ultra-sensitive chem-bio detection

    NASA Astrophysics Data System (ADS)

    Hu, Juejun; Musgrave, J. David; Carlie, Nathan; Agarwal, Anu; Richardson, Kathleen; Kimerling, Lionel C.

    2011-05-01

    Nano-cavity photothermal spectroscopy is a novel technique for ultra-sensitive chem-bio detection. We illustrate that through simultaneous localization of optical and thermal interactions in a planar nano-cavity, detection sensitivity can be improved by > 104 compared to state-of-the-art. Key to nano-cavity photothermal sensing is the use of novel infraredtransparent chalcogenide glasses for resonant cavity fabrication, as these glasses feature a photothermal figure-of-merit over two orders of magnitude higher than conventional materials. We demonstrate planar optical resonant cavity devices in these glasses with record cavity quality factors up to 5 × 105, leading to high photothermal detection sensitivity.

  2. A highly sensitive, integrable, multimode, interferometric, evanescent-wave chem/bio sensor

    NASA Astrophysics Data System (ADS)

    Lillie, Jeffrey J.

    A fully integrated optical chem/bio sensor complete with integrated source, chemically sensitive waveguide, detector arrays, and associated signal processing electronics on a Si-CMOS chip is a challenging, but highly desirable goal. An evanescent-wave multimode interferometric sensing element is a sensitive method for sensing, which is easily integrated on Si-CMOS. This work is concerned with the design, analysis, and demonstration of a planar multimode interferometric chem/bio sensor that is compatible with the fabrication constraints of Si-CMOS. A 4000-micron-long interferometric that can be adapted for different agents by a particular sensing layer has been fabricated on silicon using silicon dioxide and silicon oxynitride. Hexaflouro-isopropanol substituted polynorbornene is the sensing layer. This sensor has also been fabricated on a Si-CMOS circuit with embedded photodetectors. A sensor on silicon was demonstrated with a minimum detectable index change of 2.0x10 -6 using an accurate gas delivery system and a custom hermetic waveguide test chamber. A modal pattern analysis strategy has also been developed to extract the optimal SNR from the measured modal patterns. An understanding of the noise processes and spatial bandwidth effects has enabled an experimentally-based prediction of the index sensitivity of a fully integrated multimode chem/bio sensor on Si-CMOS at 9.2x10-7. Theoretically, the sensitivity enhancement of high over low index sensing layers and transverse-magnetic over transverse electric modes is described. Also, the sensitivity enhancement of higher-order-transverse modes has been quantified. The wide-angle beam propagation method has been used to simulate the sensor. This simulation showed the relation between the modal pattern repetition period and sensor sensitivity. Further, the modal coupling properties of the multimode y-junction have been described. A second multimode y-junction has been designed to change the modal excitation under the

  3. ChemCam First Discovery of High Silica Sediments in Gale Crater

    NASA Astrophysics Data System (ADS)

    Frydenvang, J.; Gasda, P. J.; Wiens, R. C.; Newsom, H. E.; Bridges, J.; Gasnault, O.; Maurice, S.; Forni, O.; Mangold, N.; Cousin, A.; Payré, V.; Anderson, R. B.; Mitrofanov, I. G.; Jun, I.; Rice, M. S.; Milliken, R.; Edwards, P.; Vaniman, D. T.; Morris, R. V.; Blake, D. F.; Gellert, R.; Thompson, L. M.; Clark, B. C.; Hurowitz, J.; Sumner, D. Y.; Ehlmann, B. L.; Fraeman, A.; Kinch, K. M.; Madsen, M. B.; Calef, F.; Grotzinger, J. P.; Vasavada, A. R.

    2015-12-01

    On sol 991, The Curiosity rover ascended a steep slope to Marias Pass in Gale Crater. Close to the top, ChemCam analyzed the rock target Elk from an apparent bright unit. Utilizing the new elemental calibration implemented for ChemCam in the summer of 2015, four of five points on Elk were measured to contain 76-82 wt% SiO2 and >3 wt% TiO2, whereas the last point showed elevated CaSO4. The Elk target is identified to be part of the Murray formation, and hence related to the Pahrump area mudstones that were subjected to intensive studies by the Curiosity rover team over the sols 758-948. While the Murray formation west of Elk did show elevated SiO2 (~65 wt%) compared to the Pahrump area, no targets with similarly high SiO2 wt% as Elk were observed, thus prompting - together with detection of anomalously high DAN H signals in the same area - the Curiosity rover to return to the Elk target area for additional analyses. This return led to numerous additional high Si observations (targets Pistol, Mary, Shepard, Dublin Gulch and Frog) that all corroborated the initial high Si observation at Elk. Additionally, the Alpha Particle X-ray Spectrometer (APXS) analyzed the target Lamoose and found SiO2 content in excess of 72 wt% and moderately elevated TiO2. Considering the difference in footprint (1.7 cm for APXS vs ~400μm for ChemCam) and the fact that the target couldn't be brushed, this is considered a good corroboration of the very high Si observed with ChemCam. These targets suggest that the Elk-area targets represent an end-member of the Murray formation, but there are multiple working hypotheses for the origin of the high SiO2 and TiO2 in these: 1. primary precipitates from the water column of a lake, 2. a post-depositional leaching/weathering front and 3. a hydrothermal silica precipitate.

  4. Comment on ``Quasirelativistic theory equivalent to fully relativistic theory'' [J. Chem. Phys. 123, 241102 (2005)

    NASA Astrophysics Data System (ADS)

    Filatov, Michael

    2006-09-01

    The connection between the exact quasirelativistic approach developed in the title reference [W. Kutzelnigg and W. Liu, J. Chem. Phys. 123, 241102 (2005)] and the method of elimination of the small component in matrix form developed previously by Dyall is explicitly worked out. An equation that links Hermitian and non-Hermitian formulations of the exact quasirelativistic theory is derived. Besides establishing a kinship between the existing formulations, the proposed equation can be employed for the derivation of new formulations of the exact quasirelativistic theory.

  5. Comment on 'Thermodynamic cycles and the calculation of p Ka' [Chem. Phys. Lett. 367 (2003) 145

    NASA Astrophysics Data System (ADS)

    da Silva, Clarissa O.; da Silva, Edilson C.; Nascimento, Marco A. C.

    2003-11-01

    In a recent Letter, Pliego [Chem. Phys. Lett. 367 (2003) 145] has raised some questions about the methodology that we have employed for calculating p Ka values in aqueous solutions. In this comment we show that the problem with Pliego's analysis is the fact that he used Ben-Naim's definition of Δ Gsol for both the solute and the solvent, which implies that the concentration, for both components, should be equal to 1 M. For the solute, this is a reference state fully compatible with the quantum description, but for the solvent this choice is unphysical, as discussed in the Letter.

  6. ChemCam passive reflectance spectroscopy of surface materials at the Curiosity landing site, Mars

    NASA Astrophysics Data System (ADS)

    Johnson, Jeffrey R.; Bell, J. F.; Bender, S.; Blaney, D.; Cloutis, E.; DeFlores, L.; Ehlmann, B.; Gasnault, O.; Gondet, B.; Kinch, K.; Lemmon, M.; Le Mouélic, S.; Maurice, S.; Rice, M.; Wiens, R. C.

    2015-03-01

    The spectrometers on the Mars Science Laboratory (MSL) ChemCam instrument were used in passive mode to record visible/near-infrared (400-840 nm) radiance from the martian surface. Using the onboard ChemCam calibration targets' housing as a reflectance standard, we developed methods to collect, calibrate, and reduce radiance observations to relative reflectance. Such measurements accurately reproduce the known reflectance spectra of other calibration targets on the rover, and represent the highest spatial resolution (0.65 mrad) and spectral sampling (<1 nm) visible/near-infrared reflectance spectra from a landed platform on Mars. Relative reflectance spectra of surface rocks and soils match those from orbital observations and multispectral data from the MSL Mastcam camera. Preliminary analyses of the band depths, spectral slopes, and reflectance ratios of the more than 2000 spectra taken during the first year of MSL operations demonstrate at least six spectral classes of materials distinguished by variations in ferrous and ferric components. Initial comparisons of ChemCam spectra to laboratory spectra of minerals and Mars analog materials demonstrate similarities with palagonitic soils and indications of orthopyroxene in some dark rocks. Magnesium-rich "raised ridges" tend to exhibit distinct near-infrared slopes. The ferric absorption downturn typically found for martian materials at <600 nm is greatly subdued in brushed rocks and drill tailings, consistent with their more ferrous nature. Calcium-sulfate veins exhibit the highest relative reflectances observed, but are still relatively red owing to the effects of residual dust. Such dust is overall less prominent on rocks sampled within the "blast zone" immediately surrounding the landing site. These samples were likely affected by the landing thrusters, which partially removed the ubiquitous dust coatings. Increased dust coatings on the calibration targets during the first year of the mission were documented by

  7. Exploration of Mars with the ChemCam LIBS Instrument and the Curiosity Rover

    NASA Technical Reports Server (NTRS)

    Newsom, Horton E.

    2016-01-01

    The Mars Science Laboratory (MSL) Curiosity rover landed on Mars in August 2012, and has been exploring the planet ever since. Dr. Horton E. Newsom will discuss the MSL's design and main goal, which is to characterize past environments that may have been conducive to the evolution and sustainability of life. He will also discuss Curiosity's science payload, and remote sensing, analytical capabilities, and direct discoveries of the Chemistry & Camera (ChemCam) instrument, which is the first Laser Induced Breakdown Spectrometer (LIBS) to operate on another planetary surface and determine the chemistry of the rocks and soils.

  8. Torsional Angle Driver (TorAD) System for HyperChem/Excel

    NASA Astrophysics Data System (ADS)

    Starkey, Ronald

    1999-02-01

    The torsional angle driver system for HyperChem/Excel is a package of several Excel spreadsheets and macro programs to be used with HyperChem to obtain and plot information, such as total energy, for the conformations that result from a 360° rotation about a torsional angle system in a molecule. The TorAD system also includes several HyperChem scripts to facilitate its use. TorAD was developed for use in the undergraduate organic chemistry laboratory. The results obtained with TorAD could be obtained manually with HyperChem, but it would take considerable time and would not be instructive to the students. Use of the TorAD system allows students to spend their time on the more important aspect of conformation analysisinterpretation of results. The Excel spreadsheet/macro programs in TorAD include:

    · Tor_xl_a and tor_xl obtain and plot the total energy at 5° torsional-angle intervals. The calculation method, the torsional-angle restraint, and the structure to be used at each angle can be set by the user. The advanced version, tor_xl_a, which requires HyperChem 4.5 or later, also allows torsional-angle structures to be saved for later recall as individual structures or, using a HyperChem script, in a movie format. It also provides a rapid scan of the 360° rotation where only single-point calculations, rather than geometry optimizations, are performed. The tor_xl system will perform routine tasks in a manner suitable for most instructional settings. · Tor_Comp performs molecular mechanics optimizations at 5° intervals and obtains and plots four energy parameters (total, torsional, nonbonded, and bond [bend plus stretch] energy) as a function of torsional angle. The calculation method and the restraint can be specified. · TorDipol produces a plot of the total energy and the calculated dipole moment at 5° steps of the torsional angle. The default calculation is the semi-empirical AM

  9. Monolithically-integrated MicroChemLab for gas-phase chemical analysis.

    SciTech Connect

    Kottenstette, Richard Joseph; Adkins, Douglas Ray; Manley, Robert George; Lewis, Patrick Raymond; Bauer, Joseph M.; Manginell, Ronald Paul; Okandan, Murat; Shul, Randy John; Sokolowski, Sara Suzette

    2003-06-01

    Sandia National Labs has developed an autonomous, hand-held system for sensitive/selective detection of gas-phase chemicals. Through the sequential connection of microfabricated preconcentrators (PC), gas chromatography columns (GC) and a surface acoustic wave (SAW) detector arrays, the MicroChemLab{trademark} system is capable of selective and sensitive chemical detection in real-world environments. To date, interconnection of these key components has primarily been achieved in a hybrid fashion on a circuit board modified to include fluidic connections. The monolithic integration of the PC and GC with a silicon-based acoustic detector is the subject of this work.

  10. Modeling of Lightning-Related Plumes into the Chemistry and Transport GEOS-Chem Global Model: Impact on the Upper Tropospheric Chemistry.

    NASA Astrophysics Data System (ADS)

    Gressent, A.

    2014-12-01

    This work is dedicated to the study of the lightning-related plumes in terms of origin, quantification of the plumes trace gas, and impact on the budget of ozone in particular in the upper troposphere (critical region regarding the greenhouse effect). Recently, Gressent et al., 2014, demonstrated that the majority (74%) of large scale plumes (>300km) from lightning emissions (LNOx) is related to warm conveyor belts and extra-tropical cyclones originating from North America and entering the intercontinental pathway between North America and Europe, leading to a negative (positive) west to east NOy (O3) zonal gradient with -0.4 (+18) ppb difference during spring and -0.6 (+14) ppb difference in summer. In order to better constraint lightning emissions impact in global models, a plume parameterization has been implemented in the 3D chemistry and transport GEOS-Chem global model (Harvard University). Such parameterization was successfully developed for aircraft exhausts application (Cariolle et al., 2009). It allows reproducing sub-grid processes related to lightning NOx chemistry and the chemical evolution during transport in the atmosphere. The issue is here based on the evaluation of parameters such as the plume lifetime and the effective reaction rate constant within the plume. The Dynamically Simple Model of Atmospheric Chemical Complexity (DSMACC) is used to determine such critical values and to better understand the chemical interactions between NOx and O3 species within the undiluted fraction of the plume. Additionally high-resolved simulations of the French meso-scale Meso-NH model are applied over specific case studies of thunderstorms in order to consider the dynamical conditions necessary to represent the plume dilution to the background atmosphere. Finally, sensitivity tests are carried out with the GEOS-Chem model to evaluate the impact of this plume-in-grid model on the ozone and nitrogen species budget.

  11. Simulated photodetachment spectra of AlH2-

    NASA Astrophysics Data System (ADS)

    Mok, Daniel K. W.; Lee, Edmond P. F.; Chau, Foo-tim; Dyke, John M.

    2013-07-01

    We have carried out high-level ab initio calculations on AlH2 and its anion, as well as Franck-Condon factor calculations, which include anharmonicity and Duschinsky rotation, to simulate the photodetachment spectrum of AlH2-, with the aim of assigning the very recently reported photodetachment spectrum of AlH2- [X. Zhang, H. Wang, E. Collins, A. Lim, G. Ganteför, B. Kiran, H. Schnöckel, B. Eichhorn, and K. Bowen, J. Chem. Phys. 138, 124303 (2013)], 10.1063/1.4796200. However, our simulated spectra do not support the assignment of the reported experimental spectrum to AlH2-.

  12. Effects on Student Achievement in General Chemistry Following Participation in an Online Preparatory Course. ChemPrep, a Voluntary, Self-Paced, Online Introduction to Chemistry

    NASA Astrophysics Data System (ADS)

    Botch, Beatrice; Day, Roberta; Vining, William; Stewart, Barbara; Rath, Kenneth; Peterfreund, Alan; Hart, David

    2007-03-01

    ChemPrep was developed to be a stand-alone preparatory short-course to help students succeed in general chemistry. It is Web-based and delivered using the OWL system. Students reported that the ChemPrep materials (short information pages, parameterized questions with detailed feedback, tutorials, and answers to questions through the OWL message system) permitted them to work independently without the need for textbook or lecture. On average, students who completed ChemPrep had higher grades in the subsequent GenChem, Nursing, and Honors chemistry courses, with a greater percentage achieving a grade of C- or higher. Participation in ChemPrep was voluntary, and more women than men responded. Students in the Honors course enrolled in ChemPrep in higher percentages than students in GenChem and Nursing. SAT and departmental math placement exam scores were used as proxy measures of prior achievement and ability. Based on these, Honors chemistry ChemPrep users were on par with their peers but performed better in the course than non-users. In GenChem and Nursing chemistry courses, ChemPrep helped students of high prior achievement and ability perform better than their achievement scores would predict. Weaker or less motivated students did not respond to the voluntary offerings of ChemPrep in the same numbers as stronger or more motivated students, and we are seeking alternate ways to reach this population.

  13. ALS - resources

    MedlinePlus

    Resources - ALS ... The following organizations are good resources for information on amyotrophic lateral sclerosis : Muscular Dystrophy Association -- www.mda.org/disease/amyotrophic-lateral-sclerosis National Amyotrophic Lateral Sclerosis (ALS) ...

  14. Using Combustion Tracers to Estimate Surface Black Carbon Distributions in WRF-Chem

    NASA Astrophysics Data System (ADS)

    Raman, A.; Arellano, A. F.

    2015-12-01

    Black Carbon (BC) emissions significantly affect the global and regional climate, air quality, and human health. However, BC observations are currently limited in space and time; leading to considerable uncertainties in the estimates of BC distribution from regional and global models. Here, we investigate the usefulness of carbon monoxide (CO) in quantifying BC across continental United States (CONUS). We use high resolution EPA AQS observations of CO and IMPROVE BC to estimate BC/CO ratios. We model the BC and CO distribution using the community Weather Research and Forecasting model with Chemistry (WRF-Chem). We configured WRF-Chem using MOZART chemistry, NEI 2005, MEGAN, and FINNv1.5 for anthropogenic, biogenic and fire emissions, respectively. In this work, we address the following three key questions: 1) What are the discrepancies in the estimates of BC and CO distributions across CONUS during summer and winter periods?, 2) How do BC/CO ratios change for different spatial and temporal regimes?, 3) Can we get better estimates of BC from WRF-Chem if we use BC/CO ratios along with optimizing CO concentrations? We compare ratios derived from the model and observations and develop characteristic ratios for several geographical and temporal regimes. We use an independent set of measurements of BC and CO to evaluate these ratios. Finally, we use a Bayesian synthesis inversion to optimize CO from WRF-Chem using regionally tagged CO tracers. We multiply the characteristic ratios we derived with the optimized CO to obtain BC distributions. Our initial results suggest that the maximum ratios of BC versus CO occur in the western US during the summer (average: 4 ng/m3/ppbv) and in the southeast during the winter (average: 5 ng/m3/ppbv). However, we find that these relationships vary in space and time and are highly dependent on fuel usage and meteorology. We find that optimizing CO using EPA-AQS provides improvements in BC but only over areas where BC/CO ratios are close

  15. The potassic sedimentary rocks in Gale Crater, Mars, as seen by ChemCam Onboard Curiosity

    USGS Publications Warehouse

    Le Deit, Laetitia; Mangold, Nicolas; Forni, Olivier; Cousin, Agnes; Lasue, Jeremie; Schröder, Susanne; Wiens, Roger C.; Sumner, Dawn Y.; Fabre, Cecile; Stack, Katherine M.; Anderson, Ryan; Blaney, Diana L.; Clegg, Samuel M.; Dromart, Gilles; Fisk, Martin; Gasnault, Olivier; Grotzinger, John P.; Gupta, Sanjeev; Lanza, Nina; Le Mouélic, Stephane; Maurice, Sylvestre; McLennan, Scott M.; Meslin, Pierre-Yves; Nachon, Marion; Newsom, Horton E.; Payre, Valerie; Rapin, William; Rice, Melissa; Sautter, Violaine; Treiman, Alan H.

    2016-01-01

    The Mars Science Laboratory rover Curiosity encountered potassium-rich clastic sedimentary rocks at two sites in Gale Crater, the waypoints Cooperstown and Kimberley. These rocks include several distinct meters thick sedimentary outcrops ranging from fine sandstone to conglomerate, interpreted to record an ancient fluvial or fluvio-deltaic depositional system. From ChemCam Laser-Induced Breakdown Spectroscopy (LIBS) chemical analyses, this suite of sedimentary rocks has an overall mean K2O abundance that is more than 5 times higher than that of the average Martian crust. The combined analysis of ChemCam data with stratigraphic and geographic locations reveals that the mean K2O abundance increases upward through the stratigraphic section. Chemical analyses across each unit can be represented as mixtures of several distinct chemical components, i.e., mineral phases, including K-bearing minerals, mafic silicates, Fe-oxides, and Fe-hydroxide/oxyhydroxides. Possible K-bearing minerals include alkali feldspar (including anorthoclase and sanidine) and K-bearing phyllosilicate such as illite. Mixtures of different source rocks, including a potassium-rich rock located on the rim and walls of Gale Crater, are the likely origin of observed chemical variations within each unit. Physical sorting may have also played a role in the enrichment in K in the Kimberley formation. The occurrence of these potassic sedimentary rocks provides additional evidence for the chemical diversity of the crust exposed at Gale Crater.

  16. Recent Highlights of ChemCam’s exploration of Gale Crater

    NASA Astrophysics Data System (ADS)

    Blaney, Diana L.; Wiens, Roger C.; Maurice, Sylvestre; Anderson, Ryan; Clegg, Samuel; Le Deit, Laetitia; Forni, Olivier; Gasnault, Olivier; Johnson, Jeffry R.; Lanza, Nina; Lasue, Jeremie A.; Mangold, Nicholas; Nachon, Marion; Newsom, Horton; Pilleri , Agnes; Sautter, Violaine

    2014-11-01

    ChemCam has been exploring Gale Crater and documenting the chemistry along our traverse to Mount Sharp. More than 160,000 LIBS spectra and 2,000 images have been returned to Earth from locations along the 9 km route. Key discoveries documented by ChemCam along the traverse since leaving the Yellow Knife Bay drilling location include: 1) abundant alkali feldspar present in conglomerates and float rocks; 2) MnO present at up to several wt. % in specific coatings and in the Kimberly outcrop; its presence suggests highly oxidized fluids existed during emplacement; 3) fluorine present in key lithologies; the associated chemistry indicates the occurrence of fluor-apatites in igneous rocks and micas in conglomerates; 4) Cap rocks showing a wide range of compositions that span the compositions of outcrops seen at previous locations (e.g. “Shaler”, “Point Lake”) 5) a pair of iron meteorites, “Lebanon” and “Littleton”, 6) Chlorine-bearing soils in “Hidden Valley” and corresponding light toned outcrops and 7) an assessment of coatings in Gale that indicate alteration rates are generally slower than rates of aeolian abrasion. The talk will also include discussion of most recent results and their implications for fluvial processes at Gale.

  17. Nanoplatforms for Detection, Remediation and Protection Against Chem-Bio Warfare

    NASA Astrophysics Data System (ADS)

    Denkbaş, E. B.; Bayram, C.; Kavaz, D.; Çirak, T.; Demirbilek, M.

    Chemical and biological substances have been used as warfare agents by terrorists by varying degree of sophistication. It is critical that these agents be detected in real-time with high level of sensitively, specificity, and accuracy. Many different types of techniques and systems have been developed to detect these agents. But there are some limitations in these conventional techniques and systems. Limitations include the collection, handling and sampling procedures, detection limits, sample transfer, expensive equipment, personnel training, and detection materials. Due to the unique properties such as quantum effect, very high surface/volume ratio, enhanced surface reactivity, conductivity, electrical and magnetic properties of the nanomaterials offer great opportunity to develop very fast, sensitive, accurate and cost effective detection techniques and systems to detect chemical and biological (chem.-bio) warfare agents. Furthermore, surface modification of the materials is very easy and effective way to get functional or smart surfaces to be used as nano-biosensor platform. In that respect many different types of nanomaterials have been developed and used for the detection, remediation and protection, such as gold and silver nanoparticles, quantum dots, Nano chips and arrays, fluorescent polymeric and magnetic nanoparticles, fiber optic and cantilever based nanobiosensors, nanofibrillar nanostructures etc. This study summarizes preparation and characterization of nanotechnology based approaches for the detection of and remediation and protection against chem.-bio warfare agents.

  18. AerChemMIP: Quantifying the effects of chemistry and aerosols in CMIP6

    DOE PAGES

    Collins, William J.; Lamarque, Jean -François; Schulz, Michael; ...

    2017-02-09

    The Aerosol Chemistry Model Intercomparison Project (AerChemMIP) is endorsed by the Coupled-Model Intercomparison Project 6 (CMIP6) and is designed to quantify the climate and air quality impacts of aerosols and chemically reactive gases. These are specifically near-term climate forcers (NTCFs: methane, tropospheric ozone and aerosols, and their precursors), nitrous oxide and ozone-depleting halocarbons. The aim of AerChemMIP is to answer four scientific questions. 1. How have anthropogenic emissions contributed to global radiative forcing and affected regional climate over the historical period? 2. How might future policies (on climate, air quality and land use) affect the abundances of NTCFs and theirmore » climate impacts? 3.How do uncertainties in historical NTCF emissions affect radiative forcing estimates? 4. How important are climate feedbacks to natural NTCF emissions, atmospheric composition, and radiative effects? These questions will be addressed through targeted simulations with CMIP6 climate models that include an interactive representation of tropospheric aerosols and atmospheric chemistry. These simulations build on the CMIP6 Diagnostic, Evaluation and Characterization of Klima (DECK) experiments, the CMIP6 historical simulations, and future projections performed elsewhere in CMIP6, allowing the contributions from aerosols and/or chemistry to be quantified. As a result, specific diagnostics are requested as part of the CMIP6 data request to highlight the chemical composition of the atmosphere, to evaluate the performance of the models, and to understand differences in behaviour between them.« less

  19. AerChemMIP: quantifying the effects of chemistry and aerosols in CMIP6

    NASA Astrophysics Data System (ADS)

    Collins, William J.; Lamarque, Jean-François; Schulz, Michael; Boucher, Olivier; Eyring, Veronika; Hegglin, Michaela I.; Maycock, Amanda; Myhre, Gunnar; Prather, Michael; Shindell, Drew; Smith, Steven J.

    2017-02-01

    The Aerosol Chemistry Model Intercomparison Project (AerChemMIP) is endorsed by the Coupled-Model Intercomparison Project 6 (CMIP6) and is designed to quantify the climate and air quality impacts of aerosols and chemically reactive gases. These are specifically near-term climate forcers (NTCFs: methane, tropospheric ozone and aerosols, and their precursors), nitrous oxide and ozone-depleting halocarbons. The aim of AerChemMIP is to answer four scientific questions. 1. How have anthropogenic emissions contributed to global radiative forcing and affected regional climate over the historical period? 2. How might future policies (on climate, air quality and land use) affect the abundances of NTCFs and their climate impacts? 3.How do uncertainties in historical NTCF emissions affect radiative forcing estimates? 4. How important are climate feedbacks to natural NTCF emissions, atmospheric composition, and radiative effects? These questions will be addressed through targeted simulations with CMIP6 climate models that include an interactive representation of tropospheric aerosols and atmospheric chemistry. These simulations build on the CMIP6 Diagnostic, Evaluation and Characterization of Klima (DECK) experiments, the CMIP6 historical simulations, and future projections performed elsewhere in CMIP6, allowing the contributions from aerosols and/or chemistry to be quantified. Specific diagnostics are requested as part of the CMIP6 data request to highlight the chemical composition of the atmosphere, to evaluate the performance of the models, and to understand differences in behaviour between them.

  20. ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2016-01-01

    Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

  1. High resolution satellite derived erodibility factors for WRF/Chem windblown dust simulations in Argentina

    NASA Astrophysics Data System (ADS)

    Cremades, Pablo Gabriel; Fernandez, Rafael Pedro; Allend, David; Mulena, Celeste; Puliafito, Salvador Enrique

    2017-04-01

    A proper representation of dust sources is critical to accurately predict atmospheric particle concentrations in regional windblown dust simulations. The Weather Research and Forecasting model with Chemistry (WRF/Chem) includes a topographic-based erodibility map originally conceived for global scale modeling, which fails to identify the geographical location of dust sources in many regions of Argentina. Therefore, this study aims at developing a method to obtain a high-resolution erodibility map suitable for regional or local scale modeling using WRF/Chem. We present two independent approaches based on global methods to estimate soil erodibility using satellite retrievals, i.e. topography from the Shuttle Radar Topography Mission (SRTM) and surface reflectance from the Moderate Resolution Imaging Spectroradiometer (MODIS). Simulation results of a severe Zonda wind episode in the arid central-west Argentina serve as bases for the analysis of these methods. Simulated dust concentration at surface level is compared with particulate matter measurements at one site in Mendoza city. In addition, we use satellite aerosol optical depth (AOD) retrievals to investigate model performance in reproducing spatial distribution of dust emissions. The erodibility map based on surface reflectance from MODIS improves the representation of small scale features, and increases the overall dust aerosol loading with respect to the standard map included by default. Simulated concentrations are in good agreement with measurements as well as satellite derived dust spatial distribution.

  2. WRF-Chem simulation of East Asian air quality: Sensitivity to temporal and vertical emissions distributions

    NASA Astrophysics Data System (ADS)

    Wang, Xueyuan; Liang, Xin-Zhong; Jiang, Weimei; Tao, Zhining; Wang, Julian X. L.; Liu, Hongnian; Han, Zhiwei; Liu, Shuyan; Zhang, Yuyan; Grell, Georg A.; Peckham, Steven E.

    2010-02-01

    This study develops fine temporal (seasonal, day-of-week, diurnal) and vertical allocations of anthropogenic emissions for the TRACE-P inventory and evaluates their impacts on the East Asian air quality prediction using WRF-Chem simulations in July 2001 at 30-km grid spacing against available surface measurements from EANET and NEMCC. For NO 2 and SO 2, the diurnal and vertical redistributions of emissions play essential roles, while the day-of-week variation is less important. When all incorporated, WRF-Chem best simulates observations of surface NO 2 and SO 2 concentrations, while using the default emissions produces the worst result. The sensitivity is especially large over major cities and industrial areas, where surface NO 2 and SO 2 concentrations are reduced by respectively 3-7 and 6-12 ppbv when using the scaled emissions. The incorporation of all the three redistributions of emissions simulates surface O 3 concentrations higher by 4-8 ppbv at night and 2-4 ppbv in daytime over broad areas of northern, eastern and central China. To this sensitivity, the diurnal redistribution contributes more than the other two.

  3. Ultrafast PubChem searching combined with improved filtering rules for elemental composition analysis.

    PubMed

    Lommen, Arjen

    2014-06-03

    A new and improved software tool for elemental composition annotation of molecular ions detected in mass spectrometry, based on improved filtering rules followed by ultrafast querying in publicly available compound databases, is provided. Pubchem is used as a general source of 1.3 million unique chemical formulas. A plant metabolomics database containing ca. 100,000 formulas is used as a source of naturally occurring compounds. Four modes with different sets of rules for heuristic filtering of candidate formulas coming from elemental composition analysis are incorporated and tested on both databases. The elemental composition analysis is then coupled to ultrafast PubChem searching based on a mass-indexed intermediate system. The performance of the filters is compared and discussed. When reactive compounds are assumed not to be present, 99.95% of the 1.3 million PubChem formulas is correctly found, while ca. 30% less formulas per mass are given compared to previously published rules. For the ca. 100,000 plant metabolomics based formulas, 100% fit the improved rules.

  4. Statistical Downscaling of WRF-Chem Model: An Air Quality Analysis over Bogota, Colombia

    NASA Astrophysics Data System (ADS)

    Kumar, Anikender; Rojas, Nestor

    2015-04-01

    Statistical downscaling is a technique that is used to extract high-resolution information from regional scale variables produced by coarse resolution models such as Chemical Transport Models (CTMs). The fully coupled WRF-Chem (Weather Research and Forecasting with Chemistry) model is used to simulate air quality over Bogota. Bogota is a tropical Andean megacity located over a high-altitude plateau in the middle of very complex terrain. The WRF-Chem model was adopted for simulating the hourly ozone concentrations. The computational domains were chosen of 120x120x32, 121x121x32 and 121x121x32 grid points with horizontal resolutions of 27, 9 and 3 km respectively. The model was initialized with real boundary conditions using NCAR-NCEP's Final Analysis (FNL) and a 1ox1o (~111 km x 111 km) resolution. Boundary conditions were updated every 6 hours using reanalysis data. The emission rates were obtained from global inventories, namely the REanalysis of the TROpospheric (RETRO) chemical composition and the Emission Database for Global Atmospheric Research (EDGAR). Multiple linear regression and artificial neural network techniques are used to downscale the model output at each monitoring stations. The results confirm that the statistically downscaled outputs reduce simulated errors by up to 25%. This study provides a general overview of statistical downscaling of chemical transport models and can constitute a reference for future air quality modeling exercises over Bogota and other Colombian cities.

  5. Inclusion of biomass burning in WRF-Chem: Impact of wildfires on weather forecasts

    SciTech Connect

    Grell, G. A.; Freitas, Saulo; Stuefer, Martin; Fast, Jerome D.

    2011-06-06

    A plume rise algorithm for wildfires was included in WRF-Chem, and applied to look at the impact of intense wildfires during the 2004 Alaska wildfire season on weather forecasts using model resolutions of 10km and 2km. Biomass burning emissions were estimated using a biomass burning emissions model. In addition, a 1-D, time-dependent cloud model was used online in WRF-Chem to estimate injection heights as well as the final emission rates. It was shown that with the inclusion of the intense wildfires of the 2004 fire season in the model simulations, the interaction of the aerosols with the atmospheric radiation led to significant modifications of vertical profiles of temperature and moisture in cloud-free areas. On the other hand, when clouds were present, the high concentrations of fine aerosol (PM2.5) and the resulting large numbers of Cloud Condensation Nuclei (CCN) had a strong impact on clouds and microphysics, with decreased precipitation coverage and precipitation amounts during the first 12 hours of the integration, but significantly stronger storms during the afternoon hours.

  6. ChemCam results from the Shaler Outcrop in Gale Crater, Mars

    USGS Publications Warehouse

    Anderson, Ryan Bradley; Edgar, L.; Bridges, J.C.; Williams, A.; Williams, J.; Ollila, A.; Forni, O.; Mangold, N.; Lanza, N.; Sautter, V.; Gupta, S.; Blaney, D.; Clark, B.; Clegg, G.; Dromart, G.; Gasnault, O.; Lasue, J.; Le Mouélic, S.; Léveillé, Richard; Lewin, E.; Lewis, K.; Maurice, S.; Nachon, Marion; Newsom, H.; Vaniman, D.; Wiens, R.C.

    2014-01-01

    The "Shaler" outcrop in Gale crater is approximately 0.7 m thick and >20 m long, and exhibits multiple well-exposed platy and cross-stratified facies [1] interpreted to be primarily fluvial sandstone deposits. The outcrop is a part of the upper Glenelg member in the Yellowknife Bay (YKB) stratigraphic section [2]. Curiosity first encountered the "Shaler" outcrop on sol 121 of the mission, and returned to the outcrop on sols 309- 324. The rugged nature of the outcrop and short time available for analysis limited opportunities for contact science, but ChemCam’s ability to remotely collect compositional and textural observations resulted in a large data set from Shaler. ChemCam conducted analyses of 29 non-soil targets at Shaler, 26 of which used laser-induced breakdown spectroscopy (LIBS) for a total of 9,180 spectra. Three observations used only the remote micro-imager (RMI). Each of the 26 LIBS targets were analyzed at between 5 and 25 points, providing a measure of the target homogeneity and in some cases transecting fine strata. 

  7. The Martian O2 and H2O cycles observed with ChemCam Passive Sky Spectroscopy

    NASA Astrophysics Data System (ADS)

    McConnochie, T. H.; Smith, M. D.; Bender, S. C.; Wolff, M. J.; Johnson, J. R.; Lemmon, M. T.; Wiens, R. C.; Maurice, S.; Gasnault, O.; Blaney, D.; DeFlores, L. P.; Harri, A. M.; Kemppinen, O.; Genzer, M.; Moores, J.; Wong, M. H.; Trainer, M. G.; Martín-Torres, J.; Zorzano, M. P.; Franz, H.; Barraclough, B. L.; Atreya, S. K.; Mahaffy, P. R.

    2014-12-01

    The Mars Science Laboratory's (MSL) ChemCam spectrometer, designed primarily for laser-induced breakdown spectroscopy, has proven to also be every effective as a passive spectrometer. We will describe measurements O2, H2O, and aerosols from ChemCam passive sky observations. We will then discuss the evidence they provide for a seasonally active Martian O2 cycle as well as their implications for the Martian water cycle. ChemCam passive sky observations proceed by acquiring spectra of scattered light from the atmosphere at two different elevation angles, constructing a ratio spectrum to eliminate the solar spectrum and instrument response uncertainties, and then fitting a discrete ordinates multiple scattering radiative transfer model. O2 was thought to have a long, greater than 10 Martian year, photochemical lifetime (e. g. Krasnopolsky 2010, Icarus 207) and thus was expected to show a seasonal behavior identical to other non-condensable inert gases. ChemCam measurements demonstrate that this is not the case, showing that O2 decreases rapidly relative to SAM-QMS-measured Ar and CRISM-measured CO during the Ls = 350° to Ls = 30° period and then doubles its mixing ratio relative to those gases during the Ls = 50° to Ls = 130° period. SAM-QMS O2 measurements confirm the ChemCam results, showing essentially identical O2 mixing ratios and seasonal variations. The ChemCam water vapor measurements, when combined with the in-situ sampling of the REMS humidity sensor and with global scale orbiter data sets, provide information on the vertical distribution of water vapor and yield insights into the local and regional scale dynamics in the vicinity of Gale Crater. We observe a close match between mixing ratios inferred from REMS humidity sensor measurements and column average mixing ratios inferred from ChemCam in some seasons, but significant differences in other seasons, suggesting seasonal variations in vertical mixing processes.

  8. Comparison of biomass burning inventories processed by GEOS-Chem and ACCESS2.0 with total column and satellite data in Australia.

    NASA Astrophysics Data System (ADS)

    Desservettaz, M.; Fisher, J. A.; Jones, N. B.; Bukosa, B.; Greenslade, J.; Luhar, A.; Woodhouse, M.; Griffith, D. W. T.; Velazco, V. A.

    2016-12-01

    Australia contributes approximately 6% of global biomass burning CO2 emissions, mostly from savanna type fires. This estimate comes from biomass burning inventories that use emission factors derived from field campaigns performed outside Australia. The relevance of these emission factors to the Australian environment has not previously been evaluated and therefore needs to be tested. Here we compare predictions from the chemical transport model GEOS-Chem and the global chemistry-climate model ACCESS-UKCA run using different biomass burning inventories to total column measurements of CO, C2H6 and HCHO, in order to identify the most representative inventory for Australian fire emissions. The measurements come from the Network for Detection of Atmospheric Composition Change (NDACC) and Total Carbon Column Observing Network (TCCON) solar remote sensing Fourier transform spectrometers and satellite measurements from IASI and OMI over Australia. We evaluate three inventories: the Global Fire Emission Database version 4 - GFED4 (Giglio et al. 2013), the Fire Inventory from NCAR - FINN (Wiedinmyer et al. 2011), the Quick Fire Emission Database - QFED from NASA and the MACCity emission inventory (from the MACC/CityZEN EU projects; Angiola et al. 2010). From this evaluation we aim to give recommendations for the most appropriate inventory to use for different Australian environments. We also plan to examine any significant concentration variations arising from the differences between the two model setups.

  9. Calibration of the MSL/ChemCam/LIBS Remote Sensing Composition Instrument

    NASA Technical Reports Server (NTRS)

    Wiens, R. C.; Maurice S.; Bender, S.; Barraclough, B. L.; Cousin, A.; Forni, O.; Ollila, A.; Newsom, H.; Vaniman, D.; Clegg, S.; Lasue, J. A.; Blaney, D.; DeFlores, L.; Morris, R. V.

    2011-01-01

    The ChemCam instrument suite on board the 2011 Mars Science Laboratory (MSL) Rover, Curiosity, will provide remote-sensing composition information for rock and soil samples within seven meters of the rover using a laser-induced breakdown spectroscopy (LIBS) system, and will provide context imaging with a resolution of 0.10 mradians using the remote micro-imager (RMI) camera. The high resolution is needed to image the small analysis footprint of the LIBS system, at 0.2-0.6 mm diameter. This fine scale analytical capability will enable remote probing of stratigraphic layers or other small features the size of "blueberries" or smaller. ChemCam is intended for rapid survey analyses within 7 m of the rover, with each measurement taking less than 6 minutes. Repeated laser pulses remove dust coatings and provide depth profiles through weathering layers, allowing detailed investigation of rock varnish features as well as analysis of the underlying pristine rock composition. The LIBS technique uses brief laser pulses greater than 10 MW/square mm to ablate and electrically excite material from the sample of interest. The plasma emits photons with wavelengths characteristic of the elements present in the material, permitting detection and quantification of nearly all elements, including the light elements H, Li, Be, B, C, N, O. ChemCam LIBS projects 14 mJ of 1067 nm photons on target and covers a spectral range of 240-850 nm with resolutions between 0.15 and 0.60 nm FWHM. The Nd:KGW laser is passively cooled and is tuned to provide maximum power output from -10 to 0 C, though it can operate at 20% degraded energy output at room temperature. Preliminary calibrations were carried out on the flight model (FM) in 2008. However, the detectors were replaced in 2009, and final calibrations occurred in April-June, 2010. This presentation describes the LIBS calibration and characterization procedures and results, and details plans for final analyses during rover system thermal testing

  10. Evaluation and comparison of O3 forecasts of ALARO-CAMx and WRF-Chem

    NASA Astrophysics Data System (ADS)

    Flandorfer, Claudia; Hirtl, Marcus

    2015-04-01

    ZAMG runs two models for Air-Quality forecasts operationally: ALARO-CAMx and WRF-Chem. ALARO-CAMx is a combination of the meteorological model ALARO and the photochemical dispersion model CAMx and is operated at ZAMG by order of the regional governments since 2005. The emphasis of this modeling system is on predicting ozone peaks in the north-east Austrian flatlands. Two modeling domains are used with the highest resolution (5 km) in the alpine region. Various extensions with external data sources have been conducted in the past to improve the daily forecasts of the model, e.g. data assimilation of O3- and PM10 observations from the Austrian measurement network (with optimum interpolation technique); MACC-II boundary conditions; combination of high resolved emission inventories for Austria with TNO and EMEP data. The biogenic emissions are provided by the SMOKE model. The model runs 2 times per day for a period of 48 hours. The second model which is operational is the on-line coupled model WRF-Chem. Meteorology is simulated simultaneously with the emission, turbulent mixing, transport, transformation, and fate of trace gases and aerosols. 2 domains are used for the simulations. The mother domain covers Europe with a resolution of 12 km. The inner domain includes the alpine region with a horizontal resolution of 4km. 45 model levels are used in the vertical. The model runs 2 times per day for a period of 72 hours and is initialized with ECMWF forecasts. The evaluation of both models is conducted for summer 2014 with the main focus on the forecasts of ozone. The measurements of the Air-Quality stations are compared with the punctual forecasts at the sites of the stations and with the area forecasts for every province of Austria. Beside the evaluation a comparison of the forecasts of ALARO-CAMx and WRF-Chem is done. The summer 2014 was the coldest and the dullest in the last 9 years. Due to this only two exceedances of the information threshold were measured (June

  11. Collaboration of EarthChem and EARTHTIME to Develop a Geochronology and Thermochronology Database

    NASA Astrophysics Data System (ADS)

    Walker, J.; Ash, J.; Bowring, J. F.; Bowring, S. A.; Deino, A. L.; Kislytsyn, R.; Koppers, A. A.; McLean, N. M.; Lehnert, K. A.

    2011-12-01

    A significant factor in data reporting and developing databases for geochronological and thermochronological studies is to capture all of the metadata needed to completely document the analytical work and the interpretations of the analyst. This information is mostly or completely present in data reduction programs used by researchers, but harvesting and preserving this information in either publications or databases has proven difficult to impossible to accomplish. This mostly owes to the fact that data reporting is not an easy or seamless part of the researchers workflow. To make progress on this issue, the EarthChem and EARTHTIME efforts are collaborating to foster the next generation of data management and discovery for age information by integrating data reporting with data reduction to the extent possible. EarthChem workers have met with groups working on the Ar-Ar, U-Pb, and (U-Th)/He systems to establish data reporting requirements as well as XML schemas to be used for transferring data from reduction programs to database. At present, we have systems working for the U-Pb_Redux, ArArCalc, MassSpec, and Helios programs. In each program, the user can select to upload data and metadata to the Geochron system hosted at EarthChem (http://geochronportal.org). There are two additional requirements for upload. The first is having a unique identifier (IGSN) obtained either manually or via web services contained within the reduction program from the SESAR system (http://geosamples.org). The second is that the user selects whether the sample is to be available for discovery (public) or remain hidden (private). Search for data at the Geochron portal can be done using age, method, mineral, or location parameters. Data can be downloaded in the full XML format for ingestion back into the reduction program or as abbreviated tables. For researching not using these programs, we plan to make available either web-based forms or spread sheets that can preserve important

  12. A case study on the aerosol-meteorology feedback for Europe with WRF/Chem

    NASA Astrophysics Data System (ADS)

    Forkel, R.; Werhahn, J.; McKeen, S.; Peckham, S.; Grell, G.; Suppan, P.

    2012-04-01

    A main topic of the investigations with online coupled meteorology-chemistry models, such as WRF/Chem is the feedback of air pollution on meteorology. For the current case study three WRF/Chem simulations for Europe and the North Atlantic are compared: a baseline case without any aerosol feedback on meteorology, a simulation with the direct effect of aerosol on radiation included, and a simulation including the direct effect as well as the indirect aerosol effect. An episode covering June and July in 2006 was considered. WRF/Chem's 3-modal MADE/SORGAM aerosol module was applied for this investigation, which was motivated by the AQMEII (Air Quality Model Evaluation International Initiative) model inter-comparison exercise. For the simulation including just the direct effect, the aerosol-radiation induced changes in temperature, boundary layer height, and clouds ("semi-direct effect") were found to dominate after some time. Over Central Europe the mean reduction of global radiation due to aerosol extinction alone was mostly 3 - 7 W m-2, but changes in cloud cover due to semi-direct effects resulted in monthly mean changes of ± 50 W m-2. The inclusion of the indirect aerosol effect resulted in an up to 70% lower cloud water content and a significantly higher mean rain water content over the North Atlantic. The simulated low cloud droplet and CCN concentrations there are a result of the low aerosol concentrations in this area. However, model analysis suggests these results are sensitive to boundary conditions and a possible underestimation of aerosol sources over the North Atlantic. In spite of the higher aerosol concentrations over continental Europe, the inclusion of the indirect aerosol effect also results sometimes in smaller cloud droplet numbers than the fixed droplet number that is assumed in the absence of aerosol-cloud interactions. The agreement between observed and simulated global radiation over Europe was found to be better for cloudy conditions when the

  13. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem.

    PubMed

    Kim, Sunghwan; Thiessen, Paul A; Bolton, Evan E; Bryant, Stephen H

    2015-07-01

    PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, developed and maintained by the US National Institutes of Health (NIH). PubChem contains more than 180 million depositor-provided chemical substance descriptions, 60 million unique chemical structures and 225 million bioactivity assay results, covering more than 9000 unique protein target sequences. As an information resource for the chemical biology research community, it routinely receives more than 1 million requests per day from an estimated more than 1 million unique users per month. Programmatic access to this vast amount of data is provided by several different systems, including the US National Center for Biotechnology Information (NCBI)'s Entrez Utilities (E-Utilities or E-Utils) and the PubChem Power User Gateway (PUG)-a common gateway interface (CGI) that exchanges data through eXtended Markup Language (XML). Further simplifying programmatic access, PubChem provides two additional general purpose web services: PUG-SOAP, which uses the simple object access protocol (SOAP) and PUG-REST, which is a Representational State Transfer (REST)-style interface. These interfaces can be harnessed in combination to access the data contained in PubChem, which is integrated with the more than thirty databases available within the NCBI Entrez system.

  14. Proteolytic cleavage of chemerin protein is necessary for activation to the active form, Chem157S, which functions as a signaling molecule in glioblastoma.

    PubMed

    Yamaguchi, Yasuto; Du, Xiao-Yan; Zhao, Lei; Morser, John; Leung, Lawrence L K

    2011-11-11

    Chemerin is a chemoattractant involved in innate and adaptive immunity as well as an adipokine implicated in adipocyte differentiation. Chemerin circulates as an inactive precursor in blood whose bioactivity is closely regulated through proteolytic processing at its C terminus. We developed methodology for production of different recombinant chemerin isoforms (chem163S, chem157S, and chem155A) which allowed us to obtain large quantities of these proteins with purity of >95%. Chem158K was generated from chem163S by plasmin cleavage. Characterization by mass spectrometry and Edman degradation demonstrated that both the N and C termini were correct for each isoform. Ca(2+) mobilization assays showed that the EC(50) values for chem163S and chem158K were 54.2 ± 19.9 nm and 65.2 ± 13.2 nm, respectively, whereas chem157S had a ∼50-fold higher potency with an EC(50) of 1.2 ± 0.7 nm. Chem155A had no agonist activity and weak antagonist activity, causing a 50% reduction of chem157S activity at a molar ratio of 100:1. Similar results were obtained in a chemotaxis assay. Because chem158K is the dominant form in cerebrospinal fluid from patients with glioblastoma (GBM), we examined the significance of chemerin in GBM biology. In silico analysis showed chemerin mRNA was significantly increased in tissue from grade III and IV gliomas. Furthermore, U-87 MG cells, a human GBM line, express the chemerin receptors, chemokine-like receptor 1 and chemokine receptor-like 2, and chem157S triggered Ca(2+) flux. This study emphasized the necessity of appropriate C-terminal proteolytic processing to generate the likely physiologic form of active chemerin, chem157S, and suggested a possible role in malignant GBM.

  15. Structuring Chemical Space: Similarity-Based Characterization of the PubChem Database.

    PubMed

    Cincilla, Giovanni; Thormann, Michael; Pons, Miquel

    2010-01-12

    The ensemble of conceivable molecules is referred to as the Chemical Space. In this article we describe a hierarchical version of the Affinity Propagation (AP) clustering algorithm and apply it to analyze the LINGO-based similarity matrix of a 500 000-molecule subset of the PubChem database, which contains more than 19 million compounds. The combination of two highly efficient methods, namely the AP clustering algorithm and LINGO-based molecular similarity calculations, allows the unbiased analysis of large databases. Hierarchical clustering generates a numerical diagonalization of the similarity matrix. The target-independent, intrinsic structure of the database , derived without any previous information on the physical or biological properties of the compounds, maps together molecules experimentally shown to bind the same biological target or to have similar physical properties.

  16. Assessments of Potential Rock Coatings at Rocknest, Gale Crater with ChemCam

    NASA Technical Reports Server (NTRS)

    Blaney, D. L.; Anderson, R.; Berger, G.; Bridges, J.; Bridges, N.; Clark, B.; Clegg, S.; Ehlman, B.; Goetz, W.; King, P.; Lanza, N.; Mangold, N.; Meslin, P.-Y.; Newsom, H.

    2013-01-01

    Many locations on Mars have low color contrast between the rocks and soils due to the rocks being "dusty"--basically having a surface that is spectrally similar to Martian soil. In general this has been interpreted as soil and/or dust clinging to the rock though either mechanical or electrostic processes. However, given the apparent mobility of thin films of water forming cemented soils on Mars and at Gale Crater, the possibility exists that some of these "dusty" surfaces may actually be coatings formed by thin films of water locally mobilizing soil/air fall material at the rock interface. This type of coating was observed by Spirit during an investigation of the rock Mazatzal which showed enhanced salts above "normal soil" and an enhancement of nano phase iron oxide that was 10 micronmeters thick. We decided to use ChemCam to investigate the possibility of similar rock coatings forming at the Rocknest site at Gale Crater.

  17. In situ detection of boron by ChemCam on Mars

    NASA Astrophysics Data System (ADS)

    Gasda, Patrick J.; Haldeman, Ethan B.; Wiens, Roger C.; Rapin, William; Bristow, Thomas F.; Bridges, John C.; Schwenzer, Susanne P.; Clark, Benton; Herkenhoff, Kenneth; Frydenvang, Jens; Lanza, Nina L.; Maurice, Sylvestre; Clegg, Samuel; Delapp, Dorothea M.; Sanford, Veronica L.; Bodine, Madeleine R.; McInroy, Rhonda

    2017-09-01

    We report the first in situ detection of boron on Mars. Boron has been detected in Gale crater at levels <0.05 wt % B by the NASA Curiosity rover ChemCam instrument in calcium-sulfate-filled fractures, which formed in a late-stage groundwater circulating mainly in phyllosilicate-rich bedrock interpreted as lacustrine in origin. We consider two main groundwater-driven hypotheses to explain the presence of boron in the veins: leaching of borates out of bedrock or the redistribution of borate by dissolution of borate-bearing evaporite deposits. Our results suggest that an evaporation mechanism is most likely, implying that Gale groundwaters were mildly alkaline. On Earth, boron may be a necessary component for the origin of life; on Mars, its presence suggests that subsurface groundwater conditions could have supported prebiotic chemical reactions if organics were also present and provides additional support for the past habitability of Gale crater.

  18. Design and Development of ChemInfoCloud: An Integrated Cloud Enabled Platform for Virtual Screening.

    PubMed

    Karthikeyan, Muthukumarasamy; Pandit, Deepak; Bhavasar, Arvind; Vyas, Renu

    2015-01-01

    The power of cloud computing and distributed computing has been harnessed to handle vast and heterogeneous data required to be processed in any virtual screening protocol. A cloud computing platorm ChemInfoCloud was built and integrated with several chemoinformatics and bioinformatics tools. The robust engine performs the core chemoinformatics tasks of lead generation, lead optimisation and property prediction in a fast and efficient manner. It has also been provided with some of the bioinformatics functionalities including sequence alignment, active site pose prediction and protein ligand docking. Text mining, NMR chemical shift (1H, 13C) prediction and reaction fingerprint generation modules for efficient lead discovery are also implemented in this platform. We have developed an integrated problem solving cloud environment for virtual screening studies that also provides workflow management, better usability and interaction with end users using container based virtualization, OpenVz.

  19. Aerosol impact on seasonal prediction using FIM-Chem-iHYCOM coupled model

    NASA Astrophysics Data System (ADS)

    sun, shan; Grell, Georg; Bleck, Rainer

    2016-04-01

    A coupled model consisting of the weather model FIM and the ocean model iHYCOM, both operating on an icosahedral horizontal grid, is being developed for subseasonal to seasonal prediction. Initial results indicate that the model skill is comparable to that of the operational model CFSv2 used by NCEP. In addition, an online atmospheric chemistry module is coupled to FIM. The purpose of onging experiments with the FIM-Chem-iHYCOM combination is to investigate the aerosol impact on the atmospheric and oceanic circulation at the seasonal scale. We compare the model sensitivity with various chemistry emissions, including aerosols, fire and anthropogenic emissions. Additional emphasis of this work is on the effect of aerosols on cloudiness and precipitation, either directly or indirectly through changes in SST. To isolate the latter effect, we conduct parallel experiments with observed SST.

  20. Assessments of Potential Rock Coatings at Rocknest, Gale Crater with ChemCam

    NASA Technical Reports Server (NTRS)

    Blaney, D. L.; Anderson, R.; Berger, G.; Bridges, J.; Bridges, N.; Clark, B.; Clegg, S.; Ehlman, B.; Goetz, W.; King, P.; hide

    2013-01-01

    Many locations on Mars have low color contrast between the rocks and soils due to the rocks being "dusty"--basically having a surface that is spectrally similar to Martian soil. In general this has been interpreted as soil and/or dust clinging to the rock though either mechanical or electrostic processes. However, given the apparent mobility of thin films of water forming cemented soils on Mars and at Gale Crater, the possibility exists that some of these "dusty" surfaces may actually be coatings formed by thin films of water locally mobilizing soil/air fall material at the rock interface. This type of coating was observed by Spirit during an investigation of the rock Mazatzal which showed enhanced salts above "normal soil" and an enhancement of nano phase iron oxide that was 10 micronmeters thick. We decided to use ChemCam to investigate the possibility of similar rock coatings forming at the Rocknest site at Gale Crater.

  1. Comment on ``Minimum free-energy pathway of nucleation'' [J. Chem. Phys. 135, 134508 (2011)

    NASA Astrophysics Data System (ADS)

    Schmelzer, Jürn W. P.; Abyzov, Alexander S.

    2012-03-01

    In their recent paper [J. Chem. Phys. 135, 134508 (2011)], Philippe and Blavette, 10.1063/1.3644935 claimed to have found for the first time—based on minimum free energy considerations—that the nucleation pathway in solid solutions involves a universal two-step behavior: nuclei sharply enrich up to near equilibrium values of the concentration and then grow. This claim of priority is not correct. The same scenario was proposed by us long ago [J. W. P. Schmelzer, A. R. Gokhman, and V. M. Fokin, J. Colloid Interface Sci. 272, 109 (2004)], 10.1016/j.jcis.2003.08.038 and then applied and further developed. In particular, it was shown by us that only the account of both thermodynamic and kinetic factors allows one to determine correctly the most probable path of evolution in nucleation-growth processes. The two-step scenario is retained, however, also in these generalizations of our original approach.

  2. Comment on ``Global thermodynamics of hydrophobic cavitation, dewetting, and hydration'' [J. Chem. Phys. 123, 184504 (2005)

    NASA Astrophysics Data System (ADS)

    Graziano, Giuseppe

    2006-07-01

    It is pointed out that in a Ben-Amotz in a recent article [J. Chem. Phys.123, 184504 (2005)] attributed a noncorrect meaning to the entropy convergence temperature, claiming that the latter corresponds to the temperature at which the hydration entropy of a series of solutes crosses zero. A short resumé of the entropy convergence phenomenon and of the provided statistical mechanical analyses is accomplished. In addition, it is brought out that the different temperature dependence of the cavity entropy change on increasing the cavity diameter, pointed out by Ben-Amotz, originates from the assumption that the work of cavity creation should be proportional to the experimental surface tension of liquid water for cavities large on a molecular scale.

  3. The PubChemQC project: A large chemical database from the first principle calculations

    NASA Astrophysics Data System (ADS)

    Maho, Nakata

    2015-12-01

    In this research, we have been constructing a large database of molecules by ab initio calculations. Currently, we have over 1.53 million entries of 6-31G* B3LYP optimized geometries and ten excited states by 6-31+G* TDDFT calculations. To calculate molecules, we only refer the InChI (International Chemical Identifier) representation of chemical formula by the International Union of Pure and Applied Chemistry (IUPAC), thus, no reference to experimental data. These results are open to public at http://pubchemqc.riken.jp/. The molecular data have been taken from the PubChem Project (http://pubchem.ncbi.nlm.nih.gov/) which is one of the largest in the world (approximately 63 million molecules are listed) and free (public domain) database. Our final goal is, using these data, to develop a molecular search engine or molecular expert system to find molecules which have desired properties.

  4. Towards a forecasting system of air quality for Asia using the WRF-Chem model

    NASA Astrophysics Data System (ADS)

    Katinka Petersen, Anna; Kumar, Rajesh; Brasseur, Guy; Granier, Claire

    2013-04-01

    The degradation of air quality in Asia resulting from the intensification of human activities, and the related impacts on the health of billions of people have become an urgent matter of concern. The World Health Organization states that each year nearly 3.3 million people die worldwide prematurely because of air pollution. The situation is particularly acute in Asia. Improving air quality over the Asian continent has become a major challenge for national, regional and local authorities. A prerequisite for air quality improvement is the development of a reliable monitoring system with surface instrumentation and space platforms as well as an analysis and prediction system based on an advanced chemical-meteorological model. The aim is to use the WRF-Chem model for the prediction of daily air quality for the Asian continent with spatial resolution that will be increased in densely populated areas by grid nesting. The modeling system covers a nearly the entire Asian continent so that transport processes of chemical compounds within the continent are simulated and analyzed. To additionally account for the long-range effects and assess their relative importance against regional emissions, the regional chemical transport modeling system uses information from a global modeling system as boundary conditions. The first steps towards a forecasting system over Asia are to test the model performance over this large model domain and the different emissions inventories available for Asia. In this study, the WRF-Chem model was run for a domain covering 60°E to 150°E, 5°S to 50°N at a resolution of 60 km x 60 km for January 2006 with three alternative emission inventories available for Asia (MACCITY, INTEX-B and REAS). We present an intercomparison of the three different simulations and evaluate the simulations with satellite and in situ observations, with focus on ozone, particulate matter, nitrogen oxides and carbon monoxide. The differences between the simulations using

  5. Chemistry of diagenetic features analyzed by ChemCam at Pahrump Hills, Gale crater, Mars

    USGS Publications Warehouse

    Nachon, Marion; Mangold, Nicolas; Forni, Olivier; Kah, Linda C.; Cousin, Agnes; Wiens, Roger C.; Anderson, Ryan; Blaney, Diana L.; Blank, Jen G.; Calef, Fred J.; Clegg, Samuel M.; Fabre, Cecile; Fisk, Martin R.; Gasnault, Olivier; Grotzinger, John P.; Kronyak, Rachel; Lanza, Nina L.; Lasue, Jeremie; Le Deit, Laetitia; Le Mouelic, Stephane; Maurice, Sylvestre; Meslin, Pierre-Yves; Oehler, D. Z.; Payre, Valerie; Rapin, William; Schroder, Susanne; Stack, Katherine M.; Sumner, Dawn

    2017-01-01

    The Curiosity rover's campaign at Pahrump Hills provides the first analyses of lower Mount Sharp strata. Here we report ChemCam elemental composition of a diverse assemblage of post-depositional features embedded in, or cross-cutting, the host rock. ChemCam results demonstrate their compositional diversity, especially compared to the surrounding host rock: (i) Dendritic aggregates and relief enhanced features, characterized by a magnesium enhancement and sulfur detection, and interpreted as Mg-sulfates; (ii) A localized observation that displays iron enrichment associated with sulfur, interpreted as Fe-sulfate; (iii) Dark raised ridges with varying Mg- and Ca-enriched compositions compared to host rock; (iv) Several dark-toned veins with calcium enhancement associated with fluorine detection, interpreted as fluorite veins. (v) Light-toned veins with enhanced calcium associated with sulfur detection, and interpreted as Ca-sulfates. The diversity of the Pahrump Hills diagenetic assemblage suggests a complex post-depositional history for fine-grained sediments for which the origin has been interpreted as fluvial and lacustrine. Assessment of the spatial and relative temporal distribution of these features shows that the Mg-sulfate features are predominant in the lower part of the section, suggesting local modification of the sediments by early diagenetic fluids. In contrast, light-toned Ca-sulfate veins occur in the whole section and cross-cut all other features. A relatively late stage shift in geochemical conditions could explain this observation. The Pahrump Hills diagenetic features have no equivalent compared to targets analyzed in other locations at Gale crater. Only the light-toned Ca-sulfate veins are present elsewhere, along Curiosity's path, suggesting they formed through a common late-stage process that occurred at over a broad area.

  6. Mixed Waste Treatment Using the ChemChar Thermolytic Detoxification Technique

    SciTech Connect

    Kuchynka, D.J.

    1997-01-01

    This R and D program addresses the treatment of mixed waste employing the ChemChar Thermolytic Detoxification process. Surrogate mixed waste streams will be treated in a four inch diameter, continuous feed, adiabatic reactor with the goal of meeting all regulatory treatment levels for the contaminants in the surrogates with the concomitant production of contaminant free by-products. Successful completion of this program will show that organic contaminants in mixed waste surrogates will be converted to a clean, energy rich synthesis gas capable of being used, without further processing, for power or heat generation. The inorganic components in the surrogates will be found to be adsorbed on a macroporous coal char activated carbon substrate which is mixed with the waste prior to treatment. These contaminants include radioactive metal surrogate species, RCRA hazardous metals and any acid gases formed during the treatment process. The program has three main tasks that will be performed to meet the above objectives. The first task is the design and construction of the four inch reactor at Mirage Systems in Sunnyvale, CA. The second task is production and procurement of the activated carbon char employed in the ChemChartest runs and identification of two surrogate mixed wastes. The last task is testing and operation of the reactor on char/surrogate waste mixtures to be performed at the University of Missouri. The deliverables for the project are a Design Review Report, Operational Test Plan, Topical Report and Final Report. This report contains only the results of the design and construction carbon production-surrogate waste identification tasks.Treatment of the surrogate mixed wastes has just begun and will not be reported in this version of the Final Report. The latter will be reported in the final version of the Final Report.

  7. WRF/Chem model analyses of the BEACHON-ROMBAS 2011 filed study

    NASA Astrophysics Data System (ADS)

    Hodzic, A.; gochis, D.

    2012-04-01

    The scientific understanding of the formation and aging of organic aerosols in forest environments is still limited especially in presence of anthropogenic pollutants. The Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen (BEACHON) project was initiated by NCAR in 2008 to provide a detailed characterization of biosphere-hydrosphere-atmosphere interactions through combination of long-term field measurements, laboratory studies and multi-scale modeling. The BEACHON-ROMBAS intensive aerosol study took place from 25 July to 25 August 2011 at the Manitou Observatory Forest in Colorado with the specific objective of characterizing the formation and growth of biogenic particles in the forest canopy, and quantifying the perturbations that occur in presence of anthropogenic emissions. Here we will present the first results of the high-resolution simulations (4km) that were performed over the Colorado mountains using the Weather Research and Forecasting model with chemistry (WRF/Chem) during summer 2011 and used to interpret and analyze the meteorological and chemical data collected during the campaign. The meteorological and passive tracer analyses were used to identify the main meteorological regimes, and characterize the periods of a strong anthropogenic influence. Of particular interest were the periods featuring the transport of the front-range urban pollution or the four corners power plant plume over the forest site. For each of these periods the WRF/Chem model predictions of main organic aerosol components were assessed and compared with the AMS data. In addition, the sensitivity of the model results to changes and inaccuracies in the landuse is discussed.

  8. Viral vectors for gene modification of plants as chem/bio sensors.

    SciTech Connect

    Manginell, Monica; Harper, Jason C.; Arango, Dulce C.; Brozik, Susan Marie; Dolan, Patricia L.

    2006-11-01

    Chemical or biological sensors that are specific, sensitive, and robust allowing intelligence gathering for verification of nuclear non-proliferation treaty compliance and detouring production of weapons of mass destruction are sorely needed. Although much progress has been made in the area of biosensors, improvements in sensor lifetime, robustness, and device packaging are required before these devices become widely used. Current chemical and biological detection and identification techniques require less-than-covert sample collection followed by transport to a laboratory for analysis. In addition to being expensive and time consuming, results can often be inconclusive due to compromised sample integrity during collection and transport. We report here a demonstration of a plant based sensor technology which utilizes mature and seedling plants as chemical sensors. One can envision genetically modifying native plants at a site of interest that can report the presence of specific toxins or chemicals. In this one year project we used a developed inducible expression system to show the feasibility of plant sensors. The vector was designed as a safe, non-infectious vector which could be used to invade, replicate, and introduce foreign genes into mature host plants that then allow the plant to sense chem/bio agents. The genes introduced through the vector included a reporter gene that encodes for green fluorescent protein (GFP) and a gene that encodes for a mammalian receptor that recognizes a chemical agent. Specifically, GFP was induced by the presence of 17-{beta}-Estradiol (estrogen). Detection of fluorescence indicated the presence of the target chemical agent. Since the sensor is a plant, costly device packaging development or manufacturing of the sensor were not required. Additionally, the biological recognition and reporting elements are maintained in a living, natural environment and therefore do not suffer from lifetime disadvantages typical of most biosensing

  9. ChemModLab: a web-based cheminformatics modeling laboratory.

    PubMed

    Hughes-Oliver, Jacqueline M; Brooks, Atina D; Welch, William J; Khaledi, Morteza G; Hawkins, Douglas; Young, S Stanley; Patil, Kirtesh; Howell, Gary W; Ng, Raymond T; Chu, Moody T

    ChemModLab, written by the ECCR @ NCSU consortium under NIH support, is a toolbox for fitting and assessing quantitative structure-activity relationships (QSARs). Its elements are: a cheminformatic front end used to supply molecular descriptors for use in modeling; a set of methods for fitting models; and methods for validating the resulting model. Compounds may be input as structures from which standard descriptors will be calculated using the freely available cheminformatic front end PowerMV; PowerMV also supports compound visualization. In addition, the user can directly input their own choices of descriptors, so the capability for comparing descriptors is effectively unlimited. The statistical methodologies comprise a comprehensive collection of approaches whose validity and utility have been accepted by experts in the fields. As far as possible, these tools are implemented in open-source software linked into the flexible R platform, giving the user the capability of applying many different QSAR modeling methods in a seamless way. As promising new QSAR methodologies emerge from the statistical and data-mining communities, they will be incorporated in the laboratory. The web site also incorporates links to public-domain data sets that can be used as test cases for proposed new modeling methods. The capabilities of ChemModLab are illustrated using a variety of biological responses, with different modeling methodologies being applied to each. These show clear differences in quality of the fitted QSAR model, and in computational requirements. The laboratory is web-based, and use is free. Researchers with new assay data, a new descriptor set, or a new modeling method may readily build QSAR models and benchmark their results against other findings. Users may also examine the diversity of the molecules identified by a QSAR model. Moreover, users have the choice of placing their data sets in a public area to facilitate communication with other researchers; or can keep

  10. A new WRF-Chem treatment for studying regional scale impacts of cloud-aerosol interactions in parameterized cumuli

    NASA Astrophysics Data System (ADS)

    Berg, L. K.; Shrivastava, M.; Easter, R. C.; Fast, J. D.; Chapman, E. G.; Liu, Y.

    2014-04-01

    A new treatment of cloud-aerosol interactions within parameterized shallow and deep convection has been implemented in WRF-Chem that can be used to better understand the aerosol lifecycle over regional to synoptic scales. The modifications to the model to represent cloud-aerosol interactions include treatment of the cloud droplet number mixing ratio; key cloud microphysical and macrophysical parameters (including the updraft fractional area, updraft and downdraft mass fluxes, and entrainment) averaged over the population of shallow clouds, or a single deep convective cloud; and vertical transport, activation/resuspension, aqueous chemistry, and wet removal of aerosol and trace gases in warm clouds. These changes have been implemented in both the WRF-Chem chemistry packages as well as the Kain-Fritsch cumulus parameterization that has been modified to better represent shallow convective clouds. Preliminary testing of the modified WRF-Chem has been completed using observations from the Cumulus Humilis Aerosol Processing Study (CHAPS) as well as a high-resolution simulation that does not include parameterized convection. The simulation results are used to investigate the impact of cloud-aerosol interactions on regional scale transport of black carbon (BC), organic aerosol (OA), and sulfate aerosol. Based on the simulations presented here, changes in the column integrated BC can be as large as -50% when cloud-aerosol interactions are considered (due largely to wet removal), or as large as +40% for sulfate in non-precipitating conditions due to the sulfate production in the parameterized clouds. The modifications to WRF-Chem version 3.2.1 are found to account for changes in the cloud drop number concentration (CDNC) and changes in the chemical composition of cloud-drop residuals in a way that is consistent with observations collected during CHAPS. Efforts are currently underway to port the changes described here to WRF-Chem version 3.5, and it is anticipated that they

  11. A fast stratospheric chemistry solver: the E4CHEM submodel for the atmospheric chemistry global circulation model EMAC

    NASA Astrophysics Data System (ADS)

    Baumgaertner, A. J. G.; Jöckel, P.; Steil, B.; Tost, H.; Sander, R.

    2010-06-01

    The atmospheric chemistry general circulation model ECHAM5/MESSy (EMAC) and the atmospheric chemistry box model CAABA are extended by a computationally very efficient submodel for atmospheric chemistry, E4CHEM. It focuses on stratospheric chemistry but also includes background tropospheric chemistry. It is based on the chemistry of MAECHAM4-CHEM and is intended to serve as a simple and fast alternative to the flexible but also computationally more demanding submodel MECCA. In a model setup with E4CHEM, EMAC is now also suitable for simulations of longer time scales. The reaction mechanism contains basic O3, CH4, CO, HOx, NOx, and ClOx gas phase chemistry. In addition, E4CHEM includes optional fast routines for heterogeneous reactions on sulphate aerosols and polar stratospheric clouds (substituting the existing submodels PSC and HETCHEM), and scavenging (substituting the existing submodel SCAV). We describe the implementation of E4CHEM into the MESSy structure of CAABA and EMAC. For some species the steady state in the box model differs by up to 100% when compared to results from CAABA/MECCA due to different reaction rates. After an update of the reaction rates in E4CHEM the mixing ratios in both boxmodel and 3-D model simulations are in satisfactory agreement with the results from a simulation where MECCA with a similar chemistry scheme was employed. Finally, a comparison against a simulation with a more complex and already evaluated chemical mechanism is presented in order to discuss shortcomings associated with the simplification of the chemical mechanism.

  12. A fast stratospheric chemistry solver: the E4CHEM submodel for the atmospheric chemistry global circulation model EMAC

    NASA Astrophysics Data System (ADS)

    Baumgaertner, A. J. G.; Jöckel, P.; Steil, B.; Tost, H.; Sander, R.

    2010-02-01

    The atmospheric chemistry general circulation model ECHAM5/MESSy (EMAC) and the atmospheric chemistry box model CAABA are extended by a computationally very efficient submodel for atmospheric chemistry, E4CHEM. It focuses on stratospheric chemistry but also includes background tropospheric chemistry. It is based on the chemistry of MAECHAM4-CHEM and is intended to serve as a simple and fast alternative to the flexible but also computationally more demanding submodel MECCA. In a model setup with E4CHEM, EMAC is now also suitable for simulations of longer time scales. The reaction mechanism contains basic O3, CH4, CO, HOx, NOx and ClOx gas phase chemistry. In addition, E4CHEM includes optional fast routines for heterogeneous reactions on sulphate aerosols and polar stratospheric clouds (substituting the existing submodels PSC and HETCHEM), and scavenging (substituting the existing submodel SCAV). We describe the implementation of E4CHEM into the MESSy structure of CAABA and EMAC. For some species the steady state in the box model differs by up to 100% when compared to results from CAABA/MECCA due to different reaction rates. After an update of the reaction rates in E4CHEM the mixing ratios in both boxmodel and 3-D model simulations are in satisfactory agreement with the results from a simulation where MECCA with a similar chemistry scheme was employed. Finally, a comparison against a simulation with a more complex and already evaluated chemical mechanism is presented in order to discuss shortcomings associated with the simplification of the chemical mechanism.

  13. A New WRF-Chem Treatment for Studying Regional Scale Impacts of Cloud-Aerosol Interactions in Parameterized Cumuli

    SciTech Connect

    Berg, Larry K.; Shrivastava, ManishKumar B.; Easter, Richard C.; Fast, Jerome D.; Chapman, Elaine G.; Liu, Ying

    2015-01-01

    A new treatment of cloud-aerosol interactions within parameterized shallow and deep convection has been implemented in WRF-Chem that can be used to better understand the aerosol lifecycle over regional to synoptic scales. The modifications to the model to represent cloud-aerosol interactions include treatment of the cloud dropletnumber mixing ratio; key cloud microphysical and macrophysical parameters (including the updraft fractional area, updraft and downdraft mass fluxes, and entrainment) averaged over the population of shallow clouds, or a single deep convective cloud; and vertical transport, activation/resuspension, aqueous chemistry, and wet removal of aerosol and trace gases in warm clouds. Thesechanges have been implemented in both the WRF-Chem chemistry packages as well as the Kain-Fritsch cumulus parameterization that has been modified to better represent shallow convective clouds. Preliminary testing of the modified WRF-Chem has been completed using observations from the Cumulus Humilis Aerosol Processing Study (CHAPS) as well as a high-resolution simulation that does not include parameterized convection. The simulation results are used to investigate the impact of cloud-aerosol interactions on the regional scale transport of black carbon (BC), organic aerosol (OA), and sulfate aerosol. Based on the simulations presented here, changes in the column integrated BC can be as large as -50% when cloud-aerosol interactions are considered (due largely to wet removal), or as large as +35% for sulfate in non-precipitating conditions due to the sulfate production in the parameterized clouds. The modifications to WRF-Chem version 3.2.1 are found to account for changes in the cloud drop number concentration (CDNC) and changes in the chemical composition of cloud-drop residuals in a way that is consistent with observations collected during CHAPS. Efforts are currently underway to port the changes described here to WRF-Chem version 3.5, and it is anticipated that they

  14. ChemCam Observations of Manganese in Rock Targets (Sols 778-1384): An Indicator of Redox and Habitability Conditions

    NASA Astrophysics Data System (ADS)

    Lanza, N.; Lamm, S. N.; Frydenvang, J.; Wiens, R. C.; Kirk, M. F.

    2016-12-01

    Recent results from the Curiosity Mars rover have identified enrichments of manganese in rock targets throughout Gale crater. Some of these are inferred to be Mn-oxide minerals. High concentrations of Mn on Earth are typically found as secondary mineral deposits, requiring abundant liquid water and highly oxidizing conditions to form. The earliest terrestrial manganese deposits are associated with the rise of free oxygen in the atmosphere 2.5 Gya. Thus the discovery of Mn-oxides on Mars raises the possibility that the martian atmosphere once contained more oxygen. Here we assess Mn abundance in all rocks analyzed by ChemCam along the rover's traverse over sols 778-1384. During this time 477 rocks were analyzed with a total of 3296 sampling locations. Of these, 125 ( 4%) on 61 rocks (12%) were found to contain abundances of Mn 2-sigma over the mean, corresponding to 1.3 wt% MnO. This is similar to results for rock targets from the first 777 sols of the traverse. Relationships between Mn and major and minor elements were also assessed for all rock targets. Higher Mn is associated with lower Si and higher Fe, Na, Al, and Li. Elevated Mn was found in a range of rock types, including conglomerates, fine-grained sandstones, and veins. LIBS data were examined for potential shot-to-shot trends to determine whether Mn is associated with surface features such as coatings or layers; no strong trends were identified. Remote Micro-Imager (RMI) images of rock targets were analyzed for texture, grain size, and albedo. No specific rock features were correlated with Mn abundance. Of sampling locations with Mn abundances above 2-sigma, over 50% were in the Stimson formation, the youngest geologic unit identified in Gale to date. Our results suggest that Mn in this region may have be concentrated prior to incorporation into sediments, and the observed compositional and spatial variations may be the result of differing source regions. Work is ongoing to better understand the nature of

  15. Interpreting aerosol lifetimes using the GEOS-Chem model and constraints from radionuclide measurements

    NASA Astrophysics Data System (ADS)

    Croft, B.; Pierce, J. R.; Martin, R. V.

    2014-04-01

    Aerosol removal processes control global aerosol abundance, but the rate of that removal remains uncertain. A recent study of aerosol-bound radionuclide measurements after the Fukushima Daiichi nuclear power plant accident documents 137Cs removal (e-folding) times of 10.0-13.9 days, suggesting that mean aerosol lifetimes in the range of 3-7 days in global models might be too short by a factor of two. In this study, we attribute this discrepancy to differences between the e-folding and mean aerosol lifetimes. We implement a simulation of 137Cs and 133Xe into the GEOS-Chem chemical transport model and examine the removal rates for the Fukushima case. We find a general consistency between modelled and measured e-folding times. The simulated 137Cs global burden e-folding time is about 14 days. However, the simulated mean lifetime of aerosol-bound 137Cs over a 6-month post-accident period is only 1.8 days. We find that the mean lifetime depends strongly on the removal rates in the first few days after emissions, before the aerosols leave the boundary layer and are transported to altitudes and latitudes where lifetimes with respect to wet removal are longer by a few orders of magnitude. We present sensitivity simulations that demonstrate the influence of differences in altitude and location of the radionuclides on the mean lifetime. Global mean lifetimes are shown to strongly depend on the altitude of injection. The global mean 137Cs lifetime is more than one order of magnitude greater for the injection at 7 km than into the boundary layer above the Fukushima site. Instantaneous removal rates are slower during the first few days after the emissions for a free tropospheric versus boundary layer injection and this strongly controls the mean lifetimes. Global mean aerosol lifetimes for the GEOS-Chem model are 3-6 days, which is longer than that for the 137Cs injected at the Fukushima site (likely due to precipitation shortly after Fukushima emissions), but similar to the

  16. Effect of MERRA-2 initial and boundary conditions on WRF-Chem aerosol simulations over the Arabian Peninsula

    NASA Astrophysics Data System (ADS)

    Ukhov, Alexander; Stenchikov, Georgiy

    2017-04-01

    In this study, we test the sensitivity of the horizontal and vertical distributions of aerosols to the initial and boundary conditions (IC&BC) of the aerosol/chemistry. We use the WRF-Chem model configured over the Arabian Peninsula to study both dust and anthropogenic aerosols. Currently, in the WRF-Chem the aerosol/chemistry IC&BC are constructed using either default aerosol/chemistry profiles with no inflow of aerosols and chemicals through the lateral boundaries or using the aerosol/chemistry fields from MOZART, the model for ozone and related chemical tracers from the NCAR. Here, we construct aerosol/chemistry IC&BC using MERRA-2 output. MERRA-2 is a recently developed reanalysis that assimilates ground-based and satellite observations to provide the improved distributions of aerosols and chemical species. We ran WRF-Chem simulations for July-August 2015 using GOCART/AFWA dust emission and GOCART aerosol schemes. We used the EDGAR HTAP V4 dataset to calculate SO2 emissions. Comparison of three runs initiated using the same ERA-Interim reanalysis fields but different aerosol/chemistry IC&BC (default WRF-Chem, MOZART, and MERRA-2) with AERONET, Micropulse Lidar, Balloon, and satellite observations shows that the MERRA-2 IC&BC are superior.

  17. ChemVoyage: A Web-Based, Simulated Learning Environment with Scaffolding and Linking Visualization to Conceptualization

    ERIC Educational Resources Information Center

    McRae, Christopher; Karuso, Peter; Liu, Fei

    2012-01-01

    The Web is now a standard tool for information access and dissemination in higher education. The prospect of Web-based, simulated learning platforms and technologies, however, remains underexplored. We have developed a Web-based tutorial program (ChemVoyage) for a third-year organic chemistry class on the topic of pericyclic reactions to…

  18. ChemEd Bridges: Building Bridges between Two-Year College Chemistry Faculty and the National Chemical Education Community

    ERIC Educational Resources Information Center

    Ungar, Harry; Brown, David R.

    2010-01-01

    ChemEd Bridges is an NSF-funded project that provides career and professional development opportunities for chemistry faculty members who teach at two-year colleges (2YCs). We broaden the interests and the horizons of these faculty members by building bridges between them and the broader community of chemical educators. In particular, we have…

  19. Comment on "Soret motion in non-ionic binary molecular mixtures" [J. Chem. Phys. 135, 054102 (2011)].

    PubMed

    Semenov, Semen N; Schimpf, Martin E

    2012-09-28

    The material transport equations derived in the article by Leroyer and Würger [J. Chem. Phys. 135, 054102 (2011)] do not adequately provide a description of material transport in liquid binary systems. An alternate approach based on non-equilibrium thermodynamics is presented.

  20. The "Virtual ChemLab" Project: A Realistic and Sophisticated Simulation of Organic Synthesis and Organic Qualitative Analysis

    ERIC Educational Resources Information Center

    Woodfield, Brian F.; Andrus, Merritt B.; Waddoups, Gregory L.; Moore, Melissa S.; Swan, Richard; Allen, Rob; Bodily, Greg; Andersen, Tricia; Miller, Jordan; Simmons, Bryon; Stanger, Richard

    2005-01-01

    A set of sophisticated and realistic laboratory simulations is created for use in freshman- and sophomore-level chemistry classes and laboratories called 'Virtual ChemLab'. A detailed assessment of student responses is provided and the simulation's pedagogical utility is described using the organic simulation.

  1. ChemVoyage: A Web-Based, Simulated Learning Environment with Scaffolding and Linking Visualization to Conceptualization

    ERIC Educational Resources Information Center

    McRae, Christopher; Karuso, Peter; Liu, Fei

    2012-01-01

    The Web is now a standard tool for information access and dissemination in higher education. The prospect of Web-based, simulated learning platforms and technologies, however, remains underexplored. We have developed a Web-based tutorial program (ChemVoyage) for a third-year organic chemistry class on the topic of pericyclic reactions to…

  2. Iron and Magnesium Enrichments in Ca-Sulfate Veins as Observed by ChemCam at Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    L'Haridon, J.; Mangold, N.; Rapin, W.; Forni, O.; Meslin, P.-Y.; Cousin, A.; Payré, V.; Johnson, J.; Dehouck, E.; Nachon, M.; Le Deit, L.; Gasnault, O.; Maurice, S.; Wiens, R.

    2017-10-01

    ChemCam observations of Fe and Mg enrichments in Ca-sulfate bearing veins attest of variations in the pH and redox conditions that prevailed in the parent fluid during the diagenesis of the sedimentary rocks of Gale Crater.

  3. Rotational Analysis of FTIR Spectra from Cigarette Smoke: An Application of Chem Spec II Software in the Undergraduate Laboratory

    ERIC Educational Resources Information Center

    Ford, Alan R.; Burns, William A.; Reeve, Scott W.

    2004-01-01

    A version of the classic gas phase infrared experiment was developed for students at Arkansas State University based on the shortcomings of the rotationally resolved infrared experiment. Chem Spec II is a noncommercial Windows-based software package developed to aid in the potentially complicated problem of assigning quantum numbers to observed…

  4. ChemEd Bridges: Building Bridges between Two-Year College Chemistry Faculty and the National Chemical Education Community

    ERIC Educational Resources Information Center

    Ungar, Harry; Brown, David R.

    2010-01-01

    ChemEd Bridges is an NSF-funded project that provides career and professional development opportunities for chemistry faculty members who teach at two-year colleges (2YCs). We broaden the interests and the horizons of these faculty members by building bridges between them and the broader community of chemical educators. In particular, we have…

  5. Evaluating the Effectiveness of the Open-Access ChemWiki Resource as a Replacement for Traditional General Chemistry Textbooks

    ERIC Educational Resources Information Center

    Allen, Gregory; Guzman-Alvarez, Alberto; Smith, Amy; Gamage, Alan; Molinaro, Marco; Larsen, Delmar S.

    2015-01-01

    Open educational resources (OERs) provide a potential alternative to costly textbooks and can allow content to be edited and adapted to a variety of classroom environments. At the University of California, Davis, the OER "ChemWiki" project, as part of the greater STEMWiki Hyperlibrary, was developed to supplant traditional post-secondary…

  6. The "Virtual ChemLab" Project: A Realistic and Sophisticated Simulation of Organic Synthesis and Organic Qualitative Analysis

    ERIC Educational Resources Information Center

    Woodfield, Brian F.; Andrus, Merritt B.; Waddoups, Gregory L.; Moore, Melissa S.; Swan, Richard; Allen, Rob; Bodily, Greg; Andersen, Tricia; Miller, Jordan; Simmons, Bryon; Stanger, Richard

    2005-01-01

    A set of sophisticated and realistic laboratory simulations is created for use in freshman- and sophomore-level chemistry classes and laboratories called 'Virtual ChemLab'. A detailed assessment of student responses is provided and the simulation's pedagogical utility is described using the organic simulation.

  7. Chemistry Outreach Project to High Schools Using a Mobile Chemistry Laboratory, ChemKits, and Teacher Workshops

    ERIC Educational Resources Information Center

    Long, Gary L.; Bailey, Carol A.; Bunn, Barbara B.; Slebodnick, Carla; Johnson, Michael R.; Derozier, Shad

    2012-01-01

    The Chemistry Outreach Program (ChOP) of Virginia Tech was a university-based outreach program that addressed the needs of high school chemistry classes in underfunded rural and inner-city school districts. The primary features of ChOP were a mobile chemistry laboratory (MCL), a shipping-based outreach program (ChemKits), and teacher workshops.…

  8. Comment on "On the Crooks fluctuation theorem and the Jarzynski equality" [J. Chem. Phys. 129, 091101 (2008)].

    PubMed

    Adib, Artur B

    2009-06-28

    It has recently been argued that a self-consistency condition involving the Jarzynski equality (JE) and the Crooks fluctuation theorem (CFT) is violated for a simple Brownian process [L. Y. Chen, J. Chem. Phys.129, 091101 (2008)]. This note adopts the definitions in the original formulation of the JE and CFT and demonstrates the contrary.

  9. Chemistry Outreach Project to High Schools Using a Mobile Chemistry Laboratory, ChemKits, and Teacher Workshops

    ERIC Educational Resources Information Center

    Long, Gary L.; Bailey, Carol A.; Bunn, Barbara B.; Slebodnick, Carla; Johnson, Michael R.; Derozier, Shad

    2012-01-01

    The Chemistry Outreach Program (ChOP) of Virginia Tech was a university-based outreach program that addressed the needs of high school chemistry classes in underfunded rural and inner-city school districts. The primary features of ChOP were a mobile chemistry laboratory (MCL), a shipping-based outreach program (ChemKits), and teacher workshops.…

  10. Rotational Analysis of FTIR Spectra from Cigarette Smoke: An Application of Chem Spec II Software in the Undergraduate Laboratory

    ERIC Educational Resources Information Center

    Ford, Alan R.; Burns, William A.; Reeve, Scott W.

    2004-01-01

    A version of the classic gas phase infrared experiment was developed for students at Arkansas State University based on the shortcomings of the rotationally resolved infrared experiment. Chem Spec II is a noncommercial Windows-based software package developed to aid in the potentially complicated problem of assigning quantum numbers to observed…

  11. Fabrication of Sulfate-bearing Ceramic Calibration Targets for the ChemCam Laser Spectroscopy Instrument, Mars Science Lander

    NASA Astrophysics Data System (ADS)

    Vaniman, D. T.; Clegg, S.; Lanza, N.; Newsom, H.; Wiens, R. C.; Chemcam Team

    2009-03-01

    A need for sulfur-bearing calibration targets for LIBS analysis by ChemCam on the Mars Science Lander required development of low-fire ceramics. A range of sulfur contents can be obtained that mimic soil or rock at the potential landing sites.

  12. Evaluating the Effectiveness of the Open-Access ChemWiki Resource as a Replacement for Traditional General Chemistry Textbooks

    ERIC Educational Resources Information Center

    Allen, Gregory; Guzman-Alvarez, Alberto; Smith, Amy; Gamage, Alan; Molinaro, Marco; Larsen, Delmar S.

    2015-01-01

    Open educational resources (OERs) provide a potential alternative to costly textbooks and can allow content to be edited and adapted to a variety of classroom environments. At the University of California, Davis, the OER "ChemWiki" project, as part of the greater STEMWiki Hyperlibrary, was developed to supplant traditional post-secondary…

  13. ChemCam investigation of resistant fracture-fill cements at Yellowknife Bay, Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Leveille, R. J.; Wiens, R. C.; Anderson, R. B.; Berger, G.; Bridges, J.; Clark, B. C.; Cousin, A.; Edgar, L. A.; Fabre, C.; Forni, O.; Grotzinger, J. P.; Kah, L. C.; Lanza, N.; Lasue, J.; Le Mouelic, S.; Leshin, L. A.; Mangold, N.; Maurice, S.; McLennan, S. M.; Meslin, P.; Mezzacappa, A.; Newsom, H. E.; Ollila, A.; Schröder, S.; Siebach, K. L.; Thompson, L.; Team, M.

    2013-12-01

    ChemCam is a remote sensing instrument on the Curiosity rover and it is capable of providing rapid geochemical analyses of targets up to 7m away. It can also provide detailed, high spatial resolution (sub-mm), three-dimensional chemical data. Here, we describe Remote Microscopic Imager (RMI) mosaics and detailed LIBS analyses, including rasters and depth profiles of distinctive fracture-filling isopachous cements. In addition, APXS analyses and Mastcam colour images provide additional information and geological context. These resistant features generally appear as centimeter-thick, sub-parallel raised ridges, often sub-vertical and generally composed of two to four layers. Major, minor and trace element data reveal that the cements have a distinct composition compared to the host sedimentary rock and at least two generations of cements can be identified based on composition. At McGrath, a tilted, three-layer vein was investigated by performing a 20-point line raster across the exposed layers (on edge) as well as depth profiles by firing 150 laser shots at a single point. Both of these analyses show that the two outer layers have a similar composition, while the center layer is distinctly different, revealing a cement stratigraphy. In particular, the outer layers show elevated MgO (14-18 wt. %) and possibly elevated Li compared to the middle layer. These compositions suggest that two generations of cements formed from two fluids of different composition or that the precipitating fluid's composition evolved over time, and that Mg-rich phyllosilicates may occur in the cements. Additional rasters and depth profiles were also performed on similar targets. These vein-like features record aqueous processes likely related to early and shallow diagenesis in a habitable lacustrine/fluvial sedimentary environment in Yellowknife Bay. Diagenetic features, such as these Mg-rich veins, as well as Ca-sulfate veins, concretions, and nodules may be common on Mars, as they are found

  14. ChemCam results from the Shaler outcrop in Gale crater, Mars

    USGS Publications Warehouse

    Anderson, Ryan B.; Bridges, J.C.; Williams, A.; Edgar, L.; Ollila, A.; Williams, J.; Nachon, Marion; Mangold, N.; Fisk, M.; Schieber, J.; Gupta, S.; Dromart, G.; Wiens, R.; Le Mouélic, Stéphane; Forni, O.; Lanza, N.; Mezzacappa, Alissa; Sautter, V.; Blaney, D.; Clark, B.; Clegg, S.; Gasnault, O.; Lasue, J.; Léveillé, Richard; Lewin, E.; Lewis, K.W.; Maurice, S.; Newsom, H.; Schwenzer, S.P.; Vaniman, D.

    2015-01-01

    The ChemCam campaign at the fluvial sedimentary outcrop “Shaler” resulted in observations of 28 non-soil targets, 26 of which included active laser induced breakdown spectroscopy (LIBS), and all of which included Remote Micro-Imager (RMI) images. The Shaler outcrop can be divided into seven facies based on grain size, texture, color, resistance to erosion, and sedimentary structures. The ChemCam observations cover Facies 3 through 7. For all targets, the majority of the grains were below the limit of the RMI resolution, but many targets had a portion of resolvable grains coarser than ∼0.5 mm. The Shaler facies show significant scatter in LIBS spectra and compositions from point to point, but several key compositional trends are apparent, most notably in the average K2O content of the observed facies. Facies 3 is lower in K2O than the other facies and is similar in composition to the “snake,” a clastic dike that occurs lower in the Yellowknife Bay stratigraphic section. Facies 7 is enriched in K2O relative to the other facies and shows some compositional and textural similarities to float rocks near Yellowknife Bay. The remaining facies (4, 5, and 6) are similar in composition to the Sheepbed and Gillespie Lake members, although the Shaler facies have slightly elevated K2O and FeOT. Several analysis points within Shaler suggest the presence of feldspars, though these points have excess FeOT which suggests the presence of Fe oxide cement or inclusions. The majority of LIBS analyses have compositions which indicate that they are mixtures of pyroxene and feldspar. The Shaler feldspathic compositions are more alkaline than typical feldspars from shergottites, suggesting an alkaline basaltic source region, particularly for the K2O-enriched Facies 7. Apart from possible iron-oxide cement, there is little evidence for chemical alteration at Shaler, although calcium-sulfate veins comparable to those observed lower in the stratigraphic section are present. The

  15. Iodine's impact on tropospheric oxidants: a global model study in GEOS-Chem

    NASA Astrophysics Data System (ADS)

    Sherwen, T.; Evans, M. J.; Carpenter, L. J.; Andrews, S. J.; Lidster, R. T.; Dix, B.; Koenig, T. K.; Sinreich, R.; Ortega, I.; Volkamer, R.; Saiz-Lopez, A.; Prados-Roman, C.; Mahajan, A. S.; Ordóñez, C.

    2016-02-01

    We present a global simulation of tropospheric iodine chemistry within the GEOS-Chem chemical transport model. This includes organic and inorganic iodine sources, standard gas-phase iodine chemistry, and simplified higher iodine oxide (I2OX, X = 2, 3, 4) chemistry, photolysis, deposition, and parametrized heterogeneous reactions. In comparisons with recent iodine oxide (IO) observations, the simulation shows an average bias of ˜ +90 % with available surface observations in the marine boundary layer (outside of polar regions), and of ˜ +73 % within the free troposphere (350 hPa < p < 900 hPa) over the eastern Pacific. Iodine emissions (3.8 Tg yr-1) are overwhelmingly dominated by the inorganic ocean source, with 76 % of this emission from hypoiodous acid (HOI). HOI is also found to be the dominant iodine species in terms of global tropospheric IY burden (contributing up to 70 %). The iodine chemistry leads to a significant global tropospheric O3 burden decrease (9.0 %) compared to standard GEOS-Chem (v9-2). The iodine-driven OX loss rate1 (748 Tg OX yr-1) is due to photolysis of HOI (78 %), photolysis of OIO (21 %), and reaction between IO and BrO (1 %). Increases in global mean OH concentrations (1.8 %) by increased conversion of hydroperoxy radicals exceeds the decrease in OH primary production from the reduced O3 concentration. We perform sensitivity studies on a range of parameters and conclude that the simulation is sensitive to choices in parametrization of heterogeneous uptake, ocean surface iodide, and I2OX (X = 2, 3, 4) photolysis. The new iodine chemistry combines with previously implemented bromine chemistry to yield a total bromine- and iodine-driven tropospheric O3 burden decrease of 14.4 % compared to a simulation without iodine and bromine chemistry in the model, and a small increase in OH (1.8 %). This is a significant impact and so halogen chemistry needs to be considered in both climate and air quality models. 1 Here OX is defined as O3 + NO2 + 2

  16. Constraints on Eurasian ship NOx emissions using OMI NO2 observations and GEOS-Chem

    NASA Astrophysics Data System (ADS)

    Vinken, Geert C. M.; Boersma, Folkert; van Donkelaar, Aaron; Zhang, Lin

    2013-04-01

    Ships emit large quantities of nitrogen oxides (NOx = NO + NO2), important precursors for ozone (O3) and particulate matter formation. Ships burn low-grade marine heavy fuel due to the limited regulations that exist for the maritime sector in international waters. Previous studies showed that global ship NOx emission inventories amount to 3.0-10.4 Tg N per year (15-30% of total NOx emissions), with most emissions close to land and affecting air quality in densely populated coastal regions. Bottom-up inventories depend on the extrapolation of a relatively small number of measurements that are often unable to capture annual emission changes and can suffer from large uncertainties. Satellites provide long-term, high-resolution retrievals that can be used to improve emission estimates. In this study we provide top-down constraints on ship NOx emissions in major European ship routes, using observed NO2 columns from the Ozone Monitoring Instrument (OMI) and NO2 columns simulated with the nested (0.5°×0.67°) version of the GEOS-Chem chemistry transport model. We use a plume-in-grid treatment of ship NOx emissions to account for in-plume chemistry in our model. We ensure consistency between the retrievals and model simulations by using the high-resolution GEOS-Chem NO2 profiles as a priori. We find evidence that ship emissions in the Mediterranean Sea are geographically misplaced by up to 150 km and biased high by a factor of 4 as compared to the most recent (EMEP) ship emission inventory. Better agreement is found over the shipping lane between Spain and the English Channel. We extend our approach and also provide constraints for major ship routes in the Red Sea and Indian Ocean. Using the full benefit of the long-term retrieval record of OMI, we present a new Eurasian ship emission inventory for the years 2005 to 2010, based on the EMEP and AMVER-ICOADS inventories, and top-down constraints from the satellite retrievals. Our work shows that satellite retrievals can

  17. Evaluation of WRF-CHEM Model: A case study of Air Pollution Episode in Istanbul Metropolitan

    NASA Astrophysics Data System (ADS)

    Aydınöz, Esra; Gürer, Kemal; Toros, Hüseyin

    2014-05-01

    Istanbul is the largest city in Europe with a population of about 14 million and nearly 3.2 million registered vehicles. Considering that the city is at the junction of major transportation routes on both land and sea, emissions from all motor vehicles operating in the city and those that are in transit is the major source of pollution. The natural gas is used as the major heat source and the impact of other heating sources on the pollution episodes is not clearly known. During 19-29 December 2013 İstanbul metropolitan area experienced a severe PM10 episode with average episode concentration of 127µgm-3 . The episode was associated with a high pressure system with center pressure of 1030 mb residing over Balkans and north of Black Sea and thereby influencing Istanbul. We carried out simulations using the Weather Research and Forecasting model with Chemistry (WRF-CHEM) v3.5 to examine the meteorological conditions and to produce estimates of PM10 over Istanbul for 17-31 December 2013. The three nested domains was setup using 18, 6 and 2 km horizontal grid spacing with (90x90), (115x115) and (130x130) grid points in 1st, 2nd and 3rd domains, respectively. The each domain was run using one way nesting option after preparing the results from the mother domain as an input to subsequent inner domain. 34 vertical levels were used with the lowest layer depth of 15 m above the surface and extending to 15 km at the model top. The model was configured using the model options after many tests to find optimal model parameters and was initialized using global emissions data available publicly. The local emissions database is still in works and is not available to use in the model instead of global data. The estimated PM10 concentrations were compared against the observed conditions. This work shows the first attempt of using WRF-CHEM in Turkey to estimate the pollutant concentrations instead of using other air pollution models such as WRF/CMAQ combination. At the time of

  18. Using WRF-Chem to investigate the impact of night time nitrate radical chemistry and N2O5 heterogeneous chemistry on the chemical composition of the UK troposphere.

    NASA Astrophysics Data System (ADS)

    Archer-Nicholls, S.; Lowe, D.; Utembe, S.; McFiggans, G.

    2012-04-01

    It is believed that NO3 is the primary oxidant at night time, significantly impacting ozone formation, rain acidification and the formation and transformation of aerosols, particularly through the formation of the ammonium nitrate particulate (Allan et. al., 2000). However, many of the basic chemical processes controlling the formation and removal of NO3, in particular, the N2O5 heterogeneous reactions, are often not represented in models, although general parameterisations have been developed (c.f. Bertram & Thornton, 2009). The ROle of Night time chemistry in controlling the Oxidising Capacity of the atmOsphere (RONOCO) campaign is a project being funded by NERC and being carried out by a collaboration of UK Universities. It aims to better understand the role of the NO3 radical on the chemistry of the night time atmosphere, its oxidation capacity and thus its overall effects on the composition of the troposphere. The Weather Research and Forecasting model with Chemistry (WRF-Chem) is a state of the art regional climate model with fully coupled online air quality and meteorological components allowing for better resolution of aerosol and gas-phase chemistry (Grell et. al., 2005). It has been extended to include the Common Representative Intermediates scheme (CRIv2-R5) (Watson et. al., 2008), a reduced chemical scheme designed to simulate the atmospheric degradation of 220 species of hydrocarbons and VOCs. The MOSAIC aerosol scheme (Zaveri et. al., 2008), has been extended to include a reduced complexity condensed organic phase consisting of 13 semi-volatile and 2 involatile species (Topping et. al., 2012), as well as the N2O5 heterogeneous reaction scheme of Bertram & Thornton (2009). We aim to use WRF-Chem to compare the oxidation capacity of nighttime NO3 chemistry with that of daytime OH chemistry. The model was run using two nested grids: a 15km resolution domain over western Europe, containing a 5km resolution domain over the UK. The RONOCO campaign consisted

  19. Source apportionment of atmospheric mercury pollution in China using the GEOS-Chem model.

    PubMed

    Wang, Long; Wang, Shuxiao; Zhang, Lei; Wang, Yuxuan; Zhang, Yanxu; Nielsen, Chris; McElroy, Michael B; Hao, Jiming

    2014-07-01

    China is the largest atmospheric mercury (Hg) emitter in the world. Its Hg emissions and environmental impacts need to be evaluated. In this study, China's Hg emission inventory is updated to 2007 and applied in the GEOS-Chem model to simulate the Hg concentrations and depositions in China. Results indicate that simulations agree well with observed background Hg concentrations. The anthropogenic sources contributed 35-50% of THg concentration and 50-70% of total deposition in polluted regions. Sensitivity analysis was performed to assess the impacts of mercury emissions from power plants, non-ferrous metal smelters and cement plants. It is found that power plants are the most important emission sources in the North China, the Yangtze River Delta (YRD) and the Pearl River Delta (PRD) while the contribution of non-ferrous metal smelters is most significant in the Southwest China. The impacts of cement plants are significant in the YRD, PRD and Central China. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Preliminary performance assessment of biotoxin detection for UWS applications using a MicroChemLab device.

    SciTech Connect

    VanderNoot, Victoria A.; Haroldsen, Brent L.; Renzi, Ronald F.; Shokair, Isaac R.

    2010-03-01

    In a multiyear research agreement with Tenix Investments Pty. Ltd., Sandia has been developing field deployable technologies for detection of biotoxins in water supply systems. The unattended water sensor or UWS employs microfluidic chip based gel electrophoresis for monitoring biological analytes in a small integrated sensor platform. This instrument collects, prepares, and analyzes water samples in an automated manner. Sample analysis is done using the {mu}ChemLab{trademark} analysis module. This report uses analysis results of two datasets collected using the UWS to estimate performance of the device. The first dataset is made up of samples containing ricin at varying concentrations and is used for assessing instrument response and detection probability. The second dataset is comprised of analyses of water samples collected at a water utility which are used to assess the false positive probability. The analyses of the two sets are used to estimate the Receiver Operating Characteristic or ROC curves for the device at one set of operational and detection algorithm parameters. For these parameters and based on a statistical estimate, the ricin probability of detection is about 0.9 at a concentration of 5 nM for a false positive probability of 1 x 10{sup -6}.

  1. CAM-chem: description and evaluation of interactive atmospheric chemistry in the Community Earth System Model

    SciTech Connect

    Lamarque, J.-F.; Emmons, L.; Hess, Peter; Kinnison, Douglas E.; Tilmes, S.; Vitt, Francis; Heald, C. L.; Holland, Elisabeth A.; Lauritzen, P. H.; Neu, J.; Orlando, J. J.; Rasch, Philip J.; Tyndall, G. S.

    2012-03-27

    We discuss and evaluate the representation of atmospheric chemistry in the global Community Atmosphere Model (CAM) version 4, the atmospheric component of the Community Earth System Model (CESM). We present a variety of configurations for the representation of tropospheric and stratospheric chemistry, wet removal, and online and offline meteorology. Results from simulations illustrating these configurations are compared with surface, aircraft and satellite observations. Major biases include a negative bias in the high-latitude CO distribution, a positive bias in upper-tropospheric/lower-stratospheric ozone, and a positive bias in summertime surface ozone (over the United States and Europe). The tropospheric net chemical ozone production varies significantly between configurations, partly related to variations in stratosphere-troposphere exchange. Aerosol optical depth tends to be underestimated over most regions, while comparison with aerosol surface measurements over the United States indicate reasonable results for sulfate, especially in the online simulation. Other aerosol species exhibit significant biases. Overall, the model-data comparison indicates that the offline simulation driven by GEOS5 meteorological analyses provides the best simulation, possibly due in part to the increased vertical resolution (52 levels instead of 26 for online dynamics). The CAM-chem code as described in this paper, along with all the necessary datasets needed to perform the simulations described here, are available for download at www.cesm.ucar.edu.

  2. Evaluating stomatal ozone fluxes in WRF-Chem: Comparing ozone uptake in Mediterranean ecosystems

    NASA Astrophysics Data System (ADS)

    Rydsaa, J. H.; Stordal, F.; Gerosa, G.; Finco, A.; Hodnebrog, Ø.

    2016-10-01

    The development of modelling tools for estimating stomatal uptake of surface ozone in vegetation is important for the assessment of potential damage induced due to both current and future near surface ozone concentrations. In this study, we investigate the skill in estimating ozone uptake in plants by the Weather Research and Forecasting model coupled with chemistry (WRF-Chem) V3.6.1, with the Wesely dry deposition scheme. To validate the stomatal uptake of ozone, the model simulations were compared with field measurements of three types of Mediterranean vegetation, over seven different periods representing various meteorological conditions. Some systematic biases in modelled ozone fluxes are revealed; the lack of an explicit and time varying dependency on plants' water availability results in overestimated daytime ozone stomatal fluxes particularly in dry periods. The optimal temperature in the temperature response function is likely too low for the woody species tested here. Also, too low nighttime stomatal conductance leads to underestimation of ozone uptake during night. We demonstrate that modelled stomatal ozone flux is improved by accounting for vapor pressure deficit in the ambient air. Based on the results of the overall comparison to measured fluxes, we propose that additional improvements to the stomatal conductance parameterization should be implemented before applying the modelling system for estimating ozone doses and potential damage to vegetation.

  3. The Virtual ChemLab Project: A Realistic and Sophisticated Simulation of Inorganic Qualitative Analysis

    NASA Astrophysics Data System (ADS)

    Woodfield, Brian F.; Catlin, Heidi R.; Waddoups, Gregory L.; Moore, Melissa S.; Swan, Richard; Allen, Rob; Bodily, Greg

    2004-11-01

    We have created a set of sophisticated and realistic laboratory simulations for use in freshman- and sophomore-level chemistry classes and laboratories called Virtual ChemLab. We have completed simulations for Inorganic Qualitative Analysis, Organic Synthesis and Organic Qualitative Analysis, Experiments in Quantum Chemistry, Gas Properties, Titration Experiments, and Calorimetric and Thermochemical Experiments. The purpose of our simulations is to reinforce concepts taught in the classroom, provide an environment for creative learning, and emphasize the thinking behind instructional laboratory experiments. We have used the inorganic simulation extensively with thousands of students in our department at Brigham Young University. We have learned from our evaluation that: (i) students enjoy using these simulations and find them to be an asset in learning effective problem-solving strategies, (ii) students like the fact that they can both reproduce experimental procedures and explore various topics in ways they choose, and (iii) students naturally divide themselves into two groups: creative learners, who excel in an open-ended environment of virtual laboratories, and structured learners, who struggle in this same environment. In this article, we describe the Inorganic Qualitative Analysis simulation; we also share specific evaluation findings from using the inorganic simulation in classroom and laboratory settings.

  4. Modeling urban air pollution in Budapest using WRF-Chem model

    NASA Astrophysics Data System (ADS)

    Kovács, Attila; Leelőssy, Ádám; Lagzi, István; Mészáros, Róbert

    2017-04-01

    Air pollution is a major problem for urban areas since the industrial revolution, including Budapest, the capital and largest city of Hungary. The main anthropogenic sources of air pollutants are industry, traffic and residential heating. In this study, we investigated the contribution of major industrial point sources to the urban air pollution in Budapest. We used the WRF (Weather Research and Forecasting) nonhydrostatic mesoscale numerical weather prediction system online coupled with chemistry (WRF-Chem, version 3.6).The model was configured with three nested domains with grid spacings of 15, 5 and 1 km, representing Central Europe, the Carpathian Basin and Budapest with its surrounding area. Emission data was obtained from the National Environmental Information System. The point source emissions were summed in their respective cells in the second nested domain according to latitude-longitude coordinates. The main examined air pollutants were carbon monoxide (CO) and nitrogen oxides (NOx), from which the secondary compound, ozone (O3) forms through chemical reactions. Simulations were performed under different weather conditions and compared to observations from the automatic monitoring site of the Hungarian Air Quality Network. Our results show that the industrial emissions have a relatively weak role in the urban background air pollution, confirming the effect of industrial developments and regulations in the recent decades. However, a few significant industrial sources and their impact area has been demonstrated.

  5. QSARINS-chem: Insubria datasets and new QSAR/QSPR models for environmental pollutants in QSARINS.

    PubMed

    Gramatica, Paola; Cassani, Stefano; Chirico, Nicola

    2014-05-15

    A database of environmentally hazardous chemicals, collected and modeled by QSAR by the Insubria group, is included in the updated version of QSARINS, software recently proposed for the development and validation of QSAR models by the genetic algorithm-ordinary least squares method. In this version, a module, named QSARINS-Chem, includes several datasets of chemical structures and their corresponding endpoints (physicochemical properties and biological activities). The chemicals are accessible in different ways (CAS, SMILES, names and so forth) and their three-dimensional structure can be visualized. Some of the QSAR models, previously published by our group, have been redeveloped using the free online software for molecular descriptor calculation, PaDEL-Descriptor. The new models can be easily applied for future predictions on chemicals without experimental data, also verifying the applicability domain to new chemicals. The QSAR model reporting format (QMRF) of these models is also here downloadable. Additional chemometric analyses can be done by principal component analysis and multicriteria decision making for screening and ranking chemicals to prioritize the most dangerous. Copyright © 2014 Wiley Periodicals, Inc.

  6. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

    NASA Astrophysics Data System (ADS)

    Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

    2015-01-01

    A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

  7. Recalibration of the Mars Science Laboratory ChemCam instrument with an expanded geochemical database

    DOE PAGES

    Clegg, Samuel M.; Wiens, Roger C.; Anderson, Ryan; ...

    2016-12-24

    The ChemCam Laser-Induced Breakdown Spectroscopy (LIBS) instrument onboard the Mars Science Laboratory (MSL) rover Curiosity has obtained > 300,000 spectra of rock and soil analysis targets since landing at Gale Crater in 2012, and the spectra represent perhaps the largest publicly-available LIBS datasets. The compositions of the major elements, reported as oxides, have been re-calibrated using a laboratory LIBS instrument, Mars-like atmospheric conditions, and a much larger set of standards (408) that span a wider compositional range than previously employed. The new calibration uses a combination of partial least squares (PLS1) and Independent Component Analysis (ICA) algorithms, together with amore » calibration transfer matrix to minimize differences between the conditions under which the standards were analyzed in the laboratory and the conditions on Mars. While the previous model provided good results in the compositional range near the average Mars surface composition, the new model fits the extreme compositions far better. Examples are given for plagioclase feldspars, where silicon was previously significantly over-estimated, and for calcium-sulfate veins, where silicon compositions near zero were inaccurate. Here, the uncertainties of major element abundances are described as a function of the abundances, and are overall significantly lower than the previous model, enabling important new geochemical interpretations of the data.« less

  8. Recalibration of the Mars Science Laboratory ChemCam instrument with an expanded geochemical database

    SciTech Connect

    Clegg, Samuel M.; Wiens, Roger C.; Anderson, Ryan; Forni, Olivier; Frydenvang, Jens; Lasue, Jeremie; Cousin, Agnes; Payré, Valérie; Boucher, Tommy; Dyar, M. Darby; McLennan, Scott M.; Morris, Richard V.; Graff, Trevor G.; Mertzman, Stanley A.; Ehlmann, Bethany L.; Belgacem, Ines; Newsom, Horton; Clark, Ben C.; Melikechi, Noureddine; Mezzacappa, Alissa; McInroy, Rhonda E.; Martinez, Ronald; Gasda, Patrick; Gasnault, Olivier; Maurice, Sylvestre

    2016-12-24

    The ChemCam Laser-Induced Breakdown Spectroscopy (LIBS) instrument onboard the Mars Science Laboratory (MSL) rover Curiosity has obtained > 300,000 spectra of rock and soil analysis targets since landing at Gale Crater in 2012, and the spectra represent perhaps the largest publicly-available LIBS datasets. The compositions of the major elements, reported as oxides, have been re-calibrated using a laboratory LIBS instrument, Mars-like atmospheric conditions, and a much larger set of standards (408) that span a wider compositional range than previously employed. The new calibration uses a combination of partial least squares (PLS1) and Independent Component Analysis (ICA) algorithms, together with a calibration transfer matrix to minimize differences between the conditions under which the standards were analyzed in the laboratory and the conditions on Mars. While the previous model provided good results in the compositional range near the average Mars surface composition, the new model fits the extreme compositions far better. Examples are given for plagioclase feldspars, where silicon was previously significantly over-estimated, and for calcium-sulfate veins, where silicon compositions near zero were inaccurate. Here, the uncertainties of major element abundances are described as a function of the abundances, and are overall significantly lower than the previous model, enabling important new geochemical interpretations of the data.

  9. Identification of "Known Unknowns" Utilizing Accurate Mass Data and ChemSpider

    NASA Astrophysics Data System (ADS)

    Little, James L.; Williams, Antony J.; Pshenichnov, Alexey; Tkachenko, Valery

    2012-01-01

    In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

  10. In Situ Detection of Boron by ChemCam on Mars

    DOE PAGES

    Gasda, Patrick J.; Haldeman, Ethan Brian; Wiens, Roger Craig; ...

    2017-09-05

    Here, we report the first in situ detection of boron on Mars. Boron has been detected in Gale crater at levels <0.05 wt % B by the NASA Curiosity rover ChemCam instrument in calcium-sulfate-filled fractures, which formed in a late-stage groundwater circulating mainly in phyllosilicate-rich bedrock interpreted as lacustrine in origin. We also consider two main groundwater-driven hypotheses to explain the presence of boron in the veins: leaching of borates out of bedrock or the redistribution of borate by dissolution of borate-bearing evaporite deposits. Our results suggest that an evaporation mechanism is most likely, implying that Gale groundwaters were mildlymore » alkaline. On Earth, boron may be a necessary component for the origin of life; on Mars, its presence suggests that subsurface groundwater conditions could have supported prebiotic chemical reactions if organics were also present and provides additional support for the past habitability of Gale crater.« less

  11. Modeling Transport in Gas Chromatography Columns for the Micro-ChemLab

    SciTech Connect

    ADKINS,DOUGLAS R.; FRYE-MASON,GREGORY CHARLES; HUDSON,MARY L.; KOTTENSTETTE,RICHARD; MATZKE,CAROLYN M.; SALINGER,ANDREW G.; SHADID,JOHN N.; WONG, CHUNGNIN CHANN

    1999-09-01

    The gas chromatography (GC) column is a critical component in the microsystem for chemical detection ({mu}ChemLab{trademark}) being developed at Sandia. The goal is to etch a meter-long GC column onto a 1-cm{sup 2} silicon chip while maintaining good chromatographic performance. Our design strategy is to use a modeling and simulation approach. We have developed an analytical tool that models the transport and surface interaction process to achieve an optimized design of the GC column. This analytical tool has a flow module and a separation module. The flow module considers both the compressibility and slip flow effects that may significantly influence the gas transport in a long and narrow column. The separation module models analyte transport and physico-chemical interaction with the coated surface in the GC column. It predicts the column efficiency and performance. Results of our analysis will be presented in this paper. In addition to the analytical tool, we have also developed a time-dependent adsorption/desorption model and incorporated this model into a computational fluid dynamics (CFD) code to simulate analyte transport and separation process in GC columns. CFD simulations can capture the complex three-dimensional flow and transport dynamics, whereas the analytical tool cannot. Different column geometries have been studied, and results will be presented in this paper. Overall we have demonstrated that the modeling and simulation approach can guide the design of the GC column and will reduce the number of iterations in the device development.

  12. Radiative effects of black carbon aerosols on Indian monsoon: a study using WRF-Chem model

    NASA Astrophysics Data System (ADS)

    Soni, Pramod; Tripathi, Sachchida Nand; Srivastava, Rajesh

    2017-02-01

    The Weather Research and Forecasting model with Chemistry (WRF-Chem) is utilized to examine the radiative effects of black carbon (BC) aerosols on the Indian monsoon, for the year 2010. Five ensemble simulations with different initial conditions (1st to 5th December, 2009) were performed and simulation results between 1st January, 2010 to 31st December, 2010 were used for analysis. Most of the BC which stays near the surface during the pre-monsoon season gets transported to higher altitudes with the northward migration of the Inter Tropical Convergence Zone (ITCZ) during the monsoon season. In both the seasons, strong negative SW anomalies are present at the surface along with positive anomalies in the atmosphere, which results in the surface cooling and lower tropospheric heating, respectively. During the pre-monsoon season, lower troposphere heating causes increased convection and enhanced meridional wind circulation, bringing moist air from Indian Ocean and Bay of Bengal to the North-East India, leading to increased rainfall there. However, during the monsoon season, along with cooling over the land regions, a warming over the Bay of Bengal is simulated. This differential heating results in an increased westerly moisture flux anomaly over central India, leading to increased rainfall over northern parts of India but decreased rainfall over southern parts. Decreased rainfall over southern India is also substantiated by the presence of increased evaporation over Bay of Bengal and decrease over land regions.

  13. Identification of "known unknowns" utilizing accurate mass data and ChemSpider.

    PubMed

    Little, James L; Williams, Antony J; Pshenichnov, Alexey; Tkachenko, Valery

    2012-01-01

    In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

  14. Recent advancements in the gas-phase MicroChemLab

    NASA Astrophysics Data System (ADS)

    Manginell, Ronald P.; Lewis, Patrick R.; Adkins, Douglas R.; Kottenstette, Richard J.; Wheeler, David; Sokolowski, Sara; Trudell, Dan; Byrnes, Joy; Okandan, Murat; Bauer, Joseph M.; Manley, Robert G.

    2004-12-01

    Sandia's hand-held MicroChemLabTM system uses a micromachined preconcentrator (PC), a gas chromatography channel (GC) and a quartz surface acoustic wave array (SAW) detector for sensitive/selective detection of gas-phase chemical analytes. Requisite system size, performance, power budget and time response mandate microfabrication of the key analytical system components. In the fielded system hybrid integration has been employed, permitting optimization of the individual components. Recent improvements in the hybrid-integrated system, using plastic, metal or silicon/glass manifolds, is described, as is system performance against semivolatile compounds and toxic industrial chemicals. The design and performance of a new three-dimensional micropreconcentrator is also introduced. To further reduce system dead volume, eliminate unheated transfer lines and simplify assembly, there is an effort to monolithically integrate the silicon PC and GC with a suitable silicon-based detector, such as a magnetically-actuated flexural plate wave sensor (magFPW) or a magnetically-actuated pivot plate resonator (PPR).

  15. Assessing the ability of WRF-Chem to forecast aerosol optical depth over Poland

    NASA Astrophysics Data System (ADS)

    Werner, Małgorzata; Kryza, Maciej; Markowicz, Krzysztof

    2017-04-01

    Aerosol particles affect Earth's energy budget by scattering and absorbing solar radiation and by altering cloud properties and also influence weather and air quality. The ability of models to describe aerosol optical properties is relevant to reduce uncertainty in aerosol direct radiative forcing and further improve forecasts of meteorology and air quality. Here we evaluate the performance of high-resolution simulations with the Weather Research and Forecasting model with Chemistry (WRF-Chem) in capturing temporal distribution of aerosol optical depth (AOD at 550 nm) over Poland. The simulations are run operationally for this area to forecast air quality since June 2016. The model is run with two domains - mother domain over Europe at 12 km x 12 km and inner domain over Poland at 4 km x 4 km. The model results were compared with ground-based observations from 2 stations from Aerosol Research Network Poland-AOD. The results show that the model can reproduce the variability of observed AOD, however in general overestimates measured values.

  16. WRF-chem sensitivity to vertical resolution during a saharan dust event

    NASA Astrophysics Data System (ADS)

    Teixeira, J. C.; Carvalho, A. C.; Tuccella, Paolo; Curci, Gabriele; Rocha, A.

    2016-08-01

    The Saharan dust event that occurred between the 22nd and 30th of June 2012 influenced the atmospheric radiative properties over North Africa, the Iberian Peninsula, the Western Mediterranean basin, extending its effects to France and Southern England. This event is well documented in satellite imagery, as well as on the air quality stations over the Iberian Peninsula and the AERONET NASA network. In order to assess the effect of the model vertical resolution on the extinction coefficient fields, as a proxy to the particulate matter concentrations in the atmosphere, the WRF-Chem model was applied during this period over a mother domain with a resolution of 18 km, covering Europe and North Africa. To this end five model setups differing in the number of vertical levels were tested. Model skills were evaluated by comparing the model results with CALIPSO and EARLINET LIDAR data. Results show that the model is able to simulate the higher level aerosol transport but it is susceptible to the vertical resolution used. This is due to the thickness of the transport layers which is, eventually, thinner than the vertical resolution of the model. When comparing model results to the observed vertical profiles, it becomes evident that the broad features of the extinction coefficient profile are generally reproduced in all model configurations, but finer details are captured only by the higher resolution simulations.

  17. Mouse ChemR23 is expressed in dendritic cell subsets and macrophages, and mediates an anti-inflammatory activity of chemerin in a lung disease model.

    PubMed

    Luangsay, Souphalone; Wittamer, Valérie; Bondue, Benjamin; De Henau, Olivier; Rouger, Laurie; Brait, Maryse; Franssen, Jean-Denis; de Nadai, Patricia; Huaux, François; Parmentier, Marc

    2009-11-15

    Chemerin is the ligand of the ChemR23 receptor and a chemoattractant factor for human immature dendritic cells (DCs), macrophages, and NK cells. In this study, we characterized the mouse chemerin/ChemR23 system in terms of pharmacology, structure-function, distribution, and in vivo biological properties. Mouse chemerin is synthesized as an inactive precursor (prochemerin) requiring, as in human, the precise processing of its C terminus for generating an agonist of ChemR23. Mouse ChemR23 is highly expressed in immature plasmacytoid DCs and at lower levels in myeloid DCs, macrophages, and NK cells. Mouse prochemerin is expressed in most epithelial cells acting as barriers for pathogens but not in leukocytes. Chemerin promotes calcium mobilization and chemotaxis on DCs and macrophages and these functional responses were abrogated in ChemR23 knockout mice. In a mouse model of acute lung inflammation induced by LPS, chemerin displayed potent anti-inflammatory properties, reducing neutrophil infiltration and inflammatory cytokine release in a ChemR23-dependent manner. ChemR23 knockout mice were unresponsive to chemerin and displayed an increased neutrophil infiltrate following LPS challenge. Altogether, the mouse chemerin/ChemR23 system is structurally and functionally conserved between human and mouse, and mouse can therefore be considered as a good model for studying the anti-inflammatory role of this system in the regulation of immune responses and inflammatory diseases.

  18. Effects on Student Achievement in General Chemistry following Participation in an Online Preparatory Course: ChemPrep, a Voluntary, Self-Paced, Online Introduction to Chemistry

    ERIC Educational Resources Information Center

    Botch, Beatrice; Day, Roberta; Vining, William; Stewart, Barbara; Rath, Kenneth; Peterfreund, Alan; Hart, David

    2007-01-01

    ChemPrep was developed to be a stand-alone preparatory short-course to help students succeed in general chemistry. It is Web-based and delivered using the OWL system. Students reported that the ChemPrep materials (short information pages, parameterized questions with detailed feedback, tutorials, and answers to questions through the OWL message…

  19. An Experimental Study Involving the Use of Contract Evaluation in a CHEM Study and in a Traditional High School Chemistry Course.

    ERIC Educational Resources Information Center

    Penn, Roger Frederick

    This study was concerned with a comparison of the effects of utilizing contract and traditional student evaluation methods in a CHEM Study and in a traditional high school chemistry course. The sample consisted of 49 students enrolled in a CHEM Study course and 63 in a traditional chemistry course. Student evaluations were conducted using the…

  20. A Comparison of CHEM Study Classes and Traditional Curriculum Classes with Respect to Achievement and Attitudinal Measures. Research Paper No. 4.

    ERIC Educational Resources Information Center

    Lawrenz, Frances; Gullickson, Arlen

    A comparison of CHEM Study and traditional chemistry classes showed no difference in student achievement in chemistry. The curricula did not have a differential effect on high vs. low ability groups. However, a difference in student attitude toward CHEM study and the traditional text, "Modern Chemistry," was observed. The students found…

  1. Effects on Student Achievement in General Chemistry following Participation in an Online Preparatory Course: ChemPrep, a Voluntary, Self-Paced, Online Introduction to Chemistry

    ERIC Educational Resources Information Center

    Botch, Beatrice; Day, Roberta; Vining, William; Stewart, Barbara; Rath, Kenneth; Peterfreund, Alan; Hart, David

    2007-01-01

    ChemPrep was developed to be a stand-alone preparatory short-course to help students succeed in general chemistry. It is Web-based and delivered using the OWL system. Students reported that the ChemPrep materials (short information pages, parameterized questions with detailed feedback, tutorials, and answers to questions through the OWL message…

  2. Visible and Near-Infrared (VNIR) Spectroscopy of Altered Basalts with Application to the ChemCam Library for Mars Science Laboratory

    NASA Astrophysics Data System (ADS)

    Hadnott, B.; Ehlmann, B. L.

    2012-12-01

    The discovery of Fe, Mg, and Al clays on Mars using VNIR spectroscopy from orbit indicates past low temperature/pressure hydrothermal and weathering environments. Laboratory analysis of Mars-analog rocks from these settings on Earth was used to build the ChemCam sample library for Mars Science Laboratory, permitting for more accurate compositional analysis of Martian samples, improved linkages between VNIR's mineralogic and ChemCam's elemental data, and improved recognition of different environmental settings for aqueous alteration. VNIR spectroscopy was used to analyze 4 suites of altered basaltic rocks—one from San Carlos, AZ and three from various locations in Iceland. Continuum shape and absorption features were found to vary, depending on the environment and extent of alteration. Relatively unaltered rocks had electronic absorptions related to ferrous iron. The strength of the 1.9- μm (μm = microns) H2O absorption correlated with the degree of aqueous alteration. Samples with strong 1.9- μm absorptions often exhibited absorption bands at 1.4, 2.2, and 2.3 μm indicating the presence of clay minerals and/or features at 0.5-0.8 μm indicative of ferric iron oxides. Diagnostic absorption features and continuum slopes have been used to identify a representative subset of rocks from each suite for further analysis for the ChemCam library. Noteworthy spectral features for all suites included variation of absorption bands from 2.0-2.5 μm. Most samples contained an absorption band near 2.21 μm, indicating the presence of Si-OH or Al-OH; a 2.3 μm band is also present in some samples, indicating the presence of Mg-OH and Fe-OH, with subtle shifts between 2.29 and 2.35 μm indicating the major cation and constituent phase (e.g. amorphous phase, smectite or chlorite). Overall continuum slope correlated with the degree of alteration. Flat slopes contained weak 1.9 μm bands (little alteration) and sometimes ferrous iron absorptions of primary minerals. Negative

  3. Development of a grid-independent GEOS-Chem chemical transport model (v9-02) as an atmospheric chemistry module for Earth system models

    NASA Astrophysics Data System (ADS)

    Long, M. S.; Yantosca, R.; Nielsen, J. E.; Keller, C. A.; da Silva, A.; Sulprizio, M. P.; Pawson, S.; Jacob, D. J.

    2015-03-01

    The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been re-engineered to also serve as an atmospheric chemistry module for Earth system models (ESMs). This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of the GEOS-Chem scientific code, permitting the exact same GEOS-Chem code to be used as an ESM module or as a stand-alone CTM. In this manner, the continual stream of updates contributed by the CTM user community is automatically passed on to the ESM module, which remains state of science and referenced to the latest version of the standard GEOS-Chem CTM. A major step in this re-engineering was to make GEOS-Chem grid independent, i.e., capable of using any geophysical grid specified at run time. GEOS-Chem data sockets were also created for communication between modules and with external ESM code. The grid-independent, ESMF-compatible GEOS-Chem is now the standard version of the GEOS-Chem CTM. It has been implemented as an atmospheric chemistry module into the NASA GEOS-5 ESM. The coupled GEOS-5-GEOS-Chem system was tested for scalability and performance with a tropospheric oxidant-aerosol simulation (120 coupled species, 66 transported tracers) using 48-240 cores and message-passing interface (MPI) distributed-memory parallelization. Numerical experiments demonstrate that the GEOS-Chem chemistry module scales efficiently for the number of cores tested, with no degradation as the number of cores increases. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemistry module means that the relative cost goes down with increasing number of cores in a massively parallel environment.

  4. Operational on-line coupled chemical weather forecasts for Europe with WRF/Chem

    NASA Astrophysics Data System (ADS)

    Hirtl, Marcus; Mantovani, Simone; Krüger, Bernd C.; Flandorfer, Claudia; Langer, Matthias

    2014-05-01

    Air quality is a key element for the well-being and quality of life of European citizens. Air pollution measurements and modeling tools are essential for the assessment of air quality according to EU legislation. The responsibilities of ZAMG as the national weather service of Austria include the support of the federal states and the public in questions connected to the protection of the environment in the frame of advisory and counseling services as well as expert opinions. ZAMG conducts daily Air-Quality forecasts using the on-line coupled model WRF/Chem. Meteorology is simulated simultaneously with the emissions, turbulent mixing, transport, transformation, and fate of trace gases and aerosols. The emphasis of the application is on predicting pollutants over Austria. Two domains are used for the simulations: the mother domain covers Europe with a resolution of 12 km, the inner domain includes the alpine region with a horizontal resolution of 4 km; 45 model levels are used in the vertical direction. The model runs 2 times per day for a period of 72 hours and is initialized with ECMWF forecasts. On-line coupled models allow considering two-way interactions between different atmospheric processes including chemistry (both gases and aerosols), clouds, radiation, boundary layer, emissions, meteorology and climate. In the operational set-up direct-, indirect and semi-direct effects between meteorology and air chemistry are enabled. The model is running on the HPCF (High Performance Computing Facility) of the ZAMG. In the current set-up 1248 CPUs are used. As the simulations need a big amount of computing resources, a method to safe I/O-time was implemented. Every MPI task writes all its output into the shared memory filesystem of the compute nodes. Once the WRF/Chem integration is finished, all split NetCDF-files are merged and saved on the global file system. The merge-routine is based on parallel-NetCDF. With this method the model runs about 30% faster on the SGI

  5. Application of the WRF-Chem model for the simulation of air quality over Cyprus

    NASA Astrophysics Data System (ADS)

    Kushta, Jonilda; Proestos, Yiannis; Georgiou, George; Christoudias, Theodoros; Lelieveld, Jos

    2017-04-01

    The fully coupled WRF-Chem (Weather Research and Forecasting with Chemistry) model is used to simulate air quality over Cyprus. Cyprus is an island country with complex topography, located in the eastern corner of East Mediterranean region, affected year-long by local, regional and long range transported pollution. An extensive sensitivity analysis of the model performance has been performed over the area of interest with three domains of respective grid spacing of 40, 8 and 2 km. Different configurations have been deployed regarding horizontal resolution, simulation timestep, boundary conditions, NOx emissions and speciation method of emitted NMVOCs (Non Methane Volatile Organic Compounds). The WRF-Chem model simulated hourly concentrations of air pollutants for a month-long period (July 2014) during which measurements are available over 13 stations (4 of which background stations, 1 industrial and 8 urban/traffic stations). The model was initialized with meteorological initial and boundary conditions (ICBC) using NCAR-NCEP's F Global Forecast System output (GFS) at a 1o x1o spatial resolution. The ICBC for the chemical species are derived from the MOZART global model results (2.5o x 2.5o). Both ICBCs datasets are updated every 6 hours. The emission inventory used in the study is the EDGAR-HTAP v2 dataset with a horizontal grid resolution of 0.1o × 0.1o, while an additional dataset with speciated NMVOCs (instead of summed volatile species) is also tested. The diurnal cycle of the atmospheric concentrations of ozone averaged over the island, exhibits a maximum of 114 μg/m3 when the boundary conditions are derived from MOZART and 94 μg/m3 when the boundary conditions are not included (local background and production), suggesting a constant inflow of ozone from long range transport of about 20 μg/m3. The contribution of pollution from regional sources is more pronounced at the western border due to the characteristic summer time north-northeasterly etesian flow

  6. Consoer et al PFOS dataset

    EPA Pesticide Factsheets

    This ScienceHub entry was developed for the published paper: Consoer et al., 2016, Toxicokinetics of perfluorooctane sulfonate in rainow trout (Oncorhynchus mykiss), Environ. Toxicol. Chem. 35:717-727. Individual rainbow trout were exposed to PFOS by bolus injection (elimination studies) or by adding PFOS to incoming water (branchial uptake studies). The trout were fitted with indwelling catheters and urinary cannulae to permit periodic collection of blood and urine. Additional sampling was conducted to evaluate PFOS uptake from and elimination to respired water. Data obtained from each fish was evaluated using a clearance-volume pharmacokinetic model. Modeled kinetic parameters were then averaged to develop summary statistics which were used as a basis for interpreting modeled results and making comparisons to a previous study of rainbow trout exposed to perfluorooctanoate (PFOA; Consoer et al., 2014, Aquat. Toxicol. 156:65-73). The results of this study, combined with that of the previous PFOA study, suggest that PFOA is a substrate for renal transporters in fish while glomerular filtration alone may be sufficient to explain the observed renal elimination of PFOS. These findings demonstrate that models developed to predict the bioaccumulation of perfluoroalkyl acids by fish must account for differences in renal clearance of individual compounds.This dataset is associated with the following publication:Consoer, D., A. Hoffman , P. Fitzsimmons , P. Kosia

  7. ChemDataExtractor: A Toolkit for Automated Extraction of Chemical Information from the Scientific Literature.

    PubMed

    Swain, Matthew C; Cole, Jacqueline M

    2016-10-24

    The emergence of "big data" initiatives has led to the need for tools that can automatically extract valuable chemical information from large volumes of unstructured data, such as the scientific literature. Since chemical information can be present in figures, tables, and textual paragraphs, successful information extraction often depends on the ability to interpret all of these domains simultaneously. We present a complete toolkit for the automated extraction of chemical entities and their associated properties, measurements, and relationships from scientific documents that can be used to populate structured chemical databases. Our system provides an extensible, chemistry-aware, natural language processing pipeline for tokenization, part-of-speech tagging, named entity recognition, and phrase parsing. Within this scope, we report improved performance for chemical named entity recognition through the use of unsupervised word clustering based on a massive corpus of chemistry articles. For phrase parsing and information extraction, we present the novel use of multiple rule-based grammars that are tailored for interpreting specific document domains such as textual paragraphs, captions, and tables. We also describe document-level processing to resolve data interdependencies and show that this is particularly necessary for the autogeneration of chemical databases since captions and tables commonly contain chemical identifiers and references that are defined elsewhere in the text. The performance of the toolkit to correctly extract various types of data was evaluated, affording an F-score of 93.4%, 86.8%, and 91.5% for extracting chemical identifiers, spectroscopic attributes, and chemical property attributes, respectively; set against the CHEMDNER chemical name extraction challenge, ChemDataExtractor yields a competitive F-score of 87.8%. All tools have been released under the MIT license and are available to download from http://www.chemdataextractor.org .

  8. Feldspars Detected by ChemCam in Gale Crater with Implications for Future Martian Exploration

    NASA Astrophysics Data System (ADS)

    Gasda, P. J.; Carlson, E.; Wiens, R. C.; Bridges, J.; Sautter, V.; Cousin, A.; Maurice, S.; Gasnault, O.; Clegg, S. M.

    2015-12-01

    Feldspar is a common igneous mineral that can shed light on parent magma temperatures, pressures, and compositions. During the first 801 sols of the NASA Mars Science Laboratory mission, we have detected 125 possible feldspar grains using the ChemCam LIBS instrument. We analyzed spectra from successive laser shots at the same location and approximate whole rock compositions for each target. Feldspar-containing targets range from tephrite-basanite to trachyandesite. The most common feldspar type is andesine; no targets are >An60. Over 30% are anorthoclase, and ~10% have potassium contents up to Or60. Individual shot measurements in a single spot suggest some feldspars are zoned. Most of these rocks are either float or incorporated into conglomerates, and thus we do not know their provenance. Many of the samples may originate from the Gale crater walls, indicative of Southern Highland ancient crust. Some may also be flung from further away (e.g., emplaced by impact processes). Hence, these rocks may give us a general clue to the variety of evolved igneous materials on Mars. The ubiquity of feldspars at Gale suggests that they have been significantly underestimated for the Southern Highlands, if not for the whole of Mars. For example, significant abundance of andesitic feldspars in both the southern highland and northern lowlands of Mars would imply that Martian volcanism has produced a greater extent of evolved igneous materials to a greater degree than previously thought. Remote sensing instruments are insensitive to plagioclase due to dust cover, lack of exposures, or low feldspar FeO content. However, the Mars 2020 rover will be equipped with 3 new instruments, the arm-mounted SHERLOC Raman, PIXL μXRF, and the mast-mounted SuperCam combined Raman-LIBS instruments, which should help characterize Martian feldspars. Additionally, the SuperCam instrument plans to include three feldspars in its suite of 20+ onboard standards to improve feldspar chemical analysis.

  9. Numerical air quality forecasting over eastern China: An operational application of WRF-Chem

    NASA Astrophysics Data System (ADS)

    Zhou, Guangqiang; Xu, Jianming; Xie, Ying; Chang, Luyu; Gao, Wei; Gu, Yixuan; Zhou, Ji

    2017-03-01

    The Regional Atmospheric Environmental Modeling System for eastern China (RAEMS) is an operational numerical system to forecast near surface atmospheric pollutants such as PM2.5 and O3 over the eastern China region. This system was based on the fully online coupled weather research and forecasting/chemistry (WRF-Chem) model. Anthropogenic emissions were based on the multi-resolution emission inventory for China (MEIC), and biogenic emissions were online calculated using model of emissions of gases and aerosols from nature (MEGAN2). Authorized by the China Meteorological Administration (CMA), this system started to provide operational forecast in 2013. With a large domain covering eastern China, the system produces daily 72-hr forecast. In this work, a comprehensive evaluation was carried out against measurements for two full years (2014-2015). Evaluation results show that the RAEMS is skillful in forecasting temporal variation and spatial distribution of major air pollutants over the eastern China region. The performance is consistent in different forecast length of 24 h, 48 h, and 72 h. About half of cities have correlation coefficients greater than 0.6 for PM2.5 and 0.7 for daily maximum 8-h averaged (DM8H) ozone. The forecasted PM2.5 is generally in good agreement with observed concentrations, with most cities having normalized mean biases (NMB) within ±25%. Forecasted ozone diurnal variation is very similar to that of observed, and makes small peak time error for DM8H ozone. It also shows good capability in capturing ozone pollution as indicated by high critical success indexes (CSI). The modeling system also exhibits acceptable performance for PM10, NO2, SO2, and CO. Meanwhile, degraded performance for PM2.5 is found under heavy polluted conditions, and there is a general over estimation in ozone concentrations.

  10. Mixed waste treatment using the ChemChar thermolytic detoxification technique

    SciTech Connect

    Kuchynka, D.

    1995-12-31

    The diversity of mixed waste matrices contained at Department of Energy sites that require treatment preclude a single, universal treatment technology capable of handling sludges, solids, heterogeneous debris, aqueous and organic liquids and soils. Versatility of the treatment technology, volume reduction and containment of the radioactive component of the mixed waste streams are three criteria to be considered when evaluating potential treatment technologies. The ChemChar thermolytic detoxification process being developed under this R and D contract is a thermal, chemically reductive technology that converts the organic portion of a mixed waste stream to an energy-rich synthesis gas while simultaneously absorbing volatile inorganic species (metals and acid gases) on a macroporous, carbon-based char. The latter is mixed with the waste stream prior to entering the reactor. Substoichiometric amounts of oxidant are fed into the top portion of the cylindrical reactor generating a thin, radial thermochemical reaction zone. This zone generates all the necessary heat to promote the highly endothermic reduction of the organic components in the waste in the lower portion of the reactor, producing, principally, hydrogen and carbon monoxide. The solid by-product is a regenerated carbon char that, depending on the inorganic loading, is capable for reuse. The in situ scrubbing of contaminants by the char within the reactor coupled with a char filter for final polishing produce an exceptionally clean synthesis gas effluent suitable for on-site generation of heat, steam or electricity. Despite the elevated temperatures in the thermochemical reaction zone, the reductive nature of the process precludes formation of nitrogen oxides and halogenated organic compound by-products.

  11. WRF-Chem Simulation of Air Quality Over China in 2013

    NASA Astrophysics Data System (ADS)

    Zhong, M.; Saikawa, E.; Liu, Y.; Kishimoto, P. N.; Karplus, V. J.; Naik, V.; Horowitz, L. W.; Takigawa, M.

    2015-12-01

    We use the Weather Research and Forecasting model coupled with Chemistry version 3.5 (WRF-Chem) to investigate air quality over China in 2013, and compare model simulations with ground-level measurements from more than 800 monitoring sites, and satellite retrievals. We create the provincial total anthropogenic emissions in 2013 using the China Regional Economic Model (C-REM) and map these provincial emissions based on the spatial distribution of the Regional Emission Inventory in Asia (REAS) version 2. The initial and lateral chemical boundary conditions are taken from a present-day simulation of the NOAA Geophysical Fluid Dynamics Laboratory (GFDL) global chemistry-climate model AM3. We use the Regional Acid Deposition version 2 (RADM2) atmospheric chemical mechanism for gas-phase chemistry and the Model Aerosol Dynamics for Europe with the Secondary Organic Aerosol Model (MADE/SORGAM) along with some aqueous reactions for aerosol chemistry. Our preliminary results show that model meets the air quality model performance criteria for fine particulate matter (PM2.5), with mean fractional bias (MFB) less than 50%, at 95% of observation sites in April, 2013. The model tends to overestimate monthly mean PM2.5 in Central China (MFB = 23.8%), East China (MFB = 2.03%), Northwest China (MFB = 7.12%), South China (MFB = 26.9%), and Taiwan (MFB = 22.3%), but underestimate in North China (MFB = -9.7%), Northeast China (MFB = -20.5%), and Southwest China (MFB = -11.2%). Overall, model performs excellent in predicting PM2.5 using the newly created anthropogenic emissions in China, with monthly mean PM2.5 MFB of 5.5% in nationwide. We will present results of model-measurement comparisons and model-satellite retrievals comparisons for more months in the year of 2013.

  12. How wild is your model fire? Constraining WRF-Chem wildfire smoke simulations with satellite observations

    NASA Astrophysics Data System (ADS)

    Fischer, E. V.; Ford, B.; Lassman, W.; Pierce, J. R.; Pfister, G.; Volckens, J.; Magzamen, S.; Gan, R.

    2015-12-01

    Exposure to high concentrations of particulate matter (PM) present during acute pollution events is associated with adverse health effects. While many anthropogenic pollution sources are regulated in the United States, emissions from wildfires are difficult to characterize and control. With wildfire frequency and intensity in the western U.S. projected to increase, it is important to more precisely determine the effect that wildfire emissions have on human health, and whether improved forecasts of these air pollution events can mitigate the health risks associated with wildfires. One of the challenges associated with determining health risks associated with wildfire emissions is that the low spatial resolution of surface monitors means that surface measurements may not be representative of a population's exposure, due to steep concentration gradients. To obtain better estimates of ambient exposure levels for health studies, a chemical transport model (CTM) can be used to simulate the evolution of a wildfire plume as it travels over populated regions downwind. Improving the performance of a CTM would allow the development of a new forecasting framework that could better help decision makers estimate and potentially mitigate future health impacts. We use the Weather Research and Forecasting model with online chemistry (WRF-Chem) to simulate wildfire plume evolution. By varying the model resolution, meteorology reanalysis initial conditions, and biomass burning inventories, we are able to explore the sensitivity of model simulations to these various parameters. Satellite observations are used first to evaluate model skill, and then to constrain the model results. These data are then used to estimate population-level exposure, with the aim of better characterizing the effects that wildfire emissions have on human health.

  13. WRF-Chem Simulations of Aerosols and Anthropogenic Aerosol Radiative Forcing in East Asia

    SciTech Connect

    Gao, Yi; Zhao, Chun; Liu, Xiaohong; Zhang, Meigen; Leung, Lai-Yung R.

    2014-08-01

    This study aims to provide a first comprehensive evaluation of WRF-Chem for modeling aerosols and anthropogenic aerosol radiative forcing (RF) over East Asia. Several numerical experiments were conducted from November 2007 to December 2008. Comparison between model results and observations shows that the model can generally reproduce the observed spatial distributions of aerosol concentration, aerosol optical depth (AOD) and single scattering albedo (SSA) from measurements at different sites, including the relatively higher aerosol concentration and AOD over East China and the relatively lower AOD over Southeast Asia, Korean, and Japan. The model also depicts the seasonal variation and transport of pollutions over East Asia. Particulate matter of 10 um or less in the aerodynamic diameter (PM10), black carbon (BC), sulfate (SO42-), nitrate (NO3-) and ammonium (NH4+) concentrations are higher in spring than other seasons in Japan due to the pollutant transport from polluted area of East Asia. AOD is high over Southwest and Central China in winter, spring and autumn and over North China in summer while is low over South China in summer due to monsoon precipitation. SSA is lowest in winter and highest in summer. The model also captures the dust events at the Zhangye site in the semi-arid region of China. Anthropogenic aerosol RF is estimated to range from -5 to -20 W m-2 over land and -20 to -40 W m-2 over ocean at the top of atmosphere (TOA), 5 to 30 W m-2 in the atmosphere (ATM) and -15 to -40 W m-2 at the bottom (BOT). The warming effect of anthropogenic aerosol in ATM results from BC aerosol while the negative aerosol RF at TOA is caused by scattering aerosols such as SO4 2-, NO3 - and NH4+. Positive BC RF at TOA compensates 40~50% of the TOA cooling associated with anthropogenic aerosol.

  14. The ChemCam Remote Micro-Imager at Gale crater: Review of the first year of operations on Mars

    NASA Astrophysics Data System (ADS)

    Le Mouélic, S.; Gasnault, O.; Herkenhoff, K. E.; Bridges, N. T.; Langevin, Y.; Mangold, N.; Maurice, S.; Wiens, R. C.; Pinet, P.; Newsom, H. E.; Deen, R. G.; Bell, J. F.; Johnson, J. R.; Rapin, W.; Barraclough, B.; Blaney, D. L.; Deflores, L.; Maki, J.; Malin, M. C.; Pérez, R.; Saccoccio, M.

    2015-03-01

    The Mars Science Laboratory rover, "Curiosity" landed near the base of a 5 km-high mound of layered material in Gale crater. Mounted on the rover mast, the ChemCam instrument is designed to remotely determine the composition of soils and rocks located a few meters from the rover, using a Laser-Induced Breakdown Spectrometer (LIBS) coupled to a Remote Micro-Imager (RMI). We provide an overview of the diverse imaging investigations that were carried out by ChemCam's RMI during the first year of operation on Mars. 1182 individual panchromatic RMI images were acquired from Sol 10 to Sol 360 to document the ChemCam LIBS measurements and to characterize soils, rocks and rover hardware. We show several types of derived imaging products, including mosaics of images taken before and after laser shots, difference images to enhance the most subtle laser pits, merges with color Mastcam-100 images, micro-topography using the Z-stack technique, and time lapse movies. The very high spatial resolution of RMI is able to resolve rock textures at sub-mm scales, which provides clues regarding the origin (igneous versus sedimentary) of rocks, and to reveal information about their diagenetic and weathering evolution. In addition to its scientific value over the range accessible by LIBS (1-7 m), we also show that RMI can also serve as a powerful long distance reconnaissance tool to characterize the landscape at distances up to several kilometers from the rover.

  15. Inclusion of ash and SO2 emissions from volcanic eruptions in WRF-Chem: development and some applications

    NASA Astrophysics Data System (ADS)

    Stuefer, M.; Freitas, S. R.; Grell, G.; Webley, P.; Peckham, S.; McKeen, S. A.; Egan, S. D.

    2013-04-01

    We describe a new functionality within the Weather Research and Forecasting (WRF) model with coupled Chemistry (WRF-Chem) that allows simulating emission, transport, dispersion, transformation and sedimentation of pollutants released during volcanic activities. Emissions from both an explosive eruption case and a relatively calm degassing situation are considered using the most recent volcanic emission databases. A preprocessor tool provides emission fields and additional information needed to establish the initial three-dimensional cloud umbrella/vertical distribution within the transport model grid, as well as the timing and duration of an eruption. From this source condition, the transport, dispersion and sedimentation of the ash cloud can be realistically simulated by WRF-Chem using its own dynamics and physical parameterization as well as data assimilation. Examples of model applications include a comparison of tephra fall deposits from the 1989 eruption of Mount Redoubt (Alaska) and the dispersion of ash from the 2010 Eyjafjallajökull eruption in Iceland. Both model applications show good coincidence between WRF-Chem and observations.

  16. Air Quality Modeling for the Urban Jackson, Mississippi Region Using a High Resolution WRF/Chem Model

    PubMed Central

    Yerramilli, Anjaneyulu; Dodla, Venkata B.; Desamsetti, Srinivas; Challa, Srinivas V.; Young, John H.; Patrick, Chuck; Baham, Julius M.; Hughes, Robert L.; Yerramilli, Sudha; Tuluri, Francis; Hardy, Mark G.; Swanier, Shelton J.

    2011-01-01

    In this study, an attempt was made to simulate the air quality with reference to ozone over the Jackson (Mississippi) region using an online WRF/Chem (Weather Research and Forecasting–Chemistry) model. The WRF/Chem model has the advantages of the integration of the meteorological and chemistry modules with the same computational grid and same physical parameterizations and includes the feedback between the atmospheric chemistry and physical processes. The model was designed to have three nested domains with the inner-most domain covering the study region with a resolution of 1 km. The model was integrated for 48 hours continuously starting from 0000 UTC of 6 June 2006 and the evolution of surface ozone and other precursor pollutants were analyzed. The model simulated atmospheric flow fields and distributions of NO2 and O3 were evaluated for each of the three different time periods. The GIS based spatial distribution maps for ozone, its precursors NO, NO2, CO and HONO and the back trajectories indicate that all the mobile sources in Jackson, Ridgeland and Madison contributing significantly for their formation. The present study demonstrates the applicability of WRF/Chem model to generate quantitative information at high spatial and temporal resolution for the development of decision support systems for air quality regulatory agencies and health administrators. PMID:21776240

  17. NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods

    PubMed Central

    Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene

    2015-01-01

    There is rising evidence of an inverse association between chronic diseases and diets characterized by rich fruit and vegetable consumption. Dietary components may act directly or indirectly on the human genome and modulate multiple processes involved in disease risk and disease progression. However, there is currently no exhaustive resource on the health benefits associated to specific dietary interventions, or a resource covering the broad molecular content of food. Here we present the first release of NutriChem, available at http://cbs.dtu.dk/services/NutriChem-1.0, a database generated by text mining of 21 million MEDLINE abstracts for information that links plant-based foods with their small molecule components and human disease phenotypes. NutriChem contains text-mined data for 18478 pairs of 1772 plant-based foods and 7898 phytochemicals, and 6242 pairs of 1066 plant-based foods and 751 diseases. In addition, it includes predicted associations for 548 phytochemicals and 252 diseases. To the best of our knowledge this database is the only resource linking the chemical space of plant-based foods with human disease phenotypes and provides a foundation for understanding mechanistically the consequences of eating behaviors on health. PMID:25106869

  18. E-chem page: A Support System for Remote Diagnosis of Water Quality in Boiling Water Reactors

    SciTech Connect

    Naohiro Kusumi; Takayasu Kasahara; Kazuhiko Akamine; Kenji Tada; Naoshi Usui; Nobuyuki Oota

    2002-07-01

    It is important to control and maintain water quality for nuclear power plants. Chemical engineers sample and monitor reactor water from various subsystems and analyze the chemical quality as routine operations. With regard to controlling water quality, new technologies have been developed and introduced to improve the water quality from both operation and material viewpoints. To maintain the quality, it is important to support chemical engineers in evaluating the water quality and realizing effective retrieval of stored data and documents. We have developed a remote support system using the Internet to diagnose BWR water quality, which we call e-chem page. The e-chem page integrates distributed data and information in a Web server, and makes it easy to evaluate the data on BWR water chemistry. This system is composed of four functions: data transmission, water quality evaluation, inquiry and history retrieval system, and reference to documents on BWR water chemistry. The developed system is now being evaluated in trial operations by Hitachi, Ltd. and an electric power company. In addition diagnosis technology applying independent component analysis (ICA) is being developed to improve predictive capability of the system. This paper describes the structure and function of the e-chem page and presents results of obtained with the proposed system for the prediction of chemistry conditions in reactor water. (authors)

  19. NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods.

    PubMed

    Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene

    2015-01-01

    There is rising evidence of an inverse association between chronic diseases and diets characterized by rich fruit and vegetable consumption. Dietary components may act directly or indirectly on the human genome and modulate multiple processes involved in disease risk and disease progression. However, there is currently no exhaustive resource on the health benefits associated to specific dietary interventions, or a resource covering the broad molecular content of food. Here we present the first release of NutriChem, available at http://cbs.dtu.dk/services/NutriChem-1.0, a database generated by text mining of 21 million MEDLINE abstracts for information that links plant-based foods with their small molecule components and human disease phenotypes. NutriChem contains text-mined data for 18478 pairs of 1772 plant-based foods and 7898 phytochemicals, and 6242 pairs of 1066 plant-based foods and 751 diseases. In addition, it includes predicted associations for 548 phytochemicals and 252 diseases. To the best of our knowledge this database is the only resource linking the chemical space of plant-based foods with human disease phenotypes and provides a foundation for understanding mechanistically the consequences of eating behaviors on health. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. PubChemQC Project: A Large-Scale First-Principles Electronic Structure Database for Data-Driven Chemistry.

    PubMed

    Nakata, Maho; Shimazaki, Tomomi

    2017-06-26

    Large-scale molecular databases play an essential role in the investigation of various subjects such as the development of organic materials, in silico drug design, and data-driven studies with machine learning. We have developed a large-scale quantum chemistry database based on first-principles methods. Our database currently contains the ground-state electronic structures of 3 million molecules based on density functional theory (DFT) at the B3LYP/6-31G* level, and we successively calculated 10 low-lying excited states of over 2 million molecules via time-dependent DFT with the B3LYP functional and the 6-31+G* basis set. To select the molecules calculated in our project, we referred to the PubChem Project, which was used as the source of the molecular structures in short strings using the InChI and SMILES representations. Accordingly, we have named our quantum chemistry database project "PubChemQC" ( http://pubchemqc.riken.jp/ ) and placed it in the public domain. In this paper, we show the fundamental features of the PubChemQC database and discuss the techniques used to construct the data set for large-scale quantum chemistry calculations. We also present a machine learning approach to predict the electronic structure of molecules as an example to demonstrate the suitability of the large-scale quantum chemistry database.

  1. Air quality modeling for the urban Jackson, Mississippi Region using a high resolution WRF/Chem model.

    PubMed

    Yerramilli, Anjaneyulu; Dodla, Venkata B; Desamsetti, Srinivas; Challa, Srinivas V; Young, John H; Patrick, Chuck; Baham, Julius M; Hughes, Robert L; Yerramilli, Sudha; Tuluri, Francis; Hardy, Mark G; Swanier, Shelton J

    2011-06-01

    In this study, an attempt was made to simulate the air quality with reference to ozone over the Jackson (Mississippi) region using an online WRF/Chem (Weather Research and Forecasting-Chemistry) model. The WRF/Chem model has the advantages of the integration of the meteorological and chemistry modules with the same computational grid and same physical parameterizations and includes the feedback between the atmospheric chemistry and physical processes. The model was designed to have three nested domains with the inner-most domain covering the study region with a resolution of 1 km. The model was integrated for 48 hours continuously starting from 0000 UTC of 6 June 2006 and the evolution of surface ozone and other precursor pollutants were analyzed. The model simulated atmospheric flow fields and distributions of NO2 and O3 were evaluated for each of the three different time periods. The GIS based spatial distribution maps for ozone, its precursors NO, NO2, CO and HONO and the back trajectories indicate that all the mobile sources in Jackson, Ridgeland and Madison contributing significantly for their formation. The present study demonstrates the applicability of WRF/Chem model to generate quantitative information at high spatial and temporal resolution for the development of decision support systems for air quality regulatory agencies and health administrators.

  2. An arrayed nanocavity structure for novel spectroscopic chem/bio-sensing

    NASA Astrophysics Data System (ADS)

    Zhao, H. Z.; Ren, L.; Kirkpatrick, T.; Rizal, B.; Durning, R.; Ren, Z. F.; Naughton, M. J.; Chiles, T. C.; Cai, D.

    2010-03-01

    Chemical sensors based on coaxial nanocavity arrays are demonstrated. The high throughput array is developed by overlaying porous Al2O3 and Al layers on vertically aligned carbon nanotube arrays. Adsorption of molecules, such as vapors of water, methanol and ethanol, into the porous Al2O3 layer (the cavity) changes the dielectric properties of the device and leads to detectable changes in the capacitance/impedance of the nanocoax sensor. The detections were conducted in both time and frequency domains with impedance spectroscopy (1Hz-1MHz). Different chemicals exhibited different dose responses and response dynamics. A potentially characteristic 14 kHz shift of peak frequencies was observed between the spectra of acetone and ethanol. This demonstrates the concept of spectroscopic chemical sensing using high density arrays of vertical nanocavity structures. Such techniques will also be applied to biological sensing.

  3. Theory of absorption-induced transparency

    NASA Astrophysics Data System (ADS)

    Rodrigo, Sergio G.; Martín-Moreno, L.

    2014-09-01

    Absorption induced transparency consists in a transmission peak observed in holey metal films when a molecular dye is deposited on top of it [Hutchison et al., Angew. Chem. Int. Ed. 50, 2085 (2011)]. This transmission feature appears unexpectedly close to one of the absorption energies of the molecules, hence its name. Tentative explanations pointed to strong-coupling interactions between plasmons and molecules. However, we recently demonstrated the actual mechanism behind, which takes place through a strong modification of the propagation constant of holes. We also found that absorption induced transparency occurs in single holes and it is not restricted to the optical range.

  4. AL Amyloidosis

    PubMed Central

    2012-01-01

    Definition of the disease AL amyloidosis results from extra-cellular deposition of fibril-forming monoclonal immunoglobulin (Ig) light chains (LC) (most commonly of lambda isotype) usually secreted by a small plasma cell clone. Most patients have evidence of isolated monoclonal gammopathy or smoldering myeloma, and the occurrence of AL amyloidosis in patients with symptomatic multiple myeloma or other B-cell lymphoproliferative disorders is unusual. The key event in the development of AL amyloidosis is the change in the secondary or tertiary structure of an abnormal monoclonal LC, which results in instable conformation. This conformational change is responsible for abnormal folding of the LC, rich in β leaves, which assemble into monomers that stack together to form amyloid fibrils. Epidemiology AL amyloidosis is the most common type of systemic amyloidois in developed countries with an estimated incidence of 9 cases/million inhabitant/year. The average age of diagnosed patients is 65 years and less than 10% of patients are under 50. Clinical description The clinical presentation is protean, because of the wide number of tissues or organs that may be affected. The most common presenting symptoms are asthenia and dyspnoea, which are poorly specific and may account for delayed diagnosis. Renal manifestations are the most frequent, affecting two thirds of patients at presentation. They are characterized by heavy proteinuria, with nephrotic syndrome and impaired renal function in half of the patients. Heart involvement, which is present at diagnosis in more than 50% of patients, leading to restrictive cardiopathy, is the most serious complication and engages prognosis. Diagnostic methods The diagnosis relies on pathological examination of an involved site showing Congo red-positive amyloid deposits, with typical apple-green birefringence under polarized light, that stain positive with an anti-LC antibody by immunohistochemistry and/or immunofluorescence. Due to the

  5. Anti-allergic Hydroxy Fatty Acids from Typhonium blumei Explored through ChemGPS-NP.

    PubMed

    Korinek, Michal; Tsai, Yi-Hong; El-Shazly, Mohamed; Lai, Kuei-Hung; Backlund, Anders; Wu, Shou-Fang; Lai, Wan-Chun; Wu, Tung-Ying; Chen, Shu-Li; Wu, Yang-Chang; Cheng, Yuan-Bin; Hwang, Tsong-Long; Chen, Bing-Hung; Chang, Fang-Rong

    2017-01-01

    Increasing prevalence of allergic diseases with an inadequate variety of treatment drives forward search for new alternative drugs. Fatty acids, abundant in nature, are regarded as important bioactive compounds and powerful nutrients playing an important role in lipid homeostasis and inflammation. Phytochemical study on Typhonium blumei Nicolson and Sivadasan (Araceae), a folk anti-cancer and anti-inflammatory medicine, yielded four oxygenated fatty acids, 12R-hydroxyoctadec-9Z,13E-dienoic acid methyl ester (1) and 10R-hydroxyoctadec-8E,12Z-dienoic acid methyl ester (2), 9R-hydroxy-10E-octadecenoic acid methyl ester (3), and 12R(*)-hydroxy-10E-octadecenoic acid methyl ester (4). Isolated compounds were identified by spectroscopic methods along with GC-MS analysis. Isolated fatty acids together with a series of saturated, unsaturated and oxygenated fatty acids were evaluated for their anti-inflammatory and anti-allergic activities in vitro. Unsaturated (including docosahexaenoic and eicosapentaenoic acids) as well as hydroxylated unsaturated fatty acids exerted strong anti-inflammatory activity in superoxide anion generation (IC50 2.14-3.73 μM) and elastase release (IC50 1.26-4.57 μM) assays. On the other hand, in the anti-allergic assays, the unsaturated fatty acids were inactive, while hydroxylated fatty acids showed promising inhibitory activity in A23187- and antigen-induced degranulation assays (e.g., 9S-hydroxy-10E,12Z-octadecadienoic acid, IC50 92.4 and 49.7 μM, respectively). According to our results, the presence of a hydroxy group in the long chain did not influence the potent anti-inflammatory activity of free unsaturated acids. Nevertheless, hydroxylation of fatty acids (or their methyl esters) seems to be a key factor for the anti-allergic activity observed in the current study. Moreover, ChemGPS-NP was explored to predict the structure-activity relationship of fatty acids. The anti-allergic fatty acids formed different cluster distant from

  6. Sensitivity analysis of the microphysics scheme in WRF-Chem contributions to AQMEII phase 2

    NASA Astrophysics Data System (ADS)

    Baró, Rocio; Jiménez-Guerrero, Pedro; Balzarini, Alessandra; Curci, Gabriele; Forkel, Renate; Grell, Georg; Hirtl, Marcus; Honzak, Luka; Langer, Matthias; Pérez, Juan L.; Pirovano, Guido; San José, Roberto; Tuccella, Paolo; Werhahn, Johannes; Žabkar, Rahela

    2015-08-01

    The parameterization of cloud microphysics is a crucial part of fully-coupled meteorology-chemistry models, since microphysics governs the formation, growth and dissipation of hydrometeors and also aerosol cloud interactions. The main objective of this study, which is based on two simulations for Europe contributing to Phase 2 of the Air Quality Model Evaluation International Initiative (AQMEII) is to assess the sensitivity of WRF-Chem to the selection of the microphysics scheme. Two one-year simulations including aerosol cloud interactions with identical physical-chemical parameterizations except for the microphysics scheme (Morrison -MORRAT vs Lin -LINES) are compared. The study covers the difference between the simulations for two three-month periods (cold and a warm) during the year 2010, allowing thus a seasonal analysis. Overall, when comparing to observational data, no significant benefits from the selection of the microphysical schemes can be derived from the results. However, these results highlight a marked north-south pattern of differences, as well as a decisive impact of the aerosol pollution on the results. The MORRAT simulation resulted in higher cloud water mixing ratios over remote areas with low CCN concentrations, whereas the LINES simulation yields higher cloud water mixing ratios over the more polluted areas. Regarding the droplet number mixing ratio, the Morrison scheme was found to yield higher values both during winter and summer for nearly the entire model domain. As smaller and more numerous cloud droplets are more effective in scattering shortwave radiation, the downwelling shortwave radiation flux at surface was found to be up to 30 W m-2 lower for central Europe for the MORRAT simulation as compared to the simulation using the LINES simulation during wintertime. Finally, less convective precipitation is simulated over land with MORRAT during summertime, while no almost difference was found for the winter. On the other hand, non

  7. Overview of the diagenetic features analyzed by ChemCam onboard Curiosity

    NASA Astrophysics Data System (ADS)

    Mangold, N.; Forni, O.; Nachon, M.; Blaney, D. L.; Wiens, R. C.; Kah, L. C.; Kronyak, R. E.; Clegg, S. M.; Cousin, A.; Fisk, M. R.; Gasnault, O.; Grotzinger, J. P.; Lanza, N.; Lasue, J.; Le Deit, L.; Le Mouelic, S.; Maurice, S.; Meslin, P. Y.; Rapin, W.; Newsom, H. E.; Sumner, D. Y.

    2015-12-01

    The Curiosity rover has encountered a variety of sedimentary rocks with significant variations in both texture and composition. Most of the sandstones and mudstones are interpreted as having been deposited in a fluvio-lacustrine environment, as analyzed in details in the waypoints named Yellowknife Bay, Kimberley and Pahrump. All of these sediments have been crossed by diagenetic features of different composition. Light-toned Ca-sulfate veins observed initially at Yellowknife Bay were observed along the traverse, and in high density at the Pahrump location. As they appear in all sediments and show straight fractures, they correspond to late-stage diagenetic features, due to fluid circulation, with fractures probably due to hydraulic stress at depth. In contrast to light-toned veins, earlier-stage diagenetic features have shown variable composition in the three areas. At Yellowknife Bay, raised ridges display enriched Mg proportion, probably linked to Mg-clay whereas outcrops at Kimberley display fracture fills enriched in Mn and Zn. Pahrump displays a large variety of diagenetic features distinct from these previous examples. Mg-enriched concretions contain S and abundant Ni. Mg enrichments have also been observed in resistant zones along fractures and in resistant layers. Locally concretions also display high Fe, S-bearing material interpreted as Fe-sulfate, probably jarosite. A special location named Garden City at the top of the Parhump sequence displays a complex area with light-toned veins surrounded by darker veins. The latter display strong Ca signatures correlated with F, interpreted as fluorite. No C or S emissions were observed that could alternatively explain the high Ca abundance by carbonates or sulfates. The dark tone of the F-bearing minerals may be due to the presence of Fe. These specific dark veins could derive from the leaching of F-apatite, a mineral that has been observed both in the sandstones and in some of the igneous clasts analyzed by Chem

  8. WRF-Chem simulations of aerosols and anthropogenic aerosol radiative forcing in East Asia

    NASA Astrophysics Data System (ADS)

    Gao, Yi; Zhao, Chun; Liu, Xiaohong; Zhang, Meigen; Leung, L. Ruby

    2014-08-01

    This study aims to provide a first comprehensive evaluation of WRF-Chem for modeling aerosols and anthropogenic aerosol radiative forcing (RF, including direct, semi-direct and indirect forcing) over East Asia. Several numerical experiments were conducted from November 2007 to December 2008. Comparison between model results and observations shows that the model can generally reproduce the observed spatial distributions of aerosol concentration, aerosol optical depth (AOD) and single scattering albedo (SSA) from measurements at many sites, including the relatively higher aerosol concentration and AOD over East China and the relatively lower AOD over Southeast Asia, Korea, and Japan. The model also depicts the seasonal variation and transport of pollutions over East Asia. Particulate matter of 10 μm or less in the aerodynamic diameter (PM10), black carbon (BC), sulfate (SO42-), nitrate (NO3-) and ammonium (NH4+) concentrations are higher in spring than other seasons in Japan, which indicates the possible influence of pollutant transport from polluted area of East Asia. The model underestimates SO42- and organic carbon (OC) concentrations over mainland China by about a factor of 2, while overestimates NO3- concentration in autumn along the Yangtze River. The model captures the dust events at the Zhangye site in the semi-arid region of China. AOD is high over Southwest and Central China in winter and spring and over North China in winter, spring and summer while is low over South China in summer due to monsoon precipitation. SSA is lowest in winter and highest in summer. Anthropogenic aerosol RF is estimated to range from -5 to -20 W m-2 over land and -20 to -40 W m-2 over adjacent oceans at the top of atmosphere (TOA), 5-30 W m-2 in the atmosphere (ATM) and -15 to -40 W m-2 at the bottom (BOT). The warming effect of anthropogenic aerosol in ATM results from BC aerosol while the negative aerosol RF at TOA is caused by scattering aerosols such as SO42-, NO3- and NH4

  9. Anti-allergic Hydroxy Fatty Acids from Typhonium blumei Explored through ChemGPS-NP

    PubMed Central

    Korinek, Michal; Tsai, Yi-Hong; El-Shazly, Mohamed; Lai, Kuei-Hung; Backlund, Anders; Wu, Shou-Fang; Lai, Wan-Chun; Wu, Tung-Ying; Chen, Shu-Li; Wu, Yang-Chang; Cheng, Yuan-Bin; Hwang, Tsong-Long; Chen, Bing-Hung; Chang, Fang-Rong

    2017-01-01

    Increasing prevalence of allergic diseases with an inadequate variety of treatment drives forward search for new alternative drugs. Fatty acids, abundant in nature, are regarded as important bioactive compounds and powerful nutrients playing an important role in lipid homeostasis and inflammation. Phytochemical study on Typhonium blumei Nicolson and Sivadasan (Araceae), a folk anti-cancer and anti-inflammatory medicine, yielded four oxygenated fatty acids, 12R-hydroxyoctadec-9Z,13E-dienoic acid methyl ester (1) and 10R-hydroxyoctadec-8E,12Z-dienoic acid methyl ester (2), 9R-hydroxy-10E-octadecenoic acid methyl ester (3), and 12R*-hydroxy-10E-octadecenoic acid methyl ester (4). Isolated compounds were identified by spectroscopic methods along with GC-MS analysis. Isolated fatty acids together with a series of saturated, unsaturated and oxygenated fatty acids were evaluated for their anti-inflammatory and anti-allergic activities in vitro. Unsaturated (including docosahexaenoic and eicosapentaenoic acids) as well as hydroxylated unsaturated fatty acids exerted strong anti-inflammatory activity in superoxide anion generation (IC50 2.14–3.73 μM) and elastase release (IC50 1.26–4.57 μM) assays. On the other hand, in the anti-allergic assays, the unsaturated fatty acids were inactive, while hydroxylated fatty acids showed promising inhibitory activity in A23187- and antigen-induced degranulation assays (e.g., 9S-hydroxy-10E,12Z-octadecadienoic acid, IC50 92.4 and 49.7 μM, respectively). According to our results, the presence of a hydroxy group in the long chain did not influence the potent anti-inflammatory activity of free unsaturated acids. Nevertheless, hydroxylation of fatty acids (or their methyl esters) seems to be a key factor for the anti-allergic activity observed in the current study. Moreover, ChemGPS-NP was explored to predict the structure-activity relationship of fatty acids. The anti-allergic fatty acids formed different cluster distant from

  10. ChemR23 Dampens Lung Inflammation and Enhances Anti-viral Immunity in a Mouse Model of Acute Viral Pneumonia

    PubMed Central

    de Nadai, Patricia; Glineur, Stéphanie; De Henau, Olivier; Luangsay, Souphalone; Van Gool, Frédéric; Communi, David; De Vuyst, Paul; Desmecht, Daniel; Parmentier, Marc

    2011-01-01

    Viral diseases of the respiratory tract, which include influenza pandemic, children acute bronchiolitis, and viral pneumonia of the elderly, represent major health problems. Plasmacytoid dendritic cells play an important role in anti-viral immunity, and these cells were recently shown to express ChemR23, the receptor for the chemoattractant protein chemerin, which is expressed by epithelial cells in the lung. Our aim was to determine the role played by the chemerin/ChemR23 system in the physiopathology of viral pneumonia, using the pneumonia virus of mice (PVM) as a model. Wild-type and ChemR23 knock-out mice were infected by PVM and followed for functional and inflammatory parameters. ChemR23−/− mice displayed higher mortality/morbidity, alteration of lung function, delayed viral clearance and increased neutrophilic infiltration. We demonstrated in these mice a lower recruitment of plasmacytoid dendritic cells and a reduction in type I interferon production. The role of plasmacytoid dendritic cells was further addressed by performing depletion and adoptive transfer experiments as well as by the generation of chimeric mice, demonstrating two opposite effects of the chemerin/ChemR23 system. First, the ChemR23-dependent recruitment of plasmacytoid dendritic cells contributes to adaptive immune responses and viral clearance, but also enhances the inflammatory response. Second, increased morbidity/mortality in ChemR23−/− mice is not due to defective plasmacytoid dendritic cells recruitment, but rather to the loss of an anti-inflammatory pathway involving ChemR23 expressed by non-leukocytic cells. The chemerin/ChemR23 system plays important roles in the physiopathology of viral pneumonia, and might therefore be considered as a therapeutic target for anti-viral and anti-inflammatory therapies. PMID:22072972

  11. ChemR23 dampens lung inflammation and enhances anti-viral immunity in a mouse model of acute viral pneumonia.

    PubMed

    Bondue, Benjamin; Vosters, Olivier; de Nadai, Patricia; Glineur, Stéphanie; De Henau, Olivier; Luangsay, Souphalone; Van Gool, Frédéric; Communi, David; De Vuyst, Paul; Desmecht, Daniel; Parmentier, Marc

    2011-11-01

    Viral diseases of the respiratory tract, which include influenza pandemic, children acute bronchiolitis, and viral pneumonia of the elderly, represent major health problems. Plasmacytoid dendritic cells play an important role in anti-viral immunity, and these cells were recently shown to express ChemR23, the receptor for the chemoattractant protein chemerin, which is expressed by epithelial cells in the lung. Our aim was to determine the role played by the chemerin/ChemR23 system in the physiopathology of viral pneumonia, using the pneumonia virus of mice (PVM) as a model. Wild-type and ChemR23 knock-out mice were infected by PVM and followed for functional and inflammatory parameters. ChemR23(-/-) mice displayed higher mortality/morbidity, alteration of lung function, delayed viral clearance and increased neutrophilic infiltration. We demonstrated in these mice a lower recruitment of plasmacytoid dendritic cells and a reduction in type I interferon production. The role of plasmacytoid dendritic cells was further addressed by performing depletion and adoptive transfer experiments as well as by the generation of chimeric mice, demonstrating two opposite effects of the chemerin/ChemR23 system. First, the ChemR23-dependent recruitment of plasmacytoid dendritic cells contributes to adaptive immune responses and viral clearance, but also enhances the inflammatory response. Second, increased morbidity/mortality in ChemR23(-/-) mice is not due to defective plasmacytoid dendritic cells recruitment, but rather to the loss of an anti-inflammatory pathway involving ChemR23 expressed by non-leukocytic cells. The chemerin/ChemR23 system plays important roles in the physiopathology of viral pneumonia, and might therefore be considered as a therapeutic target for anti-viral and anti-inflammatory therapies.

  12. Calibration of the Fluorine, Chlorine and Hydrogen Content of Apatites With the ChemCam LIBS Instrument

    NASA Technical Reports Server (NTRS)

    Meslin, P.-Y.; Cicutto, L.; Forni, O.; Drouet, C.; Rapin, W.; Nachon, M.; Cousin, A.; Blank, J. G.; McCubbin, F. M.; Gasnault, O.; hide

    2016-01-01

    Determining the composition of apatites is important to understand the behavior of volatiles during planetary differentiation. Apatite is an ubiquitous magmatic mineral in the SNC meteorites. It is a significant reservoir of halogens in these meteorites and has been used to estimate the halogen budget of Mars. Apatites have been identified in sandstones and pebbles at Gale crater by ChemCam, a Laser-Induced Breakdown Spectroscometer (LIBS) instrument onboard the Curiosity rover. Their presence was inferred from correlations between calcium, fluorine (using the CaF molecular band centered near 603 nm, whose detection limit is much lower that atomic or ionic lines and, in some cases, phosphorus (whose detection limit is much larger). An initial quantification of fluorine, based on fluorite (CaF2)/basalt mixtures and obtained at the LANL laboratory, indicated that the excess of F/Ca (compared to the stoichiometry of pure fluorapatites) found on Mars in some cases could be explained by the presence of fluorite. Chlorine was not detected in these targets, at least above a detection limit of 0.6 wt% estimated from. Fluorapatite was later also detected by X-ray diffraction (with CheMin) at a level of approx.1wt% in the Windjana drill sample (Kimberley area), and several points analyzed by ChemCam in this area also revealed a correlation between Ca and F. The in situ detection of F-rich, Cl-poor apatites contrasts with the Cl-rich, F-poor compositions of apatites found in basaltic shergottites and in gabbroic clasts from the martian meteorite NWA 7034, which were also found to be more Cl-rich than apatites from basalts on Earth, the Moon, or Vesta. The in situ observations could call into question one of the few possible explanations brought forward to explain the SNC results, namely that Mars may be highly depleted in fluorine. The purpose of the present study is to refine the calibration of the F, Cl, OH and P signals measured by the ChemCam LIBS instrument, initiated

  13. Modeling of the chemical composition of fine particulate matter: Development and performance assessment of EASYWRF-Chem

    NASA Astrophysics Data System (ADS)

    Mendez, M.; Lebègue, P.; Visez, N.; Fèvre-Nollet, V.; Crenn, V.; Riffault, V.; Petitprez, D.

    2016-03-01

    The European emission Adaptation SYstem for the WRF-Chem model (EASYWRF-Chem) has been developed to generate chemical information supporting the WRF-Chem requirements from any emission inventory based on the CORINAIR methodology. Using RADM2 and RACM2 mechanisms, "emission species" are converted into "model species" thanks to the SAPRC methodology for gas phase pollutant and the PM10 and PM2.5 fractions. Furthermore, by adapting US EPA PM2.5 profiles, the processing of aerosol chemical speciation profiles separates the unspeciated PM2.5 emission into five chemical families: sulfates, nitrates, elemental carbon, organic aerosol and unspeciated aerosol. The evaluation of the model has been performed by separately comparing model outcomes with (i) meteorological measurements; (ii) NO2, O3, PM10 and PM2.5 mass concentrations from the regional air quality monitoring network; (iii) hourly-resolved data from four field campaign measurements, in winter and in summer, on two sites in the French northern region. In the latter, a High Resolution - Time of Flight - Aerosol Mass Spectrometer (HR-ToF-AMS) provided non-refractory PM1 concentrations of sulfate, nitrate and ammonium ions as well as organic matter (OM), while an aethalometer provided black carbon (BC) concentrations in the PM2.5 fraction. Meteorological data (temperature, wind, relative humidity) are well simulated for all the time series data except for specific events as wind direction changes or rainfall. For particulate matter, results are presented by considering firstly the total mass concentration of PM2.5 and PM10. EASYWRF-Chem simulations overestimated the PM10 mass concentrations by + 22% and + 4% for summer and winter periods respectively, whereas for the finer PM2.5 fraction, mass concentrations were overestimated by + 20% in summer and underestimated by - 13% in winter. Simulated sulfate concentrations were underestimated and nitrate concentrations were overestimated but hourly variations were well

  14. Al-doping influence on crystal growth of Ni-Al alloy: Experimental testing of a theoretical model

    NASA Astrophysics Data System (ADS)

    Rong, Xi-Ming; Chen, Jun; Li, Jing-Tian; Zhuang, Jun; Ning, Xi-Jing

    2015-12-01

    Recently, a condensing potential model was developed to evaluate the crystallization ability of bulk materials [Ye X X, Ming C, Hu Y C and Ning X J 2009 J. Chem. Phys. 130 164711 and Peng K, Ming C, Ye X X, Zhang W X, Zhuang J and Ning X J 2011 Chem. Phys. Lett. 501 330], showing that the best temperature for single crystal growth is about 0.6Tm, where Tm is the melting temperature, and for Ni-Al alloy, more than 6 wt% of Al-doping will badly reduce the crystallization ability. In order to verify these predictions, we fabricated Ni-Al films with different concentrations of Al on Si substrates at room temperature by pulsed laser deposition, and post-annealed the films at 833, 933, 1033 (˜ 0.6Tm), 1133, and 1233 K in vacuum furnace, respectively. The x-ray diffraction spectra show that annealing at 0.6Tm is indeed best for larger crystal grain formation, and the film crystallization ability remarkably declines with more than 6-wt% Al doping. Project supported by the Specialized Research Fund for the Doctoral Program of Higher Education, China (Grant No. 20130071110018) and the National Natural Science Foundation of China (Grant No. 11274073).

  15. Classical trajectories of the continuum states of the \\chem{\\cal{PT}} symmetric Scarf II potential

    NASA Astrophysics Data System (ADS)

    Sinha, Anjana

    2012-06-01

    We apply the factorization technique developed by Kuru et al. (Ann. Phys. (N.Y.), 323 (2008) 413) to obtain the exact analytical classical trajectories and momenta of the continuum states of the non-Hermitian but {\\cal {PT}} symmetric Scarf II potential. In particular, we observe that the strange behaviour of the quantum version at the spectral singularity has an interesting classical analogue.

  16. Modelling the urban air quality in Hamburg with the new city-scale chemistry transport model CityChem

    NASA Astrophysics Data System (ADS)

    Karl, Matthias; Ramacher, Martin; Aulinger, Armin; Matthias, Volker; Quante, Markus

    2017-04-01

    Air quality modelling plays an important role by providing guidelines for efficient air pollution abatement measures. Currently, most urban dispersion models treat air pollutants as passive tracer substances or use highly simplified chemistry when simulating air pollutant concentrations on the city-scale. The newly developed urban chemistry-transport model CityChem has the capability of modelling the photochemical transformation of multiple pollutants along with atmospheric diffusion to produce pollutant concentration fields for the entire city on a horizontal resolution of 100 m or even finer and a vertical resolution of 24 layers up to 4000 m height. CityChem is based on the Eulerian urban dispersion model EPISODE of the Norwegian Institute for Air Research (NILU). CityChem treats the complex photochemistry in cities using detailed EMEP chemistry on an Eulerian 3-D grid, while using simple photo-stationary equilibrium on a much higher resolution grid (receptor grid), i.e. close to industrial point sources and traffic sources. The CityChem model takes into account that long-range transport contributes to urban pollutant concentrations. This is done by using 3-D boundary concentrations for the city domain derived from chemistry-transport simulations with the regional air quality model CMAQ. For the study of the air quality in Hamburg, CityChem was set-up with a main grid of 30×30 grid cells of 1×1 km2 each and a receptor grid of 300×300 grid cells of 100×100 m2. The CityChem model was driven with meteorological data generated by the prognostic meteorology component of the Australian chemistry-transport model TAPM. Bottom-up inventories of emissions from traffic, industry, households were based on data of the municipality of Hamburg. Shipping emissions for the port of Hamburg were taken from the Clean North Sea Shipping project. Episodes with elevated ozone (O3) were of specific interest for this study, as these are associated with exceedances of the World

  17. Development of a Grid-Independent Geos-Chem Chemical Transport Model (v9-02) as an Atmospheric Chemistry Module for Earth System Models

    NASA Technical Reports Server (NTRS)

    Long, M. S.; Yantosca, R.; Nielsen, J. E; Keller, C. A.; Da Silva, A.; Sulprizio, M. P.; Pawson, S.; Jacob, D. J.

    2015-01-01

    The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been re-engineered to also serve as an atmospheric chemistry module for Earth system models (ESMs). This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of the GEOSChem scientific code, permitting the exact same GEOSChem code to be used as an ESM module or as a standalone CTM. In this manner, the continual stream of updates contributed by the CTM user community is automatically passed on to the ESM module, which remains state of science and referenced to the latest version of the standard GEOS-Chem CTM. A major step in this re-engineering was to make GEOS-Chem grid independent, i.e., capable of using any geophysical grid specified at run time. GEOS-Chem data sockets were also created for communication between modules and with external ESM code. The grid-independent, ESMF-compatible GEOS-Chem is now the standard version of the GEOS-Chem CTM. It has been implemented as an atmospheric chemistry module into the NASA GEOS- 5 ESM. The coupled GEOS-5-GEOS-Chem system was tested for scalability and performance with a tropospheric oxidant-aerosol simulation (120 coupled species, 66 transported tracers) using 48-240 cores and message-passing interface (MPI) distributed-memory parallelization. Numerical experiments demonstrate that the GEOS-Chem chemistry module scales efficiently for the number of cores tested, with no degradation as the number of cores increases. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemistry module means that the relative cost goes down with increasing number of cores in a massively parallel environment.

  18. CHEM2D-OPP: A New Linearized Gas-Phased Ozone Photochemistry Parameterization for HIih-Altitude NWP and Climate Models

    DTIC Science & Technology

    2006-01-01

    middle atmospheric photochemical transport model. We evaluate CHEM2D-OPP performance using both short-term (6-day) and long-term (1-year) strato - spheric...processes become progressively more important than transport effects with increasing height. We define the local photochemical tendency of strato ...ozone production rates. CHEM2D-OPP is intended for use throughout the strato - sphere and lower mesosphere. At the higher altitudes of this region

  19. Comment on ``High order finite difference algorithms for solving the Schrödinger equation in molecular dynamics'' [J. Chem. Phys. 111, 10827 (1999)

    NASA Astrophysics Data System (ADS)

    Mazziotti, David A.

    2001-10-01

    The spectral difference methods [D. A. Mazziotti, Chem. Phys. Lett. 299, 473 (1999)] for solving differential equations in chemical physics combine the useful features of matrix sparsity and rapid convergence. In their recent article [J. Chem. Phys. 111, 10827 (1999)] Guantes and Farantos incorrectly classify the Lagrange distributed approximating functional (LDAF) method in the category of finite differences. This comment clarifies the connections among higher-order finite difference, Lagrange distributed approximating functionals, and other spectral difference methods.

  20. Development of a Grid-Independent Geos-Chem Chemical Transport Model (v9-02) as an Atmospheric Chemistry Module for Earth System Models

    NASA Technical Reports Server (NTRS)

    Long, M. S.; Yantosca, R.; Nielsen, J. E; Keller, C. A.; Da Silva, A.; Sulprizio, M. P.; Pawson, S.; Jacob, D. J.

    2015-01-01

    The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been re-engineered to also serve as an atmospheric chemistry module for Earth system models (ESMs). This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of the GEOSChem scientific code, permitting the exact same GEOSChem code to be used as an ESM module or as a standalone CTM. In this manner, the continual stream of updates contributed by the CTM user community is automatically passed on to the ESM module, which remains state of science and referenced to the latest version of the standard GEOS-Chem CTM. A major step in this re-engineering was to make GEOS-Chem grid independent, i.e., capable of using any geophysical grid specified at run time. GEOS-Chem data sockets were also created for communication between modules and with external ESM code. The grid-independent, ESMF-compatible GEOS-Chem is now the standard version of the GEOS-Chem CTM. It has been implemented as an atmospheric chemistry module into the NASA GEOS- 5 ESM. The coupled GEOS-5-GEOS-Chem system was tested for scalability and performance with a tropospheric oxidant-aerosol simulation (120 coupled species, 66 transported tracers) using 48-240 cores and message-passing interface (MPI) distributed-memory parallelization. Numerical experiments demonstrate that the GEOS-Chem chemistry module scales efficiently for the number of cores tested, with no degradation as the number of cores increases. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemistry module means that the relative cost goes down with increasing number of cores in a massively parallel environment.

  1. Dynamic Solvent Effects on Electron Transfer Rates in the Inverted Regime: Ultrafast Studies on the Betaines

    DTIC Science & Technology

    1991-05-06

    vol 3, eds. H. Ratajczak and W.J. Orville-Thomas, John Wiley & Sons Ltd. (1982); (b) K. Dimroth, C. Reichardt, T. Siepmann and F. Bohlmann, Justus ... Liebigs Ann. Chem. 681, 1 (1963); (c) C. Reichardt, Angew. Chem. Int. Ed. Engl. 18, 98 (1979). 10. A.M. Kjaer and J. Ulstrup, J. Am. Chem. Soc. 109, 1934

  2. Application of WRF/Chem over East Asia: Part I. Model evaluation and intercomparison with MM5/CMAQ

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Zhang, Xin; Wang, Litao; Zhang, Qiang; Duan, Fengkui; He, Kebin

    2016-01-01

    In this work, the application of the online-coupled Weather Research and Forecasting model with chemistry (WRF/Chem) version 3.3.1 is evaluated over East Asia for January, April, July, and October 2005 and compared with results from a previous application of an offline model system, i.e., the Mesoscale Model and Community Multiple Air Quality modeling system (MM5/CMAQ). The evaluation of WRF/Chem is performed using multiple observational datasets from satellites and surface networks in mainland China, Hong Kong, Taiwan, and Japan. WRF/Chem simulates well specific humidity (Q2) and downward longwave and shortwave radiation (GLW and GSW) with normalized mean biases (NMBs) within 24%, but shows moderate to large biases for temperature at 2-m (T2) (NMBs of -9.8% to 75.6%) and precipitation (NMBs of 11.4-92.7%) for some months, and wind speed at 10-m (WS10) (NMBs of 66.5-101%), for all months, indicating some limitations in the YSU planetary boundary layer scheme, the Purdue Lin cloud microphysics, and the Grell-Devenyi ensemble scheme. WRF/Chem can simulate the column abundances of gases reasonably well with NMBs within 30% for most months but moderately to significantly underpredicts the surface concentrations of major species at all sites in nearly all months with NMBs of -72% to -53.8% for CO, -99.4% to -61.7% for NOx, -84.2% to -44.5% for SO2, -63.9% to -25.2% for PM2.5, and -68.9% to 33.3% for PM10, and aerosol optical depth in all months except for October with NMBs of -38.7% to -16.2%. The model significantly overpredicts surface concentrations of O3 at most sites in nearly all months with NMBs of up to 160.3% and NO3- at the Tsinghua site in all months. Possible reasons for large underpredictions include underestimations in the anthropogenic emissions of CO, SO2, and primary aerosol, inappropriate vertical distributions of emissions of SO2 and NO2, uncertainties in upper boundary conditions (e.g., for O3 and CO), missing or inaccurate model representations (e

  3. Response to "Comment on `Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond"' [J. Chem. Phys. 145, 147104 (2016)

    NASA Astrophysics Data System (ADS)

    Zhou, Peijie; Li, Tiejun

    2016-10-01

    The uniqueness issue of SDE decomposition theory proposed by Ao and his co-workers has recently been discussed. A comprehensive study to investigate connections among different landscape theories [J. Chem. Phys. 144, 094109 (2016)] has pointed out that the decomposition is generally not unique, while Ao et al. recently argue that such conclusions are "incorrect" because the uniqueness of the decomposition for Ornstein-Uhlenbeck (O-U) process has been claimed before. In this response, we will demonstrate that the claimed "uniqueness" of the O-U process decomposition is invalid to serve as a counterexample according to the original definition of SDE decomposition. The absence of effective and concrete boundary conditions in previous SDE decomposition papers will be pointed out, and some other issues in the comment will also be responded.

  4. Twelve-month, 12 km resolution North American WRF-Chem v3.4 air quality simulation: performance evaluation

    DOE PAGES

    Tessum, C. W.; Hill, J. D.; Marshall, J. D.

    2015-04-07

    We present results from and evaluate the performance of a 12-month, 12 km horizontal resolution year 2005 air pollution simulation for the contiguous United States using the WRF-Chem (Weather Research and Forecasting with Chemistry) meteorology and chemical transport model (CTM). We employ the 2005 US National Emissions Inventory, the Regional Atmospheric Chemistry Mechanism (RACM), and the Modal Aerosol Dynamics Model for Europe (MADE) with a volatility basis set (VBS) secondary aerosol module. Overall, model performance is comparable to contemporary modeling efforts used for regulatory and health-effects analysis, with an annual average daytime ozone (O3) mean fractional bias (MFB) of 12%more » and an annual average fine particulate matter (PM2.5) MFB of −1%. WRF-Chem, as configured here, tends to overpredict total PM2.5 at some high concentration locations and generally overpredicts average 24 h O3 concentrations. Performance is better at predicting daytime-average and daily peak O3 concentrations, which are more relevant for regulatory and health effects analyses relative to annual average values. Predictive performance for PM2.5 subspecies is mixed: the model overpredicts particulate sulfate (MFB = 36%), underpredicts particulate nitrate (MFB = −110%) and organic carbon (MFB = −29%), and relatively accurately predicts particulate ammonium (MFB = 3%) and elemental carbon (MFB = 3%), so that the accuracy in total PM2.5 predictions is to some extent a function of offsetting over- and underpredictions of PM2.5 subspecies. Model predictive performance for PM2.5 and its subspecies is in general worse in winter and in the western US than in other seasons and regions, suggesting spatial and temporal opportunities for future WRF-Chem model development and evaluation.« less

  5. Nonlinear mapping technique for data visualization and clustering assessment of LIBS data: application to ChemCam data

    NASA Astrophysics Data System (ADS)

    Lasue, Jeremie; Wiens, Roger; Stepinski, Tom; Forni, Olivier; Clegg, Samuel; Maurice, Sylvestre; Chemcam Team

    2011-02-01

    ChemCam is a remote laser-induced breakdown spectroscopy (LIBS) instrument that will arrive on Mars in 2012, on-board the Mars Science Laboratory Rover. The LIBS technique is crucial to accurately identify samples and quantify elemental abundances at various distances from the rover. In this study, we compare different linear and nonlinear multivariate techniques to visualize and discriminate clusters in two dimensions (2D) from the data obtained with ChemCam. We have used principal components analysis (PCA) and independent components analysis (ICA) for the linear tools and compared them with the nonlinear Sammon's map projection technique. We demonstrate that the Sammon's map gives the best 2D representation of the data set, with optimization values from 2.8% to 4.3% (0% is a perfect representation), together with an entropy value of 0.81 for the purity of the clustering analysis. The linear 2D projections result in three (ICA) and five times (PCA) more stress, and their clustering purity is more than twice higher with entropy values about 1.8. We show that the Sammon's map algorithm is faster and gives a slightly better representation of the data set if the initial conditions are taken from the ICA projection rather than the PCA projection. We conclude that the nonlinear Sammon's map projection is the best technique for combining data visualization and clustering assessment of the ChemCam LIBS data in 2D. PCA and ICA projections on more dimensions would improve on these numbers at the cost of the intuitive interpretation of the 2D projection by a human operator.

  6. Nonlinear mapping technique for data visualization and clustering assessment of LIBS data: application to ChemCam data.

    PubMed

    Lasue, J; Wiens, R C; Stepinski, T F; Forni, O; Clegg, S M; Maurice, S

    2011-07-01

    ChemCam is a remote laser-induced breakdown spectroscopy (LIBS) instrument that will arrive on Mars in 2012, on-board the Mars Science Laboratory Rover. The LIBS technique is crucial to accurately identify samples and quantify elemental abundances at various distances from the rover. In this study, we compare different linear and nonlinear multivariate techniques to visualize and discriminate clusters in two dimensions (2D) from the data obtained with ChemCam. We have used principal components analysis (PCA) and independent components analysis (ICA) for the linear tools and compared them with the nonlinear Sammon's map projection technique. We demonstrate that the Sammon's map gives the best 2D representation of the data set, with optimization values from 2.8% to 4.3% (0% is a perfect representation), together with an entropy value of 0.81 for the purity of the clustering analysis. The linear 2D projections result in three (ICA) and five times (PCA) more stress, and their clustering purity is more than twice higher with entropy values about 1.8. We show that the Sammon's map algorithm is faster and gives a slightly better representation of the data set if the initial conditions are taken from the ICA projection rather than the PCA projection. We conclude that the nonlinear Sammon's map projection is the best technique for combining data visualization and clustering assessment of the ChemCam LIBS data in 2D. PCA and ICA projections on more dimensions would improve on these numbers at the cost of the intuitive interpretation of the 2D projection by a human operator.

  7. Twelve-month, 12 km resolution North American WRF-Chem v3.4 air quality simulation: performance evaluation

    NASA Astrophysics Data System (ADS)

    Tessum, C. W.; Hill, J. D.; Marshall, J. D.

    2015-04-01

    We present results from and evaluate the performance of a 12-month, 12 km horizontal resolution year 2005 air pollution simulation for the contiguous United States using the WRF-Chem (Weather Research and Forecasting with Chemistry) meteorology and chemical transport model (CTM). We employ the 2005 US National Emissions Inventory, the Regional Atmospheric Chemistry Mechanism (RACM), and the Modal Aerosol Dynamics Model for Europe (MADE) with a volatility basis set (VBS) secondary aerosol module. Overall, model performance is comparable to contemporary modeling efforts used for regulatory and health-effects analysis, with an annual average daytime ozone (O3) mean fractional bias (MFB) of 12% and an annual average fine particulate matter (PM2.5) MFB of -1%. WRF-Chem, as configured here, tends to overpredict total PM2.5 at some high concentration locations and generally overpredicts average 24 h O3 concentrations. Performance is better at predicting daytime-average and daily peak O3 concentrations, which are more relevant for regulatory and health effects analyses relative to annual average values. Predictive performance for PM2.5 subspecies is mixed: the model overpredicts particulate sulfate (MFB = 36%), underpredicts particulate nitrate (MFB = -110%) and organic carbon (MFB = -29%), and relatively accurately predicts particulate ammonium (MFB = 3%) and elemental carbon (MFB = 3%), so that the accuracy in total PM2.5 predictions is to some extent a function of offsetting over- and underpredictions of PM2.5 subspecies. Model predictive performance for PM2.5 and its subspecies is in general worse in winter and in the western US than in other seasons and regions, suggesting spatial and temporal opportunities for future WRF-Chem model development and evaluation.

  8. Simulations of the Holuhraun eruption 2014 with WRF-Chem and evaluation with satellite and ground based SO2 measurements

    NASA Astrophysics Data System (ADS)

    Hirtl, Marcus; Arnold-Arias, Delia; Flandorfer, Claudia; Maurer, Christian; Mantovani, Simone; Natali, Stefano

    2016-04-01

    Volcanic eruptions, with gas or/and particle emissions, directly influence our environment, with special significance when they either occur near inhabited regions or are transported towards them. In addition to the well-known affectation of air traffic, with large economic impacts, the ground touching plumes can lead directly to an influence of soil, water and even to a decrease of air quality. The eruption of Holuhraun in August 2014 in central Iceland is the country's largest lava and gas eruption since the Lakagígar eruption in 1783. Nevertheless, very little volcanic ash was produced. The main atmospheric threat from this event was the SO2 pollution that frequently violated the Icelandic National Air Quality Standards in many population centers. However, the SO2 affectation was not limited to Iceland but extended to mainland Europe. The on-line coupled model WRF-Chem is used to simulate the dispersion of SO2 for this event that affected the central European regions. The volcanic emissions are considered in addition to the anthropogenic and biogenic ground sources at European scale. A modified version of WRF-Chem version 4.1 is used in order to use time depending injection heights and mass fluxes which were obtained from in situ observations. WRF-Chem uses complex gas- (RADM2) and aerosol- (MADE-SORGAM) chemistry and is operated on a European domain (12 km resolution), and a nested grid covering the Alpine region (4 km resolution). The study is showing the evaluation of the model simulations with satellite and ground based measurement data of SO2. The analysis is conducted on a data management platform, which is currently developed in the frame of the ESA-funded project TAMP "Technology and Atmospheric Mission Platform": it provides comprehensive functionalities to visualize and numerically compare data from different sources (model, satellite and ground-measurements).

  9. Assessing regional scale predictions of aerosols, marine stratocumulus, and their interactions during VOCALS-REx using WRF-Chem

    NASA Astrophysics Data System (ADS)

    Yang, Q.; Gustafson, W. I., Jr.; Fast, J. D.; Wang, H.; Easter, R. C.; Morrison, H.

    2011-08-01

    In the recent chemistry version (v3.3) of the Weather Research and Forecasting (WRF-Chem) model, we have coupled the Morrison double-moment microphysics scheme with interactive aerosols so that two-way aerosol-cloud interactions are included in the simulations. We have used this new WRF-Chem functionality in a study focused on assessing predictions of aerosols, marine stratocumulus clouds, and their interactions over the Southeast Pacific using measurements from the VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) and satellite retrievals. This study also serves as a detailed analysis of our WRF-Chem simulations contributed to the VOCALS model Assessment (VOCA) project. The WRF-Chem 31-day (15 October-16 November 2008) simulation with aerosol-cloud interactions (AERO hereafter) is also compared to a simulation (MET hereafter) with fixed cloud droplet number concentrations assumed by the default in Morrison microphysics scheme with no interactive aerosols. The well-predicted aerosol properties such as number, mass composition, and optical depth lead to significant improvements in many features of the simulated stratocumulus clouds: cloud optical properties and microphysical properties such as cloud top effective radius, cloud water path, and cloud optical thickness, and cloud macrostructure such as cloud depth and cloud base height. In addition to accounting for the aerosol direct and semi-direct effects, these improvements feed back to the prediction of boundary-layer characteristics and energy budgets. Particularly, inclusion of interactive aerosols in AERO strengthens the temperature and humidity gradients within the capping inversion layer and lowers the marine boundary layer depth by 150 m from that of the MET simulation. Mean top-of-the-atmosphere outgoing shortwave fluxes, surface latent heat, and surface downwelling longwave fluxes are in better agreement with observations in AERO, compared to the MET simulation. Nevertheless, biases

  10. Comment on “On the quantum theory of molecules” [J. Chem. Phys. 137, 22A544 (2012)

    SciTech Connect

    Sutcliffe, Brian T.; Woolley, R. Guy

    2014-01-21

    In our previous paper [B. T. Sutcliffe and R. G. Woolley, J. Chem. Phys. 137, 22A544 (2012)] we argued that the Born-Oppenheimer approximation could not be based on an exact transformation of the molecular Schrödinger equation. In this Comment we suggest that the fundamental reason for the approximate nature of the Born-Oppenheimer model is the lack of a complete set of functions for the electronic space, and the need to describe the continuous spectrum using spectral projection.

  11. Assessment of particulate accumulation climatology under inversions in Glacier Bay for the 2008 tourist season using WRF/Chem data

    NASA Astrophysics Data System (ADS)

    Pirhalla, Michael A.

    Each summer, roughly one million tourists come to Southeast Alaska aboard cruise ships to see the pristine landscape and wildlife. Tourism is an integral component in the economy for most of the towns and villages on the Alaska Panhandle. With ship emissions only modestly regulated, there have been some concerns regarding the potential environmental impacts that cruise ships have on air quality, wildlife, and visitor experience. Cruise ships travel to remote regions, and are frequently the only anthropogenic emissions source in federally protected parks, such as Glacier Bay National Park and Preserve. In the absence of winds and synoptic scale storm systems common in the Gulf of Alaska, temperature inversions frequently develop inside Glacier Bay due to radiative cooling influenced by the complex topography inside the park. Inversions act as a lid, and may trap pollutants from cruise-ship emissions depending on the meteorological conditions present. Since meteorological observations are sparse and frequently skewed to easily accessible locations, data from the Weather Research and Forecasting Model, coupled with a chemistry package (WRF/Chem), were used to examine the physical and chemical processes that are impossible to determine through direct observations. Model simulation data for 124 days during the 2008 tourist season (May 15 to September 15), including a cruise-ship emission inventory for all 225 cruise ship entries in Glacier Bay, was analyzed. Evaluation of WRF/Chem through meteorological observations reveals that the model accurately captures the synoptic conditions for most of the summer, despite problems with complex topography. WRF/Chem simulated quasi-multi-day inversion events, with strengths as high as 6.7 K (100 m)-1. Inversions were present in all grid-cell locations in Glacier Bay, with inversions occurring on average of 42% of the days during the tourist season. WRF/Chem was able to model PM 10 (particulate matter with diameter less than 10

  12. Assessing regional scale predictions of aerosols, marine stratocumulus, and their interactions during VOCALS-REx using WRF-Chem

    SciTech Connect

    Yang, Qing; Gustafson, William I.; Fast, Jerome D.; Wang, Hailong; Easter, Richard C.; Morrison, H.; Lee, Y.- N.; Chapman, Elaine G.; Spak, S. N.; Mena-Carrasco, M. A.

    2011-12-02

    In the recent chemistry version (v3.3) of the Weather Research and Forecasting (WRF-Chem) model, we have coupled the Morrison double-moment microphysics scheme with interactive aerosols so that full two-way aerosol-cloud interactions are included in simulations. We have used this new WRF-Chem functionality in a study focused on assessing predictions of aerosols, marine stratocumulus clouds, and their interactions over the Southeast Pacific using measurements from the VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) and satellite retrievals. This study also serves as a detailed analysis of our WRF-Chem simulations contributed to the VOCALS model Assessment (VOCA) project. The WRF-Chem 31-day (October 15-November 16, 2008) simulation with aerosol-cloud interactions (AERO hereafter) is also compared to a simulation (MET hereafter) with fixed cloud droplet number concentrations assumed by the default in Morrison microphysics scheme with no interactive aerosols. The well-predicted aerosol properties such as number, mass composition, and optical depth lead to significant improvements in many features of the predicted stratocumulus clouds: cloud optical properties and microphysical properties such as cloud top effective radius, cloud water path, and cloud optical thickness, and cloud macrostructure such as cloud depth and cloud base height. These improvements in addition to the aerosol direct and semi-direct effects, in turn, feed back to the prediction of boundary-layer characteristics and energy budgets. Particularly, inclusion of interactive aerosols in AERO strengths temperature and humidity gradients within capping inversion layer and lowers the MBL depth by 150 m from that of the MET simulation. Mean top-of-the-atmosphere outgoing shortwave fluxes, surface latent heat, and surface downwelling longwave fluxes are in better agreement with observations in AERO, compared to the MET simulation. Nevertheless, biases in some of the simulated

  13. ChemCam at Gale Crater: Highlights and Discoveries from Three Years of Chemical Measurements on Mars

    NASA Astrophysics Data System (ADS)

    Blaney, Diana L.; Wiens, Roger; Maurice, Sylvestre; Gasnault, Olivier; Anderson, Ryan; Bridges, John; Bridges, Nathan; Clegg, Samuel; Clark, Benton; Ehlmann, Bethany; Dyar, Melinda D.; Fisk, Martin; Francis, Raymond; Fabre, Cecile; Forni, Olivier; Frydenvang, Jens; Johnson, Jeffery; Lanza, Nina; Leveille, Richard; Lasue, Jeremie; Le Deit, Laetitia; Mangold, Nicholas; Melikechi, Noureddine; Nachon, Marion; Newsom, Horton; Payre, Valerie; Rapin, William; Sautter, Violane; Vaniman, David; Grotzinger, John; Vasavad, Ashwin; Crisp, Joy

    2015-11-01

    ChemCam has undertaken a detailed chemical investigation of the rocks and soils at Gale crater over the last three years with over six thousand separate geochemical measurements. Recent recalibration of the ChemCam data using a new library of >350 geochemical standards has enabled increased elemental accuracies over a wider compositional range. The increased accuracy combined with ChemCam’s small spot size allows for the chemistry of mineral end members including feldspars, high silica, oxide rich grains to be identified. ChemCam has observed both sedimentary and igneous compositions. Igneous compositions are generally present in conglomerates and in float rocks. Compositions show a wide range of igneous chemistry ranging from basaltic to feldspar rich assemblages.Sedimentary rocks have a wide range of compositions reflecting both differences in chemical source regions and in depositional and diagenetic histories. The “Sheepbed” mudstones cluster around Martian average crustal compositions. The “Kimberley” outcrop showed enhanced potassium reaching concentrations up to ~6 wt% K2O. More recent observations in the Murray Formation at the base of Mt. Sharp reveal mudstones that are lower in magnesium and higher in silica and aluminum than the more basaltic mudstones previously investigated. Extremely high silica (75-85 wt%) deposits have also been identified. The high silica observations were associated with increased TiO2, While the Murray mudstones are generally low in magnesium, local enhancements in magnesium have also been noted associated with resistant facies in the outcrop. Chemical trends also indicate that iron oxide phases may also be present as cements. Sandstone facies with a mafic composition are also present. Veins in the unit also show a wide range of compositions indicating fluid chemistries rich in calcium sulfate, fluorine, magnesium and iron were present. Vein chemistry could be the result of distinct fluids migrating through from a

  14. Spectroscopic Observations of Comet C/2013 A1 (Siding Spring) from Mars using ChemCam, OMEGA and SPICAM.

    NASA Astrophysics Data System (ADS)

    Lasue, J.; Gondet, B.; Bertaux, J. L.; Barraclough, B. L.; Beck, P.; Bender, S.; Bibring, J. P.; Bridges, N. T.; Chaufray, J. Y.; Gasnault, O.; Herkenhoff, K. E.; Langevin, Y.; Le Mouelic, S.; Lemmon, M. T.; Lewin, E.; McConnochie, T. H.; Martín-Torres, J.; Maurice, S.; Meslin, P. Y.; Ming, D. W.; Montmessin, F.; Owen, T. C.; Rapin, W.; Rocard, F.; Wiens, R. C.; Zorzano, M. P.

    2014-12-01

    Comet Siding Spring will graze Mars on Oct. 19th 2014. Its closest approach from the centre of the planet will be 135,000 km, and its predicted visual magnitude as low as -5.3 (JPL Horizons web site). The observing conditions will be ideal to attempt spectroscopic measurements of the inner coma from the UV to the IR at an unprecedented spectral resolution from the instruments located on and around Mars. ChemCam is a Laser-Induced Breakdown Spectroscopy instrument operating on-board the Mars Science Laboratory rover to analyse the chemical composition of rocks and can be used for passive spectroscopy. ChemCam is equipped with high resolution spectrometers covering the optical range (240-850 nm) with a pixel resolution of 0.05nm up to 470nm and 0.2nm in the near-IR range. The ChemCam passive spectroscopy field of view is 0.65 mrad wide and covers several 100km projected on the coma. Based on predicted magnitude and inner coma intensity variations, we expect to retrieve spectral signatures around the nucleus. Simultaneously the 7 instruments on board Mars Express will take measurements in nadir and limb modes. We will merge the results obtained with ChemCam with those of the 2 imaging spectrometers SPICAM (110-310 nm resolution of 0.6nm and 1-1.7 μm resolution of 1.5 nm) and OMEGA (457-910 nm resolution of 1.5 nm and 2.5-5.1 μm resolution of 15 nm) to obtain the composition and spatial variation of emitting molecules in the different parts of the coma. The instruments will also monitor the atmosphere before and after the encounter to detect any change. We will report on the preparations for the observations and the spectroscopy results, with emphasis on the detection of complex organic molecules and the spatial distribution of H2O and OH in the inner coma. A decision will be made on the adequacy of risk reduction activities for the spacecraft, and planned science operations may need to be cancelled by ESOC.This work is supported by NASA, ESA and CNES.

  15. Chem-Prep PZT 95/5 for neutron generator applications : development of laboratory-scale powder processing operations.

    SciTech Connect

    Montoya, Ted V.; Moore, Roger Howard; Spindle, Thomas Lewis Jr.

    2003-12-01

    Chemical synthesis methods are being developed as a future source of PZT 95/5 powder for neutron generator voltage bar applications. Laboratory-scale powder processes were established to produce PZT billets from these powders. The interactions between calcining temperature, sintering temperature, and pore former content were studied to identify the conditions necessary to produce PZT billets of the desired density and grain size. Several binder systems and pressing aids were evaluated for producing uniform sintered billets with low open porosity. The development of these processes supported the powder synthesis efforts and enabled comparisons between different chem-prep routes.

  16. Evaluation of the Importance of Wet Scavenging for the may 29, 2012 DC3 Severe Storm Case Using Results from Wrf-Chem Simulations

    NASA Astrophysics Data System (ADS)

    Bela, M. M.; Barth, M. C.; Toon, O.; Fried, A.; Morrison, H.; Pickering, K. E.; Cummings, K.; Li, Y.; Allen, D. J.; Manning, K.

    2013-12-01

    Deep convective thunderstorms affect the vertical distribution of chemical species through vertical transport, lightning-production of NOx, wet scavenging of soluble species as well as aqueous and ice chemistry. This work focuses on the May 29 Oklahoma thunderstorm from the DC3 (Deep Convective Clouds and Chemistry) field campaign. WRF-Chem simulations at cloud parameterizing scales (dx=15km) and cloud resolving scales (dx=3 and 1km) are conducted to investigate wet scavenging of soluble trace gases. Two different wet scavenging schemes are coupled to the Morrison microphysics scheme and MOZART chemistry. The first, based on Neu and Prather (ACP, 2012), tracks dissolved species in cloud droplets and precipitation and releases species to the gas phase from evaporating precipitation. However, it does not distinguish between precipitating liquid and ice, and species are completely retained upon hydrometeor freezing. The second, described in Barth et al. (JGR, 2001), tracks solute in individual liquid and frozen hydrometeors, and a new capability to specify the fraction of each species that is retained in ice upon hydrometeor freezing is added. The simulated meteorology, evaluated with the NEXRAD radar reflectivity, is shown to represent the structure and evolution of the storm, although the simulated storm triggers about an hour early, has a larger area of high reflectivity and extends further north than observed in NEXRAD. Vertical distributions of trace gases with varying solubilities within the storm and immediately surrounding the storm are compared with observations from the GV and DC-8 aircraft in storm inflow and outflow regions. Using the Neu and Prather scheme or using the Barth scheme with zero or complete ice retention, observed mean vertical profiles of some soluble species in outflow are better represented in the model with scavenging, while others are overly scavenged. Finally, sensitivity studies are conducted to determine ice retention factors for each

  17. ChemCam Analysis of Soil Diversity along Bradbury-Glenelg Traverse

    NASA Astrophysics Data System (ADS)

    Meslin, Pierre-Yves; Cousin, Agnès; Berger, Gilles; Forni, Olivier; Gasnault, Olivier; Lasue, Jérémie; Mangold, Nicolas; Schröder, Susanne; Maurice, Sylvestre; Wiens, Roger; Vaniman, Dave; Anderson, Ryan; Blaney, Diana; Newsom, Horton; Ollila, Ann; Clegg, Sam; Ehlmann, Bethany; Fabre, Cécile; Lanza, Nina; MSL Science Team

    2013-04-01

    The ChemCam (CCAM) instrument onboard the NASA Mars Science Laboratory rover, which combines a Laser-Induced Breakdown (LIBS) Spectrometer and a Remote Micro-Imager (RMI), provides the first insight on martian soil and dust chemical variability at the submillimeter scale. It is capable of isolating various soil components that bulk measurements would average out, and it can provide a depth profile of chemical composition to depths of a few mms in soils. It is also sensitive to the presence of hydrogen. CCAM is used for remote sensing at typical distances of 2 to 7 m. It has been used intensively since its first active use on Sol 13. A large fraction of the data has been obtained on soil targets (126 LIBS points during the 100 first sols of the mission), which are defined here as a loose, unconsolidated material, with grain sizes typically < 3 mm. Both Partial Least Square (PLS), Independent and Principal Component Analysis (PCA, ICA) and clustering analysis have been used to analyze the chemical diversity of these targets. They reveal a compositional trend between at least two major end-members: a mafic component (Type 1), similar to the composition of the average martian soil and to the composition of the dust measured by CCAM on rock surfaces, and an alkaline-, aluminum- and silica-rich component (Type 2), more representative of some local rocks found in the vicinity of the landing site. Some variability in Ca and SiO2 contents is also observed within the Rocknest ripple, an aeolian bedform extensively analyzed by CCAM and other MSL instruments, suggesting the presence of a high-Ca phase likely associated with either S, P, Cl or F, as also observed in neighboring rock targets. These soil targets, however, clearly differ from the rocks found in the Rocknest area, having more Mg and less Fe+Ti than the latter. A qualitative analysis of CCAM data also suggests that Type 1 corresponds mostly to soils that are fine-grained at the LIBS scale, while Type 2 corresponds

  18. Evaluation of lightning-induced tropospheric ozone enhancements observed by ozone lidar and simulated by WRF/Chem

    NASA Astrophysics Data System (ADS)

    Wang, Lihua; Follette-Cook, Melanie B.; Newchurch, M. J.; Pickering, Kenneth E.; Pour-Biazar, Arastoo; Kuang, Shi; Koshak, William; Peterson, Harold

    2015-08-01

    High spatial- and temporal-resolution ozone lidar profiles, in conjunction with ozonesonde and satellite observations, are well suited to characterize short-term ozone variations due to different physical and chemical processes, such as the impact of lightning-generated NOx (LNOx) on tropospheric ozone. This work presents the hourly variation of tropospheric-ozone profiles measured by an ozone lidar at the University of Alabama in Huntsville, on July 14, 18, and 27, 2011. These ozone lidar data are compared with two WRF/Chem simulations, one with lightning NO (LNO) emissions and the other without. On July 14, 2011, the ozone lidar observed an ozone laminar structure with elevated ozone concentrations of 65∼80 ppbv below 2 km, low ozone (50∼65) ppbv between 2 and 5 km, and high ozone up to 165 ppbv between 5 and 12 km AGL. WRF/Chem simulations, in conjunction with backward trajectory analysis, suggest that lightning events occurring within upwind regions resulted in an ozone enhancement of 28 ppbv at 7.5 km AGL over Huntsville. On July 27, LNO emissions were transported to Huntsville from upwind and account for 75% of NOx and an 8.3 ppbv of ozone enhancement at ∼10 km; the model overestimates ozone between 2.5 and 5 km AGL.

  19. Implementation and evaluation of online gas-phase chemistry within a regional climate model (RegCM-CHEM4)

    SciTech Connect

    Shalaby, A. K.; Zakey, A. S.; Tawfik, A. B.; Solmon, F.; Giorgi, Filippo; Stordal, F.; Sillman, S.; Zaveri, Rahul A.; Steiner, A. L.

    2012-05-22

    The RegCM-CHEM4 is a new online climate-chemistry model based on the International Centre for Theoretical Physics (ICTP) regional climate model (RegCM4). Tropospheric gas-phase chemistry is integrated into the climate model using the condensed version of the Carbon Bond Mechanism (CBM-Z; Zaveri and Peters, 1999) with a fast solver based on radical balances. We evaluate the model over Continental Europe for two different time scales: (1) an event-based analysis of the ozone episode associated with the heat wave of August 2003 and (2) a climatological analysis of a sixyear simulation (2000-2005). For the episode analysis, model simulations show good agreement with European Monitoring and Evaluation Program (EMEP) observations of hourly ozone over different regions in Europe and capture ozone concentrations during and after the August 2003 heat wave event. For long-term climate simulations, the model captures the seasonal cycle of ozone concentrations with some over prediction of ozone concentrations in non-heat wave summers. Overall, the ozone and ozone precursor evaluation shows the feasibility of using RegCM-CHEM4 for decadal-length simulations of chemistry-climate interactions.

  20. WRF-Chem Simulations of Lightning-NOx Production and Transport in Oklahoma and Colorado Thunderstorms Observed During DC3

    NASA Technical Reports Server (NTRS)

    Cummings, Kristin A.; Pickering, Kenneth E.; Barth, M.; Bela, M.; Li, Y.; Allen, D.; Bruning, E.; MacGorman, D.; Rutledge, S.; Basarab, B.; hide

    2016-01-01

    The focus of this analysis is on lightning-generated nitrogen oxides (LNOx) and their distribution for two thunderstorms observed during the Deep Convective Clouds and Chemistry (DC3) field campaign in May-June 2012. The Weather Research and Forecasting Chemistry (WRF-Chem) model is used to perform cloud-resolved simulations for the May 29-30 Oklahoma severe convection, which contained one supercell, and the June 6-7 Colorado squall line. Aircraft and ground-based observations (e.g., trace gases, lightning and radar) collected during DC3 are used in comparisons against the model-simulated lightning flashes generated by the flash rate parameterization schemes (FRPSs) incorporated into the model, as well as the model-simulated LNOx predicted in the anvil outflow. Newly generated FRPSs based on DC3 radar observations and Lightning Mapping Array data are implemented in the model, along with previously developed schemes from the literature. The results of these analyses will also be compared between storms to investigate which FRPSs were most appropriate for the two types of convection and to examine the variation in the LNOx production. The simulated LNOx results from WRF-Chem will also be compared against other previously studied mid-latitude thunderstorms.

  1. GeoSys.Chem: Estimate of reservoir fluid characteristics as first step in geochemical modeling of geothermal systems

    NASA Astrophysics Data System (ADS)

    Verma, Mahendra P.

    2012-12-01

    A computer code GeoSys.Chem for the calculation of deep geothermal reservoir fluid characteristics from the measured physical-chemical parameters of separated water and condensed vapor samples obtained from drilled wells is presented. It was written as a dynamic link library (DLL) in Visual Basic in Visual Studio 2010 (VB.NET). Using this library a demonstration program GeoChem was developed in VB.NET, which accepts the input data file in the XML format. A stepwise calculation of deep reservoir fluid characteristics of 11 production wells of Los Azufres geothermal system is performed. The calculated concentration of CO2 (e.g.=1270 mmole/kg in the well AZ-09) in the vapor, discharged into the atmosphere at the weir box, from the water sample indicates some problem in the analysis of carbonic species concentrations. In the absence of good quality analysis of carbonic species it is suggested to consider the CO2 in the vapor sample at the separator and the total dissolved carbonic species concentration in the water sample (i.e., without considering the liberation of CO2 in the atmospheric vapor at the weir box) for the geothermal reservoir fluid composition calculations. Similarly, it presents various diagrams developed in Excel for the thermodynamic evolution of Los Azufres geothermal reservoir.

  2. The potassic sedimentary rocks in Gale Crater, Mars, as seen by ChemCam on board Curiosity

    NASA Astrophysics Data System (ADS)

    Le Deit, L.; Mangold, N.; Forni, O.; Cousin, A.; Lasue, J.; Schröder, S.; Wiens, R. C.; Sumner, D.; Fabre, C.; Stack, K. M.; Anderson, R. B.; Blaney, D.; Clegg, S.; Dromart, G.; Fisk, M.; Gasnault, O.; Grotzinger, J. P.; Gupta, S.; Lanza, N.; Le Mouélic, S.; Maurice, S.; McLennan, S. M.; Meslin, P.-Y.; Nachon, M.; Newsom, H.; Payré, V.; Rapin, W.; Rice, M.; Sautter, V.; Treiman, A. H.

    2016-05-01

    The Mars Science Laboratory rover Curiosity encountered potassium-rich clastic sedimentary rocks at two sites in Gale Crater, the waypoints Cooperstown and Kimberley. These rocks include several distinct meters thick sedimentary outcrops ranging from fine sandstone to conglomerate, interpreted to record an ancient fluvial or fluvio-deltaic depositional system. From ChemCam Laser-Induced Breakdown Spectroscopy (LIBS) chemical analyses, this suite of sedimentary rocks has an overall mean K2O abundance that is more than 5 times higher than that of the average Martian crust. The combined analysis of ChemCam data with stratigraphic and geographic locations reveals that the mean K2O abundance increases upward through the stratigraphic section. Chemical analyses across each unit can be represented as mixtures of several distinct chemical components, i.e., mineral phases, including K-bearing minerals, mafic silicates, Fe-oxides, and Fe-hydroxide/oxyhydroxides. Possible K-bearing minerals include alkali feldspar (including anorthoclase and sanidine) and K-bearing phyllosilicate such as illite. Mixtures of different source rocks, including a potassium-rich rock located on the rim and walls of Gale Crater, are the likely origin of observed chemical variations within each unit. Physical sorting may have also played a role in the enrichment in K in the Kimberley formation. The occurrence of these potassic sedimentary rocks provides additional evidence for the chemical diversity of the crust exposed at Gale Crater.

  3. Retention of chromium (VI) on a macroporous char following ChemChar gasification and successive leaching with water and acids.

    PubMed

    Marrero, Thomas W; Manahan, Stanley E

    2005-01-01

    A granular macroporous char, triple-reverse-burn (TRB) char, was loaded with 23.40 mg Cr/g TRB char from an aqueous solution, and the retained metal was leached by water, 0.66 M nitric acid, concentrated nitric acid, and concentrated hydrochloric acid before and after treatment by a reductive thermal gasification process (ChemChar process developed by ChemChar Research, Inc., Columbia, Missouri). The chromium leachate was analyzed by flame atomic adsorption. Reverse- and forward-mode gasifications were performed on the metal-laden char. With the exception of a 10% mass loss of carbon, the reverse mode gasification process does not change the physical characteristics of the granular char, but does increase the retention of the chromium from 16.7 to 24.2%, depending on the leachant. The forward mode gasification process produces a vitrified (or glasslike) ash residue. There was an 11.6 to 13.1% increase in the retention of the chromium by the slag and ash when compared to the nongasified chromium-loaded TRB char. Chromium (VI) was effectively removed from solution by TRB char and found to be retained to a higher degree on the char after a reductive thermal treatment.

  4. Reduction and scientific analysis of data from the charge-energy-mass (CHEM) spectrometer on the AMPTE/CCE spacecraft

    NASA Technical Reports Server (NTRS)

    Gloeckler, G.; Hamilton, D. C.; Ipavich, F. M.

    1987-01-01

    The Charge-Energy-Mass (CHEM) spectrometer instrument on the AMPTE/Charge Composition Explorer (CCE) spacecraft is designed to measure the mass and charge-state abundance of magnetospheric and magnetosheath ions between 0.3 and 315 keV/e, an energy range that includes the bulk of the ring current and the dynamically important portion of the plasma sheet population. Continuing research is being conducted using the AMPTE mission data set, and in particular, that of the CHEM spectrometer which has operated flawlessly since launch and still provides excellent quality data. The requirted routine data processing and reduction, and software develpment continues to be performed. Scientific analysis of composition data in a number of magnetospheric regions including the ring current region, near-earth plasma sheet and subsolar magnetosheath continues to be undertaken. Correlative studies using data from the sister instrument SULEICA, which determines the mass and charge states of ions in the energy range of approximately 10 to 250 keV/e on the IRM, as well as other data from the CCE and IRM spacecraft, particularly in the upstream region and plasma sheet have also been undertaken.

  5. Global Sensitivity Analysis of GEOS-Chem Modeled OH, HO2, and Ozone During the INTEX Campaigns (2004, 2006)

    NASA Astrophysics Data System (ADS)

    Christian, K. E.; Brune, W. H.; Mao, J.

    2016-12-01

    Developing predictive capability for future atmospheric oxidation capability requires a detailed analysis of model uncertainties and sensitivity of the modeled oxidation capacity to model input variables. We present results from a global sensitivity analysis of GEOS-Chem, a popular chemical transport model, using the Random Sampling-High Dimensional Model Representation (RS-HDMR) method. Analyzing the period of NASA's Intercontinental Chemical Transport Experiment (INTEX) A & B campaigns (2004, 2006) over North America and the Northern Pacific Ocean, the uncertainties and sensitivities of modeled OH, HO2, and ozone concentrations to model inputs perturbed simultaneously within their respective uncertainties will be presented. Sensitivities of the modeled oxidants were determined for around 50 model input factors using the RS-HDMR method. We have determined a solid estimate of GEOS-Chem model uncertainty for the period of the INTEX campaigns and the emissions, chemical, or meteorological factors to which OH, HO2, and ozone are most sensitive. This analysis indicates that OH, HO2, and ozone are most sensitive to a combination of emissions factors, specifically CO, isoprene, and lightning and anthropogenic NOx and to chemical factors, such as the NO2 + OH reaction rate, the photolysis of NO2 and ozone, and aerosol uptake of HO2. Comparing these sensitivities to measurements taken from the Airborne Tropospheric Hydrogen Oxides Sensor (ATHOS), we will show where the model disagrees with measurements and which emissions, chemical, and meteorological input factors contribute the most to this disagreement.

  6. Gaseous Chemistry and Aerosol Mechanism Developments for Version 3.5.1 of the Online Regional Model, WRF-Chem

    SciTech Connect

    Archer-Nicholls, Scott; Lowe, Douglas; Utembe, Steve; Allan, James D.; Zaveri, Rahul A.; Fast, Jerome D.; Hodnebrog, Oivind; H. Denier van der Gon; McFiggans, Gordon

    2014-11-08

    We have made a number of developments in the regional coupled model WRF-Chem, with the aim of making the model more suitable for prediction of atmospheric composition and of interactions between air quality and weather. We have worked on the European domain, with a particular focus on making the model suitable for the study of night time chemistry and oxidation by the nitrate radical in the UK atmosphere. A reduced form of the Common Reactive Intermediates gas-phase chemical mechanism (CRIv2-R5) has been implemented to enable more explicit simulation of VOC degradation. N2O5 heterogeneous chemistry has been added to the existing sectional MOSAIC aerosol module, and coupled to both the CRIv2-R5 and existing CBM-Z gas phase scheme. Modifications have also been made to the sea-spray aerosol emission representation, allowing the inclusion of primary organic material in sea-spray aerosol. Driven by appropriate emissions, wind fields and chemical boundary conditions, implementation of the different developments is illustrated in order to demonstrate the impact that these changes have in the North-West European domain. These developments are now part of the freely available WRF-Chem distribution.

  7. Photoelectron circular dichroism of chiral molecules studied with a continuum-state-corrected strong-field approximation

    NASA Astrophysics Data System (ADS)

    Dreissigacker, Ingo; Lein, Manfred

    2014-05-01

    Motivated by recent experiments on circular dichroism in the photoelectron momentum distributions from strong-field ionization of chiral molecules [C. Lux et al., Angew. Chem. Int. Ed. 51, 5001 (2012), 10.1002/anie.201109035; C. S. Lehmann et al., J. Chem. Phys. 139, 234307 (2013), 10.1063/1.4844295], we investigate the origin of this effect theoretically. We show that it is not possible to describe photoelectron circular dichroism with the commonly used strong-field approximation due to its plane-wave nature. We therefore apply the Born approximation to the scattering state and use this as a continuum-state correction in the strong-field approximation. We obtain electron distributions for the molecules camphor and fenchone. In order to gain physical insight into the process, we study the contributions of individual molecular orientations.

  8. Incorporation of new particle formation and early growth treatments into WRF/Chem: Model improvement, evaluation, and impacts of anthropogenic aerosols over East Asia

    NASA Astrophysics Data System (ADS)

    Cai, Changjie; Zhang, Xin; Wang, Kai; Zhang, Yang; Wang, Litao; Zhang, Qiang; Duan, Fengkui; He, Kebin; Yu, Shao-Cai

    2016-01-01

    New particle formation (NPF) provides an important source of aerosol particles and cloud condensation nuclei, which may result in enhanced cloud droplet number concentration (CDNC) and cloud shortwave albedo. In this work, several nucleation parameterizations and one particle early growth parameterization are implemented into the online-coupled Weather Research and Forecasting model coupled with chemistry (WRF/Chem) to improve the model's capability in simulating NPF and early growth of ultrafine particles over East Asia. The default 8-bin over the size range of 39 nm-10 μm used in the Model for Simulating Aerosol Interactions and Chemistry aerosol module is expanded to the 12-bin over 1 nm-10 μm to explicitly track the formation and evolution of new particles. Although model biases remain in simulating H2SO4, condensation sink, growth rate, and formation rate, the evaluation of July 2008 simulation identifies a combination of three nucleation parameterizations (i.e., COMB) that can best represent the atmospheric nucleation processes in terms of both surface nucleation events and the resulting vertical distribution of ultrafine particle concentrations. COMB consists of a power law of Wang et al. (2011) based on activation theory for urban areas in planetary boundary layer (PBL), a power law of Boy et al. (2008) based on activation theory for non-urban areas in PBL, and the ion-mediated nucleation parameterization of YU10 for above PBL. The application and evaluation of the improved model with 12-bin and the COMB nucleation parameterization in East Asia during January, April, July, and October in 2001 show that the model has an overall reasonably good skill in reproducing most observed meteorological variables and surface and column chemical concentrations. Relatively large biases in simulated precipitation and wind speeds are due to inaccurate surface roughness and limitations in model treatments of cloud formation and aerosol-cloud-precipitation interactions

  9. ChemSkill Builder 2000, Version 6.1 [CD-ROM] (by James D. Spain and Harold J. Peters)

    NASA Astrophysics Data System (ADS)

    Keeney-Kennicutt, Reviewed By Wendy L.

    2000-07-01

    One of the major challenges for faculty teaching general chemistry is how to encourage students to practice solving problems. We know that for students to develop chemical intuition and problem-solving skills, they must "get their hands dirty" as they decipher and unravel problems inherent to our discipline. One tool that I've used since its release in 1996 is the ChemSkill Builder, an electronic homework package. The latest version, ChemSkill Builder (CSB) 2000, version 6.1, is an excellent, effective integration of teaching and testing most quantitative and conceptual learning objectives in an interactive way. It is inexpensive and easy to use for both students and faculty. The CSB 2000 package of personalized problem sets, specifically designed to complement most general chemistry courses, is a program on CD-ROM for PC Windows users (3.1, 95, or 98), with more than 1500 questions and a 3 1/2-in. record-management disk. There is a separate grade-management disk for the instructor. It has 24 gradable chapters, each with 5 or 6 sections, plus two new chapters that are not graded: Polymer Chemistry and an Appendix of Chemical Skills. Each section begins with a short review of the topic and many have interactive explanations. If students miss an answer, they are given a second chance for 70% credit. If they still miss, the worked-out solution is presented in detail. Students can work each section as many times as they wish to improve their scores. Periodically, the students download their data directly into a PC set up by the instructor. The data can be easily converted into an ASCII file and merged with a spreadsheet. The use of CD-ROM solves the sporadic problems associated with previous versions on 3 1/2-in. disks: software glitches, failed disks, and system incompatibilities. The quality and number of graphics and interactive exercises are much improved in this latest version. I particularly enjoyed the interactive explanations of significant figures and

  10. Geochemistry of the Bagnold dune field as observed by ChemCam and comparison with other aeolian deposits at Gale crater: ChemCam results from Bagnold Dunes, Mars

    DOE PAGES

    Agnes, Cousin; Dehouck, Erwin; Meslin, Pierre-Yves; ...

    2017-06-27

    The Curiosity rover conducted the first field investigation of an active extraterrestrial dune. Our study of the Bagnold dunes focuses on the ChemCam chemical results and also presents findings on the grain size distributions based on the ChemCam RMI and MAHLI images. These active dunes are composed of grains that are mostly <250 μm. Their composition is overall similar to that of the aeolian deposits analyzed all along the traverse (“Aeolis Palus soils”). Nevertheless, the dunes contain less volatiles (Cl, H, S) than the Aeolis Palus soils, which appears to be due to a lower content of volatile-rich fine-grained particlesmore » (<100 μm), or a lower content of volatile-rich amorphous component, possibly as a result of: 1) a lower level of chemical alteration; 2) the removal of an alteration rind at the surface of the grains during transport; 3) a lower degree of interaction with volcanic gases/aerosols; or 4) physical sorting that removed the smallest and most altered grains. Analyses of the >150 μm grain-size dump piles have shown that coarser grains (150-250 μm) are enriched in the mafic elements Fe and Mn, suggesting a larger content in olivine compared to smaller grains (<150 μm) of the Bagnold dunes. Furthermore, the chemistry of soils analyzed in the vicinity of the dunes indicates that they are similar to the dune material. Altogether these observations suggest that the olivine content determined by X-ray diffraction of the <150 μm grain-size sample should be considered as a lower limit for the Bagnold dunes.« less

  11. Addition of NH3 to Al3O3-

    NASA Astrophysics Data System (ADS)

    Wyrwas, Richard B.; Jarrold, Caroline Chick; Das, Ujjal; Raghavachari, Krishnan

    2006-05-01

    Recent computational studies on the addition of ammonia (NH3) to the Al3O3- cluster anion [A. Guevara-Garcia, A. Martinez, and J. V. Ortiz, J. Chem. Phys. 122, 214309 (2005)] have motivated experimental and additional computational studies, reported here. Al3O3- is observed to react with a single NH3 molecule to form the Al3O3NH3- ion in mass spectrometric studies. This is in contrast to similarly performed studies with water, in which the Al3O5H4- product was highly favored. However, the anion PE spectrum of the ammoniated species is very similar to that of Al3O4H2-. The adiabatic electron affinity of Al3O3NH3 is determined to be 2.35(5)eV. Based on comparison between the spectra and calculated electron affinities, it appears that NH3 adds dissociatively to Al3O3-, suggesting that the time for the Al3O3-•NH3 complex to either overcome or tunnel through the barrier to proton transfer (which is higher for NH3 than for water) is short relative to the time for collisional cooling in the experiment.

  12. DayCent-Chem Simulations of Ecological and Biogeochemical Processes of Eight Mountain Ecosystems in the United States

    USGS Publications Warehouse

    Hartman, Melannie D.; Baron, Jill S.; Clow, David W.; Creed, Irena F.; Driscoll, Charles T.; Ewing, Holly A.; Haines, Bruce D.; Knoepp, Jennifer; Lajtha, Kate; Ojima, Dennis S.; Parton, William J.; Renfro, Jim; Robinson, R. Bruce; Van Miegroet, Helga; Weathers, Kathleen C.; Williams, Mark W.

    2009-01-01

    Atmospheric deposition of nitrogen (N) and sulfur (S) cause complex responses in ecosystems, from fertilization to forest ecosystem decline, freshwater eutrophication to acidification, loss of soil base cations, and alterations of disturbance regimes. DayCent-Chem, an ecosystem simulation model that combines ecosystem nutrient cycling and plant dynamics with aqueous geochemical equilibrium calculations, was developed to address ecosystem responses to combined atmospheric N and S deposition. It is unique among geochemically-based models in its dynamic biological cycling of N and its daily timestep for investigating ecosystem and surface water chemical response to episodic events. The model was applied to eight mountainous watersheds in the United States. The sites represent a gradient of N deposition across locales, from relatively pristine to N-saturated, and a variety of ecosystem types and climates. Overall, the model performed best in predicting stream chemistry for snowmelt-dominated sites. It was more difficult to predict daily stream chemistry for watersheds with deep soils, high amounts of atmospheric deposition, and a large degree of spatial heterogeneity. DayCent-Chem did well in representing plant and soil carbon and nitrogen pools and fluxes. Modeled stream nitrate (NO3-) and ammonium (NH4+) concentrations compared well with measurements at all sites, with few exceptions. Simulated daily stream sulfate (SO42-) concentrations compared well to measured values for sites where SO42- deposition has been low and where SO42- adsorption/desorption reactions did not seem to be important. The concentrations of base cations and silica in streams are highly dependent on the geochemistry and weathering rates of minerals in each catchment, yet these were rarely, if ever, known. Thus, DayCent-Chem could not accurately predict weathering products for some catchments. Additionally, few data were available for exchangeable soil cations or the magnitude of base cation

  13. Evaluation and comparison of O3 and PM10 forecasts of ALARO-CAMx and WRF-Chem

    NASA Astrophysics Data System (ADS)

    Flandorfer, Claudia; Hirtl, Marcus

    2017-04-01

    ZAMG runs two models for Air-Quality forecasts operationally: ALARO-CAMx and WRF-Chem. ALARO-CAMx is a combination of the meteorological model ALARO and the photochemical dispersion model CAMx and is operated at ZAMG by order of the regional governments since 2005. The emphasis of this modeling system is to predict ozone peaks in the North-east Austrian flatlands. Two modeling domains are used with the highest resolution (5 km) in the Alpine region. Various new features have been implemented in the model in the past to improve the daily forecasts, e.g. data assimilation of O3 and PM10 observations from the Austrian measurement network (with optimum interpolation technique), MACC-II boundary conditions and the combination of high resolved emission inventories for Austria with TNO and EMEP data. The biogenic emissions are provided by the SMOKE model. The model runs 2 times per day for a period of 48 hours. The second model which is operational is the on-line coupled model WRF-Chem. Meteorology is simulated simultaneously with the emission, turbulent mixing, transport, transformation as well as the fate of trace gases and aerosols. 2 domains are used for the simulations. The mother domain covers Europe with a resolution of 12 km. The inner domain includes the Alpine region with a horizontal resolution of 4km. The model runs 2 times per day for a period of 72 hours and is initialized with ECMWF forecasts. The evaluation of both models is conducted for the months January to September 2016 with the main focus on the forecasts of ozone. The measurements of the Air-Quality stations are compared with the area forecasts for every province of Austria. Besides the evaluation a comparison of the forecasts of ALARO-CAMx and WRF-Chem is done. The summer 2016 was one of the 11th warmest summers since the beginning of the meteorological measurements in Austria, but one of the 15th rainiest summers, too. Due to the meteorological conditions, only two exceedances of the information

  14. Application of the Technicon Chem 1+ chemistry analyzer to the Syva Emit ethyl alcohol assay in plasma and urine.

    PubMed

    Urry, F M; Kralik, M; Wozniak, E; Crockett, H; Jennison, T A

    1993-09-01

    The performance of the Technicon Chem 1+ chemistry analyzer with the Syva Emit ethyl alcohol assay in plasma and urine was evaluated. Spiked specimens from 0 to 600 mg/dL were tested, and expected versus measured concentrations were monitored. Linear regression line equations of y = 0.9314x + 5.4 and y = 0.9005x + 4.6, and correlation coefficients (r) of 0.9997 and 0.9995, were obtained for plasma and urine, respectively. A limit of detection of 5 mg/dL for plasma and urine, and a limit of quantitation of 20 mg/dL for plasma and 15 mg/dL for urine were obtained. Recovery was within 10% of expected concentration from 20 to 600 mg/dL. Precision was evaluated, giving the following coefficients of variation: within-run precision: plasma, 1.31-2.20; urine, 1.16-1.21; total precision: plasma, 2.72-3.38; urine, 2.98-4.64. No carry-over was detected when alternating 600 mg/dL and negative specimens. No interference from acetone, isopropanol, or methanol was detected. No significant differences in evaporation of alcohol at two concentrations, or from the two matrices were observed. Evaporation from a small cup (200 microL) was more than twice as great as from a large cup (2 mL). The Chem 1+ was compared to a gas chromatographic method. Plasma specimens of 0-352 mg/dL produced a linear regression line of y = 1.0112x + 6.0, r = 0.9859; urine specimens of 0-313 mg/dL produced a line of y = 1.0493x - 0.3, r = 0.9910. The capability to separate positive and negative specimens at 20% around a cutoff concentration of 20 mg/dL was examined. Four hundred specimens were analyzed, with only one specimen incorrectly classified (a false positive). The Chem 1+ chemistry analyzer demonstrated reliable performance of the Emit ethyl alcohol assay of plasma and urine specimens.

  15. Top-Down Inversion of Aerosol Emissions through Adjoint Integration of Satellite Radiance and GEOS-Chem Chemical Transport Model

    NASA Astrophysics Data System (ADS)

    Xu, X.; Wang, J.; Henze, D. K.; Qu, W.; Kopacz, M.

    2012-12-01

    The knowledge of aerosol emissions from both natural and anthropogenic sources are needed to study the impacts of tropospheric aerosol on atmospheric composition, climate, and human health, but large uncertainties persist in quantifying the aerosol sources with the current bottom-up methods. This study presents a new top-down approach that spatially constrains the amount of aerosol emissions from satellite (MODIS) observed reflectance with the adjoint of a chemistry transport model (GEOS-Chem). We apply this technique with a one-month case study (April 2008) over the East Asia. The bottom-up estimated sulfate-nitrate-ammonium precursors, such as sulfur dioxide (SO2), ammonia (NH3), and nitrogen oxides (NOx), all from INTEX-B 2006 inventory, emissions of black carbon (BC), organic carbon (OC) from Bond-2007 inventory, and mineral dust simulated from DEAD dust mobilization scheme, are spatially optimized from the GEOS-Chem model and its adjoint constrained by the aerosol optical depth (AOD) that are derived from MODIS reflectance with the GEOS-Chem aerosol single scattering properties. The adjoint inverse modeling for the study period yields notable decreases in anthropogenic aerosol emissions over China: 436 Gg (33.5%) for SO2, 378 Gg (34.5%) for NH3, 319 (18.8%) for NOx, 10 Gg (9.1%) for BC, and 30 Gg (15.0%) for OC. The total amount of the mineral dust emission is reduced by 56.4% from the DEAD mobilization module which simulates dust production of 19020 Gg. Sub-regional adjustments are significant and directions of changes are spatially different. The model simulation with optimized aerosol emissions shows much better agreement with independent observations from sun-spectrophotometer observed AOD from AERONET, MISR (Multi-angle Imaging SpectroRadiometer) AOD, OMI (Ozone Monitoring Instrument) NO2 and SO2 columns, and surface aerosol concentrations measured over both anthropogenic pollution and dust source regions. Assuming the used bottom-up anthropogenic

  16. Modelling of Impulsional pH Variations Using ChemFET-Based Microdevices: Application to Hydrogen Peroxide Detection

    PubMed Central

    Diallo, Abdou Karim; Djeghlaf, Lyes; Launay, Jerome; Temple-Boyer, Pierre

    2014-01-01

    This work presents the modelling of impulsional pH variations in microvolume related to water-based electrolysis and hydrogen peroxide electrochemical oxidation using an Electrochemical Field Effect Transistor (ElecFET) microdevice. This ElecFET device consists of a pH-Chemical FET (pH-ChemFET) with an integrated microelectrode around the dielectric gate area in order to trigger electrochemical reactions. Combining oxidation/reduction reactions on the microelectrode, water self-ionization and diffusion properties of associated chemical species, the model shows that the sensor response depends on the main influential parameters such as: (i) polarization parameters on the microelectrode, i.e., voltage (Vp) and time (tp); (ii) distance between the gate sensitive area and the microelectrode (d); and (iii) hydrogen peroxide concentration ([H2O2]). The model developed can predict the ElecFET response behaviour and creates new opportunities for H2O2-based enzymatic detection of biomolecules. PMID:24556666

  17. Application of WRF/Chem over North America under the AQMEII Phase 2: Part I. Comprehensive evaluation of 2006 simulation

    NASA Astrophysics Data System (ADS)

    Yahya, Khairunnisa; Wang, Kai; Gudoshava, Masilin; Glotfelty, Timothy; Zhang, Yang

    2015-08-01

    The Weather Research and Forecasting model with Chemistry (WRF/Chem) version 3.4.1 has been modified to include the Carbon Bond 2005 (CB05) gas-phase mechanism, the Modal for Aerosol Dynamics for Europe (MADE) and the Volatility Basis Set (VBS) approach for secondary organic aerosol (hereafter WRF/Chem-CB05-MADE/VBS), and aerosol-cloud-radiation feedbacks to improve predictions of secondary organic aerosols (SOA) and to study meteorology-chemistry feedbacks. In this Part I paper, a comprehensive evaluation is performed for WRF/Chem-CB05-MADE/VBS to simulate air quality over a large area in North America for the full year of 2006. Operational, diagnostic, and mechanistic evaluations have been carried out for major meteorological variables, gas and aerosol species, as well as aerosol-cloud-radiation variables against surface measurements, sounding data, and satellite data on a seasonal and annual basis. The model performs well for most meteorological variables with moderate to relatively high correlation and low mean biases (MBs), but with a cold bias of 0.8-0.9 °C in temperature, a moderate overprediction with normalized mean biases (NMBs) of 17-22% in wind speed, and large underpredictions with NMBs of -65% to -62% in cloud optical depths and cloud condensation nuclei over the ocean. Those biases are attributed to uncertainty in physical parameterizations, incomplete treatments of hydrometeors, and inaccurate aerosol predictions. The model shows moderate underpredictions in the mixing ratios of O3 with an annual NMB of -12.8% over rural and national park sites, which may be caused by biases in temperature and wind speed, underestimate in wildfire emissions, and underestimate in biogenic organic emissions (reflected by an NMB of -79.1% in simulated isoprene mixing ratio). The model performs well for PM2.5 concentrations with annual NMBs within ±10%; but with possible bias compensation for PM2.5 species concentrations. The model simulates well the domainwide

  18. Global sensitivity analysis of the GEOS-Chem chemical transport model: ozone and hydrogen oxides during ARCTAS (2008)

    NASA Astrophysics Data System (ADS)

    Christian, Kenneth E.; Brune, William H.; Mao, Jingqiu

    2017-03-01

    Developing predictive capability for future atmospheric oxidation capacity requires a detailed analysis of model uncertainties and sensitivity of the modeled oxidation capacity to model input variables. Using oxidant mixing ratios modeled by the GEOS-Chem chemical transport model and measured on the NASA DC-8 aircraft, uncertainty and global sensitivity analyses were performed on the GEOS-Chem chemical transport model for the modeled oxidants hydroxyl (OH), hydroperoxyl (HO2), and ozone (O3). The sensitivity of modeled OH, HO2, and ozone to model inputs perturbed simultaneously within their respective uncertainties were found for the flight tracks of NASA's Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) A and B campaigns (2008) in the North American Arctic. For the spring deployment (ARCTAS-A), ozone was most sensitive to the photolysis rate of NO2, the NO2 + OH reaction rate, and various emissions, including methyl bromoform (CHBr3). OH and HO2 were overwhelmingly sensitive to aerosol particle uptake of HO2 with this one factor contributing upwards of 75 % of the uncertainty in HO2. For the summer deployment (ARCTAS-B), ozone was most sensitive to emission factors, such as soil NOx and isoprene. OH and HO2 were most sensitive to biomass emissions and aerosol particle uptake of HO2. With modeled HO2 showing a factor of 2 underestimation compared to measurements in the lowest 2 km of the troposphere, lower uptake rates (γHO2 < 0. 055), regardless of whether or not the product of the uptake is H2O or H2O2, produced better agreement between modeled and measured HO2.

  19. Representation of the Community Earth System Model (CESM1) CAM4-chem within the Chemistry-Climate Model Initiative (CCMI)

    NASA Astrophysics Data System (ADS)

    Tilmes, Simone; Lamarque, Jean-Francois; Emmons, Louisa K.; Kinnison, Doug E.; Marsh, Dan; Garcia, Rolando R.; Smith, Anne K.; Neely, Ryan R.; Conley, Andrew; Vitt, Francis; Martin, Maria Val; Tanimoto, Hiroshi; Simpson, Isobel; Blake, Don R.; Blake, Nicola

    2016-05-01

    The Community Earth System Model (CESM1) CAM4-chem has been used to perform the Chemistry Climate Model Initiative (CCMI) reference and sensitivity simulations. In this model, the Community Atmospheric Model version 4 (CAM4) is fully coupled to tropospheric and stratospheric chemistry. Details and specifics of each configuration, including new developments and improvements are described. CESM1 CAM4-chem is a low-top model that reaches up to approximately 40 km and uses a horizontal resolution of 1.9° latitude and 2.5° longitude. For the specified dynamics experiments, the model is nudged to Modern-Era Retrospective Analysis for Research and Applications (MERRA) reanalysis. We summarize the performance of the three reference simulations suggested by CCMI, with a focus on the last 15 years of the simulation when most observations are available. Comparisons with selected data sets are employed to demonstrate the general performance of the model. We highlight new data sets that are suited for multi-model evaluation studies. Most important improvements of the model are the treatment of stratospheric aerosols and the corresponding adjustments for radiation and optics, the updated chemistry scheme including improved polar chemistry and stratospheric dynamics and improved dry deposition rates. These updates lead to a very good representation of tropospheric ozone within 20 % of values from available observations for most regions. In particular, the trend and magnitude of surface ozone is much improved compared to earlier versions of the model. Furthermore, stratospheric column ozone of the Southern Hemisphere in winter and spring is reasonably well represented. All experiments still underestimate CO most significantly in Northern Hemisphere spring and show a significant underestimation of hydrocarbons based on surface observations.

  20. Evaluation of UTLS Carbon Monoxide Simulations in GMI and GEOS-Chem Chemical Transport Models using Aura MLS Observations

    NASA Technical Reports Server (NTRS)

    Huang, Lei; Jiang, Jonathan H.; Murray, Lee T.; Damon, Megan R.; Su, Hui; Livesey, Nathaniel J.

    2016-01-01

    This study evaluates the distribution and variation of carbon monoxide (CO) in the upper troposphere and lower stratosphere (UTLS) during 2004-2012 as simulated by two chemical transport models, using the latest version of Aura Microwave Limb Sounder (MLS) observations. The simulated spatial distributions, temporal variations and vertical transport of CO in the UTLS region are compared with those observed by MLS. We also investigate the impact of surface emissions and deep convection on CO concentrations in the UTLS over different regions, using both model simulations and MLS observations. Global Modeling Initiative (GMI) and GEOS-Chem simulations of UTLS CO both show similar spatial distributions to observations. The global mean CO values simulated by both models agree with MLS observations at 215 and 147 hPa, but are significantly underestimated by more than 40% at 100 hPa. In addition, the models underestimate the peak CO values by up to 70% at 100 hPa, 60% at 147 hPa and 40% at 215 hPa, with GEOS-Chem generally simulating more CO at 100 hPa and less CO at 215 hPa than GMI. The seasonal distributions of CO simulated by both models are in better agreement with MLS in the Southern Hemisphere (SH) than in the Northern Hemisphere (NH), with disagreements between model and observations over enhanced CO regions such as southern Africa. The simulated vertical transport of CO shows better agreement with MLS in the tropics and the SH subtropics than the NH subtropics. We also examine regional variations in the relationships among surface CO emission, convection and UTLS CO concentrations. The two models exhibit emission-convection- CO relationships similar to those observed by MLS over the tropics and some regions with enhanced UTLS CO.

  1. ChemCam investigation of the John Klein and Cumberland drill holes and tailings, Gale crater, Mars

    NASA Astrophysics Data System (ADS)

    Jackson, R. S.; Wiens, R. C.; Vaniman, D. T.; Beegle, L.; Gasnault, O.; Newsom, H. E.; Maurice, S.; Meslin, P.-Y.; Clegg, S.; Cousin, A.; Schröder, S.; Williams, J. M.

    2016-10-01

    The ChemCam instrument on the Mars Science Laboratory rover analyzed the rock surface, drill hole walls, tailings, and unprocessed and sieved dump piles to investigate chemical variations with depth in the first two martian drill holes and possible fractionation or segregation effects of the drilling and sample processing. The drill sites are both in Sheepbed Mudstone, the lowest exposed member of the Yellowknife Bay formation. Yellowknife Bay is composed of detrital basaltic materials in addition to clay minerals and an amorphous component. The drill tailings are a mixture of basaltic sediments and diagenetic material like calcium sulfate veins, while the shots on the drill site surface and walls of the drill holes are closer to those pure end members. The sediment dumped from the sample acquisition, processing, and handling subsystem is of similar composition to the tailings; however, due to the specifics of the drilling process the tailings and dump piles come from different depths within the hole. This allows the ChemCam instrument to analyze samples representing the bulk composition from different depths. On the pre-drill surfaces, the Cumberland site has a greater amount of CaO and evidence for calcium sulfate veins, than the John Klein site. However, John Klein has a greater amount of calcium sulfate veins below the surface, as seen in mapping, drill hole wall analysis, and observations in the drill tailings and dump pile. In addition, the Cumberland site does not have any evidence of variations in bulk composition with depth down the drill hole, while the John Klein site has evidence for a greater amount of CaO (calcium sulfates) in the top portion of the hole compared to the middle section of the hole, where the drill sample was collected.

  2. Evaluation of UTLS carbon monoxide simulations in GMI and GEOS-Chem chemical transport models using Aura MLS observations

    NASA Astrophysics Data System (ADS)

    Huang, Lei; Jiang, Jonathan H.; Murray, Lee T.; Damon, Megan R.; Su, Hui; Livesey, Nathaniel J.

    2016-05-01

    This study evaluates the distribution and variation of carbon monoxide (CO) in the upper troposphere and lower stratosphere (UTLS) during 2004-2012 as simulated by two chemical transport models, using the latest version of Aura Microwave Limb Sounder (MLS) observations. The simulated spatial distributions, temporal variations and vertical transport of CO in the UTLS region are compared with those observed by MLS. We also investigate the impact of surface emissions and deep convection on CO concentrations in the UTLS over different regions, using both model simulations and MLS observations. Global Modeling Initiative (GMI) and GEOS-Chem simulations of UTLS CO both show similar spatial distributions to observations. The global mean CO values simulated by both models agree with MLS observations at 215 and 147 hPa, but are significantly underestimated by more than 40 % at 100 hPa. In addition, the models underestimate the peak CO values by up to 70 % at 100 hPa, 60 % at 147 hPa and 40 % at 215 hPa, with GEOS-Chem generally simulating more CO at 100 hPa and less CO at 215 hPa than GMI. The seasonal distributions of CO simulated by both models are in better agreement with MLS in the Southern Hemisphere (SH) than in the Northern Hemisphere (NH), with disagreements between model and observations over enhanced CO regions such as southern Africa. The simulated vertical transport of CO shows better agreement with MLS in the tropics and the SH subtropics than the NH subtropics. We also examine regional variations in the relationships among surface CO emission, convection and UTLS CO concentrations. The two models exhibit emission-convection-CO relationships similar to those observed by MLS over the tropics and some regions with enhanced UTLS CO.

  3. Evaluation of UTLS Carbon Monoxide Simulations in GMI and GEOS-Chem Chemical Transport Models using Aura MLS Observations

    NASA Technical Reports Server (NTRS)

    Huang, Lei; Jiang, Jonathan H.; Murray, Lee T.; Damon, Megan R.; Su, Hui; Livesey, Nathaniel J.

    2016-01-01

    This study evaluates the distribution and variation of carbon monoxide (CO) in the upper troposphere and lower stratosphere (UTLS) during 2004-2012 as simulated by two chemical transport models, using the latest version of Aura Microwave Limb Sounder (MLS) observations. The simulated spatial distributions, temporal variations and vertical transport of CO in the UTLS region are compared with those observed by MLS. We also investigate the impact of surface emissions and deep convection on CO concentrations in the UTLS over different regions, using both model simulations and MLS observations. Global Modeling Initiative (GMI) and GEOS-Chem simulations of UTLS CO both show similar spatial distributions to observations. The global mean CO values simulated by both models agree with MLS observations at 215 and 147 hPa, but are significantly underestimated by more than 40% at 100 hPa. In addition, the models underestimate the peak CO values by up to 70% at 100 hPa, 60% at 147 hPa and 40% at 215 hPa, with GEOS-Chem generally simulating more CO at 100 hPa and less CO at 215 hPa than GMI. The seasonal distributions of CO simulated by both models are in better agreement with MLS in the Southern Hemisphere (SH) than in the Northern Hemisphere (NH), with disagreements between model and observations over enhanced CO regions such as southern Africa. The simulated vertical transport of CO shows better agreement with MLS in the tropics and the SH subtropics than the NH subtropics. We also examine regional variations in the relationships among surface CO emission, convection and UTLS CO concentrations. The two models exhibit emission-convection- CO relationships similar to those observed by MLS over the tropics and some regions with enhanced UTLS CO.

  4. The ChemCam Remote Micro-Imager on MSL: Observations From the First Year on Mars

    NASA Astrophysics Data System (ADS)

    Le Mouelic, S.; Gasnault, O.; Bridges, N. T.; Herkenhoff, K. E.; Langevin, Y.; Pinet, P. C.; Maurice, S.; Wiens, R. C.; Mangold, N.; Johnson, J. R.; Bell, J. F.; Blaney, D. L.; Barraclough, B. L.

    2013-12-01

    The Remote Microscopic Imager (RMI) portion of the ChemCam instrument on the Mars Science Laboratory 'Curiosity' rover acquires panchromatic images with a 1024x1024 pixel CCD. The main objective of the RMI is to provide geomorphologic context of the ChemCam Laser Induced Breakdown Spectroscopy (LIBS) analyses, locate the laser pits, and document the changes induced by the laser shots on the targets. Thanks to its very narrow pixel angular size of 20 microrad, RMI by itself adds a significant scientific value to the study of soils and rocks by revealing their fine texture and morphology, and can also occasionally serve as a reconnaissance tool for distant targets as the rover drives along. During the first year of operations on Mars, the RMI has been used in a variety of situations, providing more than 1000 images of rover hardware, soils and rock targets located at distances ranging from 1.2 meters up to several kilometers from the camera. Several types of products have been derived from these raw data. These include mosaics of images taken before and after the LIBS shots, difference images to identify the most subtle laser pits on hard rocks, merges with the color information acquired by the Mastcam cameras, and micro-topographic information from focal sections, also known as the z-stack technique. Further applications are also under investigation, such as night sky imaging or stereogrammetry using RMI and Mastcam 100 images. The RMI has the highest spatial resolution of the cameras on MSL's remote sensing mast, and is therefore very useful, along with Curiosity's other imaging instruments, in deciphering the history of rocks and soils at Gale crater.

  5. Representation of the Community Earth System Model (CESM1) CAM4-chem within the Chemistry-Climate Model Initiative (CCMI)

    DOE PAGES

    Tilmes, Simone; Lamarque, Jean -Francois; Emmons, Louisa K.; ...

    2016-05-20

    The Community Earth System Model (CESM1) CAM4-chem has been used to perform the Chemistry Climate Model Initiative (CCMI) reference and sensitivity simulations. In this model, the Community Atmospheric Model version 4 (CAM4) is fully coupled to tropospheric and stratospheric chemistry. Details and specifics of each configuration, including new developments and improvements are described. CESM1 CAM4-chem is a low-top model that reaches up to approximately 40 km and uses a horizontal resolution of 1.9° latitude and 2.5° longitude. For the specified dynamics experiments, the model is nudged to Modern-Era Retrospective Analysis for Research and Applications (MERRA) reanalysis. We summarize the performance ofmore » the three reference simulations suggested by CCMI, with a focus on the last 15 years of the simulation when most observations are available. Comparisons with selected data sets are employed to demonstrate the general performance of the model. We highlight new data sets that are suited for multi-model evaluation studies. Most important improvements of the model are the treatment of stratospheric aerosols and the corresponding adjustments for radiation and optics, the updated chemistry scheme including improved polar chemistry and stratospheric dynamics and improved dry deposition rates. These updates lead to a very good representation of tropospheric ozone within 20 % of values from available observations for most regions. In particular, the trend and magnitude of surface ozone is much improved compared to earlier versions of the model. Furthermore, stratospheric column ozone of the Southern Hemisphere in winter and spring is reasonably well represented. In conclusion, all experiments still underestimate CO most significantly in Northern Hemisphere spring and show a significant underestimation of hydrocarbons based on surface observations.« less

  6. The anthropogenic contribution to atmospheric black carbon concentrations in southern Africa: a WRF-Chem modeling study

    NASA Astrophysics Data System (ADS)

    Kuik, F.; Lauer, A.; Beukes, J. P.; Van Zyl, P. G.; Josipovic, M.; Vakkari, V.; Laakso, L.; Feig, G. T.

    2015-08-01

    South Africa has one of the largest industrialized economies in Africa. Emissions of air pollutants are particularly high in the Johannesburg-Pretoria metropolitan area, the Mpumalanga Highveld and the Vaal Triangle, resulting in local air pollution. This study presents and evaluates a setup for conducting modeling experiments over southern Africa with the Weather Research and Forecasting model including chemistry and aerosols (WRF-Chem), and analyzes the contribution of anthropogenic emissions to the total black carbon (BC) concentrations from September to December 2010. The modeled BC concentrations are compared with measurements obtained at the Welgegund station situated ca. 100 km southwest of Johannesburg. An evaluation of WRF-Chem with observational data from ground-based measurement stations, radiosondes, and satellites shows that the meteorology is modeled mostly reasonably well, but precipitation amounts are widely overestimated and the onset of the wet season is modeled approximately 1 month too early in 2010. Modeled daily mean BC concentrations show a temporal correlation of 0.66 with measurements, but the total BC concentration is underestimated in the model by up to 50 %. Sensitivity studies with anthropogenic emissions of BC and co-emitted species turned off show that anthropogenic sources can contribute up to 100 % to BC concentrations in the industrialized and urban areas, and anthropogenic BC and co-emitted species together can contribute up to 60 % to PM1 levels. Particularly the co-emitted species contribute significantly to the aerosol optical depth (AOD). Furthermore, in areas of large-scale biomass-burning atmospheric heating rates are increased through absorption by BC up to an altitude of about 600hPa.

  7. Towards a Comprehensive Dynamic-chemistry Assimilation for Eos-Chem: Plans and Status in NASA's Data Assimilation Office

    NASA Technical Reports Server (NTRS)

    Pawson, Steven; Lin, Shian-Jiann; Rood, Richard B.; Stajner, Ivanka; Nebuda, Sharon; Nielsen, J. Eric; Douglass, Anne R.

    2000-01-01

    In order to support the EOS-Chem project, a comprehensive assimilation package for the coupled chemical-dynamical system is being developed by the Data Assimilation Office at NASA GSFC. This involves development of a coupled chemistry/meteorology model and of data assimilation techniques for trace species and meteorology. The model is being developed using the flux-form semi-Lagrangian dynamical core of Lin and Rood, the physical parameterizations from the NCAR Community Climate Model, and atmospheric chemistry modules from the Atmospheric Chemistry and Dynamics branch at NASA GSFC. To date the following results have been obtained: (i) multi-annual simulations with the dynamics-radiation model show the credibility of the package for atmospheric simulations; (ii) initial simulations including a limited number of middle atmospheric trace gases reveal the realistic nature of transport mechanisms, although there is still a need for some improvements. Samples of these results will be shown. A meteorological assimilation system is currently being constructed using the model; this will form the basis for the proposed meteorological/chemical assimilation package. The latter part of the presentation will focus on areas targeted for development in the near and far terms, with the objective of Providing a comprehensive assimilation package for the EOS-Chem science experiment. The first stage will target ozone assimilation. The plans also encompass a reanalysis (ReSTS) for the 1991-1995 period, which includes the Mt. Pinatubo eruption and the time when a large number of UARS observations were available. One of the most challenging aspects of future developments will be to couple theoretical advances in tracer assimilation with the practical considerations of a real environment and eventually a near-real-time assimilation system.

  8. Representation of the Community Earth System Model (CESM1) CAM4-chem within the Chemistry-Climate Model Initiative (CCMI)

    SciTech Connect

    Tilmes, Simone; Lamarque, Jean -Francois; Emmons, Louisa K.; Kinnison, Doug E.; Marsh, Dan; Garcia, Rolando R.; Smith, Anne K.; Neely, Ryan R.; Conley, Andrew; Vitt, Francis; Val Martin, Maria; Tanimoto, Hiroshi; Simpson, Isobel; Blake, Don R.; Blake, Nicola

    2016-05-20

    The Community Earth System Model (CESM1) CAM4-chem has been used to perform the Chemistry Climate Model Initiative (CCMI) reference and sensitivity simulations. In this model, the Community Atmospheric Model version 4 (CAM4) is fully coupled to tropospheric and stratospheric chemistry. Details and specifics of each configuration, including new developments and improvements are described. CESM1 CAM4-chem is a low-top model that reaches up to approximately 40 km and uses a horizontal resolution of 1.9° latitude and 2.5° longitude. For the specified dynamics experiments, the model is nudged to Modern-Era Retrospective Analysis for Research and Applications (MERRA) reanalysis. We summarize the performance of the three reference simulations suggested by CCMI, with a focus on the last 15 years of the simulation when most observations are available. Comparisons with selected data sets are employed to demonstrate the general performance of the model. We highlight new data sets that are suited for multi-model evaluation studies. Most important improvements of the model are the treatment of stratospheric aerosols and the corresponding adjustments for radiation and optics, the updated chemistry scheme including improved polar chemistry and stratospheric dynamics and improved dry deposition rates. These updates lead to a very good representation of tropospheric ozone within 20 % of values from available observations for most regions. In particular, the trend and magnitude of surface ozone is much improved compared to earlier versions of the model. Furthermore, stratospheric column ozone of the Southern Hemisphere in winter and spring is reasonably well represented. In conclusion, all experiments still underestimate CO most significantly in Northern Hemisphere spring and show a significant underestimation of hydrocarbons based on surface observations.

  9. Spatial, temporal and vertical distribution of ammonia concentrations over Europe - comparing a static and dynamic approach with WRF-Chem

    NASA Astrophysics Data System (ADS)

    Werner, M.; Kryza, M.; Geels, C.; Ellermann, T.; Ambelas Skjøth, C.

    2015-08-01

    The study focuses on the application of a dynamic ammonia emission into the Weather Research and Forecasting Chemistry model (WRF-Chem) and the influence on the simulated ammonia concentrations and the overall model performance. We have focused on agricultural ammonia sources and have analysed both hourly and daily patterns of ammonia emissions and concentrations at measurement sites located in agricultural areas or influenced by this activity. For selected episodes, we have also investigated the 3-D patterns of the ammonia concentrations in the atmosphere. The application of the dynamic ammonia emission into the WRF-Chem model (the "DYNAMIC" simulation) results in an improvement of the modelled daily ammonia concentrations in comparison to a static approach (the "BASE" simulation), which is currently widely used in chemical transport models. In the case of hourly resolution, we have observed an improvement for the DYNAMIC approach for the winter and autumn seasons, but for the entire year the modelled hourly ammonia peaks are shifted toward the afternoon hours if compared with measurements. This study indicates that the current description of the diurnal cycle of the ammonia concentration from fields is not accurate and more research is needed in order to improve the processes that describe the emission from fertilised fields. The results suggest that the governing processes in relation to the diurnal cycle are the atmospheric mixing and the emission strength. Therefore, an improved description of the diurnal profile of ammonia concentrations within atmospheric models requires a better description of the planetary boundary layer height and a stronger daily pattern of ammonia emission, e.g. through increased evaporation or increased fluxes from the surface.

  10. Modeling Gas-phase Glyoxal and Associated Secondary Organic Aerosol Formation in a Megacity using WRF/Chem

    NASA Astrophysics Data System (ADS)

    Wang, K.; Hodzic, A.; Barth, M. C.; Jimenez, J. L.; Volkamer, R.; Ervens, B.; Zhang, Y.

    2011-12-01

    Organic aerosol (OA) as one of a major fine particulate matter in the atmosphere plays an important role in air pollution, human health, and climate forcing. OA is composed of directly emitted primary organic aerosol and chemically produced secondary organic aerosols (SOA). Despite much recent progress in understanding SOA formation, current air quality models cannot explain the magnitude and growth of atmospheric SOA, due to high uncertainties in sources, properties, and chemical reactions of precursors and formation pathways of SOA. Recent laboratory and modeling studies showed that glyoxal may serve as an important SOA precursor in the condensed solution of inorganic or organic aerosol particles (e.g., ammonium sulfate, fulvic acid, and amino acids). In this study, the Weather Research and Forecasting model with chemistry (WRF/Chem) is modified to account for the latest observed gas-phase yields of glyoxal from various volatile organic compounds (VOCs) and the associated SOA formation in the aqueous aerosol phase. The SOA formation in the aqueous aerosol phase is implemented using two approaches. In the first approach, two simplified parameterizations are used to represent the lumped particle-phase chemical processes under dark conditions and photochemical surface uptake. In the second approach, more detailed kinetic glyoxal reactions such as reversible glyoxal uptake, dimer formation of glyoxal, and oligomerization are treated and resolved explicitly. The updated WRF/Chem is assessed over the Mexico City and the surrounding region during March 2006 using the MILAGRO campaign data. Various observations such as organic matter from Aerodyne Aerosol Mass Spectrometer and VOCs from Proton-transfer Ion Trap Mass Spectrometry were compared. The preliminary results showed that the addition of the SOA formation from glyoxal in aqueous particles brings SOA predictions into a better agreement with field observations, in particular in presence of high relative humidity

  11. The impact of resolution on meteorological, chemical and aerosol properties in regional simulations with WRF-Chem

    NASA Astrophysics Data System (ADS)

    Crippa, Paola; Sullivan, Ryan C.; Thota, Abhinav; Pryor, Sara C.

    2017-01-01

    Limited area (regional) models applied at high resolution over specific regions of interest are generally expected to more accurately capture the spatiotemporal variability of key meteorological and climate parameters. However, improved performance is not inevitable, and there remains a need to optimize use of numerical resources and to quantify the impact on simulation fidelity that derives from increased resolution. The application of regional models for climate forcing assessment is currently limited by the lack of studies quantifying the sensitivity to horizontal spatial resolution and the physical-dynamical-chemical schemes driving the simulations. Here we investigate model skill in simulating meteorological, chemical and aerosol properties as a function of spatial resolution, by applying the Weather Research and Forecasting model with coupled Chemistry (WRF-Chem) over eastern North America at different resolutions. Using Brier skill scores and other statistical metrics it is shown that enhanced resolution (from 60 to 12 km) improves model performance for all of the meteorological parameters and gas-phase concentrations considered, in addition to both mean and extreme aerosol optical depth (AOD) in three wavelengths in the visible relative to satellite observations, principally via increase of potential skill. Some of the enhanced model performance for AOD appears to be attributable to improved simulation of meteorological conditions and the concentration of key aerosol precursor gases (e.g., SO2 and NH3). Among other reasons, a dry bias in the specific humidity in the boundary layer and a substantial underestimation of total monthly precipitation in the 60 km simulations are identified as causes for the better performance of WRF-Chem simulations at 12 km.

  12. A new WRF-Chem treatment for studying regional-scale impacts of cloud processes on aerosol and trace gases in parameterized cumuli

    NASA Astrophysics Data System (ADS)

    Berg, L. K.; Shrivastava, M.; Easter, R. C.; Fast, J. D.; Chapman, E. G.; Liu, Y.; Ferrare, R. A.

    2015-02-01

    A new treatment of cloud effects on aerosol and trace gases within parameterized shallow and deep convection, and aerosol effects on cloud droplet number, has been implemented in the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) version 3.2.1 that can be used to better understand the aerosol life cycle over regional to synoptic scales. The modifications to the model include treatment of the cloud droplet number mixing ratio; key cloud microphysical and macrophysical parameters (including the updraft fractional area, updraft and downdraft mass fluxes, and entrainment) averaged over the population of shallow clouds, or a single deep convective cloud; and vertical transport, activation/resuspension, aqueous chemistry, and wet removal of aerosol and trace gases in warm clouds. These changes have been implemented in both the WRF-Chem chemistry packages as well as the Kain-Fritsch (KF) cumulus parameterization that has been modified to better represent shallow convective clouds. Testing of the modified WRF-Chem has been completed using observations from the Cumulus Humilis Aerosol Processing Study (CHAPS). The simulation results are used to investigate the impact of cloud-aerosol interactions on regional-scale transport of black carbon (BC), organic aerosol (OA), and sulfate aerosol. Based on the simulations presented here, changes in the column-integrated BC can be as large as -50% when cloud-aerosol interactions are considered (due largely to wet removal), or as large as +40% for sulfate under non-precipitating conditions due to sulfate production in the parameterized clouds. The modifications to WRF-Chem are found to account for changes in the cloud droplet number concentration (CDNC) and changes in the chemical composition of cloud droplet residuals in a way that is consistent with observations collected during CHAPS. Efforts are currently underway to port the changes described here to the latest version of WRF-Chem, and it is anticipated

  13. Volcanic ash transport integrated in the WRF-Chem model: a description of the application and verification results from the 2010 Eyjafjallajökull eruption.

    NASA Astrophysics Data System (ADS)

    Stuefer, Martin; Webley, Peter; Grell, Georg; Freitas, Saulo; Kim, Chang Ki; Egan, Sean

    2013-04-01

    Regional volcanic ash dispersion models are usually offline decoupled from the numerical weather prediction model. Here we describe a new functionality using an integrated modeling system that allows simulating emission, transport, and sedimentation of pollutants released during volcanic activities. A volcanic preprocessor tool has been developed to initialize the Weather Research Forecasting model with coupled Chemistry (WRF-Chem) with volcanic ash and sulphur dioxide emissions. Volcanic ash variables were added into WRF-Chem, and the model was applied to study the 2010 eruption of Eyjafjallajökull. We evaluate our results using WRF-Chem with available ash detection data from satellite and airborne sensors, and from ground based Lidar measurements made available through the AeroCom project. The volcanic ash was distributed into 10 different bins according to the particle size ranging from 2 mm to less than 3.9 μm; different particle size distributions derived from historic eruptions were tested. An umbrella shaped initial ash cloud and an empirical relationship between mass eruption rates and eruption heights were used to initialize WRF-Chem. We show WRF-Chem model verification for the Eyjafjallajökull eruptions, which occurred during the months of April and May 2010. The volcanic ash plume dispersed extensively over Europe. Comparisons with satellite remote sensing volcanic ash retrievals showed good agreement during the events, also ground-based LIDAR compared well to the model simulations. The model sensitivity analysis of the Eyjafjallajökull event showed a considerable bias of ass mass concentrations afar from the volcano depending on initial ash size and eruption rate assumptions. However the WRF-Chem model initialized with reliable eruption source parameters produced good quality forecasts, and will be tested for operational volcanic ash transport predictions.

  14. Examining natural rock varnish and weathering rinds with laser-induced breakdown spectroscopy for application to ChemCam on Mars.

    PubMed

    Lanza, Nina L; Clegg, Samuel M; Wiens, Roger C; McInroy, Rhonda E; Newsom, Horton E; Deans, Matthew D

    2012-03-01

    A laser-induced breakdown spectroscopy (LIBS) instrument is traveling to Mars as part of ChemCam on the Mars Science Laboratory rover. Martian rocks have weathered exteriors that obscure their bulk compositions. We examine weathered rocks with LIBS in a martian atmosphere to improve interpretations of ChemCam rock analyses on Mars. Profile data are analyzed using principal component analysis, and coatings and rinds are examined using scanning electron microscopy and electron probe microanalysis. Our results show that LIBS is sensitive to minor compositional changes with depth and correctly identifies rock type even if the series of laser pulses does not penetrate to unweathered material.

  15. Abu al-Layth al-Libi

    DTIC Science & Technology

    2015-02-01

    jihadi doctrine, al-Libi enrolled himself in the recently erected and highly popular al-Faruq 2 “Al-Sahab Releases ‘Winds of Paradise , Part III...February 2008, http://news.bbc.co.uk/2/hi/south_asia/7220823.stm. 3 “Al-Sahab Releases ‘Winds of Paradise , Part III,’” Global Terrorism Research Project...5 “Al-Sahab Releases ‘Winds of Paradise , Part III,’” Global Terrorism Research Project. 6 Ibid. The date provided in the video is 1410

  16. What Is ALS?

    MedlinePlus

    ... Javits, actor David Niven, “Sesame Street” creator Jon Stone, boxing champion Ezzard Charles, NBA Hall of Fame ... Help for People with ALS and Caregivers Read stories from families living with ALS Forms of ALS ...

  17. Multiyear applications of WRF/Chem over continental U.S.: Model evaluation, variation trend, and impacts of boundary conditions

    NASA Astrophysics Data System (ADS)

    Yahya, Khairunnisa; He, Jian; Zhang, Yang

    2015-12-01

    Multiyear applications of an online-coupled meteorology-chemistry model allow an assessment of the variation trends in simulated meteorology, air quality, and their interactions to changes in emissions and meteorology, as well as the impacts of initial and boundary conditions (ICONs/BCONs) on simulated aerosol-cloud-radiation interactions over a period of time. In this work, the Weather Research and Forecasting model with Chemistry version 3.4.1 (WRF/Chem v. 3.4.1) with the 2005 Carbon Bond mechanism coupled with the Volatility Basis Set module for secondary organic aerosol formation (WRF/Chem-CB05-VBS) is applied for multiple years (2001, 2006, and 2010) over continental U.S. This work also examines the changes in simulated air quality and meteorology due to changes in emissions and meteorology and the model's capability in reproducing the observed variation trends in species concentrations from 2001 to 2010. In addition, the impacts of the chemical ICONs/BCONs on model predictions are analyzed. ICONs/BCONs are downscaled from two global models, the modified Community Earth System Model/Community Atmosphere model version 5.1 (CESM/CAM v5.1) and the Monitoring Atmospheric Composition and Climate model (MACC). The evaluation of WRF/Chem-CB05-VBS simulations with the CESM ICONs/BCONs for 2001, 2006, and 2010 shows that temperature at 2 m (T2) is underpredicted for all three years likely due to inaccuracies in soil moisture and soil temperature, resulting in biases in surface relative humidity, wind speed, and precipitation. With the exception of cloud fraction, other aerosol-cloud variables including aerosol optical depth, cloud droplet number concentration, and cloud optical thickness are underpredicted for all three years, resulting in overpredictions of radiation variables. The model performs well for O3 and particulate matter with diameter less than or equal to 2.5 (PM2.5) for all three years comparable to other studies from literature. The model is able to

  18. Comparison of Deep Convective Transport in Cumulus-Parameterized and Cloud-Resolved WRF-Chem Simulations of Different Scale Storms during the DC3 Field Campaign

    NASA Astrophysics Data System (ADS)

    Li, Y.; Pickering, K. E.; Barth, M. C.; Bela, M.; Cummings, K.; Allen, D. J.; Carey, L. D.; Mecikalski, R.; Fierro, A. O.

    2016-12-01

    Deep convective transport of surface moisture and pollution from the planetary boundary layer (PBL) to the upper troposphere and lower stratosphere (UTLS) can affects the atmospheric radiation budget and climate. This study uses WRF-Chem to analyze deep convective transport in thunderstorms at three different spatial scales from the 2012 Deep Convective Clouds and Chemistry (DC3) field campaign: the May 21 Alabama airmass thunderstorm, May 29 Oklahoma multicell severe convection, and the June 11 mesoscale convective system (MCS). Lightning data assimilation (LDA) is used to improve the WRF-Chem simulations. WRF-Chem with LDA successfully reproduced storm locations, vertical structures and chemical fields. The analysis shows that deep convective transport of pollutants is strongest in the May 29 multi-cell severe convection and weakest in the June 11 MCS case. Tracer experiments demonstrate that the strong rear inflow jet in the June 11 MCS case brought cleaner mid-level air down to the low-level, which then entered the updraft. The injection of this cleaner air weakened the deep convective transport of boundary layer trace gases in the June 11 case by diluting boundary layer air. The cloud-resolved vertical transport results are used to evaluate cloud-parameterized deep convective vertical transport in WRF-Chem run at 15 km horizontal resolution. We examine convective transport from three parameterizations, the modified Kain-Fritsch, Grell 3D, and Grell-Freitas schemes.

  19. ConfChem Conference on Flipped Classroom: Reclaiming Face Time--How an Organic Chemistry Flipped Classroom Provided Access to Increased Guided Engagement

    ERIC Educational Resources Information Center

    Trogden, Bridget G.

    2015-01-01

    Students' active engagement is one of the most critical challenges to any successful learning environment. The blending of active engagement along with rich, meaningful content is necessary for chemical educators to re-examine the purpose of the chemistry classroom. The Spring 2014 ConfChem conference, Flipped Classroom, was held from May 9 to…

  20. ConfChem Conference on Flipped Classroom: Reclaiming Face Time--How an Organic Chemistry Flipped Classroom Provided Access to Increased Guided Engagement

    ERIC Educational Resources Information Center

    Trogden, Bridget G.

    2015-01-01

    Students' active engagement is one of the most critical challenges to any successful learning environment. The blending of active engagement along with rich, meaningful content is necessary for chemical educators to re-examine the purpose of the chemistry classroom. The Spring 2014 ConfChem conference, Flipped Classroom, was held from May 9 to…

  1. Impact of Gas-Phase Mechanisms on Weather Research Forecasting Model with Chemistry (WRF/Chem) Predictions: Mechanism Implementation and Comparative Evaluation

    EPA Science Inventory

    Gas-phase mechanisms provide important oxidant and gaseous precursors for secondary aerosol formation. Different gas-phase mechanisms may lead to different predictions of gases, aerosols, and aerosol direct and indirect effects. In this study, WRF/Chem-MADRID simulations are cond...

  2. Impact of Gas-Phase Mechanisms on Weather Research Forecasting Model with Chemistry (WRF/Chem) Predictions: Mechanism Implementation and Comparative Evaluation

    EPA Science Inventory

    Gas-phase mechanisms provide important oxidant and gaseous precursors for secondary aerosol formation. Different gas-phase mechanisms may lead to different predictions of gases, aerosols, and aerosol direct and indirect effects. In this study, WRF/Chem-MADRID simulations are cond...

  3. Comment on "Simulation of Surface Ozone Pollution in the Central Gulf Coast Region Using WRF/Chem Model: Sensitivity to PBL and Land Surface Physics"

    EPA Science Inventory

    A recently published meteorology and air quality modeling study has several serious deficiencies deserving comment. The study uses the weather research and forecasting/chemistry (WRF/Chem) model to compare and evaluate boundary layer and land surface modeling options. The most se...

  4. 20170403 - Identifying "known unknowns": A comparison between ChemSpider and the US EPA's CompTox Dashboard (ACS Spring National meeting) 1 of 7

    EPA Science Inventory

    Non-targeted analysis (NTA) workflows in high-resolution mass spectrometry require mechanisms for compound identification. One strategy for tentative identification is the use of online chemical databases such as ChemSpider. Databases like this use molecular formulae and monois...

  5. The Chemerin/ChemR23 System Does Not Affect the Pro-Inflammatory Response of Mouse and Human Macrophages Ex Vivo

    PubMed Central

    Luangsay, Souphalone; Devosse, Thalie; de Nadaï, Patricia; Springael, Jean-Yves; Parmentier, Marc; Vosters, Olivier

    2012-01-01

    Macrophages constitute a major component of innate immunity and play an essential role in defense mechanisms against external aggressions and in inflammatory responses. Chemerin, a chemoattractant protein, is generated in inflammatory conditions, and recruits cells expressing the G protein-coupled receptor ChemR23, including macrophages. Chemerin was initially expected to behave as a pro-inflammatory agent. However, recent data described more complex activities that are either pro- or anti-inflammatory, according to the disease model investigated. In the present study, peritoneal macrophages were generated from WT or ChemR23−/− mice, stimulated with lipopolyssaccharide in combination or not with IFN-γ and the production of pro- (TNF-α, IL-1β and IL-6) and anti-inflammatory (IL-10) cytokines was evaluated using qRT-PCR and ELISA. Human macrophages generated from peripheral blood monocytes were also tested in parallel. Peritoneal macrophages from WT mice, recruited by thioglycolate or polyacrylamide beads, functionally expressed ChemR23, as assessed by flow cytometry, binding and chemotaxis assays. However, chemerin had no effect on the strong upregulation of cytokine release by these cells upon stimulation by LPS or LPS/IFN-γ, whatever the concentration tested. Similar data were obtained with human macrophages. In conclusion, our results rule out the direct anti-inflammatory effect of chemerin on macrophages ex vivo, described previously in the literature, despite the expression of a functional ChemR23 receptor in these cells. PMID:22768214

  6. The chemerin/ChemR23 system does not affect the pro-inflammatory response of mouse and human macrophages ex vivo.

    PubMed

    Bondue, Benjamin; De Henau, Olivier; Luangsay, Souphalone; Devosse, Thalie; de Nadaï, Patricia; Springael, Jean-Yves; Parmentier, Marc; Vosters, Olivier

    2012-01-01

    Macrophages constitute a major component of innate immunity and play an essential role in defense mechanisms against external aggressions and in inflammatory responses. Chemerin, a chemoattractant protein, is generated in inflammatory conditions, and recruits cells expressing the G protein-coupled receptor ChemR23, including macrophages. Chemerin was initially expected to behave as a pro-inflammatory agent. However, recent data described more complex activities that are either pro- or anti-inflammatory, according to the disease model investigated. In the present study, peritoneal macrophages were generated from WT or ChemR23(-/-) mice, stimulated with lipopolyssaccharide in combination or not with IFN-γ and the production of pro- (TNF-α, IL-1β and IL-6) and anti-inflammatory (IL-10) cytokines was evaluated using qRT-PCR and ELISA. Human macrophages generated from peripheral blood monocytes were also tested in parallel. Peritoneal macrophages from WT mice, recruited by thioglycolate or polyacrylamide beads, functionally expressed ChemR23, as assessed by flow cytometry, binding and chemotaxis assays. However, chemerin had no effect on the strong upregulation of cytokine release by these cells upon stimulation by LPS or LPS/IFN-γ, whatever the concentration tested. Similar data were obtained with human macrophages. In conclusion, our results rule out the direct anti-inflammatory effect of chemerin on macrophages ex vivo, described previously in the literature, despite the expression of a functional ChemR23 receptor in these cells.

  7. University-School Partnerships: On the Impact on Students of Summer Schools (for School Students Aged 17-18) Run by Bristol ChemLabs

    ERIC Educational Resources Information Center

    Shaw, A. J.; Harrison, T. G.; Croker, S. J.; Medley, M.; Sellou, L.; Shallcross, K. L.; Williams, S, J.; Grayson, D. J.; Shallcross, D. E.

    2010-01-01

    Chemistry summer schools for 17-18 year old school students in the UK were run by Bristol ChemLabS, a Centre for Excellence in Teaching and Learning in Chemistry at the University of Bristol. Students attending were all studying Chemistry at post-16 level (A level in the UK) and experienced not only new practical techniques but also lectures on…

  8. Note: Derivation of two-photon circular dichroism—Addendum to “Two-photon circular dichroism” [J. Chem. Phys. 62, 1006 (1975)

    SciTech Connect

    Friese, Daniel H.

    2015-09-07

    This addendum shows the detailed derivation of the fundamental equations for two-photon circular dichroism which are given in a very condensed form in the original publication [I. Tinoco, J. Chem. Phys. 62, 1006 (1975)]. In addition, some minor errors are corrected and some of the derivations in the original publication are commented.

  9. ChemEd X Data: Exposing Students to Open Scientific Data for Higher-Order Thinking and Self-Regulated Learning

    ERIC Educational Resources Information Center

    Eklund, Brandon; Prat-Resina, Xavier

    2014-01-01

    ChemEd X Data is an open web tool that collects and curates physical and chemical data of hundreds of substances. This tool allows students to navigate, select, and graphically represent data such as boiling and melting points, enthalpies of combustion, and heat capacities for hundreds of molecules. By doing so, students can independently identify…

  10. Correcting for variable laser-target distances of laser-induced breakdown spectroscopy measurements with ChemCam using emission lines of Martian dust spectra

    NASA Astrophysics Data System (ADS)

    Melikechi, N.; Mezzacappa, A.; Cousin, A.; Lanza, N. L.; Lasue, J.; Clegg, S. M.; Berger, G.; Wiens, R. C.; Maurice, S.; Tokar, R. L.; Bender, S.; Forni, O.; Breves, E. A.; Dyar, M. D.; Frydenvang, J.; Delapp, D.; Gasnault, O.; Newsom, H.; Ollila, A. M.; Lewin, E.; Clark, B. C.; Ehlmann, B. L.; Blaney, D.; Fabre, C.

    2014-06-01

    As part of the Mars Science Laboratory, the ChemCam instrument acquires remote laser induced breakdown spectra at distances that vary between 1.56 m and 7 m. This variation in distance affects the intensities of the measured LIBS emission lines in non-trivial ways. To determine the behavior of a LIBS emission line with distance, it is necessary to separate the effects of many parameters such as laser energy, laser spot size, target homogeneity, and optical collection efficiency. These parameters may be controlled in a laboratory on Earth but for field applications or in space this is a challenge. In this paper, we show that carefully selected ChemCam LIBS emission lines acquired from the Martian dust can be used to build an internal proxy spectroscopic standard. This in turn, allows for a direct measurement of the effects of the distance of various LIBS emission lines and hence can be used to correct ChemCam LIBS spectra for distance variations. When tested on pre-launch LIBS calibration data acquired under Martian-like conditions and with controlled and well-calibrated targets, this approach yields much improved agreement between targets observed at various distances. This work lays the foundation for future implementation of automated routines to correct ChemCam spectra for differences caused by variable distance.

  11. Comment on "Simulation of Surface Ozone Pollution in the Central Gulf Coast Region Using WRF/Chem Model: Sensitivity to PBL and Land Surface Physics"

    EPA Science Inventory

    A recently published meteorology and air quality modeling study has several serious deficiencies deserving comment. The study uses the weather research and forecasting/chemistry (WRF/Chem) model to compare and evaluate boundary layer and land surface modeling options. The most se...

  12. ChemEd X Data: Exposing Students to Open Scientific Data for Higher-Order Thinking and Self-Regulated Learning

    ERIC Educational Resources Information Center

    Eklund, Brandon; Prat-Resina, Xavier

    2014-01-01

    ChemEd X Data is an open web tool that collects and curates physical and chemical data of hundreds of substances. This tool allows students to navigate, select, and graphically represent data such as boiling and melting points, enthalpies of combustion, and heat capacities for hundreds of molecules. By doing so, students can independently identify…

  13. Comment on ``Surface diffusion potential energy surfaces from first principles: CO chemisorbed on Pt{110}'' [J. Chem. Phys. 111, 9461 (1999)

    NASA Astrophysics Data System (ADS)

    Graham, A. P.; Toennies, J. P.

    2001-01-01

    In a recent article Ge and King [J. Chem. Phys. 111, 9461 (1999)] question, on the basis of their recent density functional calculations, the interpretation of quasielastic helium atom scattering experiments on surface diffusion. In this comment we attempt to clarify a number of misunderstandings and justify the methods used in the data analysis.

  14. Photochemical Pollution Modeling of Ozone at Metropolitan Area of Porto Alegre - RS/Brazil using WRF/Chem

    NASA Astrophysics Data System (ADS)

    Cuchiara, G. C.; Carvalho, J.

    2013-05-01

    One of the main problems related to air pollution in urban areas is caused by photochemical oxidants, particularly troposphere ozone (O3), which is considered a harmful substance. The O3 precursors (carbon monoxide CO, nitrogen oxides NOx and hydrocarbons HCs) are predominantly of anthropogenic origin in these areas, and vehicles are the main emission sources. Due to the increased urbanization and industrial development in recent decades, air pollutant emissions have increased likewise, mainly by mobile sources in the highly urbanized and developed areas, such as the Metropolitan Area of Porto Alegre-RS (MAPA). According to legal regulations implemented in Brazil in 2005, which aimed at increasing the fraction of biofuels in the national energy matrix, 2% biodiesel were supposed to be added to the fuel mixture within three years, and up to 5% after eight years of implementation of these regulations. Our work performs an analysis of surface concentrations for O3, NOx, CO, and HCs through numerical simulations with WRF/Chem (Weather Research and Forecasting model with Chemistry). The model is validated against observational data obtained from the local urban air quality network for the period from January 5 to 9, 2009 (96 hours). One part of the study focused on the comparison of simulated meteorological variables, to observational data from two stations in MAPA. The results showed that the model simulates well the diurnal evolution of pressure and temperature at the surface, but is much less accurate for wind speed. Another part included the evaluation of model results of WRF/Chem for O3 versus observed data at air quality stations Esteio and Porto Alegre. Comparisons between simulated and observed O3 revealed that the model simulates well the evolution of the observed values, but on many occasions the model did not reproduce well the maximum and minimum concentrations. Finally, a preliminary quantitative sensitivity study on the impact of biofuel on the

  15. Assessing regional scale predictions of aerosols, marine stratocumulus, and their interactions during VOCALS-REx using WRF-Chem

    NASA Astrophysics Data System (ADS)

    Yang, Q.; Gustafson, W. I., Jr.; Fast, J. D.; Wang, H.; Easter, R. C.; Morrison, H.; Lee, Y.-N.; Chapman, E. G.; Spak, S. N.; Mena-Carrasco, M. A.

    2011-12-01

    This study assesses the ability of the recent chemistry version (v3.3) of the Weather Research and Forecasting (WRF-Chem) model to simulate boundary layer structure, aerosols, stratocumulus clouds, and energy fluxes over the Southeast Pacific Ocean. Measurements from the VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) and satellite retrievals (i.e., products from the MODerate resolution Imaging Spectroradiometer (MODIS), Clouds and Earth's Radiant Energy System (CERES), and GOES-10) are used for this assessment. The Morrison double-moment microphysics scheme is newly coupled with interactive aerosols in the model. The 31-day (15 October-16 November 2008) WRF-Chem simulation with aerosol-cloud interactions (AERO hereafter) is also compared to a simulation (MET hereafter) with fixed cloud droplet number concentrations in the microphysics scheme and simplified cloud and aerosol treatments in the radiation scheme. The well-simulated aerosol quantities (aerosol number, mass composition and optical properties), and the inclusion of full aerosol-cloud couplings lead to significant improvements in many features of the simulated stratocumulus clouds: cloud optical properties and microphysical properties such as cloud top effective radius, cloud water path, and cloud optical thickness. In addition to accounting for the aerosol direct and semi-direct effects, these improvements feed back to the simulation of boundary-layer characteristics and energy budgets. Particularly, inclusion of interactive aerosols in AERO strengthens the temperature and humidity gradients within the capping inversion layer and lowers the marine boundary layer (MBL) depth by 130 m from that of the MET simulation. These differences are associated with weaker entrainment and stronger mean subsidence at the top of the MBL in AERO. Mean top-of-atmosphere outgoing shortwave fluxes, surface latent heat, and surface downwelling longwave fluxes are in better agreement with observations

  16. Modeling Urban Air Quality in the Berlin-Brandenburg Region: Evaluation of a WRF-Chem Setup

    NASA Astrophysics Data System (ADS)

    Kuik, F.; Churkina, G.; Butler, T. M.; Lauer, A.; Mar, K. A.

    2015-12-01

    Air pollution is the number one environmental cause of premature deaths in Europe. Despite extensive regulations, air pollution remains a challenging issue, especially in urban areas. For studying air quality in the Berlin-Brandenburg region of Germany the Weather Research and Forecasting Model with Chemistry (WRF-Chem) is set up and evaluated against meteorological and air quality observations from monitoring stations as well as from a field campaign conducted in 2014 (incl. black carbon, VOCs as well as mobile measurements of particle size distribution and particle mass). The model setup includes 3 nested domains with horizontal resolutions of 15km, 3km, and 1km, online biogenic emissions using MEGAN 2.0, and anthropogenic emissions from the TNO-MACC-II inventory. This work serves as a basis for future studies on different aspects of air pollution in the Berlin-Brandenburg region, including how heat waves affect emissions of biogenic volatile organic compounds (BVOC) from urban vegetation (summer 2006) and the impact of selected traffic measures on air quality in the Berlin-Brandenburg area (summer 2014). The model represents the meteorology as observed in the region well for both periods. An exception is the heat wave period in 2006, where the temperature simulated with 3km and 1km resolutions is biased low by around 2°C for urban built-up stations. First results of simulations with chemistry show that, on average, WRF-Chem simulates concentrations of O3 well. However, the 8 hr maxima are underestimated, and the minima are overestimated. While NOx daily means are modeled reasonably well for urban stations, they are overestimated for suburban stations. PM10 concentrations are underestimated by the model. The biases and correlation coefficients of simulated O3, NOx, and PM10 in comparison to surface observations do not show improvements for the 1km domain in comparison to the 3km domain. To improve the model performance of the 1km domain we will include an

  17. Assessing regional scale predictions of aerosols, marine stratocumulus, and their interactions during VOCALS-REx using WRF-Chem

    SciTech Connect

    Yang Q.; Lee Y.; Gustafson Jr., W. I.; Fast, J. D.; Wang, H.; Easter, R. C.; Morrison, H.; Chapman, E. G.; Spak, S. N.; Mena-Carrasco, M. A.

    2011-12-02

    This study assesses the ability of the recent chemistry version (v3.3) of the Weather Research and Forecasting (WRF-Chem) model to simulate boundary layer structure, aerosols, stratocumulus clouds, and energy fluxes over the Southeast Pacific Ocean. Measurements from the VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) and satellite retrievals (i.e., products from the MODerate resolution Imaging Spectroradiometer (MODIS), Clouds and Earth's Radiant Energy System (CERES), and GOES-10) are used for this assessment. The Morrison double-moment microphysics scheme is newly coupled with interactive aerosols in the model. The 31-day (15 October-16 November 2008) WRF-Chem simulation with aerosol-cloud interactions (AERO hereafter) is also compared to a simulation (MET hereafter) with fixed cloud droplet number concentrations in the microphysics scheme and simplified cloud and aerosol treatments in the radiation scheme. The well-simulated aerosol quantities (aerosol number, mass composition and optical properties), and the inclusion of full aerosol-cloud couplings lead to significant improvements in many features of the simulated stratocumulus clouds: cloud optical properties and microphysical properties such as cloud top effective radius, cloud water path, and cloud optical thickness. In addition to accounting for the aerosol direct and semi-direct effects, these improvements feed back to the simulation of boundary-layer characteristics and energy budgets. Particularly, inclusion of interactive aerosols in AERO strengthens the temperature and humidity gradients within the capping inversion layer and lowers the marine boundary layer (MBL) depth by 130 m from that of the MET simulation. These differences are associated with weaker entrainment and stronger mean subsidence at the top of the MBL in AERO. Mean top-of-atmosphere outgoing shortwave fluxes, surface latent heat, and surface downwelling longwave fluxes are in better agreement with observations

  18. Trans-Pacific transport and evolution of aerosols: evaluation of quasi-global WRF-Chem simulation with multiple observations

    NASA Astrophysics Data System (ADS)

    Hu, Zhiyuan; Zhao, Chun; Huang, Jianping; Leung, L. Ruby; Qian, Yun; Yu, Hongbin; Huang, Lei; Kalashnikova, Olga V.

    2016-05-01

    A fully coupled meteorology-chemistry model (WRF-Chem, the Weather Research and Forecasting model coupled with chemistry) has been configured to conduct quasi-global simulation for 5 years (2010-2014) and evaluated with multiple observation data sets for the first time. The evaluation focuses on the simulation over the trans-Pacific transport region using various reanalysis and observational data sets for meteorological fields and aerosol properties. The simulation generally captures the overall spatial and seasonal variability of satellite retrieved aerosol optical depth (AOD) and absorbing AOD (AAOD) over the Pacific that is determined by the outflow of pollutants and dust and the emissions of marine aerosols. The assessment of simulated extinction Ångström exponent (EAE) indicates that the model generally reproduces the variability of aerosol size distributions as seen by satellites. In addition, the vertical profile of aerosol extinction and its seasonality over the Pacific are also well simulated. The difference between the simulation and satellite retrievals can be mainly attributed to model biases in estimating marine aerosol emissions as well as the satellite sampling and retrieval uncertainties. Compared with the surface measurements over the western USA, the model reasonably simulates the observed magnitude and seasonality of dust, sulfate, and nitrate surface concentrations, but significantly underestimates the peak surface concentrations of carbonaceous aerosol likely due to model biases in the spatial and temporal variability of biomass burning emissions and secondary organic aerosol (SOA) production. A sensitivity simulation shows that the trans-Pacific transported dust, sulfate, and nitrate can make significant contribution to surface concentrations over the rural areas of the western USA, while the peaks of carbonaceous aerosol surface concentrations are dominated by the North American emissions. Both the retrievals and simulation show small

  19. Measurement and modeling of O 3 variability in Shanghai, China: Application of the WRF-Chem model

    NASA Astrophysics Data System (ADS)

    Tie, Xuexi; Geng, Fuhai; Peng, Li; Gao, Wei; Zhao, Chunsheng

    Since 2005, Shanghai Meteorological Bureau (SMB) has established an observational network for measuring VOC, NO x, O 3 and aerosols in the Shanghai region. In this study, a rapid O 3 changes from Aug/02/2007 to Aug/11/2007 was observed in the region. During this 10 day period, the noontime O 3 maximum decreased from 100 to 130 ppbv to about 20-30 ppbv. In order to analyze the processes in controlling this rapid change of O 3 during this short period, a newly developed regional chemical/dynamical model (WRF-Chem) is applied to study O 3 variability in the Shanghai region. The model performances are evaluated by comparing the model calculation to the measurement. The result shows that the calculated magnitudes and diurnal variations of O 3 are close to the measured results in city sites, but are underestimated at a rural petroleum industrial site, suggesting that the emissions from petroleum factories around this rural site are significantly underestimated and need to be improved. The calculated rapid changes of O 3 concentrations, O 3 precursors, and aerosols are consistent with the measured results, suggesting that the model is suitable to study the causes of this rapid O 3 change. The model analysis indicates that weather conditions play important roles in controlling the surface O 3 in the Shanghai region. During summer, there is a persistent sub-tropical high pressure system (SUBH) in southeast of Shanghai over Pacific Ocean. During the earlier time of the period (Aug/02-Aug/05), the SUBH system was weak, resulting in weak surface winds. With the calm winds, a noticeable noontime sea-breeze produced an inflow from ocean to land, generating a cycling pattern of wind directions. As a result, the high O 3 concentrations were trapped in the Shanghai region, with a maximum concentration of 100-130 ppbv. By contrast, during the later time of the period (Aug/06-Aug/11), the SUBH was enhanced, resulting in strong surface winds. The high O 3 concentrations formed in the

  20. Temporal evolution of trace gases in a sub-Himalayan region of India: WRF-Chem simulations versus observation

    NASA Astrophysics Data System (ADS)

    Pathak, B.

    2015-12-01

    WRF-Chem has been used to simulate O3 and its precursors, NOx and CO and meteorological variables over the sub-Himalayn North-Eastern region of India including Bangladesh for the year 2012. The model simulation is compared with the observations carried at a location Dibrugarh (27.3ºN, 94.6ºE, 111 m amsl). WRF Chem is capable of simulating the diurnal variability in surface O3 in all the seasons with a good correlation (R2>0.57) between the simulated and observed O3. The model is found to capture the observed seasonal variations in O3 concentrations with maximum during the spring and minimum in monsoon. However, the model overestimates both the minimum and maximum levels by >10ppb in monsoon season and > 20ppb in all other three seasons. Simulated NO is underestimated, mostly during the nighttime in all three seasons (5-20 ppb) except the monsoon (~5ppb) season, when it is overestimated. Simulated NO2 and CO on the other hand, is underestimated in all the seasons. The observed difference may be contributed by the bias in the estimation of the O3 precursors, NOx and CO in the emission inventories or the error in the simulation of the meteorological variables which influences O3 concentration. For example, in the pre-monsoon and winter season, the model simulated shortwave flux overestimates the observation by ~500 Wm-2. While in the monsoon and post monsoon season, simulated shortwave flux is equivalent to the observation. The model predicts high wind speed in all the seasons especially during night-time as against observation. In the post-monsoon and winter season, the simulated wind pattern is reverse to observation with daytime low and night-time high values. Rainfall is overestimated in all the seasons. The night-time overestimation of O3 over this location may also be due to inadequacy of the model's chemistry to properly simulate the night-time level over this location.

  1. ChemCam passive reflectance spectroscopy of the Lubango, Okoruso, and Oudam drill targets in Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Johnson, J. R.; Cloutis, E.; Fraeman, A.; Wiens, R. C.; Maurice, S.; Blaney, D. L.; Gasnault, O.

    2016-12-01

    The ChemCam laser-induced breakdown spectroscopy instrument on the MSL rover Curiosity was used in passive mode (without the laser) to obtain relative reflectance spectra (400-840 nm) of drill tailings and sieved dump piles associated with the targets Lubango, Okoruso, and Oudam between mission sols 1324-1369 near the base of Mt. Sharp. The Lubango and Okoruso drill holes were studied to compare the light-toned zones in the Stimson sandstone (Lubango; 61 wt % SiO2 from ChemCam LIBS data) with nearby unaltered materials (Okoruso; 42 wt % SiO2). Passive spectra of the Lubango tailings (derived from 1-2 cm near the surface) were 50% brighter than the sieved samples (obtained from >2 cm depths). All samples exhibited flat spectra with a slight decrease in reflectance toward the near-infrared. The presence of a weak band near 433 nm (from trace ferric materials such as ferric sulfate) was likely enhanced by the relatively transparent, silica-rich matrix. Lubango was spectrally similar to Greenhorn, another high-silica alteration zone observed in the Stimson unit (Sol 1139). Okoruso passive spectra exhibited flat but increasing reflectance towards the near-infrared with a minor downturn past 800 nm likely related to minor pyroxene. The spectra were darker than the Lubango sieved samples, with no evidence for a 433 nm band. They were similar to the spectra of Big Sky (the unaltered Stimson companion observation to Greenhorn). The Oudam drill tailings pile was observed at two locations: along its outer edge and at a more inward location. Both areas exhibited broad bands near 535 nm and 670 nm and a near-infrared dropoff consistent with hematite. Peak reflectances were near 785 nm for the edge sample but closer to 765 nm for the inner surface (similar to the hematite-bearing Confidence Hills sample from Sol 762). The difference likely results from the presence of other ferric materials in addition to hematite along the edge. This may indicate minor variations in oxidation

  2. Trans-Pacific transport and evolution of aerosols: Evaluation of quasi-global WRF-Chem simulation with multiple observations

    DOE PAGES

    Hu, Zhiyuan; Zhao, Chun; Huang, Jianping; ...

    2016-05-10

    A fully coupled meteorology-chemistry model (WRF-Chem, the Weather Research and Forecasting model coupled with chemistry) has been configured to conduct quasi-global simulation for 5 years (2010–2014) and evaluated with multiple observation data sets for the first time. The evaluation focuses on the simulation over the trans-Pacific transport region using various reanalysis and observational data sets for meteorological fields and aerosol properties. The simulation generally captures the overall spatial and seasonal variability of satellite retrieved aerosol optical depth (AOD) and absorbing AOD (AAOD) over the Pacific that is determined by the outflow of pollutants and dust and the emissions of marine aerosols.more » The assessment of simulated extinction Ångström exponent (EAE) indicates that the model generally reproduces the variability of aerosol size distributions as seen by satellites. In addition, the vertical profile of aerosol extinction and its seasonality over the Pacific are also well simulated. The difference between the simulation and satellite retrievals can be mainly attributed to model biases in estimating marine aerosol emissions as well as the satellite sampling and retrieval uncertainties. Compared with the surface measurements over the western USA, the model reasonably simulates the observed magnitude and seasonality of dust, sulfate, and nitrate surface concentrations, but significantly underestimates the peak surface concentrations of carbonaceous aerosol likely due to model biases in the spatial and temporal variability of biomass burning emissions and secondary organic aerosol (SOA) production. A sensitivity simulation shows that the trans-Pacific transported dust, sulfate, and nitrate can make significant contribution to surface concentrations over the rural areas of the western USA, while the peaks of carbonaceous aerosol surface concentrations are dominated by the North American emissions. Both the retrievals and simulation show

  3. Trans-Pacific transport and evolution of aerosols: Evaluation of quasi-global WRF-Chem simulation with multiple observations

    SciTech Connect

    Hu, Zhiyuan; Zhao, Chun; Huang, Jianping; Leung, L. Ruby; Qian, Yun; Yu, Hongbin; Huang, Lei; Kalashnikova, Olga V.

    2016-05-10

    A fully coupled meteorology-chemistry model (WRF-Chem, the Weather Research and Forecasting model coupled with chemistry) has been configured to conduct quasi-global simulation for 5 years (2010–2014) and evaluated with multiple observation data sets for the first time. The evaluation focuses on the simulation over the trans-Pacific transport region using various reanalysis and observational data sets for meteorological fields and aerosol properties. The simulation generally captures the overall spatial and seasonal variability of satellite retrieved aerosol optical depth (AOD) and absorbing AOD (AAOD) over the Pacific that is determined by the outflow of pollutants and dust and the emissions of marine aerosols. The assessment of simulated extinction Ångström exponent (EAE) indicates that the model generally reproduces the variability of aerosol size distributions as seen by satellites. In addition, the vertical profile of aerosol extinction and its seasonality over the Pacific are also well simulated. The difference between the simulation and satellite retrievals can be mainly attributed to model biases in estimating marine aerosol emissions as well as the satellite sampling and retrieval uncertainties. Compared with the surface measurements over the western USA, the model reasonably simulates the observed magnitude and seasonality of dust, sulfate, and nitrate surface concentrations, but significantly underestimates the peak surface concentrations of carbonaceous aerosol likely due to model biases in the spatial and temporal variability of biomass burning emissions and secondary organic aerosol (SOA) production. A sensitivity simulation shows that the trans-Pacific transported dust, sulfate, and nitrate can make significant contribution to surface concentrations over the rural areas of the western USA, while the peaks of carbonaceous aerosol surface concentrations are dominated by the North American emissions. Both the retrievals and simulation show small

  4. Decadal application of WRF/Chem for regional air quality and climate modeling over the U.S. under the representative concentration pathways scenarios. Part 1: Model evaluation and impact of downscaling

    NASA Astrophysics Data System (ADS)

    Yahya, Khairunnisa; Wang, Kai; Campbell, Patrick; Chen, Ying; Glotfelty, Timothy; He, Jian; Pirhalla, Michael; Zhang, Yang

    2017-03-01

    An advanced online-coupled meteorology-chemistry model, i.e., the Weather Research and Forecasting Model with Chemistry (WRF/Chem), is applied for current (2001-2010) and future (2046-2055) decades under the representative concentration pathways (RCP) 4.5 and 8.5 scenarios to examine changes in future climate, air quality, and their interactions. In this Part I paper, a comprehensive model evaluation is carried out for current decade to assess the performance of WRF/Chem and WRF under both scenarios and the benefits of downscaling the North Carolina State University's (NCSU) version of the Community Earth System Model (CESM_NCSU) using WRF/Chem. The evaluation of WRF/Chem shows an overall good performance for most meteorological and chemical variables on a decadal scale. Temperature at 2-m is overpredicted by WRF (by ∼0.2-0.3 °C) but underpredicted by WRF/Chem (by ∼0.3-0.4 °C), due to higher radiation from WRF. Both WRF and WRF/Chem show large overpredictions for precipitation, indicating limitations in their microphysics or convective parameterizations. WRF/Chem with prognostic chemical concentrations, however, performs much better than WRF with prescribed chemical concentrations for radiation variables, illustrating the benefit of predicting gases and aerosols and representing their feedbacks into meteorology in WRF/Chem. WRF/Chem performs much better than CESM_NCSU for most surface meteorological variables and O3 hourly mixing ratios. In addition, WRF/Chem better captures observed temporal and spatial variations than CESM_NCSU. CESM_NCSU performance for radiation variables is comparable to or better than WRF/Chem performance because of the model tuning in CESM_NCSU that is routinely made in global models.

  5. Assessing the CAM5 Physics Suite in the WRF-Chem Model: Implementation, Resolution Sensitivity, and a First Evaluation for a Regional Case Study

    SciTech Connect

    Ma, Po-Lun; Rasch, Philip J.; Fast, Jerome D.; Easter, Richard C.; Gustafson, William I.; Liu, Xiaohong; Ghan, Steven J.; Singh, Balwinder

    2014-05-06

    A suite of physical parameterizations (deep and shallow convection, turbulent boundary layer, aerosols, cloud microphysics, and cloud fraction) from the global climate model Community Atmosphere Model version 5.1 (CAM5) has been implemented in the regional model Weather Research and Forecasting with chemistry (WRF-Chem). A downscaling modeling framework with consistent physics has also been established in which both global and regional simulations use the same emissions and surface fluxes. The WRF-Chem model with the CAM5 physics suite is run at multiple horizontal resolutions over a domain encompassing the northern Pacific Ocean, northeast Asia, and northwest North America for April 2008 when the ARCTAS, ARCPAC, and ISDAC field campaigns took place. These simulations are evaluated against field campaign measurements, satellite retrievals, and ground-based observations, and are compared with simulations that use a set of common WRF-Chem Parameterizations. This manuscript describes the implementation of the CAM5 physics suite in WRF-Chem provides an overview of the modeling framework and an initial evaluation of the simulated meteorology, clouds, and aerosols, and quantifies the resolution dependence of the cloud and aerosol parameterizations. We demonstrate that some of the CAM5 biases, such as high estimates of cloud susceptibility to aerosols and the underestimation of aerosol concentrations in the Arctic, can be reduced simply by increasing horizontal resolution. We also show that the CAM5 physics suite performs similarly to a set of parameterizations commonly used in WRF-Chem, but produces higher ice and liquid water condensate amounts and near-surface black carbon concentration. Further evaluations that use other mesoscale model parameterizations and perform other case studies are needed to infer whether one parameterization consistently produces results more consistent with observations.

  6. Characterization of LIBS emission lines for the identification of chlorides, carbonates, and sulfates in salt/basalt mixtures for the application to MSL ChemCam data

    NASA Astrophysics Data System (ADS)

    Anderson, D. E.; Ehlmann, B. L.; Forni, O.; Clegg, S. M.; Cousin, A.; Thomas, N. H.; Lasue, J.; Delapp, D. M.; McInroy, R. E.; Gasnault, O.; Dyar, M. D.; Schröder, S.; Maurice, S.; Wiens, R. C.

    2017-04-01

    Ancient environmental conditions on Mars can be probed through the identification of minerals on its surface, including water-deposited salts and cements dispersed in the pore space of sedimentary rocks. Laser-induced breakdown spectroscopy (LIBS) analyses by the Martian rover Curiosity's ChemCam instrument can indicate salts, and ChemCam surveys aid in identifying and selecting sites for further, detailed in situ analyses. We performed laboratory LIBS experiments under simulated Mars conditions with a ChemCam-like instrument on a series of mixtures containing increasing concentrations of salt in a basaltic background to investigate the potential for identifying and quantifying chloride, carbonate, and sulfate salts found only in small amounts, dispersed in bulk rock with ChemCam, rather than concentrated in veins. Data indicate that the presence of emission lines from the basalt matrix limited the number of Cl, C, and S emission lines found to be useful for quantitative analysis; nevertheless, several lines with intensities sensitive to salt concentration were identified. Detection limits for the elements based on individual emission lines ranged from 20 wt % carbonate (2 wt % C), 5-30 wt % sulfate (1-8 wt % S), and 5-10 wt % chloride (3-6 wt % Cl) depending on the basaltic matrix and/or salt cation. Absolute quantification of Cl, C, and S in the samples via univariate analysis depends on the cation-anion pairing in the salt but appears relatively independent of matrices tested, following normalization. These results are promising for tracking relative changes in the salt content of bulk rock on the Martian surface with ChemCam.

  7. The Role of Organic Nitrates in the Chemistry of the Continents: An Assessment Using WRF-CHEM

    NASA Astrophysics Data System (ADS)

    Zare, A.; Cohen, R. C.; Romer, P.

    2015-12-01

    Nitrogen oxides (NOx) play a fundamental role in the chemistry of atmospheric oxidation and affect air quality and climate. Recent experiments have shown that formation of organic nitrates is a more important immediate sink of NOx than nitric acid in the rural continental locations. In particular, in regions with high emissions of biogenic volatile organic compounds (BVOCs), isoprene and monoterpene derived organic nitrates can be expected to control the fate of nitrogen oxides, and consequently the ozone production efficiency. Thus understanding of the complex production and loss processes of organic nitrates are required for determining the lifetime of NOx in the present day and in preindustrial times. Using the chemical transport model WRF-Chem, we investigate impacts of organic nitrate chemistry on the NOx and ozone budgets of the southeastern United States. We evaluate changes to the NOx budget in response to decreases in anthropogenic NOx emissions. The model has been updated with recent advances in representation of BVOC oxidation chemistry and deposition rates, including a detailed representation of organic nitrates. We compared simulations to measurements from the Southern Oxidant and Aerosol Study (SOAS) campaign in central Alabama in summer 2013 and examine the sensitivity to emission rates.

  8. Developing a Dust Emission Climatology for Central Asia Using a Fully Coupled WFR-Chem-DuMo Model

    NASA Astrophysics Data System (ADS)

    Li, L.; Sokolik, I. N.

    2016-12-01

    Airborne mineral dust is thought to have a significant influence on the climate through the absorption and scattering of shortwave and longwave radiation (the direct effect) and by affecting cloud microphysical processes (the indirect effect). A critical physical process that determines that influence is the dust emission. However, a knowledge of long-term dust emissions is highly limited from both temporal and spatial perspectives. Land surface features (soil types and surface soil compositions) are important to simulate the low-frequency dust variability. Accordingly, in this study, we have incorporated a dust module (DuMo) into the WRF-Chem model by accounting for land cover and land use changes (LCLUCs) in the Central Asia from the 1950s to 2010s. Comparisons with previous publications suggest that the coupled model successfully reproduced the dust diurnal cycle in this region. With the source-oriented model, we have developed a quantitative climatology of dust Column Integrated Mass (CIM) for April months from 1950 to 2015. This dataset is statistically correlated with long-term satellite observations, e.g., Aerosol Optical Depth (AOD) and Absorbing Aerosol Index (AAI) in all six dust source regions of the Central Asia. The spatial and temporal variability of dust aerosols is further examined using the climatology dataset, along with dust trends and daily variations.

  9. Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds.

    PubMed

    Prasanna, M D; Vondrasek, Jiri; Wlodawer, Alexander; Rodriguez, H; Bhat, T N

    2006-06-01

    A novel technique to annotate, query, and analyze chemical compounds has been developed and is illustrated by using the inhibitor data on HIV protease-inhibitor complexes. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments. These standard fragments are defined by using criteria, such as chemical classification; structural, chemical, or functional groups; and commercial, scientific or common names or synonyms. These fragments are then organized into a data tree based on their chemical substructures. Search engines have been developed to use this data tree to enable query on inhibitors of HIV protease (http://xpdb.nist.gov/hivsdb/hivsdb.html). These search engines use a new novel technique, Chemical Block Layered Alignment of Substructure Technique (Chem-BLAST) to search on the fragments of an inhibitor to look for its chemical structural neighbors. This novel technique to annotate and query compounds lays the foundation for the use of the Semantic Web concept on chemical compounds to allow end users to group, sort, and search structural neighbors accurately and efficiently. During annotation, it enables the attachment of "meaning" (i.e., semantics) to data in a manner that far exceeds the current practice of associating "metadata" with data by creating a knowledge base (or ontology) associated with compounds. Intended users of the technique are the research community and pharmaceutical industry, for which it will provide a new tool to better identify novel chemical structural neighbors to aid drug discovery.

  10. Comparison of CAM-Chem with Trace Gas Measurements from Airborne Field Campaigns from 2009-2016.

    NASA Astrophysics Data System (ADS)

    Schauffler, S.; Atlas, E. L.; Kinnison, D. E.; Lamarque, J. F.; Saiz-Lopez, A.; Navarro, M. A.; Donets, V.; Blake, D. R.; Blake, N. J.

    2016-12-01

    Trace gas measurements collected during seven field campaigns, two with multiple deployments, will be compared with the NCAR CAM-Chem model to evaluate the model performance over multiple years. The campaigns include HIPPO (2009-2011) pole to pole observations in the Pacific on the NSF/NCAR GV over multiple seasons; SEAC4RS (Aug./Sept., 2013) in the central and southern U.S. and western Gulf of Mexico on the NASA ER-2 and DC8; ATTREX (2011-2015) on the NASA Global Hawk over multiple seasons and locations; CONTRAST (Jan/Feb, 2014) in the western Pacific on the NSF/NCAR GV; VIRGAS (Oct., 2015) in the south central US and western Gulf of Mexico on the NASA WB-57; ORCAS (Jan/Feb, 2016) over the southern ocean on the NSF/NCAR GV; and POSIDON (Oct, 2016) in the western Pacific on the NASA WB-57. We will focus on along the flight tracks comparisons with the model and will also examine comparisons of vertical distributions and various tracer-tracer correlations.

  11. Simulation of West African air pollution during the DACCIWA experiment with the GEOS-Chem West African regional model.

    NASA Astrophysics Data System (ADS)

    Morris, Eleanor; Evans, Mathew

    2017-04-01

    Pollutant emissions from West African cities are forecast to increase rapidly in future years because of extensive economic and population growth, together with poorly regulated industrialisation and urbanisation. Observational constraints in this region are few, leading to poor understanding of present-day air pollution in this region. To increase our understanding of the processes controlling air pollutants over the region, airborne observations were made from three research aircraft based out of Lomé, Togo during the DACCIWA field campaign in June-July 2016. A new 0.25x0.3125 degree West Africa regional version of the GEOS-Chem offline chemical transport model has also been developed to explore the processes controlling pollutants over the region. We evaluate the model using the aircraft data and focus on primary (CO, SO2, NOx, VOCs) and secondary pollutants (O3, aerosol). We find significant differences between the model and the measurements for certain primary compounds which is indicative of significant uncertainties in the base (EDGAR) emissions. For CO (a general tracer of pollution) we evaluate the role of different emissions sources (transport, low temperature combustion, power generation) in determining its concentration in the region. We conclude that the leading cause of uncertainty in our simulation is associated with the emissions datasets and explore the impact of using differing datasets.

  12. Incorporating recent advances in isoprene photooxidation into GEOS-Chem: Effects on oxidant, NOx, and VOC budgets

    NASA Astrophysics Data System (ADS)

    Bates, K. H.; McVay, R.; Teng, A.; Crounse, J.; Nguyen, T.; Praske, E.; Schwantes, R.; St Clair, J. M.; Allen, H.; Seinfeld, J.; Wennberg, P. O.

    2016-12-01

    Because of the large annual flux of isoprene to the atmosphere ( 500 Tg y-1), its gas-phase chemistry and that of its products can exert a strong influence on the oxidative capacity of the troposphere and on the budgets of many trace gases. Recent advances in our understanding of the isoprene photooxidation mechanism, even of minor pathways, may therefore significantly change the concentrations of oxidants and volatile organic compounds (VOCs) predicted by atmospheric models, particularly in heavily forested regions where isoprene dominates total OH reactivity and VOC budgets. Here, we in