WorldWideScience

Sample records for bioinorganic chemistry modeled

  1. Bioinorganic Chemistry

    OpenAIRE

    Bertini, Ivano; Gray, Harry B.; Lippard, Stephen J.; Valentine, Joan Selverstone

    1994-01-01

    This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material...

  2. Bioinorganic Chemistry Modeled with the TPSSh Density Functional

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2008-01-01

    In this work, the TPSSh density functional has been benchmarked against a test set of experimental structures and bond energies for 80 transition-metal-containing diatomics. It is found that the TPSSh functional gives structures of the same quality as other commonly used hybrid and nonhybrid...... promising density functional for use and further development within the field of bioinorganic chemistry....

  3. Institute of Bioinorganic and Radiopharmaceutical Chemistry. Annual report 1992

    International Nuclear Information System (INIS)

    The Institute of Bioinorganic and Radiopharmaceutical Chemistry of the Rossendorf Research Center (FZR) presents its 1992 anual report in order to in form on research activities in the first year of its existence. This volume contains 27 individual reports devoted to various aspects of radiotracers for nuclear medicine. (BBR)

  4. Institute of Bioinorganic and Radiopharmaceutical Chemistry. Annual report 2001

    International Nuclear Information System (INIS)

    In 2001 the Forschungszentrum Rossendorf e.V. continued and further developed its basic and application-oriented research. Research at the Institute of Bioinorganic and Radiopharmaceutical Chemistry, one of five institutes in the Research Centre, was focused on radiotracers as molecular probes to make the human body biochemically transparent with regard to individual molecular reactions. As illustrated by the large number of contributions in this report, the Institute is predominantly engaged in the coordination chemistry and radiopharmacology of technetium and rhenium. (orig.)

  5. Bioinorganic Chemistry of the Alkali Metal Ions.

    Science.gov (United States)

    Kim, Youngsam; Nguyen, Thuy-Tien T; Churchill, David G

    2016-01-01

    The common Group 1 alkali metals are indeed ubiquitous on earth, in the oceans and in biological systems. In this introductory chapter, concepts involving aqueous chemistry and aspects of general coordination chemistry and oxygen atom donor chemistry are introduced. Also, there are nuclear isotopes of importance. A general discussion of Group 1 begins from the prevalence of the ions, and from a comparison of their ionic radii and ionization energies. While oxygen and water molecule binding have the most relevance to biology and in forming a detailed understanding between the elements, there is a wide range of basic chemistry that is potentially important, especially with respect to biological chelation and synthetic multi-dentate ligand design. The elements are widely distributed in life forms, in the terrestrial environment and in the oceans. The details about the workings in animal, as well as plant life are presented in this volume. Important biometallic aspects of human health and medicine are introduced as well. Seeing as the elements are widely present in biology, various particular endogenous molecules and enzymatic systems can be studied. Sodium and potassium are by far the most important and central elements for consideration. Aspects of lithium, rubidium, cesium and francium chemistry are also included; they help in making important comparisons related to the coordination chemistry of Na(+) and K(+). Physical methods are also introduced. PMID:26860297

  6. Bioinorganic Chemistry of the Alkali Metal Ions.

    Science.gov (United States)

    Kim, Youngsam; Nguyen, Thuy-Tien T; Churchill, David G

    2016-01-01

    The common Group 1 alkali metals are indeed ubiquitous on earth, in the oceans and in biological systems. In this introductory chapter, concepts involving aqueous chemistry and aspects of general coordination chemistry and oxygen atom donor chemistry are introduced. Also, there are nuclear isotopes of importance. A general discussion of Group 1 begins from the prevalence of the ions, and from a comparison of their ionic radii and ionization energies. While oxygen and water molecule binding have the most relevance to biology and in forming a detailed understanding between the elements, there is a wide range of basic chemistry that is potentially important, especially with respect to biological chelation and synthetic multi-dentate ligand design. The elements are widely distributed in life forms, in the terrestrial environment and in the oceans. The details about the workings in animal, as well as plant life are presented in this volume. Important biometallic aspects of human health and medicine are introduced as well. Seeing as the elements are widely present in biology, various particular endogenous molecules and enzymatic systems can be studied. Sodium and potassium are by far the most important and central elements for consideration. Aspects of lithium, rubidium, cesium and francium chemistry are also included; they help in making important comparisons related to the coordination chemistry of Na(+) and K(+). Physical methods are also introduced.

  7. Institute of Bioinorganic and Radiopharmaceutical Chemistry. Annual report 2000

    International Nuclear Information System (INIS)

    In 2000 the Rossendorf research centre continued and further developed its basic and application-oriented research. Research at the Institute of Bioinorganic and Radiopharmaceutical Chemistry, one of five institutes in the Research Centre, was focused on radiotracers as molecular probes to make the human body biochemically transparent with regard to individual molecular reactions. In this respect the potential for diagnostic application depends on the quality and versatility of radiopharmaceutical chemistry, which is the main discipline in our Institute. Areas in which the Institute was particularly active were the design of new radiotracers, both radiometal-based and natural organic molecules, the elaboration of radiolabelling concepts and procedures and the chemical and pharmacological evaluation of new tracers. This was complemented by more clinically oriented activities in the Positron Emission Tomography Centre Rossendorf. With numerous contributions in the fields of radiopharmaceutical chemistry, tumour agents, tumour diagnosis and brain biochemistry this Annual Report will document the scientific progress made in 2000. (orig.)

  8. Theoretical bioinorganic chemistry: the electronic structure makes a difference.

    Science.gov (United States)

    Kirchner, Barbara; Wennmohs, Frank; Ye, Shengfa; Neese, Frank

    2007-04-01

    Theoretical bioinorganic and biomimetic chemistry involves the careful description of the electronic structure: for example, 'valence bond reading' of broken-symmetry density functional theory computations gives insight into the structure and bonding of metal-radical systems with complex electronic structures. Exploring the reactivities of such systems leads to the design of novel compounds with better reactivities. Combined quantum-mechanics/molecular-mechanics (QM/MM), where the QM part is a sophisticated ab initio method, aids in understanding nature's most complicated reaction mechanisms in atomic detail. First principles molecular dynamics simulations (Car-Parrinello simulations) open up exciting new avenues for studying transition metal centers and enable several questions to be addressed that cannot be resolved with either standard quantum chemical or traditional force-field methods. PMID:17349817

  9. Carbonic Anhydrase and Metalloderivatives: A Bioinorganic Chemistry Study

    Science.gov (United States)

    McQuate, Robert S.

    1977-01-01

    Discusses selected bioinorganic aspects of carbonic anhydrase and describes experiments that will reinforce the students' understanding of the presence and essential role that metal ions have in some biological systems. (SL)

  10. Integrating Bio-Inorganic and Analytical Chemistry into an Undergraduate Biochemistry Laboratory

    Science.gov (United States)

    Erasmus, Daniel J.; Brewer, Sharon E.; Cinel, Bruno

    2015-01-01

    Undergraduate laboratories expose students to a wide variety of topics and techniques in a limited amount of time. This can be a challenge and lead to less exposure to concepts and activities in bio-inorganic chemistry and analytical chemistry that are closely-related to biochemistry. To address this, we incorporated a new iron determination by…

  11. Forschungszentrum Rossendorf, Institute of Bioinorganic and Radiopharmaceutical Chemistry. Annual report 1995

    International Nuclear Information System (INIS)

    Research at the Institute of Bioinorganic and Radiopharmaceutical Chemistry of the Research Center Rossendorf is focused on radiotracers as molecular probes for diagnosis of disease. The research effort has two main components: -Positron emission tomography (PET) - technetium chemistry and radiopharmacology. The research activities of the Institute have been performed in three administratively classified groups. A PET tracer group is engaged in the chemistry and radiopharmacy of 11C and 18F compounds and in the setup of the PET center. A SPECT tracer group deals with the design, synthesis and chemical characterization of metal coordination compounds, primarily rhenium and technetium complexes. A biochemical group is working on SPECT and PET-relevant biochemical and biological projects. This includes the characterization and assessment of new compounds developed in the two synthetically oriented groups. The annual report presented here covers the research activities of the Institute of Bioinorganic and Radiopharmaceutical Chemistry in 1995. (orig.)

  12. Integrating bio-inorganic and analytical chemistry into an undergraduate biochemistry laboratory.

    Science.gov (United States)

    Erasmus, Daniel J; Brewer, Sharon E; Cinel, Bruno

    2015-01-01

    Undergraduate laboratories expose students to a wide variety of topics and techniques in a limited amount of time. This can be a challenge and lead to less exposure to concepts and activities in bio-inorganic chemistry and analytical chemistry that are closely-related to biochemistry. To address this, we incorporated a new iron determination by atomic absorption spectroscopy exercise as part of a five-week long laboratory-based project on the purification of myoglobin from beef. Students were required to prepare samples for chemical analysis, operate an atomic absorption spectrophotometer, critically evaluate their iron data, and integrate these data into a study of myoglobin.

  13. Institute of Bioinorganic and Radiopharmaceutical Chemistry. Annual report 1993

    International Nuclear Information System (INIS)

    The subjects of the present report are described in this volume in 41 reports dealing with various aspects of radiotracers for nuclear medicine. This first part describes synthetic work on 11C-tracers and precursors. The papers on technetium/rhenium chemistry describes the efforts to gain a deeper insight into the reactions taking place in intricate Tc/Re-ligand systems, to design more suitable and variable chelate units, and to start functionalizing these complexes in order to make them mimics of biochemical substrates or drugs. Progress has been achieved in the complexation of SH-containing peptides, mainly by the introduction of N-alkylation, which remarkably influences the properties of the complexes, by systematic alteration of the peptide chain length and derivatization. (orig./EF)

  14. Forschungszentrum Rossendorf. Institute of Bioinorganic and Radiopharmaceutical Chemistry. Annual report 2002

    International Nuclear Information System (INIS)

    In 2002 the Institute of Bioinorganic and Radiopharmaceutical Chemistry, one of five institutes in the Forschungszentrum Rossendorf e.V., continued and further developed its basic and application-oriented research. Research was focused on radiotracers as molecular probes to make the human body biochemically transparent with regard to individual molecular reactions. While further pursuing and extending our chemical, biological and medical activities in the PET Centre and being engaged in the coordination chemistry and radiopharmacology of technetium, rhenium and other metals, new lines of activity have also been opened up recently. This involves bioactive substances as they are present in food. Such substances may cause a health risk or may exert effects not yet fully understood. New biotechnological procedures in food processing also give rise to new questions that can be addressed by PET. As illustrated by the majority of contributions in this report, the Institute is predominantly engaged in radiopharmaceutical chemistry of both radiometals and the PET nuclides carbon-11 and fluorine-18. The improvement of labelling methods continued to remain an area of considerable endeavour. The review article on radiochemistry with the short-lived positron emitters 11C and 18F is meant to emphasize this field of research and to help to classify our contribution to this area. As for the radiometals, our studies agree with the more and more demanding insight that the coordination has a not sufficiently predictable impact on the in vivo behaviour of the molecule into which the chelate unit is integrated. Therefore, attempts to better understand and adjust the in vivo behaviour of the radiotracers are being continued. In order to reflect on and identify trends and perspectives, the Institute organized on March 7-8, 2002, an international conference on advances and perspectives in radiotracer development. The Institute's chemically and radiopharmacologically oriented activities

  15. The Inorganic Illustrator: A 3-D Graphical Supplement for Inorganic and Bioinorganic Chemistry Courses Distributed on CD-ROM

    Science.gov (United States)

    Childs, Scott L.; Hagen, Karl S.

    1996-10-01

    The visualization of molecular and solid state chemical structures in three dimensions is a particularly difficult problem for students to overcome when the primary means of communication is the two-dimensional world of textbooks, blackboards, and overhead projector screens. Recent editions of popular textbooks in organic, inorganic, and biochemistry have included stereoviews of molecules to aid the student, and stereoviews of crystal structures have been used in inorganic chemistry publications for many years. These are powerful aids for visualizing complex molecules, but with the exception of the biochemistry text mentioned above, they are limited to single, static images generally in black and white. Molecular model kits are routinely used very effectively in organic chemistry but their utility in inorganic chemistry is limited to all but the most simple molecules encountered. Now that personal computers are generally accessible and multimedia tools are starting to make an appearance in chemistry lecture halls (1), we can make our inorganic and bioinorganic chemistry and crystallography lectures come alive with the aid of the computer-based resources, which are the essence of this project. As part of this project we are accumulating a database of representative crystal structures of main group molecules, coordination complexes, organometallic compounds, small metalloproteins, bioinorganic model complexes, clusters, and solid state materials in Chem3D Plus format to be viewed with Chem3D Viewer, which is free software from Cambridge Scientific Computing. We are also generating a library of high-quality graphic images of these same molecules and structures using Cerius2 package from Molecular Simulations. These include polyhedral representations of clusters and solid state structures (see Fig. 1). Figure 1. Representation of the user interface: the title page and an example of polyhedral and ball-and-stick representation of an octanuclear iron-oxo cluster. The

  16. Uma visão da química bioinorgânica medicinal Medicinal bioinorganic chemistry

    Directory of Open Access Journals (Sweden)

    Anna Maria Canavarro Benite

    2007-01-01

    Full Text Available Metals play a vital role in human and plant physiology and important research is directed towards exploring the interrelated mechanisms that govern their interactions with biomolecules. Bioinorganic medicinal chemistry studies the functions, processing, storage and applications of metal ions and their complexes in biological systems. This paper presents a brief discussion about on interactions of metals with biomolecules that determine their intracellular accumulation, where metal ions may fulfill essential functions in cellular metabolism or, in certain cases, exert toxic effects towards cells.

  17. Molecular Modeling of Heme Proteins Using MOE: Bio-Inorganic and Structure-Function Activity for Undergraduates

    Science.gov (United States)

    Ray, Gigi B.; Cook, J. Whitney

    2005-01-01

    A biochemical molecular modeling project on heme proteins suitable for an introductory Biochemistry I class has been designed with a 2-fold objective: i) to reinforce the correlation between protein three-dimensional structure and function through a discovery oriented project, and ii) to introduce students to the fields of bioinorganic and…

  18. Development of high resolution x-ray spectrometers for the investigation of bioinorganic chemistry in metalloproteins

    Science.gov (United States)

    Drury, Owen Byron

    used to measure its oxidation state despite the very small chemical shifts. We also have taken spectra on the molybdenum M-edges and on the sulfur L-edges of inorganic model compounds.

  19. 2010 Environmental Bioinorganic Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Rachael Austin

    2010-06-18

    This interdisciplinary meeting will gather together scientists - structural biologists, chemists, geneticists, chemical and biological oceanographers, geochemists, and other specialist - who study the flows of essential and toxic elements through the environment and living systems, on timescales ranging from femptoseconds to eons. Of particular interest are the molecular mechanisms that govern element acquisition and use in organisms, and the tools and techniques used to study these phenomena. The aim of this community is to use these molecular-scale insights to understand the interconnected biotic and abiotic processes that shape the macroscopic environment and its development and change over a range of time scales.

  20. COMe: the ontology of bioinorganic proteins

    Directory of Open Access Journals (Sweden)

    Contrino Sergio

    2004-02-01

    Full Text Available Abstract Background Many characterised proteins contain metal ions, small organic molecules or modified residues. In contrast, the huge amount of data generated by genome projects consists exclusively of sequences with almost no annotation. One of the goals of the structural genomics initiative is to provide representative three-dimensional (3-D structures for as many protein/domain folds as possible to allow successful homology modelling. However, important functional features such as metal co-ordination or a type of prosthetic group are not always conserved in homologous proteins. So far, the problem of correct annotation of bioinorganic proteins has been largely ignored by the bioinformatics community and information on bioinorganic centres obtained by methods other than crystallography or NMR is only available in literature databases. Results COMe (Co-Ordination of Metals represents the ontology for bioinorganic and other small molecule centres in complex proteins. COMe consists of three types of entities: 'bioinorganic motif' (BIM, 'molecule' (MOL, and 'complex proteins' (PRX, with each entity being assigned a unique identifier. A BIM consists of at least one centre (metal atom, inorganic cluster, organic molecule and two or more endogenous and/or exogenous ligands. BIMs are represented as one-dimensional (1-D strings and 2-D diagrams. A MOL entity represents a 'small molecule' which, when in complex with one or more polypeptides, forms a functional protein. The PRX entities refer to the functional proteins as well as to separate protein domains and subunits. The complex proteins in COMe are subdivided into three categories: (i metalloproteins, (ii organic prosthetic group proteins and (iii modified amino acid proteins. The data are currently stored in both XML format and a relational database and are available at http://www.ebi.ac.uk/come/. Conclusion COMe provides the classification of proteins according to their 'bioinorganic' features

  1. 2014 Penn State Bioinorganic Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Golbeck, John [Pennsylvania State Univ., State College, PA (United States)

    2015-10-01

    The 3rd Penn State Bioinorganic Workshop took place in early June 2014 and was combined with the 3rd Penn State Frontiers in Metallobiochemistry Symposium. The workshop was even larger than the 2nd Penn State Bioinorganic Workshop we offered in 2012. It had even more participants (162 rather than 123 in 2012). Like the 2012 workshop, the 2014 workshop had three parts. The first part consisted of 16 90-minute lectures presented by faculty experts on the topic of their expertise (see below). Based on the suggestions from the 2012 workshop, we have recorded all 16 lectures professionally and make them available to the entire bioinorganic community via online streaming. In addition, hard copies of the recordings are available as backup.

  2. Applications of Inorganic Chemistry in Biology: An Interdisciplinary Graduate Course

    Science.gov (United States)

    Farrell, Nicholas; Ross, Paul; Roat, Rosette M.

    1998-06-01

    Inorganic chemistry faculty at Virginia Commonwealth University (VCU) are offering an advanced, interdisciplinary, graduate course entitled "Applications of Inorganic Chemistry in Biology". The course utilizes examples from bioinorganic chemistry to introduce advanced topics in synthesis, structural analysis, and analytical methods that are practiced by inorganic chemists. Emphasis is placed on the structure and function of trace and ultratrace transition metals in biological systems and on the use of metals for medicinal purposes. Instrumental techniques such as electron paramagnetic resonance, Mössbauer spectroscopy, and X-ray crystallography are explained in the detail necessary to familiarize students with their use for analysis of bioinorganic systems and their models. Students have take-home examinations during the term and write a term paper describing a metalloprotein whose X-ray structure data is listed in Brookhaven protein data base. The paper follows the same course pattern of classroom discussion of a bioinorganic system, concentrating on the coordination geometry and nearest neighbor contacts of the metal-binding site in the protein, substrate binding site, and relevance to the metalloprotein or enzyme function, mechanism of action of the enzyme or protein, spectroscopic studies on the metal-binding site, and model studies for the protein's metal-binding site. The instructors conclude that their basic goals for the course - introduction to advanced inorganic chemistry topics using bioinorganic examples with emphasis on primary literature sources and computer-assisted displays - are being accomplished.

  3. Metaphorical Models in Chemistry.

    Science.gov (United States)

    Rosenfeld, Stuart; Bhusan, Nalini

    1995-01-01

    What happens when students of chemistry fail to recognize the metaphorical status of certain models and interpret them literally? Suggests that such failures lead students to form perceptions of phenomena that can be misleading. Argues that the key to making good use of metaphorical models is a recognition of their metaphorical status. Examines…

  4. Ecosustainable Development of Novel Bio-inorganic Hybrid Materials as UV Protection Systems for Potential Cosmetic Applications.

    Science.gov (United States)

    Villa, Carla; Lacapra, Chiara; Rosa, Roberto; Veronesi, Paolo; Leonelli, Cristina

    2015-01-01

    A new organoclay, bio-inorganic hybrid material, was successfully prepared following the "green chemistry" principles, exploiting microwave irradiation (as an alternative energetic source) in both the solvent-free synthesis of the organic filler (UVB filter) and in its hydrothermal intercalation in a sodium Bentonite clay (renewable natural inorganic source at low temperature). The organic filler is a benzylidene camphor derivative with the same cationic moiety as the well- known UV filter camphor benzalkonium methosulfate. The aim of the research was the ecosustainable development of a new UV protection model, suitable for use in cosmetic and pharmaceutical products, with potential advantages of stability, efficiency and safety compared to the commercially available UVB sunscreens. The organically modified clay was thoroughly investigated using X-ray diffraction (XRD), infrared spectroscopy (IR), thermo gravimetric analysis and differential thermal analysis (DTA). Results confirmed the complete intercalation of the organic filler in the interlayer region of the smectite clay, leading to a new bio-inorganic hybrid material with potential for cosmetic and pharmaceutical applications in the UV protection field, as confirmed by preliminary photochemical studies. This work represents the first example in the use of Na-Bentonite cationic clay (usually employed as rheological additive) as hosting agent of the synthesized quaternary UVB filter, as well as in the complete MW-assisted preparation of the organoclay, starting from the synthesis of the organic UV sunscreen to its hydrothermal intercalation.

  5. Advanced Chemistry Basins Model

    Energy Technology Data Exchange (ETDEWEB)

    Blanco, Mario; Cathles, Lawrence; Manhardt, Paul; Meulbroek, Peter; Tang, Yongchun

    2003-02-13

    The objective of this project is to: (1) Develop a database of additional and better maturity indicators for paleo-heat flow calibration; (2) Develop maturation models capable of predicting the chemical composition of hydrocarbons produced by a specific kerogen as a function of maturity, heating rate, etc.; assemble a compositional kinetic database of representative kerogens; (3) Develop a 4 phase equation of state-flash model that can define the physical properties (viscosity, density, etc.) of the products of kerogen maturation, and phase transitions that occur along secondary migration pathways; (4) Build a conventional basin model and incorporate new maturity indicators and data bases in a user-friendly way; (5) Develop an algorithm which combines the volume change and viscosities of the compositional maturation model to predict the chemistry of the hydrocarbons that will be expelled from the kerogen to the secondary migration pathways; (6) Develop an algorithm that predicts the flow of hydrocarbons along secondary migration pathways, accounts for mixing of miscible hydrocarbon components along the pathway, and calculates the phase fractionation that will occur as the hydrocarbons move upward down the geothermal and fluid pressure gradients in the basin; and (7) Integrate the above components into a functional model implemented on a PC or low cost workstation.

  6. Heterogeneous Chemistry in Global Chemistry Transport Models

    Science.gov (United States)

    Stadtler, Scarlet; Simpson, David; Schultz, Martin; Bott, Andreas

    2016-04-01

    The impact of six tropospheric heterogeneous reactions on ozone and nitrogen species was studied using two chemical transport models EMEP MSC-W and ECHAM6-HAMMOZ. Since heterogeneous reactions depend on reactant concentrations (in this study these are N_2O_5, NO_3, NO_2, O_3, HNO_3, HO_2) and aerosol surface area S_a, the modeled surface area of both models was compared to a satellite product retrieving the surface area. This comparison shows a good agreement in global pattern and especially the capability of both models to capture the extreme aerosol loadings in East Asia. Further, the impact of the heterogeneous reactions was evaluated by the simulation of a reference run containing all heterogeneous reactions and several sensitivity runs. One reaction was turned off in each sensitivity run to compare it with the reference run. As previously shown, the analysis of the sensitivity runs shows that the globally most important heterogeneous reaction is the one of N_2O_5. Nevertheless, NO_2, NO_3, HNO3 and HO2 heterogeneous reactions gain relevance particular in East China due to presence of high NOx concentrations and high Sa in the same region. The heterogeneous reaction of O3 itself on dust is compared to the other heterogeneous reactions of minor relevance. Evaluation of the models with northern hemispheric ozone surface observations yields a better agreement of the models with observations when the heterogeneous reactions are incorporated. Impacts of emission changes on the importance of the heterogeneous chemistry will be discussed.

  7. Simplified Model for Reburning Chemistry

    DEFF Research Database (Denmark)

    Glarborg, Peter; Hansen, Stine

    2010-01-01

    In solid fuel flames, reburn-type reactions are often important for the concentrations of NOx in the near-burner region. To be able to model the nitrogen chemistry in these flames, it is necessary to have an adequate model for volatile/NO interactions. Simple models consisting of global steps...

  8. Microbial Metallomics: A Bioinorganic Perspective

    Science.gov (United States)

    Elliott, S. J.

    2004-12-01

    The term "metallome", as described by R.J.P. Williams is synonymous with the instantaneously determined concentration of all inorganic species within a cellular system [1]. Here, we refine this definition to specify that metallomics should reflect not only the overall content of inorganic species in cells, but the chemical identity of such species (i.e., in both ligated and unligated states) a well as their location. Of particular interest to the metallobiochemist are the roles inorganic species play in the up- and down-regulation of protein expression in cells. Thus, we consider that a fully realized "metallome" will reflect the biochemical pathways associated with metal ion speciation and localization within cells. Here we will describe currently proposed strategy and methodology that is used by the Elliott Lab of Boston University to capture snapshots of the proteomic and metallomic landscape of a variety of microbial systems. Two such systems will be described in some detail. The first is Methylococcus capsulatus (Bath), a methanotrophic organism that is known to undergo dramatic morphological changes upon the introduction of varying concentrations of Fe and Cu in the growth medium. In particular, the introduction of increasing concentrations of copper induces the expression of extensive intracytosolic membranes [2]. The Fe:Cu ratio also controls the expression of gene transcripts for soluble and particulate methane monooxygenase enzymes. This provides a unique opportunity to explore metal sensing, uptake, speciation and localization in methanotrophs. A developing model of protein expression and metal input will be discussed. Specific metallomic experiments regarding Shewanella oneidensis will also be discussed, in the context of an ongoing effort to understand how this organism can utilize a dazzling array of electron acceptors, including Fe(III), Mn(IV), nitrite, DMSO, TMAO, and fumarate. [1] R.J.P. Williams, Coord. Chem. Rev., 216:583-595 (2001). [2] C

  9. Artificial cytoskeletal structures within enzymatically active bio-inorganic protocells.

    Science.gov (United States)

    Kumar, Ravinash Krishna; Li, Mei; Olof, Sam N; Patil, Avinash J; Mann, Stephen

    2013-02-11

    The fabrication of enzymatically active, semi-permeable bio-inorganic protocells capable of self-assembling a cytoskeletal-like interior and undergoing small-molecule dephosphorylation reactions is described. Reversible disassembly of an amino acid-derived supramolecular hydrogel within the internalized reaction space is used to tune the enzymatic activity of the nanoparticle-bounded inorganic compartments. PMID:23027575

  10. Aqueous vanadium ion dynamics relevant to bioinorganic chemistry: A review.

    Science.gov (United States)

    Kustin, Kenneth

    2015-06-01

    Aqueous solutions of the four highest vanadium oxidation states exhibit four diverse colors, which only hint at the diverse reactions that these ions can undergo. Cationic vanadium ions form complexes with ligands; anionic vanadium ions form complexes with ligands and self-react to form isopolyanions. All vanadium species undergo oxidation-reduction reactions. With a few exceptions, elucidation of the dynamics of these reactions awaited the development of fast reaction techniques before the kinetics of elementary ligation, condensation, reduction, and oxidation of the aqueous vanadium ions could be investigated. As the biological roles played by endogenous and therapeutic vanadium expand, it is appropriate to bring the results of the diverse kinetics studies under one umbrella. To achieve this goal this review presents a systematic examination of elementary aqueous vanadium ion dynamics. PMID:25578410

  11. Expanding coordination chemistry from protein to protein assembly.

    Science.gov (United States)

    Sanghamitra, Nusrat J M; Ueno, Takafumi

    2013-05-14

    Bioinorganic chemistry is of growing importance in the fields of nanomaterial science and biotechnology. Coordination of metals by biological systems is a crucial step in intricate enzymatic reactions such as photosynthesis, nitrogen fixation and biomineralization. Although such systems employ protein assemblies as molecular scaffolds, the important roles of protein assemblies in coordination chemistry have not been systematically investigated and characterized. Many researchers are joining the field of bioinorganic chemistry to investigate the inorganic chemistry of protein assemblies. This area is emerging as an important next-generation research field in bioinorganic chemistry. This article reviews recent progress in rational design of protein assemblies in coordination chemistry for integration of catalytic reactions using metal complexes, preparation of mineral biomimetics, and mechanistic investigations of biomineralization processes with protein assemblies. The unique chemical properties of protein assemblies in the form of cages, tubes, and crystals are described in this review.

  12. Modeling the atmospheric chemistry of TICs

    Science.gov (United States)

    Henley, Michael V.; Burns, Douglas S.; Chynwat, Veeradej; Moore, William; Plitz, Angela; Rottmann, Shawn; Hearn, John

    2009-05-01

    An atmospheric chemistry model that describes the behavior and disposition of environmentally hazardous compounds discharged into the atmosphere was coupled with the transport and diffusion model, SCIPUFF. The atmospheric chemistry model was developed by reducing a detailed atmospheric chemistry mechanism to a simple empirical effective degradation rate term (keff) that is a function of important meteorological parameters such as solar flux, temperature, and cloud cover. Empirically derived keff functions that describe the degradation of target toxic industrial chemicals (TICs) were derived by statistically analyzing data generated from the detailed chemistry mechanism run over a wide range of (typical) atmospheric conditions. To assess and identify areas to improve the developed atmospheric chemistry model, sensitivity and uncertainty analyses were performed to (1) quantify the sensitivity of the model output (TIC concentrations) with respect to changes in the input parameters and (2) improve, where necessary, the quality of the input data based on sensitivity results. The model predictions were evaluated against experimental data. Chamber data were used to remove the complexities of dispersion in the atmosphere.

  13. Stratospheric General Circulation with Chemistry Model (SGCCM)

    Science.gov (United States)

    Rood, Richard B.; Douglass, Anne R.; Geller, Marvin A.; Kaye, Jack A.; Nielsen, J. Eric; Rosenfield, Joan E.; Stolarski, Richard S.

    1990-01-01

    In the past two years constituent transport and chemistry experiments have been performed using both simple single constituent models and more complex reservoir species models. Winds for these experiments have been taken from the data assimilation effort, Stratospheric Data Analysis System (STRATAN).

  14. Applications of density functional theory to iron-containing molecules of bioinorganic interest.

    Science.gov (United States)

    Hirao, Hajime; Thellamurege, Nandun; Zhang, Xi

    2014-01-01

    The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.

  15. Modelling the atmospheric chemistry of volcanic plumes

    OpenAIRE

    Surl, Luke

    2016-01-01

    Abstract Volcanoes are the principal way by which volatiles are transferred from the solid Earth to the atmosphere-hydrosphere system. Once released into the atmosphere, volcanic emissions rapidly undergo a complex series of chemical reactions. This thesis seeks to further the understanding of such processes by both observation and numerical modelling. I have adapted WRF-Chem to model passive degassing from Mount Etna, the chemistry of its plume, and its influence on the ...

  16. Volcanic Plume Chemistry: Models, Observations and Impacts

    Science.gov (United States)

    Roberts, Tjarda; Martin, Robert; Oppenheimer, Clive; Griffiths, Paul; Braban, Christine; Cox, Tony; Jones, Rod; Durant, Adam; Kelly, Peter

    2010-05-01

    Volcanic plumes are highly chemically reactive; both in the hot, near-vent plume, and also at ambient temperatures in the downwind plume, as the volcanic gases and aerosol disperse into the background atmosphere. In particular, DOAS (Differential Optical Absortpion Spectroscopy) observations have identified BrO (Bromine Monoxide) in several volcanic plumes degassing into the troposphere. These observations are explained by rapid in-plume autocatalytic BrO-chemistry that occurs whilst the plume disperses, enabling oxidants such as ozone from background air to mix with the acid gases and aerosol. Computer modelling tools have recently been developed to interpret the observed BrO and predict that substantial ozone depletion occurs downwind. Alongside these modelling developments, advances in in-situ and remote sensing techniques have also improved our observational understanding of volcanic plumes. We present simulations using the model, PlumeChem, that predict the spatial distribution of gases in volcanic plumes, including formation of reactive halogens BrO, ClO and OClO that are enhanced nearer the plume edges, and depletion of ozone within the plume core. The simulations also show that in-plume chemistry rapidly converts NOx into nitric acid, providing a mechanism to explain observed elevated in-plume HNO3. This highlights the importance of coupled BrO-NOx chemistry, both for BrO-formation and as a production mechanism for HNO3 in BrO-influenced regions of the atmosphere. Studies of coupled halogen-H2S-chemistry are consistent with in-situ Alphasense electrochemical sensor observations of H2S at a range of volcanoes, and only predict H2S-depletion if Cl is additionally elevated. Initial studies regarding the transformations of mercury within volcanic plumes suggest that significant in-plume conversion of Hg0 to Hg2+ can occur in the downwind plume. Such Hg2+ may impact downwind ecology through enhanced Hg-deposition, and causing enhanced biological uptake of

  17. Advances in atmospheric chemistry modeling: the LLNL impact tropospheric/stratospheric chemistry model

    Energy Technology Data Exchange (ETDEWEB)

    Rotman, D A; Atherton, C

    1999-10-07

    We present a unique modeling capability to understand the global distribution of trace gases and aerosols throughout both the troposphere and stratosphere. It includes the ability to simulate tropospheric chemistry that occurs both in the gas phase as well as on the surfaces of solid particles. We have used this capability to analyze observations from particular flight campaigns as well as averaged observed data. Results show the model to accurately simulate the complex chemistry occurring near the tropopause and throughout the troposphere and stratosphere.

  18. Algebraic Turbulence-Chemistry Interaction Model

    Science.gov (United States)

    Norris, Andrew T.

    2012-01-01

    The results of a series of Perfectly Stirred Reactor (PSR) and Partially Stirred Reactor (PaSR) simulations are compared to each other over a wide range of operating conditions. It is found that the PaSR results can be simulated by a PSR solution with just an adjusted chemical reaction rate. A simple expression has been developed that gives the required change in reaction rate for a PSR solution to simulate the PaSR results. This expression is the basis of a simple turbulence-chemistry interaction model. The interaction model that has been developed is intended for use with simple one-step global reaction mechanisms and for steady-state flow simulations. Due to the simplicity of the model there is very little additional computational cost in adding it to existing CFD codes.

  19. Genetic Algorithm Approaches to Prebiobiotic Chemistry Modeling

    Science.gov (United States)

    Lohn, Jason; Colombano, Silvano

    1997-01-01

    We model an artificial chemistry comprised of interacting polymers by specifying two initial conditions: a distribution of polymers and a fixed set of reversible catalytic reactions. A genetic algorithm is used to find a set of reactions that exhibit a desired dynamical behavior. Such a technique is useful because it allows an investigator to determine whether a specific pattern of dynamics can be produced, and if it can, the reaction network found can be then analyzed. We present our results in the context of studying simplified chemical dynamics in theorized protocells - hypothesized precursors of the first living organisms. Our results show that given a small sample of plausible protocell reaction dynamics, catalytic reaction sets can be found. We present cases where this is not possible and also analyze the evolved reaction sets.

  20. Quantifying atmospheric transport, chemistry, and mixing using a new trajectory-box model and a global atmospheric-chemistry GCM

    OpenAIRE

    H. Riede; Jöckel, P.; Sander, R.

    2009-01-01

    We present a novel method for the quantification of transport, chemistry, and mixing along atmospheric trajectories based on a consistent model hierarchy. The hierarchy consists of the new atmospheric-chemistry trajectory-box model CAABA/MJT and the three-dimensional (3-D) global ECHAM/MESSy atmospheric-chemistry (EMAC) general circulation model. CAABA/MJT employs the atmospheric box model CAABA in a configuration using the atmospheric-chemistry submodel MECCA (M), the photochemistry submodel...

  1. Representational Translation with Concrete Models in Organic Chemistry

    Science.gov (United States)

    Stull, Andrew T.; Hegarty, Mary; Dixon, Bonnie; Stieff, Mike

    2012-01-01

    In representation-rich domains such as organic chemistry, students must be facile and accurate when translating between different 2D representations, such as diagrams. We hypothesized that translating between organic chemistry diagrams would be more accurate when concrete models were used because difficult mental processes could be augmented by…

  2. Molecular Modeling and Computational Chemistry at Humboldt State University.

    Science.gov (United States)

    Paselk, Richard A.; Zoellner, Robert W.

    2002-01-01

    Describes a molecular modeling and computational chemistry (MM&CC) facility for undergraduate instruction and research at Humboldt State University. This facility complex allows the introduction of MM&CC throughout the chemistry curriculum with tailored experiments in general, organic, and inorganic courses as well as a new molecular modeling…

  3. Developing enhancement models for first-year chemistry concepts

    Science.gov (United States)

    Storer, Donald A.

    2000-10-01

    This dissertation consists of three units, each of which addresses a topic in one of three major categories of chemical education research as required by the Ph.D. program in chemistry with emphasis in chemical education at Miami University. Unit I, Modification of First-Year Chemistry Laboratory Experiences to Implement a Capstone, addresses the category on Development and Testing of Chemistry Courses or Learning Units and demonstrates an approach to implementing a multi-week capstone project as a part of the laboratory curriculum. The work outlined in Unit I demonstrates how this was accomplished in a traditional first-year chemistry setting by modifying the content of traditional first-year chemistry experiments and having the students complete a capstone project that addresses multiple content areas. Unit II, Assessment of a Materials Development Model, addresses the Development and Testing of Chemistry-Based Instructional Materials category. This study determines the effectiveness of a materials development model in producing a publishable quality student monograph and instructor's guide to be used in chemical technology education. The materials development model described in Unit II was used to develop a student monograph (which contains ten laboratory activities) and instructor's guide that could be used in a chemical technology education curriculum. Unit III, Predicting Performance in General Chemistry at Miami University Using ACT and SAT Test Scores, is a project in the category of Research in Student Learning of Chemistry. From a subject pool of 2,764 first-year chemistry students taking General Chemistry at Miami University, Oxford during the fall of the years 1993 and 1994, a sub-sample of 1,023 subjects for which complete data was available was used to develop regression equations based on ACT or SAT scores to predict performance in first-year chemistry.

  4. Modeling the Explicit Chemistry of Anthropogenic and Biogenic Organic Aerosols

    Energy Technology Data Exchange (ETDEWEB)

    Madronich, Sasha [Univ. Corporation for Atmospheric Research, Boulder, CO (United States)

    2015-12-09

    The atmospheric burden of Secondary Organic Aerosols (SOA) remains one of the most important yet uncertain aspects of the radiative forcing of climate. This grant focused on improving our quantitative understanding of SOA formation and evolution, by developing, applying, and improving a highly detailed model of atmospheric organic chemistry, the Generation of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) model. Eleven (11) publications have resulted from this grant.

  5. Modeling local chemistry in PWR steam generator crevices

    Energy Technology Data Exchange (ETDEWEB)

    Millett, P.J. [EPRI, Palo Alto, CA (United States)

    1997-02-01

    Over the past two decades steam generator corrosion damage has been a major cost impact to PWR owners. Crevices and occluded regions create thermal-hydraulic conditions where aggressive impurities can become highly concentrated, promoting localized corrosion of the tubing and support structure materials. The type of corrosion varies depending on the local conditions, with stress corrosion cracking being the phenomenon of most current concern. A major goal of the EPRI research in this area has been to develop models of the concentration process and resulting crevice chemistry conditions. These models may then be used to predict crevice chemistry based on knowledge of bulk chemistry, thereby allowing the operator to control corrosion damage. Rigorous deterministic models have not yet been developed; however, empirical approaches have shown promise and are reflected in current versions of the industry-developed secondary water chemistry guidelines.

  6. Comparison of tropospheric chemistry schemes for use within global models

    Directory of Open Access Journals (Sweden)

    K. M. Emmerson

    2008-11-01

    Full Text Available Methane and ozone are two important climate gases with significant tropospheric chemistry. Within chemistry-climate and transport models this chemistry is simplified for computational expediency. We compare the state of the art Master Chemical Mechanism (MCM with six tropospheric chemistry schemes (CRI-reduced, GEOS-CHEM and a GEOS-CHEM adduct, MOZART, TOMCAT and CBM-IV that could be used within composition transport models. We test the schemes within a box model framework under conditions derived from a composition transport model and from field observations from a regional scale pollution event. We find that CRI-reduced provides much skill in simulating the full chemistry, yet with greatly reduced complexity. We find significant variations between the other chemical schemes, and reach the following conclusions. 1 The inclusion of a gas phase N2O5+H2O reaction in some schemes and not others is a large source of uncertainty in the inorganic chemistry. 2 There are significant variations in the calculated concentration of PAN between the schemes, which will affect the long range transport of reactive nitrogen in global models. 3 The representation of isoprene chemistry differs hugely between the schemes, leading to significant uncertainties on the impact of isoprene on composition. 4 Night-time chemistry is badly represented with significant disagreements in the ratio of NO3 to NOx. Resolving these four issues through further investigative laboratory studies will reduce the uncertainties within the chemical schemes of global tropospheric models.

  7. Chemistry Teachers' Knowledge and Application of Models

    Science.gov (United States)

    Wang, Zuhao; Chi, Shaohui; Hu, Kaiyan; Chen, Wenting

    2014-01-01

    Teachers' knowledge and application of model play an important role in students' development of modeling ability and scientific literacy. In this study, we investigated Chinese chemistry teachers' knowledge and application of models. Data were collected through test questionnaire and analyzed quantitatively and qualitatively. The…

  8. The link between physics and chemistry in track modelling

    International Nuclear Information System (INIS)

    The physical structure of a radiation track provides the initial conditions for the modelling of radiation chemistry. These initial conditions are not perfectly understood, because there are important gaps between what is provided by a typical track structure model and what is required to start the chemical model. This paper addresses the links between the physics and chemistry of tracks, with the intention of identifying those problems that need to be solved in order to obtain an accurate picture of the initial conditions for the purposes of modelling chemistry. These problems include the reasons for the increased yield of ionisation relative to homolytic bond breaking in comparison with the gas phase. A second area of great importance is the physical behaviour of low-energy electrons in condensed matter (including thermolisation and solvation). Many of these processes are not well understood, but they can have profound effects on the transient chemistry in the track. Several phenomena are discussed, including the short distance between adjacent energy loss events, the molecular nature of the underlying medium, dissociative attachment resonances and the ability of low-energy electrons to excite optically forbidden molecular states. Each of these phenomena has the potential to modify the transient chemistry substantially and must therefore be properly characterised before the physical model of the track can be considered to be complete. (orig.)

  9. Assessing High School Chemistry Students' Modeling Sub-Skills in a Computerized Molecular Modeling Learning Environment

    Science.gov (United States)

    Dori, Yehudit Judy; Kaberman, Zvia

    2012-01-01

    Much knowledge in chemistry exists at a molecular level, inaccessible to direct perception. Chemistry instruction should therefore include multiple visual representations, such as molecular models and symbols. This study describes the implementation and assessment of a learning unit designed for 12th grade chemistry honors students. The organic…

  10. Acceleration of the chemistry solver for modeling DI engine combustion using dynamic adaptive chemistry (DAC) schemes

    Science.gov (United States)

    Shi, Yu; Liang, Long; Ge, Hai-Wen; Reitz, Rolf D.

    2010-03-01

    Acceleration of the chemistry solver for engine combustion is of much interest due to the fact that in practical engine simulations extensive computational time is spent solving the fuel oxidation and emission formation chemistry. A dynamic adaptive chemistry (DAC) scheme based on a directed relation graph error propagation (DRGEP) method has been applied to study homogeneous charge compression ignition (HCCI) engine combustion with detailed chemistry (over 500 species) previously using an R-value-based breadth-first search (RBFS) algorithm, which significantly reduced computational times (by as much as 30-fold). The present paper extends the use of this on-the-fly kinetic mechanism reduction scheme to model combustion in direct-injection (DI) engines. It was found that the DAC scheme becomes less efficient when applied to DI engine simulations using a kinetic mechanism of relatively small size and the accuracy of the original DAC scheme decreases for conventional non-premixed combustion engine. The present study also focuses on determination of search-initiating species, involvement of the NOx chemistry, selection of a proper error tolerance, as well as treatment of the interaction of chemical heat release and the fuel spray. Both the DAC schemes were integrated into the ERC KIVA-3v2 code, and simulations were conducted to compare the two schemes. In general, the present DAC scheme has better efficiency and similar accuracy compared to the previous DAC scheme. The efficiency depends on the size of the chemical kinetics mechanism used and the engine operating conditions. For cases using a small n-heptane kinetic mechanism of 34 species, 30% of the computational time is saved, and 50% for a larger n-heptane kinetic mechanism of 61 species. The paper also demonstrates that by combining the present DAC scheme with an adaptive multi-grid chemistry (AMC) solver, it is feasible to simulate a direct-injection engine using a detailed n-heptane mechanism with 543 species

  11. Chemistry

    International Nuclear Information System (INIS)

    The chemical research and development efforts related to the design and ultimate operation of molten-salt breeder reactor systems are concentrated on fuel- and coolant-salt chemistry, including the development of analytical methods for use in these systems. The chemistry of tellurium in fuel salt is being studied to help elucidate the role of this element in the intergranular cracking of Hastelloy N. Studies were continued of the effect of oxygen-containing species on the equilibrium between dissolved UF3 and dissolved UF4, and, in some cases, between the dissolved uranium fluorides and graphite, and the UC2. Several aspects of coolant-salt chemistry are under investigation. Hydroxy and oxy compounds that could be formed in molten NaBF4 are being synthesized and characterized. Studies of the chemistry of chromium (III) compounds in fluoroborate melts were continued as part of a systematic investigation of the corrosion of structural alloys by coolant salt. An in-line voltammetric method for determining U4+/U3+ ratios in fuel salt was tested in a forced-convection loop over a six-month period. (LK)

  12. Uncertainty and error in complex plasma chemistry models

    Science.gov (United States)

    Turner, Miles M.

    2015-06-01

    Chemistry models that include dozens of species and hundreds to thousands of reactions are common in low-temperature plasma physics. The rate constants used in such models are uncertain, because they are obtained from some combination of experiments and approximate theories. Since the predictions of these models are a function of the rate constants, these predictions must also be uncertain. However, systematic investigations of the influence of uncertain rate constants on model predictions are rare to non-existent. In this work we examine a particular chemistry model, for helium-oxygen plasmas. This chemistry is of topical interest because of its relevance to biomedical applications of atmospheric pressure plasmas. We trace the primary sources for every rate constant in the model, and hence associate an error bar (or equivalently, an uncertainty) with each. We then use a Monte Carlo procedure to quantify the uncertainty in predicted plasma species densities caused by the uncertainty in the rate constants. Under the conditions investigated, the range of uncertainty in most species densities is a factor of two to five. However, the uncertainty can vary strongly for different species, over time, and with other plasma conditions. There are extreme (pathological) cases where the uncertainty is more than a factor of ten. One should therefore be cautious in drawing any conclusion from plasma chemistry modelling, without first ensuring that the conclusion in question survives an examination of the related uncertainty.

  13. System dynamics modeling: from mechanics to chemistry

    OpenAIRE

    D’Anna, Michele; Fuchs, Hans; Lubini, Paolo

    2008-01-01

    In this paper, we discuss a contribution toward the use of analogical reasoning by explicit system dynamics modeling of physical processes. The relational structures found in simple models are transferred to an example of chemical processes leading to chemical equilibrium. We present an experiment on the mutarotation of D-glucose. A dynamical model will be built that makes use of amount of substance and chemical potential differences in analogy to quantities of fluid and pressure ...

  14. A Process Model for the Comprehension of Organic Chemistry Notation

    Science.gov (United States)

    Havanki, Katherine L.

    2012-01-01

    This dissertation examines the cognitive processes individuals use when reading organic chemistry equations and factors that affect these processes, namely, visual complexity of chemical equations and participant characteristics (expertise, spatial ability, and working memory capacity). A six stage process model for the comprehension of organic…

  15. A quasi chemistry-transport model mode for EMAC

    Directory of Open Access Journals (Sweden)

    R. Deckert

    2010-11-01

    Full Text Available A quasi chemistry-transport model mode (QCTM is presented for the numerical chemistry-climate simulation system ECHAM/MESSy Atmospheric Chemistry (EMAC. It allows for a quantification of chemical signals through suppression of any feedback between chemistry and dynamics. Noise would otherwise interfere too strongly. The signal follows from the difference of two QCTM simulations, reference and sensitivity. These are fed with offline chemical fields as a substitute of the feedbacks between chemistry and dynamics: offline mixing ratios of radiatively active substances enter the radiation scheme (a, offline mixing ratios of nitric acid enter the scheme for re-partitioning and sedimentation from polar stratospheric clouds (b. Offline methane oxidation is the exclusive source of chemical water-vapor tendencies (c. Any set of offline fields suffices to suppress the feedbacks, though may be inconsistent with the simulation setup. An adequate set of offline climatologies can be produced from a non-QCTM simulation of the reference setup. Test simulations reveal the particular importance of adequate offline fields associated with (a. Inconsistencies from (b are negligible when using adequate fields of nitric acid. Acceptably small inconsistencies come from (c, but should vanish for an adequate prescription of water vapor tendencies. Toggling between QCTM and non-QCTM is done via namelist switches and does not require a source code re-compilation.

  16. Chemistry

    International Nuclear Information System (INIS)

    Research progress is reported in programs on fuel-salt chemistry, properties of compounds in the Li--Te system, Te spectroscopy UF4--H equilibria, porous electrode studies of molten salts, fuel salt-coolant salt reactions, thermodynamic properties of transition-metal fluorides, and properties of sodium fluoroborate. Developmental work on analytical methods is summarized including in-line analysis of molten MSBR fuel, analysis of coolant-salts for tritium, analysis of molten LiF--BeF2--ThF4 for Fe and analysis of LiF--BeF--ThF4 for Te

  17. Understanding atmospheric peroxyformic acid chemistry: observation, modeling and implication

    Directory of Open Access Journals (Sweden)

    H. Liang

    2015-01-01

    Full Text Available The existence and importance of peroxyformic acid (PFA in the atmosphere has been under controversy. We present here, for the first time, the observation data for PFA from four field measurements carried out in China. These data provided powerful evidence that PFA can stay in the atmosphere, typically in dozens of pptv level. The relationship between PFA and other detected peroxides was examined. The results showed that PFA had a strong positive correlation with its homolog, peroxyacetic acid, due to their similar sources and sinks. Through an evaluation of PFA production and removal rates, we proposed that the reactions between peroxyformyl radical (HC(OO2 and formaldehyde or the hydroperoxyl radical (HO2 were likely to be the major source and degradation into formic acid (FA was likely to be the major sink for PFA. Based on a box model evaluation, we proposed that the HC(OO2 and PFA chemistry was a major source for FA under low NOx conditions. Furthermore, it is found that the impact of the HC(OO2 and PFA chemistry on radical cycling was dependent on the yield of HC(OO2 radical from HC(O + O2 reaction. When this yield exceeded 50%, the HC(OO2 and PFA chemistry should not be neglected for calculating the radical budget. To make clear the exact importance of HC(OO2 and PFA chemistry in the atmosphere, further kinetic, field and modeling studies are required.

  18. Using Transport Diagnostics to Understand Chemistry Climate Model Ozone Simulations

    Science.gov (United States)

    Strahan, S. E.; Douglass, A. R.; Stolarski, R. S.; Akiyoshi, H.; Bekki, S.; Braesicke, P.; Butchart, N.; Chipperfield, M. P.; Cugnet, D.; Dhomse, S.; Frith, S. M.; Gettleman, A.; Hardiman, S. C.; Kinnison, D. E.; Lamarque, J.-F.; Mancini, E.; Marchand, M.; Michou, M.; Morgenstern, O.; Nakamura, T.; Olivie, D.; Pawson, S.; Pitari, G.; Plummer, D. A.; Pyle, J. A.

    2010-01-01

    We demonstrate how observations of N2O and mean age in the tropical and midlatitude lower stratosphere (LS) can be used to identify realistic transport in models. The results are applied to 15 Chemistry Climate Models (CCMs) participating in the 2010 WMO assessment. Comparison of the observed and simulated N2O/mean age relationship identifies models with fast or slow circulations and reveals details of model ascent and tropical isolation. The use of this process-oriented N2O/mean age diagnostic identifies models with compensating transport deficiencies that produce fortuitous agreement with mean age. We compare the diagnosed model transport behavior with a model's ability to produce realistic LS O3 profiles in the tropics and midlatitudes. Models with the greatest tropical transport problems show the poorest agreement with observations. Models with the most realistic LS transport agree more closely with LS observations and each other. We incorporate the results of the chemistry evaluations in the SPARC CCMVal Report (2010) to explain the range of CCM predictions for the return-to-1980 dates for global (60 S-60 N) and Antarctic column ozone. Later (earlier) Antarctic return dates are generally correlated to higher (lower) vortex Cl(sub y) levels in the LS, and vortex Cl(sub y) is generally correlated with the model's circulation although model Cl(sub y) chemistry or Cl(sub y) conservation can have a significant effect. In both regions, models that have good LS transport produce a smaller range of predictions for the return-to-1980 ozone values. This study suggests that the current range of predicted return dates is unnecessarily large due to identifiable model transport deficiencies.

  19. Quantifying atmospheric transport, chemistry, and mixing using a new trajectory-box model and a global atmospheric-chemistry GCM

    Directory of Open Access Journals (Sweden)

    H. Riede

    2009-12-01

    Full Text Available We present a novel method for the quantification of transport, chemistry, and mixing along atmospheric trajectories based on a consistent model hierarchy. The hierarchy consists of the new atmospheric-chemistry trajectory-box model CAABA/MJT and the three-dimensional (3-D global ECHAM/MESSy atmospheric-chemistry (EMAC general circulation model. CAABA/MJT employs the atmospheric box model CAABA in a configuration using the atmospheric-chemistry submodel MECCA (M, the photochemistry submodel JVAL (J, and the new trajectory submodel TRAJECT (T, to simulate chemistry along atmospheric trajectories, which are provided offline. With the same chemistry submodels coupled to the 3-D EMAC model and consistent initial conditions and physical parameters, a unique consistency between the two models is achieved. Since only mixing processes within the 3-D model are excluded from the model consistency, comparisons of results from the two models allow to separate and quantify contributions of transport, chemistry, and mixing along the trajectory pathways. Consistency of transport between the trajectory-box model CAABA/MJT and the 3-D EMAC model is achieved via calculation of kinematic trajectories based on 3-D wind fields from EMAC using the trajectory model LAGRANTO. The combination of the trajectory-box model CAABA/MJT and the trajectory model LAGRANTO can be considered as a Lagrangian chemistry-transport model (CTM moving isolated air parcels. The procedure for obtaining the necessary statistical basis for the quantification method is described as well as the comprehensive diagnostics with respect to chemistry.

    The quantification method presented here allows to investigate the characteristics of transport, chemistry, and mixing in a grid-based 3-D model. The analysis of chemical processes within the trajectory-box model CAABA/MJT is easily extendable to include, for example, the impact of different transport pathways or of mixing processes onto

  20. Benchmarking spin-state chemistry in starless core models

    CERN Document Server

    Sipilä, O; Harju, J

    2015-01-01

    Aims. We aim to present simulated chemical abundance profiles for a variety of important species, with special attention given to spin-state chemistry, in order to provide reference results against which present and future models can be compared. Methods. We employ gas-phase and gas-grain models to investigate chemical abundances in physical conditions corresponding to starless cores. To this end, we have developed new chemical reaction sets for both gas-phase and grain-surface chemistry, including the deuterated forms of species with up to six atoms and the spin-state chemistry of light ions and of the species involved in the ammonia and water formation networks. The physical model is kept simple in order to facilitate straightforward benchmarking of other models against the results of this paper. Results. We find that the ortho/para ratios of ammonia and water are similar in both gas-phase and gas-grain models, at late times in particular, implying that the ratios are determined by gas-phase processes. We d...

  1. Modelling stratospheric chemistry in a global three-dimensional chemical transport model

    Energy Technology Data Exchange (ETDEWEB)

    Rummukainen, M. [Finnish Meteorological Inst., Sodankylae (Finland). Sodankylae Observatory

    1995-12-31

    Numerical modelling of atmospheric chemistry aims to increase the understanding of the characteristics, the behavior and the evolution of atmospheric composition. These topics are of utmost importance in the study of climate change. The multitude of gases and particulates making up the atmosphere and the complicated interactions between them affect radiation transfer, atmospheric dynamics, and the impacts of anthropogenic and natural emissions. Chemical processes are fundamental factors in global warming, ozone depletion and atmospheric pollution problems in general. Much of the prevailing work on modelling stratospheric chemistry has so far been done with 1- and 2-dimensional models. Carrying an extensive chemistry parameterisation in a model with high spatial and temporal resolution is computationally heavy. Today, computers are becoming powerful enough to allow going over to 3-dimensional models. In order to concentrate on the chemistry, many Chemical Transport Models (CTM) are still run off-line, i.e. with precalculated and archived meteorology and radiation. In chemistry simulations, the archived values drive the model forward in time, without interacting with the chemical evolution. This is an approach that has been adopted in stratospheric chemistry modelling studies at the Finnish Meteorological Institute. In collaboration with the University of Oslo, a development project was initiated in 1993 to prepare a stratospheric chemistry parameterisation, fit for global 3-dimensional modelling. This article presents the parameterisation approach. Selected results are shown from basic photochemical simulations

  2. Modelling the chemistry of star forming filaments

    CERN Document Server

    Seifried, D

    2015-01-01

    We present simulations of star forming filaments incorporating - to our knowledge - the largest chemical network used to date on-the-fly in a 3D-MHD simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this we use the newly developed package KROME (Grassi et al. 2014). We combine the KROME package with an algorithm which allows us to calculate the column density and attenuation of the interstellar radiation field necessary to properly model heating and ionisation rates. Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionisation rate. We find that towards the centre of the filaments there is gradual conversion of hydrogen from H^+ over H to H_2 as well as of C^+ over C to CO. Moreover, we find a decrease of the dust temperature towards the centre of the filaments in agreement with recent...

  3. Modeling UTLS water vapor: Transport/Chemistry interactions

    International Nuclear Information System (INIS)

    This thesis was initially meant to be a study on the impact on chemistry and climate from UTLS water vapor. However, the complexity of the UTLS water vapor and its recent changes turned out to be a challenge by it self. In the light of this, the overall motivation for the thesis became to study the processes controlling UTLS water vapor and its changes. Water vapor is the most important greenhouse gas, involved in important climate feedback loops. Thus, a good understanding of the chemical and dynamical behavior of water vapor in the atmosphere is crucial for understanding the climate changes in the last century. Additionally, parts of the work was motivated by the development of a coupled climate chemistry model based on the CAM3 model coupled with the Chemical Transport Model Oslo CTM2. The future work will be concentrated on the UTLS water vapor impact on chemistry and climate. We are currently studying long term trends in UTLS water vapor, focusing on identification of the different processes involved in the determination of such trends. The study is based on natural as well as anthropogenic climate forcings. The ongoing work on the development of a coupled climate chemistry model will continue within our group, in collaboration with Prof. Wei-Chyung Wang at the State University of New York, Albany. Valuable contacts with observational groups are established during the work on this thesis. These collaborations will be continued focusing on continuous model validation, as well as identification of trends and new features in UTLS water vapor, and other tracers in this region. (Author)

  4. A quasi chemistry-transport model mode for EMAC

    Directory of Open Access Journals (Sweden)

    R. Deckert

    2011-03-01

    Full Text Available A quasi chemistry-transport model mode (QCTM is presented for the numerical chemistry-climate simulation system ECHAM/MESSy Atmospheric Chemistry (EMAC. It allows for a quantification of chemical signals through suppression of any feedback between chemistry and dynamics. Noise would otherwise interfere too strongly. The signal is calculated from the difference of two QCTM simulations, a reference simulation and a sensitivity simulation. In order to avoid the feedbacks, the simulations adopt the following offline chemical fields: (a offline mixing ratios of radiatively active substances enter the radiation scheme, (b offline mixing ratios of nitric acid enter the scheme for re-partitioning and sedimentation from polar stratospheric clouds, (c and offline methane oxidation is the exclusive source of chemical water-vapor tendencies. Any set of offline fields suffices to suppress the feedbacks, though may be inconsistent with the simulation setup. An adequate set of offline climatologies can be produced from a non-QCTM simulation using the setup of the reference simulation. Test simulations reveal the particular importance of adequate offline fields associated with (a. Inconsistencies from (b are negligible when using adequate fields of nitric acid. Acceptably small inconsistencies come from (c, but should vanish for an adequate prescription of chemical water vapor tendencies. Toggling between QCTM and non-QCTM is done via namelist switches and does not require a source code re-compilation.

  5. Using advanced surface complexation models for modelling soil chemistry under forests: Solling forest, Germany

    International Nuclear Information System (INIS)

    Various dynamic soil chemistry models have been developed to gain insight into impacts of atmospheric deposition of sulphur, nitrogen and other elements on soil and soil solution chemistry. Sorption parameters for anions and cations are generally calibrated for each site, which hampers extrapolation in space and time. On the other hand, recently developed surface complexation models (SCMs) have been successful in predicting ion sorption for static systems using generic parameter sets. This study reports the inclusion of an assemblage of these SCMs in the dynamic soil chemistry model SMARTml and applies this model to a spruce forest site in Solling Germany. Parameters for SCMs were taken from generic datasets and not calibrated. Nevertheless, modelling results for major elements matched observations well. Further, trace metals were included in the model, also using the existing framework of SCMs. The model predicted sorption for most trace elements well. - Highlights: → Surface complexation models can be well applied in field studies. → Soil chemistry under a forest site is adequately modelled using generic parameters. → The model is easily extended with extra elements within the existing framework. → Surface complexation models can show the linkages between major soil chemistry and trace element behaviour. - Surface complexation models with generic parameters make calibration of sorption superfluous in dynamic modelling of deposition impacts on soil chemistry under nature areas.

  6. Modeling skills of pre-service chemistry teachers in predicting the structure and properties of inorganic chemistry compounds

    Science.gov (United States)

    Nursa'adah, Euis; Liliasari, Mudzakir, Ahmad

    2016-02-01

    The focus of chemistry is learning about the composition, properties, and transformations of matters. Modeling skills are required to comprehend structure and chemical composition in submicroscopic size. Modeling skills are abilities to produce chemical structure and to explain it into the macroscopic phenomenon and submicroscopic representations. Inorganic chemistry is a study of whole elements in the periodic table and their compounds, except carbon compounds and their derivatives. Knowledge about the structure and properties of chemical substances is a basic model for students in studying inorganic chemistry. Furthermore, students can design and produce to utilize materials needed in their life. This research aimed to describes modeling skills of pre-service chemistry teachers. In order, they are able to determine and synthesize useful materials. The results show that students' modeling skills were in a low level and unable connecting skill categories, even the models of inorganic compounds common. These phenomena indicated that students only describe each element when they learn inorganic chemistry. So that it will make modeling skills of students low. Later, another researches are necessary to develop learning design of inorganic chemistry based on good modeling skills of students.

  7. Thyroid hormone synthesis and anti-thyroid drugs: A bioinorganic chemistry approach

    Indian Academy of Sciences (India)

    Gouriprasanna Roy; G Mugesh

    2006-11-01

    Hydrogen peroxide, generated by thyroid oxidase enzymes, is a crucial substrate for the thyroid peroxidase (TPO)-catalysed biosynthesis of thyroid hormones, thyroxine (T4) and triiodothyronine (T3) in the thyroid gland. It is believed that the H2O2 generation is a limiting step in thyroid hormone synthesis. Therefore, the control of hydrogen peroxide concentration is one of the possible mechanisms for the inhibition of thyroid hormone biosynthesis. The inhibition of thyroid hormone synthesis is required for the treatment of hyperthyroidism and this can be achieved by one or more anti-thyroid drugs. The most widely used anti-thyroid drug methimazole (MMI) inhibits the production of thyroid hormones by irreversibly inactivating the enzyme TPO. Our studies show that the replacement of sulphur in MMI by selenium leads to a selone, which exists predominantly in its zwitterionic form. In contrast to the sulphur drug, the selenium analogue (MSeI) reversibly inhibits the peroxidase-catalysed oxidation and iodination reactions. Theoretical studies on MSeI reveal that the selenium atom in this compound carries a large negative charge. The carbon-selenium bond length in MSeI is found to be close to single-bond length. As the selenium atom exhibits a large nucleophilic character, the selenium analogue of MMI may scavenge the hydrogen peroxide present in the thyroid cells, which may lead to a reversible inhibition of thyroid hormone biosynthesis.

  8. Development of High Resolution X-Ray spectrometers for the Investigation of Bioinorganic Chemistry in Metalloproteins

    International Nuclear Information System (INIS)

    Metals play as varied a role in biology as the proteins they are part of. They are involved in structure formation, they help transfer material and information, and they catalyze chemical reactions. Other proteins transport material or information, such as hemoglobin that distributes O2 and takes up CO2, or insulin that signals cells to increase glucose uptake in response to high blood glucose levels. Again other proteins promote chemical reactions, such as photosystem II responsible for photosynthetic oxygen evolution or nitrogenase which catalyzes the reduction of N2 to NH3. All of these proteins require the presence of a metal ion for their activity.

  9. Development of High Resolution X-Ray spectrometers for the Investigation of Bioinorganic Chemistry in Metalloproteins

    Energy Technology Data Exchange (ETDEWEB)

    Drury, Owen Byron [Univ. of California, Davis, CA (United States)

    2007-01-01

    Metals play as varied a role in biology as the proteins they are part of. They are involved in structure formation, they help transfer material and information, and they catalyze chemical reactions. Other proteins transport material or information, such as hemoglobin that distributes O2 and takes up CO2, or insulin that signals cells to increase glucose uptake in response to high blood glucose levels. Again other proteins promote chemical reactions, such as photosystem II responsible for photosynthetic oxygen evolution or nitrogenase which catalyzes the reduction of N2 to NH3. All of these proteins require the presence of a metal ion for their activity.

  10. An Aerosol Physical Chemistry Model for the Upper Troposphere

    Science.gov (United States)

    Lin, Jin-Sheng

    2001-01-01

    This report is the final report for the Cooperative Agreement NCC2-1000. The tasks outlined in the various proposals are: (1) Development of an aerosol chemistry model; (2) Utilization of satellite measurements of trace gases along with analysis of temperatures and dynamic conditions to understand ice cloud formation, dehydration and sedimentation in the winter polar regions; (3) Comparison of the HALOE and SAGE II time dependencies of the Pinatubo aerosol decay. The publications are attached.

  11. MIANN models in medicinal, physical and organic chemistry.

    Science.gov (United States)

    González-Díaz, Humberto; Arrasate, Sonia; Sotomayor, Nuria; Lete, Esther; Munteanu, Cristian R; Pazos, Alejandro; Besada-Porto, Lina; Ruso, Juan M

    2013-01-01

    Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.

  12. The global change research center atmospheric chemistry model

    Energy Technology Data Exchange (ETDEWEB)

    Moraes, F.P. Jr.

    1995-01-01

    This work outlines the development of a new model of the chemistry of the natural atmosphere. The model is 2.5-dimensional, having spatial coordinates height, latitude, and, the half-dimension, land and ocean. The model spans both the troposphere and stratosphere, although the troposphere is emphasized and the stratosphere is simple and incomplete. The chemistry in the model includes the O{sub x}, HO{sub x}, NO{sub x}, and methane cycles in a highly modular fashion which allows model users great flexibility in selecting simulation parameters. A detailed modeled sensitivity analysis is also presented. A key aspect of the model is its inclusion of clouds. The model uses current understanding of the distribution and optical thickness of clouds to determine the true radiation distribution in the atmosphere. As a result, detailed studies of the radiative effects of clouds on the distribution of both oxidant concentrations and trace gas removal are possible. This work presents a beginning of this study with model results and discussion of cloud effects on the hydroxyl radical.

  13. Chemistry

    International Nuclear Information System (INIS)

    Research and development activities dealing with the chemical problems related to design and ultimate operation of molten-salt reactor systems are described. An experimental test stand was constructed to expose metallurgical test specimens to Te2 vapor at defined temperatures and deposition rates. To better define the chemistry of fluoroborate coolant, several aspects are being investigated. The behavior of hydroxy and oxy compounds in molten NaBF4 is being investigated to define reactions and compounds that may be involved in corrosion and/or could be involved in methods for trapping tritium. Two corrosion products of Hastelloy N, Na3CrF6 and Na5Cr3F14, were identified from fluoroborate systems. The evaluation of fluoroborate and alternate coolants continued. Research on the behavior of hydrogen and its isotopes is summarized. The solubilities of hydrogen, deuterium, and helium in Li2BeF4 are very low. The sorption of tritium on graphite was found to be significant (a few milligrams of tritium per kilogram of graphite), possibly providing a means of sequestering a portion of the tritium produced. Development of analytical methods continued with emphasis on voltammetric and spectrophotometric techniques for the in-line analysis of corrosion products such as Fe2+ and Cr3+ and the determination of the U3+/U4+ ratio in MSBR fuel salt. Similar studies were conducted with the NaBF4--NaF coolant salt. Information developed during the previous operation of the CSTF has been assessed and used to formulate plans for evaluation of in-line analytical methods in future CSTF operations. Electroanalytical and spectrophotometric research suggests that an electroactive protonic species is present in molten NaBF4--NaF, and that this species rapidly equilibrates with a volatile proton-containing species. Data obtained from the CSTF indicated that tritium was concentrated in the volatile species. (JGB)

  14. Modelling the sulphur chemistry evolution in Orion KL

    CERN Document Server

    Esplugues, G B; Goicoechea, J R; Cernicharo, J

    2014-01-01

    We study the sulphur chemistry evolution in the Orion KL along the gas and grain phases of the cloud. We investigate the processes that dominate the sulphur chemistry and to determine how physical and chemical parameters, such as the final star mass and the initial elemental abundances, influence the evolution of the hot core and of the surrounding outflows and shocked gas (the plateau). We independently modelled the chemistry evolution of both components using the time-dependent gas-grain model UCL_CHEM and considering two different phase calculations. Phase I starts with the collapsing cloud and the depletion of atoms and molecules onto grain surfaces. Phase II starts when a central protostar is formed and the evaporation from grains takes place. We show how the gas density, the gas depletion efficiency, the initial sulphur abundance, the shocked gas temperature and the different chemical paths on the grains leading to different reservoirs of sulphur on the mantles affect sulphur-bearing molecules at differ...

  15. Computational Tools To Model Halogen Bonds in Medicinal Chemistry.

    Science.gov (United States)

    Ford, Melissa Coates; Ho, P Shing

    2016-03-10

    The use of halogens in therapeutics dates back to the earliest days of medicine when seaweed was used as a source of iodine to treat goiters. The incorporation of halogens to improve the potency of drugs is now fairly standard in medicinal chemistry. In the past decade, halogens have been recognized as direct participants in defining the affinity of inhibitors through a noncovalent interaction called the halogen bond or X-bond. Incorporating X-bonding into structure-based drug design requires computational models for the anisotropic distribution of charge and the nonspherical shape of halogens, which lead to their highly directional geometries and stabilizing energies. We review here current successes and challenges in developing computational methods to introduce X-bonding into lead compound discovery and optimization during drug development. This fast-growing field will push further development of more accurate and efficient computational tools to accelerate the exploitation of halogens in medicinal chemistry.

  16. Evaluation of radiation scheme performance within chemistry climate models

    OpenAIRE

    Forster, P. M.; Mayer, B.; et, al.

    2011-01-01

    This paper evaluates global mean radiatively important properties of chemistry climate models (CCMs). We evaluate stratospheric temperatures and their 1980�2000 trends, January clear sky irradiances, heating rates, and greenhouse gas radiative forcings from an offline comparison of CCM radiation codes with line�by�line models, and CCMs� representation of the solar cycle. CCM global mean temperatures and their change can give an indication of errors in radiative trans...

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

    Directory of Open Access Journals (Sweden)

    A. J. G. Baumgaertner

    2010-02-01

    Full Text Available 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.

  18. Gridded global surface ozone metrics for atmospheric chemistry model evaluation

    Directory of Open Access Journals (Sweden)

    E. D. Sofen

    2015-07-01

    Full Text Available The concentration of ozone at the Earth's surface is measured at many locations across the globe for the purposes of air quality monitoring and atmospheric chemistry research. We have brought together all publicly available surface ozone observations from online databases from the modern era to build a consistent dataset for the evaluation of chemical transport and chemistry-climate (Earth System models for projects such as the Chemistry-Climate Model Initiative and Aer-Chem-MIP. From a total dataset of approximately 6600 sites and 500 million hourly observations from 1971–2015, approximately 2200 sites and 200 million hourly observations pass screening as high-quality sites in regional background locations that are appropriate for use in global model evaluation. There is generally good data volume since the start of air quality monitoring networks in 1990 through 2013. Ozone observations are biased heavily toward North America and Europe with sparse coverage over the rest of the globe. This dataset is made available for the purposes of model evaluation as a set of gridded metrics intended to describe the distribution of ozone concentrations on monthly and annual timescales. Metrics include the moments of the distribution, percentiles, maximum daily eight-hour average (MDA8, SOMO35, AOT40, and metrics related to air quality regulatory thresholds. Gridded datasets are stored as netCDF-4 files and are available to download from the British Atmospheric Data Centre (doi:10.5285/08fbe63d-fa6d-4a7a-b952-5932e3ab0452. We provide recommendations to the ozone measurement community regarding improving metadata reporting to simplify ongoing and future efforts in working with ozone data from disparate networks in a consistent manner.

  19. Gridded global surface ozone metrics for atmospheric chemistry model evaluation

    Science.gov (United States)

    Sofen, E. D.; Bowdalo, D.; Evans, M. J.; Apadula, F.; Bonasoni, P.; Cupeiro, M.; Ellul, R.; Galbally, I. E.; Girgzdiene, R.; Luppo, S.; Mimouni, M.; Nahas, A. C.; Saliba, M.; Tørseth, K.

    2016-02-01

    The concentration of ozone at the Earth's surface is measured at many locations across the globe for the purposes of air quality monitoring and atmospheric chemistry research. We have brought together all publicly available surface ozone observations from online databases from the modern era to build a consistent data set for the evaluation of chemical transport and chemistry-climate (Earth System) models for projects such as the Chemistry-Climate Model Initiative and Aer-Chem-MIP. From a total data set of approximately 6600 sites and 500 million hourly observations from 1971-2015, approximately 2200 sites and 200 million hourly observations pass screening as high-quality sites in regionally representative locations that are appropriate for use in global model evaluation. There is generally good data volume since the start of air quality monitoring networks in 1990 through 2013. Ozone observations are biased heavily toward North America and Europe with sparse coverage over the rest of the globe. This data set is made available for the purposes of model evaluation as a set of gridded metrics intended to describe the distribution of ozone concentrations on monthly and annual timescales. Metrics include the moments of the distribution, percentiles, maximum daily 8-hour average (MDA8), sum of means over 35 ppb (daily maximum 8-h; SOMO35), accumulated ozone exposure above a threshold of 40 ppbv (AOT40), and metrics related to air quality regulatory thresholds. Gridded data sets are stored as netCDF-4 files and are available to download from the British Atmospheric Data Centre (doi: 10.5285/08fbe63d-fa6d-4a7a-b952-5932e3ab0452). We provide recommendations to the ozone measurement community regarding improving metadata reporting to simplify ongoing and future efforts in working with ozone data from disparate networks in a consistent manner.

  20. Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives

    Energy Technology Data Exchange (ETDEWEB)

    Vitello, P A; Fried, L E; Howard, W M; Levesque, G; Souers, P C

    2011-07-21

    Detonation waves in insensitive, TATB based explosives are believed to have multi-time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. They use the thermo-chemical code CHEETAH linked to an ALE hydrodynamics code to model detonations. They term their model chemistry resolved kinetic flow as CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculates EOS values based on the concentrations. A HE-validation suite of model simulations compared to experiments at ambient, hot, and cold temperatures has been developed. They present here a new rate model and comparison with experimental data.

  1. Molecular Motion in Frustrated Lewis Pair Chemistry: insights from modelling

    OpenAIRE

    Pu, Maoping

    2015-01-01

    Mechanisms of reactions of the frustrated Lewis pairs (FLPs) with carbon dioxide (CO2) and hydrogen (H2) are studied by using quantum chemical modelling. FLPs are relatively novel chemical systems in which steric effects prevent a Lewis base (LB) from donating its electron pair to a Lewis acid (LA). From the main group of the periodic table, a variety of the electron pair donors and acceptors can create an FLP and the scope of the FLP chemistry is rapidly expanding at present. Representative ...

  2. The coupled atmosphere-chemistry-ocean model SOCOL-MPIOM

    Directory of Open Access Journals (Sweden)

    S. Muthers

    2014-05-01

    Full Text Available The newly developed atmosphere–ocean-chemistry-climate model SOCOL-MPIOM is presented by demonstrating the influence of the interactive chemistry module on the climate state and the variability. Therefore, we compare pre-industrial control simulations with (CHEM and without (NOCHEM interactive chemistry. In general, the influence of the chemistry on the mean state and the variability is small and mainly restricted to the stratosphere and mesosphere. The largest differences are found for the atmospheric dynamics in the polar regions, with slightly stronger northern and southern winter polar vortices in CHEM. The strengthening of the vortex is related to larger stratospheric temperature gradients, which are attributed to a parametrization of the absorption of ozone and oxygen in the Lyman-alpha, Schumann–Runge, Hartley, and Higgins bands. This effect is parametrized in the version with interactive chemistry only. A second reason for the temperature differences between CHEM and NOCHEM is related to diurnal variations in the ozone concentrations in the higher atmosphere, which are missing in NOCHEM. Furthermore, stratospheric water vapour concentrations differ substantially between the two experiments, but their effect on the temperatures is small. In both setups, the simulated intensity and variability of the northern polar vortex is inside the range of present day observations. Sudden stratospheric warming events are well reproduced in terms of their frequency, but the distribution amongst the winter months is too uniform. Additionally, the performance of SOCOL-MPIOM under changing external forcings is assessed for the period 1600–2000 using an ensemble of simulations driven by a spectral solar forcing reconstruction. The amplitude of the reconstruction is large in comparison to other state-of-the-art reconstructions, providing an upper limit for the importance of the solar signal. In the pre-industrial period (1600–1850 the simulated

  3. Application of modeling to local chemistry in PWR steam generators

    International Nuclear Information System (INIS)

    Localized corrosion of the SG tubes and other components is due to the presence of an aggressive environment in local crevices and occluded regions. In crevices and on vertical and horizontal tube surfaces, corrosion products and particulate matter can accumulate in the form of porous deposits. The SG water contains impurities at extremely low levels (ppb). Low levels of non-volatile impurities, however, can be efficiently concentrated in crevices and sludge piles by a thermal hydraulic mechanism. The temperature gradient across the SG tube coupled with local flow starvation, produces local boiling in the sludge and crevices. Since mass transfer processes are inhibited in these geometries, the residual liquid becomes enriched in many of the species present in the SG water. The resulting concentrated solutions have been shown to be aggressive and can corrode the SG materials. This corrosion may occur under various conditions which result in different types of attack such as pitting, stress corrosion cracking, wastage and denting. A major goal of EPRI's research program has been the development of models of the concentration process and the resulting chemistry. An improved understanding should eventually allow utilities to reduce or eliminate the corrosion by the appropriate manipulation of the steam generator water chemistry and or crevice conditions. The application of these models to experimental data obtained for prototypical SG tube support crevices is described in this paper. The models adequately describe the key features of the experimental data allowing extrapolations to be made to plant conditions. (author)

  4. The 1-way on-line coupled atmospheric chemistry model system MECO(n – Part 1: The limited-area atmospheric chemistry model COSMO/MESSy

    Directory of Open Access Journals (Sweden)

    A. Kerkweg

    2011-06-01

    Full Text Available The numerical weather prediction model of the Consortium for Small Scale Modelling (COSMO, maintained by the German weather service (DWD, is connected with the Modular Earth Submodel System (MESSy. This effort is undertaken in preparation of a~new, limited-area atmospheric chemistry model. This model is as consistent as possible, with respect to atmospheric chemistry and related processes, with a previously developed global atmospheric chemistry general circulation model: the ECHAM/MESSy Atmospheric Chemistry (EMAC model. The combined system constitutes a new research tool, bridging the global to the meso-γ scale for atmospheric chemistry research. MESSy provides the infrastructure and includes, among others, the process and diagnostic submodels for atmospheric chemistry simulations. Furthermore, MESSy is highly flexible allowing model setups with tailor made complexity, depending on the scientific question. Here, the connection of the MESSy infrastructure to the COSMO model is documented. Previously published prototype submodels for simplified tracer studies are generalised to be plugged-in and used in the global and the limited-area model. They are used to evaluate the tracer transport characteristics of the new COSMO/MESSy model system, an important prerequisite for future atmospheric chemistry applications. A supplementary document with further details on the technical implementation of the MESSy interface into COSMO with a complete list of modifications to the COSMO code is provided.

  5. Modeling the Relationship between High School Students' Chemistry Self-Efficacy and Metacognitive Awareness

    Science.gov (United States)

    Kirbulut, Zubeyde Demet

    2014-01-01

    In this study, the relationship between students' chemistry self-efficacy beliefs and metacognitive awareness was investigated utilizing a path model. There were 268 chemistry high school students (59% 10th grade and 41% 11th grade) participated in the study. The students took two-hour chemistry course in the 9th and 10th grade and three-hour…

  6. Meteorological implementation issues in chemistry and transport models

    Directory of Open Access Journals (Sweden)

    S. E. Strahan

    2006-01-01

    Full Text Available Offline chemistry and transport models (CTMs are versatile tools for studying composition and climate issues requiring multi-decadal simulations. They are computationally fast compared to coupled chemistry climate models, making them well-suited for integrating sensitivity experiments necessary for understanding model performance and interpreting results. The archived meteorological fields used by CTMs can be implemented with lower horizontal or vertical resolution than the original meteorological fields in order to shorten integration time, but the effects of these shortcuts on transport processes must be understood if the CTM is to have credibility. In this paper we present a series of sensitivity experiments on a CTM using the Lin and Rood advection scheme, each differing from another by a single feature of the wind field implementation. Transport effects arising from changes in resolution and model lid height are evaluated using process-oriented diagnostics that intercompare CH4, O3, and age tracer carried in the simulations. Some of the diagnostics used are derived from observations and are shown as a reality check for the model. Processes evaluated include tropical ascent, tropical-midlatitude exchange, poleward circulation in the upper stratosphere, and the development of the Antarctic vortex. We find that faithful representation of stratospheric transport in this CTM is possible with a full mesosphere, ~1 km resolution in the lower stratosphere, and relatively low vertical resolution (>4 km spacing in the middle stratosphere and above, but lowering the lid from the upper to lower mesosphere leads to less realistic constituent distributions in the upper stratosphere. Ultimately, this affects the polar lower stratosphere, but the effects are greater for the Antarctic than the Arctic. The fidelity of lower stratospheric transport requires realistic tropical and high latitude mixing barriers which are produced at 2°×2.5°, but not lower

  7. Probing flame chemistry with MBMS, theory, and modeling

    Energy Technology Data Exchange (ETDEWEB)

    Westmoreland, P.R. [Univ. of Massachusetts, Amherst (United States)

    1993-12-01

    The objective is to establish kinetics of combustion and molecular-weight growth in C{sub 3} hydrocarbon flames as part of an ongoing study of flame chemistry. Specific reactions being studied are (1) the growth reactions of C{sub 3}H{sub 5} and C{sub 3}H{sub 3} with themselves and with unsaturated hydrocarbons and (2) the oxidation reactions of O and OH with C{sub 3}`s. This approach combines molecular-beam mass spectrometry (MBMS) experiments on low-pressure flat flames; theoretical predictions of rate constants by thermochemical kinetics, Bimolecular Quantum-RRK, RRKM, and master-equation theory; and whole-flame modeling using full mechanisms of elementary reactions.

  8. Hybrid method for numerical modelling of LWR coolant chemistry

    Science.gov (United States)

    Swiatla-Wojcik, Dorota

    2016-10-01

    A comprehensive approach is proposed to model radiation chemistry of the cooling water under exposure to neutron and gamma radiation at 300 °C. It covers diffusion-kinetic processes in radiation tracks and secondary reactions in the bulk coolant. Steady-state concentrations of the radiolytic products have been assessed based on the simulated time dependent concentration profiles. The principal reactions contributing to the formation of H2, O2 and H2O2 were indicated. Simulation was carried out depending on the amount of extra hydrogen dissolved in the coolant to reduce concentration of corrosive agents. High sensitivity to the rate of reaction H+H2O=OH+H2 is shown and discussed.

  9. Online coupled meteorology and chemistry models: history, current status, and outlook

    OpenAIRE

    Zhang, Y.

    2008-01-01

    International audience The climate-chemistry-aerosol-cloud-radiation feedbacks are important processes occurring in the atmosphere. Accurately simulating those feedbacks requires fully-coupled meteorology, climate, and chemistry models and presents significant challenges in terms of both scientific understanding and computational demand. This paper reviews the history and current status of the development and application of online-coupled meteorology and chemistry models, with a focus on f...

  10. Structure and chemistry of model catalysts in ultrahigh vacuum

    Science.gov (United States)

    Walker, Joshua D.

    The study of catalysis is a key area of focus not only in the industrial sector but also in the nature and biological systems. The market for catalysis is a multi-billion dollar industry. Many of the materials and products we use on a daily basis are formed through a catalytic process. The quest to understanding and improving catalytic mechanisms is ongoing. Many model catalysts use transition metals as a support for chemical reactions to take place due to their selectivity and activity. Palladium, gold, and copper metals are studied in this work and show the ability to be catalytically reactive. It is important to understand the characteristics and properties of these surfaces. A well-known example of catalysis is the conversion of carbon monoxide (CO), a very harmful gas to carbon dioxide (CO2) which is less harmful. This reaction is mainly seen in the automotive industry. This reaction is investigated in this work on a Au(111) single crystal, which is normally inert but becomes reactivity with the adsorption of oxygen on the surface. Temperature Programmed Desorption (TPD) is used to understand some of the chemistry and effects with and without the addition of H2O. The oxidation of CO is shown to be enhanced by the addition of water, but warrants further analysis too fully understand the different mechanisms and reaction pathways existing. The field of nano-electronics is rapidly growing as technology continues to challenge scientists to create innovative ideas. The trend to produce smaller electronic products is increasing as consumer demands persist. It has been shown previously that 1,4-phenlyene diisocyanobenzene (1,4-PDI) on Au(111) react to form one-dimensional oligomer chains comprising alternating gold and 1,4-PDI units on the Au(111) surface. A similar compound 1,3-phenlyene diisocyanobenzene (1,3-PDI) was studied in order to investigate whether the oligomerization found for 1,4-PDI is a general phenomenon and to ultimately explore the effect of

  11. Modeling and management of pit lake water chemistry 1: Theory

    International Nuclear Information System (INIS)

    Highlights: • Review of pit lake literature in the context of pit lake predictions. • Review of approaches used to predict pit wall-rock runoff and leachate. • Review of approaches used to generate a pit lake water balance. • Review of approaches used to generate a hydrodynamic prediction. • Review of approaches used to generate a geochemical prediction of a future pit lake. - Abstract: Pit lakes are permanent hydrologic/landscape features that can result from open pit mining for metals, coal, uranium, diamonds, oil sands, and aggregates. Risks associated with pit lakes include local and regional impacts to water quality and related impacts to aquatic and terrestrial ecosystems. Stakeholders rely on predictive models of water chemistry to prepare for and manage these risks. This paper is the first of a two part series on the modeling and management of pit lakes. Herein, we review approaches that have been used to quantify wall-rock runoff geochemistry, wall-rock leachate geochemistry, pit lake water balance, pit lake limnology (i.e. extent of vertical mixing), and pit lake water quality, and conclude with guidance on the application of models within the mine life cycle. The purpose of this paper is to better prepare stakeholders, including future modelers, mine managers, consultants, permitting agencies, land management agencies, regulators, research scientists, academics, and other interested parties, for the challenges of predicting and managing future pit lakes in un-mined areas

  12. Photosynthetic water oxidation: insights from manganese model chemistry.

    Science.gov (United States)

    Young, Karin J; Brennan, Bradley J; Tagore, Ranitendranath; Brudvig, Gary W

    2015-03-17

    Catalysts for light-driven water oxidation are a critical component for development of solar fuels technology. The multielectron redox chemistry required for this process has been successfully deployed on a global scale in natural photosynthesis by green plants and cyanobacteria using photosystem II (PSII). PSII employs a conserved, cuboidal Mn4CaOX cluster called the O2-evolving complex (OEC) that offers inspiration for artificial O2-evolution catalysts. In this Account, we describe our work on manganese model chemistry relevant to PSII, particularly the functional model [Mn(III/IV)2(terpy)2(μ-O)2(OH2)2](NO3)3 complex (terpy = 2,2';6',2″-terpyridine), a mixed-valent di-μ-oxo Mn dimer with two terminal aqua ligands. In the presence of oxo-donor oxidants such as HSO5(-), this complex evolves O2 by two pathways, one of which incorporates solvent water in an O-O bond-forming reaction. Deactivation pathways of this catalyst include comproportionation to form an inactive Mn(IV)Mn(IV) dimer and also degradation to MnO2, a consequence of ligand loss when the oxidation state of the complex is reduced to labile Mn(II) upon release of O2. The catalyst's versatility has been shown by its continued catalytic activity after direct binding to the semiconductor titanium dioxide. In addition, after binding to the surface of TiO2 via a chromophoric linker, the catalyst can be oxidized by a photoinduced electron-transfer mechanism, mimicking the natural PSII process. Model oxomanganese complexes have also aided in interpreting biophysical and computational studies on PSII. In particular, the μ-oxo exchange rates of the Mn-terpy dimer have been instrumental in establishing that the time scale for μ-oxo exchange of high-valent oxomanganese complexes with terminal water ligands is slower than O2 evolution in the natural photosynthetic system. Furthermore, computational studies on the Mn-terpy dimer and the OEC point to similar Mn(IV)-oxyl intermediates in the O-O bond

  13. Photosynthetic water oxidation: insights from manganese model chemistry.

    Science.gov (United States)

    Young, Karin J; Brennan, Bradley J; Tagore, Ranitendranath; Brudvig, Gary W

    2015-03-17

    Catalysts for light-driven water oxidation are a critical component for development of solar fuels technology. The multielectron redox chemistry required for this process has been successfully deployed on a global scale in natural photosynthesis by green plants and cyanobacteria using photosystem II (PSII). PSII employs a conserved, cuboidal Mn4CaOX cluster called the O2-evolving complex (OEC) that offers inspiration for artificial O2-evolution catalysts. In this Account, we describe our work on manganese model chemistry relevant to PSII, particularly the functional model [Mn(III/IV)2(terpy)2(μ-O)2(OH2)2](NO3)3 complex (terpy = 2,2';6',2″-terpyridine), a mixed-valent di-μ-oxo Mn dimer with two terminal aqua ligands. In the presence of oxo-donor oxidants such as HSO5(-), this complex evolves O2 by two pathways, one of which incorporates solvent water in an O-O bond-forming reaction. Deactivation pathways of this catalyst include comproportionation to form an inactive Mn(IV)Mn(IV) dimer and also degradation to MnO2, a consequence of ligand loss when the oxidation state of the complex is reduced to labile Mn(II) upon release of O2. The catalyst's versatility has been shown by its continued catalytic activity after direct binding to the semiconductor titanium dioxide. In addition, after binding to the surface of TiO2 via a chromophoric linker, the catalyst can be oxidized by a photoinduced electron-transfer mechanism, mimicking the natural PSII process. Model oxomanganese complexes have also aided in interpreting biophysical and computational studies on PSII. In particular, the μ-oxo exchange rates of the Mn-terpy dimer have been instrumental in establishing that the time scale for μ-oxo exchange of high-valent oxomanganese complexes with terminal water ligands is slower than O2 evolution in the natural photosynthetic system. Furthermore, computational studies on the Mn-terpy dimer and the OEC point to similar Mn(IV)-oxyl intermediates in the O-O bond

  14. Spray Combustion Modeling with VOF and Finite-Rate Chemistry

    Science.gov (United States)

    Chen, Yen-Sen; Shang, Huan-Min; Liaw, Paul; Wang, Ten-See

    1996-01-01

    A spray atomization and combustion model is developed based on the volume-of-fluid (VOF) transport equation with finite-rate chemistry model. The gas-liquid interface mass, momentum and energy conservation laws are modeled by continuum surface force mechanisms. A new solution method is developed such that the present VOF model can be applied for all-speed range flows. The objectives of the present study are: (1) to develop and verify the fractional volume-of-fluid (VOF) cell partitioning approach into a predictor-corrector algorithm to deal with multiphase (gas-liquid) free surface flow problems; (2) to implement the developed unified algorithm in a general purpose computational fluid dynamics (CFD) code, Finite Difference Navier-Stokes (FDNS), with droplet dynamics and finite-rate chemistry models; and (3) to demonstrate the effectiveness of the present approach by simulating benchmark problems of jet breakup/spray atomization and combustion. Modeling multiphase fluid flows poses a significant challenge because a required boundary must be applied to a transient, irregular surface that is discontinuous, and the flow regimes considered can range from incompressible to highspeed compressible flows. The flow-process modeling is further complicated by surface tension, interfacial heat and mass transfer, spray formation and turbulence, and their interactions. The major contribution of the present method is to combine the novel feature of the Volume of Fluid (VOF) method and the Eulerian/Lagrangian method into a unified algorithm for efficient noniterative, time-accurate calculations of multiphase free surface flows valid at all speeds. The proposed method reformulated the VOF equation to strongly couple two distinct phases (liquid and gas), and tracks droplets on a Lagrangian frame when spray model is required, using a unified predictor-corrector technique to account for the non-linear linkages through the convective contributions of VOF. The discontinuities within the

  15. SREF - a Simple Removable Epoxy Foam decomposition chemistry model.

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, Michael L.

    2003-12-01

    A Simple Removable Epoxy Foam (SREF) decomposition chemistry model has been developed to predict the decomposition behavior of an epoxy foam encapsulant exposed to high temperatures. The foam is composed of an epoxy polymer, blowing agent, and surfactant. The model is based on a simple four-step mass loss model using distributed Arrhenius reaction rates. A single reaction was used to describe desorption of the blowing agent and surfactant (BAS). Three of the reactions were used to describe degradation of the polymer. The coordination number of the polymeric lattice was determined from the chemical structure of the polymer; and a lattice statistics model was used to describe the evolution of polymer fragments. The model lattice was composed of sites connected by octamethylcylotetrasiloxane (OS) bridges, mixed product (MP) bridges, and bisphenol-A (BPA) bridges. The mixed products were treated as a single species, but are likely composed of phenols, cresols, and furan-type products. Eleven species are considered in the SREF model - (1) BAS, (2) OS, (3) MP, (4) BPA, (5) 2-mers, (6) 3-mers, (7) 4-mers, (8) nonvolatile carbon residue, (9) nonvolatile OS residue, (10) L-mers, and (11) XL-mers. The first seven of these species (VLE species) can either be in the condensed-phase or gas-phase as determined by a vapor-liquid equilibrium model based on the Rachford-Rice equation. The last four species always remain in the condensed-phase. The 2-mers, 3-mers, and 4-mers are polymer fragments that contain two, three, or four sites, respectively. The residue can contain C, H, N, O, and/or Si. The L-mer fraction consists of polymer fragments that contain at least five sites (5-mer) up to a user defined maximum mer size. The XL-mer fraction consists of polymer fragments greater than the user specified maximum mer size and can contain the infinite lattice if the bridge population is less than the critical bridge population. Model predictions are compared to 133-thermogravimetric

  16. A new model for magnesium chemistry in the upper atmosphere.

    Science.gov (United States)

    Plane, John M C; Whalley, Charlotte L

    2012-06-21

    This paper describes the kinetic study of a number of gas-phase reactions involving neutral Mg-containing species, which are important for the chemistry of meteor-ablated magnesium in the upper mesosphere/lower thermosphere region. The study is motivated by the very recent observation of the global atomic Mg layer around 90 km, using satellite-born UV-visible spectroscopy. In the laboratory, Mg atoms were produced thermally in the upstream section of a fast flow tube and then converted to the molecular species MgO, MgO(2), OMgO(2), and MgCO(3) by the addition of appropriate reagents. Atomic O was added further downstream, and Mg was detected at the downstream end of the flow tube by laser-induced fluorescence. The following rate coefficients were determined at 300 K: k(MgO + O → Mg + O(2)) = (6.2 ± 1.1) × 10(-10); k(MgO(2) + O → MgO + O(2)) = (8.4 ± 2.8) × 10(-11); k(MgCO(3) + O → MgO(2) + CO(2)) ≥ 4.9 × 10(-12); and k(MgO + CO → Mg + CO(2)) = (1.1 ± 0.3) × 10(-11) cm(3) molecule(-1) s(-1). Electronic structure calculations of the relevant potential energy surfaces combined with RRKM theory were performed to interpret the experimental results and also to explore the likely reaction pathways that convert MgCO(3) and OMgO(2) into long-lived reservoir species such as Mg(OH)(2). Although no reaction was observed in the laboratory between OMgO(2) and O, this is most likely due to the rapid recombination of O(2) with the product MgO(2) to form the relatively stable O(2)MgO(2). Indeed, one significant finding is the role of O(2) in the mesosphere, where it initiates holding cycles by recombining with radical species such as MgO(2) and MgOH. A new atmospheric model was then constructed which combines these results together with recent work on magnesium ion-molecule chemistry. The model is able to reproduce satisfactorily some of the key features of the Mg and Mg(+) layers, including the heights of the layers, the seasonal variations of their column

  17. Gas-Grain Models for Interstellar Anion Chemistry

    Science.gov (United States)

    Cordiner, M. A.; Charnely, S. B.

    2012-01-01

    Long-chain hydrocarbon anions C(sub n) H(-) (n = 4, 6, 8) have recently been found to be abundant in a variety of interstellar clouds. In order to explain their large abundances in the denser (prestellar/protostellar) environments, new chemical models are constructed that include gas-grain interactions. Models including accretion of gas-phase species onto dust grains and cosmic-ray-induced desorption of atoms are able to reproduce the observed anion-to-neutral ratios, as well as the absolute abundances of anionic and neutral carbon chains, with a reasonable degree of accuracy. Due to their destructive effects, the depletion of oxygen atoms onto dust results in substantially greater polyyne and anion abundances in high-density gas (with n(sub H2) approx > / cubic cm). The large abundances of carbon-chain-bearing species observed in the envelopes of protostars such as L1527 can thus be explained without the need for warm carbon-chain chemistry. The C6H(-) anion-to-neutral ratio is found to be most sensitive to the atomic O and H abundances and the electron density. Therefore, as a core evolves, falling atomic abundances and rising electron densities are found to result in increasing anion-to-neutral ratios. Inclusion of cosmic-ray desorption of atoms in high-density models delays freeze-out, which results in a more temporally stable anion-to-neutral ratio, in better agreement with observations. Our models include reactions between oxygen atoms and carbon-chain anions to produce carbon-chain-oxide species C6O, C7O, HC6O, and HC7O, the abundances of which depend on the assumed branching ratios for associative electron detachment

  18. GAS-GRAIN MODELS FOR INTERSTELLAR ANION CHEMISTRY

    International Nuclear Information System (INIS)

    Long-chain hydrocarbon anions CnH– (n = 4, 6, 8) have recently been found to be abundant in a variety of interstellar clouds. In order to explain their large abundances in the denser (prestellar/protostellar) environments, new chemical models are constructed that include gas-grain interactions. Models including accretion of gas-phase species onto dust grains and cosmic-ray-induced desorption of atoms are able to reproduce the observed anion-to-neutral ratios, as well as the absolute abundances of anionic and neutral carbon chains, with a reasonable degree of accuracy. Due to their destructive effects, the depletion of oxygen atoms onto dust results in substantially greater polyyne and anion abundances in high-density gas (with nH2∼>105 cm–3). The large abundances of carbon-chain-bearing species observed in the envelopes of protostars such as L1527 can thus be explained without the need for warm carbon-chain chemistry. The C6H– anion-to-neutral ratio is found to be most sensitive to the atomic O and H abundances and the electron density. Therefore, as a core evolves, falling atomic abundances and rising electron densities are found to result in increasing anion-to-neutral ratios. Inclusion of cosmic-ray desorption of atoms in high-density models delays freeze-out, which results in a more temporally stable anion-to-neutral ratio, in better agreement with observations. Our models include reactions between oxygen atoms and carbon-chain anions to produce carbon-chain-oxide species C6O, C7O, HC6O, and HC7O, the abundances of which depend on the assumed branching ratios for associative electron detachment.

  19. GAS-GRAIN MODELS FOR INTERSTELLAR ANION CHEMISTRY

    Energy Technology Data Exchange (ETDEWEB)

    Cordiner, M. A. [Also at Institute for Astrophysics and Computational Sciences, Catholic University of America, Washington, DC 20064 (United States); Charnley, S. B., E-mail: martin.cordiner@nasa.gov [Astrochemistry Laboratory and Goddard Center for Astrobiology, Mailstop 691, NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, MD 20770 (United States)

    2012-04-20

    Long-chain hydrocarbon anions C{sub n}H{sup -} (n = 4, 6, 8) have recently been found to be abundant in a variety of interstellar clouds. In order to explain their large abundances in the denser (prestellar/protostellar) environments, new chemical models are constructed that include gas-grain interactions. Models including accretion of gas-phase species onto dust grains and cosmic-ray-induced desorption of atoms are able to reproduce the observed anion-to-neutral ratios, as well as the absolute abundances of anionic and neutral carbon chains, with a reasonable degree of accuracy. Due to their destructive effects, the depletion of oxygen atoms onto dust results in substantially greater polyyne and anion abundances in high-density gas (with n{sub H{sub 2}}{approx}>10{sup 5} cm{sup -3}). The large abundances of carbon-chain-bearing species observed in the envelopes of protostars such as L1527 can thus be explained without the need for warm carbon-chain chemistry. The C{sub 6}H{sup -} anion-to-neutral ratio is found to be most sensitive to the atomic O and H abundances and the electron density. Therefore, as a core evolves, falling atomic abundances and rising electron densities are found to result in increasing anion-to-neutral ratios. Inclusion of cosmic-ray desorption of atoms in high-density models delays freeze-out, which results in a more temporally stable anion-to-neutral ratio, in better agreement with observations. Our models include reactions between oxygen atoms and carbon-chain anions to produce carbon-chain-oxide species C{sub 6}O, C{sub 7}O, HC{sub 6}O, and HC{sub 7}O, the abundances of which depend on the assumed branching ratios for associative electron detachment.

  20. Modeling chemistry in and above snow at Summit, Greenland – Part 2: Impact of snowpack chemistry on the oxidation capacity of the boundary layer

    OpenAIRE

    Thomas, J.L.; Dibb, J. E.; L. G. Huey; Liao, J; Tanner, D.; Lefer, B; Glasow, R.; Stutz, J.

    2012-01-01

    The chemical composition of the boundary layer in snow covered regions is impacted by chemistry in the snowpack via uptake, processing, and emission of atmospheric trace gases. We use the coupled one-dimensional (1-D) snow chemistry and atmospheric boundary layer model MISTRA-SNOW to study the impact of snowpack chemistry on the oxidation capacity of the boundary layer. The model includes gas phase photochemistry and chemical reactions both in the interstitial air and the at...

  1. Modeling chemistry in and above snow at Summit, Greenland − Part 2: Impact of snowpack chemistry on the oxidation capacity of the boundary layer

    OpenAIRE

    Lefer, B; von Glasow, R.; Tanner, D.; Liao, J; L. G. Huey; Dibb, J. E.; Thomas, J.L.; Stutz, J.

    2012-01-01

    The chemical composition of the boundary layer in snow covered regions is impacted by chemistry in the snowpack via uptake, processing, and emission of atmospheric trace gases. We use the coupled one-dimensional (1-D) snow chemistry and atmospheric boundary layer model MISTRA-SNOW to study the impact of snowpack chemistry on the oxidation capacity of the boundary layer. The model includes gas phase photochemistry and chemical reactions both in the interstitial air and the atmosphere. Chemistr...

  2. Effects of `Environmental Chemistry' Elective Course Via Technology-Embedded Scientific Inquiry Model on Some Variables

    Science.gov (United States)

    Çalik, Muammer; Özsevgeç, Tuncay; Ebenezer, Jazlin; Artun, Hüseyin; Küçük, Zeynel

    2014-06-01

    The purpose of this study is to examine the effects of `environmental chemistry' elective course via Technology-Embedded Scientific Inquiry (TESI) model on senior science student teachers' (SSSTs) conceptions of environmental chemistry concepts/issues, attitudes toward chemistry, and technological pedagogical content knowledge (TPACK) levels. Within one group pre-test-post-test design, the study was conducted with 117 SSSTs (68 females and 49 males—aged 21-23 years) enrolled in an `environmental chemistry' elective course in the spring semester of 2011-2012 academic-years. Instruments for data collection comprised of Environmental Chemistry Conceptual Understanding Questionnaire, TPACK survey, and Chemistry Attitudes and Experiences Questionnaire. Significant increases in the SSSTs' conceptions of environmental chemistry concepts/issues, attitudes toward chemistry, and TPACK levels are attributed to the SSSTs learning how to use the innovative technologies in the contexts of the `environmental chemistry' elective course and teaching practicum. The study implies that the TESI model may serve a useful purpose in experimental science courses that use the innovative technologies. However, to generalize feasibility of the TESI model, it should be evaluated with SSSTs in diverse learning contexts.

  3. Developing computational model-based diagnostics to analyse clinical chemistry data

    NARCIS (Netherlands)

    Schalkwijk, D.B. van; Bochove, K. van; Ommen, B. van; Freidig, A.P.; Someren, E.P. van; Greef, J. van der; Graaf, A.A. de

    2010-01-01

    This article provides methodological and technical considerations to researchers starting to develop computational model-based diagnostics using clinical chemistry data.These models are of increasing importance, since novel metabolomics and proteomics measuring technologies are able to produce large

  4. Modeling the plasma chemistry of stratospheric Blue Jet streamers

    Science.gov (United States)

    Winkler, Holger; Notholt, Justus

    2014-05-01

    Stratospheric Blue Jets (SBJs) are upward propagating discharges in the altitude range 15-40 km above thunderstorms. The currently most accepted theory associates SBJs to the development of the streamer zone of a leader. The streamers emitted from the leader can travel for a few tens of kilometers predominantly in the vertical direction (Raizer et al., 2007). The strong electric fields at the streamer tips cause ionisation, dissociation, and excitation, and give rise to chemical perturbations. While in recent years the effects of electric discharges occurring in the mesosphere (sprites) have been investigated in a number of model studies, there are only a few studies on the impact of SBJs. However, chemical perturbations due to SBJs are of interest as they might influence the stratospheric ozone layer. We present results of detailed plasma chemistry simulations of SBJ streamers for both day-time and night-time conditions. Any effects of the subsequent leader are not considered. The model accounts for more than 500 reactions and calculates the evolution of the 88 species under the influence of the breakdown electric fields at the streamer tip. As the SBJ dynamics is outside the scope of this study, the streamer parameters are prescribed. For this purpose, electric field parameters based on Raizer et al. (2007) are used. The model is applied to the typical SBJ altitude range 15-40 km. The simulations indicate that SBJ streamers cause significant chemical perturbations. In particular, the liberation of atomic oxygen during the discharge leads to a formation of ozone. At the same time, reactive nitrogen and hydrogen radicals are produced which will cause catalytic ozone destruction. Reference: Raizer et al. (2007), J. Atmos. Solar-Terr. Phys., 69 (8), 925-938.

  5. Measurement-based modeling of bromine chemistry in the boundary layer: 1. Bromine chemistry at the Dead Sea

    OpenAIRE

    Tas, E.; Peleg, M.; D. U. Pedersen; Matveev, V; Pour Biazar, A.; Luria, M.

    2006-01-01

    International audience The Dead Sea is an excellent natural laboratory for the investigation of Reactive Bromine Species (RBS) chemistry, due to the high RBS levels observed in this area, combined with anthropogenic air pollutants up to several ppb. The present study investigated the basic chemical mechanism of RBS at the Dead Sea using a numerical one-dimensional chemical model. Simulations were based on data obtained from comprehensive measurements performed at sites along the Dead Sea. ...

  6. Guided-Inquiry Experiments for Physical Chemistry: The POGIL-PCL Model

    Science.gov (United States)

    Hunnicutt, Sally S.; Grushow, Alexander; Whitnell, Robert

    2015-01-01

    The POGIL-PCL project implements the principles of process-oriented, guided-inquiry learning (POGIL) in order to improve student learning in the physical chemistry laboratory (PCL) course. The inquiry-based physical chemistry experiments being developed emphasize modeling of chemical phenomena. In each experiment, students work through at least…

  7. DFT modeling of chemistry on the Z machine

    Science.gov (United States)

    Mattsson, Thomas

    2013-06-01

    Density Functional Theory (DFT) has proven remarkably accurate in predicting properties of matter under shock compression for a wide-range of elements and compounds: from hydrogen to xenon via water. Materials where chemistry plays a role are of particular interest for many applications. For example the deep interiors of Neptune, Uranus, and hundreds of similar exoplanets are composed of molecular ices of carbon, hydrogen, oxygen, and nitrogen at pressures of several hundred GPa and temperatures of many thousand Kelvin. High-quality thermophysical experimental data and high-fidelity simulations including chemical reaction are necessary to constrain planetary models over a large range of conditions. As examples of where chemical reactions are important, and demonstration of the high fidelity possible for these both structurally and chemically complex systems, we will discuss shock- and re-shock of liquid carbon dioxide (CO2) in the range 100 to 800 GPa, shock compression of the hydrocarbon polymers polyethylene (PE) and poly(4-methyl-1-pentene) (PMP), and finally simulations of shock compression of glow discharge polymer (GDP) including the effects of doping with germanium. Experimental results from Sandia's Z machine have time and again validated the DFT simulations at extreme conditions and the combination of experiment and DFT provide reliable data for evaluating existing and constructing future wide-range equations of state models for molecular compounds like CO2 and polymers like PE, PMP, and GDP. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  8. The Chemistry of Atmosphere-Forest Exchange (CAFE Model – Part 1: Model description and characterization

    Directory of Open Access Journals (Sweden)

    G. M. Wolfe

    2011-01-01

    Full Text Available We present the Chemistry of Atmosphere-Forest Exchange (CAFE model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. CAFE integrates all key processes, including turbulent diffusion, emission, deposition and chemistry, throughout the forest canopy and mixed layer. CAFE utilizes the Master Chemical Mechanism (MCM and is the first model of its kind to incorporate a suite of reactions for the oxidation of monoterpenes and sesquiterpenes, providing a more comprehensive description of the oxidative chemistry occurring within and above the forest. We use CAFE to simulate a young Ponderosa pine forest in the Sierra Nevada, CA. Utilizing meteorological constraints from the BEARPEX-2007 field campaign, we assess the sensitivity of modeled fluxes to parameterizations of diffusion, laminar sublayer resistance and radiation extinction. To characterize the general chemical environment of this forest, we also present modeled mixing ratio profiles of biogenic hydrocarbons, hydrogen oxides and reactive nitrogen. The vertical profiles of these species demonstrate a range of structures and gradients that reflect the interplay of physical and chemical processes within the forest canopy, which can influence net exchange.

  9. The Chemistry of Atmosphere-Forest Exchange (CAFE Model – Part 1: Model description and characterization

    Directory of Open Access Journals (Sweden)

    G. M. Wolfe

    2010-09-01

    Full Text Available We present the Chemistry of Atmosphere-Forest Exchange (CAFE model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. CAFE integrates all key processes, including turbulent diffusion, emission, deposition and chemistry, throughout the forest canopy and mixed layer. It is the first model of its kind to incorporate the Master Chemical Mechanism (MCM and a suite of reactions for the oxidation of monoterpenes and sesquiterpenes, providing a more comprehensive description of the oxidative chemistry occurring within and above the forest. We use CAFE to simulate a young Ponderosa pine forest in the Sierra Nevada, CA. Utilizing meteorological constraints from the BEARPEX-2007 field campaign, we assess the sensitivity of modeled fluxes to parameterizations of diffusion, laminar sublayer resistance and radiation extinction. To characterize the general chemical environment of this forest, we also present modeled mixing ratio profiles of biogenic hydrocarbons, hydrogen oxides and reactive nitrogen. The vertical profiles of these species demonstrate a range of structures and gradients that reflect the interplay of physical and chemical processes within the forest canopy, which can influence net exchange.

  10. Modeling of iodine radiation chemistry in the presence of organic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Taghipour, Fariborz; Evans, Greg J. E-mail: evansg@chem-eng.toronto.edu

    2002-06-01

    A kinetic-based model was developed that simulates the radiation chemistry of iodine in the presence of organic compounds. The model's mechanistic description of iodine chemistry and generic semi-mechanistic reactions for various classes of organics, provided a reasonable representation of experimental results. The majority of the model and experimental results of iodine volatilization rates were in agreement within an order of magnitude.

  11. Supported Organometallic Complexes: Surface Chemistry, Spectroscopy, Catalysis, and Homogeneous Models

    Energy Technology Data Exchange (ETDEWEB)

    Marks, Tobin J. [Northwestern Univ., Evanston, IL (United States); Stalzer, Madelyn M. [Northwestern Univ., Evanston, IL (United States); Delferro, Massimiliano [Northwestern Univ., Evanston, IL (United States)

    2016-09-09

    The goal of this project is to model, understand at a fundamental level, expand, and exploit pathways by which organometallic molecules of varying nuclearity undergo chemisorptive activation and catalytic activity enhancement on solid surfaces. Such processes connect to real-world, large-scale industrial hydrocarbon processes and to manufacturing cleaner, greener, more environmentally acceptable products, including those from renewable resources. This research program combines catalyst synthesis, surface chemistry and spectroscopy, homogeneous analogue catalysis, structural analysis, and computation, and involves collaboration with national laboratory and industrial researchers. The objectives are to: 1) Investigate mononuclear and binuclear organometallic chemisorption on “super Brønsted acid” and related oxide surfaces, 2) Synthesize and characterize mononuclear and polynuclear catalyst precursors for understanding-based surface and solution phase catalysis, 3) Use this information to produce new types of efficient energy storage materials, 4) Computationally model both solution phase and chemisorbed catalysts, and investigate their reactivity modes. Of relevance to national energy issues is the potential to transform/metathesize inert saturated hydrocarbons,to drive “uphill” processes by coupling to exoergic transformations, to better utilize biofeedstocks (e.g., Dow’s world-scale Brazilian non-petroleum polyethylene process), and to address challenges articulated in recent BES Catalysis BRN and Grand Research Challenges reports. The long-range objective is therefore to understand and exploit (catalyst)∙∙∙(catalyst) and (catalyst )∙∙∙(surface/cocatalyst) interactions for new, instructive reactivity patterns, and to connect activating surface environments with mechanistically less complex solution environments. The information obtained is then fed back into further catalyst discovery efforts. We have pursued correlated synthesis

  12. Reducing Uncertainty in Chemistry Climate Model Predictions of Stratospheric Ozone

    Science.gov (United States)

    Douglass, A. R.; Strahan, S. E.; Oman, L. D.; Stolarski, R. S.

    2014-01-01

    Chemistry climate models (CCMs) are used to predict the future evolution of stratospheric ozone as ozone-depleting substances decrease and greenhouse gases increase, cooling the stratosphere. CCM predictions exhibit many common features, but also a broad range of values for quantities such as year of ozone-return-to-1980 and global ozone level at the end of the 21st century. Multiple linear regression is applied to each of 14 CCMs to separate ozone response to chlorine change from that due to climate change. We show that the sensitivity of lower atmosphere ozone to chlorine change deltaO3/deltaCly is a near linear function of partitioning of total inorganic chlorine (Cly) into its reservoirs; both Cly and its partitioning are controlled by lower atmospheric transport. CCMs with realistic transport agree with observations for chlorine reservoirs and produce similar ozone responses to chlorine change. After 2035 differences in response to chlorine contribute little to the spread in CCM results as the anthropogenic contribution to Cly becomes unimportant. Differences among upper stratospheric ozone increases due to temperature decreases are explained by differences in ozone sensitivity to temperature change deltaO3/deltaT due to different contributions from various ozone loss processes, each with their own temperature dependence. In the lower atmosphere, tropical ozone decreases caused by a predicted speed-up in the Brewer-Dobson circulation may or may not be balanced by middle and high latitude increases, contributing most to the spread in late 21st century predictions.

  13. High-Latitude Stratospheric Sensitivity to QBO Width in a Chemistry-Climate Model with Parameterized Ozone Chemistry

    Science.gov (United States)

    Hurwitz, M. M.; Braesicke, P.; Pyle, J. A.

    2010-01-01

    In a pair of idealized simulations with a simplified chemistry-climate model, the sensitivity of the wintertime Arctic stratosphere to variability in the width of the quasi-biennial oscillation (QBO) is assessed. The width of the QBO appears to have equal influence on the Arctic stratosphere as does the phase (i.e. the Holton-Tan mechanism). In the model, a wider QBO acts like a preferential shift toward the easterly phase of the QBO, where zonal winds at 60 N tend to be relatively weaker, while 50 hPa geopotential heights and polar ozone values tend to be higher.

  14. Radiation chemistry of salicylic and methyl substituted salicylic acids: Models for the radiation chemistry of pharmaceutical compounds

    International Nuclear Information System (INIS)

    Salicylic acid and its derivatives are components of many medications and moieties found in numerous pharmaceutical compounds. They have been used as models for various pharmaceutical compounds in pharmacological studies, for the treatment of pharmaceuticals and personal care products (PPCPs), and, reactions with natural organic matter (NOM). In this study, the radiation chemistry of benzoic acid, salicylic acid and four methyl substituted salicylic acids (MSA) is reported. The absolute bimolecular reaction rate constants for hydroxyl radical reaction with benzoic and salicylic acids as well as 3-methyl-, 4-methyl-, 5-methyl-, and 6-methyl-salicylic acid were determined (5.86±0.54)×109, (1.07±0.07)×1010, (7.48±0.17)×109, (7.31±0.29)×109, (5.47±0.25)×109, (6.94±0.10)×109 (M−1 s−1), respectively. The hydrated electron reaction rate constants were measured (3.02±0.10)×109, (8.98±0.27)×109, (5.39±0.21)×109, (4.33±0.17)×109, (4.72±0.15)×109, (1.42±0.02)×109 (M−1 s−1), respectively. The transient absorption spectra for the six model compounds were examined and their role as model compounds for the radiation chemistry of pharmaceuticals investigated. - Highlights: • Free radical chemistry of salicylic and 4 methyl salicylic acids is investigated. • The transient absorptions spectra for model compounds are measured. • Absolute bimolecular reaction rate constants for hydroxyl radical are determined. • Solvated electron reaction rate constants are calculated. • The use of salicylic acids as models for pharmaceuticals is explored

  15. Organic chemistry in the atmosphere. [laboratory modeling of Titan atmosphere

    Science.gov (United States)

    Sagan, C.

    1974-01-01

    The existence of an at least moderately complex organic chemistry on Titan is stipulated based on clear evidence of methane, and at least presumptive evidence of hydrogen in its atmosphere. The ratio of methane to hydrogen is the highest of any atmosphere in the solar system. Irradiation of hydrogen/methane mixtures produces aromatic and aliphatic hydrocarbons. A very reasonable hypothesis assumes that the red cloud cover of Titan is made of organic chemicals. Two-carbon hydrocarbons experimentally produced from irradiated mixtures of methane, ammonia, water, and hydrogen bear out the possible organic chemistry of the Titanian environment.

  16. Chemistry and dynamics of the Arctic winter 2015/2016: Simulations with the Chemistry-Climate Model EMAC

    Science.gov (United States)

    Khosrawi, Farahnaz; Kirner, Ole; Sinnhuber, Bjoern-Martin; Ruhnke, Roland; Hoepfner, Michael; Woiwode, Wolfgang; Oelhaf, Hermann; Santee, Michelle L.; Manney, Gloria L.; Froidevaux, Lucien; Murtagh, Donal; Braesicke, Peter

    2016-04-01

    Model simulations of the Arctic winter 2015/2016 were performed with the atmospheric chemistry-climate model ECHAM5/MESSy Atmospheric Chemistry (EMAC) for the POLSTRACC (Polar Stratosphere in a Changing Climate) project. The POLSTRACC project is a HALO mission (High Altitude and LOng Range Research Aircraft) that aims to investigate the structure, composition and evolution of the Arctic Upper Troposphere Lower Stratosphere (UTLS) in a changing climate. Especially, the chemical and physical processes involved in Arctic stratospheric ozone depletion, transport and mixing processes in the UTLS at high latitudes, polar stratospheric clouds as well as cirrus clouds are investigated. The model simulations were performed with a resolution of T42L90, corresponding to a quadratic Gaussian grid of approximately 2.8°× 2.8° degrees in latitude and longitude, and 90 vertical layers from the surface up to 0.01 hPa (approx. 80 km). A Newtonian relaxation technique of the prognostic variables temperature, vorticity, divergence and surface pressure towards ECMWF data was applied above the boundary layer and below 10 hPa, in order to nudge the model dynamics towards the observed meteorology. During the Arctic winter 2015/2016 a stable vortex formed in early December, with a cold pool where temperatures reached below the Nitric Acid Trihydrate (NAT) existence temperature of 195 K, thus allowing Polar Stratospheric Clouds (PSCs) to form. The early winter has been exceptionally cold and satellite observations indicate that sedimenting PSC particles have lead to denitrification as well as dehydration of stratospheric layers. In this presentation an overview of the chemistry and dynamics of the Arctic winter 2015/2016 as simulated with EMAC will be given and comparisons to satellite observations such as e.g. Aura/MLS and Odin/SMR will be shown.

  17. Modeling chemistry in and above snow at Summit, Greenland – Part 1: Model description and results

    Directory of Open Access Journals (Sweden)

    J. L. Thomas

    2010-12-01

    Full Text Available Sun-lit snow is increasingly recognized as a chemical reactor that plays an active role in uptake, transformation, and release of atmospheric trace gases. Snow is known to influence boundary layer air on a local scale, and given the large global surface coverage of snow may also be significant on regional and global scales.

    We present a new detailed one-dimensional snow chemistry module that has been coupled to the 1-D atmospheric boundary layer model MISTRA, we refer to the coupled model as MISTRA-SNOW. The new 1-D snow module, which is dynamically coupled to the overlaying atmospheric model, includes heat transport in the snowpack, molecular diffusion, and wind pumping of gases in the interstitial air. The model includes gas phase photochemistry and chemical reactions both in the interstitial air and the atmosphere. Heterogeneous and multiphase chemistry on atmospheric aerosol is considered explicitly. The chemical interaction of interstitial air with snow grains is simulated assuming chemistry in a liquid (aqueous layer on the grain surface. The model was used to investigate snow as the source of nitrogen oxides (NOx and gas phase reactive bromine in the atmospheric boundary layer in the remote snow covered Arctic (over the Greenland ice sheet as well as to investigate the link between halogen cycling and ozone depletion that has been observed in interstitial air. The model is validated using data taken 10 June–13 June, 2008 as part of the Greenland Summit Halogen-HOx experiment (GSHOX. The model predicts that reactions involving bromide and nitrate impurities in the surface snow at Summit can sustain atmospheric NO and BrO mixing ratios measured at Summit during this period.

  18. Directed synthesis of bio-inorganic vanadium oxide composites using genetically modified filamentous phage

    International Nuclear Information System (INIS)

    Highlights: • Phage is an excellent seeding for bio-templates for environmentally benign vanadium oxide nanocomposite synthesis. • The synthesized bio-inorganic vanadium oxide showed photodegradation activities. • The fabricated wt phage/vanadium oxide composite exhibited bundle-like structure. • The fabricated RSTB-phage/vanadium oxide composite exhibited a ball with a fiber-like nanostructure. • The virus/vanadium oxide composite could be applied in photocatalysts, sensors and nanoelectronic applications. - Abstract: The growth of crystalline vanadium oxide using a filamentous bacteriophage template was investigated using sequential incubation in a V2O5 precursor. Using the genetic modification of the bacteriophage, we displayed two cysteines that constrained the RSTB-1 peptide on the major coat protein P8, resulting in vanadium oxide crystallization. The phage-driven vanadium oxide crystals with different topologies, microstructures, photodegradation and vanadium oxide composites were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), quartz microbalance and dissipation (QCM-D) and X-ray photoelectron spectroscopy (XPS). Non-specific electrostatic attraction between a wild-type phage (wt-phage) and vanadium cations in the V2O5 precursor caused phage agglomeration and fiber formation along the length of the viral scaffold. As a result, the addition of recombinant phage (re-phage) in V2O5 precursors formed heterogeneous structures, which led to efficient condensation of vanadium oxide crystal formation in lines, shown by QCM-D analysis. Furthermore, re-phage/VxOx composites showed significantly enhanced photodegradation activities compared with the synthesized wt-phage-V2O5 composite under illumination. This study demonstrates that peptide-mediated vanadium oxide mineralization is governed by a complicated interplay of peptide sequence, local structure, kinetics and the presence of a mineralizing aid, such as the

  19. Modeling chemistry in and above snow at Summit, Greenland – Part 1: Model description and results

    Directory of Open Access Journals (Sweden)

    J. L. Thomas

    2011-05-01

    Full Text Available Sun-lit snow is increasingly recognized as a chemical reactor that plays an active role in uptake, transformation, and release of atmospheric trace gases. Snow is known to influence boundary layer air on a local scale, and given the large global surface coverage of snow may also be significant on regional and global scales. We present a new detailed one-dimensional snow chemistry module that has been coupled to the 1-D atmospheric boundary layer model MISTRA. The new 1-D snow module, which is dynamically coupled to the overlaying atmospheric model, includes heat transport in the snowpack, molecular diffusion, and wind pumping of gases in the interstitial air. The model includes gas phase chemical reactions both in the interstitial air and the atmosphere. Heterogeneous and multiphase chemistry on atmospheric aerosol is considered explicitly. The chemical interaction of interstitial air with snow grains is simulated assuming chemistry in a liquid-like layer (LLL on the grain surface. The coupled model, referred to as MISTRA-SNOW, was used to investigate snow as the source of nitrogen oxides (NOx and gas phase reactive bromine in the atmospheric boundary layer in the remote snow covered Arctic (over the Greenland ice sheet as well as to investigate the link between halogen cycling and ozone depletion that has been observed in interstitial air. The model is validated using data taken 10 June–13 June, 2008 as part of the Greenland Summit Halogen-HOx experiment (GSHOX. The model predicts that reactions involving bromide and nitrate impurities in the surface snow can sustain atmospheric NO and BrO mixing ratios measured at Summit, Greenland during this period.

  20. Modeling chemistry in and above snow at Summit, Greenland - Part 1: Model description and results

    Science.gov (United States)

    Thomas, J. L.; Stutz, J.; Lefer, B.; Huey, L. G.; Toyota, K.; Dibb, J. E.; von Glasow, R.

    2011-05-01

    Sun-lit snow is increasingly recognized as a chemical reactor that plays an active role in uptake, transformation, and release of atmospheric trace gases. Snow is known to influence boundary layer air on a local scale, and given the large global surface coverage of snow may also be significant on regional and global scales. We present a new detailed one-dimensional snow chemistry module that has been coupled to the 1-D atmospheric boundary layer model MISTRA. The new 1-D snow module, which is dynamically coupled to the overlaying atmospheric model, includes heat transport in the snowpack, molecular diffusion, and wind pumping of gases in the interstitial air. The model includes gas phase chemical reactions both in the interstitial air and the atmosphere. Heterogeneous and multiphase chemistry on atmospheric aerosol is considered explicitly. The chemical interaction of interstitial air with snow grains is simulated assuming chemistry in a liquid-like layer (LLL) on the grain surface. The coupled model, referred to as MISTRA-SNOW, was used to investigate snow as the source of nitrogen oxides (NOx) and gas phase reactive bromine in the atmospheric boundary layer in the remote snow covered Arctic (over the Greenland ice sheet) as well as to investigate the link between halogen cycling and ozone depletion that has been observed in interstitial air. The model is validated using data taken 10 June-13 June, 2008 as part of the Greenland Summit Halogen-HOx experiment (GSHOX). The model predicts that reactions involving bromide and nitrate impurities in the surface snow can sustain atmospheric NO and BrO mixing ratios measured at Summit, Greenland during this period.

  1. Radiation chemistry of salicylic and methyl substituted salicylic acids: Models for the radiation chemistry of pharmaceutical compounds

    Science.gov (United States)

    Ayatollahi, Shakiba; Kalnina, Daina; Song, Weihua; Turks, Maris; Cooper, William J.

    2013-11-01

    Salicylic acid and its derivatives are components of many medications and moieties found in numerous pharmaceutical compounds. They have been used as models for various pharmaceutical compounds in pharmacological studies, for the treatment of pharmaceuticals and personal care products (PPCPs), and, reactions with natural organic matter (NOM). In this study, the radiation chemistry of benzoic acid, salicylic acid and four methyl substituted salicylic acids (MSA) is reported. The absolute bimolecular reaction rate constants for hydroxyl radical reaction with benzoic and salicylic acids as well as 3-methyl-, 4-methyl-, 5-methyl-, and 6-methyl-salicylic acid were determined (5.86±0.54)×109, (1.07±0.07)×1010, (7.48±0.17)×109, (7.31±0.29)×109, (5.47±0.25)×109, (6.94±0.10)×109 (M-1 s-1), respectively. The hydrated electron reaction rate constants were measured (3.02±0.10)×109, (8.98±0.27)×109, (5.39±0.21)×109, (4.33±0.17)×109, (4.72±0.15)×109, (1.42±0.02)×109 (M-1 s-1), respectively. The transient absorption spectra for the six model compounds were examined and their role as model compounds for the radiation chemistry of pharmaceuticals investigated.

  2. An advanced scheme for wet scavenging and liquid-phase chemistry in a regional online-coupled chemistry transport model

    Directory of Open Access Journals (Sweden)

    C. Knote

    2012-10-01

    Full Text Available Clouds are reaction chambers for atmospheric trace gases and aerosols, and the associated precipitation is a major sink for atmospheric constituents. The regional chemistry-climate model COSMO-ART has been lacking a description of wet scavenging of gases and aqueous-phase chemistry. In this work we present a coupling of COSMO-ART with a wet scavenging and aqueous-phase chemistry scheme. The coupling is made consistent with the cloud microphysics scheme of the underlying meteorological model COSMO. While the choice of the aqueous-chemistry mechanism is flexible, the effects of a simple sulfur oxidation scheme are shown in the application of the coupled system in this work. We give details explaining the coupling and extensions made, then present results from idealized flow-over-hill experiments in a 2-D model setup and finally results from a full 3-D simulation. Comparison against measurement data shows that the scheme efficiently reduces SO2 trace gas concentrations by 0.3 ppbv (−30% on average, while leaving O3 and NOx unchanged. PM10 aerosol mass, which has been overestimated previously, is now in much better agreement with measured values due to a stronger scavenging of coarse particles. While total PM2.5 changes only little, chemical composition is improved notably. Overestimations of nitrate aerosols are reduced by typically 0.5–1 μg m−3 (up to −2 μg m−3 in the Po Valley while sulfate mass is increased by 1–1.5 μg m−3 on average (up to 2.5 μg m−3 in Eastern Europe. The effect of cloud processing of aerosols on its size distribution, i. e. a shift towards larger diameters, is observed. Compared against wet deposition measurements the system underestimates the total wet deposited mass for the simulated case study. We find that while evaporation of cloud droplets dominates in higher altitudes, evaporation of precipitation can

  3. A Model for Nitrogen Chemistry in Oxy-Fuel Combustion of Pulverized Coal

    DEFF Research Database (Denmark)

    Hashemi, Hamid; Hansen, Stine; Toftegaard, Maja Bøg;

    2011-01-01

    In this work, a model for the nitrogen chemistry in the oxy-fuel combustion of pulverized coal has been developed. The model is a chemical reaction engineering type of model with a detailed reaction mechanism for the gas-phase chemistry, together with a simplified description of the mixing of flows......, stoichiometry, and inlet NO level. In general, the model provides a satisfactory description of NO formation in air and oxy-fuel combustion of coal, but under some conditions, it underestimates the impact on NO of replacing N2 with CO2. According to the model, differences in the NO yield between the oxy...

  4. Coordination chemistry and applications of versatile 4,5-diazafluorene derivatives.

    Science.gov (United States)

    Annibale, Vincent T; Song, Datong

    2016-01-01

    This perspective review will examine the coordination chemistry and applications of metal complexes of 4,5-diazafluorene derivatives. The versatile derivatives of 4,5-diazafluorene can serve multiple roles, and display a number of coordination modes. The ambidentate derivatives with multiple coordination sites can allow for the syntheses of coordination polymers, multimetallic, and macrocyclic complexes. In addition, certain 4,5-diazafluorene derivatives can serve as spectator ligands to support reactivity at the metal centre, or as reactive actor ligands engaging in atypical reactivity patterns. The applications of metal complexes of 4,5-diazafluorene derivatives in catalysis, photochemistry and photophysics, as well as in bioinorganic chemistry are also surveyed.

  5. A Strategy for Process-Oriented Validation of Coupled Chemistry-Climate Models

    OpenAIRE

    Eyring, V.; Harris, N. R. P.; Rex, M.; Shepherd, T. G.; Fahey, D. W.; Amanatidis, G. T.; J. Austin; M. P. Chipperfield; Dameris, M.; P. M. De F. Forster; Gettelman, A.; Graf, H. F.; Nagashima, T.; Newman, P. A.; Pawson, S.

    2005-01-01

    Accurate and reliable predictions and an understanding of future changes in the stratosphere are of major importance to our understanding of climate change. Simulating the interaction between chemistry and climate is of particular importance, because continued increases in greenhouse gases and a slow decrease in halogen loading are expected. These both influence the abundance of stratospheric ozone. In recent years a number of coupled chemistry climate models (CCMs) with different levels of c...

  6. Effects of '"Environmental Chemistry" Elective Course via Technology-Embedded Scientific Inquiry Model on Some Variables

    Science.gov (United States)

    Çalik, Muammer; Özsevgeç, Tuncay; Ebenezer, Jazlin; Artun, Hüseyin; Küçük, Zeynel

    2014-01-01

    The purpose of this study is to examine the effects of "environmental chemistry" elective course via Technology-Embedded Scientific Inquiry (TESI) model on senior science student teachers' (SSSTs) conceptions of environmental chemistry concepts/issues, attitudes toward chemistry, and technological pedagogical content knowledge…

  7. What Can the Bohr-Sommerfeld Model Show Students of Chemistry in the 21st Century?

    Science.gov (United States)

    Niaz, Mansoor; Cardellini, Liberato

    2011-01-01

    Bohr's model of the atom is considered to be important by general chemistry textbooks. A shortcoming of this model was that it could not explain the spectra of atoms containing more than one electron. To increase the explanatory power of the model, Sommerfeld hypothesized the existence of elliptical orbits. This study aims to elaborate a framework…

  8. Global cloud and precipitation chemistry and wet deposition: tropospheric model simulations with ECHAM5/MESSy1

    Directory of Open Access Journals (Sweden)

    H. Tost

    2007-01-01

    Full Text Available The representation of cloud and precipitation chemistry and subsequent wet deposition of trace constituents in global atmospheric chemistry models is associated with large uncertainties. To improve the simulated trace gas distributions we apply the new submodel SCAV, which includes detailed cloud and precipitation chemistry and present results of the atmospheric chemistry general circulation model ECHAM5/MESSy1. A good agreement with observed wet deposition fluxes for species causing acid rain is obtained. The new scheme enables prognostic calculations of the pH of clouds and precipitation, and these results are also in accordance with observations. We address the influence of detailed cloud and precipitation chemistry on trace constituents based on sensitivity simulations. The results confirm previous results from regional scale and box models, and we extend the analysis to the role of aqueous phase chemistry on the global scale. Some species are directly affected through multiphase removal processes, and many also indirectly through changes in oxidant concentrations, which in turn have an impact on the species lifetime. While the overall effect on tropospheric ozone is relatively small (<10%, regional effects on O3 can reach ~20%, and several important compounds (e.g., H2O2, HCHO are substantially depleted by clouds and precipitation.

  9. Global cloud and precipitation chemistry and wet deposition: tropospheric model simulations with ECHAM5/MESSy1

    Directory of Open Access Journals (Sweden)

    J. Lelieveld

    2007-05-01

    Full Text Available The representation of cloud and precipitation chemistry and subsequent wet deposition of trace constituents in global atmospheric chemistry models is associated with large uncertainties. To improve the simulated trace gas distributions we apply the new submodel SCAV, which includes detailed cloud and precipitation chemistry and present results of the atmospheric chemistry general circulation model ECHAM5/MESSy1. A good agreement with observed wet deposition fluxes for species causing acid rain is obtained. The new scheme enables prognostic calculations of the pH of clouds and precipitation, and these results are also in accordance with observations. We address the influence of detailed cloud and precipitation chemistry on trace constituents based on sensitivity simulations. The results confirm previous results from regional scale and box models, and we extend the analysis to the role of aqueous phase chemistry on the global scale. Some species are directly affected through multiphase removal processes, and many also indirectly through changes in oxidant concentrations, which in turn have an impact on the species lifetime. While the overall effect on tropospheric ozone is relatively small (3 can reach ≈20%, and several important compounds (e.g., H2O2, HCHO are substantially depleted by clouds and precipitation.

  10. Online coupled meteorology and chemistry models: history, current status, and outlook

    Directory of Open Access Journals (Sweden)

    Y. Zhang

    2008-02-01

    Full Text Available The climate-chemistry-aerosol-cloud-radiation feedbacks are important processes occurring in the atmosphere. Accurately simulating those feedbacks requires fully-coupled meteorology, climate, and chemistry models and presents significant challenges in terms of both scientific understanding and computational demand. This paper reviews the history and current status of development and application of online coupled models. Several representative online coupled meteorology and chemistry models developed in the U.S. such as GATOR-GCMOM, WRF/Chem, CAM3, MIRAGE, and Caltech unified GCM are included along with case studies. Major model features, physical/chemical treatments, as well as typical applications are compared with a focus on aerosol microphysics treatments, aerosol feedbacks to planetary boundary layer meteorology, and aerosol-cloud interactions. Recommendations for future development and improvement of online coupled models are provided.

  11. Combustion chemistry of alcohols: Experimental and modeled structure of a premixed 2-methylbutanol flame

    KAUST Repository

    Lucassen, Arnas

    2014-06-14

    This paper presents a detailed investigation of 2-methylbutanol combustion chemistry in low-pressure premixed flames. This chemistry is of particular interest to study because this compound is potentially a lignocellulosic-based, next-generation biofuel. The detailed chemical structure of a stoichiometric low-pressure (25 Torr) flame was determined using flame-sampling molecular-beam mass spectrometry. A total of 55 species were identified and subsequently quantitative mole fraction profiles as function of distance from the burner surface were determined. In an independent effort, a detailed flame chemistry model for 2-methylbutanol was assembled based on recent knowledge gained from combustion chemistry studies for butanol isomers ([Sarathy et al. Combust. Flame 159 (6) (2012) 2028-2055]) and iso-pentanol (3-methylbutanol) [Sarathy et al. Combust. Flame 160 (12) (2013) 2712-2728]. Experimentally determined and modeled mole fraction profiles were compared to demonstrate the model\\'s capabilities. Examples of individual mole fraction profiles are discussed together with the most significant fuel consumption pathways to highlight the combustion chemistry of 2-methylbutanol. Discrepancies between experimental and modeling results are used to suggest areas where improvement of the kinetic model would be needed. © 2014.

  12. Non-OH chemistry in oxidation flow reactors for the study of atmospheric chemistry systematically examined by modeling

    Directory of Open Access Journals (Sweden)

    Z. Peng

    2015-09-01

    Full Text Available Oxidation flow reactors (OFRs using low-pressure Hg lamp emission at 185 and 254 nm produce OH radicals efficiently and are widely used in atmospheric chemistry and other fields. However, knowledge of detailed OFR chemistry is limited, allowing speculation in the literature about whether some non-OH reactants, including several not relevant for tropospheric chemistry, may play an important role in these OFRs. These non-OH reactants are UV radiation, O(1D, O(3P, and O3. In this study, we investigate the relative importance of other reactants to OH for the fate of reactant species in OFR under a wide range of conditions via box modeling. The relative importance of non-OH species is less sensitive to UV light intensity than to relative humidity (RH and external OH reactivity (OHRext, as both non-OH reactants and OH scale roughly proportional to UV intensity. We show that for field studies in forested regions and also the urban area of Los Angeles, reactants of atmospheric interest are predominantly consumed by OH. We find that O(1D, O(3P, and O3 have relative contributions to VOC consumption that are similar or lower than in the troposphere. The impact of O atoms can be neglected under most conditions in both OFR and troposphere. Under "pathological OFR conditions" of low RH and/or high OHRext, the importance of non-OH reactants is enhanced because OH is suppressed. Some biogenics can have substantial destructions by O3, and photolysis at non-tropospheric wavelengths (185 and 254 nm may also play a significant role in the degradation of some aromatics under pathological conditions. Working under low O2 with the OFR185 mode allows OH to completely dominate over O3 reactions even for the biogenic species most reactive with O3. Non-tropospheric VOC photolysis may have been a problem in some laboratory and source studies, but can be avoided or lessened in future studies by diluting source emissions and working at lower precursor concentrations in lab

  13. Modeling chemistry in and above snow at Summit, Greenland - Part 1: Model description and results

    OpenAIRE

    Thomas, J. L.; Stutz, J.; Lefer, B.; L. G. Huey; K. Toyota; J. E. Dibb; Glasow, R.

    2011-01-01

    Sun-lit snow is increasingly recognized as a chemical reactor that plays an active role in uptake, transformation, and release of atmospheric trace gases. Snow is known to influence boundary layer air on a local scale, and given the large global surface coverage of snow may also be significant on regional and global scales. We present a new detailed one-dimensional snow chemistry module that has been coupled to the 1-D atmospheric boundary layer model MISTRA. The new 1-D sn...

  14. Directed synthesis of bio-inorganic vanadium oxide composites using genetically modified filamentous phage

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Michael; Baik, Seungyun [Environmental Safety Group, Korea Institute of Science and Technology Europe (KIST-Europe) Forschungsgesellschaft mbH, Campus E 7 1, Saarbruecken (Germany); Jeon, Hojeong; Kim, Yuchan [Center for Biomaterials, Biomedical Research Institute Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Kim, Jungtae [Environmental Safety Group, Korea Institute of Science and Technology Europe (KIST-Europe) Forschungsgesellschaft mbH, Campus E 7 1, Saarbruecken (Germany); Kim, Young Jun, E-mail: youngjunkim@kist-europe.de [Environmental Safety Group, Korea Institute of Science and Technology Europe (KIST-Europe) Forschungsgesellschaft mbH, Campus E 7 1, Saarbruecken (Germany)

    2015-05-15

    Highlights: • Phage is an excellent seeding for bio-templates for environmentally benign vanadium oxide nanocomposite synthesis. • The synthesized bio-inorganic vanadium oxide showed photodegradation activities. • The fabricated wt phage/vanadium oxide composite exhibited bundle-like structure. • The fabricated RSTB-phage/vanadium oxide composite exhibited a ball with a fiber-like nanostructure. • The virus/vanadium oxide composite could be applied in photocatalysts, sensors and nanoelectronic applications. - Abstract: The growth of crystalline vanadium oxide using a filamentous bacteriophage template was investigated using sequential incubation in a V{sub 2}O{sub 5} precursor. Using the genetic modification of the bacteriophage, we displayed two cysteines that constrained the RSTB-1 peptide on the major coat protein P8, resulting in vanadium oxide crystallization. The phage-driven vanadium oxide crystals with different topologies, microstructures, photodegradation and vanadium oxide composites were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), quartz microbalance and dissipation (QCM-D) and X-ray photoelectron spectroscopy (XPS). Non-specific electrostatic attraction between a wild-type phage (wt-phage) and vanadium cations in the V{sub 2}O{sub 5} precursor caused phage agglomeration and fiber formation along the length of the viral scaffold. As a result, the addition of recombinant phage (re-phage) in V{sub 2}O{sub 5} precursors formed heterogeneous structures, which led to efficient condensation of vanadium oxide crystal formation in lines, shown by QCM-D analysis. Furthermore, re-phage/V{sub x}O{sub x} composites showed significantly enhanced photodegradation activities compared with the synthesized wt-phage-V{sub 2}O{sub 5} composite under illumination. This study demonstrates that peptide-mediated vanadium oxide mineralization is governed by a complicated interplay of peptide sequence, local structure

  15. The Lagrangian chemistry and transport model ATLAS: simulation and validation of stratospheric chemistry and ozone loss in the winter 1999/2000

    Directory of Open Access Journals (Sweden)

    I. Wohltmann

    2010-06-01

    Full Text Available ATLAS is a new global Lagrangian Chemistry and Transport Model (CTM, which includes a stratospheric chemistry scheme with 46 active species, 171 reactions, heterogeneous chemistry on polar stratospheric clouds and a Lagrangian denitrification module. Lagrangian (trajectory-based models have several important advantages over conventional Eulerian models, including the absence of spurious numerical diffusion, efficient code parallelization and no limitation of the largest time step by the Courant-Friedrichs-Lewy criterion. This work describes and validates the stratospheric chemistry scheme of the model. Stratospheric chemistry is simulated with ATLAS for the Arctic winter 1999/2000, with a focus on polar ozone depletion and denitrification. The simulations are used to validate the chemistry module in comparison with measurements of the SOLVE/THESEO 2000 campaign. A Lagrangian denitrification module, which is based on the simulation of the nucleation, sedimentation and growth of a large number of polar stratospheric cloud particles, is used to model the substantial denitrification that occured in this winter.

  16. The Lagrangian chemistry and transport model ATLAS: simulation and validation of stratospheric chemistry and ozone loss in the winter 1999/2000

    Directory of Open Access Journals (Sweden)

    I. Wohltmann

    2010-11-01

    Full Text Available ATLAS is a new global Lagrangian Chemistry and Transport Model (CTM, which includes a stratospheric chemistry scheme with 46 active species, 171 reactions, heterogeneous chemistry on polar stratospheric clouds and a Lagrangian denitrification module. Lagrangian (trajectory-based models have several important advantages over conventional Eulerian models, including the absence of spurious numerical diffusion, efficient code parallelization and no limitation of the largest time step by the Courant-Friedrichs-Lewy criterion. This work describes and validates the stratospheric chemistry scheme of the model. Stratospheric chemistry is simulated with ATLAS for the Arctic winter 1999/2000, with a focus on polar ozone depletion and denitrification. The simulations are used to validate the chemistry module in comparison with measurements of the SOLVE/THESEO 2000 campaign. A Lagrangian denitrification module, which is based on the simulation of the nucleation, sedimentation and growth of a large number of polar stratospheric cloud particles, is used to model the substantial denitrification that occured in this winter.

  17. Toward an Earth system model: atmospheric chemistry, coupling, and petascale computing

    International Nuclear Information System (INIS)

    Atmospheric chemicals and aerosols are interactive components of the Earth system, with implications for climate. As part of the SciDAC climate consortium of labs we have implemented a flexible state-of-the-art atmospheric chemistry and aerosol capability into the Community Climate System Model (CCSM). We have also developed a fast chemistry mechanism that agrees well with observations and is computationally more efficient than our more complex chemistry mechanisms. We are working with other colleagues to couple this capability with the biospheric and aerosol-cloud interaction capabilities that are being developed for the CCSM model to create an Earth system model. However, to realise the potential of this Earth system model will require a move from terascale to petascale computing, and the greatest benefit will come from well balanced computers and a balance between capability and capacity computing

  18. Chemistry in plumes of high-flying aircraft with H2 combustion engines: a modelling study

    Directory of Open Access Journals (Sweden)

    G. Weibring

    Full Text Available Recent discussions on high-speed civil transport (HSCT systems have renewed the interest in the chemistry of supersonic-aircraft plumes. The engines of these aircraft emit large concentrations of radicals like O, H, OH, and NO. In order to study the effect of these species on the composition of the atmosphere, the detailed chemistry of an expanding and cooling plume is examined for different expansion models.

    For a representative flight at 26 km the computed trace gas concentrations do not differ significantly for different models of the expansion behaviour. However, it is shown that the distributions predicted by all these models differ significantly from those adopted in conventional meso-scale and global models in which the plume chemistry is not treated in detail. This applies in particular to the reservoir species HONO and H2O2.

  19. Skill in forecasting extreme ozone pollution episodes with a global atmospheric chemistry model

    Directory of Open Access Journals (Sweden)

    J. L. Schnell

    2014-03-01

    Full Text Available From the ensemble of stations that monitor surface air quality over the United States and Europe, we identify extreme ozone pollution events and find that they occur predominantly in clustered, multi-day episodes with spatial extents of more than 1000 km. Such scales are amenable to forecasting with current global atmospheric chemistry models. We develop an objective mapping algorithm that uses the heterogeneous observations of the individual surface sites to calculate surface ozone averaged over 1° by 1° grid cells, matching the resolution of a global model. Air quality extreme (AQX events are identified locally as statistical extremes of the ozone climatology and not as air quality exceedances. With the University of California, Irvine chemistry-transport model (CTM we find there is skill in hindcasting these extreme episodes, and thus identify a new diagnostic using global chemistry-climate models (CCM to identify changes in the characteristics of extreme pollution episodes in a warming climate.

  20. Modeling the surface chemistry of biomass model compounds on oxygen-covered Rh(100).

    Science.gov (United States)

    Caglar, B; Niemantsverdriet, J W Hans; Weststrate, C J Kees-Jan

    2016-08-24

    Rhodium-based catalysts are potential candidates to process biomass and serve as a representation of the class of noble metal catalysts for biomass-related processes. Biomass can be processed in aqueous media (hydrolysis and aqueous phase reforming), and in this case the surface chemistry involves hydroxyl (OH) species. In our study this was modelled by the presence of pre-adsorbed oxygen. Ethylene glycol, with a hydroxyl group on every carbon atom, serves as a model compound to understand the conversion of biomass derived molecules into desirable chemicals on catalytically active metal surfaces. Ethanol (containing one OH group) serves as a reference molecule for ethylene glycol (containing two OH groups) to understand the interaction of C-OH functionalities with a Rh(100) surface. The surface chemistry of ethylene glycol and ethanol in the presence of pre-adsorbed oxygen on a Rh(100) surface has been studied via temperature programmed reaction spectroscopy (TPRS) and reflection absorption infrared spectroscopy (RAIRS) using various coverages of O(ad) and ethylene glycol and ethanol. Pre-adsorbed oxygen alters the decomposition chemistry of both compounds, thereby affecting the product distribution. Under an oxygen-lean condition, the selectivity to produce methane from ethanol is enhanced significantly (4.5-fold with respect to that obtained on the oxygen-free surface). For ethylene glycol, oxygen-lean conditions promote the formation of formaldehyde, with 10-15% selectivity. In addition, with Oad present the fraction of molecules that decompose on the surface increases 2-fold for ethanol and 1.5-fold for ethylene glycol, due to fast O-H bond activation by pre-adsorbed oxygen. Under oxygen-rich conditions, the decomposition products are mainly oxidized to carbon dioxide and water for both molecules. In this condition, the promotion effect provided by adsorbed oxygen for the dissociative adsorption of ethanol and ethylene glycol is reduced due to the site blocking

  1. Integrated sorption and diffusion model for bentonite. Part 2. Porewater chemistry, sorption and diffusion modeling in compacted systems

    International Nuclear Information System (INIS)

    It is important to understand the coupled processes of sorption and diffusion of radionuclides (RNs) in compacted bentonite, and to develop mechanistic models that can aid in the prediction of the long-term performance of geological disposal systems of radioactive waste. The integrated sorption and diffusion (ISD) model was developed based on the consistent combination of clay–water interaction, sorption and diffusion models. The diffusion model based on the electrical double layer theory describing relative ionic concentrations and viscoelectric effects at the negatively charged clay surface was coupled with porewater chemistry and sorption models. This ISD model was successfully tested for various actinides with a complex chemistry (Np(V), Am(III), U(VI) under conditions where variably charged carbonate complexes are formed) considered in Part 1, by using published diffusion and sorption data (Da, De, Kd) as a function of partial montmorillonite density. Quantitative agreements were observed by considering uncertainty in porewater chemistry and dominant aqueous species. It can therefore be concluded that the ISD model developed here is able to adequately explain the sorption and diffusion behavior of various RNs with a complex chemistry in compacted bentonites. The performed modeling indicates that uncertainties are mainly related to porewater chemistry and RN speciation and that these parameters need to be carefully evaluated. (author)

  2. Non-linear regression model for spatial variation in precipitation chemistry for South India

    Science.gov (United States)

    Siva Soumya, B.; Sekhar, M.; Riotte, J.; Braun, Jean-Jacques

    Chemical composition of rainwater changes from sea to inland under the influence of several major factors - topographic location of area, its distance from sea, annual rainfall. A model is developed here to quantify the variation in precipitation chemistry under the influence of inland distance and rainfall amount. Various sites in India categorized as 'urban', 'suburban' and 'rural' have been considered for model development. pH, HCO 3, NO 3 and Mg do not change much from coast to inland while, SO 4 and Ca change is subjected to local emissions. Cl and Na originate solely from sea salinity and are the chemistry parameters in the model. Non-linear multiple regressions performed for the various categories revealed that both rainfall amount and precipitation chemistry obeyed a power law reduction with distance from sea. Cl and Na decrease rapidly for the first 100 km distance from sea, then decrease marginally for the next 100 km, and later stabilize. Regression parameters estimated for different cases were found to be consistent ( R2 ˜ 0.8). Variation in one of the parameters accounted for urbanization. Model was validated using data points from the southern peninsular region of the country. Estimates are found to be within 99.9% confidence interval. Finally, this relationship between the three parameters - rainfall amount, coastline distance, and concentration (in terms of Cl and Na) was validated with experiments conducted in a small experimental watershed in the south-west India. Chemistry estimated using the model was in good correlation with observed values with a relative error of ˜5%. Monthly variation in the chemistry is predicted from a downscaling model and then compared with the observed data. Hence, the model developed for rain chemistry is useful in estimating the concentrations at different spatio-temporal scales and is especially applicable for south-west region of India.

  3. Prion疾病与生物无机化学%Prion Diseases and Bio-inorganic Chemistry

    Institute of Scientific and Technical Information of China (English)

    黄仲贤; 陆君霞; 王韵华

    2000-01-01

    介绍了除病菌、病毒以外的第三种病原体-病蛋白Prion.这种病原蛋白的本质是正常蛋白的异常折叠,因此又被称为蛋白分子的"构象病".还介绍了这种病蛋白的可能致病机理.铜离子对这种病蛋白生成的重要作用,充分显示了生物无机化学这门新兴学科的重要性和前沿性.

  4. Bioinorganic Chemistry in Thyroid Gland: Effect of Antithyroid Drugs on Peroxidase-Catalyzed Oxidation and Iodination Reactions

    Directory of Open Access Journals (Sweden)

    G. Mugesh

    2006-11-01

    Full Text Available Propylthiouracil (PTU and methimazole (MMI are the most commonly used antithyroid drugs. The available data suggest that these drugs may block the thyroid hormone synthesis by inhibiting the thyroid peroxidase (TPO or diverting oxidized iodides away from thyroglobulin. It is also known that PTU inhibits the selenocysteine-containing enzyme ID-1 by reacting with the selenenyl iodide intermediate (E-SeI. In view of the current interest in antithyroid drugs, we have recently carried out biomimetic studies to understand the mechanism by which the antithyroid drugs inhibit the thyroid hormone synthesis and found that the replacement of sulfur with selenium in MMI leads to an interesting compound that may reversibly block the thyroid hormone synthesis. Our recent results on the inhibition of lactoperoxidase (LPO-catalyzed oxidation and iodination reactions by antithyroid drugs are described.

  5. Electron-nuclear double resonance spectroscopy (and electron spin-echo envelope modulation spectroscopy) in bioinorganic chemistry

    OpenAIRE

    Hoffman, Brian M.

    2003-01-01

    This perspective discusses the ways that advanced paramagnetic resonance techniques, namely electron-nuclear double resonance (ENDOR) and electron spin-echo envelope modulation (ESEEM) spectroscopies, can help us understand how metal ions function in biological systems.

  6. A Performance Enhanced Interactive Learning Workshop Model as a Supplement for Organic Chemistry Instruction

    Science.gov (United States)

    Phillips, Karen E. S.; Grose-Fifer, Jilliam

    2011-01-01

    In this study, the authors describe a Performance Enhanced Interactive Learning (PEIL) workshop model as a supplement for organic chemistry instruction. This workshop model differs from many others in that it includes public presentations by students and other whole-class-discussion components that have not been thoroughly investigated in the…

  7. The two-way nested global chemistry-transport zoom model TM5: algorithm and applications

    NARCIS (Netherlands)

    Krol, M.; Houweling, S.; Bregman, B.; van den Broek, M.; Segers, A.; van Velthoven, P.; Peters, W.; Dentener, F.; Bergamaschi, P.

    2005-01-01

    This paper describes the global chemistry Transport Model, version 5 (TM5) which allows two-way nested zooming. The model is used for global studies which require high resolution regionally but can work on a coarser resolution globally. The zoom algorithm introduces refinement in both space and time

  8. An Integrated Visualization and Basic Molecular Modeling Laboratory for First-Year Undergraduate Medicinal Chemistry

    Science.gov (United States)

    Hayes, Joseph M.

    2014-01-01

    A 3D model visualization and basic molecular modeling laboratory suitable for first-year undergraduates studying introductory medicinal chemistry is presented. The 2 h practical is embedded within a series of lectures on drug design, target-drug interactions, enzymes, receptors, nucleic acids, and basic pharmacokinetics. Serving as a teaching aid…

  9. Modelling the chemistry of star-forming filaments - I. H2 and CO chemistry

    Science.gov (United States)

    Seifried, D.; Walch, S.

    2016-06-01

    We present simulations of star-forming filaments incorporating on of the largest chemical network used to date on-the-fly in a 3D-magnetohydrodynamic (MHD) simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this, we use the newly developed package KROME (Grassi et al.). We combine the KROME package with an algorithm which allows us to calculate the column density and attenuation of the interstellar radiation field necessary to properly model heating and ionization rates. Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionization rate. We find that, towards the centre of the filaments, there is gradual conversion of hydrogen from H to H2 as well as of C+ over C to CO. Moreover, we find a decrease of the dust temperature towards the centre of the filaments in agreement with recent HERSCHEL observations.

  10. Modeling Human Serum Albumin Tertiary Structure to Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics

    Science.gov (United States)

    Petrovic, Dus?an; Zlatovic´, Mario

    2015-01-01

    A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL…

  11. Single-step chemistry model and transport coefficient model for hydrogen combustion

    Institute of Scientific and Technical Information of China (English)

    WANG ChangJian; WEN Jennifer; LU ShouXiang; GUO Jin

    2012-01-01

    To satisfy the needs of large-scale hydrogen combustion and explosion simulation,a method is presented to establish single-step chemistry model and transport model for fuel-air mixture.If the reaction formula for hydrogen-air mixture is H2+0.5O2→H2O,the reaction rate model is ω =1.13×1015[H2][O2]exp(-46.37T0/T) mol (cm3 s)-1,and the transport coefficient model is μ=K/Cp=pD=7.0×10-5T 0.7 g (cm s)-1.By using current models and the reference model to simulate steady Zeldovich-von Neumann-Doering (ZND) wave and free-propagating laminar flame,it is found that the results are well agreeable.Additionally,deflagration-to-detonation transition in an obstructed channel was also simulated.The numerical results are also well consistent with the experimental results.These provide a reasonable proof for current method and new models.

  12. MATCH–SALSA – Multi-scale Atmospheric Transport and CHemistry model coupled to the SALSA aerosol microphysics model – Part 1: Model description and evaluation

    OpenAIRE

    Andersson, C.; Bergström, R; Bennet, C.; Robertson, L.; Thomas, M.; Korhonen, H.; Lehtinen, K. E. J.; H. Kokkola

    2014-01-01

    We have implemented the sectional aerosol dynamics model SALSA in the European scale chemistry-transport model MATCH (Multi-scale Atmospheric Transport and Chemistry). The new model is called MATCH–SALSA. It includes aerosol microphysics, with several formulations for nucleation, wet scavenging and condensation. The model reproduces observed higher particle number concentration (PNC) in central Europe and lower concentrations in remote regions. The model PNC size ...

  13. Solid-State Synthesis, Characterization, and Biological Activity of the Bioinorganic Complex of Aspartic Acid and Arsenic Triiodide

    Directory of Open Access Journals (Sweden)

    Guo-Qing Zhong

    2013-01-01

    Full Text Available The bioinorganic complex of aspartic acid and arsenic triiodide was synthesized by a solid-state reaction at room temperature. The formula of the complex is AsI3[HOOCCH2CH(NH2COOH]2.5. The crystal structure of the complex belongs to monoclinic system with lattice parameters: a=1.0019 nm, b=1.5118 nm, c=2.1971 nm, and β=100.28°. The infrared spectra can demonstrate the complex formation between the arsenic ion and aspartic acid, and the complex may be a dimer with bridge structure. The result of primary biological test indicates that the complex possesses better biological activity for the HL-60 cells of the leukemia than arsenic triiodide.

  14. Merging curriculum design with chemical epistemology: A case of teaching and learning chemistry through modeling

    Science.gov (United States)

    Erduran, Sibel

    The central problem underlying this dissertation is the design of learning environments that enable the teaching and learning of chemistry through modeling. Significant role of models in chemistry knowledge is highlighted with a shift in emphasis from conceptual to epistemological accounts of models. Research context is the design and implementation of student centered Acids & Bases Curriculum, developed as part of Project SEPIA. Qualitative study focused on 3 curriculum activities conducted in one 7th grade class of 19 students in an urban, public middle school in eastern United States. Questions guiding the study were: (a) How can learning environments be designed to promote growth of chemistry knowledge through modeling? (b) What epistemological criteria facilitate learning of growth of chemistry knowledge through modeling? Curriculum materials, and verbal data from whole class conversations and student group interviews were analyzed. Group interviews consisted of same 4 students, selected randomly before curriculum implementation, and were conducted following each activity to investigate students' developing understandings of models. Theoretical categories concerning definition, properties and kinds of models as well as educational and chemical models informed curriculum design, and were redefined as codes in the analysis of verbal data. Results indicate more diversity of codes in student than teacher talk across all activities. Teacher concentrated on educational and chemical models. A significant finding is that model properties such as 'compositionality' and 'projectability' were not present in teacher talk as expected by curriculum design. Students did make reference to model properties. Another finding is that students demonstrate an understanding of models characterized by the seventeenth century Lemery model of acids and bases. Two students' developing understandings of models across curriculum implementation suggest that curriculum bears some change in

  15. Impact of an accurate modeling of primordial chemistry in high resolution studies

    CERN Document Server

    Bovino, S; Latif, M A; Schleicher, D R G

    2013-01-01

    The formation of the first stars in the Universe is regulated by a sensitive interplay of chemistry and cooling with the dynamics of a self-gravitating system. As the outcome of the collapse and the final stellar masses depend sensitively on the thermal evolution, it is necessary to accurately model the thermal evolution in high resolution simulations. As previous investigations raised doubts regarding the convergence of the temperature at high resolution, we investigate the role of the numerical method employed to model the chemistry and the thermodynamics. Here we compare the standard implementation in the adaptive-mesh refinement code \\verb|ENZO|, employing a first order backward differentiation formula (BDF), with the 5th order accurate BDF solver \\verb|DLSODES|. While the standard implementation in \\verb|ENZO| shows a strong dependence on the employed resolution, the results obtained with \\verb|DLSODES| are considerably more robust, both with respect to the chemistry and thermodynamics, but also for dyna...

  16. A new Geoengineering Model Intercomparison Project (GeoMIP experiment designed for climate and chemistry models

    Directory of Open Access Journals (Sweden)

    S. Tilmes

    2014-08-01

    Full Text Available A new Geoengineering Model Intercomparison Project (GeoMIP experiment "G4 specified stratospheric aerosols" (short name: G4SSA is proposed to investigate the impact of stratospheric aerosol geoengineering on atmospheric composition, climate, and the environment. In contrast to the earlier G4 GeoMIP experiment, which requires an emission of sulphur dioxide (SO2 into the model, a prescribed aerosol forcing file is provided to the community, to be consistently applied to future model experiments between 2020 and 2100. This stratospheric aerosol distribution, with a total burden of about 2 Tg S has been derived using the ECHAM5-HAM microphysical model, based on a continuous annual tropical emission of 8 Tg SO2 year−1. A ramp-up of geoengineering in 2020 and a ramp-down in 2070 over a period of two years are included in the distribution, while a background aerosol burden should be used for the last 3 decades of the experiment. The performance of this experiment using climate and chemistry models in a multi-model comparison framework will allow us to better understand the significance of the impact of geoengineering and the abrupt termination after 50 years on climate and composition of the atmosphere in a changing environment. The zonal and monthly mean stratospheric aerosol input dataset is available at https://www2.acd.ucar.edu/gcm/geomip-g4-specified-stratospheric-aerosol-data-set.

  17. Representativeness errors in comparing chemistry transport and chemistry climate models with satellite UV/Vis tropospheric column retrievals

    Directory of Open Access Journals (Sweden)

    K. F. Boersma

    2015-09-01

    Full Text Available UV/Vis satellite retrievals of trace gas columns of nitrogen dioxide (NO2, sulphur dioxide (SO2, and formaldehyde (HCHO are useful to test and improve models of atmospheric composition, for data assimilation, air quality hindcasting and forecasting, and to provide top-down constraints on emissions. However, because models and satellite measurements do not represent the exact same geophysical quantities, the process of confronting model fields with satellite measurements is complicated by representativeness errors, which degrade the quality of the comparison beyond contributions from modelling and measurement errors alone. Here we discuss three types of representativeness errors that arise from the act of carrying out a model-satellite comparison: (1 horizontal representativeness errors due to imperfect collocation of the model grid cell and an ensemble of satellite pixels called superobservation, (2 temporal representativeness errors originating mostly from differences in cloud cover between the modelled and observed state, and (3 vertical representativeness errors because of reduced satellite sensitivity towards the surface accompanied with necessary retrieval assumptions on the state of the atmosphere. To minimize the impact of these representativeness errors, we recommend that models and satellite measurements be sampled as consistently as possible, and our paper provides a number of recipes to do so. A practical confrontation of tropospheric NO2 columns simulated by the TM5 chemistry transport model (CTM with Ozone Monitoring Instrument (OMI tropospheric NO2 retrievals suggests that horizontal representativeness errors, while unavoidable, are limited to within 5–10 % in most cases and of random nature. These errors should be included along with the individual retrieval errors in the overall superobservation error. Temporal sampling errors from mismatches in cloud cover, and, consequently, in photolysis rates, are on the order of 10 % for

  18. Representativeness errors in comparing chemistry transport and chemistry climate models with satellite UV-Vis tropospheric column retrievals

    Science.gov (United States)

    Boersma, K. F.; Vinken, G. C. M.; Eskes, H. J.

    2016-03-01

    Ultraviolet-visible (UV-Vis) satellite retrievals of trace gas columns of nitrogen dioxide (NO2), sulfur dioxide (SO2), and formaldehyde (HCHO) are useful to test and improve models of atmospheric composition, for data assimilation, air quality hindcasting and forecasting, and to provide top-down constraints on emissions. However, because models and satellite measurements do not represent the exact same geophysical quantities, the process of confronting model fields with satellite measurements is complicated by representativeness errors, which degrade the quality of the comparison beyond contributions from modelling and measurement errors alone. Here we discuss three types of representativeness errors that arise from the act of carrying out a model-satellite comparison: (1) horizontal representativeness errors due to imperfect collocation of the model grid cell and an ensemble of satellite pixels called superobservation, (2) temporal representativeness errors originating mostly from differences in cloud cover between the modelled and observed state, and (3) vertical representativeness errors because of reduced satellite sensitivity towards the surface accompanied with necessary retrieval assumptions on the state of the atmosphere. To minimize the impact of these representativeness errors, we recommend that models and satellite measurements be sampled as consistently as possible, and our paper provides a number of recipes to do so. A practical confrontation of tropospheric NO2 columns simulated by the TM5 chemistry transport model (CTM) with Ozone Monitoring Instrument (OMI) tropospheric NO2 retrievals suggests that horizontal representativeness errors, while unavoidable, are limited to within 5-10 % in most cases and of random nature. These errors should be included along with the individual retrieval errors in the overall superobservation error. Temporal sampling errors from mismatches in cloud cover, and, consequently, in photolysis rates, are of the order of 10

  19. Results of an interactively coupled atmospheric chemistry - general circulation model. Comparison with observations

    Energy Technology Data Exchange (ETDEWEB)

    Hein, R.; Dameris, M.; Schnadt, C. [and others

    2000-01-01

    An interactively coupled climate-chemistry model which enables a simultaneous treatment of meteorology and atmospheric chemistry and their feedbacks is presented. This is the first model, which interactively combines a general circulation model based on primitive equations with a rather complex model of stratospheric and tropospheric chemistry, and which is computational efficient enough to allow long-term integrations with currently available computer resources. The applied model version extends from the Earth's surface up to 10 hPa with a relatively high number (39) of vertical levels. We present the results of a present-day (1990) simulation and compare it to available observations. We focus on stratospheric dynamics and chemistry relevant to describe the stratospheric ozone layer. The current model version ECHAM4.L39(DLR)/CHEM can realistically reproduce stratospheric dynamics in the Arctic vortex region, including stratospheric warming events. This constitutes a major improvement compared to formerly applied model versions. However, apparent shortcomings in Antarctic circulation and temperatures persist. The seasonal and interannual variability of the ozone layer is simulated in accordance with observations. Activation and deactivation of chlorine in the polar stratospheric vortices and their interhemispheric differences are reproduced. The consideration of the chemistry feedback on dynamics results in an improved representation of the spatial distribution of stratospheric water vapor concentrations, i.e., the simulated meriodional water vapor gradient in the stratosphere is realistic. The present model version constitutes a powerful tool to investigate, for instance, the combined direct and indirect effects of anthropogenic trace gas emissions, and the future evolution of the ozone layer. (orig.)

  20. An optimization approach to kinetic model reduction for combustion chemistry

    CERN Document Server

    Lebiedz, Dirk

    2013-01-01

    Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on optimization of trajectories and show its applicability to realistic combustion models. As most model reduction methods, it identifies points on a slow invariant manifold based on time scale separation in the dynamics of the reaction system. The numerical approximation of points on the manifold is achieved by solving a semi-infinite optimization problem, where the dynamics enter the problem as constraints. The proof of existence of a solution for an arbitrarily chosen dimension of the reduced model (slow manifold) is extended to the case of realistic combustion models including thermochemistry by considering the properties of proper maps. The model reduction approach is finally applied to three models based on realistic reaction mechanisms: 1. ozone decomposition as a small t...

  1. Practical approaches to biological inorganic chemistry

    CERN Document Server

    Louro, Ricardo O

    2012-01-01

    The book reviews the use of spectroscopic and related methods to investigate the complex structures and mechanisms of biological inorganic systems that contain metals. Each chapter presents an overview of the technique including relevant theory, clearly explains what it is and how it works and then presents how the technique is actually used to evaluate biological structures. Practical examples and problems are included to illustrate each technique and to aid understanding. Designed for students and researchers who want to learn both the basics, and more advanced aspects of bioinorganic chemistry. It includes many colour illustrations enable easier visualization of molecular mechanisms and structures. It provides worked examples and problems that are included to illustrate and test the reader's understanding of each technique. It is written by a multi-author team who use and teach the most important techniques used today to analyse complex biological structures.

  2. The Role of Water Chemistry in Marine Aquarium Design: A Model System for a General Chemistry Class

    Science.gov (United States)

    Keaffaber, Jeffrey J.; Palma, Ramiro; Williams, Kathryn R.

    2008-01-01

    Water chemistry is central to aquarium design, and it provides many potential applications for discussion in undergraduate chemistry and engineering courses. Marine aquaria and their life support systems feature many chemical processes. A life support system consists of the entire recirculation system, as well as the habitat tank and all ancillary…

  3. Chemistry, Life, the Universe, and Everything: A New Approach to General Chemistry, and a Model for Curriculum Reform

    Science.gov (United States)

    Cooper, Melanie; Klymkowsky, Michael

    2013-01-01

    The history of general chemistry is one of almost constant calls for reform, yet over the past 60 years little of substance has changed. Those reforms that have been implemented are almost entirely concerned with how the course is taught, rather than what is to be learned. Here we briefly discuss the history of the general chemistry curriculum and…

  4. Modelling iodide – iodate speciation in atmospheric aerosol: Contributions of inorganic and organic iodine chemistry

    Directory of Open Access Journals (Sweden)

    S. Pechtl

    2007-01-01

    Full Text Available The speciation of iodine in atmospheric aerosol is currently poorly understood. Models predict negligible iodide concentrations but accumulation of iodate in aerosol, both of which is not confirmed by recent measurements. We present an updated aqueous phase iodine chemistry scheme for use in atmospheric chemistry models and discuss sensitivity studies with the marine boundary layer model MISTRA. These studies show that iodate can be reduced in acidic aerosol by inorganic reactions, i.e., iodate does not necessarily accumulate in particles. Furthermore, the transformation of particulate iodide to volatile iodine species likely has been overestimated in previous model studies due to negligence of collision-induced upper limits for the reaction rates. However, inorganic reaction cycles still do not seem to be sufficient to reproduce the observed range of iodide – iodate speciation in atmospheric aerosol. Therefore, we also investigate the effects of the recently suggested reaction of HOI with dissolved organic matter to produce iodide. If this reaction is fast enough to compete with the inorganic mechanism, it would not only directly lead to enhanced iodide concentrations but, indirectly via speed-up of the inorganic iodate reduction cycles, also to a decrease in iodate concentrations. Hence, according to our model studies, organic iodine chemistry, combined with inorganic reaction cycles, is able to reproduce observations. The presented chemistry cycles are highly dependent on pH and thus offer an explanation for the large observed variability of the iodide – iodate speciation in atmospheric aerosol.

  5. Online-coupled meteorology and chemistry models: history, current status, and outlook

    Directory of Open Access Journals (Sweden)

    Y. Zhang

    2008-06-01

    Full Text Available The climate-chemistry-aerosol-cloud-radiation feedbacks are important processes occurring in the atmosphere. Accurately simulating those feedbacks requires fully-coupled meteorology, climate, and chemistry models and presents significant challenges in terms of both scientific understanding and computational demand. This paper reviews the history and current status of the development and application of online-coupled meteorology and chemistry models, with a focus on five representative models developed in the US including GATOR-GCMOM, WRF/Chem, CAM3, MIRAGE, and Caltech unified GCM. These models represent the current status and/or the state-of-the science treatments of online-coupled models worldwide. Their major model features, typical applications, and physical/chemical treatments are compared with a focus on model treatments of aerosol and cloud microphysics and aerosol-cloud interactions. Aerosol feedbacks to planetary boundary layer meteorology and aerosol indirect effects are illustrated with case studies for some of these models. Future research needs for model development, improvement, application, as well as major challenges for online-coupled models are discussed.

  6. MATCH-SALSA – Multi-scale Atmospheric Transport and CHemistry model coupled to the SALSA aerosol microphysics model – Part 1: Model description and evaluation

    OpenAIRE

    Andersson, C.; Bergström, R; Bennet, C.; Robertson, L.; Thomas, M.; Korhonen, H.; Lehtinen, K. E. J.; H. Kokkola

    2015-01-01

    We have implemented the sectional aerosol dynamics model SALSA (Sectional Aerosol module for Large Scale Applications) in the European-scale chemistry-transport model MATCH (Multi-scale Atmospheric Transport and Chemistry). The new model is called MATCH-SALSA. It includes aerosol microphysics, with several formulations for nucleation, wet scavenging and condensation. The model reproduces observed higher particle number concentration (PNC) in central Europe and lower c...

  7. Difficulties in generalizing modelling strategies in science: the case of physics and chemistry

    OpenAIRE

    Greca, Ileana M.; Flávia M. T. dos Santos

    2005-01-01

    A review of the papers published in science education shows that the teaching centred in modelling is seemed as one of the most effective strategies for the improvement of the understanding of scientific concepts. However, a more carefully analyse also shows that what is being called as model or modelling process is very wide, and does not consider the differences in the specificities of the sciences. In this paper we try to discuss the differences and similitude in physics and chemistry mode...

  8. The global impact of supersaturation in a coupled chemistry-climate model

    OpenAIRE

    A. Gettelman; Kinnison, D E

    2007-01-01

    International audience Ice supersaturation is important for understanding condensation in the upper troposphere. Many general circulation models however do not permit supersaturation. In this study, a coupled chemistry climate model, the Whole Atmosphere Community Climate Model (WACCM), is modified to include supersaturation for the ice phase. Rather than a study of a detailed parameterization of supersaturation, the study is intended as a sensitivity experiment, to understand the potentia...

  9. Performance of European chemistry transport models as function of horizontal resolution

    NARCIS (Netherlands)

    Schaap, M.; Cuvelier, C.; Hendriks, C.; Bessagnet, B.; Baldasano, J.M.; Colette, A.; Thunis, P.; Karam, D.; Fagerli, H.; Graff, A.; Kranenburg, R.; Nyiri, A.; Pay, M.T.; Rouïl, L.; Schulz, M.; Simpson, D.; Stern, R.; Terrenoire, E.; Wind, P.

    2015-01-01

    Air pollution causes adverse effects on human health as well as ecosystems and crop yield and also has an impact on climate change trough short-lived climate forcers. To design mitigation strategies for air pollution, 3D Chemistry Transport Models (CTMs) have been developed to support the decision p

  10. Turbulent combustion modelling of a confined premixed jet flame including heat loss effects using tabulated chemistry

    NARCIS (Netherlands)

    Gövert, S.; Mira, D.; Kok, J.B.W.; Vázquez, M.; Houzeaux, G.

    2015-01-01

    The present work addresses the coupling of a flamelet database, to a low-Mach approximation of the Navier–Stokes equations using scalar controlling variables. The model is characterized by the chemistry tabulation based on laminar premixed flamelets in combination with an optimal choice of the react

  11. Mathematics Models in Chemistry--An Innovation for Non-Mathematics and Non-Science Majors

    Science.gov (United States)

    Rash, Agnes M.; Zurbach, E. Peter

    2004-01-01

    The intention of this article is to present a year-long interdisciplinary course, Mathematical Models in Chemistry. The course is comprised of eleven units, each of which has both a mathematical and a chemical component. A syllabus of the course is given and the format of the class is explained. The interaction of the professors and the content is…

  12. Modeling Chemistry for Effective Chemical Education: An Interview with Ronald J. Gillespie

    Science.gov (United States)

    Cardellini, Liberato

    2010-01-01

    Ronald J. Gillespie, the inventor of the Valence Shell Electron Pair Repulsion (VSEPR) model, relates how his career as researcher in Christopher Ingold's laboratories started. Gillespie developed a passion for chemistry and chemical education, searching for more appropriate and interesting ways to transmit the essential knowledge and enthusiasm…

  13. A detailed approach to model transport, heterogeneous chemistry, and electrochemistry in solid-oxide fuel cells

    OpenAIRE

    Janardhanan, Vinod

    2007-01-01

    This book lays out a numerical framework for the detailed description of heterogeneous chemistry, electrochemistry and porous media transport in solid-oxide fuel cells (SOFC). Assuming hydrogen as the only electrochemically active species, a modified Butler-Volmer equation is used to model the electrochemical charge transfer.

  14. CAChe Molecular Modeling: A Visualization Tool Early in the Undergraduate Chemistry Curriculum.

    Science.gov (United States)

    Crouch, R. David; And Others

    1996-01-01

    Describes a "Synthesis and Reactivity" curriculum that focuses on the correlation of laboratory experiments with lecture topics and the extension of laboratory exercises beyond the usual four-hour period. Highlights experiments developed and an out-of-class computational chemistry exercise using CAChe, a versatile molecular modeling software…

  15. Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

    Science.gov (United States)

    Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

    2011-01-01

    We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

  16. Why has the bohr-sommerfeld model of the atom been ignoredby general chemistry textbooks?

    Science.gov (United States)

    Niaz, Mansoor; Cardellini, Liberato

    2011-12-01

    Bohr's model of the atom is considered to be important by general chemistry textbooks. A major shortcoming of this model was that it could not explain the spectra of atoms containing more than one electron. In order to increase the explanatory power of the model, Sommerfeld hypothesized the existence of elliptical orbits. This study has the following objectives: 1) Formulation of criteria based on a history and philosophy of science framework; and 2) Evaluation of university-level general chemistry textbooks based on the criteria, published in Italy and U.S.A. Presentation of a textbook was considered to be "satisfactory" if it included a description of the Bohr-Sommerfeld model along with diagrams of the elliptical orbits. Of the 28 textbooks published in Italy that were analyzed, only five were classified as "satisfactory". Of the 46 textbooks published in U.S.A., only three were classified as "satisfactory". This study has the following educational implications: a) Sommerfeld's innovation (auxiliary hypothesis) by introducing elliptical orbits, helped to restore the viability of Bohr's model; b) Bohr-Sommerfeld's model went no further than the alkali metals, which led scientists to look for other models; c) This clearly shows that scientific models are tentative in nature; d) Textbook authors and chemistry teachers do not consider the tentative nature of scientific knowledge to be important; e) Inclusion of the Bohr-Sommerfeld model in textbooks can help our students to understand how science progresses.

  17. Physical chemistry of charged interfaces: multi-scale modelling and applications to energy

    International Nuclear Information System (INIS)

    This article presents the advantages of a multi-scale modelling strategy for the understanding of systems with charged interfaces. On the one hand, one can simulate a complex system at different levels, depending on the relevant length and time scales for a given physical chemistry problem. On the other hand, one should make the link between the various levels of description, e.g. following a bottom-up approach. The case of charged porous materials, in particular clay minerals, is illustrated here by discussing physical chemistry issues that arise in the context of geological disposal of nuclear wastes and CO2 sequestration. (author)

  18. On the use of mass-conserving wind fields in chemistry-transport models

    Directory of Open Access Journals (Sweden)

    B. Bregman

    2003-01-01

    Full Text Available A new method has been developed that provides mass-conserving wind fields for global chemistry-transport models. In previous global Eulerian modeling studies a mass-imbalance was found between the model mass transport and the surface pressure tendencies. Several methods have been suggested to correct for this imbalance, but so far no satisfactory solution has been found. Our new method solves these problems by using the wind fields in a spherical harmonical form (divergence and vorticity by mimicing the physics of the weather forecast model as closely as possible. A 3-D chemistry-transport model was used to show that the calculated ozone fields with the new processing method agree remarkably better with ozone observations in the upper troposphere and lower stratosphere. In addition, the calculated age of air in the lower stratosphere show better agreement with observations, although the air remains still too young in the extra-tropical stratosphere.

  19. ECHMERIT V1.0 – a new global fully coupled mercury-chemistry and transport model

    Directory of Open Access Journals (Sweden)

    N. Pirrone

    2009-05-01

    Full Text Available Mercury is a global pollutant due to its long lifetime in the atmosphere. Its hemispheric transport patterns and eventual deposition are therefore of major concern. For the purpose of global atmospheric mercury chemistry and transport modelling the ECHMERIT model was developed. ECHMERIT, based on the global circulation model ECHAM5 differs from most global mercury models in that the emissions, chemistry (including general tropospheric chemistry and mercury chemistry, transport and deposition are coupled on-line to the GCM. The chemistry mechanism includes an online calculation of photolysis rate constants using the Fast-J photolysis mechanism, the CBM-Z tropospheric gas-phase mechanism and aqueous-phase chemistry based on the MECCA mechanism. Additionally, a mercury chemistry mechanism that incorporates gas and aqueous phase mercury chemistry is included. A detailed description of the model, including the wet and dry deposition modules, and the implemented emissions is given in this technical report. First model testing and evaluation show a satisfactory model performance for surface ozone and mercury concentrations (with a mean bias of 1.46 ppb for ozone and a mean bias of 13.55 ppq for TGM when compared with EMEP station data. Requirements regarding measurement data and emission inventories which could considerably improve model skill are discussed.

  20. ECHMERIT V1.0 – a new global fully coupled mercury-chemistry and transport model

    Directory of Open Access Journals (Sweden)

    G. Jung

    2009-11-01

    Full Text Available Mercury is a global pollutant due to its long lifetime in the atmosphere. Its hemispheric transport patterns and eventual deposition are therefore of major concern. For the purpose of global atmospheric mercury chemistry and transport modelling the ECHMERIT model was developed. ECHMERIT, based on the global circulation model ECHAM5 differs from most global mercury models in that the emissions, chemistry (including general tropospheric chemistry and mercury chemistry, transport and deposition are coupled on-line to the GCM. The chemistry mechanism includes an online calculation of photolysis rate constants using the Fast-J photolysis mechanism, the CBM-Z tropospheric gas-phase mechanism and aqueous-phase chemistry based on the MECCA mechanism. Additionally, a mercury chemistry mechanism that incorporates gas and aqueous phase mercury chemistry is included. A detailed description of the model, including the wet and dry deposition modules, and the implemented emissions is given in this technical report. First model testing and evaluation show a satisfactory model performance for surface ozone and mercury mixing ratios (with a mean bias of 1.46 nmol/mol for ozone and a mean bias of 13.55 fmol/mol for TGM when compared with EMEP station data. Requirements regarding measurement data and emission inventories which could considerably improve model skill are discussed.

  1. Validation of Global Ozone Monitoring Experiment zone profiles and evaluation of stratospheric transport in a global chemistry transport model

    NARCIS (Netherlands)

    Laat, A.T.J.de; Landgraf, J.; Aben, I.; Hasekamp, O.; Bregman, B.

    2007-01-01

    This paper presents a validation of Global Ozone Monitoring Experiment (GOME) ozone (O3) profiles which are used to evaluate stratospheric transport in the chemistry transport model (CTM) Tracer Model version 5 (TM5) using a linearized stratospheric O3 chemistry scheme. A comparison of GOME O3 profi

  2. Implementation and evaluation of pH-dependent cloud chemistry and wetdeposition in the chemical transport model REM-Calgrid

    NARCIS (Netherlands)

    Banzhaf, S.; Schaap, M.; Kerschbaumer, A.; Reimer, E.; Stern, R.; Swaluw, E. van der; Builtjes, P.

    2012-01-01

    The Chemistry Transport Model REM-Calgrid (RCG) has been improved by implementing an enhanced description of aqueous-phase chemistry and wet deposition processes including droplet pH. A sensitivity study on cloud and rain droplet pH has been performed to investigate its impact on model sulphate prod

  3. Simulation of hydrogen mitigation in catalytic recombiner: Part-I: Surface chemistry modelling

    Energy Technology Data Exchange (ETDEWEB)

    Prabhudharwadkar, Deoras M. [Department of Mechanical Engineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400076, Maharashtra (India); Aghalayam, Preeti A. [Department of Chemical Engineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400076 (India); Iyer, Kannan N., E-mail: kiyer@iitb.ac.i [Department of Mechanical Engineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400076, Maharashtra (India)

    2011-05-15

    This paper aims at accurate modelling of a Passive Catalytic Recombiner used for hydrogen mitigation in the nuclear power plant containments. In order to assess the performance of the recombiner through numerical simulations, it is required to accurately predict the catalytic reactions. There are various detailed reaction mechanisms available in the literature for prediction of hydrogen-oxygen reaction over a platinum surface. While a single step reaction rate expression is always sought in order to obtain numerical predictions economically, a detailed reaction mechanism that includes several elementary reactions and intermediate species is likely to produce more accurate predictions. The paper compares the solution from two of competing models, one a single step reaction and the other a multiple reaction model. A new single step rate expression is also derived from the detailed mechanism after simplifying it for the present problem. The paper also considers the diffusion controlled model that assumes rapid reaction rates for which the surface chemistry is not required at all. In order to find the best suited approach to model the surface chemistry, CFD simulations were performed with FLUENT code using available experimental data from the literature. The current study reports comparison up to 4% H{sub 2} mole fraction in dry air with catalyst temperature varying from 300 K to 800 K. It is demonstrated that the new single step model is able to satisfactorily predict the data as well as the detailed chemistry model. The diffusion controlled model is shown to over-predict the data.

  4. Meso-scale modeling of air pollution transport/chemistry/deposition and its application

    International Nuclear Information System (INIS)

    Transport/chemistry/deposition model for atmospheric trace chemical species is now regarded as an important tool for an understanding of the effects of various human activities, such as fuel combustion and deforestation, on human health, eco-system, and climate and for planning of appropriate control of emission sources. Several 'comprehensive' models have been proposed such as RADM (Chang, et al., 1987), STEM-II (Carmichael, et al., 1986), and CMAQ (Community Multi-scale Air Quality model, e.g., EPA website, 2003); the 'comprehensive' models include not only gas/aerosol phase chemistry but also aqueous phase chemistry in cloud/rain water in addition to the processes of advection, diffusion, wet deposition (mass transfer between aqueous and gas/aerosol phases), and dry deposition. The target of the development of the 'comprehensive' model will be that the model can correctly reproduce mass balance of various chemical species in the atmosphere with keeping adequate accuracy for calculated concentration distributions of chemical species. For the purpose, one of the important problems is a reliable wet deposition modeling, and here, we introduce two types of methods of 'cloud-resolving' and 'non-cloud-resolving' modeling for the wet deposition of pollutants. (author)

  5. Chemistry of Dark Clouds: Databases, Networks, and Models

    CERN Document Server

    Agundez, Marcelino

    2013-01-01

    Chemical models have been developed over the years by astrophysicists to study the pro- cesses at play in the various environments of the interstellar medium (ISM) that define the chemical composition of the gas and the dust. These qualitative aspects of the model predictions have been improved from a chemical point of view thanks to many recent developments of the experimental technics and theoretical methods that aim at studying the individual reactions in conditions as close to the ISM conditions as possible and characterize the rate constants of their efficiency. These models have also been more and more associated with dynamical evolution of the ISM physical conditions (for star forming regions for instance) since the chemical composition is far from steady-state in such regions. In this paper, we try to assess the state of the art concerning the chemical modeling of dark clouds, the initial step for the formation of stars and disks.

  6. Energetic electron precipitation impacts on the middle atmosphere: From satellite observations to chemistry-climate modeling

    Science.gov (United States)

    Sinnhuber, Miriam; Bender, Stefan; Burrows, John P.; Funke, Bernd; Fytterer, Tilo; Nieder, Holger; Reddmann, Thomas; Stiller, Gabriele; Versick, Stefan; von Clarmann, Thomas; Maik Wissing, Jan

    2016-04-01

    Precipitation of energetic particles - mainly protons from solar coronal mass ejections or electrons accelerated in auroral or geomagnetic storms - directly affects the mesosphere and lower thermosphere. Nitric oxides (N, NO, NO2) and hydrogen radicals (H, OH) are formed by particle impact dissociation and ionization and subsequent ion chemistry reactions. However, the stratosphere and possibly even tropospheric weather systems can be affected indirectly by downward transport of particle-induced nitric oxides from their source regions into the stratosphere during polar winter, subsequent ozone depletion, and dynamical feedbacks with radiative (ozone) heating and cooling. This so-called "EPP indirect effect" forms one aspect of solar-climate interactions which will be recommended to include in chemistry-climate models, e.g., in the upcoming CMIP-6 experiment. We will present recent observations of mesospheric nitric oxide formation due to particle precipitation, as well as downwelling of particle induced NOy. Observations are compared to results from three 3-dimensional global chemistry-climate and chemistry-transport models of the middle atmosphere, and the subsequent ozone depletion is assessed using CCM / CTM model results.

  7. Advanced modelling of the multiphase DMS chemistry with the CAPRAM DMS module 1.0

    Science.gov (United States)

    Hoffmann, Erik Hans; Tilgner, Andreas; Schrödner, Roland; Wolke, Ralf; Herrmann, Hartmut

    2016-04-01

    Oceans are the general emitter of dimethyl sulphide (DMS), the major natural sulphur source (Andreae, 1990), and cover approximately 70 % of earth's surface. The main DMS oxidation products are SO2, H2SO4 and methyl sulfonic acid (MSA). Hence, DMS is very important for formation of non-sea salt sulphate (nss SO42-) aerosols and secondary particulate matter and thus global climate. Despite many previous model studies, there are still important knowledge gaps, especially in aqueous phase DMS chemistry, of its atmospheric fate (Barnes et al., 2006). Therefore, a comprehensive multiphase DMS chemistry mechanism, the CAPRAM DMS module 1.0 (DM1.0), has been developed. The DM1.0 includes 103 gas phase reactions, 5 phase transfers and 54 aqueous phase reactions. It was coupled with the multiphase chemistry mechanism MCMv3.2/CAPRAM4.0α (Rickard et al., 2015; Bräuer et al., 2016) and the extended CAPRAM halogen module 2.1 (HM2.1, Bräuer et al., 2013) for investigation of multiphase DMS oxidation in the marine boundary layer. Then, a pristine ocean scenario was simulated using the air parcel model SPACCIM (Wolke et al., 2005) including 8 non-permanent cloud passages - 4 at noon and 4 at midnight. This allows the investigation of the influence of deliquesced particles and clouds on multiphase DMS chemistry during both daytime and nighttime conditions as well as under cloud formation and evaporation. To test the influence of various subsystems on multiphase DMS chemistry different sensitivity runs were performed. Investigations of multiphase chemistry of DMS and its important oxidation products were done using concentration-time profiles and detailed time-resolved reaction flux analyses. The model studies revealed the importance of aqueous phase chemistry for DMS and its oxidation products. Overall about 7.0% of DMS is effectively oxidised by O3 in the aqueous phase of clouds. The simulations revealed the importance of halogen and aqueous phase chemistry for DMS and its

  8. Modeling lightning-NOx chemistry at sub-grid scale in a global chemical transport model

    Directory of Open Access Journals (Sweden)

    A. Gressent

    2015-12-01

    Full Text Available For the first time, a plume-in-grid approach is implemented in a chemical transport model (CTM to parameterize the effects of the non-linear reactions occurring within high concentrated NOx plumes from lightning NOx emissions (LNOx in the upper troposphere. It is characterized by a set of parameters including the plume lifetime, the effective reaction rate constant related to NOx-O3 chemical interactions and the fractions of NOx conversion into HNO3 within the plume. Parameter estimates were made using the DSMACC chemical box model, simple plume dispersion simulations and the mesoscale 3-D Meso-NH model. In order to assess the impact of the LNOx plume approach on the NOx and O3 distributions at large scale, simulations for the year 2006 were performed using the GEOS-Chem global model with a horizontal resolution of 2° × 2.5°. The implementation of the LNOx parameterization implies NOx and O3 decrease at large scale over the region characterized by a strong lightning activity (up to 25 and 8 %, respectively, over Central Africa in July and a relative increase downwind of LNOx emissions (up to 18 and 2 % for NOx and O3, respectively, in July are derived. The calculated variability of NOx and O3 mixing ratios around the mean value according to the known uncertainties on the parameter estimates is maximum over continental tropical regions with ΔNOx [−33.1; +29.7] ppt and ΔO3 [−1.56; +2.16] ppb, in January, and ΔNOx [−14.3; +21] ppt and ΔO3 [−1.18; +1.93] ppb, in July, mainly depending on the determination of the diffusion properties of the atmosphere and the initial NO mixing ratio injected by lightning. This approach allows (i to reproduce a more realistic lightning NOx chemistry leading to better NOx and O3 distributions at the large scale and (ii focus on other improvements to reduce remaining uncertainties from processes related to NOx chemistry in CTM.

  9. Non-OH chemistry in oxidation flow reactors for the study of atmospheric chemistry systematically examined by modeling

    Science.gov (United States)

    Peng, Zhe; Day, Douglas A.; Ortega, Amber M.; Palm, Brett B.; Hu, Weiwei; Stark, Harald; Li, Rui; Tsigaridis, Kostas; Brune, William H.; Jimenez, Jose L.

    2016-04-01

    Oxidation flow reactors (OFRs) using low-pressure Hg lamp emission at 185 and 254 nm produce OH radicals efficiently and are widely used in atmospheric chemistry and other fields. However, knowledge of detailed OFR chemistry is limited, allowing speculation in the literature about whether some non-OH reactants, including several not relevant for tropospheric chemistry, may play an important role in these OFRs. These non-OH reactants are UV radiation, O(1D), O(3P), and O3. In this study, we investigate the relative importance of other reactants to OH for the fate of reactant species in OFR under a wide range of conditions via box modeling. The relative importance of non-OH species is less sensitive to UV light intensity than to water vapor mixing ratio (H2O) and external OH reactivity (OHRext), as both non-OH reactants and OH scale roughly proportionally to UV intensity. We show that for field studies in forested regions and also the urban area of Los Angeles, reactants of atmospheric interest are predominantly consumed by OH. We find that O(1D), O(3P), and O3 have relative contributions to volatile organic compound (VOC) consumption that are similar or lower than in the troposphere. The impact of O atoms can be neglected under most conditions in both OFR and troposphere. We define "riskier OFR conditions" as those with either low H2O ( 200 s-1 in OFR254). We strongly suggest avoiding such conditions as the importance of non-OH reactants can be substantial for the most sensitive species, although OH may still dominate under some riskier conditions, depending on the species present. Photolysis at non-tropospheric wavelengths (185 and 254 nm) may play a significant (> 20 %) role in the degradation of some aromatics, as well as some oxidation intermediates, under riskier reactor conditions, if the quantum yields are high. Under riskier conditions, some biogenics can have substantial destructions by O3, similarly to the troposphere. Working under low O2 (volume mixing

  10. Gas-grain models for interstellar anion chemistry

    OpenAIRE

    Cordiner, M. A.; Charnley, S. B.

    2012-01-01

    Long-chain hydrocarbon anions CnH- (n=4, 6, 8) have recently been found to be abundant in a variety of interstellar clouds. In order to explain their large abundances in the denser (prestellar/protostellar) environments, new chemical models are constructed that include gas-grain interactions. Models including accretion of gas-phase species onto dust grains and cosmic-ray-induced desorption of atoms are able to reproduce the observed anion-to-neutral ratios, as well as the absolute abundances ...

  11. Titan Chemistry: Results From A Global Climate Model

    Science.gov (United States)

    Wilson, Eric; West, R. A.; Friedson, A. J.; Oyafuso, F.

    2008-09-01

    We present results from a 3-dimesional global climate model of Titan's atmosphere and surface. This model, a modified version of NCAR's CAM-3 (Community Atmosphere Model), has been optimized for analysis of Titan's lower atmosphere and surface. With the inclusion of forcing from Saturn's gravitational tides, interaction from the surface, transfer of longwave and shortwave radiation, and parameterization of haze properties, constrained by Cassini observations, a dynamical field is generated, which serves to advect 14 long-lived species. The concentrations of these chemical tracers are also affected by 82 chemical reactions and the photolysis of 21 species, based on the Wilson and Atreya (2004) model, that provide sources and sinks for the advected species along with 23 additional non-advected radicals. In addition, the chemical contribution to haze conversion is parameterized along with the microphysical processes that serve to distribute haze opacity throughout the atmosphere. References Wilson, E.H. and S.K. Atreya, J. Geophys. Res., 109, E06002, 2004.

  12. Kinetic models in spin chemistry. 1. The hyperfine interaction

    DEFF Research Database (Denmark)

    Mojaza, M.; Pedersen, J. B.

    2012-01-01

    Kinetic models for quantum systems are quite popular due to their simplicity, although they are difficult to justify. We show that the transformation from quantum to kinetic description can be done exactly for the hyperfine interaction of one nuclei with arbitrary spin; more spins are described w...... induced enhancement of the reaction yield. (C) 2012 Elsevier B.V. All rights reserved....

  13. Aerosol–cloud interactions studied with the chemistry-climate model EMAC

    OpenAIRE

    Chang, D Y; Tost, H.; Steil, B.; Lelieveld, J.

    2014-01-01

    This study uses the EMAC atmospheric chemistry-climate model to simulate cloud properties and estimate cloud radiative effects induced by aerosols. We have tested two prognostic cloud droplet nucleation parameterizations, i.e., the standard STN (osmotic coefficient model) and hybrid (HYB, replacing the osmotic coefficient by the κ hygroscopicity parameter) schemes to calculate aerosol hygroscopicity and critical supersaturation, and consider aerosol–cloud fe...

  14. Theoretical chemistry periodicities in chemistry and biology

    CERN Document Server

    Eyring, Henry

    1978-01-01

    Theoretical Chemistry: Periodicities in Chemistry and Biology, Volume 4 covers the aspects of theoretical chemistry. The book discusses the stably rotating patterns of reaction and diffusion; the chemistry of inorganic systems exhibiting nonmonotonic behavior; and population cycles. The text also describes the mathematical modeling of excitable media in neurobiology and chemistry; oscillating enzyme reactions; and oscillatory properties and excitability of the heart cell membrane. Selected topics from the theory of physico-chemical instabilities are also encompassed. Chemists, mechanical engin

  15. An insight into chemical kinetics and turbulence-chemistry interaction modeling in flameless combustion

    Directory of Open Access Journals (Sweden)

    Amir Azimi, Javad Aminian

    2015-01-01

    Full Text Available Computational Fluid Dynamics (CFD study of flameless combustion condition is carried out by solving the Reynolds-Averaged Navier-Stokes (RANS equations in the open-source CFD package of OpenFOAM 2.1.0. Particular attention is devoted to the comparison of three global and detailed chemical mechanisms using the Partially Stirred Reactor (PaSR combustion model for the turbulence-chemistry interaction treatment. The OpenFOAM simulations are assessed against previously published CFD results using the Eddy Dissipation Concept (EDC combustion model as well as the experimental data available in the literature. Results show that global chemical mechanisms provide acceptable predictions of temperature and major species fields in flameless mode with much lower computational costs comparing with the detailed chemical mechanisms. However, incorporation of detailed chemical mechanisms with proper combustion models is crucial to account for finite-rate chemistry effects and accurately predict net production of minor species.

  16. Physical chemistry and modelling of the sintering of actinide oxides

    International Nuclear Information System (INIS)

    This report gives a synthesis of the work I have carried out or to which I have numerically contributed to from 1996 up to 2012 in the Department of Plutonium Uranium and minor Actinides in Cadarache CEA Center. Their main goal is the study and the modeling of the sintering process of nuclear fuels which is the unifying thread of this document. Both in order to take into account the physical and chemical features of the actinide bearing oxide material and in order to combine the different transport phenomena leading to sintering, a sub-granular scale model is under development. Extension to a varying chemical composition as well as exchanges with the gaseous phase are foreseen. A simulation on a larger scale (pellet scale) is ongoing in the framework of a PhD thesis. Validation means have been tested with (U,Pu)O2 material on the scale of the pellet (Small Angle Neutron Diffusion), on the scale of powder granules (X-Ray High Resolution Micro-Tomography) and with CeO2 at the 'Institut de Chimie Separative' in Marcoule on a single crystal scale (Environmental Scanning Electron Microscope). The required microstructure homogeneity for nuclear fuels has led to a campaign of experimental studies about the role of Cr2O3 as a sintering aid. Whole of these studies improve our understanding of fuel sintering and hence leads to an improved mastering of this process. (author)

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

    Science.gov (United States)

    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.

  18. The GEOS Chemistry Climate Model: Implications of Climate Feedbacks on Ozone Depletion and Recovery

    Science.gov (United States)

    Stolarski, Richard S.; Pawson, Steven; Douglass, Anne R.; Newman, Paul A.; Kawa, S. Randy; Nielsen, J. Eric; Rodriquez, Jose; Strahan, Susan; Oman, Luke; Waugh, Darryn

    2008-01-01

    The Goddard Earth Observing System Chemistry Climate Model (GEOS CCM) has been developed by combining the atmospheric chemistry and transport modules developed over the years at Goddard and the GEOS general circulation model, also developed at Goddard. The first version of the model was used in the CCMVal intercomparison exercises that contributed to the 2006 WMO/UNEP Ozone Assessment. The second version incorporates the updated version of the GCM (GEOS 5) and will be used for the next round of CCMVal evaluations and the 2010 Ozone Assessment. The third version, now under development, incorporates the combined stratosphere and troposphere chemistry package developed under the Global Modeling Initiative (GMI). We will show comparison to past observations that indicate that we represent the ozone trends over the past 30 years. We will also show the basic temperature, composition, and dynamical structure of the simulations. We will further show projections into the future. We will show results from an ensemble of transient and time-slice simulations, including simulations with fixed 1960 chlorine, simulations with a best guess scenario (Al), and simulations with extremely high chlorine loadings. We will discuss planned extensions of the model to include emission-based boundary conditions for both anthropogenic and biogenic compounds.

  19. The 1-way on-line coupled atmospheric chemistry model system MECO(n – Part 1: Description of the limited-area atmospheric chemistry model COSMO/MESSy

    Directory of Open Access Journals (Sweden)

    A. Kerkweg

    2012-01-01

    Full Text Available The numerical weather prediction model of the Consortium for Small Scale Modelling (COSMO, maintained by the German weather service (DWD, is connected with the Modular Earth Submodel System (MESSy. This effort is undertaken in preparation of a new, limited-area atmospheric chemistry model. Limited-area models require lateral boundary conditions for all prognostic variables. Therefore the quality of a regional chemistry model is expected to improve, if boundary conditions for the chemical constituents are provided by the driving model in consistence with the meteorological boundary conditions. The new developed model is as consistent as possible, with respect to atmospheric chemistry and related processes, with a previously developed global atmospheric chemistry general circulation model: the ECHAM/MESSy Atmospheric Chemistry (EMAC model. The combined system constitutes a new research tool, bridging the global to the meso-γ scale for atmospheric chemistry research. MESSy provides the infrastructure and includes, among others, the process and diagnostic submodels for atmospheric chemistry simulations. Furthermore, MESSy is highly flexible allowing model setups with tailor made complexity, depending on the scientific question. Here, the connection of the MESSy infrastructure to the COSMO model is documented and also the code changes required for the generalisation of regular MESSy submodels. Moreover, previously published prototype submodels for simplified tracer studies are generalised to be plugged-in and used in the global and the limited-area model. They are used to evaluate the TRACER interface implementation in the new COSMO/MESSy model system and the tracer transport characteristics, an important prerequisite for future atmospheric chemistry applications. A supplementary document with further details on the technical implementation of the MESSy interface into COSMO with a complete list of modifications to the COSMO code is provided.

  20. Modelling trends in tropical column ozone with the UKCA chemistry-climate model

    Science.gov (United States)

    Keeble, James; Bednarz, Ewa; Banerjee, Antara; Abraham, Luke; Harris, Neil; Maycock, Amanda; Pyle, John

    2016-04-01

    Trends in tropical column ozone under a number of different emissions scenarios are explored with the UM-UKCA coupled chemistry climate model. A transient 1960-2100 simulation was run following the RCP6 scenario. Tropical averaged (10S-10N) total column ozone values decrease from the 1970s, reaching a minimum around 2000, and return to their 1980 values around 2040, consistent with the use and emission of ozone depleting substances, and their later controls under the Montreal Protocol. However, when the total column is subdivided into three partial columns, extending from the surface to the tropopause, the tropopause to 30km, and 30km to 50km, significant differences to the total column trend are seen. Modelled tropospheric column values increase from 1960-2000 before remaining steady throughout the 21st Century. Lower stratospheric column values decrease rapidly from 1960-2000, remain steady until 2050 before slowly decreasing to 2100, never recovering to their 1980s values. Upper stratospheric values decrease from 1960-2000, before rapidly increasing throughout the 21st Century, recovering to 1980s values by ~2020 and are significantly increased above the 1980s values by 2100. Using a series of idealised model simulations with varying concentrations of greenhouse gases and ozone depleting substances, we assess the physical processes driving the partial column response in the troposphere, lower stratosphere and upper stratosphere, and assess how these processes change under different emissions scenarios. Finally, we present a simple, linearised model for predicting tropical column ozone values based on greenhouse gas and ozone depleting substance scenarios.

  1. Update on microkinetic modeling of lean NOx trap chemistry.

    Energy Technology Data Exchange (ETDEWEB)

    Larson, Richard S.; Daw, C. Stuart (Oak Ridge National Laboratory, Oak Ridge, TN); Pihl, Josh A. (Oak Ridge National Laboratory, Oak Ridge, TN); Choi, Jae-Soon (Oak Ridge National Laboratory, Oak Ridge, TN); Chakravarthy, V, Kalyana (Oak Ridge National Laboratory, Oak Ridge, TN)

    2010-04-01

    Our previously developed microkinetic model for lean NOx trap (LNT) storage and regeneration has been updated to address some longstanding issues, in particular the formation of N2O during the regeneration phase at low temperatures. To this finalized mechanism has been added a relatively simple (12-step) scheme that accounts semi-quantitatively for the main features observed during sulfation and desulfation experiments, namely (a) the essentially complete trapping of SO2 at normal LNT operating temperatures, (b) the plug-like sulfation of both barium oxide (NOx storage) and cerium oxide (oxygen storage) sites, (c) the degradation of NOx storage behavior arising from sulfation, (d) the evolution of H2S and SO2 during high temperature desulfation (temperature programmed reduction) under H2, and (e) the complete restoration of NOx storage capacity achievable through the chosen desulfation procedure.

  2. Metal transport across biomembranes: emerging models for a distinct chemistry.

    Science.gov (United States)

    Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

    2012-04-20

    Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

  3. A new 2D climate model with chemistry and self consistent eddy-parameterization. The impact of airplane NO{sub x} on the chemistry of the atmosphere

    Energy Technology Data Exchange (ETDEWEB)

    Gepraegs, R.; Schmitz, G.; Peters, D. [Institut fuer Atmosphaerenphysik, Kuehlungsborn (Germany)

    1997-12-31

    A 2D version of the ECHAM T21 climate model has been developed. The new model includes an efficient spectral transport scheme with implicit diffusion. Furthermore, photodissociation and chemistry of the NCAR 2D model have been incorporated. A self consistent parametrization scheme is used for eddy heat- and momentum flux in the troposphere. It is based on the heat flux parametrization of Branscome and mixing-length formulation for quasi-geostrophic vorticity. Above 150 hPa the mixing-coefficient K{sub yy} is prescribed. Some of the model results are discussed, concerning especially the impact of aircraft NO{sub x} emission on the model chemistry. (author) 6 refs.

  4. Comparison of the Research Effectiveness of Chemistry Nobelists and Fields Medalist Mathematicians with Google Scholar: the Yule-Simon Model

    CERN Document Server

    Bensman, Stephen J; Sage, Daniel S

    2014-01-01

    This paper uses the Yule-Simon model to estimate to what extent the work of chemistry Nobelists and Fields medalist mathematicians is incorporated into the knowledge corpus of their disciplines as measured by Google Scholar inlinks. Due to differences in the disciplines and prizes, it finds that the work of chemistry Nobelists is better incorporated than that of Fields medalists.

  5. Attribution of stratospheric ozone trends to chemistry and transport: a modelling study

    Directory of Open Access Journals (Sweden)

    G. Kiesewetter

    2010-07-01

    Full Text Available The decrease of the concentration of ozone depleting substances (ODS in the stratosphere over the past decade raises the question to what extent observed changes in stratospheric ozone over this period are consistent with known changes in chemical composition and possible changes in atmospheric transport. Here we present a series of ozone sensitivity calculations with a stratospheric chemistry transport model (CTM driven with meteorological reanalyses from the European Centre for Medium Range Weather Forecast, covering the period 1978–2009. In order to account for the reversal in ODS trends, ozone trends are analysed in two periods, 1979–1999 and 2000–2009. Effects of ODS changes on the ozone chemistry are either accounted for or left out, allowing for a distinct attribution of ozone trends to the different factors of variability, namely ODS acting via gas phase chemistry, ODS acting via polar heterogeneous chemistry, and changes in transport and temperature. Modeled column ozone trends are in excellent agreement with observed trends from the Total Ozone Mapping Spectrometer (TOMS and Solar Backscatter UV (SBUV/2 as well as the Global Ozone Monitoring Experiment (GOME/GOME2 and Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY instruments. For the 1979–1999 period we find that changes in ODS are the dominant source of the ozone trend, while changes in transport also contribute signifcantly to the overall trend. In contrast, for the period 2000–2009 the effect of ODS changes on total ozone is small. Observed ozone changes can be reproduced well with the CTM driven with meteorological reanalyses, indicating that the observed evolution of ozone over the past decade is consistent with our current understanding of chemistry and transport.

  6. Ship plume dispersion rates in convective boundary layers for chemistry models

    Directory of Open Access Journals (Sweden)

    F. Chosson

    2008-08-01

    Full Text Available Detailed ship plume simulations in various convective boundary layer situations have been performed using a Lagrangian Dispersion Model driven by a Large Eddy Simulation Model. The simulations focus on the early stage (1–2 h of plume dispersion regime and take into account the effects of plume rise on dispersion. Results are presented in an attempt to provide to atmospheric chemistry modellers a realistic description of characteristic dispersion impact on exhaust ship plume chemistry. Plume dispersion simulations are used to derive analytical dilution rate functions. Even though results exhibit striking effects of plume rise parameter on dispersion patterns, it is shown that initial buoyancy fluxes at ship stack have a minor effect on plume dilution rate. After initial high dispersion regimes a simple characteristic dilution time scale can be used to parameterize the subgrid plume dilution effect in large-scale chemistry models. The results show that this parameter is directly related to the typical turn-over time scale of the convective boundary layer.

  7. Comprehensive mechanisms for combustion chemistry: Experiment, modeling, and sensitivity analysis

    Energy Technology Data Exchange (ETDEWEB)

    Dryer, F.L.; Yetter, R.A. [Princeton Univ., NJ (United States)

    1993-12-01

    This research program is an integrated experimental/numerical effort to study pyrolysis and oxidation reactions and mechanisms for small-molecule hydrocarbon structures under conditions representative of combustion environments. The experimental aspects of the work are conducted in large diameter flow reactors, at pressures from one to twenty atmospheres, temperatures from 550 K to 1200 K, and with observed reaction times from 10{sup {minus}2} to 5 seconds. Gas sampling of stable reactant, intermediate, and product species concentrations provides not only substantial definition of the phenomenology of reaction mechanisms, but a significantly constrained set of kinetic information with negligible diffusive coupling. Analytical techniques used for detecting hydrocarbons and carbon oxides include gas chromatography (GC), and gas infrared (NDIR) and FTIR methods are utilized for continuous on-line sample detection of light absorption measurements of OH have also been performed in an atmospheric pressure flow reactor (APFR), and a variable pressure flow (VPFR) reactor is presently being instrumented to perform optical measurements of radicals and highly reactive molecular intermediates. The numerical aspects of the work utilize zero and one-dimensional pre-mixed, detailed kinetic studies, including path, elemental gradient sensitivity, and feature sensitivity analyses. The program emphasizes the use of hierarchical mechanistic construction to understand and develop detailed kinetic mechanisms. Numerical studies are utilized for guiding experimental parameter selections, for interpreting observations, for extending the predictive range of mechanism constructs, and to study the effects of diffusive transport coupling on reaction behavior in flames. Modeling using well defined and validated mechanisms for the CO/H{sub 2}/oxidant systems.

  8. Modelling interstellar physics and chemistry: implications for surface and solid-state processes.

    Science.gov (United States)

    Williams, David; Viti, Serena

    2013-07-13

    We discuss several types of regions in the interstellar medium of the Milky Way and other galaxies in which the chemistry appears to be influenced or dominated by surface and solid-state processes occurring on or in interstellar dust grains. For some of these processes, for example, the formation of H₂ molecules, detailed experimental and theoretical approaches have provided excellent fundamental data for incorporation into astrochemical models. In other cases, there is an astrochemical requirement for much more laboratory and computational study, and we highlight these needs in our description. Nevertheless, in spite of the limitations of the data, it is possible to infer from astrochemical modelling that surface and solid-state processes play a crucial role in astronomical chemistry from early epochs of the Universe up to the present day.

  9. An insight into chemical kinetics and turbulence-chemistry interaction modeling in flameless combustion

    OpenAIRE

    Amir Azimi, Javad Aminian

    2015-01-01

    Computational Fluid Dynamics (CFD) study of flameless combustion condition is carried out by solving the Reynolds-Averaged Navier-Stokes (RANS) equations in the open-source CFD package of OpenFOAM 2.1.0. Particular attention is devoted to the comparison of three global and detailed chemical mechanisms using the Partially Stirred Reactor (PaSR) combustion model for the turbulence-chemistry interaction treatment. The OpenFOAM simulations are assessed against previously published CFD results usi...

  10. Description and evaluation of tropospheric chemistry and aerosols in the Community Earth System Model (CESM1.2)

    OpenAIRE

    Tilmes, S.; J.-F. Lamarque; Emmons, L. K.; Kinnison, D E; P.-L. Ma; Liu, X.; Ghan, S; Bardeen, C.; Arnold, S.; Deeter, M.; F. Vitt; T. Ryerson; J. W. Elkins; Moore, F.; R. Spackman

    2014-01-01

    The Community Atmosphere Model (CAM), version 5, is now coupled to extensive tropospheric and stratospheric chemistry, called CAM5-chem, and is available in addition to CAM4-chem in the Community Earth System Model (CESM) version 1.2. Both configurations are well suited as tools for atmospheric-chemistry modeling studies in the troposphere and lower stratosphere, whether with internally derived "free running" (FR) meteorology, or "specified dynamics" (SD). The main focus of thi...

  11. An aqueous chemistry module for a three-dimensional cloud resolving model: Sulfate redistribution

    Directory of Open Access Journals (Sweden)

    Vujović Dragana

    2012-01-01

    Full Text Available An aqueous chemistry module is created and included into a complex 3D cloud-resolving mesoscale ARPS model to examine the characteristics of in-cloud sulfate. The complex orography of Serbia is included in the model. The chemical species included in the module are sulfur dioxide, sulfate ion, ammonium ion, hydrogen peroxide and ozone. Six water categories are considered: water vapor, cloud water, rain, cloud ice, snow and hail. Each chemical species in each microphysical category is represented by a differential equation of mass continuity. This paper gives a detailed description of the chemistry module and demonstrates the utility of an atmospheric model coupled with the chemistry module in forecasting the redistribution of chemical species in all water categories. The main mean microphysical and chemical conversion rates of sulfate averaged over a 2 h simulation period for a base run are for the oxidation of S(IV in rain water and cloud water, SO4 2− scavenging by Brownian diffusion in cloud droplets and cloud ice as well as the impact scavenging of SO4 2− by rain. The calculated values of sulfates in all water categories and the shape of sulfate profiles depend on radar reflectivity.

  12. A simple one-step chemistry model for partially premixed hydrocarbon combustion

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Tarrazo, Eduardo [Instituto Nacional de Tecnica Aeroespacial, Madrid (Spain); Sanchez, Antonio L. [Area de Mecanica de Fluidos, Universidad Carlos III de Madrid, Leganes 28911 (Spain); Linan, Amable [ETSI Aeronauticos, Pl. Cardenal Cisneros 3, Madrid 28040 (Spain); Williams, Forman A. [Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093-0411 (United States)

    2006-10-15

    This work explores the applicability of one-step irreversible Arrhenius kinetics with unity reaction order to the numerical description of partially premixed hydrocarbon combustion. Computations of planar premixed flames are used in the selection of the three model parameters: the heat of reaction q, the activation temperature T{sub a}, and the preexponential factor B. It is seen that changes in q with equivalence ratio f need to be introduced in fuel-rich combustion to describe the effect of partial fuel oxidation on the amount of heat released, leading to a universal linear variation q(f) for f>1 for all hydrocarbons. The model also employs a variable activation temperature T{sub a}(f) to mimic changes in the underlying chemistry in rich and very lean flames. The resulting chemistry description is able to reproduce propagation velocities of diluted and undiluted flames accurately over the whole flammability limit. Furthermore, computations of methane-air counterflow diffusion flames are used to test the proposed chemistry under nonpremixed conditions. The model not only predicts the critical strain rate at extinction accurately but also gives near-extinction flames with oxygen leakage, thereby overcoming known predictive limitations of one-step Arrhenius kinetics. (author)

  13. Evaluation of the ACCESS - chemistry-climate model for the Southern Hemisphere

    Science.gov (United States)

    Stone, Kane A.; Morgenstern, Olaf; Karoly, David J.; Klekociuk, Andrew R.; French, W. John; Abraham, N. Luke; Schofield, Robyn

    2016-02-01

    Chemistry-climate models are important tools for addressing interactions of composition and climate in the Earth system. In particular, they are used to assess the combined roles of greenhouse gases and ozone in Southern Hemisphere climate and weather. Here we present an evaluation of the Australian Community Climate and Earth System Simulator - chemistry-climate model (ACCESS-CCM), focusing on the Southern Hemisphere and the Australian region. This model is used for the Australian contribution to the international Chemistry-Climate Model Initiative, which is soliciting hindcast, future projection and sensitivity simulations. The model simulates global total column ozone (TCO) distributions accurately, with a slight delay in the onset and recovery of springtime Antarctic ozone depletion, and consistently higher ozone values. However, October-averaged Antarctic TCO from 1960 to 2010 shows a similar amount of depletion compared to observations. Comparison with model precursors shows large improvements in the representation of the Southern Hemisphere stratosphere, especially in TCO concentrations. A significant innovation is seen in the evaluation of simulated vertical profiles of ozone and temperature with ozonesonde data from Australia, New Zealand and Antarctica from 38 to 90° S. Excess ozone concentrations (greater than 26 % at Davis and the South Pole during winter) and stratospheric cold biases (up to 10 K at the South Pole during summer and autumn) outside the period of perturbed springtime ozone depletion are seen during all seasons compared to ozonesondes. A disparity in the vertical location of ozone depletion is seen: centred around 100 hPa in ozonesonde data compared to above 50 hPa in the model. Analysis of vertical chlorine monoxide profiles indicates that colder Antarctic stratospheric temperatures (possibly due to reduced mid-latitude heat flux) are artificially enhancing polar stratospheric cloud formation at high altitudes. The model's inability to

  14. The Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP: overview and description of models, simulations and climate diagnostics

    Directory of Open Access Journals (Sweden)

    J.-F. Lamarque

    2012-08-01

    Full Text Available The Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP consists of a series of timeslice experiments targeting the long-term changes in atmospheric composition between 1850 and 2100, with the goal of documenting radiative forcing and the associated composition changes. Here we introduce the various simulations performed under ACCMIP and the associated model output. The ACCMIP models have a wide range of horizontal and vertical resolutions, vertical extent, chemistry schemes and interaction with radiation and clouds. While anthropogenic and biomass burning emissions were specified for all time slices in the ACCMIP protocol, it is found that the natural emissions lead to a significant range in emissions, mostly for ozone precursors. The analysis of selected present-day climate diagnostics (precipitation, temperature, specific humidity and zonal wind reveals biases consistent with state-of-the-art climate models. The model-to-model comparison of changes in temperature, specific humidity and zonal wind between 1850 and 2000 and between 2000 and 2100 indicates mostly consistent results, but with outliers different enough to possibly affect their representation of climate impact on chemistry.

  15. Evaluation of the Australian Community Climate and Earth-System Simulator Chemistry-Climate Model

    Directory of Open Access Journals (Sweden)

    K. A. Stone

    2015-07-01

    Full Text Available Chemistry climate models are important tools for addressing interactions of composition and climate in the Earth System. In particular, they are used for assessing the combined roles of greenhouse gases and ozone in Southern Hemisphere climate and weather. Here we present an evaluation of the Australian Community Climate and Earth System Simulator-Chemistry Climate Model, focusing on the Southern Hemisphere and the Australian region. This model is used for the Australian contribution to the international Chemistry-Climate Model Initiative, which is soliciting hindcast, future projection and sensitivity simulations. The model simulates global total column ozone (TCO distributions accurately, with a slight delay in the onset and recovery of springtime Antarctic ozone depletion, and consistently higher ozone values. However, October averaged Antarctic TCO from 1960 to 2010 show a similar amount of depletion compared to observations. A significant innovation is the evaluation of simulated vertical profiles of ozone and temperature with ozonesonde data from Australia, New Zealand and Antarctica from 38 to 90° S. Excess ozone concentrations (up to 26.4 % at Davis during winter and stratospheric cold biases (up to 10.1 K at the South Pole outside the period of perturbed springtime ozone depletion are seen during all seasons compared to ozonesondes. A disparity in the vertical location of ozone depletion is seen: centered around 100 hPa in ozonesonde data compared to above 50 hPa in the model. Analysis of vertical chlorine monoxide profiles indicates that colder Antarctic stratospheric temperatures (possibly due to reduced mid-latitude heat flux are artificially enhancing polar stratospheric cloud formation at high altitudes. The models inability to explicitly simulated supercooled ternary solution may also explain the lack of depletion at lower altitudes. The simulated Southern Annular Mode (SAM index compares well with ERA-Interim data. Accompanying

  16. Modeling chemistry in and above snow at Summit, Greenland − Part 2: Impact of snowpack chemistry on the oxidation capacity of the boundary layer

    Directory of Open Access Journals (Sweden)

    B. Lefer

    2012-02-01

    Full Text Available The chemical composition of the boundary layer in snow covered regions is impacted by chemistry in the snowpack via uptake, processing, and emission of atmospheric trace gases. We use the coupled one-dimensional (1-D snow chemistry and atmospheric boundary layer model MISTRA-SNOW to study the impact of snowpack chemistry on the oxidation capacity of the boundary layer. The model includes gas phase photochemistry and chemical reactions both in the interstitial air and the atmosphere. Chemistry on snow grains is simulated assuming a liquid-like layer (LLL, treated as an aqueous layer on the snow grain surface. The model has been recently compared with BrO and NO data taken on 10 June–13 June 2008 as part of the Greenland Summit Halogen-HOx experiment (GSHOX. In the present study, we use the same focus period to investigate the influence of snowpack derived chemistry on OH and HOx + RO2 in the boundary layer. We compare model results with chemical ionization mass spectrometry (CIMS measurements of the hydroxyl radical (OH and of the hydroperoxyl radical (HO2 plus the sum of all organic peroxy radicals (RO2 taken at Summit during summer 2008. Using sensitivity runs we show that snowpack influenced nitrogen cycling and bromine chemistry both increase the oxidation capacity of the boundary layer and that together they increase the mid-day OH concentrations by approximately a factor of 2. We show for the first time, using an unconstrained coupled one-dimensional snowpack-boundary layer model, that air-snow interactions impact the oxidation capacity of the boundary layer and that it is not possible to match measured OH levels without snowpack NOx and halogen emissions. Model predicted HONO compared with mistchamber measurements suggests there may be an unknown HONO source at Summit. Other model predicted HOx precursors, H2O2 and HCHO, compare well with measurements taken in summer 2000. Over 3 days, snow sourced NOx contributes an additional 2 ppb to

  17. Advances in analytical methodology for bioinorganic speciation analysis: metallomics, metalloproteomics and heteroatom-tagged proteomics and metabolomics.

    Science.gov (United States)

    Szpunar, Joanna

    2005-04-01

    The recent developments in analytical techniques capable of providing information on the identity and quantity of heteroatom-containing biomolecules are critically discussed. Particular attention is paid to the emerging areas of bioinorganic analysis including: (i) a comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type (metallomics), (ii) the study of the part of the metallome involving the protein ligands (metalloproteomics), and (iii) the use of a heteroelement, naturally present in a protein or introduced in a tag added by means of derivatisation, for the spotting and quantification of proteins (heteroatom-tagged proteomics). Inductively coupled plasma mass spectrometry (ICP MS), used as detector in chromatography and electrophoresis, and supported by electrospray and MALDI MS, appears as the linchpin analytical technique for these emerging areas. This review focuses on the recent advances in ICP MS in biological speciation analysis including sensitive detection of non-metals, especially of sulfur and phosphorus, couplings to capillary and nanoflow HPLC and capillary electrophoresis, laser ablation ICP MS detection of proteins in gel electrophoresis, and isotope dilution quantification of biomolecules. The paper can be considered as a followup of a previous review by the author on a similar topic (J. Szpunar, Analyst, 2000, 125, 963).

  18. Measurement-based modeling of bromine chemistry in the boundary layer: 1. Bromine chemistry at the Dead Sea

    Directory of Open Access Journals (Sweden)

    E. Tas

    2006-01-01

    Full Text Available The Dead Sea is an excellent natural laboratory for the investigation of Reactive Bromine Species (RBS chemistry, due to the high RBS levels observed in this area, combined with anthropogenic air pollutants up to several ppb. The present study investigated the basic chemical mechanism of RBS at the Dead Sea using a numerical one-dimensional chemical model. Simulations were based on data obtained from comprehensive measurements performed at sites along the Dead Sea. The simulations showed that the high BrO levels measured frequently at the Dead Sea could only partially be attributed to the highly concentrated Br− present in the Dead Sea water. Furthermore, the RBS activity at the Dead Sea cannot solely be explained by a pure gas phase mechanism. This paper presents a chemical mechanism which can account for the observed chemical activity at the Dead Sea, with the addition of only two heterogeneous processes: the "Bromine Explosion" mechanism and the heterogeneous decomposition of BrONO2. Ozone frequently dropped below a threshold value of ~1 to 2 ppbv at the Dead Sea evaporation ponds, and in such cases, O3 became a limiting factor for the production of BrOx (BrO+Br. The entrainment of O3 fluxes into the evaporation ponds was found to be essential for the continuation of RBS activity, and to be the main reason for the jagged diurnal pattern of BrO observed in the Dead Sea area, and for the positive correlation observed between BrO and O3 at low O3 concentrations. The present study has shown that the heterogeneous decomposition of BrONO2 has a great potential to affect the RBS activity in areas influenced by anthropogenic emissions, mainly due to the positive correlation between the rate of this process and the levels of NO2. Further investigation of the influence of the decomposition of BrONO2 may be especially important in understanding the RBS activity at mid-latitudes.

  19. Measurement-based modeling of bromine chemistry in the boundary layer: 1. Bromine chemistry at the Dead Sea

    Directory of Open Access Journals (Sweden)

    A. Pour Biazar

    2006-06-01

    Full Text Available The Dead Sea is an excellent natural laboratory for the investigation of Reactive Bromine Species (RBS chemistry, due to the high RBS levels observed in this area, combined with anthropogenic air pollutants up to several ppb. The present study investigated the chemical mechanism of RBS at the Dead Sea using a numerical one-dimensional chemical model. Simulations were based on data obtained from comprehensive measurements performed at sites along the Dead Sea. The simulations showed that the high BrO levels measured frequently at the Dead Sea could only partially be attributed to the highly concentrated Br− present in the Dead Sea water. Further, the RBS activity at the Dead Sea cannot solely be explained by a pure gas phase mechanism. This paper presents a chemical mechanism which can account for the observed chemical activity at the Dead Sea, with the addition of only two heterogeneous processes: the "Bromine Explosion" mechanism and the heterogeneous decomposition of BrONO2. Ozone frequently dropped below a threshold value of ~1 to 2 ppbv at the Dead Sea evaporation ponds, and in such cases, O3 became a limiting factor for the production of BrOx (BrO+Br. The entrainment of O3 fluxes into the evaporation ponds was found to be essential for the continuation of RBS activity, and to be the main reason for the positive correlation observed between BrO and O3 at low O3 concentrations, and for the jagged diurnal pattern of BrO observed in the Dead Sea area. The present study has shown that the heterogeneous decomposition of BrONO2 has the potential to greatly affect the RBS activity in areas under anthropogenic influence, mainly due to the positive correlation between the rate of this process and the levels of NO2. Further investigation of the influence of the decomposition of BrONO2 may be especially important in understanding the RBS activity at mid-latitudes.

  20. Modelling atmospheric chemistry and long-range transport of emerging Asian pollutants

    CERN Document Server

    Wang, Kuo-Ying

    2008-01-01

    Modeling is a very important tool for scientific processes, requiring long-term dedication, desire, and continuous reflection. In this work, we discuss several aspects of modeling, and the reasons for doing it. We discuss two major modeling systems that have been built by us over the last 10 years. It is a long and arduous process but the reward of understanding can be enormous, as demonstrated in the examples shown in this work. We found that long-range transport of emerging Asian pollutants can be interpreted using a Lagrangian framework for wind analysis. More detailed processes still need to be modeled but an accurate representation of the wind structure is the most important thing above all others. Our long-term chemistry integrations reveal the capability of the IMS model in simulating tropospheric chemistry on a climate scale. These long-term integrations also show ways for further model development. Modeling is a quantitative process, and the understanding can be sustained only when theories are vigor...

  1. Development and validation of chemistry agnostic flow battery cost performance model and application to nonaqueous electrolyte systems: Chemistry agnostic flow battery cost performance model

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, Alasdair [Pacific Northwest National Laboratory (PNNL), 902 Battelle Boulevard, P.O. Box 999 Richland WA 99352 USA; Thomsen, Edwin [Pacific Northwest National Laboratory (PNNL), 902 Battelle Boulevard, P.O. Box 999 Richland WA 99352 USA; Reed, David [Pacific Northwest National Laboratory (PNNL), 902 Battelle Boulevard, P.O. Box 999 Richland WA 99352 USA; Stephenson, David [Pacific Northwest National Laboratory (PNNL), 902 Battelle Boulevard, P.O. Box 999 Richland WA 99352 USA; Sprenkle, Vincent [Pacific Northwest National Laboratory (PNNL), 902 Battelle Boulevard, P.O. Box 999 Richland WA 99352 USA; Liu, Jun [Pacific Northwest National Laboratory (PNNL), 902 Battelle Boulevard, P.O. Box 999 Richland WA 99352 USA; Viswanathan, Vilayanur [Pacific Northwest National Laboratory (PNNL), 902 Battelle Boulevard, P.O. Box 999 Richland WA 99352 USA

    2016-01-01

    A chemistry agnostic cost performance model is described for a nonaqueous flow battery. The model predicts flow battery performance by estimating the active reaction zone thickness at each electrode as a function of current density, state of charge, and flow rate using measured data for electrode kinetics, electrolyte conductivity, and electrode-specific surface area. Validation of the model is conducted using a 4kW stack data at various current densities and flow rates. This model is used to estimate the performance of a nonaqueous flow battery with electrode and electrolyte properties used from the literature. The optimized cost for this system is estimated for various power and energy levels using component costs provided by vendors. The model allows optimization of design parameters such as electrode thickness, area, flow path design, and operating parameters such as power density, flow rate, and operating SOC range for various application duty cycles. A parametric analysis is done to identify components and electrode/electrolyte properties with the highest impact on system cost for various application durations. A pathway to 100$kWh-1 for the storage system is identified.

  2. Ozone Budgets from a Global Chemistry/ Transport Model and Comparison to Observations from POLARIS

    Science.gov (United States)

    Kawa, S. Randy

    1999-01-01

    The objective of the Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) field mission was to obtain data to better characterize the summertime seasonal decrease of ozone at mid to high latitudes. The decrease in ozone occurs mainly in the lower stratosphere and is expected to result from in situ chemical destruction. Instrumented balloons and aircraft were used in POLARIS, along with satellites, to measure ozone and chemical species which are involved with stratospheric ozone chemistry. In order to close the seasonal ozone budget, however, ozone transport must also be estimated. Comparison to a global chemistry and transport model (CTM) of the stratosphere indicates how well the summertime ozone loss processes are simulated and thus how well we can predict the ozone response to changing amounts of chemical source gases. Moreover, the model gives insight into the possible relative magnitude of transport contributions to the seasonal ozone decline. Initial comparison to the Goddard CTM, which uses transport winds and temperatures from meteorological data assimilation, shows a high ozone bias in the model and an attenuated summertime ozone loss cycle. Comparison of the model chemical partitioning, and ozone catalytic loss rates to those derived from measurements shows fairly close agreement both at ER-2 altitudes (20 km) and higher. This suggests that the model transport is too active in resupplying ozone to the high latitude region, although chemistry failings cannot be completely ruled out. Comparison of ozone and related species will be shown along with a full diagnosis of the model ozone budget and its possible sources of error.

  3. Do organic surface films on sea salt aerosols influence atmospheric chemistry? ─ a model study

    Directory of Open Access Journals (Sweden)

    R. von Glasow

    2007-11-01

    Full Text Available Organic material from the ocean's surface can be incorporated into sea salt aerosol particles often producing a surface film on the aerosol. Such an organic coating can reduce the mass transfer between the gas phase and the aerosol phase influencing sea salt chemistry in the marine atmosphere. To investigate these effects and their importance for the marine boundary layer (MBL we used the one-dimensional numerical model MISTRA. We considered the uncertainties regarding the magnitude of uptake reduction, the concentrations of organic compounds in sea salt aerosols and the oxidation rate of the organics to analyse the possible influence of organic surfactants on gas and liquid phase chemistry with a special focus on halogen chemistry. By assuming destruction rates for the organic coating based on laboratory measurements we get a rapid destruction of the organic monolayer within the first meters of the MBL. Larger organic initial concentrations lead to a longer lifetime of the coating but lead also to an unrealistically strong decrease of O3 concentrations as the organic film is destroyed by reaction with O3. The lifetime of the film is increased by assuming smaller reactive uptake coefficients for O3 or by assuming that a part of the organic surfactants react with OH. With regard to tropospheric chemistry we found that gas phase concentrations for chlorine and bromine species decreased due to the decreased mass transfer between gas phase and aerosol phase. Aqueous phase chlorine concentrations also decreased but aqueous phase bromine concentrations increased. Differences for gas phase concentrations are in general smaller than for liquid phase concentrations. The effect on gas phase NO2 or NO is very small (reduction less than 5% whereas liquid phase NO2 concentrations increased in some cases by nearly 100%. We list suggestions for further laboratory studies which are needed for improved model studies.

  4. SIMULATION OF NOx FORMATION IN TURBULENT SWIRLING COMBUSTION USING A USM TURBULENCE-CHEMISTRY MODEL

    Institute of Scientific and Technical Information of China (English)

    周力行; 乔丽; 张健

    2003-01-01

    A unified second-order moment (USM) turbulence-chemistry model for simulating NOx formation in turbulent combustion is proposed.All of correlations,including the correlation of the reaction-rate coefficient fluctuation with the concentration fluctuation,are closed by the transport equations in the same form.This model discards the approximation of series expansion of the exponential function or the approximation of using the product of several 1-D PDF's instead of a joint PDF.It is much simpler than other refined models,such as the PDF transport equation model and the conditional moment closure model.The proposed model is used to simulate methane-air swirling turbulent combustion and NOx formation.The prediction results are in good agreement with the experimental results.

  5. Parameterization and evaluation of sulfate adsorption in a dynamic soil chemistry model

    International Nuclear Information System (INIS)

    Including sulfate adsorption improves the dynamic behavior of the SAFE model. - Sulfate adsorption was implemented in the dynamic, multi-layer soil chemistry model SAFE. The process is modeled by an isotherm in which sulfate adsorption is considered to be fully reversible and dependent on sulfate concentration as well as pH in soil solution. The isotherm was parameterized by a site-specific series of simple batch experiments at different pH (3.8-5.0) and sulfate concentration (10-260 μmol l-1) levels. Application of the model to the Lake Gaardsjoen roof covered site shows that including sulfate adsorption improves the dynamic behavior of the model and sulfate adsorption and desorption delay acidification and recovery of the soil. The modeled adsorbed pool of sulfate at the site reached a maximum level of 700 mmol/m2 in the late 1980s, well in line with experimental data

  6. Computational Models and Virtual Reality. New Perspectives of Research in Chemistry

    Directory of Open Access Journals (Sweden)

    Klaus Mainzer

    1999-11-01

    Full Text Available Molecular models are typical topics of chemical research depending on the technical standards of observation, computation, and representation. Mathematically, molecular structures have been represented by means of graph theory, topology, differential equations, and numerical procedures. With the increasing capabilities of computer networks, computational models and computer-assisted visualization become an essential part of chemical research. Object-oriented programming languages create a virtual reality of chemical structures opening new avenues of exploration and collaboration in chemistry. From an epistemic point of view, virtual reality is a new computer-assisted tool of human imagination and recognition.

  7. An exploratory study of proficient undergraduate Chemistry II students' application of Lewis's model

    Science.gov (United States)

    Lewis, Sumudu R.

    This exploratory study was based on the assumption that proficiency in chemistry must not be determined exclusively on students' declarative and procedural knowledge, but it should be also described as the ability to use variety of reasoning strategies that enrich and diversify procedural methods. The study furthermore assumed that the ability to describe the structure of a molecule using Lewis's model and use it to predict its geometry as well as some of its properties is indicative of proficiency in the essential concepts of covalent bonding and molecule structure. The study therefore inquired into the reasoning methods and procedural techniques of proficient undergraduate Chemistry II students when solving problems, which require them to use Lewis's model. The research design included an original survey, designed by the researcher for this study, and two types of interviews, with students and course instructors. The purpose of the survey was two-fold. First and foremost, the survey provided a base for the student interview selection, and second it served as the foundation for the inquiry into the strategies the student use when solving survey problems. Twenty two students were interviewed over the course of the study. The interview with six instructors allowed to identify expected prior knowledge and skills, which the students should have acquired upon completion of the Chemistry I course. The data, including videos, audios, and photographs of the artifacts produced by students during the interviews, were organized and analyzed manually and using QSR NVivo 10. The research found and described the differences between proficient and non-proficient students' reasoning and procedural strategies when using Lewis's model to describe the structure of a molecule. One of the findings clearly showed that the proficient students used a variety of cues to reason, whereas other students used one memorized cue, or an algorithm, which often led to incorrect representations in

  8. Modeling aluminum-silicon chemistries and application to Australian acidic playa lakes as analogues for Mars

    Science.gov (United States)

    Marion, G.M.; Crowley, J.K.; Thomson, B.J.; Kargel, J.S.; Bridges, N.T.; Hook, S.J.; Baldridge, A.; Brown, A.J.; Ribeiro da Luz, B.; de Souza, Filho C.R.

    2009-01-01

    Recent Mars missions have stimulated considerable thinking about the surficial geochemical evolution of Mars. Among the major relevant findings are the presence in Meridiani Planum sediments of the mineral jarosite (a ferric sulfate salt) and related minerals that require formation from an acid-salt brine and oxidizing environment. Similar mineralogies have been observed in acidic saline lake sediments in Western Australia (WA), and these lakes have been proposed as analogues for acidic sedimentary environments on Mars. The prior version of the equilibrium chemical thermodynamic FREZCHEM model lacked Al and Si chemistries that are needed to appropriately model acidic aqueous geochemistries on Earth and Mars. The objectives of this work were to (1) add Al and Si chemistries to the FREZCHEM model, (2) extend these chemistries to low temperatures (silicon mineral parameterizations were based on Gibbs free energy and enthalpy data. New aluminum and silicon parameterizations added 12 new aluminum/silicon minerals to this Na-K-Mg-Ca-Fe(II)-Fe(III)-Al-H-Cl-Br-SO4-NO3-OH-HCO3-CO3-CO2-O2-CH4-Si-H2O system that now contain 95 solid phases. There were similarities, differences, and uncertainties between Australian acidic, saline playa lakes and waters that likely led to the Burns formation salt accumulations on Mars. Both systems are similar in that they are dominated by (1) acidic, saline ground waters and sediments, (2) Ca and/or Mg sulfates, and (3) iron precipitates such as jarosite and hematite. Differences include: (1) the dominance of NaCl in many WA lakes, versus the dominance of Fe-Mg-Ca-SO4 in Meridiani Planum, (2) excessively low K+ concentrations in Meridiani Planum due to jarosite precipitation, (3) higher acid production in the presence of high iron concentrations in Meridiani Planum, and probably lower rates of acid neutralization and hence, higher acidities on Mars owing to colder temperatures, and (4) lateral salt patterns in WA lakes. The WA playa lakes

  9. Improved simulation of isoprene oxidation chemistry with the ECHAM5/MESSy chemistry-climate model: lessons from the GABRIEL airborne field campaign

    OpenAIRE

    Butler, T M; Taraborrelli, D.; C. Brühl; H. Fischer; Harder, H.; Martinez, M.; Williams, J; Lawrence, M. G.; Lelieveld, J.

    2008-01-01

    The GABRIEL airborne field measurement campaign, conducted over the Guyanas in October 2005, produced measurements of hydroxyl radical (OH) concentration which are significantly higher than can be simulated using current generation models of atmospheric chemistry. Based on the hypothesis that this "missing OH" is due to an as-yet undiscovered mechanism for recycling OH during the oxidation chain of isoprene, we determine that an OH recycling of about 40–50% (compared with ...

  10. Solution chemistry for models of enterobactin and tannin with uranyl ion

    International Nuclear Information System (INIS)

    In order to develop optimum design of sequestering agents the solution chemistry for models of enterobactin such as Tiron [4,5-dihydroxy-5-benzendisulfonate], nCat[4-nitrocatechol],3,4,3-LICAMS [N1,N5,N10,N14-tetra(2,3-dihydroxy-5-sulfobenzoyl)-tetraazatetradecane] with UO22+ has been investigated. Tannin, which is a polyphenol and inexpensive substance, may probably be used in separation science of nuclear industry. Therefore, the solution chemistry of Tannin with uranyl ion has also been studied. The behaviour of solution chemistry, including eight systems--Tiron and Tiron-U(VI) nCat and nCat-U(VI),3,4,3-LICAMS and 3,4,3-LICAMS-U(VI) as well as Tannin and Tannin-U(VI), has been examined by pH-spectrophotometrc titration method. These experiments have established that U(VI) complexes with these ligands via phenolic groups. This work has offered important data for the design of actinide-specific sequestering agents

  11. Causes and impacts of changes in the stratospheric meridional circulation in a chemistry-climate model

    Energy Technology Data Exchange (ETDEWEB)

    Garny, Hella

    2011-05-13

    The stratospheric meridional circulation is projected to be subject to changes due to enhanced greenhouse-gas concentrations in the atmosphere. This study aims to diagnose and explain long-term changes in the stratospheric meridional circulation using the chemistry-climate model E39CA. The diagnosed strengthening of the circulation is found to be driven by increases in tropical sea surface temperatures which lead to a strengthening and upward shift of the subtropical jets. This enables enhanced vertical propagation of large scale waves into the lower stratosphere, and therefore stronger local wave forcing of the meridional circulation in the tropical lower stratosphere. The impact of changes in transport on the ozone layer is analysed using a newly developed method that allows the separation of the effects of transport and chemistry changes on ozone. It is found that future changes of mean stratospheric ozone concentrations are largely determined by changes in chemistry, while changes in transport of ozone play a minor role. (orig.)

  12. A Two-Zone Multigrid Model for SI Engine Combustion Simulation Using Detailed Chemistry

    Directory of Open Access Journals (Sweden)

    Hai-Wen Ge

    2010-01-01

    Full Text Available An efficient multigrid (MG model was implemented for spark-ignited (SI engine combustion modeling using detailed chemistry. The model is designed to be coupled with a level-set-G-equation model for flame propagation (GAMUT combustion model for highly efficient engine simulation. The model was explored for a gasoline direct-injection SI engine with knocking combustion. The numerical results using the MG model were compared with the results of the original GAMUT combustion model. A simpler one-zone MG model was found to be unable to reproduce the results of the original GAMUT model. However, a two-zone MG model, which treats the burned and unburned regions separately, was found to provide much better accuracy and efficiency than the one-zone MG model. Without loss in accuracy, an order of magnitude speedup was achieved in terms of CPU and wall times. To reproduce the results of the original GAMUT combustion model, either a low searching level or a procedure to exclude high-temperature computational cells from the grouping should be applied to the unburned region, which was found to be more sensitive to the combustion model details.

  13. A report on workshops: General circulation model study of climate- chemistry interaction

    International Nuclear Information System (INIS)

    This report summarizes the discussion on General Circulation Model Study of Climate-Chemistry Interaction from two workshops, the first held 19--21 August 1992 at Oslo, Norway and the second 26--27 May 1993 at Albany, New York, USA. The workshops are the IAMAP activities under the Trace Constituent Working Group. The main objective of the two workshops was to recommend specific general circulation model (GCM) studies of the ozone distribution and the climatic effect of its changes. The workshops also discussed the climatic implications of increasing sulfate aerosols because of its importance to regional climate. The workshops were organized into four working groups: observation of atmospheric O3; modeling of atmospheric chemical composition; modeling of sulfate aerosols; and aspects of climate modeling

  14. Design performances and chemistry program supporting the FA3 /UKEPRTM activity management: experience and modeling balance

    International Nuclear Information System (INIS)

    EPRTM reactor accounts with an evolutionary design that provides the appropriate features to ensure the safety implementation of different chemistry and radiochemistry options. ALARP considerations have been taken into account by EDF-AREVA for making decisions relating to the activity management in the primary circuit of Flamanville 3-EPRTM and UK-EPRTM reactors. The water chemistry and radiochemistry concept implemented in FA3-EPRTM and UK-EPRTM reactors is the result of an exhaustive selection process based on the balance between the theoretical developments, the laboratory tests and the NPP experience concerning the diverse areas associated with: - The source term identification and characterization: The understanding of the origin and behavior of fission products/actinides, corrosion products and activation products constitutes the essential support for the selection of suitable parameters and criteria to monitor the system integrity, the tramp-uranium and radiation build-up and the discharges to the environment. - The source term quantification: The balance between the baseline data from PWR forerunner reactors and the assessments performed by modeling constitutes the major demonstration of the source term accuracy. This approach ensures that activity risks are understood and can be managed with the EPRTM design options. - The EPRTM design options evaluation: The sensitivity analysis results show the influence of the fuel management, the material choice and the chemistry conditioning on several domains such as the activity coolant and the fuel/ex-core crud management. EDF-AREVA demonstrates by means of this process that the design, sizing and chemistry conditioning of EPRTM reactor primary circuit are adapted to guarantee the correct activity management. The methodology developed, based on qualitative and quantitative assessments, intends to propose to the Nuclear Industry several alternatives for evaluating and/or improving the compliance with requirements

  15. Ship plume dispersion rates in convective boundary layers for chemistry models

    Directory of Open Access Journals (Sweden)

    F. Chosson

    2008-04-01

    Full Text Available Detailed ship plume simulations in various convective boundary layer situations have been performed using a Lagrangian Dispersion Model driven by a Large Eddy Simulation Model. The simulations focus on early stage (1–2 h of plume dispersion regime and take into account the effects of plume rise on dispersion. Results are presented in an attempt to provide to chemical modellers community a realistic description of the impact of characteristic dispersion on exhaust ship plume chemistry. Plume dispersion simulations are used to derive analytical dilution rate functions. Even though results exhibit striking effects of plume rise parameter on dispersion patterns, it is shown that initial buoyancy fluxes at ship stack have minor effect on plume dilution rate. After initial high dispersion regimes a simple characteristic dilution time scale can be used to parameterize the subgrid plume dilution effects in large scale chemistry models. The results show that this parameter is directly related to the typical turn-over time scale of the convective boundary layer.

  16. Assessment of the Breakup of the Antarctic Polar Vortex in Two New Chemistry-Climate Models

    Science.gov (United States)

    Hurwitz, M. M.; Newman, P. A.; Oman, L. D.; Li, F.; Morgenstern, O.; Braesicke, P.; Pyle, J. A.

    2010-01-01

    Successful simulation of the breakup of the Antarctic polar vortex depends on the representation of tropospheric stationary waves at Southern Hemisphere middle latitudes. This paper assesses the vortex breakup in two new chemistry-climate models (CCMs). The stratospheric version of the UK Chemistry and Aerosols model is able to reproduce the observed timing of the vortex breakup. Version 2 of the Goddard Earth Observing System (GEOS V2) model is typical of CCMs in that the Antarctic polar vortex breaks up too late; at 10 hPa, the mean transition to easterlies at 60 S is delayed by 12-13 days as compared with the ERA-40 and National Centers for Environmental Prediction reanalyses. The two models' skill in simulating planetary wave driving during the October-November period accounts for differences in their simulation of the vortex breakup, with GEOS V2 unable to simulate the magnitude and tilt of geopotential height anomalies in the troposphere and thus underestimating the wave driving. In the GEOS V2 CCM the delayed breakup of the Antarctic vortex biases polar temperatures and trace gas distributions in the upper stratosphere in November and December.

  17. Development and application of the High resolution VOC Atmospheric Chemistry in Canopies (Hi-VACC) model

    Science.gov (United States)

    Kenny, W.; Bohrer, G.; Chatziefstratiou, E.

    2013-12-01

    We have been working to develop a new post-processing model - High resolution VOC Atmospheric Chemistry in Canopies (Hi-VACC) - which will be able to resolve the dispersion and chemistry of reacting chemical species given their emission rates from the vegetation and soil, driven by high resolution meteorological forcing and wind fields from various high resolution atmospheric regional and large-eddy simulations. Hi-VACC reads in fields of pressure, temperature, humidity, air density, short-wave radiation, wind (3-D u, v and w components) and sub-grid-scale turbulence that were simulated by a high resolution atmospheric model. This meteorological forcing data is provided as snapshots of 3-D fields. Presently, the advection-diffusion portion of the model is fully developed, and we have tested it using a number of RAMS-based Forest Large Eddy Simulation (RAFLES) runs. Here, we present results from utilizing Hi-VACC in a few different contexts where it performs smoke and particle dispersion well. These include simulations of smoke dispersion from a theoretical forest fire in a domain in The Pine Barrens in New Jersey, as well as simulations to test the effects of heat flux on a scalar plume dispersing over a vegetative windbreak in an agricultural setting. Additional, we show initial results from testing the coupled chemistry component of Hi-VACC. One of the primary benefits of Hi-VACC is that users of other models can utilize this tool with only minimal work on their part -- processing their output fields into the appropriate HI-VACC input format. We have developed our model such that for whatever atmospheric model is being used with it, a MATLAB function must be written to extract the necessary information from the output files of that model and shape it into the proper format. This is the only model-specific work required. As such, this sort of smoke dispersion modeling performed by Hi-VACC - as well as its other capabilities - can be easily performed in other

  18. Coupled Chemistry Climate Model Simulations of Stratospheric Temperature for the Recent Past

    Science.gov (United States)

    Austin, J.

    2007-12-01

    Temperature results for the recent past from multi-decadal simulations of eleven coupled chemistry climate models are analysed using multi-linear regression including a trend, solar cycle and volcanic aerosol terms. The climatology of the models since 1980 is in good agreement with observations for the troposphere but diverge from each other and from observations in the stratosphere. Overall, the models agree better with observations than previous assessments. As a function of latitude and pressure, the simulated trends vary substantially from model to model, although all models show several consistent features. These include statistically significant cooling trends from about the lower stratosphere upwards in the low and middle latitudes. Several models have statistically significant cooling in the lower stratosphere over the polar region. The temporal variation in the global average temperature in the lower stratosphere indicates a clear increase during volcanic eruptions, superimposed on an overall cooling. The model responses to the volcanic aerosol varies by about a factor of two with several models substantially overpredicting the observed response during the 1980s and 1990s. The globally averaged temperature simulated by the models is generally in agreement with corrected satellite observations over much of their range. Model trend comparisons are also shown for the polar spring and illlustrate even larger inter-model differences. These differences are caused by different simulations of trends in planetary waves and ozone amounts, and illustrate the challenge of predicting ozone recovery in polar regions.

  19. The global impact of supersaturation in a coupled chemistry-climate model

    Directory of Open Access Journals (Sweden)

    A. Gettelman

    2007-01-01

    Full Text Available Ice supersaturation is important for understanding condensation in the upper troposphere. Many general circulation models however do not permit supersaturation. In this study, a coupled chemistry climate model, the Whole Atmosphere Community Climate Model (WACCM, is modified to include supersaturation for the ice phase. Rather than a study of a detailed parameterization of supersaturation, the study is intended as a sensitivity experiment, to understand the potential impact of supersaturation, and of expected changes to stratospheric water vapor, on climate and chemistry. High clouds decrease and water vapor in the stratosphere increases at a similar rate to the prescribed supersaturation (20% supersaturation increases water vapor by nearly 20%. The stratospheric Brewer-Dobson circulation slows at high southern latitudes, consistent with slight changes in temperature likely induced by changes to cloud radiative forcing. The cloud changes also cause an increase in the seasonal cycle of near tropopause temperatures, increasing them in boreal summer over boreal winter. There are also impacts on chemistry, with small increases in ozone in the tropical lower stratosphere driven by enhanced production. The radiative impact of changing water vapor is dominated by the reduction in cloud forcing associated with fewer clouds (~+0.6 Wm−2 with a small component likely from the radiative effect (greenhouse trapping of the extra water vapor (~+0.2 Wm−2, consistent with previous work. Representing supersaturation is thus important, and changes to supersaturation resulting from changes in aerosol loading for example, might have a modest impact on global radiative forcing, mostly through changes to clouds. There is no evidence of a strong impact of water vapor on tropical tropopause temperatures.

  20. The global impact of supersaturation in a coupled chemistry-climate model

    Directory of Open Access Journals (Sweden)

    A. Gettelman

    2006-12-01

    Full Text Available Ice supersaturation is important for understanding condensation in the upper troposphere. Most general circulation models however do not permit supersaturation. In this study, a coupled chemistry climate model, the Whole Atmosphere Community Climate Model (WACCM, is modified to include supersaturation for the ice phase. The study is intended as a sensitivity experiment, to understand the potential impact of supersaturation, and of expected changes to stratospheric water vapor, on climate and chemistry. Results indicate that high clouds decrease and water vapor in the stratosphere increases nearly linearly with supersaturation (20% supersaturation increases water vapor by nearly 20%. The stratospheric Brewer-Dobson circulation slows at high southern latitudes, consistent with slight changes in temperature likely induced by changes to cloud radiative forcing. The cloud changes also cause an increase in the seasonal cycle of near tropopause temperatures, increasing them in boreal summer over boreal winter. There are also impacts on chemistry, with small increases in ozone in the tropical lower stratosphere driven by enhanced production. The radiative impact of changing water vapor is dominated by the reduction in cloud forcing associated with fewer clouds (~+0.6 Wm−2 with a small component likely from radiative effect (greenhouse trapping of the extra water vapor (~+0.2 Wm−2, consistent with previous work. Representing supersaturation is thus important, and changes to supersaturation resulting from changes in aerosol loading for example, might have a modest impact on global radiative forcing, mostly through changes to clouds. We do not see evidence of a strong impact of water vapor on tropical tropopause temperatures.

  1. Direct variational data assimilation algorithm for atmospheric chemistry data with transport and transformation model

    Science.gov (United States)

    Penenko, Alexey; Penenko, Vladimir; Nuterman, Roman; Baklanov, Alexander; Mahura, Alexander

    2015-11-01

    Atmospheric chemistry dynamics is studied with convection-diffusion-reaction model. The numerical Data Assimilation algorithm presented is based on the additive-averaged splitting schemes. It carries out ''fine-grained'' variational data assimilation on the separate splitting stages with respect to spatial dimensions and processes i.e. the same measurement data is assimilated to different parts of the split model. This design has efficient implementation due to the direct data assimilation algorithms of the transport process along coordinate lines. Results of numerical experiments with chemical data assimilation algorithm of in situ concentration measurements on real data scenario have been presented. In order to construct the scenario, meteorological data has been taken from EnviroHIRLAM model output, initial conditions from MOZART model output and measurements from Airbase database.

  2. A chemistry-transport model simulation of middle atmospheric ozone from 1980 to 2019 using coupled chemistry GCM winds and temperatures

    Science.gov (United States)

    Damski, J.; Thölix, L.; Backman, L.; Kaurola, J.; Taalas, P.; Austin, J.; Butchart, N.; Kulmala, M.

    2007-05-01

    A global 40-year simulation from 1980 to 2019 was performed with the FinROSE chemistry-transport model based on the use of coupled chemistry GCM-data. The main focus of our analysis is on climatological-scale processes in high latitudes. The resulting trend estimates for the past period (1980-1999) agree well with observation-based trend estimates. The results for the future period (2000-2019) suggest that the extent of seasonal ozone depletion over both northern and southern high-latitudes has likely reached its maximum. Furthermore, while climate change is expected to cool the stratosphere, this cooling is unlikely to accelerate significantly high latitude ozone depletion. However, the recovery of seasonal high latitude ozone losses will not take place during the next 15 years.

  3. The Meteorology-Chemistry Interface Processor (MCIP for the CMAQ modeling system

    Directory of Open Access Journals (Sweden)

    T. L. Otte

    2009-12-01

    Full Text Available The Community Multiscale Air Quality (CMAQ modeling system, a state-of-the-science regional air quality modeling system developed by the US Environmental Protection Agency, is being used for a variety of environmental modeling problems including regulatory applications, air quality forecasting, evaluation of emissions control strategies, process-level research, and interactions of global climate change and regional air quality. The Meteorology-Chemistry Interface Processor (MCIP is a vital piece of software within the CMAQ modeling system that serves to, as best as possible, maintain dynamic consistency between the meteorological model and the chemical transport model. MCIP acts as both a post-processor to the meteorological model and a pre-processor to the CMAQ modeling system. MCIP's functions are to ingest the meteorological model output fields in their native formats, perform horizontal and vertical coordinate transformations, diagnose additional atmospheric fields, define gridding parameters, and prepare the meteorological fields in a form required by the CMAQ modeling system. This paper provides an updated overview of MCIP, documenting the scientific changes that have been made since it was first released as part of the CMAQ modeling system in 1998.

  4. Characteristics and Levels of Sophistication: An Analysis of Chemistry Students' Ability to Think with Mental Models

    Science.gov (United States)

    Wang, Chia-Yu; Barrow, Lloyd H.

    2011-08-01

    This study employed a case-study approach to reveal how an ability to think with mental models contributes to differences in students' understanding of molecular geometry and polarity. We were interested in characterizing features and levels of sophistication regarding first-year university chemistry learners' mental modeling behaviors while the learners were solving problems associated with spatial information. To serve this purpose, we conducted case studies on nine students who were sampled from high-scoring, moderate-scoring, and low-scoring students. Our findings point to five characteristics of mental modeling ability that distinguish students in the high-, moderate-, and low-ability groups from one another. Although the levels of mental modeling abilities have been described in categories (high, moderate, and low), they can be thought of as a continuum with the low-ability group reflecting students who have very limited ability to generate and use mental models whereas students in the high-ability group not only construct and use mental models as a thinking tool, but also analyze the problems to be solved, evaluate their mental models, and oversee entire mental modeling processes. Cross-case comparisons for students with different levels of mental modeling ability indicate that experiences of generating and manipulating a mental model based on imposed propositions are crucial for a learner's efforts to incorporate content knowledge with visual-spatial thinking skills. This paper summarizes potential factors that undermine learners' comprehension of molecular geometry and polarity and that influence mastery of this mental modeling ability.

  5. A model study of the plasma chemistry of stratospheric Blue Jets

    Science.gov (United States)

    Winkler, Holger; Notholt, Justus

    2015-04-01

    Stratospheric Blue Jets (BJs) are upward propagating discharges in the altitude range 15-40 km above thunderstorms. They appear as conical bodies of blue light originating at the top of thunderclouds and proceed upward with velocities of the order of 100 km/s. Electric discharges in the atmosphere are known to have chemical effects. Of particular interest is the liberation of atomic oxygen and the formation of reactive nitrogen radicals. We have used a numerical plasma chemistry model in order to simulate the chemical processes in stratospheric BJs. It was applied to BJ streamers in the altitude range 18-38 km. The model results show that there is a production of ozone from atomic oxygen liberated at the streamer tips. At the same time, significant amounts of nitric oxide are produced. Compared to earlier plasma chemistry simulations of BJ streamers, the production of NO and O3 is by orders of magnitude larger. Additionally, the chemical processes in the leader part of a BJ have been simulated for the first time. In the leader channel, driven by high-temperature reactions, the concentration of N2O and NO increases by several orders of magnitude, and there is a significant depletion of ozone. The model results might gain importance by the fact that the chemical perturbations in BJs are largest at altitudes of the stratospheric ozone layer.

  6. On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

    Science.gov (United States)

    Turi, László

    2016-04-01

    We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

  7. An evaluation of the performance of chemistry transport models by comparison with research aircraft observations. Part 1: Concepts and overall model performance

    OpenAIRE

    Brunner, D.; Staehelin, J; Rogers, H. L.; Köhler, M. O.; Pyle, J.A.; Hauglustaine, D.; Jourdain, L.; Berntsen, T. K.; Gauss, M.; I. S. A. Isaksen; MEIJER E.; Van Velthoven, P.; Pitari, G.; Mancini, E; Grewe, G.

    2003-01-01

    A rigorous evaluation of five global Chemistry-Transport and two Chemistry-Climate Models operated by several different groups in Europe, was performed. Comparisons were made of the models with trace gas observations from a number of research aircraft measurement campaigns during the four-year period 1995-1998. Whenever possible the models were run over the same four-year period and at each simulation time step the instantaneous tracer fields were interpolated to all coinciding observati...

  8. An evaluation of the performance of chemistry transport models by comparison with research aircraft observations. Part 1: Concepts and overall model performance

    OpenAIRE

    Brunner, D.; Staehelin, J; Rogers, H. L.; Köhler, M. O.; Pyle, J.A.; Hauglustaine, D.; Jourdain, L.; Berntsen, T. K.; Gauss, M.; I. S. A. Isaksen; MEIJER E.; Van Velthoven, P.; Pitari, G.; Mancini, E; Grewe, V

    2003-01-01

    A rigorous evaluation of five global Chemistry-Transport and two Chemistry-Climate Models operated by several different groups in Europe was performed by comparing the models with trace gas observations from a number of research aircraft measurement campaigns. Whenever possible the models were run over the four-year period 1995–1998 and at each simulation time step the instantaneous tracer fields were interpolated to all coinciding observation points. This approach allows for a ...

  9. An evaluation of the performance of chemistry transport models by comparison with research aircraft observations. Part 1: Concepts and overall model performance

    OpenAIRE

    Brunner, D.; Staehelin, J; Rogers, H. L.; Köhler, M. O.; Pyle, J.A.; Hauglustaine, D.; Jourdain, L.; Berntsen, T. K.; Gauss, M.; I. S. A. Isaksen; MEIJER E.; Van Velthoven, P.; Pitari, G.; Mancini, E; Grewe, V

    2003-01-01

    International audience A rigorous evaluation of five global Chemistry-Transport and two Chemistry-Climate Models operated by several different groups in Europe was performed by comparing the models with trace gas observations from a number of research aircraft measurement campaigns. Whenever possible the models were run over the four-year period 1995–1998 and at each simulation time step the instantaneous tracer fields were interpolated to all coinciding observation points. This approach a...

  10. An evaluation of the performance of chemistry transport models by comparison with research aircraft observations. Part 1: Concepts and overall model performance

    OpenAIRE

    Brunner, D.; Staehelin, J; Rogers, H. L.; Köhler, M. O.; Pyle, J.A.; Hauglustaine, D.; Jourdain, L.; Berntsen, T. K.; Gauss, M.; I. S. A. Isaksen; MEIJER E.; Van Velthoven, P.; Pitari, G.; Mancini, E; Grewe, G.

    2003-01-01

    International audience A rigorous evaluation of five global Chemistry-Transport and two Chemistry-Climate Models operated by several different groups in Europe, was performed. Comparisons were made of the models with trace gas observations from a number of research aircraft measurement campaigns during the four-year period 1995-1998. Whenever possible the models were run over the same four-year period and at each simulation time step the instantaneous tracer fields were interpolated to all...

  11. An evaluation of the performance of chemistry transport models by comparison with research aircraft observations. Part 1: Concepts and overall model performance

    OpenAIRE

    Brunner, D.; Staehelin, J; Rogers, H. L.; Köhler, M. O.; Pyle, J.A.; Hauglustaine, D.; Jourdain, L.; Berntsen, T. K.; Gauss, M.; I. S. A. Isaksen; MEIJER E.; Van Velthoven, P.; Pitari, G.; Mancini, E; Grewe, G.

    2003-01-01

    A rigorous evaluation of five global Chemistry-Transport and two Chemistry-Climate Models operated by several different groups in Europe, was performed. Comparisons were made of the models with trace gas observations from a number of research aircraft measurement campaigns during the four-year period 1995-1998. Whenever possible the models were run over the same four-year period and at each simulation time step the instantaneous tracer fields were interpol...

  12. Radon global simulations with the multiscale chemistry and transport model MOCAGE

    International Nuclear Information System (INIS)

    We present an evaluation of the representation of subgrid scale transport in the new multiscale global chemistry and transport model MOCAGE. The approach is an off-line computation of vertical mass fluxes due to convective and turbulent processes, using only large-scale variables archived in meteorological analyses. Radon is a naturally emitted gas with a radioactive half-life of 3.8 days and is a useful tracer of tropospheric transport processes. A 1-yr (1999) simulation of atmospheric radon concentration has been performed, using 6-hourly meteorological analyses for the forcings. Two different mass flux convection schemes have been tested: a simplified version of the Tiedtke scheme and Kain-Fritsch-Bechtold. We compare model outputs with observations at different time and space scales, showing good overall results. A new interpretation is given to the more contrasted results obtained in Antarctica, as for other models. The state-of-the-art representation of synoptic scale activity around Antarctica is markedly worse than in other parts of the world, both due to oversimplifications of the seasonal evolution of the extent of sea ice, and to the scarcity of observations. Twelve-hourly simulated concentrations are evaluated at two sites for 1999. At Amsterdam Island results are satisfactory: correlation between observed and modelled concentrations is of the order of 0.5. The model reproduces well 'radonic storm' events. At the coastal site of Mace Head in Ireland, simulations are available at two different horizontal resolutions. The correlation between observations and the model is of the order of 0.7. This result is mainly determined by the synoptic scale context, even though local-scale circulations such as breezes interfere on occasions. Finally, it appears that the off-line approach in MOCAGE for subgrid transport is a practical one for chemistry and transport multiscale modelling

  13. Representing ozone extremes in European megacities: the importance of resolution in a global chemistry climate model

    Directory of Open Access Journals (Sweden)

    Z. S. Stock

    2013-10-01

    Full Text Available The continuing growth of the world's urban population has led to an increasing number of cities with more than 10 million inhabitants. The higher emissions of pollutants, coupled to higher population density, makes predictions of air quality in these megacities of particular importance from both a science and a policy perspective. Global climate models are typically run at coarse resolution to enable both the efficient running of long time integrations, and the ability to run multiple future climate scenarios. However, when considering surface ozone concentrations at the local scale, coarse resolution can lead to inaccuracies arising from the highly non-linear ozone chemistry and the sensitivity of ozone to the distribution of its precursors on smaller scales. In this study, we use UM-UKCA, a global atmospheric chemistry model, coupled to the UK Met Office Unified Model, to investigate the impact of model resolution on tropospheric ozone, ranging from global to local scales. We focus on the model's ability to represent the probability of high ozone concentrations in the summer and low ozone concentrations, associated with polluted megacity environments, in the winter, and how this varies with horizontal resolution. We perform time-slice integrations with two model configurations at typical climate resolution (CR, ~150 km and at a higher resolution (HR, ~40 km. The CR configuration leads to overestimation of ozone concentrations on both regional and local scales, while it gives broadly similar results to the HR configuration on the global scale. The HR configuration is found to produce a more realistic diurnal cycle of ozone concentrations and to give a better representation of the probability density function of ozone values in urban areas such as the megacities of London and Paris. We discuss the possible causes for the observed difference in model behaviour between CR and HR configurations and estimate the relative contribution of chemical and

  14. Representing ozone extremes in European megacities: the importance of resolution in a global chemistry climate model

    Science.gov (United States)

    Stock, Z. S.; Russo, M. R.; Pyle, J. A.

    2014-04-01

    The continuing growth of the world's urban population has led to an increasing number of cities with more than 10 million inhabitants. The higher emissions of pollutants, coupled to higher population density, makes predictions of air quality in these megacities of particular importance from both a science and a policy perspective. Global climate models are typically run at coarse resolution to enable both the efficient running of long time integrations, and the ability to run multiple future climate scenarios. However, when considering surface ozone concentrations at the local scale, coarse resolution can lead to inaccuracies arising from the highly nonlinear ozone chemistry and the sensitivity of ozone to the distribution of its precursors on smaller scales. In this study, we use UM-UKCA, a global atmospheric chemistry model, coupled to the UK Met Office Unified Model, to investigate the impact of model resolution on tropospheric ozone, ranging from global to local scales. We focus on the model's ability to represent the probability of high ozone concentrations in the summer and low ozone concentrations, associated with polluted megacity environments, in the winter, and how this varies with horizontal resolution. We perform time-slice integrations with two model configurations at typical climate resolution (CR, ~150 km) and at a higher resolution (HR, ~40 km). The CR configuration leads to overestimation of ozone concentrations on both regional and local scales, while it gives broadly similar results to the HR configuration on the global scale. The HR configuration is found to produce a more realistic diurnal cycle of ozone concentrations and to give a better representation of the probability density function of ozone values in urban areas such as the megacities of London and Paris. We find the observed differences in model behaviour between CR and HR configurations to be largely caused by chemical differences during the winter and meteorological differences

  15. Parallelization and load balancing of a comprehensive atmospheric chemistry transport model

    Science.gov (United States)

    Elbern, Hendrik

    Chemistry transport models are generally claimed to be well suited for massively parallel processing on distributed memory architectures since the arithmetic-to-communication ratio is usually high. However, this observation proves insufficient to account for an efficient parallel performance with increasing complexity of the model. The modeling of the local state of the atmosphere ensues very different branches of the modules' code and greater differences in the computational work load and, consequently, runtime of individual processors occur to a much larger extent during a time step than reported for meteorological models. Variable emissions, changes in actinic fluxes, and all processes associated with cloud modeling are highly variable in time and space and are identified to induce large load imbalances which severely affect the parallel efficiency. This is more so, when the model domain encompasses more heterogeneous meteorological or regional regimes, which impinge dissimilarly on simulations of atmospheric chemistry processes. These conditions hold for the EURAD model applied in this study, which covers the European continental scale as integration domain. Based on a master-worker configuration with a horizontal grid partitioning approach, a method is proposed where the integration domain of the individual processors is locally adjusted to accommodate for load imbalances. This ensures a minimal communication volume and data exchange only with the next neighbors. The interior boundary adjustments of the processors are combined with routine boundary exchange which is required each time step anyway. Two dynamic load balancing schemes were implemented and compared against a conventional equal area partition and a static load balancing scheme. The methods are devised for massively parallel distributed memory computers of both, Single and Multiple Instruction stream Multiple Data stream (SIMD, MIMD) types. A midsummer episode of highly elevated ozone concentrations

  16. Modeling the present and future impact of aviation on climate: an AOGCM approach with online coupled chemistry

    OpenAIRE

    P. Huszar; Teyssèdre, H.; M. Michou; Voldoire, A.; Olivié, D. J. L.; D. Saint-Martin; Cariolle, D.; Senesi, S.; D. Salas y Melia; Alias, A.; Karcher, F.; Ricaud, P.; T. Halenka

    2013-01-01

    Our work is among the first that use an atmosphere-ocean general circulation model (AOGCM) with online chemistry to evaluate the impact of future aviation emissions on temperature. Other particularities of our study include non-scaling to the aviation emissions, and the analysis of models' transient response using ensemble simulations. The model we use is the Météo-France CNRM-CM5.1 earth system model extended with the REPROBUS chemistry scheme. The time horizon of our interest is 1940–2100, ...

  17. Influence of convective transport on tropospheric ozone and its precursors in a chemistry-climate model

    Directory of Open Access Journals (Sweden)

    R. M. Doherty

    2005-06-01

    Full Text Available The impact of convection on tropospheric O3 and its precursors has been examined in a coupled chemistry-climate model. There are two ways that convection affects O3. First, convection affects O3 by vertical mixing of O3 itself. Convection lifts lower tropospheric air to regions where the ozone lifetime is longer, whilst mass-balance subsidence mixes O3-rich upper tropospheric (UT air downwards to regions where the O3 lifetime is shorter. This tends to decrease UT ozone and the overall tropospheric column of O3. Secondly, convection affects O3 by vertical mixing of ozone precursors. This affects O3 chemical production and destruction. Convection transports isoprene and its degradation products to the UT where they interact with lightning NOx to produce PAN, at the expense of NOx. The combined effect of NOx to PAN conversions and downward transport of lightning NOx results in UT NOx decreases. Convective lofting of NOx from surface sources appears relatively unimportant. Despite UT NOx decreases, UT O3 production increases as a result of UT HOx increases driven by isoprene oxidation chemistry. However, UT O3 tends to decrease, as the effect of convective overturning of O3 itself dominates over changes in O3 chemistry. The changes in tropical UT O3 are transported polewards resulting in a 15% decrease in the global tropospheric O3 burden. These results contrast with an earlier study that uses a model of similar chemical complexity. Differences in chemistry schemes - in particular isoprene-driven changes, as well as differences in convection schemes themselves, are the most likely causes of such discrepancies. Further modelling studies are needed to constrain this uncertainty range.

  18. Quantitative performance metrics for stratospheric-resolving chemistry-climate models

    Directory of Open Access Journals (Sweden)

    D. W. Waugh

    2008-06-01

    Full Text Available A set of performance metrics is applied to stratospheric-resolving chemistry-climate models (CCMs to quantify their ability to reproduce key processes relevant for stratospheric ozone. The same metrics are used to assign a quantitative measure of performance ("grade" to each model-observations comparison shown in Eyring et al. (2006. A wide range of grades is obtained, both for different diagnostics applied to a single model and for the same diagnostic applied to different models, highlighting the wide range in ability of the CCMs to simulate key processes in the stratosphere. No model scores high or low on all tests, but differences in the performance of models can be seen, especially for transport processes where several models get low grades on multiple tests. The grades are used to assign relative weights to the CCM projections of 21st century total ozone. However, only small differences are found between weighted and unweighted multi-model mean total ozone projections. This study raises several issues with the grading and weighting of CCMs that need further examination, but it does provide a framework that will enable quantification of model improvements and assignment of relative weights to the model projections.

  19. Modeling water chemistry change and contaminant transport in riverbank filtration systems

    Science.gov (United States)

    Mustafa, Shaymaa; Bahar, Arifah; Aziz, Zainal Abdul; Suratman, Saim

    2016-06-01

    Riverbank filtration system is river water treatment approach based on natural removal of contaminants due to physical, chemical and biological processes. In this article, an analytical model is developed by using Green's function method to simulate the effects of pumping well and microbial activity that occurs in riverbed sediments on contaminant transport and evolution of water chemistry. The model is tested with data collected previously for RBF site in France. The results are compared with numerical simulation conducted in the literature by using finite difference method. Graphically, it is noticed that both numerical and analytical results have almost the same behavior. Also it is found that the model can simulate the decreasing of one pollutant concentration at the zone where the bacteria starts to consume this pollutant.

  20. A pebbles accretion model with chemistry and implications for the solar system

    CERN Document Server

    Ali-Dib, Mohamad

    2016-01-01

    We investigate the chemical composition of the solar system's giant planets atmospheres using a physical formation model with chemistry. The model incorporate disk evolution, pebbles and gas accretion, type I and II migration, simplified disk photoevaporation and solar system chemical measurements. We track the chemical compositions of the formed giant planets and compare them to the observed values. Two categories of models are studied: with and without disk chemical enrichment via photoevaporation. Predictions for the Oxygen and Nitrogen abundances, core masses, and total amount of heavy elements for the planets are made for each case. We find that in the case without disk PE, both Jupiter and Saturn will have a small residual core and comparable total amounts of heavy elements in the envelopes. We predict oxygen abundances enrichments in the same order as carbon, phosphorus and sulfur for both planets. Cometary Nitrogen abundances does not allow to easily reproduce Jupiter's nitrogen observations. In the c...

  1. The Effect of Learning Cycle Model on Preservice Chemistry Teachers’ Understanding of Oxidation Reduction Topic and Thinking Skills

    Directory of Open Access Journals (Sweden)

    Senar Temel

    2012-06-01

    Full Text Available In the study, it was aimed to examine preservice chemistry teachers’ understanding level of oxidation and reduction topic before and after the learning cycle model application and to determine the effect of this model on their understanding level of this topic and lower and higher order thinking skills. In the study, it was aimed to examine preservice chemistry teachers’ understanding level of oxidation and reduction topic before and after the learning cycle model application and to determine the effect of this model on their understanding level of this topic and lower and higher order thinking skills. Thirty preservice chemistry teachers from Hacettepe University, Faculty of Education, Department of Chemistry Education participated in the study. Data were obtained by Oxidation Reduction Achievement Test which is consisted of twelve open ended questions prepared according to Bloom Taxonomy. At the end of the study, it was determined that preservice chemistry teachers’ understanding level of oxidation reduction topic is low before the learning cycle model application but a significant increase in their understanding level of this topic was determined after the application. It was concluded that the learning cycle model provides a significant increase in their higher and lower order thinking skills via paired sample t-tests.

  2. Status of Numerical Modelling of Polar Stratospheric Clouds and Their Effect on Stratospheric Chemistry

    Science.gov (United States)

    Wang, X.; Michelangeli, D. V.; Kletskin, I.

    2003-04-01

    A multi-dimensional stratospheric model for aerosols including detailed Polar Stratospheric Cloud (PSC) microphysical processes, heterogeneous chemistry and comprehensive gas phase chemistry is being developed to study the formation and evolution of PSCs and the effect of heterogeneous reactions occurring on the surface of PSCs on polar stratospheric ozone. The model can be used in parcel mode or one, two, three dimensions. Background sulfate aerosols, frozen sulfate aerosols (sulfuric acid tetrahydrate, SAT) , Type 1a PSCs (nitric acid trihydrate, NAT ), Type 1b PSCs (supercooled ternary solution, STS ), and Type 2 PSCs (water ice crystals) are all treated as interactive elements in the model. The possible microphysical processes included in the model are: uptake of HNO_3 and H_2O on background sulphate droplets to form Type 1b and evaporation of HNO_3 and H_2O from Type 1b to return background sulphate droplets; homogenous freezing of Type 1b to form Type 2 PSCs; heterogeneous nucleation of SAT to form NAT particles, and NAT to form Type 2 PSC ice; deliquescence of SAT to form Type 1b STS and melting of SAT to form background sulphate droplets. In addition, the model involves the growth of ice and NAT by H_2O and HNO_3 deposition, evaporation, coagulation, sedimentation and transport processes. Heterogeneous reactions of nitrogen, chlorine, and bromine compounds in and on sulphate droplets, ternary, and ice particles are considered in the model. In this paper, preliminary simulation results of sensitivity tests are presented to display the basic features of PSCs and their effects on polar ozone. Comparisons with satellite measurements will be discussed.

  3. Lumping, testing, tuning: The invention of an artificial chemistry in atmospheric transport modeling

    Science.gov (United States)

    Heymann, Matthias

    Since the late 1950s computer simulation has been used to investigate the transport of pollutants in the atmosphere. About 20 years later also the chemical transformation of atmospheric pollutants was included in computer models of photochemical smog formation. Due to limited knowledge of atmospheric chemistry and due to limited computer capacity, chemical processes in the atmosphere were modeled with the help of simplified chemical models. In these models chemical substances are lumped together forming artificial virtual compounds with virtual characteristics. The paper aims at studying the practices developed in chemical model building and the creation of confidence in these models. Core of the paper will be the analysis of the Urban Airshed Model (UAM) for the Los Angeles region, a pioneering development in the early 1970s. The construction of the UAM involved the "lumping" of chemical processes and extensive testing and tuning. These practices led to a consistent model representation, in which diverse pieces of information fitted and were mutually stabilized. The pragmatic achievement of consistency created confidence, even though empirical tests of the models remained ambiguous and problematic.

  4. Treatment of Electronic Energy Level Transition and Ionization Following the Particle-Based Chemistry Model

    Science.gov (United States)

    Liechty, Derek S.; Lewis, Mark

    2010-01-01

    A new method of treating electronic energy level transitions as well as linking ionization to electronic energy levels is proposed following the particle-based chemistry model of Bird. Although the use of electronic energy levels and ionization reactions in DSMC are not new ideas, the current method of selecting what level to transition to, how to reproduce transition rates, and the linking of the electronic energy levels to ionization are, to the author s knowledge, novel concepts. The resulting equilibrium temperatures are shown to remain constant, and the electronic energy level distributions are shown to reproduce the Boltzmann distribution. The electronic energy level transition rates and ionization rates due to electron impacts are shown to reproduce theoretical and measured rates. The rates due to heavy particle impacts, while not as favorable as the electron impact rates, compare favorably to values from the literature. Thus, these new extensions to the particle-based chemistry model of Bird provide an accurate method for predicting electronic energy level transition and ionization rates in gases.

  5. Quantum mechanical methods for the investigation of metalloproteins and related bioinorganic compounds.

    Science.gov (United States)

    Bertini, Luca; Bruschi, Maurizio; Cosentino, Ugo; Greco, Claudio; Moro, Giorgio; Zampella, Giuseppe; De Gioia, Luca

    2014-01-01

    It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H2, O2, and N2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.

  6. Sulfur cycle and sulfate radiative forcing simulated from a coupled global climate-chemistry model

    Directory of Open Access Journals (Sweden)

    I.-C. Tsai

    2009-10-01

    Full Text Available The sulfur cycle and radiative effects of sulfate aerosol on climate are studied with a Global tropospheric Climate-Chemistry Model in which chemistry, radiation and dynamics are fully coupled. Production and removal mechanisms of sulfate are analyzed for the conditions of natural and anthropogenic sulfur emissions. Results show that the 1985 anthropogenic emission doubled the global SO2 and sulfate loadings from its natural value of 0.15 and 0.27 Tg S, respectively. Under natural conditions, the fraction of sulfate produced in-cloud is 87%, and the lifetime of SO2 and sulfate are 1.8 and 4.0 days, respectively; whereas with anthropogenic emissions, changes in in-cloud sulfate production are small, while SO2 and sulfate lifetimes are significant reduced (1.0 and 2.4 days, respectively. The doubling of sulfate results in a direct radiative forcing of −0.32 and −0.14 W m−2 under clear-sky and all-sky conditions, respectively, and a significant first indirect forcing of −1.69 W m−2. The first indirect forcing is sensitive to the relationship between aerosol concentration and cloud droplet number concentration. Two aspects of chemistry-climate interaction are addressed. Firstly, the coupling effects lead to 10% and 2% decreases in sulfate loading, respectively, for the cases of natural and anthropogenic added sulfur emissions. Secondly, only the indirect effect of sulfate aerosols yields significantly stronger signals in changes of near surface temperature and sulfate loading than changes due to intrinsic climate variability, while other responses to the indirect effect and all responses to the direct effect are weak.

  7. Sulfur cycle and sulfate radiative forcing simulated from a coupled global climate-chemistry model

    Directory of Open Access Journals (Sweden)

    I.-C. Tsai

    2010-04-01

    Full Text Available The sulfur cycle and radiative effects of sulfate aerosol on climate are studied with a Global tropospheric Climate-Chemistry Model in which chemistry, radiation and dynamics are fully coupled. Production and removal mechanisms of sulfate are analyzed for the conditions of natural and anthropogenic sulfur emissions. Results show that the 1985 anthropogenic emission tripled the global SO2 and sulfate loadings from its natural value of 0.16 and 0.10 Tg S, respectively. Under natural conditions, the fraction of sulfate produced in-cloud is 74%; whereas with anthropogenic emissions, the fraction of in-cloud sulfate production slightly increased to 76%. Lifetimes of SO2 and sulfate under polluted conditions are estimated to be 1.7 and 2.0 days, respectively. The tripling of sulfate results in a direct radiative forcing of −0.43 W m−2 (clear-sky or −0.24 W m−2 (all-sky, and a significant first indirect forcing of −1.85 W m−2, leading to a mean global cooling of about 0.1 K. Regional forcing and responses are significantly stronger than the global values. The first indirect forcing is sensitive to the relationship between aerosol concentration and cloud droplet number concentration which requires further investigation. Two aspects of chemistry-climate interaction are addressed. Firstly, the coupling effects lead to a slight decrease of 1% in global sulfate loading for both the cases of natural and anthropogenic added sulfur emissions. Secondly, only the indirect effect of sulfate aerosols yields significantly stronger signals in changes of near surface temperature and sulfate loading than changes due to intrinsic climate variability, while other responses to the indirect effect and all responses to the direct effect are below noise level.

  8. Deconstructing Constructivism: Modeling Causal Relationships Among Constructivist Learning Environment Factors and Student Outcomes in Introductory Chemistry

    Science.gov (United States)

    Komperda, Regis

    The purpose of this dissertation is to test a model of relationships among factors characterizing aspects of a student-centered constructivist learning environment and student outcomes of satisfaction and academic achievement in introductory undergraduate chemistry courses. Constructivism was chosen as the theoretical foundation for this research because of its widespread use in chemical education research and practice. In a constructivist learning environment the role of the teacher shifts from delivering content towards facilitating active student engagement in activities that encourage individual knowledge construction through discussion and application of content. Constructivist approaches to teaching introductory chemistry courses have been adopted by some instructors as a way to improve student outcomes, but little research has been done on the causal relationships among particular aspects of the learning environment and student outcomes. This makes it difficult for classroom teachers to know which aspects of a constructivist teaching approach are critical to adopt and which may be modified to better suit a particular learning environment while still improving student outcomes. To investigate a model of these relationships, a survey designed to measure student perceptions of three factors characterizing a constructivist learning environment in online courses was adapted for use in face-to-face chemistry courses. These three factors, teaching presence, social presence, and cognitive presence, were measured using a slightly modified version of the Community of Inquiry (CoI) instrument. The student outcomes investigated in this research were satisfaction and academic achievement, as measured by standardized American Chemical Society (ACS) exam scores and course grades. Structural equation modeling (SEM) was used to statistically model relationships among the three presence factors and student outcome variables for 391 students enrolled in six sections of a

  9. Evaluation of a regional chemistry transport model using a newly developed regional OMI NO2 retrieval

    Directory of Open Access Journals (Sweden)

    G. Kuhlmann

    2014-12-01

    Full Text Available In this paper, we evaluate a high-resolution chemistry transport model (CTM (3 km x 3 km spatial resolution with the new Hong Kong (HK NO2 retrieval developed for the Ozone Monitoring Instrument (OMI on-board the Aura satellite. The three-dimensional atmospheric chemistry was modelled in the Pearl River Delta (PRD region in southern China by the Models-3 Community Multiscale Air Quality (CMAQ modelling system from October 2006 to January 2007. In the HK NO2 retrieval, tropospheric air mass factors (AMF were recalculated using high-resolution ancillary parameters of surface reflectance, NO2 profile shapes and aerosol profiles of which the latter two were taken from the CMAQ simulation. We also tested four different aerosol parametrizations. Ground level measurements by the PRD Regional Air Quality Monitoring (RAQM network were used as additional independent measurements. The HK NO2 retrieval increases the NO2 vertical column densities (VCD by (+31 ± 38 %, when compared to NASA's standard product (SP2, and reduces the mean bias (MB between satellite and ground measurements by 26 percentage points from −41 to −15 %. The correlation coefficient r is low for both satellite datasets (r = 0.35 due to the high spatial variability of NO2 concentrations. The correlation between CMAQ and the RAQM network is low (r ≈ 0.3 and the model underestimates the NO2 concentrations in the north-western model domain (Foshan and Guangzhou. We compared the CMAQ NO2 time series of the two main plumes with our regional OMI NO2 product. The model overestimates the NO2 VCDs by about 15 % in Hong Kong and Shenzhen, while the correlation coefficient is satisfactory (r = 0.56. In Foshan and Guangzhou, the correlation is low (r = 0.37 and the model underestimates the VCDs strongly (MB = −40 %. In addition, we estimated that the OMI VCDs are also underestimated by about 10 to 20 % in Foshan and Guangzhou because of the influence of the model parameters on the AMF

  10. Comparing mesoscale chemistry-transport model and remote-sensed Aerosol Optical Depth

    CERN Document Server

    Carnevale, C; Pisoni, E; Volta, M

    2010-01-01

    A comparison of modeled and observed Aerosol Optical Depth (AOD) is presented. 3D Eulerian multiphase chemistry-transport model TCAM is employed for simulating AOD at mesoscale. MODIS satellite sensor and AERONET photometer AOD are used for comparing spatial patterns and temporal timeseries. TCAM simulations for year 2004 over a domain containing Po-Valley and nearly whole Northern Italy are employed. For the computation of AOD, a configuration of external mixing of the chemical species is considered. Furthermore, a parametrization of the effect of moisture affecting both aerosol size and composition is used. An analysis of the contributions of the granulometric classes to the extinction coefficient reveals the dominant role of the inorganic compounds of submicron size. For the analysis of spatial patterns, summer and winter case study are considered. TCAM AOD reproduces spatial patterns similar to those retrieved from space, but AOD values are generally smaller by an order of magnitude. However, accounting a...

  11. AN APPLICATION OF THE LOGISTIC REGRESSION MODEL IN THE EXPERIMENTAL PHYSICAL CHEMISTRY

    Directory of Open Access Journals (Sweden)

    Elpidio Corral-López

    2015-06-01

    Full Text Available The calculation of intensive properties molar volumes of ethanol-water mixtures by experimental densities and tangent method in the Physical Chemistry Laboratory presents the problem of making manually the molar volume curve versus mole fraction and the trace of the tangent line trace. The advantage of using a statistical model the Logistic Regression on a Texas VOYAGE graphing calculator allowed trace the curve and the tangents in situ, and also evaluate the students work during the experimental session. The error percentage between the molar volumes calculated using literature data and those obtained with statistical method is minimal, which validates the model. It is advantageous use the calculator with this application as a teaching support tool, reducing the evaluation time of 3 weeks to 3 hours.

  12. Applications of Raman Spectroscopy to Inorganic Chemistry

    Institute of Scientific and Technical Information of China (English)

    RobinJHClarkFRS

    1995-01-01

    The renaissance in Raman spectroscopy some 25-30 years ago had particular and immediate impact on Inorganic Chemistry,viz in areas such as the study of deeply coloued compounds,structural changes on change of state,equilibria,vapour phase band contour analysis,Raman band intensities and the nature of the chemical bond,metal-metal bonding,species in melts,identification of species in solution and of radicals by time-resolved techniques,in bioinorganic chemistry,and of linear-chain semiconductors.More recently,much attention has been directed at the quantitative level at the evaluation of geometric changes in molecules on excitation by resonance Raman spectroscopy.At the qualitative level Raman microscopy is now recognised to be the most effective technique for the identification of pigments-particularly the inorganic ones-on medieval manuscripts and especially of the components(down to grain sizes of -1 um)of pigment mixtures,It is thus a very important technique at the Arts/Science borderling in conservation science.

  13. Higher Order Chemistry Models in the CFD Simulation of Laser-Ablated Carbon Plumes

    Science.gov (United States)

    Scott, C. D.; Greendyke, R. B.; Creel, J. R.; Payne, B. T.

    2005-01-01

    oven facility is heated to a temperature of 1473 K prior to nanotube production runs. Upon laser irradiation, part of the carbon target ablates immediately and forms a carbon vapor plume that penetrates into the argon base flow towards the laser initially at supersonic velocities. In the previous studies either a single carbon species, C3, was used to model the plume development, or a simplified 11 species carbon model reduced down from the Krestinin and Moravsky model for full fullerene chemistry was used. While both of these options yielded significant results, it was felt that the actual chemistry occ&g in the carbon plume might have a greater affect on the plume than assumed. Indeed, in the earlier attempts at modeling the carbon plume, several thermophysical characteristics could never be matched to experimental observations of plume development - mainly the propagation distance of the plume itself. In the present study, two additional chemistry models will be used to duplicate the previous studies simulations of the carbon plume. The first chemistry model used in this study is again a reduced form of the Krestinin and Moravsky rates. However the highest order carbon species allowed has been increased from C6 to C30 - therefore allowing the simulation of up to a half of the standard C60 fullerene. The second chemistry model investigated is a reduced form of a full carbon nanotube model developed at NASA-JSC. The C30 studies have already been accomplished at the present time, and the reduced SWNT model studies are currently underway. To pursue the current study, one sacrifice had to be made in that the simulation grid spacing had to be increased from 0.5 mm spacing to 1 mm spacing for the sake of computational efficiency since computational effort is proportional to the square of the number of grid points multiplied by the number of species considered. propagation that is far more in line with the experimental results observed by Puretzky et al as shown in Fig. 2

  14. A cognitive model of second-year organic chemistry students' conceptualizations of mental molecular rotation

    Science.gov (United States)

    Briggs, Michael W.

    The goal of this research was to answer the question, "What is a plausible explanation (model) of the cognitive structure and processes that facilitate mental molecular rotation?". This work used phenomenographic methodology and techniques of interview and think-aloud protocol. Constructivism was the theoretical framework. At the outset of the research, I designed nine tasks to obtain participant articulations of conceptualizations of mental molecular rotations. Articulations from five second-year organic chemistry students attending a Midwestern research university became the research data. Analysis produced four emerging themes along two axes: visualization representation and modeling cognition. These two axes formed a mental space, which was modeled by structure and processes that facilitated mental molecular rotation. A theoretical cognitive model of mental molecular rotation was based on the work of two researchers: Robbie Case and Richard Lesh. Lesh's "mental model" is composed of cognitive elements and operations, which are distributed over heeded local and global cognitive sub-models whereas Case deals with unheeded central conceptual structures. The models and structures interact to produce new knowledge and facilitate the use of existing knowledge. Two predictions of the theory of mental molecular rotation were elaborated. Students without a set of operations in a central conceptual structure will not be able to mentally rotate molecules. This is true even if a set of components, other than "operation", is constructed. The artifacts of mental molecular rotation can be used to determine the state of construction of the central conceptual structure responsible for mental molecular rotation.

  15. Characterization and modeling of major constituent equilibrium chemistry of a blended cement mortar

    Directory of Open Access Journals (Sweden)

    Meeussen J.C.L.

    2013-07-01

    Full Text Available Cementitious materials containing ground granulated iron blast furnace slag and coal combustion fly ash as admixtures are being used extensively for nuclear waste containment applications. Whereas the solid phases of ordinary Portland cement (OPC have been studied in great detail, the chemistry of cement, fly ash and slag blends has received relatively less study. Given that OPC is generally more reactive than slag and fly ash, the mineralogy of OPC provides a logical starting point for describing the major constituent chemistry of blended cement mortars. To this end, a blended cement mortar containing Portland cement, granulated blast furnace slag, fly ash and quartz sand was modeled using a set of solid phases known to form in hydrated OPC with the geochemical speciation solver LeachXS/ORCHESTRA. Comparison of modeling results to the experimentally determined pH-dependent batch leaching concentrations (USEPA Method 1313 indicates that major constituent concentrations are described reasonably well with the Portland cement mineral set; however, modeled and measured aluminum concentrations differ greatly. Scanning electron microscopic analysis of the mortar reveals the presence of Al-rich phyllosilicate minerals heretofore unreported in similar cementitious blends: kaolinite and potassic phyllosilicates similar in composition to illite and muscovite. Whereas the potassic phyllosilicates are present in the quartz sand aggregate, the formation of kaolinite appears to be authigenic. The inclusion of kaolinite in speciation modeling provides a substantially improved description of the release of Al and therefore, suggests that the behavior of phyllosilicate phases may be important for predicting long-term physico-chemical behavior of such systems.

  16. What do we learn on bromoform transport and chemistry in deep convection from fine scale modelling?

    Directory of Open Access Journals (Sweden)

    V. Marécal

    2011-11-01

    Full Text Available Bromoform is one of the main sources of halogenated Very Short-Lived Species (VSLS that possibly contributes when degradated to the inorganic halogen loading in the stratosphere. Because of its short lifetime of about four weeks, its pathway to the stratosphere is mainly the transport by convection up to the tropical tropopause layer (TTL and then by radiative ascent in the low stratosphere. Some of its degradation product gases (PGs that are soluble can be scavenged and not reach the TTL.

    In this paper we present a detailed modelling study of the transport and the degradation of bromoform and its PGs in convection. We use a 3-D-cloud resolving model coupled with a chemistry model including gaseous and aqueous chemistry. We run idealised simulations up to 10 days, initialised using a tropical radiosounding for atmospheric conditions and using outputs from a global chemistry-transport model for chemical species. Bromoform is initialised only in the low levels. The first simulation is run with stable atmospheric conditions. It shows that the sum of the bromoform and its PGs significantly decreases with time because of dry deposition and that PGs are mainly in the form of HBr after 2 days of simulation. The other simulation is similar to the first simulation but includes perturbations of temperature and of moisture leading to the development of a convective cloud reaching the TTL. Results of this simulation show an efficient vertical transport of the bromoform from the boundary layer in the upper troposphere and TTL (mixing ratio up to 45% of the initial boundary layer mixing ratio. The organic PGs, which are for the most abundant of them not very soluble, are also uplifted efficiently. For the inorganic PGs, which are more abundant than organic PGs, their mixing ratios in the upper troposphere and in the TTL depend on the partitioning between inorganic soluble and inorganic non soluble species in the convective cloud. Important soluble

  17. Comparing three vegetation monoterpene emission models to measured gas concentrations with a model of meteorology, air chemistry and chemical transport

    Energy Technology Data Exchange (ETDEWEB)

    Smolander, S.; He, Q.; Mogensen, Ditte; Zhou, L.; Back, J.; Ruuskanen, T.; Noe, S.; Guenther, Alex B.; Aaltonen, H.; Kulmala, M.; Boy, Michael

    2014-10-07

    Biogenic volatile organic compounds (BVOCs) are essential in atmospheric chemistry because of their chemical reactions that produce and destroy tropospheric ozone, their effects on aerosol formation and growth, and their potential influence on global warming. As one of the important BVOC groups, monoterpenes have been a focus of scientific attention in atmospheric research. Detailed regional measurements and model estimates are needed to study emission potential and the monoterpene budget on a global scale. Since the use of empirical measurements for upscaling is limited by many physical and biological factors such as genetic variation, temperature and light, water availability, seasonal changes, and environmental stresses, comprehensive inventories over larger areas are difficult to obtain.

  18. Building an Understanding of How Model-Based Inquiry Is Implemented in the High School Chemistry Classroom

    Science.gov (United States)

    Dass, Katarina; Head, Michelle L.; Rushton, Gregory T.

    2015-01-01

    Modeling as a scientific practice in K-12 classrooms has received a wealth of attention in the U.S. and abroad due to the advent of revised national science education standards. The study described herein investigated how a group of high school chemistry teachers developed their understanding of the nature and function of models in the precollege…

  19. The atmospheric chemistry general circultation model ECHAM5/MESSy1: Consistent simulation of ozone from the surface to the mesosphere

    NARCIS (Netherlands)

    Jöckel, P.; Tost, H.; Pozzer, A.; Brülh, Ch.; Buchholz, J.; Ganzeveld, L.N.; Hoor, P.; Kerkweg, A.; Lawrence, M.G.; Sander, R.; Steil, B.; Stiller, G.; Tanarhte, M.; Taraborrelli, D.; Aardenne, van J.A.; Lelieveld, J.

    2006-01-01

    The new Modular Earth Submodel System (MESSy) describes atmospheric chemistry and meteorological processes in a modular framework, following strict coding standards. It has been coupled to the ECHAM5 general circulation model, which has been slightly modified for this purpose. A 90-layer model setup

  20. Aerosol and cloud chemistry of amines from CCS - reactivity experiments and numerical modeling

    Science.gov (United States)

    Weller, Christian; Tilgner, Andreas; Herrmann, Hartmut

    2013-04-01

    Capturing CO2 from the exhaust of power plants using amine scrubbing is a common technology. Therefore, amines can be released during the carbon capture process. To investigate the tropospheric chemical fate of amines from CO2 capturing processes and their oxidation products, the impact of aqueous aerosol particles and cloud droplets on the amine chemistry has been considered. Aqueous phase reactivity experiments of NO3 radicals and ozone with relevant amines and their corresponding nitrosamines were performed. Furthermore, nitrosamine formation and nitrosamine photolysis was investigated during laboratory experiments. These experiments implicated that aqueous phase photolysis can be an effective sink for nitrosamines and that ozone is unreactive towards amines and nitrosamines. Multiphase phase oxidation schemes of amines, nitrosamines and amides were developed, coupled to the existing multiphase chemistry mechanism CAPRAM and built into the Lagrangian parcel model SPACCIM using published and newly measured data. As a result, both deliquescent particles and cloud droplets are important compartments for the multiphase processing of amines and their products. Amines can be readily oxidised by OH radicals in the gas and cloud phase during daytime summer conditions. However, amine oxidation is restricted during winter conditions with low photochemical activity leading to long lifetimes of amines. The importance of the gas and aqueous phase depends strongly on the partitioning of the different amines. Furthermore, the simulations revealed that the aqueous formation of nitrosamines in aerosol particles and could droplets is not a relevant process under tropospheric conditions.

  1. A three-dimensional general circulation model with coupled chemistry for the middle atmosphere

    Science.gov (United States)

    Rasch, P. J.; Boville, B. A.; Brasseur, G. P.

    1995-05-01

    We document a new middle atmosphere general circulation model that includes ozone photochemistry. The dynamical model component is based on the NCAR middle atmosphere version of the Community Climate Model. The chemistry model component simulates the evolution of 24 chemically reactive gases. The horizontal resolution is approximately 3° in latitude and 6° in longitude. It includes 44 levels, with a maximum vertical grid spacing of about 2.5 km and a top level at around 75 km. The chemical model distinguishes between species where we judge transport to be critical and those for which it may be neglected. Nine longer-lived species (N2O, CH4, H2O, HNO3, N2O5, CO, ClONO2, HCl, and HOCl) and four chemical families (NOy, NOx, Ox and Clx) are advected. Concentrations of 15 species which are typically shorter-lived or are members of the chemical families are diagnosed using quasi-equilibrium assumptions ( O(1D), OH, Cl, O(3P), O3, HO2, NO2, ClO, NO, HNO4, NO3, N, OClO, Cl2O2, H2O2). Distributions for a number of other species are prescribed. Results are presented from a 2-year simulation, which include only gas phase photochemical reactions and in which the ozone distribution forecast from the chemistry module does not affect the radiative forcing of the dynamical fields. The calculated distributions of trace species and their seasonal evolution are often quite realistic, particularly in the northern hemisphere extratropics. Distributions of long-lived species such as N2O and CH4 correspond well to satellite observations. Some features, such as the double peak structure occurring during equinoxes, are not reproduced. The latitudinal variation and seasonal evolution of the ozone column abundance is quite realistic. The calculated vertical distribution of the ozone mixing ratio exhibits significant differences from measured values. The model underestimates significantly the ozone in the upper stratosphere (40 km) and in the extratropics, where the maximum values occur at

  2. Improvements in the modeling of crevice chemistry in PWR steam generators using the MULTEQ code

    International Nuclear Information System (INIS)

    The MULTEQ Code was developed to model the high temperature chemistry of the concentrated solutions which form in PWR Steam Generator (SG) crevices and flow restricted regions. Earlier versions of the code modeled the evaporation process as either a constant mass or constant volume system with a well-mixed liquid solution. Experiments performed in simulated heated crevices and more complex thermal hydraulic models suggest that the solution is not well-mixed. The degree of mixing strongly effects the behavior of both volatile and insoluble species in the crevice. The well-mixed models predict much lower concentrations of volatile species in the crevice than is observed in laboratory experiments and inferred from corrosion in the field. By removing both the steam and precipitates formed in a step-wise fashion, the constant mass model approximates the behavior in a solution which is not well-mixed. The basis for this new model is fully described in the paper. 9 refs., 4 figs

  3. Plutonium chemistry: a synthesis of experimental data and a quantitative model for plutonium oxide solubility

    International Nuclear Information System (INIS)

    The chemistry of plutonium is important for assessing potential behavior of radioactive waste under conditions of geologic disposal. This paper reviews experimental data on dissolution of plutonium oxide solids, describes a hybrid kinetic-equilibrium model for predicting steady-state Pu concentrations, and compares laboratory results with predicted Pu concentrations and oxidation-state distributions. The model is based on oxidation of PuO2 by water to produce PuO2+x, an oxide that can release Pu(V) to solution. Kinetic relationships between formation of PuO2+x, dissolution of Pu(V), disproportionation of Pu(V) to Pu(IV) and Pu(VI), and reduction of Pu(VI) are given and used in model calculations. Data from tests of pyrochemical salt wastes in brines are discussed and interpreted using the conceptual model. Essential data for quantitative modeling at conditions relevant to nuclear waste repositories are identified and laboratory experiments to determine rate constants for use in the model are discussed

  4. Laboratory chemistry relevant to understanding and modeling the ionosphere of Titan.

    Science.gov (United States)

    Adams, Nigel G; Mathews, L Dalila; Osborne, David

    2010-01-01

    Laboratory data have a dual and critical role in interpreting information obtained from the Cassini spacecraft in its passes through the Titan ionosphere. Firstly, in situ mass spectra are obtained by Cassini and their conversion into atmospheric molecular composition requires chemical modeling to create agreement between the observed mass spectra and those determined from the models. Secondly, once agreement is obtained, then the chemical model can be considered to represent the evolution of the Titan atmosphere. As a contribution to these endeavors in the past, laboratory measurements have been made in the Selected Ion Flow Tube (SIFT) of the reactions of a series of ring molecules with the important ionospheric ion CH3+. These reactions showed that a dominant reaction channel is association. In the present study, this work has been extended to reactions of another important Titan ion C3H3+. These ion-molecule reactions have also been studied at room temperature using a SIFT. Reactions have been studied in detail with benzene, toluene and pyridine and show again that association is very important. The loss of ionization in the ionosphere is then controlled by electron-ion dissociative recombination of the association ions and their progeny. The recombination reactions have been studied as a function of temperature (300 to 550 K) using a flowing afterglow. These combined data have been used to develop a subset of the chemistry and test its viability. They have indicated that association of the important Titan ions with the abundant nitrogen, followed by switching of the nitrogen for the ring compounds, can build up larger species, perhaps resulting in multi-rings. Recombination of such species can affect the ionization balance and provide species which can contribute to the parallel neutral chemistry. Species are suggested that should be looked for in the in situ mass spectra. PMID:21302554

  5. Improving Students' Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture

    Science.gov (United States)

    Springer, Michael T.

    2014-01-01

    Several articles suggest how to incorporate computer models into the organic chemistry laboratory, but relatively few papers discuss how to incorporate these models broadly into the organic chemistry lecture. Previous research has suggested that "manipulating" physical or computer models enhances student understanding; this study…

  6. Implementation of REDIM reduced chemistry to model an axisymmetric laminar diffusion methane-air flame

    Science.gov (United States)

    Henrique de Almeida Konzen, Pedro; Richter, Thomas; Riedel, Uwe; Maas, Ulrich

    2011-06-01

    The goal of this work is to analyze the use of automatically reduced chemistry by the Reaction-Diffusion Manifold (REDIM) method in simulating axisymmetric laminar coflow diffusion flames. Detailed chemical kinetic models are usually computationally prohibitive for simulating complex reacting flows, and therefore reduced models are required. Automatic reduction model approaches usually exploit the natural multi-scale structure of combustion systems. The novel REDIM approach applies the concept of invariant manifolds to treat also the influence of the transport processes on the reduced model, which overcomes a fundamental problem of model reduction in neglecting the coupling of molecular transport with thermochemical processes. We have considered a previously well studied atmospheric pressure nitrogen-diluted methane-air flame as a test case to validate the methodology presented here. First, one-dimensional and two-dimensional REDIMs were computed and tabulated in lookup tables. Then, the full set of governing equations are projected on the REDIM and implemented in the object-oriented C++ Gascoigne code with a new add-on library to deal with the REDIM tables. The projected set of governing equations have been discretized by the Finite Element Method (FEM) and solved by a GMRES iteration preconditioned by a geometric multigrid method. Local grid refinement, adaptive mesh and parallelization are applied to ensure efficiency and precision. The numerical results obtained using the REDIM approach have shown very good agreement with detailed numerical simulations and experimental data.

  7. Simulations of physics and chemistry of polar stratospheric clouds with a general circulation model

    Energy Technology Data Exchange (ETDEWEB)

    Buchholz, J.

    2005-04-20

    A polar stratospheric cloud submodel has been developed and incorporated in a general circulation model including atmospheric chemistry (ECHAM5/MESSy). The formation and sedimentation of polar stratospheric cloud (PSC) particles can thus be simulated as well as heterogeneous chemical reactions that take place on the PSC particles. For solid PSC particle sedimentation, the need for a tailor-made algorithm has been elucidated. A sedimentation scheme based on first order approximations of vertical mixing ratio profiles has been developed. It produces relatively little numerical diffusion and can deal well with divergent or convergent sedimentation velocity fields. For the determination of solid PSC particle sizes, an efficient algorithm has been adapted. It assumes a monodisperse radii distribution and thermodynamic equilibrium between the gas phase and the solid particle phase. This scheme, though relatively simple, is shown to produce particle number densities and radii within the observed range. The combined effects of the representations of sedimentation and solid PSC particles on vertical H{sub 2}O and HNO{sub 3} redistribution are investigated in a series of tests. The formation of solid PSC particles, especially of those consisting of nitric acid trihydrate, has been discussed extensively in recent years. Three particle formation schemes in accordance with the most widely used approaches have been identified and implemented. For the evaluation of PSC occurrence a new data set with unprecedented spatial and temporal coverage was available. A quantitative method for the comparison of simulation results and observations is developed and applied. It reveals that the relative PSC sighting frequency can be reproduced well with the PSC submodel whereas the detailed modelling of PSC events is beyond the scope of coarse global scale models. In addition to the development and evaluation of new PSC submodel components, parts of existing simulation programs have been

  8. Simulation of polar stratospheric clouds in the chemistry-climate-model EMAC via the submodel PSC

    Directory of Open Access Journals (Sweden)

    O. Kirner

    2011-03-01

    Full Text Available The submodel PSC of the ECHAM5/MESSy Atmospheric Chemistry model (EMAC has been developed to simulate the main types of polar stratospheric clouds (PSC. The parameterisation of the supercooled ternary solutions (STS, type 1b PSC in the submodel is based on Carslaw et al. (1995b, the thermodynamic approach to simulate ice particles (type 2 PSC on Marti and Mauersberger (1993. For the formation of nitric acid trihydrate (NAT particles (type 1a PSC two different parameterisations exist. The first is based on an instantaneous thermodynamic approach from Hanson and Mauersberger (1988, the second is new implemented and considers the growth of the NAT particles with the aid of a surface growth factor based on Carslaw et al. (2002. It is possible to choose one of this NAT parameterisation in the submodel. This publication explains the background of the submodel PSC and the use of the submodel with the goal of simulating realistic PSC in EMAC.

  9. The Role of Heterogeneous Chemistry of Volatile ORganic Compounds: A Modeling and Laboratory Study

    Energy Technology Data Exchange (ETDEWEB)

    Gregory R. Carmichael; Vicki H. Grassian

    2007-03-01

    Overview The outputs of this research have been reported annually via the RIMS system. This report serves as an update and final report. The focus of our DOE BES funded project is on the importance of heterogeneous reactions in the troposphere. The primary objectives of our study were to: (i) Evaluate the extent to which heterogeneous chemistry affects the photochemical oxidant cycle, particularly, sources and sinks of tropospheric ozone; and (ii) Conduct laboratory studies on heterogeneous reactions involving NOy, O3 and VOCs on aerosol surfaces. These objectives were pursued through a multidisciplinary approach that combines modeling and laboratory components as discussed in more detail below. In addition, in response to the reconfiguring of the Atmospheric Science Program to focus on aerosol radiative forcing of climate, we also began to investigate the radiative properties of atmospheric aerosol.

  10. Comparisons of Atmospheric Chemistry Models and Observational Data in Google Earth

    Science.gov (United States)

    Burek, M.; Nackowicz, M.

    2007-12-01

    We have developed a set of tools to enable Google Earth to support the scientific analysis of a chemistry and air quality field campaign in Mexico during spring of 2006. Using a variety of information types (gridded three- dimensional model results, surface observations and aircraft-based observations) we are able to provide the scientists with additional information on the overall structure of the chemical conditions at the time and location of the observations. Because the visualization is performed using Goggle Earth, the KML files produced can easily be distributed to the community. It is our goal that the tools we are building will enable the overall community (research and education) to access and visualize significant portions of the information available at the NCAR Community Data Portal.

  11. Variational fine-grained data assimilation schemes for atmospheric chemistry transport and transformation models

    Science.gov (United States)

    Penenko, Alexey; Penenko, Vladimir; Tsvetova, Elena

    2015-04-01

    The paper concerns data assimilation problem for an atmospheric chemistry transport and transformation models. Data assimilation is carried out within variation approach on a single time step of the approximated model. A control function is introduced into the model source term (emission rate) to provide flexibility to adjust to data. This function is evaluated as the minimum of the target functional combining control function norm to a misfit between measured and model-simulated analog of data. This provides a flow-dependent and physically-plausible structure of the resulting analysis and reduces the need to calculate model error covariance matrices that are sought within conventional approach to data assimilation. Extension of the atmospheric transport model with a chemical transformations module influences data assimilation algorithms performance. This influence is investigated with numerical experiments for different meteorological conditions altering convection-diffusion processes characteristics, namely strong, medium and low wind conditions. To study the impact of transformation and data assimilation, we compare results for a convection-diffusion model (without data assimilation), convection-diffusion with assimilation, convection-diffusion-reaction (without data assimilation) and convection-diffusion-reaction-assimilation models. Both high dimensionalities of the atmospheric chemistry models and a real-time mode of operation demand for computational efficiency of the algorithms. Computational issues with complicated models can be solved by using a splitting technique. As the result a model is presented as a set of relatively independent simple models equipped with a kind of coupling procedure. With regard to data assimilation two approaches can be identified. In a fine-grained approach data assimilation is carried out on the separate splitting stages [1,2] independently on shared measurement data. The same situation arises when constructing a hybrid model

  12. Zinc and cadmium. 4; Transition metal chemistry review 1984. Pt. C

    Energy Technology Data Exchange (ETDEWEB)

    Dakternieks, D. (Deakin University, Geelong (Australia). Department of Chemical and Analitical Sciences)

    1990-02-01

    This review of the inorganic and coordination chemistry of zinc and cadmium covers material which appeared in volumes 102 and 103 of Chemical Abstracts. Zinc and cadmium are treated together and, as was the case last year, much of the reported chemistry is routine and has not been reported in detail. Rigorous classification of ligands continues to be a difficulty for compounds containing several different potential donor atoms and the reader may need to refer to more than one section. Although the scopeof this review does not encompass bio-inorganic in general, some more interesting aspects of application of {sup 113}Cd probes for biological systems have veen included this year. (author). 164 refs.; 9 schemes.

  13. Interactive chemistry in the Laboratoire de Météorologie Dynamique general circulation model: model description and impact analysis of biogenic hydrocarbons on tropospheric chemistry

    Directory of Open Access Journals (Sweden)

    G. A. Folberth

    2006-01-01

    Full Text Available We present a description and evaluation of LMDz-INCA, a global three-dimensional chemistry-climate model, pertaining to its recently developed NMHC version. In this substantially extended version of the model a comprehensive representation of the photochemistry of non-methane hydrocarbons (NMHC and volatile organic compounds (VOC from biogenic, anthropogenic, and biomass-burning sources has been included. The tropospheric annual mean methane (9.2 years and methylchloroform (5.5 years chemical lifetimes are well within the range of previous modelling studies and are in excellent agreement with estimates established by means of global observations. The model provides a reasonable simulation of the horizontal and vertical distribution and seasonal cycle of CO and key non-methane VOC, such as acetone, methanol, and formaldehyde as compared to observational data from several ground stations and aircraft campaigns. LMDz-INCA in the NMHC version reproduces tropospheric ozone concentrations fairly well throughout most of the troposphere. The model is applied in several sensitivity studies of the biosphere-atmosphere photochemical feedback. The impact of surface emissions of isoprene, acetone, and methanol is studied. These experiments show a substantial impact of isoprene on tropospheric ozone and carbon monoxide concentrations revealing an increase in surface O3 and CO levels of up to 30 ppbv and 60 ppbv, respectively. Isoprene also appears to significantly impact the global OH distribution resulting in a decrease of the global mean tropospheric OH concentration by approximately 0.7×105 molecules cm-3 or roughly 8% and an increase in the global mean tropospheric methane lifetime by approximately seven months. A global mean ozone net radiative forcing due to the isoprene induced increase in the tropospheric ozone burden of 0.09 W m-2 is found. The key role of isoprene photooxidation in the global tropospheric redistribution of NOx is demonstrated. LMDz

  14. Parameterization of plume chemistry into large-scale atmospheric models: Application to aircraft NOx emissions

    Science.gov (United States)

    Cariolle, D.; Caro, D.; Paoli, R.; Hauglustaine, D. A.; CuéNot, B.; Cozic, A.; Paugam, R.

    2009-10-01

    A method is presented to parameterize the impact of the nonlinear chemical reactions occurring in the plume generated by concentrated NOx sources into large-scale models. The resulting plume parameterization is implemented into global models and used to evaluate the impact of aircraft emissions on the atmospheric chemistry. Compared to previous approaches that rely on corrected emissions or corrective factors to account for the nonlinear chemical effects, the present parameterization is based on the representation of the plume effects via a fuel tracer and a characteristic lifetime during which the nonlinear interactions between species are important and operate via rates of conversion for the NOx species and an effective reaction rates for O3. The implementation of this parameterization insures mass conservation and allows the transport of emissions at high concentrations in plume form by the model dynamics. Results from the model simulations of the impact on atmospheric ozone of aircraft NOx emissions are in rather good agreement with previous work. It is found that ozone production is decreased by 10 to 25% in the Northern Hemisphere with the largest effects in the north Atlantic flight corridor when the plume effects on the global-scale chemistry are taken into account. These figures are consistent with evaluations made with corrected emissions, but regional differences are noticeable owing to the possibility offered by this parameterization to transport emitted species in plume form prior to their dilution at large scale. This method could be further improved to make the parameters used by the parameterization function of the local temperature, humidity and turbulence properties diagnosed by the large-scale model. Further extensions of the method can also be considered to account for multistep dilution regimes during the plume dissipation. Furthermore, the present parameterization can be adapted to other types of point-source NOx emissions that have to be

  15. Atmospheric impact of the 1783–1784 Laki eruption: Part I Chemistry modelling

    Directory of Open Access Journals (Sweden)

    D. S. Stevenson

    2003-01-01

    Full Text Available Results from the first chemistry-transport model study of the impact of the 1783–1784 Laki fissure eruption (Iceland: 64°N, 17°W upon atmospheric composition are presented. The eruption released an estimated 61 Tg(S as SO2 into the troposphere and lower stratosphere. The model has a high resolution tropopause region, and detailed sulphur chemistry. The simulated SO2 plume spreads over much of the Northern Hemisphere, polewards of ~40°N. About 70% of the SO2 gas is directly deposited to the surface before it can be oxidised to sulphuric acid aerosol. The main SO2 oxidants, OH and H2O2, are depleted by up to 40% zonally, and the lifetime of SO2 consequently increases. Zonally averaged tropospheric SO2 concentrations over the first three months of the eruption exceed 20 ppbv, and sulphuric acid aerosol reaches ~2 ppbv. These compare to modelled pre-industrial/present-day values of 0.1/0.5 ppbv SO2 and 0.1/1.0 ppbv sulphate. A total sulphuric acid aerosol yield of 17–22 Tg(S is produced. The mean aerosol lifetime is 6–10 days, and the peak aerosol loading of the atmosphere is 1.4–1.7 Tg(S (equivalent to 5.9–7.1 Tg of hydrated sulphuric acid aerosol. These compare to modelled pre-industrial/present-day sulphate burdens of 0.28/0.81 Tg(S, and lifetimes of 6/5 days, respectively. Due to the relatively short atmospheric residence times of both SO2 and sulphate, the aerosol loading approximately mirrors the temporal evolution of emissions associated with the eruption. The model produces a reason-able simulation of the acid deposition found in Greenland ice cores. These results appear to be relatively insensitive to the vertical profile of emissions assumed, although if more of the emissions reached higher levels (>12 km, this would give longer lifetimes and larger aerosol yields. Introducing the emissions in episodes generates similar results to using monthly mean emissions, because the atmospheric lifetimes are similar to the repose periods

  16. A Unified Monte Carlo Treatment of Gas-Grain Chemistry for Large Reaction Networks. II. A Multiphase Gas-Surface-Layered Bulk Model

    OpenAIRE

    Vasyunin, A. I.; Herbst, E.

    2012-01-01

    The observed gas-phase molecular inventory of hot cores is believed to be significantly impacted by the products of chemistry in interstellar ices. In this study, we report the construction of a full macroscopic Monte Carlo model of both the gas-phase chemistry and the chemistry occurring in the icy mantles of interstellar grains. Our model treats icy grain mantles in a layer-by-layer manner, which incorporates laboratory data on ice desorption correctly. The ice treatment includes a distinct...

  17. QBO Influence on Polar Stratospheric Variability in the GEOS Chemistry-Climate Model

    Science.gov (United States)

    Hurwitz, M. M.; Oman, L. D.; Li, F.; Slong, I.-S.; Newman, P. A.; Nielsen, J. E.

    2010-01-01

    The quasi-biennial oscillation modulates the strength of both the Arctic and Antarctic stratospheric vortices. Model and observational studies have found that the phase and characteristics of the quasi-biennial oscillation (QBO) contribute to the high degree of variability in the Arctic stratosphere in winter. While the Antarctic stratosphere is less variable, recent work has shown that Southern Hemisphere planetary wave driving increases in response to "warm pool" El Nino events that are coincident with the easterly phase of the QBO. These events hasten the breakup of the Antarctic polar vortex. The Goddard Earth Observing System (GEOS) chemistry-climate model (CCM) is now capable of generating a realistic QBO, due a new parameterization of gravity wave drag. In this presentation, we will use this new model capability to assess the influence of the QBO on polar stratospheric variability. Using simulations of the recent past, we will compare the modeled relationship between QBO phase and mid-winter vortex strength with the observed Holton-Tan relation, in both hemispheres. We will use simulations of the 21 St century to estimate future trends in the relationship between QBO phase and vortex strength. In addition, we will evaluate the combined influence of the QBO and El Nino/Southern Oscillation (ENSO) on the timing of the breakup of the polar stratospheric vortices in the GEOS CCM. We will compare the influence of these two natural phenomena with trends in the vortex breakup associated with ozone recovery and increasing greenhouse gas concentrations.

  18. Evaluation of the MOCAGE Chemistry Transport Model during the ICARTT/ITOP Experiment

    Science.gov (United States)

    Bousserez, N.; Attie, J. L.; Peuch, V. H.; Michou, M.; Pfister, G.; Edwards, D.; Emmons, L.; Arnold, S.; Heckel, A.; Richter, A.; Shlager, H.; Lewis A.; Avery, M.; Sachse, G.; Browell, E.; Ferrare, R.

    2007-01-01

    We evaluate the Meteo-France global chemistry transport 3D model MOCAGE (MOdele de Chimie Atmospherique a Grande Echelle) using the important set of aircraft measurements collected during the ICARRT/ITOP experiment. This experiment took place between US and Europe during summer 2004 (July 15-August 15). Four aircraft were involved in this experiment providing a wealth of chemical data in a large area including the North East of US and western Europe. The model outputs are compared to the following species of which concentration is measured by the aircraft: OH, H2O2, CO, NO, NO2, PAN, HNO3, isoprene, ethane, HCHO and O3. Moreover, to complete this evaluation at larger scale, we used also satellite data such as SCIAMACHY NO2 and MOPITT CO. Interestingly, the comprehensive dataset allowed us to evaluate separately the model representation of emissions, transport and chemical processes. Using a daily emission source of biomass burning, we obtain a very good agreement for CO while the evaluation of NO2 points out incertainties resulting from inaccurate ratio of emission factors of NOx/CO. Moreover, the chemical behavior of O3 is satisfactory as discussed in the paper.

  19. On the Impact of Execution Models: A Case Study in Computational Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Chavarría-Miranda, Daniel; Halappanavar, Mahantesh; Krishnamoorthy, Sriram; Manzano Franco, Joseph B.; Vishnu, Abhinav; Hoisie, Adolfy

    2015-05-25

    Efficient utilization of high-performance computing (HPC) platforms is an important and complex problem. Execution models, abstract descriptions of the dynamic runtime behavior of the execution stack, have significant impact on the utilization of HPC systems. Using a computational chemistry kernel as a case study and a wide variety of execution models combined with load balancing techniques, we explore the impact of execution models on the utilization of an HPC system. We demonstrate a 50 percent improvement in performance by using work stealing relative to a more traditional static scheduling approach. We also use a novel semi-matching technique for load balancing that has comparable performance to a traditional hypergraph-based partitioning implementation, which is computationally expensive. Using this study, we found that execution model design choices and assumptions can limit critical optimizations such as global, dynamic load balancing and finding the correct balance between available work units and different system and runtime overheads. With the emergence of multi- and many-core architectures and the consequent growth in the complexity of HPC platforms, we believe that these lessons will be beneficial to researchers tuning diverse applications on modern HPC platforms, especially on emerging dynamic platforms with energy-induced performance variability.

  20. Net Influence of an Internally Generated Guasi-biennial Oscillation on Modelled Stratospheric Climate and Chemistry

    Science.gov (United States)

    Hurwitz, Margaret M.; Oman, Luke David; Newman, Paul A.; Song, InSun

    2013-01-01

    A Goddard Earth Observing System Chemistry- Climate Model (GEOSCCM) simulation with strong tropical non-orographic gravity wave drag (GWD) is compared to an otherwise identical simulation with near-zero tropical non-orographic GWD. The GEOSCCM generates a quasibiennial oscillation (QBO) zonal wind signal in response to a tropical peak in GWD that resembles the zonal and climatological mean precipitation field. The modelled QBO has a frequency and amplitude that closely resembles observations. As expected, the modelled QBO improves the simulation of tropical zonal winds and enhances tropical and subtropical stratospheric variability. Also, inclusion of the QBO slows the meridional overturning circulation, resulting in a generally older stratospheric mean age of air. Slowing of the overturning circulation, changes in stratospheric temperature and enhanced subtropical mixing all affect the annual mean distributions of ozone, methane and nitrous oxide. Furthermore, the modelled QBO enhances polar stratospheric variability in winter. Because tropical zonal winds are easterly in the simulation without a QBO, there is a relative increase in tropical zonal winds in the simulation with a QBO. Extratropical differences between the simulations with and without a QBO thus reflect the westerly shift in tropical zonal winds: a relative strengthening of the polar stratospheric jet, polar stratospheric cooling and a weak reduction in Arctic lower stratospheric ozone.

  1. Performance of Versions 1,2 and 3 of the Goddard Earth Observing System (GEOS) Chemistry-Climate Model (CCM)

    Science.gov (United States)

    Pawson, Steven; Stolarski, Richard S.; Nielsen, J. Eric; Duncan, Bryan N.

    2008-01-01

    Version 1 of the Goddard Earth Observing System Chemistry-Climate Model (GEOS CCM) was used in the first CCMVa1 model evaluation and forms the basis for several studies of links between ozone and the circulation. That version of the CCM was based on the GEOS-4 GCM. Versions 2 and 3 of the GEOS CCM are based on the GEOS-5 GCM, which retains the "Lin-Rood" dynamical core but has a totally different set of physical parameterizatiOns to GEOS-4. In Version 2 of the GEOS CCM the Goddard stratospheric chemistry module is retained. Difference between Versions 1 and 2 thus reflect the physics changes of the underlying GCMs. Several comparisons between these two models are made, several of which reveal improvements in Version 2 (including a more realistic representation of the interannual variability of the Antarctic vortex). In Version 3 of the GEOS CCM, the stratospheric chemistry mechanism is replaced by the "GMI COMBO" code that includes tropospheric chemistry and different computational approaches. An advantage of this model version. is the reduction of high ozone biases that prevail at low chlorine loadings in Versions 1 and 2. This poster will compare and contrast various aspects of the three model versions that are relevant for understanding interactions between ozone and climate.

  2. Attribution of stratospheric ozone trends to chemistry and transport: a modelling study

    Directory of Open Access Journals (Sweden)

    G. Kiesewetter

    2010-12-01

    Full Text Available The decrease of the concentration of ozone depleting substances (ODSs in the stratosphere over the past decade raises the question to what extent observed changes in stratospheric ozone over this period are consistent with known changes in the chemical composition and possible changes in atmospheric transport. Here we present a series of ozone sensitivity calculations with a stratospheric chemistry transport model (CTM driven by meteorological reanalyses from the European Centre for Medium-Range Weather Forecasts, covering the period 1978–2009. In order to account for the reversal in ODS trends, ozone trends are analysed as piecewise linear trends over two periods, 1979–1999 and 2000–2009. Modelled column ozone (TO3 inter-annual variability and trends are in excellent agreement with observations from the Total Ozone Mapping Spectrometer (TOMS and Solar Backscatter UV (SBUV/2 as well as the Global Ozone Monitoring Experiment (GOME/GOME2 and Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY instruments. In the period 1979–1999, modelled TO3 trends at mid-latitudes are dominated by changes in in situ gas-phase chemistry, which contribute to about 50% or more of the TO3 trend in most seasons. Changes in meteorology contribute around 35% to mid-latitude TO3 trends, with strong differences between different seasons. In springtime, export of ozone depleted air from polar latitudes contributes about 35–50% to the modelled TO3 trend at SH mid-latitudes and about 15–30% at NH mid-latitudes. Over the period 2000–2009 positive linear trends in modelled TO3, which agree well with observed TO3 trends, are dominated by changes in meteorology, as expected for the yet small decrease in stratospheric halogen loading over this period. While the TO3 trends themselves are not statistically significant over the period 2000–2009, changes in linear trends between 1978–1999 and 2000–2009 are significant at mid- and high

  3. The millennium water vapour drop in chemistry-climate model simulations

    Science.gov (United States)

    Brinkop, Sabine; Dameris, Martin; Jöckel, Patrick; Garny, Hella; Lossow, Stefan; Stiller, Gabriele

    2016-07-01

    This study investigates the abrupt and severe water vapour decline in the stratosphere beginning in the year 2000 (the "millennium water vapour drop") and other similarly strong stratospheric water vapour reductions by means of various simulations with the state-of-the-art Chemistry-Climate Model (CCM) EMAC (ECHAM/MESSy Atmospheric Chemistry Model). The model simulations differ with respect to the prescribed sea surface temperatures (SSTs) and whether nudging is applied or not. The CCM EMAC is able to most closely reproduce the signature and pattern of the water vapour drop in agreement with those derived from satellite observations if the model is nudged. Model results confirm that this extraordinary water vapour decline is particularly obvious in the tropical lower stratosphere and is related to a large decrease in cold point temperature. The drop signal propagates under dilution to the higher stratosphere and to the poles via the Brewer-Dobson circulation (BDC). We found that the driving forces for this significant decline in water vapour mixing ratios are tropical sea surface temperature (SST) changes due to a coincidence with a preceding strong El Niño-Southern Oscillation event (1997/1998) followed by a strong La Niña event (1999/2000) and supported by the change of the westerly to the easterly phase of the equatorial stratospheric quasi-biennial oscillation (QBO) in 2000. Correct (observed) SSTs are important for triggering the strong decline in water vapour. There are indications that, at least partly, SSTs contribute to the long period of low water vapour values from 2001 to 2006. For this period, the specific dynamical state of the atmosphere (overall atmospheric large-scale wind and temperature distribution) is important as well, as it causes the observed persistent low cold point temperatures. These are induced by a period of increased upwelling, which, however, has no corresponding pronounced signature in SSTs anomalies in the tropics. Our free

  4. An evaluation of the performance of chemistry transport models, Part 2: detailed comparison with two selected campaigns

    Directory of Open Access Journals (Sweden)

    D. Brunner

    2004-11-01

    Full Text Available This is the second part of a rigorous model evaluation study involving five global Chemistry-Transport and two Chemistry-Climate Models operated by different groups in Europe. Simulated trace gas fields were interpolated to the exact times and positions of the observations to account for the actual weather conditions and hence for the specific histories of the sampled air masses. In this part of the study we focus on a detailed comparison with two selected campaigns, PEM-Tropics A and SONEX, contrasting the clean environment of the tropical Pacific with the more polluted North Atlantic region. The study highlights the different strengths and weaknesses of the models in accurately simulating key processes in the UT/LS region including stratosphere-troposphere-exchange, rapid convective transport, lightning emissions, radical chemistry and ozone production. Model simulated Radon, which was used as an idealized tracer for continental influence, was occasionally much better correlated with measured CO than simulated CO pointing towards deficiencies in the used biomass burning emission fields. The abundance and variability of HOx radicals is in general well represented in the models as inferred directly from the comparison with measured OH and HO2 and indirectly from the comparison with hydrogen peroxide concentrations. Components of the NOy family such as PAN, HNO3 and NO were found to compare less favorably. Interestingly, models showing good agreement with observations in the case of PEM-Tropics A often failed in the case of SONEX and vice versa. A better description of NOx and NOy emissions, chemistry and sinks is thought to be key to future model improvements with respect to the representation of chemistry in the UT/LS region.

  5. The chemistry CATT–BRAMS model (CCATT–BRAMS 4.5: a regional atmospheric model system for integrated air quality and weather forecasting and research

    Directory of Open Access Journals (Sweden)

    K. M. Longo

    2013-02-01

    Full Text Available The Coupled Chemistry Aerosol-Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CCATT–BRAMS, version 4.5 is an online regional chemical transport model designed for local and regional studies of atmospheric chemistry from surface to the lower stratosphere suitable both for operational and research purposes. It includes gaseous/aqueous chemistry, photochemistry, scavenging and dry deposition. The CCATT–BRAMS model takes advantages of the BRAMS specific development for the tropics/subtropics and of the recent availability of preprocessing tools for chemical mechanisms and of fast codes for photolysis rates. BRAMS includes state-of-the-art physical parameterizations and dynamic formulations to simulate atmospheric circulations of scales down to meters. The online coupling between meteorology and chemistry allows the system to be used for simultaneous atmospheric weather and chemical composition forecasts as well as potential feedbacks between them. The entire system comprises three preprocessing software tools for chemical mechanism (which are user defined, aerosol and trace gases emission fields and atmospheric and chemistry fields for initial and boundary conditions. In this paper, the model description is provided along evaluations performed using observational data obtained from ground-based stations, instruments aboard of aircrafts and retrieval from space remote sensing. The evaluation takes into account model application on different scales from megacities and Amazon Basin up to intercontinental region of the Southern Hemisphere.

  6. The Chemistry CATT-BRAMS model (CCATT-BRAMS 4.5: a regional atmospheric model system for integrated air quality and weather forecasting and research

    Directory of Open Access Journals (Sweden)

    K. M. Longo

    2013-09-01

    Full Text Available Coupled Chemistry Aerosol-Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CCATT-BRAMS, version 4.5 is an on-line regional chemical transport model designed for local and regional studies of atmospheric chemistry from the surface to the lower stratosphere suitable both for operational and research purposes. It includes gaseous/aqueous chemistry, photochemistry, scavenging and dry deposition. The CCATT-BRAMS model takes advantage of BRAMS-specific development for the tropics/subtropics as well as the recent availability of preprocessing tools for chemical mechanisms and fast codes for photolysis rates. BRAMS includes state-of-the-art physical parameterizations and dynamic formulations to simulate atmospheric circulations down to the meter. This on-line coupling of meteorology and chemistry allows the system to be used for simultaneous weather and chemical composition forecasts as well as potential feedback between the two. The entire system is made of three preprocessing software tools for user-defined chemical mechanisms, aerosol and trace gas emissions fields and the interpolation of initial and boundary conditions for meteorology and chemistry. In this paper, the model description is provided along with the evaluations performed by using observational data obtained from ground-based stations, instruments aboard aircrafts and retrieval from space remote sensing. The evaluation accounts for model applications at different scales from megacities and the Amazon Basin up to the intercontinental region of the Southern Hemisphere.

  7. Uncertainties and assessments of chemistry-climate models of the stratosphere

    Directory of Open Access Journals (Sweden)

    J. Austin

    2003-01-01

    Full Text Available In recent years a number of chemistry-climate models have been developed with an emphasis on the stratosphere. Such models cover a wide range of time scales of integration and vary considerably in complexity. The results of specific diagnostics are here analysed to examine the differences amongst individual models and observations, to assess the consistency of model predictions, with a particular focus on polar ozone. For example, many models indicate a significant cold bias in high latitudes, the "cold pole problem', particularly in the southern hemisphere during winter and spring. This is related to wave propagation from the troposphere which can be improved by improving model horizontal resolution and with the use of non-orographic gravity wave drag. As a result of the widely differing modelled polar temperatures, different amounts of polar stratospheric clouds are simulated which in turn result in varying ozone values in the models. The results are also compared to determine the possible future behaviour of ozone, with an emphasis on the polar regions and mid-latitudes. All models predict eventual ozone recovery, but give a range of results concerning its timing and extent. Differences in the simulation of gravity waves and planetary waves as well as model resolution are likely major sources of uncertainty for this issue. In the Antarctic, the ozone hole has probably reached almost its deepest although the vertical and horizontal extent of depletion may increase slightly further over the next few years. According to the model results, Antarctic ozone recovery could begin any year within the range 2001 to 2008. The limited number of models which have been integrated sufficiently far indicate that full recovery of ozone to 1980 levels may not occur in the Antarctic until about the year 2050. For the Arctic, most models indicate that small ozone losses may continue for a few more years and that recovery could begin any year within the range

  8. Risks to coral reefs from ocean carbonate chemistry changes in recent earth system model projections

    International Nuclear Information System (INIS)

    Coral reefs are among the most biodiverse ecosystems in the world. Today they are threatened by numerous stressors, including warming ocean waters and coastal pollution. Here we focus on the implications of ocean acidification for the open ocean chemistry surrounding coral reefs, as estimated from earth system models participating in the Coupled Model Intercomparison Project, Phase 5 (CMIP5). We project risks to reefs in the context of three potential aragonite saturation (Ωa) thresholds. We find that in preindustrial times, 99.9% of reefs adjacent to open ocean in the CMIP5 ensemble were located in regions with Ωa > 3.5. Under a business-as-usual scenario (RCP 8.5), every coral reef considered will be surrounded by water with Ωa 2 emissions abatement, the Ωa threshold for reefs is critical to projecting their fate. Our results indicate that to maintain a majority of reefs surrounded by waters with Ωa > 3.5 to the end of the century, very aggressive reductions in emissions are required. The spread of Ωa projections across models in the CMIP5 ensemble is narrow, justifying a high level of confidence in these results. (letter)

  9. Assimilation of surface NO2 and O3 observations into the SILAM chemistry transport model

    Science.gov (United States)

    Vira, J.; Sofiev, M.

    2015-02-01

    This paper describes the assimilation of trace gas observations into the chemistry transport model SILAM (System for Integrated modeLling of Atmospheric coMposition) using the 3D-Var method. Assimilation results for the year 2012 are presented for the prominent photochemical pollutants ozone (O3) and nitrogen dioxide (NO2). Both species are covered by the AirBase observation database, which provides the observational data set used in this study. Attention was paid to the background and observation error covariance matrices, which were obtained primarily by the iterative application of a posteriori diagnostics. The diagnostics were computed separately for 2 months representing summer and winter conditions, and further disaggregated by time of day. This enabled the derivation of background and observation error covariance definitions, which included both seasonal and diurnal variation. The consistency of the obtained covariance matrices was verified using χ2 diagnostics. The analysis scores were computed for a control set of observation stations withheld from assimilation. Compared to a free-running model simulation, the correlation coefficient for daily maximum values was improved from 0.8 to 0.9 for O3 and from 0.53 to 0.63 for NO2.

  10. Lidar signal simulation for the evaluation of aerosols in chemistry transport models

    Directory of Open Access Journals (Sweden)

    S. Stromatas

    2012-12-01

    Full Text Available We present an adaptable tool, the OPTSIM (OPTical properties SIMulation software, for the simulation of optical properties and lidar attenuated backscattered profiles (β' from aerosol concentrations calculated by chemistry transport models (CTM. It was developed to model both Level 1 observations and Level 2 aerosol lidar retrievals in order to compare model results to measurements: the level 2 enables to estimate the main properties of aerosols plume structures, but may be limited due to specific assumptions. The level 1, originally developed for this tool, gives access to more information about aerosols properties (β' requiring, at the same time, less hypothesis on aerosols types. In addition to an evaluation of the aerosol loading and optical properties, active remote sensing allows the analysis of aerosols' vertical structures. An academic case study for two different species (black carbon and dust is presented and shows the consistency of the simulator. Illustrations are then given through the analysis of dust events in the Mediterranean region during the summer 2007. These are based on simulations by the CHIMERE regional CTM and observations from the CALIOP space-based lidar, and highlight the potential of this approach to evaluate the concentration, size and vertical structure of the aerosol plumes.

  11. Risks to coral reefs from ocean carbonate chemistry changes in recent earth system model projections

    Science.gov (United States)

    Ricke, K. L.; Orr, J. C.; Schneider, K.; Caldeira, K.

    2013-09-01

    Coral reefs are among the most biodiverse ecosystems in the world. Today they are threatened by numerous stressors, including warming ocean waters and coastal pollution. Here we focus on the implications of ocean acidification for the open ocean chemistry surrounding coral reefs, as estimated from earth system models participating in the Coupled Model Intercomparison Project, Phase 5 (CMIP5). We project risks to reefs in the context of three potential aragonite saturation (Ωa) thresholds. We find that in preindustrial times, 99.9% of reefs adjacent to open ocean in the CMIP5 ensemble were located in regions with Ωa > 3.5. Under a business-as-usual scenario (RCP 8.5), every coral reef considered will be surrounded by water with Ωa 3.5 to the end of the century, very aggressive reductions in emissions are required. The spread of Ωa projections across models in the CMIP5 ensemble is narrow, justifying a high level of confidence in these results.

  12. Argument-Driven Inquiry: An Introduction to a New Instructional Model for Use in Undergraduate Chemistry Labs

    Science.gov (United States)

    Walker, Joi Phelps; Sampson, Victor; Zimmerman, Carol O.

    2011-01-01

    This article presents a new instructional model called Argument-Driven Inquiry (ADI) that can be used in undergraduate college chemistry laboratory courses. ADI is designed to provide students with an opportunity to develop their own method to generate data, to carry out investigations, use data to answer research questions, write, and be more…

  13. Can a coupled meteorology–chemistry model reproduce the historical trend in aerosol direct radiative effects over the Northern Hemisphere?

    Science.gov (United States)

    The ability of a coupled meteorology–chemistry model, i.e., Weather Research and Forecast and Community Multiscale Air Quality (WRF-CMAQ), to reproduce the historical trend in aerosol optical depth (AOD) and clear-sky shortwave radiation (SWR) over the Northern Hemisphere h...

  14. The Influence of Self-Efficacy and Motivational Factors on Academic Performance in General Chemistry Course: A Modeling Study

    Science.gov (United States)

    Alci, Bulent

    2015-01-01

    This study aims to determine the predictive and explanatory model in terms of university students' academic performance in "General Chemistry" course and their motivational features. The participants were 169 university students in the 1st grade at university. Of the participants, 132 were female and 37 were male students. Regarding…

  15. The Use of Molecular Modeling as "Pseudoexperimental" Data for Teaching VSEPR as a Hands-On General Chemistry Activity

    Science.gov (United States)

    Martin, Christopher B.; Vandehoef, Crissie; Cook, Allison

    2015-01-01

    A hands-on activity appropriate for first-semester general chemistry students is presented that combines traditional VSEPR methods of predicting molecular geometries with introductory use of molecular modeling. Students analyze a series of previously calculated output files consisting of several molecules each in various geometries. Each structure…

  16. Use of a PhET Interactive Simulation in General Chemistry Laboratory: Models of the Hydrogen Atom

    Science.gov (United States)

    Clark, Ted M.; Chamberlain, Julia M.

    2014-01-01

    An activity supporting the PhET interactive simulation, Models of the Hydrogen Atom, has been designed and used in the laboratory portion of a general chemistry course. This article describes the framework used to successfully accomplish implementation on a large scale. The activity guides students through a comparison and analysis of the six…

  17. ConfChem Conference on Flipped Classroom: Improving Student Engagement in Organic Chemistry Using the Inverted Classroom Model

    Science.gov (United States)

    Rossi, Robert D.

    2015-01-01

    Improving student engagement in STEM (science, technology, engineering, and mathematics) courses generally, and organic chemistry specifically, has long been a goal for educators. Recently educators at all academic levels have been exploring the "inverted classroom" or "flipped classroom" pedagogical model for improving student…

  18. Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins

    Science.gov (United States)

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-01-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and…

  19. Modelling the multiphase chemistry occurring in orographic hill cap clouds during HCCT-2010

    Science.gov (United States)

    Tilgner, A.; Herrmann, H.; Bräuer, P.; Wolke, R.

    2013-12-01

    Tropospheric clouds and deliquesced particles are a complex multiphase and multi-component environment with simultaneously occurring gas and aqueous phase chemical transformations. Such aqueous phase chemical processes in cloud droplets are expected to proceed very efficient on short timescales and hence they are able to alter the chemical aerosol composition and the deduced physical properties on a global scale. Besides the physico-chemical aerosol processing, chemical aerosol-cloud interactions have significant effects on the whole multiphase oxidation budget. In order to improve the still limited understanding of the aerosol-cloud interactions, Lagrangian-type field experiments, where an orographic cloud is used as a natural flow-through reactor, are used for studying such processes in more detail. In Sept./Oct. 2010, the cloud passage experiment HCCT-2010 (Hill Cap Cloud Thuringia 2010) was conducted at Mt. Schmücke in Thuringia, Germany to study aerosol cloud interactions. As known from former cloud passage experiments, particularly associated model investigations including comparisons of model results with observations have considerably contributed to the interpretation of the measured field data. In the present study, the parcel model SPACCIM (SPectral Aerosol Cloud Chemistry Interaction Model) was applied to investigate the effects of multiphase chemical processing of tropospheric aerosol particles and trace gases resulting from a passage through an orographic cloud at Mt. Schmücke during HCCT-2010. The applied model combines a complex microphysical scheme with the detailed near-explicit multiphase chemistry mechanism MCMv3.1- CAPRAM3.5α with 11381 gas phase and over 3700 aqueous phase reactions. The measured physical and chemical data at the upwind site provided the basis for the model initialisation under real environmental conditions. SPACCIM simulations have been carried out for few cloud events, which provided appropriate meteorological and overflow

  20. Controls of Ca/Mg/Fe activity ratios in pore water chemistry models of the Callovian-Oxfordian clay formation

    Energy Technology Data Exchange (ETDEWEB)

    Lerouge, C.; Grangeon, S.; Wille, G.; Flehoc, C.; Gailhanou, H.; Gaucher, E.C.; Tournassat, C. [BRGM av. Claude Guillemin BP6009 45060 Orleans cedex 2 (France); Vinsot, A. [ANDRA Meuse/Haute-Marne Underground research Laboratory (URL), RD 960, 55290 Bure (France); Made, B.; Altmann, S. [ANDRA - Parc de la Croix Blanche, 1-7 rue Jean Monnet, 92298 Chatenay-Malabry Cedex (France)

    2013-07-01

    In the pore water chemistry model of the Callovian-Oxfordian clay formation, the divalent cations Ca, Mg, and Fe are controlled by equilibrium reactions with pure carbonates: calcite for Ca, dolomite for Mg, and siderite for Fe. Results of a petrological study and computing of the Ca/Mg and Ca/Fe activity ratios based on natural pore water chemistry provide evidence that equilibrium with pure calcite and pure dolomite is a reasonable assumption for undisturbed pore waters; on the other hand, siderite cannot be considered at equilibrium with pore waters at the formation scale. (authors)

  1. Improved simulation of isoprene oxidation chemistry with the ECHAM5/MESSy chemistry-climate model: lessons from the GABRIEL airborne field campaign

    Directory of Open Access Journals (Sweden)

    T. M. Butler

    2008-08-01

    Full Text Available The GABRIEL airborne field measurement campaign, conducted over the Guyanas in October 2005, produced measurements of hydroxyl radical (OH concentration which are significantly higher than can be simulated using current generation models of atmospheric chemistry. Based on the hypothesis that this "missing OH" is due to an as-yet undiscovered mechanism for recycling OH during the oxidation chain of isoprene, we determine that an OH recycling of about 40–50% (compared with 5–10% in current generation isoprene oxidation mechanisms is necessary in order for our modelled OH to approach the lower error bounds of the OH observed during GABRIEL. Such a large amount of OH in our model leads to unrealistically low mixing ratios of isoprene. In order for our modelled isoprene mixing ratios to match those observed during the campaign, we also require that the effective rate constant for the reaction of isoprene with OH be reduced by about 50% compared with the lower bound of the range recommended by IUPAC. We show that a reasonable explanation for this lower effective rate constant could be the segregation of isoprene and OH in the mixed layer. Our modelling results are consistent with a global, annual isoprene source of about 500 Tg(C yr−1, allowing experimentally derived and established isoprene flux rates to be reconciled with global models.

  2. Improved simulation of isoprene oxidation chemistry with the ECHAM5/MESSy chemistry-climate model: lessons from the GABRIEL airborne field campaign

    Directory of Open Access Journals (Sweden)

    T. M. Butler

    2008-03-01

    Full Text Available The GABRIEL airborne field measurement campaign, conducted over the Guyanas in October 2005, produced measurements of hydroxyl radical (OH concentration which are significantly higher than can be simulated using current generation models of atmospheric chemistry. Based on the hypothesis that this "missing OH" is due to an as-yet undiscovered mechanism for recycling OH during the oxidation chain of isoprene, we determine that an OH recycling of about 40–50% (compared with 5–10% in current generation isoprene oxidation mechanisms is necessary in order for our modelled OH to approach the lower error bounds of the OH observed during GABRIEL. Such a large amount of OH in our model leads to unrealistically low mixing ratios of isoprene. In order for our modelled isoprene mixing ratios to match those observed during the campaign, we also require that the effective rate constant for the reaction of isoprene with OH be reduced by about 50% compared with the lower bound of the range recommended by IUPAC. We show that a reasonable explanation for this lower effective rate constant could be the segregation of isoprene and OH in the mixed layer. Our modelling results are consistent with a global, annual isoprene source of about 500 Tg(C yr−1, allowing experimentally derived and established isoprene flux rates to be reconciled with global models.

  3. Investigation of aviation emission impacts on global tropospheric chemistry and climate using a size-resolved aerosol-chemistry model

    Science.gov (United States)

    Kapadia, Zarashpe; Spracklen, Dominick; Arnold, Stephen; Borman, Duncan; Mann, Graham; Pringle, Kirsty; Monks, Sarah; Reddington, Carly; Rap, Alexandru; Scott, Catherine

    2014-05-01

    Aviation is responsible for 3% of global anthropogenic CO2 emissions, but 2-14% of anthropogenic induced climate warming due to contributions from short lived climate forcers. The global civil aviation fleet is projected to double by 2026 in relation to a 2006 baseline and so will play a substantial role in future climate change. Uncertainty in the net impact of aviation on climate is largely due to uncertainty in the impacts of aviation emissions on ozone and aerosol. To study the impact of aviation emissions we use the GLOMAP-mode global aerosol microphysics model coupled to the 3-D chemical transport model TOMCAT. GLOMAP-mode has been extended to include treatment of nitrate aerosol. We include a full suite of non-CO2 aviation emissions (including NOX, SO2, HCs, BC and OC) in the model. We combined the simulated changes in ozone and aerosol with a 3D radiative transfer model to quantify the radiative effect due to aviation non-CO2 emissions. We find that aviation emissions increase O3 concentrations by up to 5.3% in the upper troposphere (UT), broadly matching previous studies. Black carbon (BC) and organic carbon (OC) concentrations increase by 26.5% and 14.6% respectively in the UT, whereas nitrate aerosol is reduced in some regions due to co-emission of NOX and SO2 In the UT, aviation emissions increase both total aerosol number as well as the concentration of particles greater than 70 nm diameter (N70). Entrainment of these particles into the free troposphere results in aviation emissions also increasing N70 in the boundary layer, causing a cooling through the first aerosol indirect effect. We explore differences in these responses compared with those simulated when using the recommended aviation emissions from CMIP5 (5th Climate Model Intercomparison Project), which only include NOX and BC emissions. Our results suggest that aviation emissions of SO2 and HCs neglected by CMIP5 produce important effects on ozone, aerosol number, and N70. We suggest CMIP5

  4. History of the water chemistry for the few tube test model

    International Nuclear Information System (INIS)

    The water chemistry activities carried out in support of the Few Tube Test are described. This test was conducted to provide design confirmation data for the Clinch River Breeder Reactor Project (CRBRP) steam generators. Proposed CRBRP chemistry was followed; all volatile treatment (AVT) of water was carried out with on-line monitoring capability

  5. Fostering green chemistry through a collaborative business model: A chemical leasing case study from Serbia

    NARCIS (Netherlands)

    Lozano, R.; Carpenter, A.; Satric, V.

    2013-01-01

    Green and sustainable chemistry have been developed to help reduce the production and use of harmful chemicals. The two main approaches that have been used in fostering green and sustainable chemistry have been through policy initiatives and science/technology. This paper focuses on a complementary

  6. Improving the Representation of Near Source and Downwind Smoke Plume Chemistry in Regional and Global Air Quality Models

    Science.gov (United States)

    Alvarado, M. J.; Lonsdale, C. R.; Yokelson, R. J.; Travis, K.; Lin, J. C.; McNeill, V. F.; Blake, D. R.; Griffith, D. W. T.; Johnson, T. J.; Kreidenweis, S. M.; Lee, T.; May, A.; McMeeking, G. R.; Meinardi, S.; Simpson, I. J.; Sullivan, A.; Urbanski, S. P.; Weise, D.

    2015-12-01

    The complex photochemistry within a biomass burning smoke plume can cause large changes in the concentration, size distribution, composition, and optical properties of the fine particles (PM2.5) emitted by the fires, as well as significant formation of ozone (O3) and organic nitrate species like peroxyacetyl nitrate (PAN). The Aerosol Simulation Program (ASP) is designed to simulate this chemical evolution of biomass burning plumes under a wide variety of conditions, and can be used to parameterize this chemistry in regional and global air quality models. Here we present ASP simulations of the evolution of biomass burning aerosol from South Carolina prescribed fires in October and November of 2011. This data set contains more detailed measurements of the non-methane organic compounds (NMOCs) in the smoke than the data sets previously used to develop and test ASP, allowing for a more detailed evaluation of the model's gas- and particle-phase chemistry. We also assess the potential impact of secondary organic aerosol (SOA) from glyoxal and isoprene epoxydiols (IEPOX) on the growth of biomass burning aerosols by incorporating the simpleGAMMA (Gas-Aerosol Model for Mechanism Analysis) model into ASP. Finally, we will discuss our efforts to use the ASP model to build a sub-grid scale parameterization of the near-source chemistry of biomass burning plumes for use in regional and global air quality models, using examples from the global chemical transport model GEOS-Chem and the stochastic Lagrangian air quality model STILT-Chem.

  7. Modeling Macro- and Micro-Scale Turbulent Mixing and Chemistry in Engine Exhaust Plumes

    Science.gov (United States)

    Menon, Suresh

    1998-01-01

    Simulation of turbulent mixing and chemical processes in the near-field plume and plume-vortex regimes has been successfully carried out recently using a reduced gas phase kinetics mechanism which substantially decreased the computational cost. A detailed mechanism including gas phase HOx, NOx, and SOx chemistry between the aircraft exhaust and the ambient air in near-field aircraft plumes is compiled. A reduced mechanism capturing the major chemical pathways is developed. Predictions by the reduced mechanism are found to be in good agreement with those by the detailed mechanism. With the reduced chemistry, the computer CPU time is saved by a factor of more than 3.5 for the near-field plume modeling. Distributions of major chemical species are obtained and analyzed. The computed sensitivities of major species with respect to reaction step are deduced for identification of the dominant gas phase kinetic reaction pathways in the jet plume. Both the near field plume and the plume-vortex regimes were investigated using advanced mixing models. In the near field, a stand-alone mixing model was used to investigate the impact of turbulent mixing on the micro- and macro-scale mixing processes using a reduced reaction kinetics model. The plume-vortex regime was simulated using a large-eddy simulation model. Vortex plume behind Boeing 737 and 747 aircraft was simulated along with relevant kinetics. Many features of the computed flow field show reasonable agreement with data. The entrainment of the engine plumes into the wing tip vortices and also the partial detrainment of the plume were numerically captured. The impact of fluid mechanics on the chemical processes was also studied. Results show that there are significant differences between spatial and temporal simulations especially in the predicted SO3 concentrations. This has important implications for the prediction of sulfuric acid aerosols in the wake and may partly explain the discrepancy between past numerical studies

  8. Investigating Differences in Isoprene Oxidation Chemistry Between Gas-Phase Mechanisms Using a Constrained Chemical Box Model

    Science.gov (United States)

    Marvin, M. R.; Wolfe, G. M.; Salawitch, R. J.; Canty, T. P.; Hanisco, T. F.; Kaiser, J.; Keutsch, F. N.; Graus, M.; Warneke, C.; De Gouw, J. A.; Gilman, J.; Lerner, B. M.; Peischl, J.; Veres, P. R.; Min, K. E.; Holloway, J. S.; Aikin, K. C.; Ryerson, T. B.; Roberts, J. M.; Brown, S. S.; Pollack, I. B.; Hatch, C. D.; Lee, B. H.; Lopez-Hilfiker, F.; Thornton, J. A.; Diskin, G. S.; Sachse, G. W.; Huey, L. G.; Liu, X.; Wisthaler, A.; Mikoviny, T.; Wennberg, P. O.; St Clair, J.; Crounse, J.; Teng, A.

    2015-12-01

    Oxidation of isoprene by OH can significantly influence concentrations of important atmospheric pollutants such as ozone and secondary organic aerosols, but the chemistry that describes the relationships between these species is complex and not fully understood. Debate on the topic has led to differences in the isoprene oxidation schemes of several gas-phase chemical mechanisms currently applied in air chemistry models. We use the University of Washington Chemical Model (UWCMv3) to evaluate these mechanisms with respect to isoprene chemistry based on observations from the SENEX and SEAC4RS aircraft campaigns. The campaigns provide constraints on compounds measured over the Southeast United States, where isoprene concentrations are high and other conditions (e.g., NOx levels) vary widely. The payloads for both missions include observations of a wide range of isoprene oxidation products, which can provide insight into specific oxidation pathways. Analysis will focus on the characterization and comparison of isoprene oxidation chemistry for established gas-phase mechanisms that are prevalent in atmospheric modeling today, including the Carbon Bond mechanism (CB05 and CB6r2) and the Master Chemical Mechanism (versions 3.2 and 3.3).

  9. Experimental and modelling studies of the near-field chemistry for Nirex repository concepts

    International Nuclear Information System (INIS)

    A research programme is described which is designed to investigate the chemical conditions in the near field of a concrete based repository and the behaviour of the radiologically important nuclides under these conditions. The chemical conditions are determined by the corrosion of the iron components of the repository and by the soluble components of the concrete. Both of these have been investigated experimentally and models developed which have been validated by further experiment. The effect of these reactions on the repository pH and Eh, and how these develop in time and space have been modelled using a coupled chemical equilibrium and transport code. The solubility of the important nuclides are being studied experimentally under these conditions, and under sensible variations. These data have been used to refine the thermodynamic data base used for the geochemical code PHREEQE. The sorption behaviour of plutonium and americium, under the same conditions, have been studied; the sorption coefficients were found to be large and independent of the concrete formulation, particle size and solid liquid ratio. Recent experimental results from sorption/exchange experiments with lead and 14-carbon are also reported. The programme has also investigated experimentally the possible perturbation of the repository chemistry by microbial action and by natural and added organic material. A final set of experiments combine all the repository components and the waste in a long term equilibration experiment. (author)

  10. A Molecular-Modeling Toolbox Aimed at Bridging the Gap between Medicinal Chemistry and Computational Sciences

    Directory of Open Access Journals (Sweden)

    Sameh Eid

    2013-01-01

    Full Text Available In the current era of high-throughput drug discovery and development, molecular modeling has become an indispensable tool for identifying, optimizing and prioritizing small-molecule drug candidates. The required background in computational chemistry and the knowledge of how to handle the complex underlying protocols, however, might keep medicinal chemists from routinely using in silico technologies. Our objective is to encourage those researchers to exploit existing modeling technologies more frequently through easy-to-use graphical user interfaces. In this account, we present two innovative tools (which we are prepared to share with academic institutions facilitating computational tasks commonly utilized in drug discovery and development: (1 the VirtualDesignLab estimates the binding affinity of small molecules by simulating and quantifying their binding to the three-dimensional structure of a target protein; and (2 the MD Client launches molecular dynamics simulations aimed at exploring the time-dependent stability of ligand–protein complexes and provides residue-based interaction energies. This allows medicinal chemists to identify sites of potential improvement in their candidate molecule. As a case study, we present the application of our tools towards the design of novel antagonists for the FimH adhesin.

  11. Superheavy Element Chemistry by Relativistic Density Functional Theory Electronic Structure Modeling

    Science.gov (United States)

    Zaitsevskii, A. V.; Polyaev, A. V.; Demidov, Yu. A.; Mosyagin, N. S.; Lomachuk, Yu. V.; Titov, A. V.

    2015-06-01

    Two-component density functional theory in its non-collinear formulation combined with the accurate relativistic electronic structure model defined by shape-consistent small-core pseudopotentials (PP/RDFT) provides a robust basis of efficient computational schemes for predicting energetic and structural properties of complex polyatomic systems including superheavy elements (SHEs). Because of the exceptional role of thermochromatography in the experiments on the "chemical" identification of SHEs with atomic numbers Z ≥ 112, we focus on the description of the adsorption of single SHE atoms on the surfaces of solids through cluster modeling of adsorption complexes. In some cases our results differ significantly from those of previous theoretical studies. The results of systematic comparative studies on chemical bonding in simple molecules of binary compounds of SHEs and their nearest homologs with most common light elements, obtained at the PP/RDFT level and visualized through the "chemical graphs", provide the understanding of the general chemistry of SHEs which at present cannot be derived from the experimental data. These results are used to discuss the main trends in changing chemical properties of the elements in the given group of the periodic table and demonstrate the specificity of SHEs.

  12. Women's career choices in chemistry: Motivations, perceptions, and a conceptual model

    Science.gov (United States)

    Grunert, Megan L.

    Statistics showing the under-representation of women at all levels within the physical sciences abound, particularly at the graduate and faculty levels. Women chemists choosing an academic career tend to select teaching institutions over research institutions. This study examined women at the graduate and faculty levels through interviews and the construction of participant narratives to better understand why many women opt out of a career in academic research. Specific attention was paid to women's decision-making processes and what motivates women to choose careers, the rewards and challenges associated with different careers, and the perception of different careers contribute to their decisions. The participant narratives were analyzed on a cross-case basis and constructivist grounded theory was used to develop a model about women's decision-making regarding their careers. Additionally, preliminary work has suggested that graduate students have inaccurate perceptions of careers in academia. Interviews with faculty at teaching and research institutions provided a clearer picture of what each type of career entails. Career-choice motivators, rewards, and challenges were identified for each of the faculty groups. It was found that graduate student women have inaccurate perceptions of academic research careers, which affects how they make career decisions. A model of career choice shows interactions between motivation and perception that guide the career decision-making process. By better understanding these women and their motivations, changes can be made to foster inclusion and accommodation for women and other underrepresented groups in academic chemistry.

  13. Comparative analysis for various redox flow batteries chemistries using a cost performance model

    Science.gov (United States)

    Crawford, Alasdair; Viswanathan, Vilayanur; Stephenson, David; Wang, Wei; Thomsen, Edwin; Reed, David; Li, Bin; Balducci, Patrick; Kintner-Meyer, Michael; Sprenkle, Vincent

    2015-10-01

    The total energy storage system cost is determined by means of a robust performance-based cost model for multiple flow battery chemistries. Systems aspects such as shunt current losses, pumping losses and various flow patterns through electrodes are accounted for. The system cost minimizing objective function determines stack design by optimizing the state of charge operating range, along with current density and current-normalized flow. The model cost estimates are validated using 2-kW stack performance data for the same size electrodes and operating conditions. Using our validated tool, it has been demonstrated that an optimized all-vanadium system has an estimated system cost of costs facilitated by economies of scale from larger production volumes, coupled with performance improvements enabled by technology development, the system cost is expected to decrease to 160 kWh-1 for a 4-h application, and to 100 kWh-1 for a 10-h application. This tool has been shared with the redox flow battery community to enable cost estimation using their stack data and guide future direction.

  14. Developing Chemistry and Kinetic Modeling Tools for Low-Temperature Plasma Simulations

    Science.gov (United States)

    Jenkins, Thomas; Beckwith, Kris; Davidson, Bradley; Kruger, Scott; Pankin, Alexei; Roark, Christine; Stoltz, Peter

    2015-09-01

    We discuss the use of proper orthogonal decomposition (POD) methods in VSim, a FDTD plasma simulation code capable of both PIC/MCC and fluid modeling. POD methods efficiently generate smooth representations of noisy self-consistent or test-particle PIC data, and are thus advantageous in computing macroscopic fluid quantities from large PIC datasets (e.g. for particle-based closure computations) and in constructing optimal visual representations of the underlying physics. They may also confer performance advantages for massively parallel simulations, due to the significant reduction in dataset sizes conferred by truncated singular-value decompositions of the PIC data. We also demonstrate how complex LTP chemistry scenarios can be modeled in VSim via an interface with MUNCHKIN, a developing standalone python/C++/SQL code that identifies reaction paths for given input species, solves 1D rate equations for the time-dependent chemical evolution of the system, and generates corresponding VSim input blocks with appropriate cross-sections/reaction rates. MUNCHKIN also computes reaction rates from user-specified distribution functions, and conducts principal path analyses to reduce the number of simulated chemical reactions. Supported by U.S. Department of Energy SBIR program, Award DE-SC0009501.

  15. Online T5 learning model to enhance chemistry students’ understanding of NMR spectroscopy

    Directory of Open Access Journals (Sweden)

    Saksri Supasorn

    2014-08-01

    Full Text Available Regular lecture-based teaching approaches sometimes fail to enhance students’ understanding of some practice-based chemistry topics such as Nuclear Magnetic Resonance (NMR spectroscopy. A new task-based approach called the T5 learning model was introduced for 48 students studying NMR in the Spectroscopic Methods for Chemical Identification course in 2011. Four different NMR learning environments based on T5 learning models were developed. The students were requested to participate in the following online processes in each environment: 1 complete an individual task, 2 provide feedback and evaluate three anonymous peer tasks, 3 adjust their individual task and evaluate peer feedback, 4 complete a team task and evaluate the effort of each group member, and 5 get feedback from instructor to fulfill understanding. The result showed that the students obtained post-achievement NMR score (mean 24.25, SD 4.80 statistically significantly higher than pre- achievement score (mean 12.29, SD 1.69 at p-value of 0.05. In addition, the implementation of T5-D4LP NMR course in each year during 2010-2012 showed that the students achieved high score (about 70% in the NMR topics. The student evaluation of the T5 NMR learning environments revealed that they agreed that peer feedback with instructor facilitation engaged them in deep learning and effectively promoted their conceptual understanding.

  16. Lidar signal simulation for the evaluation of aerosols in chemistry-transport models

    Directory of Open Access Journals (Sweden)

    S. Stromatas

    2012-06-01

    Full Text Available We present an adaptable tool, the OPTSIM (OPTical properties SIMulation software, for the simulation of optical properties and lidar attenuated backscattered profiles (β' from aerosol concentrations calculated by chemistry-transport models (CTM. It was developed to support model evaluation using an original approach based on the lidar Level 1 observations (β', avoiding the use of Level 2 aerosol retrievals which include specific assumptions on aerosol types that may not be in agreement with the CTM. In addition to an evaluation of the aerosol loading and optical properties, active remote sensing allows the analysis of aerosols' vertical structures. An academic case study for two different species (black carbon and dust is presented and shows the consistency of the simulator. Illustrations are then given through the analysis of dust events in the Mediterranean region during the summer 2007. These are based on simulations by the CHIMERE regional CTM and observations from the CALIOP space-based lidar, and highlight the potential of this approach to evaluate the concentration, size and vertical structure of the aerosol plumes.

  17. Error apportionment for atmospheric chemistry-transport models - a new approach to model evaluation

    Science.gov (United States)

    Solazzo, Efisio; Galmarini, Stefano

    2016-05-01

    In this study, methods are proposed to diagnose the causes of errors in air quality (AQ) modelling systems. We investigate the deviation between modelled and observed time series of surface ozone through a revised formulation for breaking down the mean square error (MSE) into bias, variance and the minimum achievable MSE (mMSE). The bias measures the accuracy and implies the existence of systematic errors and poor representation of data complexity, the variance measures the precision and provides an estimate of the variability of the modelling results in relation to the observed data, and the mMSE reflects unsystematic errors and provides a measure of the associativity between the modelled and the observed fields through the correlation coefficient. Each of the error components is analysed independently and apportioned to resolved processes based on the corresponding timescale (long scale, synoptic, diurnal, and intra-day) and as a function of model complexity.The apportionment of the error is applied to the AQMEII (Air Quality Model Evaluation International Initiative) group of models, which embrace the majority of regional AQ modelling systems currently used in Europe and North America.The proposed technique has proven to be a compact estimator of the operational metrics commonly used for model evaluation (bias, variance, and correlation coefficient), and has the further benefit of apportioning the error to the originating timescale, thus allowing for a clearer diagnosis of the processes that caused the error.

  18. MATCH–SALSA – Multi-scale Atmospheric Transport and CHemistry model coupled to the SALSA aerosol microphysics model – Part 1: Model description and evaluation

    Directory of Open Access Journals (Sweden)

    C. Andersson

    2014-05-01

    Full Text Available We have implemented the sectional aerosol dynamics model SALSA in the European scale chemistry-transport model MATCH (Multi-scale Atmospheric Transport and Chemistry. The new model is called MATCH–SALSA. It includes aerosol microphysics, with several formulations for nucleation, wet scavenging and condensation. The model reproduces observed higher particle number concentration (PNC in central Europe and lower concentrations in remote regions. The model PNC size distribution peak occurs at the same or smaller particle size as the observed peak at five measurement sites spread across Europe. Total PNC is underestimated at Northern and Central European sites and accumulation mode PNC is underestimated at all investigated sites. On the other hand the model performs well for particle mass, including secondary inorganic aerosol components. Elemental and organic carbon concentrations are underestimated at many of the sites. Further development is needed, primarily for treatment of secondary organic aerosol, both in terms of biogenic emissions and chemical transformation, and for nitrogen gas-particle partitioning. Updating the biogenic SOA scheme will likely have a large impact on modeled PM2.5 and also affect the model performance for PNC through impacts on nucleation and condensation. An improved nitrogen partitioning model may also improve the description of condensational growth.

  19. Bad chemistry

    OpenAIRE

    Petsko, Gregory A

    2004-01-01

    General chemistry courses haven't changed significantly in forty years. Because most basic chemistry students are premedical students, medical schools have enormous influence and could help us start all over again to create undergraduate chemistry education that works.

  20. Regional scale effects of the aerosol cloud interaction simulated with an online coupled comprehensive chemistry model

    Directory of Open Access Journals (Sweden)

    M. Bangert

    2011-01-01

    Full Text Available We have extended the coupled mesoscale atmosphere and chemistry model COSMO-ART to account for the transformation of aerosol particles into cloud condensation nuclei and to quantify their interaction with warm cloud microphysics on the regional scale. The new model system aims to fill the gap between cloud resolving models and global scale models. It represents the very complex microscale aerosol and cloud physics as detailed as possible, whereas the continental domain size and efficient codes will allow for both studying weather and regional climate. The model system is applied in a first extended case study for Europe for a cloudy five day period in August 2005.

    The model results show that the mean cloud droplet number concentration of clouds is correlated with the structure of the terrain, and we present a terrain slope parameter TS to classify this dependency. We propose to use this relationship to parameterise the PDF of subgrid-scale cloud updraft velocity in the activation parameterisations of climate models.

    The simulations show that the presence of CCN and clouds are closely related spatially. We find high aerosol and CCN number concentrations in the vicinity of clouds at high altitudes. The nucleation of secondary particles is enhanced above the clouds. This is caused by an efficient formation of gaseous aerosol precursors above the cloud due to more available radiation, transport of gases in clean air above the cloud, and humid conditions. Therefore the treatment of complex photochemistry is crucial in atmospheric models to simulate the distribution of CCN.

    The mean cloud droplet number concentration and droplet diameter showed a close link to the change in the aerosol. To quantify the net impact of an aerosol change on the precipitation we calculated the precipitation susceptibility β for the whole model domain over a period of two days with an hourly resolution. The distribution function of

  1. Isoprene concentrations over Russia: ground-based measurements and chemistry-transport modeling

    Science.gov (United States)

    Berezina, Elena; Konovalov, Igor; Berezin, Evgeny; Skorokhod, Andrey; Elansky, Nikolay; Belikov, Igor

    2016-04-01

    Near-surface isoprene concentration was measured over Russia using the proton mass spectrometry method (PTR-MS) in TROICA (TRanscontinental Observations Into the Chemistry of the Atmosphere) experiments along the Trans-Siberian railway from 21.06.08 to 04.08.08 (TROICA-12) and from 08.10.09 to 23.10.09 (TROICA-13). The highest isoprene concentration is observed in the Far East (up to 3 ppb) due to the emissions from the major isoprene source - deciduous forests. The TROICA measurements were compared to the corresponding simulations performed with the CHIMERE chemistry transport model (CTM) using the MEGAN biogenic emission inventory. Simulated and measured isoprene concentrations are highly correlated (r = 0.8), but the simulated isoprene concentration is about 4-6 times higher than the measured one. The selection of daytime and background (from isoprene/benzene ratios) isoprene concentrations don't significantly increase the experimental values; moreover, even the isoprene concentration corrected for atmospheric photochemical losses (that is, the near-source concentration) is found to be 1.5 times lower than the simulated data. Therefore, the systematic discrepancy between the measurements and simulations could not be unambiguously attributed to the representativity error. The weak exponential dependence of summer isoprene concentration on temperature both for the model (R2 = 0.3) and for the experimental data (R2 = 0.4) is observed. However, a much stronger linear correlation (r ~ 0.9) is found between the isoprene concentration and temperature in Russian regions separated according to the type of vegetation. The differences between the simulated and experimental dependences of isoprene concentration on temperature are not statistically significant. The above results prompt the conclusion that the parameterization of isoprene emissions in the CHIMERE CTM is qualitatively adequate, but the isoprene emission factors applicable for Russian forest are likely

  2. Wexler's Great Smoke Pall: a chemistry-climate model analysis of a singularly large emissions pulse

    Science.gov (United States)

    Field, R. D.; Voulgarakis, A.

    2011-12-01

    We model the effects of the smoke plume from what was arguably the largest forest fire in recorded history. The Chinchaga fire burned continuously during the summer of 1950 in northwestern Canada during a very dry fire season. On September 22nd, the fire made a major advance, burning an area of approximately 1400 km2. Ground and aircraft observations showed that from September 22 to 28, the smoke plume from the emissions pulse travelled over northern Canada, southward over the Great Lakes region and eastern US, across the Atlantic, and to Western Europe. Over the Great Lakes region, the plume remained thick enough to create twilight conditions in the mid-afternoon, and was estimated to have caused a 4 oC cooling at the surface. While many instances of long-range transport of wildfire emissions have been detected over the past decade, we know of no other wildfire which created such an acute effect on downward shortwave radiation at such a long distance. As a result, the fire was an important analogue event used in estimating the effects of a nuclear winter. Simulations with the nudged version of the GISS chemistry-climate model accurately capture the long-range transport pattern of the smoke emissions in the free-troposphere. The timing and location of aircraft observations of the plume over the eastern US, North Atlantic and the United Kingdom were well-matched to modeled anomalies of CO and aerosol optical depth. Further work will examine the model's ability to create twilight conditions during the day, and to provide an estimate of the consequent cooling effects at the surface from this remarkable emissions pulse.

  3. Nitrogen oxide chemistry in an urban plume: investigation of the chemistry of peroxy and multifunctional organic nitrates with a Lagrangian model

    Directory of Open Access Journals (Sweden)

    I. M. Pérez

    2009-12-01

    Full Text Available Air quality in the outflow from urban centers affects millions of people, as well as, natural and managed ecosystems downwind. In locations where there are large sources of biogenic VOCs downwind of urban centers, the outflow is characterized by a high VOC reactivity due to biogenic emissions and low NOx. However most field and chamber studies have focused on limiting cases of high NOx or of near zero NOx. Recent measurements of a wide suite of VOCs, O3 and meteorological parameters at several locations within the Sacramento urban plume have provided a detailed benchmark for testing our understanding of chemistry in a plume transitioning from high NOx to low NOx and high VOC reactivity. As an additional simplification, the strong mountain valley circulation in the region makes this urban plume a physical realization of a nearly idealized Lagrangian plume. Here, we describe a model of this plume. We use a Lagrangian model representing chemistry based on the Master Chemical Mechanism (MCM v3.1 along with mixing and deposition. We discuss the effects of entrainment of background air, the branching ratio for the production of isoprene nitrates and the effects of soil NOx emissions on the composition of the evolving plume. The model predicts that after 2–3 h of chemical processing only 45% of the peroxynitrates (ΣPNs are PAN and that most (69% RONO2 are secondary alkyl nitrate products of the reaction of OH with RONO2. We find the model is more consistent with the observations if: a the yield of ΣPNs from large and multi-functional aldehydes is close to zero; and b the reaction between OH and RONO2 produces multifunctional nitrates as opposed to either HNO3 or NO2 as is typical in most currently adopted reaction mechanisms. Model results also show that adding NOx emissions throughout the transect increases

  4. MATCH-SALSA - Multi-scale Atmospheric Transport and CHemistry model coupled to the SALSA aerosol microphysics model - Part 1: Model description and evaluation

    Science.gov (United States)

    Andersson, C.; Bergström, R.; Bennet, C.; Robertson, L.; Thomas, M.; Korhonen, H.; Lehtinen, K. E. J.; Kokkola, H.

    2015-02-01

    We have implemented the sectional aerosol dynamics model SALSA (Sectional Aerosol module for Large Scale Applications) in the European-scale chemistry-transport model MATCH (Multi-scale Atmospheric Transport and Chemistry). The new model is called MATCH-SALSA. It includes aerosol microphysics, with several formulations for nucleation, wet scavenging and condensation. The model reproduces observed higher particle number concentration (PNC) in central Europe and lower concentrations in remote regions. The modeled PNC size distribution peak occurs at the same or smaller particle size as the observed peak at four measurement sites spread across Europe. Total PNC is underestimated at northern and central European sites and accumulation-mode PNC is underestimated at all investigated sites. The low nucleation rate coefficient used in this study is an important reason for the underestimation. On the other hand, the model performs well for particle mass (including secondary inorganic aerosol components), while elemental and organic carbon concentrations are underestimated at many of the sites. Further development is needed, primarily for treatment of secondary organic aerosol, in terms of biogenic emissions and chemical transformation. Updating the biogenic secondary organic aerosol (SOA) scheme will likely have a large impact on modeled PM2.5 and also affect the model performance for PNC through impacts on nucleation and condensation.

  5. Implementation and evaluation of online gas-phase chemistry within a regional climate model (RegCM-CHEM4)

    Energy Technology Data Exchange (ETDEWEB)

    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.

  6. Implementation and evaluation of online gas-phase chemistry within a regional climate model (RegCM-CHEM4

    Directory of Open Access Journals (Sweden)

    A. K. Shalaby

    2012-01-01

    Full Text Available 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 six-year 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.

  7. A linear CO chemistry parameterization in a chemistry-transport model: evaluation and application to data assimilation

    Directory of Open Access Journals (Sweden)

    M. Claeyman

    2010-03-01

    Full Text Available This paper presents an evaluation of a new linear parameterization valid for the troposphere and the stratosphere, based on a first order approximation of the carbon monoxide (CO continuity equation. This linear scheme (hereinafter noted LINCO has been implemented in the 3-D Chemical Transport Model (CTM MOCAGE of Météo-France. On the one hand, a one and a half years of LINCO simulation has been compared to output obtained from a detailed chemical scheme output. In spite of small differences, the seasonal and global CO distributions obtained by both schemes present similar general characteristics. The mean differences between both schemes remain small within about ±25 ppbv (part per billion by volume in the troposphere and ±15 ppbv in the stratosphere. On the other hand, LINCO has been compared to diverse observations from satellite instruments covering the troposphere (Measurements Of Pollution In The Troposphere: MOPITT and the stratosphere (Microwave Limb Sounder: MLS and also from aircraft (Measurements of ozone and water vapour by Airbus in-service aircraft: MOZAIC programme mostly flying in the upper troposphere and lower stratosphere. A good agreement is generally found in the troposphere and the lower stratosphere. In the troposphere, the LINCO seasonal variations as well as the vertical and horizontal distributions are quite close to MOPITT CO observations. However, a bias of ~−40 ppbv is observed at 700 hPa between LINCO and MOPITT which is probably caused by too low emission values. In the stratosphere, MLS and LINCO present similar large-scale patterns, except over the poles where the CO concentration is underestimated by the model. We suggest that the underestimation of CO at polar latitudes is not related to the linear scheme but is induced by a too rapid transport by the meridional circulation. In the UTLS (Upper Troposphere Lower Stratosphere, LINCO tends to slightly overestimate the MOZAIC aircraft observations, with

  8. Modeling lightning-NOx chemistry on a sub-grid scale in a global chemical transport model

    Science.gov (United States)

    Gressent, Alicia; Sauvage, Bastien; Cariolle, Daniel; Evans, Mathew; Leriche, Maud; Mari, Céline; Thouret, Valérie

    2016-05-01

    For the first time, a plume-in-grid approach is implemented in a chemical transport model (CTM) to parameterize the effects of the nonlinear reactions occurring within high concentrated NOx plumes from lightning NOx emissions (LNOx) in the upper troposphere. It is characterized by a set of parameters including the plume lifetime, the effective reaction rate constant related to NOx-O3 chemical interactions, and the fractions of NOx conversion into HNO3 within the plume. Parameter estimates were made using the Dynamical Simple Model of Atmospheric Chemical Complexity (DSMACC) box model, simple plume dispersion simulations, and the 3-D Meso-NH (non-hydrostatic mesoscale atmospheric model). In order to assess the impact of the LNOx plume approach on the NOx and O3 distributions on a large scale, simulations for the year 2006 were performed using the GEOS-Chem global model with a horizontal resolution of 2° × 2.5°. The implementation of the LNOx parameterization implies an NOx and O3 decrease on a large scale over the region characterized by a strong lightning activity (up to 25 and 8 %, respectively, over central Africa in July) and a relative increase downwind of LNOx emissions (up to 18 and 2 % for NOx and O3, respectively, in July). The calculated variability in NOx and O3 mixing ratios around the mean value according to the known uncertainties in the parameter estimates is at a maximum over continental tropical regions with ΔNOx [-33.1, +29.7] ppt and ΔO3 [-1.56, +2.16] ppb, in January, and ΔNOx [-14.3, +21] ppt and ΔO3 [-1.18, +1.93] ppb, in July, mainly depending on the determination of the diffusion properties of the atmosphere and the initial NO mixing ratio injected by lightning. This approach allows us (i) to reproduce a more realistic lightning NOx chemistry leading to better NOx and O3 distributions on the large scale and (ii) to focus on other improvements to reduce remaining uncertainties from processes related to NOx chemistry in CTM.

  9. Simulation of polar stratospheric clouds in the chemistry-climate-model EMAC via the submodel PSC

    Directory of Open Access Journals (Sweden)

    O. Kirner

    2010-11-01

    Full Text Available The submodel PSC of the ECHAM5/MESSy Atmospheric Chemistry model (EMAC has been developed to simulate the main types of polar stratospheric clouds (PSC. The parameterisation of the supercooled ternary solutions (STS, type 1b PSC in the submodel is based on Carslaw et al. (1995b, the thermodynamical approach to simulate ice particles (type 2 PSC on Marti and Mauersberger (1993. For the formation of nitric acid trihydrate (NAT particles (type 1a PSC two different parameterisations exist. The first one is based on an instantaneous thermodynamical approach from Hanson and Mauersberger (1988, the second one (new implemented by Kirner, 2008 considers the growth of the NAT particles with aid of a surface growth factor based on Carslaw et al. (2002. Via namelist switches the NAT parameterisation, as well as some parameters for the NAT and ice formation can be chosen. This publication explains the background of the submodel PSC and the use of the submodel with the goal to simulate realistic PSC in EMAC.

  10. One-dimensional numerical modeling of Blue Jet and its impact on stratospheric chemistry

    Science.gov (United States)

    Duruisseau, F.; Thiéblemont, R.; Huret, N.

    2011-12-01

    In the stratosphere the ozone layer is very sensitive to the NOx abundance. The ionisation of N2 and O2 molecules by TLE's (Transient Luminous Events) is a source of NOx which is currently not well quantified and could act as a loss of ozone. In this study a one dimensional explicit parameterization of a Blue-Jet propagation based on that proposed by Raizer et al. (2006 and 2007) has been developed. This parameterization considers Blue-Jet as a streamer initiated by a bidirectional leader discharge, emerging from the anvil and sustained by moderate cloud charge. The streamer growth varies with the electrical field induced by initial cloud charge and the initial altitude. This electrical parameterization and the chemical mechanisms associated with the discharge have been implemented into a detailed chemical model of stratospheric ozone including evolution of nitrogen, chlorine and bromine species. We will present several tests performed to validate the electrical code and evaluate the propagation velocity and the maximum altitude attains by the blue jet as a function of electrical parameters. The results obtained giving the spatiotemporal evolution of the electron density are then used to initiate the specific chemistry associated with the Blue Jet. Preliminary results on the impact of such discharge on the ozone content and the whole stratospheric system will be presented.

  11. Numerical study on the ozone formation inside street canyons using a chemistry box model

    Institute of Scientific and Technical Information of China (English)

    Chun-Ho Liu; Dennis Y. C. Leung

    2008-01-01

    Tropospheric ozone is a secondary air pollutant produced in the presence of nitrogen oxides, volatile organic compounds (VOCs), and solar radiation. In an urban environment, ground-level vehicular exhaust is the major anthropogenic source of ozone precursors. In the cases of street canyons, pollutant dilution is weakened by the surrounding buildings that create localized high concentration of nitrogen oxides and VOCs, and thus leads to high potential of ozone formation. By considering the major physical and chemical processes, a chemistry box model is employed to investigate the characteristics of ozone formation due to vehicular exhaust inside street canyons under the worst case scenario, i.e. the calm wind condition. It is found that a high level of ozone concentration, of the order of 100 ppbv and higher, would occur inside the street canyons, in particular, when the emission rate (concentration) ratio of VOCs to nitrogen oxides is greater than 10. This elevated ozone concentration appears at the transition from VOCs to nitrogen oxides sensitivity and may extend to a few hundreds.

  12. Review of the materials-chemistry models in the VICTORIA code

    Science.gov (United States)

    Olander, D. R.; Mubayi, Vinod

    Recently a Peer Review Committee established by the US Nuclear Regulatory Commission issued its report on VICTORIA, a detailed mechanistic computer code that addresses the release of fission products from degraded reactor fuel and the ex-core behavior of the released material. The present paper summarizes the findings of the report relevant to the materials-chemistry aspects of the code that apply chiefly to the high-temperature, steam-hydrogen environment of the degrading fuel and cladding. In addition to reviewing the theoretical foundation of the mechanisms used in the code, the assessment utilizes the `test problem' technique. In this method, the code (or its methods) are applied to very simple fuel and cladding systems with variations of input conditions, code flags, and material properties. The output is judged against expected behavior for each change. The topics treated include the thermochemical database, the code's method of treating interphase equilibria, the model of fission product release, and the treatment of cladding oxidation and hydrogen production.

  13. A green chemistry-based classification model for the synthesis of silver nanoparticles

    Science.gov (United States)

    The assessment of implementation of green chemistry principles in the synthesis of nanomaterials is a complex decision-making problem that necessitates integration of several evaluation criteria. Multiple Criteria Decision Aiding (MCDA) provides support for such a challenge. One ...

  14. An Adaptive Chemistry Approach to Modeling Emissions Performance of Gas Turbine Combustors Project

    Data.gov (United States)

    National Aeronautics and Space Administration — In this proposed SBIR project, we seek to implement the Adaptive Chemistry methodology in existing CFD codes used to investigate the emissions performance of gas...

  15. Predicting tropospheric ozone and hydroxyl radical in a global, three-dimensional, chemistry, transport, and deposition model

    Energy Technology Data Exchange (ETDEWEB)

    Atherton, C.S.

    1995-01-05

    Two of the most important chemically reactive tropospheric gases are ozone (O{sub 3}) and the hydroxyl radical (OH). Although ozone in the stratosphere is a necessary protector against the sun`s radiation, tropospheric ozone is actually a pollutant which damages materials and vegetation, acts as a respiratory irritant, and is a greenhouse gas. One of the two main sources of ozone in the troposphere is photochemical production. The photochemistry is initiated when hydrocarbons and carbon monoxide (CO) react with nitrogen oxides (NO{sub x} = NO + NO{sub 2}) in the presence of sunlight. Reaction with the hydroxyl radical, OH, is the main sink for many tropospheric gases. The hydroxyl radical is highly reactive and has a lifetime on the order of seconds. Its formation is initiated by the photolysis of tropospheric ozone. Tropospheric chemistry involves a complex, non-linear set of chemical reactions between atmospheric species that vary substantially in time and space. To model these and other species on a global scale requires the use of a global, three-dimensional chemistry, transport, and deposition (CTD) model. In this work, I developed two such three dimensional CTD models. The first model incorporated the chemistry necessary to model tropospheric ozone production from the reactions of nitrogen oxides with carbon monoxide (CO) and methane (CH{sub 4}). The second also included longer-lived alkane species and the biogenic hydrocarbon isoprene, which is emitted by growing plants and trees. The models` ability to predict a number of key variables (including the concentration of O{sub 3}, OH, and other species) were evaluated. Then, several scenarios were simulated to understand the change in the chemistry of the troposphere since preindustrial times and the role of anthropogenic NO{sub x} on present day conditions.

  16. LES of a Meso Combustion Chamber with a Detailed Chemistry Model: Comparison between the Flamelet and EDC Models

    Directory of Open Access Journals (Sweden)

    Angelo Minotti

    2010-12-01

    Full Text Available The goal of this paper is to contribute to the design of high-performance mesocombustors, a field currently under rapid development, in particular for propulsion, e.g., for UAVs, and micro/meso-electrical power generators. This study is focused on a cylindrical combustor of 29 cm3, fuelled by methane and air, which provides 2 kW of thermal power. The device was entirely designed and built at the Sapienza University of Rome and coupled with an ultra-micro turbine. Two 3D LES simulations with detailed chemistry are presented. They differ only for the combustion models, so that a model comparison can be carried out. The calculated maximum temperature inside the chamber, the gas exhaust temperature and the combustion efficiency are compared and discussed. The results, reported at two different physical times, show the effects of the different combustion models, which predict different temperature and species concentration maps, but similar values for the combustion efficiency. Thermal, chemical and kinematic maps show that the Eddy Dissipation Concept allows for a more accurate estimatation of the performance parameters for application to first-order design procedures.

  17. Comparing in Cylinder Pressure Modelling of a DI Diesel Engine Fuelled on Alternative Fuel Using Two Tabulated Chemistry Approaches.

    Science.gov (United States)

    Ngayihi Abbe, Claude Valery; Nzengwa, Robert; Danwe, Raidandi

    2014-01-01

    The present work presents the comparative simulation of a diesel engine fuelled on diesel fuel and biodiesel fuel. Two models, based on tabulated chemistry, were implemented for the simulation purpose and results were compared with experimental data obtained from a single cylinder diesel engine. The first model is a single zone model based on the Krieger and Bormann combustion model while the second model is a two-zone model based on Olikara and Bormann combustion model. It was shown that both models can predict well the engine's in-cylinder pressure as well as its overall performances. The second model showed a better accuracy than the first, while the first model was easier to implement and faster to compute. It was found that the first method was better suited for real time engine control and monitoring while the second one was better suited for engine design and emission prediction.

  18. Multilayer modeling of porous grain surface chemistry I. The GRAINOBLE model

    CERN Document Server

    Taquet, Vianney; Kahane, Claudine

    2011-01-01

    Mantles of iced water, mixed with CO, H2CO, and CH3OH are formed during the so called prestellar core phase. In addition, radicals are also thought to be formed on the grain surfaces, and to react to form complex organic molecules later on, during the warm-up phase of the protostellar evolution. The aim of this work is to study the formation of the grain mantles during the prestellar core phase and the abundance of H2CO, CH3OH, and radicals trapped in them. We have developed a macrosopic statistic multilayer model that follows the formation of grain mantles with time and that includes two effects that may increase the number of radicals trapped in the mantles: i) at each time of the mantle formation, only the surface layer is chemically active rather than the entire bulk, and ii) the porous structure of grains allows to trap reactive particles. The model considers a network of H, O and CO forming neutral species such as water, CO, formaldehyde, and methanol, plus several radicals. We run a large grid of model...

  19. Surface chemistry and size influence the release of model therapeutic nanoparticles from poly(ethylene glycol) hydrogels

    International Nuclear Information System (INIS)

    Nanoparticles have emerged as promising therapeutic and diagnostic tools, due to their unique physicochemical properties. The specific core and surface chemistries, as well as nanoparticle size, play critical roles in particle transport and interaction with biological tissue. Localized delivery of therapeutics from hydrogels is well established, but these systems generally release molecules with hydrodynamic radii less than ∼5 nm. Here, model nanoparticles with biologically relevant surface chemistries and diameters between 10 and 35 nm are analyzed for their release from well-characterized hydrogels. Functionalized gold nanoparticles or quantum dots were encapsulated in three-dimensional poly(ethylene glycol) hydrogels with varying mesh size. Nanoparticle size, surface chemistry, and hydrogel mesh size all influenced the release of particles from the hydrogel matrix. Size influenced nanoparticle release as expected, with larger particles releasing at a slower rate. However, citrate-stabilized gold nanoparticles were not released from hydrogels. Negatively charged carboxyl or positively charged amine-functionalized quantum dots were released from hydrogels at slower rates than neutrally charged PEGylated nanoparticles of similar size. Transmission electron microscopy images of gold nanoparticles embedded within hydrogel sections demonstrated uniform particle distribution and negligible aggregation, independent of surface chemistry. The nanoparticle-hydrogel interactions observed in this work will aid in the development of localized nanoparticle delivery systems.

  20. Development of prognostic aerosol–cloud interactions combining a chemistry transport model and a regional climate model

    Directory of Open Access Journals (Sweden)

    M. A. Thomas

    2015-02-01

    Full Text Available To reduce uncertainties and hence, to obtain a better estimate of aerosol (direct and indirect radiative forcing, next generation climate models aim for a tighter coupling between chemistry transport models and regional climate models and a better representation of aerosol–cloud interactions. In this study, this coupling is done by first forcing the Rossby Center regional climate model, RCA4 by ERA-Interim lateral boundaries (LBCs and SST using the standard CDNC (cloud droplet number concentration formulation (hereafter, referred to as the "stand-alone RCA4 version" or "CTRL" simulation. In this simulation, the CDNCs are assigned fixed numbers based on if the underlying surface is land or oceanic. The meteorology from this simulation is then used to drive the chemistry transport model, MATCH which is coupled online with the aerosol dynamics model, SALSA. CDNC fields obtained from MATCH-SALSA are then fed back into a new RCA4 simulation. In this new simulation (referred to as "MOD" simulation, all parameters remain the same as in the first run except for the CDNCs provided by MATCH-SALSA. Simulations are carried out with this model set up for the period 2005–2012 over Europe and the differences in cloud microphysical properties and radiative fluxes as a result of local CDNC changes and possible model responses are analyzed. Our study shows substantial improvements in the cloud microphysical properties with the input of the MATCH-SALSA derived 3-D CDNCs compared to the stand-alone RCA4 version. This model set up improves the spatial, seasonal and vertical distribution of CDNCs with higher concentration observed over central Europe during summer half of the year and over Eastern Europe and Russia during the winter half of the year. Realistic cloud droplet radii (CD radii values have been simulated with the maxima reaching 13 μm whereas in the stand-alone version, the values reached only 5 μm. A substantial improvement in the distribution of

  1. Mathematical Chemistry

    OpenAIRE

    Trinajstić, Nenad; Gutman, Ivan

    2002-01-01

    A brief description is given of the historical development of mathematics and chemistry. A path leading to the meeting of these two sciences is described. An attempt is made to define mathematical chemistry, and journals containing the term mathematical chemistry in their titles are noted. In conclusion, the statement is made that although chemistry is an experimental science aimed at preparing new compounds and materials, mathematics is very useful in chemistry, among other things, to produc...

  2. Gas-phase chemistry in the online multiscale NMMB/BSC Chemical Transport Model: Description and evaluation at global scale

    OpenAIRE

    Badia, Alba; JORBA Oriol; Voulgarakis, Apostolos; Dabdub, Donald; Pérez, Carlos; Hilboll, Andreas; Gonçalves, María; Janjic, Zavisa

    2016-01-01

    This paper presents a comprehensive description and benchmark evaluation of the tropospheric gas-phase chemistry component of the NMMB/BSC Chemical Transport Model (NMMB/BSC-CTM), an online chemical weather prediction system conceived for both the regional and the global scale. We provide an extensive evaluation of a global annual cycle simulation using a variety of background surface stations (EMEP, WDCGG and CASTNET), ozonesondes (WOUDC, CMD and SHADOZ), aircraft data (MOZAIC and several ca...

  3. The description and validation of the computationally Efficient CH4–CO–OH (ECCOHv1.01) chemistry module for 3-D model applications

    OpenAIRE

    Elshorbany, Yasin F.; Duncan, Bryan N.; Strode, Sarah A.; Wang, James S.; Kouatchou, Jules

    2016-01-01

    We present the Efficient CH4–CO–OH (ECCOH) chemistry module that allows for the simulation of the methane, carbon monoxide, and hydroxyl radical (CH4–CO–OH) system, within a chemistry climate model, carbon cycle model, or Earth system model. The computational efficiency of the module allows many multi-decadal sensitivity simulations of the CH4–CO–OH system, which primarily determines the global atmospheric oxidizing capacity. This capability is important for capturing the no...

  4. Development of a grid-independent GEOS-chem chemical transport model as an atmospheric chemistry module for Earth System Models

    Science.gov (United States)

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

    2014-11-01

    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 Modelling 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 via the ESMF. 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 MPI parallelization. Numerical experiments demonstrate that the GEOS-Chem chemistry module scales efficiently for the number of processors tested. 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 MPI processes.

  5. Development of a grid-independent GEOS-Chem chemical transport model (v9-02) as an atmospheric chemistry module for Earth system models

    Science.gov (United States)

    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.

  6. Assessing the Chemistry of Tidally Locked Earth-like Planets around M-type Stars Using a 3D Coupled Chemistry-Climate Model (CESM/WACCM)

    Science.gov (United States)

    Lanzano, Alexander

    2016-10-01

    Given recent discoveries there is a very real potential for tidally-locked Earth-like planets to exist orbiting M stars. To determine whether these planets may be habitable it is necessary to understand the nature of their atmospheres. In our investigation we simulate the evolution of present-day Earth while placed in tidally-locked orbit (meaning the same side of the planet always faces the star) around an M dwarf star. We are particularly interested in the evolution of the planet's ozone layer and whether it will shield the planet, and therefore life, from harmful radiation.To accomplish the above objectives we use a state-of-the-art 3-D terrestrial model, the Whole Atmosphere Community Climate Model (WACCM), which fully couples chemistry and climate, and therefore allows self-consistent simulations of atmospheric constituents and their effects on a planet's climate, surface radiation and thus habitability. Preliminary results show that this model is stable and that a tidally-locked Earth is protected from harmful UV radiation produced by G stars. The next step shall be to adapt this model for an M star by including its UV and visible spectrum.This investigation will both provide an insight into the potential for habitable exoplanets and further define the nature of the habitable zones for M class stars. We will also be able to narrow the definition of the habitable zones around distant stars, which will help us identify these planets in the future. Furthermore, this project will allow for a more thorough analysis of data from past and future exoplanet observing missions by defining the atmospheric composition of Earth-like planets around a variety of types of stars.

  7. Simulating organic species with the global atmospheric chemistry general circulation model ECHAM5/MESSy1: a comparison of model results with observation

    NARCIS (Netherlands)

    Pozzer, A.; Jöckel, P.; Tost, H.; Sander, R.; Ganzeveld, L.N.; Kerkweg, A.; Lelieveld, J.

    2007-01-01

    The atmospheric-chemistry general circulation model ECHAM5/MESSy1 is evaluated with observations of different organic ozone precursors. This study continues a prior analysis which focused primarily on the representation of atmospheric dynamics and ozone. We use the results of the same reference simu

  8. Use of chemistry software to teach and assess model-based reaction and equation knowledge

    Directory of Open Access Journals (Sweden)

    Kevin Pyatt

    2014-12-01

    Full Text Available This study investigated the challenges students face when learning chemical reactions in a first-year chemistry course and the effectiveness of a curriculum and software implementation that was used to teach and assess student understanding of chemical reactions and equations. This study took place over a two year period in a public suburban high-school, in southwestern USA. Two advanced placement (AP chemistry classes participated, referred to here as study group A (year 1, N = 14; and study group B (year 2, N = 21. The curriculum for a first-year chemistry course (group A was revised to include instruction on reaction-types. The second year of the study involved the creation and implementation of a software solution which promoted mastery learning of reaction-types. Students in both groups benefited from the reaction-type curriculum and achieved proficiency in chemical reactions and equations.  The findings suggest there was an added learning benefit to using the reaction-type software solution. This study also found that reaction knowledge was a moderate to strong predictor of chemistry achievement. Based on regression analysis, reaction knowledge significantly predicted chemistry achievement for both groups.

  9. he Impact of Primary Marine Aerosol on Atmospheric Chemistry, Radiation and Climate: A CCSM Model Development Study

    Energy Technology Data Exchange (ETDEWEB)

    Keene, William C. [University of Virginia; Long, Michael S. [University of Virginia

    2013-05-20

    This project examined the potential large-scale influence of marine aerosol cycling on atmospheric chemistry, physics and radiative transfer. Measurements indicate that the size-dependent generation of marine aerosols by wind waves at the ocean surface and the subsequent production and cycling of halogen-radicals are important but poorly constrained processes that influence climate regionally and globally. A reliable capacity to examine the role of marine aerosol in the global-scale atmospheric system requires that the important size-resolved chemical processes be treated explicitly. But the treatment of multiphase chemistry across the breadth of chemical scenarios encountered throughout the atmosphere is sensitive to the initial conditions and the precision of the solution method. This study examined this sensitivity, constrained it using high-resolution laboratory and field measurements, and deployed it in a coupled chemical-microphysical 3-D atmosphere model. First, laboratory measurements of fresh, unreacted marine aerosol were used to formulate a sea-state based marine aerosol source parameterization that captured the initial organic, inorganic, and physical conditions of the aerosol population. Second, a multiphase chemical mechanism, solved using the Max Planck Institute for Chemistry's MECCA (Module Efficiently Calculating the Chemistry of the Atmosphere) system, was benchmarked across a broad set of observed chemical and physical conditions in the marine atmosphere. Using these results, the mechanism was systematically reduced to maximize computational speed. Finally, the mechanism was coupled to the 3-mode modal aerosol version of the NCAR Community Atmosphere Model (CAM v3.6.33). Decadal-scale simulations with CAM v.3.6.33, were run both with and without reactive-halogen chemistry and with and without explicit treatment of particulate organic carbon in the marine aerosol source function. Simulated results were interpreted (1) to evaluate influences

  10. Investigations of Global Chemistry-Climate Interactions and Organic Aerosol Using Atmospheric Modeling

    Science.gov (United States)

    Pye, Havala Olson Taylor

    Aerosol, or particulate matter (PM), is an important component of the atmosphere responsible for negative health impacts, environmental degradation, reductions in visibility, and climate change. In this work, the global chemical transport model, GEOS-Chem, is used as a tool to examine chemistry-climate interactions and organic aerosols. GEOS-Chem is used to simulate present-day (year 2000) and future (year 2050) sulfate, nitrate, and ammonium aerosols and investigate the potential effects of changes in climate and emissions on global budgets and U.S. air quality. Changes in a number of meteorological parameters, such as temperature and precipitation, are potentially important for aerosols and could lead to increases or decreases in PM concentrations. Although projected changes in sulfate and nitrate precursor emissions favor lower PM concentrations over the U.S., projected increases in ammonia emissions could result in higher nitrate concentrations. The organic aerosol simulation in GEOS-Chem is updated to include aerosol from primary semivolatile organic compounds (SVOCS), intermediate volatility compounds (IVOCs), NOx dependent terpene aerosol, and aerosol from isoprene + NO3 reaction. SVOCs are identified as the largest global source of organic aerosol even though their atmospheric transformation is highly uncertain and emissions are probably underestimated. As a result of significant nighttime terpene emissions, fast reaction of monoterpenes with the nitrate radical, and high aerosol yields from NO3 oxidation, biogenic hydrocarbons reacting with the nitrate radical are expected to be a major contributor to surface level aerosol concentrations in anthropogenically influenced areas such as the United States. Globally, 69 to 88 Tg/yr of aerosol is predicted to be produced annually, approximately 22 to 24 Tg/yr of which is from biogenic hydrocarbons.

  11. Pore water chemistry reveals gradients in mineral transformation across a model basaltic hillslope

    Science.gov (United States)

    Pohlmann, Michael; Dontsova, Katerina; Root, Robert; Ruiz, Joaquin; Troch, Peter; Chorover, Jon

    2016-06-01

    The extent of weathering incongruency during soil formation from rock controls local carbon and nutrient cycling in ecosystems, as well as the evolution of hydrologic flow paths. Prior studies of basalt weathering, including those that have quantified the dynamics of well-mixed, bench-scale laboratory reactors or characterized the structure and integrated response of field systems, indicate a strong influence of system scale on weathering rate and trajectory. For example, integrated catchment response tends to produce lower weathering rates than do well mixed reactors, but the mechanisms underlying these disparities remain unclear. Here we present pore water geochemistry and physical sensor data gathered during two controlled rainfall-runoff events on a large-scale convergent model hillslope mantled with 1 m uniform depth of granular basaltic porous media. The dense sampler and sensor array (1488 samplers and sensors embedded in 330 m3 of basalt) showed that rainfall-induced dissolution of basaltic glass produced supersaturation of pore waters with respect to multiple secondary solids including allophane, gibbsite, ferrihydrite, birnessite and calcite. The spatial distribution of saturation state was heterogeneous, suggesting an accumulation of solutes leading to precipitation of secondary solids along hydrologic flow paths. Rapid dissolution of primary silicates was widespread throughout the entire hillslope, irrespective of up-gradient flowpath length. However, coherent spatial variations in solution chemistry and saturation indices were observed in depth profiles and between distinct topographic regions of the hillslope. Colloids (110-2000 nm) enriched in iron (Fe), aluminum (Al), and phosphorus (P) were mobile in soil pore waters.

  12. Satellite Observations and Chemistry Climate Models - A Meandering Path Towards Better Predictions

    Science.gov (United States)

    Douglass, Anne R.

    2011-01-01

    Knowledge of the chemical and dynamical processes that control the stratospheric ozone layer has grown rapidly since the 1970s, when ideas that depletion of the ozone layer due to human activity were put forth. The concept of ozone depletion due to anthropogenic chlorine increase is simple; quantification of the effect is much more difficult. The future of stratospheric ozone is complicated because ozone is expected to increase for two reasons: the slow decrease in anthropogenic chlorine due to the Montreal Protocol and its amendments and stratospheric cooling caused by increases in carbon dioxide and other greenhouse gases. Prediction of future ozone levels requires three-dimensional models that represent physical, photochemical and radiative processes, i.e., chemistry climate models (CCMs). While laboratory kinetic and photochemical data are necessary inputs for a CCM, atmospheric measurements are needed both to reveal physical and chemical processes and for comparison with simulations to test the conceptual model that CCMs represent. Global measurements are available from various satellites including but not limited to the LIMS and TOMS instruments on Nimbus 7 (1979 - 1993), and various instruments on the Upper Atmosphere Research Satellite (1991 - 2005), Envisat (2002 - ongoing), Sci-Sat (2003 - ongoing) and Aura (2004 - ongoing). Every successful satellite instrument requires a physical concept for the measurement, knowledge of physical chemical properties of the molecules to be measured, and stellar engineering to design an instrument that will survive launch and operate for years with no opportunity for repair but providing enough information that trend information can be separated from any instrument change. The on-going challenge is to use observations to decrease uncertainty in prediction. This talk will focus on two applications. The first considers transport diagnostics and implications for prediction of the eventual demise of the Antarctic ozone hole

  13. Aerosol–cloud interactions studied with the chemistry-climate model EMAC

    Directory of Open Access Journals (Sweden)

    D. Y. Chang

    2014-08-01

    Full Text Available This study uses the EMAC atmospheric chemistry-climate model to simulate cloud properties and estimate cloud radiative effects induced by aerosols. We have tested two prognostic cloud droplet nucleation parameterizations, i.e., the standard STN (osmotic coefficient model and hybrid (HYB, replacing the osmotic coefficient by the κ hygroscopicity parameter schemes to calculate aerosol hygroscopicity and critical supersaturation, and consider aerosol–cloud feedbacks with a focus on warm clouds. Both prognostic schemes (STN and HYB account for aerosol number, size and composition effects on droplet nucleation, and are tested in combination with two different cloud cover parameterizations, i.e., a relative humidity threshold and a statistical cloud cover scheme (RH-CLC and ST-CLC. The use of either STN and HYB leads to very different cloud radiative effects, particularly over the continents. The STN scheme predicts highly effective CCN activation in warm clouds and hazes/fogs near the surface. The enhanced CCN activity increases the cloud albedo effect of aerosols and cools the Earth's surface. The cooler surface enhances the hydrostatic stability of the lower continental troposphere and thereby reduces convection and convective precipitation. In contrast, the HYB simulations calculate lower, more realistic CCN activation and consequent cloud albedo effect, leading to relatively stronger convection and high cloud formation. The enhanced high clouds increase greenhouse warming and moderate the cooling effect of the low clouds. With respect to the cloud radiative effects, the statistical ST-CLC scheme shows much higher sensitivity to aerosol–cloud coupling for all continental regions than the RH-CLC threshold scheme, most pronounced for low clouds but also for high clouds. Simulations of the short wave cloud radiative effect at the top of the atmosphere in ST-CLC are a factor of 2–8 more sensitive to aerosol coupling than the RH

  14. A hydrochemical modelling framework for combined assessment of spatial and temporal variability in stream chemistry: application to Plynlimon, Wales

    Directory of Open Access Journals (Sweden)

    H.J. Foster

    2001-01-01

    Full Text Available Recent concern about the risk to biota from acidification in upland areas, due to air pollution and land-use change (such as the planting of coniferous forests, has generated a need to model catchment hydro-chemistry to assess environmental risk and define protection strategies. Previous approaches have tended to concentrate on quantifying either spatial variability at a regional scale or temporal variability at a given location. However, to protect biota from ‘acid episodes’, an assessment of both temporal and spatial variability of stream chemistry is required at a catchment scale. In addition, quantification of temporal variability needs to represent both episodic event response and long term variability caused by deposition and/or land-use change. Both spatial and temporal variability in streamwater chemistry are considered in a new modelling methodology based on application to the Plynlimon catchments, central Wales. A two-component End-Member Mixing Analysis (EMMA is used whereby low and high flow chemistry are taken to represent ‘groundwater’ and ‘soil water’ end-members. The conventional EMMA method is extended to incorporate spatial variability in the two end-members across the catchments by quantifying the Acid Neutralisation Capacity (ANC of each in terms of a statistical distribution. These are then input as stochastic variables to a two-component mixing model, thereby accounting for variability of ANC both spatially and temporally. The model is coupled to a long-term acidification model (MAGIC to predict the evolution of the end members and, hence, the response to future scenarios. The results can be plotted as a function of time and space, which enables better assessment of the likely effects of pollution deposition or land-use changes in the future on the stream chemistry than current methods which use catchment average values. The model is also a useful basis for further research into linkage between hydrochemistry

  15. NOx production due to energetic particle precipitation in the MLT region - results from an ion-chemistry model

    Science.gov (United States)

    Nieder, Holger; Sinnhuber, Miriam

    2013-04-01

    The chemistry in the mesosphere/lower thermosphere (MLT) region is driven by forcing from solar radiation and energetic particles. The resulting ionisation, dissociation and excitation of the constituents lead to production of neutral reactive species such as NOx (N, NO, NO2) and HOx (H, OH, HO2), both directly from dissociation of neutrals and indirectly from subsequent ion-neutral reactions. As NOx is long-lived during polar winter, it can be transported down to the stratosphere and contribute to catalytic ozone depletion. To study the effective NOx production rates during an ionisation event, runs with a one-dimensional state-of-the-art ion chemistry model (UBIC) are carried out and analysed. The model starts with a neutral atmosphere and uses direct ion and neutral production rates from Porter et al. (1976) and Rusch et al. (1981), adapted for the MLT region. Including raw ionisation rates from external sources such as AIMOS is possible. The ion-neutral reactions in the charged atmosphere are computed until equilibrium is reached, resulting in an effective production rate including impact of ion-neutral reactions. The indirect NOx production rate is found to depend on atmospheric parameters such as pressure, temperature and the abundance of NOx, atomic oxygen and H2O. For the MLT region, this leads to an increasing amount of NOx per ionpair created with increasing altitude due to an increasing atomic oxygen VMR. Values of >1.8 NOx per ionpair can be obtained. The results are made available to a 3D Chemistry Transport Model using a database-approach and multilinear interpolation for readout. Efficiency of this approach and first results from a 3D CTM using the ion-chemistry results are discussed.

  16. Modelling the chemistry and transport of bromoform within a sea breeze driven convective system during the SHIVA Campaign

    Directory of Open Access Journals (Sweden)

    P. D. Hamer

    2013-08-01

    Full Text Available We carry out a case study of the transport and chemistry of bromoform and its product gases (PGs in a sea breeze driven convective episode on 19 November 2011 along the North West coast of Borneo during the "Stratospheric ozone: Halogen Impacts in a Varying Atmosphere" (SHIVA campaign. We use ground based, ship, aircraft and balloon sonde observations made during the campaign, and a 3-D regional online transport and chemistry model capable of resolving clouds and convection explicitly that includes detailed bromine chemistry. The model simulates the temperature, wind speed, wind direction fairly well for the most part, and adequately captures the convection location, timing, and intensity. The simulated transport of bromoform from the boundary layer up to 12 km compares well to aircraft observations to support our conclusions. The model makes several predictions regarding bromine transport from the boundary layer to the level of convective detrainment (11 to 12 km. First, the majority of bromine undergoes this transport as bromoform. Second, insoluble organic bromine carbonyl species are transported to between 11 and 12 km, but only form a small proportion of the transported bromine. Third, soluble bromine species, which include bromine organic peroxides, hydrobromic acid (HBr, and hypobromous acid (HOBr, are washed out efficiently within the core of the convective column. Fourth, insoluble inorganic bromine species (principally Br2 are not washed out of the convective column, but are also not transported to the altitude of detrainment in large quantities. We expect that Br2 will make a larger relative contribution to the total vertical transport of bromine atoms in scenarios with higher CHBr3 mixing ratios in the boundary layer, which have been observed in other regions. Finally, given the highly detailed description of the chemistry, transport and washout of bromine compounds within our simulations, we make a series of recommendations about

  17. Evaluation of stratospheric chlorine chemistry for the Arctic spring 2005 using modelled and measured OClO column densities

    Directory of Open Access Journals (Sweden)

    H. Oetjen

    2011-01-01

    Full Text Available Chlorine dioxide, OClO, column amounts retrieved from measurements of the SCIAMACHY satellite instrument are presented and validated by comparison with simultaneous ground-based DOAS observations. In addition, the measurements are compared to model calculations taking into account the photochemical change along the light path.

    Although OClO does not participate directly in the destruction of ozone, its accurate measurement as well as modelling is crucial to understand the highly perturbed chlorine chemistry in the polar vortices. SCIAMACHY OClO slant columns retrieved during spring 2005 have been quantitatively validated by comparison with slant columns retrieved from measurements made in Ny-Ålesund (79° N, 12° E and Summit (73° N, 38° W as well qualitatively for Bremen (53° N, 9° E. Fair to good agreement is found depending on location as well as time of year.

    OClO slant column densities modelled with a set of stacked box models and considering the light path through the atmosphere are also included in this comparison. The model predictions differ significantly from the measured quantities. OClO amounts are underestimated for conditions of strong chlorine activation and at large solar zenith angles. Sensitivity studies for several parameters in the stacked box model have been performed and it is inferred that using the chemistry known to date, the observed OClO cannot be adequately reproduced within the range of uncertainties given for the various model parameters.

  18. Evaluation of stratospheric chlorine chemistry for the Arctic spring 2005 using modelled and measured OClO column densities

    Directory of Open Access Journals (Sweden)

    H. Oetjen

    2009-12-01

    Full Text Available Chlorine dioxide, OClO, column amounts retrieved from measurements of the SCIAMACHY satellite instrument are presented and validated by comparison with simultaneous ground-based DOAS observations. In addition, the measurements are compared to model calculations taking into account the photochemical change along the light path.

    Although OClO does not participate directly in the destruction of ozone, its accurate measurement as well as modelling is crucial to understand the highly perturbed chlorine chemistry in the polar vortices. SCIAMACHY OClO slant columns retrieved during spring 2005 have been quantitatively validated by comparison with slant columns retrieved from measurements made in Ny-Ålesund (79° N, 12° E, Summit (73° N, 38° W and Bremen (53° N, 9° E. Overall, good agreement is found.

    OClO slant column densities modelled with a set of stacked box models and considering the light path through the atmosphere are also included in this comparison. The model predictions differ significantly from the measured quantities. OClO amounts are underestimated for conditions of strong chlorine activation and at large solar zenith angles. Sensitivity studies for several parameters in the stacked box model have been performed and it is inferred that using the chemistry known to date, the observed OClO cannot be adequately reproduced within the range of uncertainties given for the various model parameters.

  19. Mathematical Modeling of Complex Reaction Systems for Computer-Aided Control and its Illustration on Atmospheric Chemistry

    Science.gov (United States)

    Amiryan, A.

    2015-12-01

    Modeling of sequential process has its own importance in Atmospheric Chemistry. Numerical calculations which allow to predict separate stages and components of chemical reaction make possible the reaction management, such is the new and perspective direction in chemical researches. Chemical processes basically pass multiple simple stages where various atoms and radicals participate. The complex chain of chemical reactionary systems complicates their research and the research is impossible without new methods of mathematical simulation and high technologies which allow not only to explain results of experiments but also to predict dynamics of processes. A new program package is suggested for solving research problems of chemical kinetics. The program is tested on different illustrative examples on Atmospheric Chemistry and installed in various scientific and educational institutions.

  20. A new version of the CNRM Chemistry-Climate Model, CNRM-CCM: description and improvements from the CCMVal-2 simulations

    OpenAIRE

    M. Michou; D. Saint-Martin; Teyssèdre, H.; Alias, A.; Karcher, F.; Olivié, D.; Voldoire, A.; B. Josse; Peuch, V.-H.; Clark, H.; Lee, J. N.; F. Chéroux

    2011-01-01

    This paper presents a new version of the Météo-France CNRM Chemistry-Climate Model, so-called CNRM-CCM. It includes some fundamental changes from the previous version (CNRM-ACM) which was extensively evaluated in the context of the CCMVal-2 validation activity. The most notable changes concern the radiative code of the GCM, and the inclusion of the detailed stratospheric chemistry of our Chemistry-Transport model MOCAGE on-line within the GCM. A 47-yr transient simulation (1960–2006) ...

  1. Exploring Atmospheric Aqueous Chemistry (and Secondary Organic Aerosol Formation) through OH Radical Oxidation Experiments, Droplet Evaporation and Chemical Modeling

    Science.gov (United States)

    Turpin, B. J.; Kirkland, J. R.; Lim, Y. B.; Ortiz-Montalvo, D. L.; Sullivan, A.; Häkkinen, S.; Schwier, A. N.; Tan, Y.; McNeill, V. F.; Collett, J. L.; Skog, K.; Keutsch, F. N.; Sareen, N.; Carlton, A. G.; Decesari, S.; Facchini, C.

    2013-12-01

    Gas phase photochemistry fragments and oxidizes organic emissions, making water-soluble organics ubiquitous in the atmosphere. My group and others have found that several water-soluble compounds react further in the aqueous phase forming low volatility products under atmospherically-relevant conditions (i.e., in clouds, fogs and wet aerosols). Thus, secondary organic aerosol can form as a result of gas followed by aqueous chemistry (aqSOA). We have used aqueous OH radical oxidation experiments coupled with product analysis and chemical modeling to validate and refine the aqueous chemistry of glyoxal, methylglyoxal, glycolaldehyde, and acetic acid. The resulting chemical model has provided insights into the differences between oxidation chemistry in clouds and in wet aerosols. Further, we conducted droplet evaporation experiments to characterize the volatility of the products. Most recently, we have conducted aqueous OH radical oxidation experiments with ambient mixtures of water-soluble gases to identify additional atmospherically-important precursors and products. Specifically, we scrubbed water-soluble gases from the ambient air in the Po Valley, Italy using four mist chambers in parallel, operating at 25-30 L min-1. Aqueous OH radical oxidation experiments and control experiments were conducted with these mixtures (total organic carbon ≈ 100 μM-C). OH radicals (3.5E-2 μM [OH] s-1) were generated by photolyzing H2O2. Precursors and products were characterized using electrospray ionization mass spectrometry (ESI-MS), ion chromatography (IC), IC-ESI-MS, and ultra high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Chemical modeling suggests that organic acids (e.g., oxalate, pyruvate, glycolate) are major products of OH radical oxidation at cloud-relevant concentrations, whereas organic radical - radical reactions result in the formation of oligomers in wet aerosols. Products of cloud chemistry and droplet evaporation have

  2. The Breath of Chemistry

    DEFF Research Database (Denmark)

    Josephsen, Jens

    The present preliminary text is a short thematic presentation in biological inorganic chemistry meant to illustrate general and inorganic (especially coordination) chemistry in biochemistry. The emphasis is on molecular models to explain features of the complicated mechanisms essential to breathing...

  3. Computational Modeling of the Optical Rotation of Amino Acids: An "in Silico" Experiment for Physical Chemistry

    Science.gov (United States)

    Simpson, Scott; Autschbach, Jochen; Zurek, Eva

    2013-01-01

    A computational experiment that investigates the optical activity of the amino acid valine has been developed for an upper-level undergraduate physical chemistry laboratory course. Hybrid density functional theory calculations were carried out for valine to confirm the rule that adding a strong acid to a solution of an amino acid in the l…

  4. Applying Modeling Instruction to High School Chemistry to Improve Students' Conceptual Understanding

    Science.gov (United States)

    Dukerich, Larry

    2015-01-01

    With the release of the Next Generation Science Standards, high school chemistry teachers are now pondering the implications of their recommendations for their teaching. They may agree that traditional instruction, as the Framework points out, "emphasizes discrete facts with a focus on breadth over depth, and does not provide students with…

  5. Earth System Chemistry Integrated Modelling (ESCiMo with the Modular Earth Submodel System (MESSy, version 2.51

    Directory of Open Access Journals (Sweden)

    P. Jöckel

    2015-10-01

    Full Text Available With version 2.51 of the ECHAM/MESSy Atmospheric Chemistry (EMAC model three types of reference simulations as recommended by the Chemistry-Climate Model Initiative (CCMI have been performed: hindcast simulations (1950–2011, hindcast simulations with specified dynamics (1978–2013, i.e., nudged towards ERA-Interim reanalysis data, and combined hindcast and projection simulations (1950–2100. The manuscript summarises the updates of the model system and details the different model setups used, including the on-line calculated diagnostics. Simulations have been performed with two different nudging setups, with and without interactive tropospheric aerosol, and with and without a coupled ocean model. Two different vertical resolutions have been applied. The on-line calculated sources and sinks of reactive species are quantified and a first evaluation of the simulation results from a global perspective is provided as a quality check of the data. The focus is on the inter-comparison of the different model setups. The simulation data will become publicly available via CCMI and the CERA database of the German Climate Computing Centre (DKRZ. This manuscript is intended to serve as an extensive reference for further analyses of the ESCiMo simulations.

  6. Modelling of a 400 kW natural gas diffusion flame using finite-rate chemistry schemes

    International Nuclear Information System (INIS)

    The Eddy-Dissipation Combustion Model combined with three different reaction mechanisms is applied to simulate a fuel-rich 400 kW natural gas diffusion flame. The chemical schemes include a global 2-step and a global 4-step approach as well as a reduced 4-step mechanism systematically derived from an elementary scheme. The species and temperature distributions resulting from the different schemes are studied in detail and compared to each other and to experiments. Furthermore the method of implementing finite-rate chemistry to the Eddy-Dissipation Combustion Model is discussed. (author)

  7. Modelling multi-phase halogen chemistry in the coastal marine boundary layer: investigation of the relative importance of local chemistry vs. long-range transport

    Directory of Open Access Journals (Sweden)

    D. Lowe

    2011-02-01

    Full Text Available Measurements of significant concentrations of IO, I2 and BrO in a semi-polluted coast environment at Roscoff, in North-West France, have been made as part of the Reactive Halogens in the Marine Boundary Layer (RHaMBLe campaign undertaken in September 2006. We use a one-dimensional column model, with idealised I2 emissions predicted using macroalgael maps and tidal data from the littoral area surrounding Roscoff, to investigate the probable causes for these observations. The coupled microphysical and chemical aerosol model simulates mixed-phase halogen chemistry using two separate particle modes, seasalt and non-seasalt, each comprising of eight size-sections. This work confirms the finding of a previous study that the BrO measurements are most likely caused by unknown, local sources. We find that the remote observations of IO and I2 are best replicated using the I2 recycling mechanism suggested by previous studies, but that such a mechanism is not wholly necessary. However in-situ measurements of I2 can only be explained by invoking an I2 recycling mechanism. We suggest that focussed observations of the changes in NOx and NOy concentrations, as well as changes in the nitrate fraction of the non-seasalt aerosol mode, in the presence of I2 bursts could be used to determine the atmospheric relevance of the predicted I2 recycling mechanism.

  8. Chemistry Notes

    Science.gov (United States)

    School Science Review, 1976

    1976-01-01

    Described are eight chemistry experiments and demonstrations applicable to introductory chemistry courses. Activities include: measure of lattice enthalpy, Le Chatelier's principle, decarboxylation of soap, use of pocket calculators in pH measurement, and making nylon. (SL)

  9. Colour Chemistry

    Science.gov (United States)

    Griffiths, J.; Rattee, I. D.

    1973-01-01

    Discusses the course offerings in pure color chemistry at two universities and the three main aspects of study: dyestuff chemistry, color measurement, and color application. Indicates that there exists a constant challenge to ingenuity in the subject discipline. (CC)

  10. The Chemistry of Atmosphere-Forest Exchange (CAFE Model – Part 2: Application to BEARPEX-2007 observations

    Directory of Open Access Journals (Sweden)

    G. M. Wolfe

    2011-02-01

    Full Text Available In a companion paper, we introduced the Chemistry of Atmosphere-Forest Exchange (CAFE model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. Here, we apply CAFE to noontime observations from the 2007 Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX-2007. In this work we evaluate the CAFE modeling approach, demonstrate the significance of in-canopy chemistry for forest-atmosphere exchange and identify key shortcomings in the current understanding of intra-canopy processes.

    CAFE generally reproduces BEARPEX-2007 observations but requires an enhanced radical recycling mechanism to overcome a factor of 6 underestimate of hydroxyl (OH concentrations observed during a warm (~29 °C period. Modeled fluxes of acyl peroxy nitrates (APN are quite sensitive to gradients in chemical production and loss, demonstrating that chemistry may perturb forest-atmosphere exchange even when the chemical timescale is long relative to the canopy mixing timescale. The model underestimates peroxy acetyl nitrate (PAN fluxes by 50% and the exchange velocity by nearly a factor of three under warmer conditions, suggesting that near-surface APN sinks are underestimated relative to the sources. Nitric acid typically dominates gross dry N deposition at this site, though other reactive nitrogen (NOy species can comprise up to 28% of the N deposition budget under cooler conditions. Upward NO2 fluxes cause the net above-canopy NOy flux to be ~30% lower than the gross depositional flux. CAFE under-predicts ozone fluxes and exchange velocities by ~20%. Large uncertainty in the parameterization of cuticular and ground deposition precludes conclusive attribution of non-stomatal fluxes to chemistry or surface uptake. Model-measurement comparisons of vertical concentration gradients for several emitted species suggests that the lower canopy airspace may be

  11. 2010 INORGANIC CHEMISTRY GORDON RESEARCH CONFERENCE JUNE 20 - 25, 2010

    Energy Technology Data Exchange (ETDEWEB)

    JOHN LOCKEMEYER

    2010-06-25

    The Inorganic Chemistry GRC is one of the longest-standing of the GRCs, originating in 1951. Over the years, this conference has played a role in spawning many other GRCs in specialized fields, due to the involvement of elements from most of the periodic table. These include coordination, organometallic, main group, f-element, and solid state chemistries; materials science, catalysis, computational chemistry, nanotechnology, bioinorganic, environmental, and biomedical sciences just to name a few. The 2010 Inorganic Chemistry GRC will continue this tradition, where scientists at all levels from academic, industrial, and national laboratories meet to define the important problems in the field and to highlight emerging opportunities through exchange of ideas and discussion of unpublished results. Invited speakers will present on a wide variety of topics, giving attendees a look at areas both inside and outside of their specialized areas of interest. In addition to invited speakers, the poster sessions at GRCs are a key feature of the conference. All conferees at the Inorganic Chemistry GRC are invited to present a poster on their work, and here the informal setting promotes the free exchange of ideas and fosters new relationships. As in previous years, we will offer poster presenters the opportunity to compete for one of several program spots in which they can give an oral presentation based on the subject matter of their poster. This is a great way to get your work noticed by the scientists attending the meeting, especially for those early in their career path such as junior faculty members, postdoctoral fellows, and those at comparable ranks. Anyone interested in participating in the poster competition should bring an electronic slide presentation and a small hard copy of their poster to submit to the committee.

  12. Positronium chemistry

    CERN Document Server

    Green, James

    1964-01-01

    Positronium Chemistry focuses on the methodologies, reactions, processes, and transformations involved in positronium chemistry. The publication first offers information on positrons and positronium and experimental methods, including mesonic atoms, angular correlation measurements, annihilation spectra, and statistical errors in delayed coincidence measurements. The text then ponders on positrons in gases and solids. The manuscript takes a look at the theoretical chemistry of positronium and positronium chemistry in gases. Topics include quenching, annihilation spectrum, delayed coincidence

  13. Combinatorial chemistry

    DEFF Research Database (Denmark)

    Nielsen, John

    1994-01-01

    An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds.......An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds....

  14. Photosynthesis-dependent Isoprene Emission from Leaf to Planet in a Global Carbon-chemistry-climate Model

    Science.gov (United States)

    Unger, N.; Harper, K.; Zeng, Y.; Kiang, N. Y.; Alienov, I.; Arneth, A.; Schurgers, G.; Amelynck, C.; Goldstein, A.; Guenther, A.; Heinesch, B.; Hewitt, C. N.; Karl, T.; Laffineur, Q.; Langford, B.; McKinney, K. A.; Misztal, P.; Potosnak, M.; Rinne, J.; Pressley, S.; Schoon, N.; Serca, D.

    2013-01-01

    We describe the implementation of a biochemical model of isoprene emission that depends on the electron requirement for isoprene synthesis into the FarquharBallBerry leaf model of photosynthesis and stomatal conductance that is embedded within a global chemistry-climate simulation framework. The isoprene production is calculated as a function of electron transport-limited photosynthesis, intercellular and atmospheric carbon dioxide concentration, and canopy temperature. The vegetation biophysics module computes the photosynthetic uptake of carbon dioxide coupled with the transpiration of water vapor and the isoprene emission rate at the 30 min physical integration time step of the global chemistry-climate model. In the model, the rate of carbon assimilation provides the dominant control on isoprene emission variability over canopy temperature. A control simulation representative of the present-day climatic state that uses 8 plant functional types (PFTs), prescribed phenology and generic PFT-specific isoprene emission potentials (fraction of electrons available for isoprene synthesis) reproduces 50 of the variability across different ecosystems and seasons in a global database of 28 measured campaign-average fluxes. Compared to time-varying isoprene flux measurements at 9 select sites, the model authentically captures the observed variability in the 30 min average diurnal cycle (R2 6496) and simulates the flux magnitude to within a factor of 2. The control run yields a global isoprene source strength of 451 TgC yr1 that increases by 30 in the artificial absence of plant water stress and by 55 for potential natural vegetation.

  15. OH and HO2 radical chemistry during PROPHET 2008 and CABINEX 2009 – Part 1: Measurements and model comparison

    Directory of Open Access Journals (Sweden)

    P. B. Shepson

    2012-12-01

    Full Text Available Hydroxyl (OH and hydroperoxyl (HO2 radicals are key species driving the oxidation of volatile organic compounds that can lead to the production of ozone and secondary organic aerosols. Previous measurements of these radicals in forest environments with high isoprene, low NOx conditions have shown serious discrepancies with modeled concentrations, bringing into question the current understanding of isoprene oxidation chemistry in these environments. During the summers of 2008 and 2009, OH and peroxy radical concentrations were measured using a laser-induced fluorescence instrument as part of the PROPHET (Program for Research on Oxidants: PHotochemistry, Emissions, and Transport and CABINEX (Community Atmosphere-Biosphere INteractions EXperiment campaigns at a forested site in northern Michigan. Supporting measurements of photolysis rates, volatile organic compounds, NOx (NO + NO2 and other inorganic species were used to constrain a zero-dimensional box model based on the Regional Atmospheric Chemistry Mechanism, modified to include the Mainz Isoprene Mechanism (RACM-MIM. The CABINEX model OH predictions were in good agreement with the measured OH concentrations, with an observed-to-modeled ratio near one (0.70 ± 0.31 for isoprene mixing ratios between 1–2 ppb on average. The measured peroxy radical concentrations, reflecting the sum of HO2 and isoprene-based peroxy radicals, were generally lower than predicted by the box model in both years.

  16. OH and HO2 radical chemistry during PROPHET 2008 and CABINEX 2009 – Part 1: Measurements and model comparison

    Directory of Open Access Journals (Sweden)

    S. M. Griffith

    2013-06-01

    Full Text Available Hydroxyl (OH and hydroperoxyl (HO2 radicals are key species driving the oxidation of volatile organic compounds that can lead to the production of ozone and secondary organic aerosols. Previous measurements of these radicals in forest environments with high isoprene, low NOx conditions have shown serious discrepancies with modeled concentrations, bringing into question the current understanding of isoprene oxidation chemistry in these environments. During the summers of 2008 and 2009, OH and peroxy radical concentrations were measured using a laser-induced fluorescence instrument as part of the PROPHET (Program for Research on Oxidants: PHotochemistry, Emissions, and Transport and CABINEX (Community Atmosphere-Biosphere INteractions EXperiment campaigns at a forested site in northern Michigan. Supporting measurements of photolysis rates, volatile organic compounds, NOx (NO + NO2 and other inorganic species were used to constrain a zero-dimensional box model based on the Regional Atmospheric Chemistry Mechanism, modified to include the Mainz Isoprene Mechanism (RACM-MIM. The CABINEX model OH predictions were in good agreement with the measured OH concentrations, with an observed-to-modeled ratio near one (0.70 ± 0.31 for isoprene mixing ratios between 1–2 ppb on average. The measured peroxy radical concentrations, reflecting the sum of HO2 and isoprene-based peroxy radicals, were generally lower than predicted by the box model in both years.

  17. Combustion chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Brown, N.J. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    This research is concerned with the development and use of sensitivity analysis tools to probe the response of dependent variables to model input variables. Sensitivity analysis is important at all levels of combustion modeling. This group`s research continues to be focused on elucidating the interrelationship between features in the underlying potential energy surface (obtained from ab initio quantum chemistry calculations) and their responses in the quantum dynamics, e.g., reactive transition probabilities, cross sections, and thermal rate coefficients. The goals of this research are: (i) to provide feedback information to quantum chemists in their potential surface refinement efforts, and (ii) to gain a better understanding of how various regions in the potential influence the dynamics. These investigations are carried out with the methodology of quantum functional sensitivity analysis (QFSA).

  18. Modelling the effects of the October 1989 solar proton event on mesospheric odd nitrogen using a detailed ion and neutral chemistry model

    Directory of Open Access Journals (Sweden)

    P. T. Verronen

    Full Text Available Solar proton events and electron precipitation affect the concentrations of middle atmospheric constituents. Ionization caused by precipitating particles enhances the production of important minor neutral constituents, such as nitric oxide, through reaction chains in which ionic reactions play an important role. The Sodankylä Ion Chemistry model (SIC has been modified and extended into a detailed ion and neutral chemistry model of the mesosphere. Our steady-state model (containing 55 ion species, 8 neutral species, and several hundred chemical reactions is used to investigate the effect of the October 1989 solar proton event on odd nitrogen at altitudes between 50–90 km. The modelling results show that the NO concentration is significantly enhanced due to the proton precipitation, reaching 107 –108 cm-3 throughout the mesosphere on the 20 October when the proton forcing was most severe. A comparison between the chemical production channels of odd nitrogen indicates that ion chemical reactions are an important factor in the total odd nitrogen production during intense ionization. The modelled electron concentration for the 23 October is compared with EISCAT incoherent scatter radar measurements and a reasonable agreement is found.

    Key words. Atmospheric composition and structure (Middle atmosphere – composition and chemistry; Ionosphere (Particle precipitation

  19. Linking soil chemistry, treeline shifts and climate change: scenario modeling using an experimental approach

    Science.gov (United States)

    Mavris, Christian; Furrer, Gerhard; Anderson, Susanne; Blum, Alex; Wells, Aaron; Dahms, Dennis; Egli, Markus

    2014-05-01

    Climate change and global warming have a strong influence on the landscape development. As cold areas become warmer, both flora and fauna must adapt to new conditions (a). It is widely accepted that climate changes deeply influence the treeline shifts. In addition to that, wildfires, plant diseases and insect infestation (i.e. mountain pine beetle) can promote a selective replacement of plants, inhibiting some and favoring others, thus modifying the ecosystem in diverse ways. There is little knowledge on the behavior of soil chemistry when such changes occur. Will elemental availability become a crucial factor as a function of climate changes? The Sinks Canyon and Stough Basin - SE flank of the Wind River Range, Wyoming, USA - offer an ideal case study. Conceptually, the areas were divided into three main subsets: tundra, forest and a subarid environment. All soils were developed on granitoid moraines (b, c). From each subset, a liquid topsoil extract was produced and mixed with the solid subsoil samples in batch reactors at 50 °C. The batch experiments were carried out over 1800 h, and the progress of the dissolution was regularly monitored by analyzing liquid aliquots using IC and ICP-OES. The nutrients were mostly released within the first hours of the experiment. Silicon and Al were continuously released into the solution, while some alkali elements - i.e. Na - showed a more complex trend. Organic acids (acetic, citric) and other ligands produced during biodegradation played an active role in mineral dissolution and nutrient release. The mineral colloids detected in the extract (X-ray diffraction) can significantly control surface reactions (adsorption/desorption) and contributed to specific cationic concentrations. The experimental set up was then compared to a computed dissolution model using SerialSTEADYQL software (d, e). Decoding the mechanisms driving mineral weathering is the key to understand the main geochemical aspects of adaptation during climate

  20. Parameterized isoprene and monoterpene emissions from the boreal forest floor: Implementation into a 1D chemistry-transport model and investigation of the influence on atmospheric chemistry

    Science.gov (United States)

    Mogensen, Ditte; Aaltonen, Hermanni; Aalto, Juho; Bäck, Jaana; Kieloaho, Antti-Jussi; Gierens, Rosa; Smolander, Sampo; Kulmala, Markku; Boy, Michael

    2015-04-01

    Volatile organic compounds (VOCs) are emitted from the biosphere and can work as precursor gases for aerosol particles that can affect the climate (e.g. Makkonen et al., ACP, 2012). VOC emissions from needles and leaves have gained the most attention, however other parts of the ecosystem also have the ability to emit a vast amount of VOCs. This, often neglected, source can be important e.g. at periods where leaves are absent. Both sources and drivers related to forest floor emission of VOCs are currently limited. It is thought that the sources are mainly due to degradation of organic matter (Isidorov and Jdanova, Chemosphere, 2002), living roots (Asensio et al., Soil Biol. Biochem., 2008) and ground vegetation. The drivers are biotic (e.g. microbes) and abiotic (e.g. temperature and moisture). However, the relative importance of the sources and the drivers individually are currently poorly understood. Further, the relative importance of these factors is highly dependent on the tree species occupying the area of interest. The emission of isoprene and monoterpenes where measured from the boreal forest floor at the SMEAR II station in Southern Finland (Hari and Kulmala, Boreal Env. Res., 2005) during the snow-free period in 2010-2012. We used a dynamic method with 3 automated chambers analyzed by Proton Transfer Reaction - Mass Spectrometer (Aaltonen et al., Plant Soil, 2013). Using this data, we have developed empirical parameterizations for the emission of isoprene and monoterpenes from the forest floor. These parameterizations depends on abiotic factors, however, since the parameterizations are based on field measurements, biotic features are captured. Further, we have used the 1D chemistry-transport model SOSAA (Boy et al., ACP, 2011) to test the seasonal relative importance of inclusion of these parameterizations of the forest floor compared to the canopy crown emissions, on the atmospheric reactivity throughout the canopy.

  1. Inactivation of various influenza strains to model avian influenza (Bird Flu) with various disinfectant chemistries.

    Energy Technology Data Exchange (ETDEWEB)

    Oberst, R. D.; Bieker, Jill Marie; Souza, Caroline Ann

    2005-12-01

    Due to the grave public health implications and economic impact possible with the emergence of the highly pathogenic avian influenza A isolate, H5N1, currently circulating in Asia we have evaluated the efficacy of various disinfectant chemistries against surrogate influenza A strains. Chemistries included in the tests were household bleach, ethanol, Virkon S{reg_sign}, and a modified version of the Sandia National Laboratories developed DF-200 (DF-200d, a diluted version of the standard DF-200 formulation). Validation efforts followed EPA guidelines for evaluating chemical disinfectants against viruses. The efficacy of the various chemistries was determined by infectivity, quantitative RNA, and qualitative protein assays. Additionally, organic challenges using combined poultry feces and litter material were included in the experiments to simulate environments in which decontamination and remediation will likely occur. In all assays, 10% bleach and Sandia DF-200d were the most efficacious treatments against two influenza A isolates (mammalian and avian) as they provided the most rapid and complete inactivation of influenza A viruses.

  2. Parameterization of dust emissions in the global atmospheric chemistry-climate model EMAC: impact of nudging and soil properties

    Directory of Open Access Journals (Sweden)

    M. Astitha

    2012-11-01

    Full Text Available Airborne desert dust influences radiative transfer, atmospheric chemistry and dynamics, as well as nutrient transport and deposition. It directly and indirectly affects climate on regional and global scales. Two versions of a parameterization scheme to compute desert dust emissions are incorporated into the atmospheric chemistry general circulation model EMAC (ECHAM5/MESSy2.41 Atmospheric Chemistry. One uses a globally uniform soil particle size distribution, whereas the other explicitly accounts for different soil textures worldwide. We have tested these two versions and investigated the sensitivity to input parameters, using remote sensing data from the Aerosol Robotic Network (AERONET and dust concentrations and deposition measurements from the AeroCom dust benchmark database (and others. The two versions are shown to produce similar atmospheric dust loads in the N-African region, while they deviate in the Asian, Middle Eastern and S-American regions. The dust outflow from Africa over the Atlantic Ocean is accurately simulated by both schemes, in magnitude, location and seasonality. Approximately 70% of the modelled annual deposition data and 70–75% of the modelled monthly aerosol optical depth (AOD in the Atlantic Ocean stations lay in the range 0.5 to 2 times the observations for all simulations. The two versions have similar performance, even though the total annual source differs by ~50%, which underscores the importance of transport and deposition processes (being the same for both versions. Even though the explicit soil particle size distribution is considered more realistic, the simpler scheme appears to perform better in several locations. This paper discusses the differences between the two versions of the dust emission scheme, focusing on their limitations and strengths in describing the global dust cycle and suggests possible future improvements.

  3. Modelling non-equilibrium secondary organic aerosol formation and evaporation with the aerosol dynamics, gas- and particle-phase chemistry kinetic multilayer model ADCHAM

    Energy Technology Data Exchange (ETDEWEB)

    Roldin, P.; Eriksson, A. C.; Nordin, E. Z.; Hermansson, E.; Mogensen, Ditte; Rusanen, A.; Boy, Michael; Swietlicki, E.; Svenningsson, Birgitta; Zelenyuk, Alla; Pagels, J.

    2014-08-11

    We have developed the novel Aerosol Dynamics, gas- and particle- phase chemistry model for laboratory CHAMber studies (ADCHAM). The model combines the detailed gas phase Master Chemical Mechanism version 3.2, an aerosol dynamics and particle phase chemistry module (which considers acid catalysed oligomerization, heterogeneous oxidation reactions in the particle phase and non-ideal interactions between organic compounds, water and inorganic ions) and a kinetic multilayer module for diffusion limited transport of compounds between the gas phase, particle surface and particle bulk phase. In this article we describe and use ADCHAM to study: 1) the mass transfer limited uptake of ammonia (NH3) and formation of organic salts between ammonium (NH4+) and carboxylic acids (RCOOH), 2) the slow and almost particle size independent evaporation of α-pinene secondary organic aerosol (SOA) particles, and 3) the influence of chamber wall effects on the observed SOA formation in smog chambers.

  4. The atmospheric chemistry general circulation model ECHAM5/MESSy1: consistent simulation of ozone from the surface to the mesosphere

    Directory of Open Access Journals (Sweden)

    P. Jöckel

    2006-01-01

    Full Text Available The new Modular Earth Submodel System (MESSy describes atmospheric chemistry and meteorological processes in a modular framework, following strict coding standards. It has been coupled to the ECHAM5 general circulation model, which has been slightly modified for this purpose. A 90-layer model setup up to 0.01 hPa was used at spectral T42 resolution to simulate the lower and middle atmosphere. With the high vertical resolution the model simulates the Quasi-Biennial Oscillation. The model meteorology has been tested to check the influence of the changes to ECHAM5 and the radiation interactions with the new representation of atmospheric composition. In the simulations presented here a Newtonian relaxation technique was applied in the tropospheric part of the domain to weakly nudge the model towards the analysed meteorology during the period 1998–2005. This allows an efficient and direct evaluation with satellite and in-situ data. It is shown that the tropospheric wave forcing of the stratosphere in the model suffices to reproduce major stratospheric warming events leading e.g. to the vortex split over Antarctica in 2002. Characteristic features such as dehydration and denitrification caused by the sedimentation of polar stratospheric cloud particles and ozone depletion during winter and spring are simulated well, although ozone loss in the lower polar stratosphere is slightly underestimated. The model realistically simulates stratosphere-troposphere exchange processes as indicated by comparisons with satellite and in situ measurements. The evaluation of tropospheric chemistry presented here focuses on the distributions of ozone, hydroxyl radicals, carbon monoxide and reactive nitrogen compounds. In spite of minor shortcomings, mostly related to the relatively coarse T42 resolution and the neglect of inter-annual changes in biomass burning emissions, the main characteristics of the trace gas distributions are generally reproduced well. The MESSy

  5. Use of the HadGEM2 climate-chemistry model to investigate interannual variability in methane sources

    Science.gov (United States)

    Hayman, Garry; O'Connor, Fiona; Clark, Douglas; Huntingford, Chris; Gedney, Nicola

    2013-04-01

    The global mean atmospheric concentration of methane (CH4) has more than doubled during the industrial era [1] and now constitutes ? 20% of the anthropogenic climate forcing by greenhouse gases [2]. The globally-averaged CH4 growth rate, derived from surface measurements, has fallen significantly from a high of 16 ppb yr-1 in the late 1970s/early 1980s and was close to zero between 1999 and 2006 [1]. This overall period of declining or low growth was however interspersed with years of positive growth-rate anomalies (e.g., in 1991-1992, 1998-1999 and 2002-2003). Since 2007, renewed growth has been evident [1, 3], with the largest increases observed over polar northern latitudes and the Southern Hemisphere in 2007 and in the tropics in 2008. The observed inter-annual variability in atmospheric methane concentrations and the associated changes in growth rates have variously been attributed to changes in different methane sources and sinks [1, 4]. In this paper, we report results from runs of the HadGEM2 climate-chemistry model [5] using year- and month-specific emission datasets. The HadGEM2 model includes the comprehensive atmospheric chemistry and aerosol package, the UK Chemistry Aerosol community model (UKCA, http://www.ukca.ac.uk/wiki/index.php). The Standard Tropospheric Chemistry scheme was selected for this work. This chemistry scheme simulates the Ox, HOx and NOx chemical cycles and the oxidation of CO, methane, ethane and propane. Year- and month-specific emission datasets were generated for the period from 1997 to 2009 for the emitted species in the chemistry scheme (CH4, CO, NOx, HCHO, C2H6, C3H8, CH3CHO, CH3CHOCH3). The approach adopted varied depending on the source sector: Anthropogenic: The emissions from anthropogenic sources were based on decadal-averaged emission inventories compiled by [6] for the Coupled Carbon Cycle Climate Model Intercomparison Project (C4MIP). These were then used to derive year-specific emission datasets by scaling the

  6. Magnetism in Chemistry

    Science.gov (United States)

    Brookes, R. W.; McFadyen, W. D.

    1975-01-01

    Discusses the technical aspects of paramagnetism and an electrostatic model called Crystal Field Theory (CFT), very often used in the case of transition metal compounds. Suggests that this discussion be included as an option for college chemistry courses. (MLH)

  7. Spatially Resolved Artificial Chemistry

    DEFF Research Database (Denmark)

    Fellermann, Harold

    2009-01-01

    Although spatial structures can play a crucial role in chemical systems and can drastically alter the outcome of reactions, the traditional framework of artificial chemistry is a well-stirred tank reactor with no spatial representation in mind. Advanced method development in physical chemistry has...... made a class of models accessible to the realms of artificial chemistry that represent reacting molecules in a coarse-grained fashion in continuous space. This chapter introduces the mathematical models of Brownian dynamics (BD) and dissipative particle dynamics (DPD) for molecular motion and reaction...

  8. Designing a Scalable Fault Tolerance Model for High Performance Computational Chemistry: A Case Study with Coupled Cluster Perturbative Triples.

    Science.gov (United States)

    van Dam, Hubertus J J; Vishnu, Abhinav; de Jong, Wibe A

    2011-01-11

    In the past couple of decades, the massive computational power provided by the most modern supercomputers has resulted in simulation of higher-order computational chemistry methods, previously considered intractable. As the system sizes continue to increase, the computational chemistry domain continues to escalate this trend using parallel computing with programming models such as Message Passing Interface (MPI) and Partitioned Global Address Space (PGAS) programming models such as Global Arrays. The ever increasing scale of these supercomputers comes at a cost of reduced Mean Time Between Failures (MTBF), currently on the order of days and projected to be on the order of hours for upcoming extreme scale systems. While traditional disk-based check pointing methods are ubiquitous for storing intermediate solutions, they suffer from high overhead of writing and recovering from checkpoints. In practice, checkpointing itself often brings the system down. Clearly, methods beyond checkpointing are imperative to handling the aggravating issue of reducing MTBF. In this paper, we address this challenge by designing and implementing an efficient fault tolerant version of the Coupled Cluster (CC) method with NWChem, using in-memory data redundancy. We present the challenges associated with our design, including an efficient data storage model, maintenance of at least one consistent data copy, and the recovery process. Our performance evaluation without faults shows that the current design exhibits a small overhead. In the presence of a simulated fault, the proposed design incurs negligible overhead in comparison to the state of the art implementation without faults. PMID:26606219

  9. Designing a Scalable Fault Tolerance Model for High Performance Computational Chemistry: A Case Study with Coupled Cluster Perturbative Triples.

    Science.gov (United States)

    van Dam, Hubertus J J; Vishnu, Abhinav; de Jong, Wibe A

    2011-01-11

    In the past couple of decades, the massive computational power provided by the most modern supercomputers has resulted in simulation of higher-order computational chemistry methods, previously considered intractable. As the system sizes continue to increase, the computational chemistry domain continues to escalate this trend using parallel computing with programming models such as Message Passing Interface (MPI) and Partitioned Global Address Space (PGAS) programming models such as Global Arrays. The ever increasing scale of these supercomputers comes at a cost of reduced Mean Time Between Failures (MTBF), currently on the order of days and projected to be on the order of hours for upcoming extreme scale systems. While traditional disk-based check pointing methods are ubiquitous for storing intermediate solutions, they suffer from high overhead of writing and recovering from checkpoints. In practice, checkpointing itself often brings the system down. Clearly, methods beyond checkpointing are imperative to handling the aggravating issue of reducing MTBF. In this paper, we address this challenge by designing and implementing an efficient fault tolerant version of the Coupled Cluster (CC) method with NWChem, using in-memory data redundancy. We present the challenges associated with our design, including an efficient data storage model, maintenance of at least one consistent data copy, and the recovery process. Our performance evaluation without faults shows that the current design exhibits a small overhead. In the presence of a simulated fault, the proposed design incurs negligible overhead in comparison to the state of the art implementation without faults.

  10. Heat Transfer Salts for Nuclear Reactor Systems - Chemistry Control, Corrosion Mitigation, and Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Mark [Univ. of Wisconsin, Madison, WI (United States); Sridharan, Kumar [Univ. of Wisconsin, Madison, WI (United States); Morgan, Dane [Univ. of Wisconsin, Madison, WI (United States); Peterson, Per [Univ. of Wisconsin, Madison, WI (United States); Calderoni, Pattrick [Univ. of Wisconsin, Madison, WI (United States); Scheele, Randall [Univ. of Wisconsin, Madison, WI (United States); Casekka, Andrew [Univ. of Wisconsin, Madison, WI (United States); McNamara, Bruce [Univ. of Wisconsin, Madison, WI (United States)

    2015-01-22

    The concept of a molten salt reactor has existed for nearly sixty years. Previously all work was done during a large collaborative effort at Oak Ridge National Laboratory, culminating in a research reactor which operated for 15,000 hours without major error. This technical success has garnished interest in modern, high temperature, reactor schemes. Research using molten fluoride salts for nuclear applications requires a steady supply of high grade molten salts. There is no bulk supplier of research grade fluoride salts in the world, so a facility which could provide all the salt needed for testing at the University of Wisconsin had to be produced. Two salt purification devices were made for this purpose, a large scale purifier, and a small scale purifier, each designed to clean the salts from impurities and reduce their corrosion potential. As of now, the small scale has performed with flibe salt, hydrogen, and hydrogen fluoride, yielding clean salt. This salt is currently being used in corrosion testing facilities at the Massachusetts Institute of Technology and the University of Wisconsin. Working with the beryllium based salts requires extensive safety measures and health monitoring to prevent the development of acute or chronic beryllium disease, two pulmonary diseases created by an allergic reaction to beryllium in the lungs. Extensive health monitoring, engineering controls, and environment monitoring had to be set up with the University of Wisconsin department of Environment, Health and Safety. The hydrogen fluoride required for purification was also an extreme health hazard requiring thoughtful planning and execution. These dangers have made research a slow and tedious process. Simple processes, such as chemical handling and clean-up, can take large amounts of ingenuity and time. Other work has complemented the experimental research at Wisconsin to advance high temperature reactor goals. Modeling work has been performed in house to re

  11. Modeling of the lower ionospheric response and VLF signal modulation during a total solar eclipse using ionospheric chemistry and LWPC

    Science.gov (United States)

    Chakraborty, Suman; Palit, Sourav; Ray, Suman; Chakrabarti, Sandip K.

    2016-02-01

    The variation in the solar Extreme Ultraviolet (EUV) radiation flux by any measure is the most dominant natural source to produce perturbations or modulations in the ionospheric chemical and plasma properties. A solar eclipse, though a very rare phenomenon, is similarly bound to produce a significant short time effect on the local ionospheric properties. The influence of the ionizing solar flux reduction during a solar eclipse on the lower ionosphere or, more precisely, the D-region, can be studied with the observation of Very Low Frequency (VLF) radio wave signal modulation. The interpretation of such an effect on VLF signals requires a knowledge of the D-region ion chemistry, which is not well studied till date. Dominant parameters which govern the ion chemistry, such as the recombination coefficients, are poorly known. The occurrence of events such as a solar eclipse provides us with an excellent opportunity to investigate the accuracy of our knowledge of the chemical condition in this part of Earth's atmosphere and the properties which control the ionospheric stability under such disturbances. In this paper, using existing knowledge of the lower ionospheric chemical and physical properties we carry out an interpretation of the effects obtained during the total solar eclipse of 22 of July 2009 on the VLF signal. Data obtained from a week long campaign conducted by the Indian Centre for Space Physics (ICSP) over the Indian subcontinent has been used for this purpose. Both positive and negative amplitude changes during the eclipse were observed along various receiver locations. In this paper, data for a propagation path between a Indian Navy VLF transmitter named VTX3 and a pair of receivers in India are used. We start from the observed solar flux during the eclipse and calculate the ionization during the whole time span over most of the influenced region in a range of height. We incorporate a D-region ion-chemistry model to find the equilibrium ion density over

  12. D-region ion-neutral coupled chemistry (Sodankylä Ion Chemistry, SIC) within the Whole Atmosphere Community Climate Model (WACCM 4) - WACCM-SIC and WACCM-rSIC

    Science.gov (United States)

    Kovács, Tamás; Plane, John M. C.; Feng, Wuhu; Nagy, Tibor; Chipperfield, Martyn P.; Verronen, Pekka T.; Andersson, Monika E.; Newnham, David A.; Clilverd, Mark A.; Marsh, Daniel R.

    2016-09-01

    This study presents a new ion-neutral chemical model coupled into the Whole Atmosphere Community Climate Model (WACCM). The ionospheric D-region (altitudes ˜ 50-90 km) chemistry is based on the Sodankylä Ion Chemistry (SIC) model, a one-dimensional model containing 307 ion-neutral and ion recombination, 16 photodissociation and 7 photoionization reactions of neutral species, positive and negative ions, and electrons. The SIC mechanism was reduced using the simulation error minimization connectivity method (SEM-CM) to produce a reaction scheme of 181 ion-molecule reactions of 181 ion-molecule reactions of 27 positive and 18 negative ions. This scheme describes the concentration profiles at altitudes between 20 km and 120 km of a set of major neutral species (HNO3, O3, H2O2, NO, NO2, HO2, OH, N2O5) and ions (O2+, O4+, NO+, NO+(H2O), O2+(H2O), H+(H2O), H+(H2O)2, H+(H2O)3, H+(H2O)4, O3-, NO2-, O-, O2, OH-, O2-(H2O), O2-(H2O)2, O4-, CO3-, CO3-(H2O), CO4-, HCO3-, NO2-, NO3-, NO3-(H2O), NO3-(H2O)2, NO3-(HNO3), NO3-(HNO3)2, Cl-, ClO-), which agree with the full SIC mechanism within a 5 % tolerance. Four 3-D model simulations were then performed, using the impact of the January 2005 solar proton event (SPE) on D-region HOx and NOx chemistry as a test case of four different model versions: the standard WACCM (no negative ions and a very limited set of positive ions); WACCM-SIC (standard WACCM with the full SIC chemistry of positive and negative ions); WACCM-D (standard WACCM with a heuristic reduction of the SIC chemistry, recently used to examine HNO3 formation following an SPE); and WACCM-rSIC (standard WACCM with a reduction of SIC chemistry using the SEM-CM method). The standard WACCM misses the HNO3 enhancement during the SPE, while the full and reduced model versions predict significant NOx, HOx and HNO3 enhancements in the mesosphere during solar proton events. The SEM-CM reduction also identifies the important ion-molecule reactions that affect the partitioning of

  13. Hydrogen chloride heterogeneous chemistry on frozen water particles in subsonic aircraft plume. Laboratory studies and modelling

    Energy Technology Data Exchange (ETDEWEB)

    Persiantseva, N.V.; Popovitcheva, O.B.; Rakhimova, T.V. [Moscow State Univ. (Russian Federation)

    1997-12-31

    Heterogeneous chemistry of HCl, as a main reservoir of chlorine content gases, has been considered after plume cooling and ice particle formation. The HCl, HNO{sub 3}, N{sub 2}O{sub 5} uptake efficiencies by frozen water were obtained in a Knudsen-cell flow reactor at the subsonic cruise conditions. The formation of ice particles in the plume of subsonic aircraft is simulated to describe the kinetics of gaseous HCl loss due to heterogeneous processes. It is shown that the HCl uptake by frozen water particles may play an important role in the gaseous HCl depletion in the aircraft plume. (author) 14 refs.

  14. A comparison of Methane data products from Chemistry Transport Models, SCIAMACHY and a network of FTIR stations

    Science.gov (United States)

    Dils, Bart; de Mazière, Martine; Vigouroux, Corinne

    2010-05-01

    Since its launch in 2002, the SCIAMACHY instrument on board ENVISAT has provided information on a large array of species affecting our environment. Methane, a species for which the retrieval algorithm development is still ongoing, is believed to be an important greenhouse gas. Thus, to effectively study the impact of CH4 on climate, information on its sources and sinks needs to be improved. To this end Eulerian Chemistry Transport models coupled with emission data are often compared with the available satellite data. However, since both model-emission databases and satellite data are still very much under development, it is very useful to compare both with independent third party data. In the framework of the EU project HYMN, the methane field as simulated by several Eulerian Chemistry Transport Models has been compared with data from a quasi-global network of groundbased Fourier Tranform Infrared (FTIR) spectrometers of NDACC. The FTIR data have been harmonized across the network in order to eliminate any station to station biases resulting from different retrieval parameter settings such as the choice of the retrieval spectral microwindows and the a priori profile selection. The models in question are TM4 developed at the Royal Netherlands Meteorological Institute (KNMI), LMDz-INCA (Laboratoire des Sciences du Climat et de l'Environnement (LSCE)) and CTM2 from the University of Oslo. The impact of several emission inventories on the modeled atmospheric CH4 distribution will be assessed. We will also discuss the inter-comparison of the latest IMAP-DOAS and WFM-DOAS CH4 SCHIAMACHY satellite products with said FTIR and model datasets, focusing on the seasonal cycle of methane.

  15. Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume

    Energy Technology Data Exchange (ETDEWEB)

    Lee-Taylor, J.; Madronich, Sasha; Aumont, B.; Baker, A.; Camredon, M.; Hodzic, Alma; Tyndall, G. S.; Apel, Eric; Zaveri, Rahul A.

    2011-12-21

    The evolution of organic aerosols (OA) in Mexico City and its outflow is investigated with the nearly explicit gas phase photochemistry model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere), wherein precursor hydrocarbons are oxidized to numerous intermediate species for which vapor pressures are computed and used to determine gas/particle partitioning in a chemical box model. Precursor emissions included observed C3-10 alkanes, alkenes, and light aromatics, as well as larger n-alkanes (up to C25) not directly observed but estimated by scaling to particulate emissions according to their volatility. Conditions were selected for comparison with observations made in March 2006 (MILAGRO). The model successfully reproduces the magnitude and diurnal shape for both primary (POA) and secondary (SOA) organic aerosols, with POA peaking in the early morning at 15-20 ug m-3, and SOA peaking at 10-15 μg m-3 during mid-day. The majority (> 75%) of the model SOA stems from the large n-alkanes, with the remainder mostly from the light aromatics. Simulated OA elemental composition reproduces observed H/C and O/C ratios reasonably well, although modeled ratios develop more slowly than observations suggest. SOA chemical composition is initially dominated by *- hydroxy ketones and nitrates from the large alkanes, with contributions from peroxy acyl nitrates and, at later times when NOx is lower, organic hydroperoxides. The simulated plume-integrated OA mass continues to increase for several days downwind despite dilution-induced particle evaporation, since oxidation chemistry leading to SOA formation remains strong. In this model, the plume SOA burden several days downwind exceeds that leaving the city by a factor of >3. These results suggest significant regional radiative impacts of SOA.

  16. Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume

    Directory of Open Access Journals (Sweden)

    J. Lee-Taylor

    2011-06-01

    Full Text Available The evolution of organic aerosols (OA in Mexico City and its outflow is investigated with the nearly explicit gas phase photochemistry model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere, wherein precursor hydrocarbons are oxidized to numerous intermediate species for which vapor pressures are computed and used to determine gas/particle partitioning in a chemical box model. Precursor emissions included observed C3–10 alkanes, alkenes, and light aromatics, as well as larger n-alkanes (up to C25 not directly observed but estimated by scaling to particulate emissions according to their volatility. Conditions were selected for comparison with observations made in March 2006 (MILAGRO. The model successfully reproduces the magnitude and diurnal shape for both primary (POA and secondary (SOA organic aerosols, with POA peaking in the early morning at 15–20 μg m−3, and SOA peaking at 10–15 μg m−3 during mid-day. The majority (≥75 % of the model SOA stems from the large n-alkanes, with the remainder mostly from the light aromatics. Simulated OA elemental composition reproduces observed H/C and O/C ratios reasonably well, although modeled ratios develop more slowly than observations suggest. SOA chemical composition is initially dominated by δ-hydroxy ketones and nitrates from the large alkanes, with contributions from peroxy acyl nitrates and, at later times when NOx is lower, organic hydroperoxides. The simulated plume-integrated OA mass continues to increase for several days downwind despite dilution-induced particle evaporation, since oxidation chemistry leading to SOA formation remains strong. In this model, the plume SOA burden several days downwind exceeds that leaving the city by a factor of >3. These results suggest significant regional radiative impacts of SOA.

  17. A Low-order Coupled Chemistry Meteorology Model for Testing Online and Offline Advanced Data Assimilation Schemes

    Science.gov (United States)

    Bocquet, M.; Haussaire, J. M.

    2015-12-01

    Bocquet and Sakov have recently introduced a low-order model based on the coupling of thechaotic Lorenz-95 model which simulates winds along a mid-latitude circle, with thetransport of a tracer species advected by this wind field. It has been used to testadvanced data assimilation methods with an online model that couples meteorology andtracer transport. In the present study, the tracer subsystem of the model is replacedwith a reduced photochemistry module meant to emulate reactive air pollution. Thiscoupled chemistry meteorology model, the L95-GRS model, mimics continental andtranscontinental transport and photochemistry of ozone, volatile organic compounds andnitrogen dioxides.The L95-GRS is specially useful in testing advanced data assimilation schemes, such as theiterative ensemble Kalman smoother (IEnKS) that combines the best of ensemble andvariational methods. The model provides useful insights prior to any implementation ofthe data assimilation method on larger models. For instance, online and offline dataassimilation strategies based on the ensemble Kalman filter or the IEnKS can easily beevaluated with it. It allows to document the impact of species concentration observationson the wind estimation. The model also illustrates a long standing issue in atmosphericchemistry forecasting: the impact of the wind chaotic dynamics and of the chemical speciesnon-chaotic but highly nonlinear dynamics on the selected data assimilation approach.

  18. Modelling transport and transformation of mercury fractions in heavily contaminated mountain streams by coupling a GIS-based hydrological model with a mercury chemistry model.

    Science.gov (United States)

    Lin, Yan; Larssen, Thorjørn; Vogt, Rolf D; Feng, Xinbin; Zhang, Hua

    2011-10-01

    Many heavily polluted areas are located in remote regions that lack routine hydrologic monitoring. A modelling method that can produce scenarios of water chemistry trends for regions that lack hydrological data is therefore needed. The Wanshan mining area, in Guizhou province in south-western China, is such a region, as it is heavily polluted with mercury (Hg). In order to model Hg transport in a stream draining the Wanshan mining area, a Geographic Information System (GIS) hydrologic model (HEC-HMS) was coupled with a simulation model for Hg fractions in water (WASP Hg). Hydrological variations in the stream flow can thereby be simulated based on readily available precipitation data. The WASP 7 MERC Hg model was used for simulating variations in total Hg, dissolved Hg and methyl-Hg concentrations. The results of HEC-HMS modelling of flow show clear seasonal variation. Winter (Oct-Dec) constitutes the dry season with low flow, while the summer season (Jun-Aug) is rainy with high flow. 48% of total annual precipitation happens in the three summer months. The stream flows at the high flow events were several times higher than normal flow. The modelled total suspended solids and Hg concentrations were tested against monitoring data from two sampling campaigns conducted in September 2007 and August 2008. The model produced reasonable simulations for TSS, THg, DHg and MeHg, with relative errors generally around 10% for the modelled parameters. High flow events are the main contributors for release of both suspended particles and Hg. The three high flow events account for about 50% of annual discharge of THg. The annual total discharge of Hg was 8.8 kg Hg high up in the stream and 2.6 kg where the stream meets a large river 20 km downstream of the pollution source. Hence, about 70% of Hg is retained in the stream through sedimentation.

  19. Tropospheric ozone changes, radiative forcing and attribution to emissions in the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP

    Directory of Open Access Journals (Sweden)

    D. S. Stevenson

    2013-03-01

    Full Text Available Ozone (O3 from 17 atmospheric chemistry models taking part in the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP has been used to calculate tropospheric ozone radiative forcings (RFs. All models applied a common set of anthropogenic emissions, which are better constrained for the present-day than the past. Future anthropogenic emissions follow the four Representative Concentration Pathway (RCP scenarios, which define a relatively narrow range of possible air pollution emissions. We calculate a value for the pre-industrial (1750 to present-day (2010 tropospheric ozone RF of 410 mW m−2. The model range of pre-industrial to present-day changes in O3 produces a spread (±1 standard deviation in RFs of ±17%. Three different radiation schemes were used – we find differences in RFs between schemes (for the same ozone fields of ±10%. Applying two different tropopause definitions gives differences in RFs of ±3%. Given additional (unquantified uncertainties associated with emissions, climate-chemistry interactions and land-use change, we estimate an overall uncertainty of ±30% for the tropospheric ozone RF. Experiments carried out by a subset of six models attribute tropospheric ozone RF to increased emissions of methane (44±12%, nitrogen oxides (31 ± 9%, carbon monoxide (15 ± 3% and non-methane volatile organic compounds (9 ± 2%; earlier studies attributed more of the tropospheric ozone RF to methane and less to nitrogen oxides. Normalising RFs to changes in tropospheric column ozone, we find a global mean normalised RF of 42 mW m−2 DU−1, a value similar to previous work. Using normalised RFs and future tropospheric column ozone projections we calculate future tropospheric ozone RFs (mW m−2; relative to 1750 for the four future scenarios (RCP2.6, RCP4.5, RCP6.0 and RCP8.5 of 350, 420, 370 and 460 (in 2030, and 200, 300, 280 and 600 (in 2100. Models show some coherent responses of ozone to climate change

  20. Tropospheric Ozone Changes, Radiative Forcing and Attribution to Emissions in the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP)

    Science.gov (United States)

    Stevenson, D.S.; Young, P.J.; Naik, V.; Lamarque, J.-F.; Shindell, D. T.; Voulgarakis, A.; Skeie, R. B.; Dalsoren, S. B.; Myhre, G.; Berntsen, T. K.; Folberth, G. A.; Rumbold, S. T.; Collins, W. J.; MacKenzie, I. A.; Doherty, R. M.; Zeng, G.; vanNoije, T. P. C.; Strunk, A.; Bergmann, D.; Cameron-Smith, P.; Plummer, D. A.; Strode, S. A.; Horowitz, L.; Lee, Y. H.; Szopa, S.; Sudo, K.; Nagashima, T.; Josse, B.; Cionni, I.; Righi, M.; Eyring, V.; Conley, A.; Bowman, K. W.; Wild, O.; Archibald, A.

    2013-01-01

    Ozone (O3) from 17 atmospheric chemistry models taking part in the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP) has been used to calculate tropospheric ozone radiative forcings (RFs). All models applied a common set of anthropogenic emissions, which are better constrained for the present-day than the past. Future anthropogenic emissions follow the four Representative Concentration Pathway (RCP) scenarios, which define a relatively narrow range of possible air pollution emissions. We calculate a value for the pre-industrial (1750) to present-day (2010) tropospheric ozone RF of 410 mW m-2. The model range of pre-industrial to present-day changes in O3 produces a spread (+/-1 standard deviation) in RFs of +/-17%. Three different radiation schemes were used - we find differences in RFs between schemes (for the same ozone fields) of +/-10 percent. Applying two different tropopause definitions gives differences in RFs of +/-3 percent. Given additional (unquantified) uncertainties associated with emissions, climate-chemistry interactions and land-use change, we estimate an overall uncertainty of +/-30 percent for the tropospheric ozone RF. Experiments carried out by a subset of six models attribute tropospheric ozone RF to increased emissions of methane (44+/-12 percent), nitrogen oxides (31 +/- 9 percent), carbon monoxide (15 +/- 3 percent) and non-methane volatile organic compounds (9 +/- 2 percent); earlier studies attributed more of the tropospheric ozone RF to methane and less to nitrogen oxides. Normalising RFs to changes in tropospheric column ozone, we find a global mean normalised RF of 42 mW m(-2) DU(-1), a value similar to previous work. Using normalised RFs and future tropospheric column ozone projections we calculate future tropospheric ozone RFs (mW m(-2); relative to 1750) for the four future scenarios (RCP2.6, RCP4.5, RCP6.0 and RCP8.5) of 350, 420, 370 and 460 (in 2030), and 200, 300, 280 and 600 (in 2100). Models show some

  1. Organic chemistry

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-08-15

    This book with sixteen chapter explains organic chemistry on linkage isomerism such as alkane, cycloalkane, alkene, aromatic compounds, stereo selective isomerization, aromatic compounds, stereo selective isomerization, organic compounds, stereo selective isomerization, organic halogen compound, alcohol, ether, aldehyde and ketone, carboxylic acid, dicarboxylic acid, fat and detergent, amino, carbohydrate, amino acid and protein, nucleotide and nucleic acid and spectroscopy, a polymer and medical chemistry. Each chapter has introduction structure and characteristic and using of organic chemistry.

  2. Social Chemistry

    OpenAIRE

    Lichtfouse, Eric; Schwarzbauer, Jan; Robert, Didier

    2012-01-01

    International audience This article is both an essay to propose social chemistry as a new scientific discipline, and a preface of the book Environmental Chemistry for a Sustainable World. Environmental chemistry is a fast emerging discipline aiming at the understanding the fate of pollutants in ecosystems and at designing novel processes that are safe for ecosystems. Past pollution should be cleaned, future pollution should be predicted and avoided (Lichtfouse et al., 2005a). Such advices ...

  3. Computational chemistry

    OpenAIRE

    Truhlar, Donald G.; McKoy, Vincent

    2000-01-01

    Computational chemistry has come of age. With significant strides in computer hardware and software over the last few decades, computational chemistry has achieved full partnership with theory and experiment as a tool for understanding and predicting the behavior of a broad range of chemical, physical, and biological phenomena. The Nobel Prize award to John Pople and Walter Kohn in 1998 highlighted the importance of these advances in computational chemistry. With massively parallel computers ...

  4. Analytical Models of Exoplanetary Atmospheres. III. Gaseous C-H-O-N Chemistry with 9 Molecules

    CERN Document Server

    Heng, Kevin

    2016-01-01

    We present novel, analytical, equilibrium-chemistry formulae for the abundances of molecules in hot exoplanetary atmospheres that include the carbon, oxygen and nitrogen networks. Our hydrogen-dominated solutions involve acetylene (C$_2$H$_2$), ammonia (NH$_3$), carbon dioxide (CO$_2$), carbon monoxide (CO), ethylene (C$_2$H$_4$), hydrogen cyanide (HCN), methane (CH$_4$), molecular nitrogen (N$_2$) and water (H$_2$O). By considering only the gaseous phase, we prove that the mixing ratio of carbon monoxide is governed by a decic equation (polynomial equation of degree 10). We validate our solutions against numerical calculations of equilibrium chemistry that perform Gibbs free energy minimization and demonstrate that they are accurate for temperatures from 500--3000 K. In hydrogen-dominated atmospheres, the ratio of abundances of HCN to CH$_4$ is nearly constant across a wide range of carbon-to-oxygen ratios, which makes it a robust diagnostic of the metallicity in the gas phase. Our validated formulae allow f...

  5. Photosynthesis-dependent isoprene emission from leaf to planet in a global carbon-chemistry-climate model

    Directory of Open Access Journals (Sweden)

    N. Unger

    2013-10-01

    Full Text Available We describe the implementation of a biochemical model of isoprene emission that depends on the electron requirement for isoprene synthesis into the Farquhar–Ball–Berry leaf model of photosynthesis and stomatal conductance that is embedded within a global chemistry-climate simulation framework. The isoprene production is calculated as a function of electron transport-limited photosynthesis, intercellular and atmospheric carbon dioxide concentration, and canopy temperature. The vegetation biophysics module computes the photosynthetic uptake of carbon dioxide coupled with the transpiration of water vapor and the isoprene emission rate at the 30 min physical integration time step of the global chemistry-climate model. In the model, the rate of carbon assimilation provides the dominant control on isoprene emission variability over canopy temperature. A control simulation representative of the present-day climatic state that uses 8 plant functional types (PFTs, prescribed phenology and generic PFT-specific isoprene emission potentials (fraction of electrons available for isoprene synthesis reproduces 50% of the variability across different ecosystems and seasons in a global database of 28 measured campaign-average fluxes. Compared to time-varying isoprene flux measurements at 9 select sites, the model authentically captures the observed variability in the 30 min average diurnal cycle (R2 = 64–96% and simulates the flux magnitude to within a factor of 2. The control run yields a global isoprene source strength of 451 TgC yr−1 that increases by 30% in the artificial absence of plant water stress and by 55% for potential natural vegetation.

  6. Description and evaluation of tropospheric chemistry and aerosols in the Community Earth System Model (CESM1.2

    Directory of Open Access Journals (Sweden)

    S. Tilmes

    2014-12-01

    Full Text Available The Community Atmosphere Model (CAM, version 5, is now coupled to extensive tropospheric and stratospheric chemistry, called CAM5-chem, and is available in addition to CAM4-chem in the Community Earth System Model (CESM version 1.2. Both configurations are well suited as tools for atmospheric-chemistry modeling studies in the troposphere and lower stratosphere, whether with internally derived "free running" (FR meteorology, or "specified dynamics" (SD. The main focus of this paper is to compare the performance of these configurations against observations from surface, aircraft, and satellite, as well as understand the origin of the identified differences. We particularly focus on comparing present-day methane lifetime estimates within the different model configurations, which range between 7.8 years in the SD configuration of CAM5-chem and 8.8 years in the FR configuration of CAM4-chem. We find that tropospheric surface area density is an important factor in controlling the burden of the hydroxyl radical (OH, which causes differences in tropical methane lifetime of about half a year between CAM4-chem and CAM5-chem. In addition, different distributions of nitrogen oxides (NOx produced from lightning production explain about half of the difference between SD and FR model versions in both CAM4-chem and CAM5-chem. Remaining differences in the tropical OH burden are due to enhanced tropical ozone burden in SD configurations compared to the FR versions, which are not only caused by differences in chemical production or loss, but also by transport and mixing. For future studies, we recommend the use of CAM5-chem, due to improved aerosol description and inclusion of aerosol-cloud interactions. However, smaller tropospheric surface area density in the current version of CAM5-chem compared to CAM4-chem results in larger oxidizing capacity in the troposphere and therefore a shorter methane lifetime.

  7. Photosynthesis-dependent isoprene emission from leaf to planet in a global carbon-chemistry-climate model

    Energy Technology Data Exchange (ETDEWEB)

    Unger, N.; Harper, K.; Zheng, Y.; Kiang, N. Y.; Aleinov, I.; Arneth, Almut; Schurgers, G.; Amelynck, C.; Goldstein, Allen H.; Guenther, Alex B.; Heinesch, B.; Hewitt, C. N.; Karl, T.; Laffineur, Q.; Langford, B.; McKinney, Karena A.; Misztal, P.; Potosnak, M.; Rinne, J.; Pressley, S.; Schoon, N.; Serca, D.

    2013-10-22

    We describe the implementation of a biochemical model of isoprene emission that depends on the electron requirement for isoprene synthesis into the Farquhar/Ball- Berry leaf model of photosynthesis and stomatal conductance that is embedded within a global chemistry-climate simulation framework. The isoprene production is calculated as a function of electron transport-limited photosynthesis, intercellular carbon dioxide concentration, and canopy temperature. The vegetation biophysics module computes the photosynthetic uptake of carbon dioxide coupled with the transpiration of water vapor and the isoprene emission rate at the 30 min physical integration time step of the global chemistry-climate model. In the model, the rate of carbon assimilation provides the dominant control on isoprene emission variability over canopy temperature. A control simulation representative of the present day climatic state that uses plant functional types (PFTs), prescribed phenology and generic PFT-specific isoprene emission potentials (fraction of electrons available for isoprene synthesis) reproduces 50% of the variability across different ecosystems and seasons in a global database of measured campaign-average fluxes. Compared to time-varying isoprene flux measurements at select sites, the model authentically captures the observed variability in the 30 min average diurnal cycle (R2 = 64-96 %) and simulates the flux magnitude to within a factor of 2. The control run yields a global isoprene source strength of 451 TgC yr-1 that increases by 30% in the artificial absence of plant water stress and by 55% for potential natural vegetation.

  8. Evaluation of aerosol properties simulated by the high resolution global coupled chemistry-aerosol-microphysics model C-IFS-GLOMAP

    Science.gov (United States)

    Dhomse, Sandip; Mann, Graham; Carslaw, Ken; Flemming, Johannes; Morcrette, Jean-Jacques; Engelen, Richard; Remy, Samuel; Boucher, Olivier; Benduhn, Francois; Hewson, Will; Woodhouse, Matthew

    2016-04-01

    The EU Framework Programme GEMS and MACC consortium projects co-ordinated by the European Centre for Medium-range Weather Forecasts (ECMWF) have developed an operational global forecasting and reanalysis system (Composition-IFS) for atmospheric composition including greenhouse gases, reactive gases and aerosol. The current operational C-IFS system uses a mass-based aerosol model coupled to data assimilation of Aerosol Optical Depth measured by satellite (MODIS) to predict global aerosol properties. During MACC, the GLOMAP-mode aerosol microphysics scheme was added to the system, providing information on aerosol size and number for improved representation of aerosol-radiation and aerosol-cloud interactions, accounting also for simulated global variations in size distribution and internally-mixed particle composition. The IFS-GLOMAP system has recently been upgraded to couple with the sulphur cycle simulated in the online TM5 tropospheric chemistry module for global reactive gases. This C-IFS-GLOMAP system is also being upgraded to use a new "nitrate-extended" version of GLOMAP which realistically treats the size-resolved gas-particle partitioning of semi volatile gases ammonia and nitric acid. In this poster we described C-IFS-GLOMAP and present an evaluation of the global sulphate aerosol distribution simulated in this coupled aerosol-chemistry C-IFS-GLOMAP, comparing to surface observations in Europe, North America and the North Atlantic and contrasting to the fixed timescale sulphate production scheme developed in GEMS. We show that the coupling to the TM5 sulphur chemistry improves the seasonal cycle of sulphate aerosol, for example addressing a persistent wintertime sulphate high bias in northern Europe. The improved skill in simulated sulphate aerosol seasonal cycle is a pre-requisite to realistically characterise nitrate aerosol since biases in sulphate affect the amount of free ammonia available to form ammonium nitrate.

  9. Long-term changes and variability in a transient simulation with a chemistry-climate model employing realistic forcing

    Directory of Open Access Journals (Sweden)

    M. Dameris

    2005-04-01

    Full Text Available A transient simulation with the interactively coupled chemistry-climate model (CCM E39/C has been carried out which covers the 40-year period between 1960 and 1999. Forcing of natural and anthropogenic origin is prescribed where the characteristics are sufficiently well known and the typical timescales are slow compared to synoptic timescale so that the simulated atmospheric chemistry and climate evolves under a ''slowly'' varying external forcing. Based on observations, sea surface temperature (SST and ice cover are prescribed. The increase of greenhouse gas and chloroflurocarbon concentrations, as well as nitrogen oxide emissions is taken into account. The 11-year solar cycle is considered in the calculation of heating rates and photolysis of chemical species. The three major volcanic eruptions during that time (Agung, 1963; El Chichon, 1982; Pinatubo, 1991 are considered. The quasi-biennial oscillation (QBO is forced by linear relaxation, also known as nudging, of the equatorial zonal wind in the lower stratosphere towards observed zonal wind profiles. Beyond a reasonable reproduction of mean parameters and long-term variability characteristics there are many apparent features of episodic similarities between simulation and observation: In the years 1986 and 1988 the Antarctic ozone holes are smaller than in the other years of the respective decade. In mid-latitudes of the Southern Hemisphere ozone anomalies, especially in 1985, 1989, 1991/1992, and 1996, resemble the corresponding observations. In the Northern Hemisphere, the first half of the 1990s is dynamically quiet, no stratospheric warming is found for a period of at least 6 years. As observed, volcanic eruptions strongly influence dynamics and chemistry, though only for few years. Obviously, planetary wave activity is strongly driven by the prescribed SST and modulated by the QBO. Preliminary evidence of realistic cause and effect relationships strongly suggest

  10. Modelling of turbulent hydrocarbon combustion. Test of different reactor concepts for describing the interactions between turbulence and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, C.; Kremer, H. [Ruhr-Universitaet Bochum, Lehrstuhl fuer Energieanlagentechnik, Bochum (Germany); Kilpinen, P.; Hupa, M. [Aabo Akademi, Turku (Finland). Combustion Chemistry Research Group

    1997-12-31

    The detailed modelling of turbulent reactive flows with CFD-codes is a major challenge in combustion science. One method of combining highly developed turbulence models and detailed chemistry in CFD-codes is the application of reactor based turbulence chemistry interaction models. In this work the influence of different reactor concepts on methane and NO{sub x} chemistry in turbulent reactive flows was investigated. Besides the classical reactor approaches, a plug flow reactor (PFR) and a perfectly stirred reactor (PSR), the Eddy-Dissipation Combustion Model (EDX) and the Eddy Dissipation Concept (EDC) were included. Based on a detailed reaction scheme and a simplified 2-step mechanism studies were performed in a simplified computational grid consisting of 5 cells. The investigations cover a temperature range from 1273 K to 1673 K and consider fuel-rich and fuel-lean gas mixtures as well as turbulent and highly turbulent flow conditions. All test cases investigated in this study showed a strong influence of the reactor residence time on the species conversion processes. Due to this characteristic strong deviations were found for the species trends resulting from the different reactor approaches. However, this influence was only concentrated on the `near burner region` and after 4-5 cells hardly any deviation and residence time dependence could be found. The importance of the residence time dependence increased when the species conversion was accelerated as it is the case for overstoichiometric combustion conditions and increased temperatures. The study focused furthermore on the fine structure in the EDC. Unlike the classical approach this part of the cell was modelled as a PFR instead of a PSR. For high temperature conditions there was hardly any difference between both reactor types. However, decreasing the temperature led to obvious deviations. Finally, the effect of the selective species transport between the cells on the conversion process was investigated

  11. The Molecular Modeling Workbook for Organic Chemistry (by Warren J. Hehre, Alan J. Shusterman, and Janet E. Nelson)

    Science.gov (United States)

    Crouch, R. David

    1999-09-01

    Wavefunction, Inc.: Irvine, CA, 1998. 307 pp. ISBN 1-890661-06-6. 30.00. This workbook is the latest in a series of "lab manuals" designed to increase the presence of molecular modeling and computational chemistry in undergraduate courses. The authors have designed the workbook to differ from its predecessors in two ways: the target audience is introductory organic chemistry students, and a CD-ROM containing files of molecules and data replaces the need for expensive molecular modeling software. It also differs from its predecessors in that the exercises in it are not really molecular modeling experiments. Instead, students are introduced to the field by viewing the results of computational work stored on the CD-ROM. The workbook is divided into 21 chapters, each of which covers a topic encountered in introductory-level organic chemistry. The sequence of chapters follows the sequence of topics that instructors of introductory organic courses might employ, allowing the workbook to be used with most modern organic chemistry texts. The heart of the workbook, though, is the CD-ROM included with the book. It contains files of molecules and their accompanying computational results as well as Spartan View, a software package that allows these models to be visualized. Although it does not allow actual calculations to be performed, Spartan View permits the user to rotate molecules, intermediates, and transition states and retrieve "precalculated" values of bond and dihedral angles, bond lengths, energies, dipole moments, charge, and frequency of vibration. Spartan View also allows the user to search molecules and intermediates for electron-rich or electron-poor regions by showing electrostatic potential as well as HOMOs and LUMOs. Some files allow for animation of reactions or conformational changes. Note, however, that since the data are just stored on the CD-ROM, not all the data are available for all files. Although performing calculations is not an option, Spartan View

  12. Application of a G-equation based combustion model and detailed chemistry to prediction of autoignition in a gasoline direct injection engine

    Energy Technology Data Exchange (ETDEWEB)

    Juneja, Harmit [Wisconsin Engine Research Consultants (WERC), Madison, WI (United States); Sczomak, David P. [General Motors Powertrain Advanced Engineering, Pontiac, MI (United States); Ge, Hai-Wen; Yang, Shiyou [Wisconsin Univ., Madison (United States); Reitz, Rolf D. [Wisconsin Univ., Madison (United States). Dept. of Mechanical Engineering

    2010-07-01

    Autoignition in an experimental single cylinder homogeneous gasoline direct injection engine was modeled using a level set method (G-equation) based combustion model incorporating detailed chemical kinetics. Several improvements have been made to the combustion model recently and implemented in the KIVA-3V code. These improvements include a transport equation residual model, the modeling of flame front quenching in highly stratified mixtures, and a recently developed primary reference fuel (PRF) chemistry mechanism. An adaptive multi grid chemistry (AMC) model was also implemented to speed-up the chemistry calculation. The integrated model was used to simulate the combustion process including the prediction of autoignition in a gasoline direct-injection engine. Experimental data in the form of a spark timing sweep covering a highly knocking to a non-knocking operating condition was used to validate the combustion modeling approach. The improved G-equation model combined with detailed chemistry matches the experimental data very well and does an excellent job at predicting the onset, location, and intensity of knock as a function of spark timing. (orig.)

  13. Use of North American and European air quality networks to evaluate global chemistry-climate modeling of surface ozone

    Directory of Open Access Journals (Sweden)

    J. L. Schnell

    2015-04-01

    Full Text Available We test the current generation of global chemistry-climate models in their ability to simulate observed, present-day surface ozone. Models are evaluated against hourly surface ozone from 4217 stations in North America and Europe that are averaged over 1° × 1° grid cells, allowing commensurate model-measurement comparison. Models are generally biased high during all hours of the day and in all regions. Most models simulate the shape of regional summertime diurnal and annual cycles well, correctly matching the timing of hourly (~ 15:00 and monthly (mid-June peak surface ozone abundance. The amplitude of these cycles is less successfully matched. The observed summertime diurnal range (~ 25 ppb is underestimated in all regions by about 7 ppb, and the observed seasonal range (~ 21 ppb is underestimated by about 5 ppb except in the most polluted regions where it is overestimated by about 5 ppb. The models generally match the pattern of the observed summertime ozone enhancement, but they overestimate its magnitude in most regions. Most models capture the observed distribution of extreme episode sizes, correctly showing that about 80% of individual extreme events occur in large-scale, multi-day episodes of more than 100 grid cells. The observed linear relationship showing increases in ozone by up to 6 ppb for larger-sized episodes is also matched.

  14. Assimilation of IASI satellite CO fields into a global chemistry transport model for validation against aircraft measurements

    Directory of Open Access Journals (Sweden)

    A. Klonecki

    2011-12-01

    Full Text Available A modelling system for assimilation of CO total columns measured by the IASI/MetOp was developed. The system, based on a sub-optimal Kalman filter coupled with the LMDz-INCA chemistry transport model, allows both assimilating long periods of historical data and making rapid forecasts of the CO concentrations in the middle troposphere based on latest available measurements. Tests of the forecast system were conducted during the international POLARCAT campaigns. A specific treatment that takes into account the representativeness of observations at the scale of the model grid is applied to the IASI CO columns and associated errors before their assimilation in the model. This paper presents the results of assimilation of eight months of historical satellite data measured in 2008. Comparisons of the assimilated CO profiles with independent in situ CO measurements from the MOZAIC program and the POLARCAT aircraft campaigns indicate that the assimilation leads to a considerable improvement of the model simulations in the middle troposphere as compared with a control run with no assimilation. Model biases in the simulation of background values are reduced and improvement in the simulation of very high concentrations is observed. The improvement is due to the transport by the model of the information present in the IASI CO retrievals. The consistency of the improvement contributes to the validation of the IASI CO data.

  15. A two-dimensional atmospheric chemistry modeling investigation of Earth's Phanerozoic O3 and near-surface ultraviolet radiation history

    Science.gov (United States)

    Harfoot, Michael B. J.; Beerling, David J.; Lomax, Barry H.; Pyle, John A.

    2007-04-01

    We use the Cambridge two-dimensional (2-D) chemistry-radiation transport model to investigate the implications for column O3 and near-surface ultraviolet radiation (UV), of variations in atmospheric O2 content over the Phanerozoic (last 540 Myr). Model results confirm some earlier 1-D model investigations showing that global annual mean O3 column increases monotonically with atmospheric O2. Sensitivity studies indicate that changes in temperature and N2O exert a minor influence on O3 relative to O2. We reconstructed Earth's O3 history by interpolating the modeled relationship between O3 and O2 onto two Phanerozoic O2 histories. Our results indicate that the largest variation in Phanerozoic column O3 occurred between 400 and 200 Myr ago, corresponding to a rise in atmospheric O2 to ˜1.5 times the present atmospheric level (PAL) and subsequent fall to ˜0.5 PAL. The O3 response to this O2 decline shows latitudinal differences, thinning most at high latitudes (30-40 Dobson units (1 DU = 0.001 atm cm) at 66°N) and least at low latitudes (5-10 DU at 9°N) where a "self-healing" effect is evident. This O3 depletion coincides with significant increases in the near-surface biologically active UV radiation at high latitudes, +28% as weighted by the Thimijan spectral weighting function. O3 and UV changes were exacerbated when we incorporated a direct feedback of the terrestrial biosphere on atmospheric chemistry, through enhanced N2O production as the climate switched from an icehouse to a greenhouse mode. On the basis of a summary of field and laboratory experimental evidence, we suggest that these UV radiation increases may have exerted subtle rather than catastrophic effects on ecosystem processes.

  16. Modeling the present and future impact of aviation on climate: an AOGCM approach with online coupled chemistry

    Directory of Open Access Journals (Sweden)

    P. Huszar

    2013-02-01

    Full Text Available This work assesses the impact of emissions from global aviation on climate, while focus is given on the temperature response. Our work is among the first that use an Atmosphere Ocean General Circulation Model (AOGCM online coupled with stratospheric chemistry and the chemistry of mid-troposphere relevant for aviation emissions. Compared to previous studies where either the chemical effects of aviation emissions were investigated using global chemistry transport models or the climate impact of aviation was under focus implementing prescribed perturbation fields or simplified chemistry schemes, our study uses emissions as inputs and provides the climate response as output. The model we use is the Météo-France CNRM-CM5.1 earth system model extended with the REPROBUS stratospheric scheme. The timehorizon of our interest is 1940–2100 assuming the A1B SRES scenario. We investigate the present and future impact of the most relevant aviation emissions (CO2, NOx, contrail and contrail induced cirrus – CIC as well as the impact of the non-CO2 emissions and the "Total" aviation impact. Aviation produced aerosol is not considered in the study.

    The general conclusion is that the aviation emissions result in a less pronounced climate signal than previous studies suggest. Moreover this signal is more unique at higher altitudes (above the mid-troposphere than near the surface.

    The global averaged near surface CO2 impact reaches around 0.1 °C by the end of the 21st century and can be even negative in the middle of the century. The non-CO2 impact remains positive during the whole 21st century reaching 0.2 °C in its second half. A similar warming is calculated for the CIC effect. The NOx emissions impact is almost negligible in our simulations, as the aviation induced ozone production was small in the model's chemical scheme. As a consequence the non-CO2 signal

  17. Good chemistry

    OpenAIRE

    Petsko, Gregory A

    2004-01-01

    The subject matter in chemistry courses reflects almost nothing of the issues that chemists are interested in. It is important to formulate a set of topics - and a Medical College Admissions Test reflecting them - that would leave chemistry departments no choice but to change their teaching.

  18. Results from a model of course-based undergraduate research in the first- and second-year chemistry curriculum

    Science.gov (United States)

    Weaver, Gabriela

    2014-03-01

    The Center for Authentic Science Practice in Education (CASPiE) is a project funded by the URC program of the NSF Chemistry Division. The purpose of CASPiE was to provide students in first and second year laboratory courses with authentic research experiences as a gateway to more traditional forms of undergraduate research. Each research experience is a 6- to 8-week laboratory project based on and contributing to the research work of the experiment's author through data or preparation of samples. The CASPiE program has resulted in a model for engaging students in undergraduate research early in their college careers. To date, CASPiE has provided that experience to over 6000 students at 17 different institutions. Evaluation data collected has included student surveys, interviews and longitudinal analysis of performance. We have found that students' perceptions of their understanding of the material and the discipline increase over the course of the semester, whereas they are seen to decrease in the control courses. Students demonstrate a greater ability to explain the meaning and purpose of their experimental procedures and results and provide extensions to the experimental design, compared not only to control courses but also compared to inquiry-based courses. Longitudinal analysis of grades indicates a possible benefit to performance in courses related to the discipline two and three years later. A similar implementation in biology courses has demonstrated an increase in critical thinking scores. Work supported by the National Science Foundation, Division of Chemistry.

  19. Implementation of the chemistry module MECCA (v2.5 in the modal aerosol version of the Community Atmosphere Model component (v3.6.33 of the Community Earth System Model

    Directory of Open Access Journals (Sweden)

    M. S. Long

    2012-06-01

    Full Text Available A coupled atmospheric chemistry and climate system model was developed using the modal aerosol version of the National Center for Atmospheric Research Community Atmosphere Model (modal-CAM and the Max Planck Institute for Chemistry's Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA to provide enhanced resolution of multiphase processes, particularly those involving inorganic halogens, and associated impacts on atmospheric composition and climate. Three Rosenbrock solvers (Ros-2, Ros-3, RODAS-3 were tested in conjunction with the basic load balancing options available to modal CAM (1 to establish an optimal configuration of the implicitly-solved multiphase chemistry module that maximizes both computational speed and repeatability of Ros-2 and RODAS-3 results versus Ros-3, and (2 to identify potential implementation strategies for future versions of this and similar coupled systems. RODAS-3 was faster than Ros-2 and Ros-3 with good reproduction of Ros-3 results, while Ros-2 was both slower and substantially less reproducible relative to Ros-3 results. Modal-CAM with MECCA chemistry was a factor of 15 slower than modal-CAM using standard chemistry. MECCA chemistry integration times demonstrated a systematic frequency distribution for all three solvers, and revealed that the change in run-time performance was due to a change in the frequency distribution chemical integration times; the peak frequency was similar for all solvers. This suggests that efficient chemistry-focused load-balancing schemes can be developed that rely on the parameters of this frequency distribution.

  20. A plant wide aqueous phase chemistry model describing pH variations and ion speciation/pairing in wastewater treatment process models

    DEFF Research Database (Denmark)

    Flores-Alsina, X.; Mbamba, C. Kazadi; Solon, K.;

    There is a growing interest within the Wastewater Treatment Plant (WWTP) modelling community to correctly describe physico-chemical processes after many years of mainly focusing on biokinetics (Batstone et al., 2012). Indeed, future modelling needs, such as a plant-wide phosphorus (P) description...... presented and interfaced with industry standard models. The module involves extensive consideration of non-ideality by including ion activities instead of molar concentrations and complex ion pairing. The general equilibria are formulated as a set of Differential Algebraic Equations (DAEs) instead of...... cationic/anionic loads. In this way, the general applicability/flexibility of the proposed approach is demonstrated by implementing the aqueous phase chemistry module in some of the most frequently used WWTP process simulation models. Finally, it is shown how traditional wastewater modelling studies can be...

  1. An evaluation of the simulation of the edge of the Antarctic vortex by chemistry-climate models

    Directory of Open Access Journals (Sweden)

    H. Struthers

    2008-12-01

    Full Text Available The dynamical barrier to meridional mixing at the edge of the Antarctic spring stratospheric vortex is examined. Diagnostics are presented which demonstrate the link between the shape of the meridional mixing barrier at the edge of the vortex and the meridional gradients in total column ozone across the vortex edge. Results derived from reanalysis and measurement data sets are compared with equivalent diagnostics from five coupled chemistry-climate models to test how well the models capture the interaction between the dynamical structure of the stratospheric vortex and the chemical processes occurring within the vortex. Results show that the accuracy of the simulation of the dynamical vortex edge varies widely amongst the models studied here. This affects the ability of the models to simulate the large observed meridional gradients in total column ozone. Three of the models in this study simulated the inner edge of the vortex to be more than 7° closer to the pole than observed. This is expected to have important implications for how well these models simulate the extent of severe springtime ozone loss that occurs within the Antarctic vortex.

  2. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    International Nuclear Information System (INIS)

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

  3. Corrosion chemistry closing comments: opportunities in corrosion science facilitated by operando experimental characterization combined with multi-scale computational modelling.

    Science.gov (United States)

    Scully, John R

    2015-01-01

    Recent advances in characterization tools, computational capabilities, and theories have created opportunities for advancement in understanding of solid-fluid interfaces at the nanoscale in corroding metallic systems. The Faraday Discussion on Corrosion Chemistry in 2015 highlighted some of the current needs, gaps and opportunities in corrosion science. Themes were organized into several hierarchical categories that provide an organizational framework for corrosion. Opportunities to develop fundamental physical and chemical data which will enable further progress in thermodynamic and kinetic modelling of corrosion were discussed. These will enable new and better understanding of unit processes that govern corrosion at the nanoscale. Additional topics discussed included scales, films and oxides, fluid-surface and molecular-surface interactions, selected topics in corrosion science and engineering as well as corrosion control. Corrosion science and engineering topics included complex alloy dissolution, local corrosion, and modelling of specific corrosion processes that are made up of collections of temporally and spatially varying unit processes such as oxidation, ion transport, and competitive adsorption. Corrosion control and mitigation topics covered some new insights on coatings and inhibitors. Further advances in operando or in situ experimental characterization strategies at the nanoscale combined with computational modelling will enhance progress in the field, especially if coupling across length and time scales can be achieved incorporating the various phenomena encountered in corrosion. Readers are encouraged to not only to use this ad hoc organizational scheme to guide their immersion into the current opportunities in corrosion chemistry, but also to find value in the information presented in their own ways. PMID:26114392

  4. Corrosion chemistry closing comments: opportunities in corrosion science facilitated by operando experimental characterization combined with multi-scale computational modelling.

    Science.gov (United States)

    Scully, John R

    2015-01-01

    Recent advances in characterization tools, computational capabilities, and theories have created opportunities for advancement in understanding of solid-fluid interfaces at the nanoscale in corroding metallic systems. The Faraday Discussion on Corrosion Chemistry in 2015 highlighted some of the current needs, gaps and opportunities in corrosion science. Themes were organized into several hierarchical categories that provide an organizational framework for corrosion. Opportunities to develop fundamental physical and chemical data which will enable further progress in thermodynamic and kinetic modelling of corrosion were discussed. These will enable new and better understanding of unit processes that govern corrosion at the nanoscale. Additional topics discussed included scales, films and oxides, fluid-surface and molecular-surface interactions, selected topics in corrosion science and engineering as well as corrosion control. Corrosion science and engineering topics included complex alloy dissolution, local corrosion, and modelling of specific corrosion processes that are made up of collections of temporally and spatially varying unit processes such as oxidation, ion transport, and competitive adsorption. Corrosion control and mitigation topics covered some new insights on coatings and inhibitors. Further advances in operando or in situ experimental characterization strategies at the nanoscale combined with computational modelling will enhance progress in the field, especially if coupling across length and time scales can be achieved incorporating the various phenomena encountered in corrosion. Readers are encouraged to not only to use this ad hoc organizational scheme to guide their immersion into the current opportunities in corrosion chemistry, but also to find value in the information presented in their own ways.

  5. Heterogeneous chemistry: a mechanism missing in current models to explain secondary inorganic aerosol formation during the January 2013 haze episode in North China

    Directory of Open Access Journals (Sweden)

    B. Zheng

    2014-06-01

    Full Text Available Severe regional haze pollution events occurred in eastern and central China in January 2013, which had adverse effects on the environment and public health. Extremely high levels of particulate matter with aerodynamic diameter of 2.5 μm or less (PM2.5 with dominant components of sulfate and nitrate are responsible for the haze pollution. Although heterogeneous chemistry is thought to play an important role in the production of sulfate and nitrate during haze episodes, few studies have comprehensively evaluated the effect of heterogeneous chemistry on haze formation in China by using the 3-D models due to of a lack of treatments for heterogeneous reactions in most climate and chemical transport models. In this work, the offline-coupled WRF-CMAQ model with newly added heterogeneous reactions is applied to East Asia to evaluate the impacts of heterogeneous chemistry and the meteorological anomaly during January 2013 on regional haze formation. The revised CMAQ with heterogeneous chemistry not only captures the magnitude and temporal variation of sulfate and nitrate, but also reproduces the enhancement of relative contribution of sulfate and nitrate to PM2.5 mass from clean days to polluted haze days. These results indicate the significant role of heterogeneous chemistry in regional haze formation and improve the understanding of the haze formation mechanisms during the January 2013 episode.

  6. Trace Chemistry

    Science.gov (United States)

    Radhakrishnan, Krishnan; Whitefield, Philip

    1999-01-01

    The goals of the trace chemistry group were to identify the processes relevant to aerosol and aerosol precursor formation occurring within aircraft gas turbine engines; that is, within the combustor, turbine, and nozzle. The topics of discussion focused on whether the chemistry of aerosol formation is homogeneous or heterogeneous; what species are important for aerosol and aerosol precursor formation; what modeling/theoretical activities to pursue; what experiments to carry out that both support modeling activities and elucidate fundamental processes; and the role of particulates in aerosol and aerosol precursor formation. The consensus of the group was that attention should be focused on SO2, SO3, and aerosols. Of immediate concern is the measurement of the concentration of the species SO3, SO2, H2SO4 OH, HO2, H2O2, O, NO, NO2, HONO, HNO3, CO, and CO2 and particulates in various engines, both those currently in use and those in development. The recommendation was that concentration measurements should be made at both the combustor exit and the engine exit. At each location the above species were classified into one of four categories of decreasing importance, Priority I through IV, as follows: Combustor exit: Priority I species - SO3:SO2 ratio, SO3, SO2, and particulates; Priority II species: OH and O; Priority III species - NO and NO2; and Priority IV species - CO and CO2. For the Engine exit: Priority I species - SO3:SO2 ratio, SO3, SO2,H2SO4, and particulates; Priority II species: OH,HO2, H2O2, and O; Priority III species - NO, NO2, HONO, and HNO3; and Priority IV species - CO and CO2. Table I summarizes the anticipated concentration range of each of these species. For particulate matter, the quantities of interest are the number density, size distribution, and composition. In order to provide data for validating multidimensional reacting flow models, it would be desirable to make 2-D, time-resolved measurements of the concentrations of the above species and

  7. Students' Involvement in Authentic Modelling Practices as Contexts in Chemistry Education

    Science.gov (United States)

    Prins, Gjalt T.; Bulte, Astrid M. W.; Van Driel, Jan H.; Pilot, Albert

    2009-01-01

    In science education students should come to understand the nature and significance of models. A promising strategy to achieve this goal is using authentic modelling practices as contexts for meaningful learning of models and modelling. An authentic practice is defined as professionals working with common motives and purposes, pertaining to a…

  8. A pebbles accretion model with chemistry and implications for the solar system in the lights of Juno

    Science.gov (United States)

    Ali-Dib, Mohamad

    2016-10-01

    The chemical compositions of the solar system giant planets are a major source of informations on their origins. Since the measurements by the Galileo probe, multiple models have been put forward to try and explain the noble gases enrichment in Jupiter. The most discussed among these are its formation in the outer cold nebula and its formation in a partially photoevaporated disk. In this work I couple a pebbles accretion model to the disk's chemistry and photoevaporation in order to make predictions from both scenarios and compare them to the upcoming Juno measurements. The model include pebbles and gas accretion, type I and II migration, photoevaporation and chemical measurements from meteorites, comets and disks. Population synthesis simulations are used to explore the models free parameters (planets initial conditions), where then the results are narrowed down using the planets chemical, dynamical and core mass costraints. We end up with a population that fits all of the constrains. These are then used to predict the oxygen abundance and core mass in Jupiter, to be compared to results of Juno. Same calculations are also done for Saturn and Neptune for comparison. I will present the results from these simulations as well as the predictions from all of the different models.Ali-Dib, M. (2016ab, submitted to MNRAS)

  9. Description of the Mountain Cloud Chemistry Program version of the PLUVIUS MOD 5. 0 reactive storm simulation model

    Energy Technology Data Exchange (ETDEWEB)

    Luecken, D.J.; Whiteman, C.D.; Chapman, E.G.; Andrews, G.L.; Bader, D.C.

    1987-07-01

    Damage to forest ecosystems on mountains in the eastern United States has prompted a study conducted for the US Environmental Protection Agency's Mountain Cloud Chemistry Program (MCCP). This study has led to the development of a numerical model called MCCP PLUVIUS, which has been used to investigate the chemical transformations and cloud droplet deposition in shallow, nonprecipitating orographic clouds. The MCCP PLUVIUS model was developed as a specialized version of the existing PLUVIUS MOD 5.0 reactive storm model. It is capable of simulating aerosol scavenging, nonreactive gas scavenging, aqueous phase SO/sub 2/ reactions, and cloud water deposition. A description of the new model is provided along with information on model inputs and outputs, as well as suggestions for its further development. The MCCP PLUVIUS incorporates a new method to determine the depth of the layer of air which flows over a mountaintop to produce an orographic cloud event. It provides a new method for calculating hydrogen ion concentrations, and provides updated expressions and values for solubility, dissociation and reaction rate constants.

  10. Modeling the present and future impact of aviation on climate: an AOGCM approach with online coupled chemistry

    Directory of Open Access Journals (Sweden)

    P. Huszar

    2013-10-01

    Full Text Available Our work is among the first that use an atmosphere-ocean general circulation model (AOGCM with online chemistry to evaluate the impact of future aviation emissions on temperature. Other particularities of our study include non-scaling to the aviation emissions, and the analysis of models' transient response using ensemble simulations. The model we use is the Météo-France CNRM-CM5.1 earth system model extended with the REPROBUS chemistry scheme. The time horizon of our interest is 1940–2100, assuming the A1B SRES scenario. We investigate the present and future impact of aviation emissions of CO2, NOx and H2O on climate, taking into account changes in greenhouse gases, contrails and contrail-induced cirrus (CIC. As in many transport-related impact studies, we distinguish between the climate impacts of CO2 emissions and those of non-CO2 emissions. Aviation-produced aerosol is not considered in the study. Our modeling system simulated a notable sea-ice bias in the Arctic, and therefore results concerning the surface should be viewed with caution. The global averaged near-surface CO2 impact reaches around 0.1 K by the end of the 21st century, while the non-CO2 impact reaches 0.2 K in the second half of the century. The NOx emissions impact is almost negligible in our simulations, as our aviation-induced ozone production is small. As a consequence, the non-CO2 signal is very similar to the CIC signal. The seasonal analysis shows that the strongest warming due to aviation is modeled for the late summer and early autumn. In the stratosphere, a significant cooling is attributed to aviation CO2 emissions (−0.25 K by 2100. A −0.3 K temperature decrease is modeled when considering all the aviation emissions, but no significant signal appears from the CIC or NOx forcings in the stratosphere.

  11. The Los Alamos National Laboratory Chemistry and Metallurgy Research Facility upgrades project - A model for waste minimization

    International Nuclear Information System (INIS)

    The Los Alamos National Laboratory (LANL) Chemistry and Metallurgy Research (CMR) Facility, constructed in 1952, is currently undergoing a major, multi-year construction project. Many of the operations required under this project (i.e., design, demolition, decontamination, construction, and waste management) mimic the processes required of a large scale decontamination and decommissioning (D ampersand D) job and are identical to the requirements of any of several upgrades projects anticipated for LANL and other Department of Energy (DOE) sites. For these reasons the CMR Upgrades Project is seen as an ideal model facility - to test the application, and measure the success of - waste minimization techniques which could be brought to bear on any of the similar projects. The purpose of this paper will be to discuss the past, present, and anticipated waste minimization applications at the facility and will focus on the development and execution of the project's open-quotes Waste Minimization/Pollution Prevention Strategic Plan.close quotes

  12. Use of North American and European Air Quality Networks to Evaluate Global Chemistry-Climate Modeling of Surface Ozone

    Science.gov (United States)

    Schnell, J. L.; Prather, M. J.; Josse, B.; Naik, V.; Horowitz, L. W.; Cameron-Smith, P.; Bergmann, D.; Zeng, G.; Plummer, D. A.; Sudo, K.; Nagashima, T.; Shindell, D. T.; Faluvegi, G.; Strode, S. A.

    2015-01-01

    We test the current generation of global chemistry-climate models in their ability to simulate observed, present-day surface ozone. Models are evaluated against hourly surface ozone from 4217 stations in North America and Europe that are averaged over 1 degree by 1 degree grid cells, allowing commensurate model-measurement comparison. Models are generally biased high during all hours of the day and in all regions. Most models simulate the shape of regional summertime diurnal and annual cycles well, correctly matching the timing of hourly (approximately 15:00 local time (LT)) and monthly (mid-June) peak surface ozone abundance. The amplitude of these cycles is less successfully matched. The observed summertime diurnal range (25 ppb) is underestimated in all regions by about 7 parts per billion, and the observed seasonal range (approximately 21 parts per billion) is underestimated by about 5 parts per billion except in the most polluted regions, where it is overestimated by about 5 parts per billion. The models generally match the pattern of the observed summertime ozone enhancement, but they overestimate its magnitude in most regions. Most models capture the observed distribution of extreme episode sizes, correctly showing that about 80 percent of individual extreme events occur in large-scale, multi-day episodes of more than 100 grid cells. The models also match the observed linear relationship between episode size and a measure of episode intensity, which shows increases in ozone abundance by up to 6 parts per billion for larger-sized episodes. We conclude that the skill of the models evaluated here provides confidence in their projections of future surface ozone.

  13. CHEMISTRY OF SO{sub 2} ON MODEL METAL AND OXIDE CATALYSTS: PHOTOEMISSION AND XANES STUDIES

    Energy Technology Data Exchange (ETDEWEB)

    RODRIGUEZ,J.A.; JIRSAK,T.; CHATURVEDI,S.; HRBEK,J.; FREITAG,A.; LARESE,J.Z.

    2000-07-09

    High-resolution synchrotron based photoemission and x-ray absorption spectroscopy have been used to study the interaction of SO{sub 2} with a series of metals and oxides. The chemistry of SO{sub 2} on metal surfaces is rich. At low coverages, the molecule fully decomposes into atomic S and O. At large coverages, the formation of SO{sub 3} and SO{sub 4} takes place. The following sequence was found for the reactivity of the metals towards SO{sub 2}: Pt {approx} Rh < Ru < Mo << Zn, Sn, Cs. Alloying can be useful for reducing the chemical affinity of a metal for SO{sub 2} and controlling S poisoning. Pd atoms bonded to Rh and Pt atoms bonded to Sn interact weakly with SO{sub 2}. In general, SO{sub 2} mainly reacts with the O centers of metal oxides. SO{sub 4} is formed on CeO{sub 2} and SO{sub 3} on ZnO. On these systems there is no decomposition of SO{sub 2}. Dissociation of the molecule is observed after introducing a large amount of Ce{sup 3+} sites in ceria, or after depositing Cu or alkali metals on the oxide surfaces. These promote the catalytic activity of the oxides during the destruction of SO{sub 2}.

  14. Click chemistry generated model DNA-peptide heteroconjugates as tools for mass spectrometry.

    Science.gov (United States)

    Flett, Fiona J; Walton, Jeffrey G A; Mackay, C Logan; Interthal, Heidrun

    2015-10-01

    UV cross-linking of nucleic acids to proteins in combination with mass spectrometry is a powerful technique to identify proteins, peptides, and the amino acids involved in intermolecular interactions within nucleic acid-protein complexes. However, the mass spectrometric identification of cross-linked nucleic acid-protein heteroconjugates in complex mixtures and MS/MS characterization of the specific sites of cross-linking is extremely challenging. As a tool for the optimization of sample preparation, ionization, fragmentation, and detection by mass spectrometry, novel synthetic DNA-peptide heteroconjugates were generated to act as mimics of UV cross-linked heteroconjugates. Click chemistry was employed to cross-link peptides to DNA oligonucleotides. These heteroconjugates were fully characterized by high resolution FTICR mass spectrometry and by collision-induced dissociation (CID) following nuclease P1 digestion of the DNA moiety to a single nucleotide monophosphate. This allowed the exact site of the cross-linking within the peptide to be unambiguously assigned. These synthetic DNA-peptide heteroconjugates have the potential to be of use for a variety of applications that involve DNA-peptide heteroconjugates.

  15. A comparison of chemistry and dust cloud formation in ultracool dwarf model atmospheres

    CERN Document Server

    Helling, Ch; Allard, F; Dehn, M; Hauschild, P; Homeier, D; Lodders, K; Marley, M; Rietmeijer, F; Tsuji, T; Woitke, P

    2008-01-01

    The atmospheres of substellar objects contain clouds of oxides, iron, silicates, and other refractory condensates. Water clouds are expected in the coolest objects. The opacity of these `dust' clouds strongly affects both the atmospheric temperature-pressure profile and the emergent flux. Thus any attempt to model the spectra of these atmospheres must incorporate a cloud model. However the diversity of cloud models in atmospheric simulations is large and it is not always clear how the underlying physics of the various models compare. Likewise the observational consequences of different modeling approaches can be masked by other model differences, making objective comparisons challenging. In order to clarify the current state of the modeling approaches, this paper compares five different cloud models in two sets of tests. Test case 1 tests the dust cloud models for a prescribed L, L--T, and T-dwarf atmospheric (temperature T, pressure p, convective velocity vconv)-structures. Test case 2 compares complete mode...

  16. Quantum chemistry

    CERN Document Server

    Lowe, John P

    1993-01-01

    Praised for its appealing writing style and clear pedagogy, Lowe's Quantum Chemistry is now available in its Second Edition as a text for senior undergraduate- and graduate-level chemistry students. The book assumes little mathematical or physical sophistication and emphasizes an understanding of the techniques and results of quantum chemistry, thus enabling students to comprehend much of the current chemical literature in which quantum chemical methods or concepts are used as tools. The book begins with a six-chapter introduction of standard one-dimensional systems, the hydrogen atom,

  17. Recent developments of surface complexation models applied to environmental aquatic chemistry

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Based on numerous latest references, the current developments in surface complexation, surface precipitation and the corresponding models (SCMs and SPMs), were reviewed. The contents involved comparison on surface charge composition and layer-structure of solid-solution interface for the classical 1-pK and 2- pK models, In addition, the fundamental concept and relations of the new models, i.e., multi-site complexation (MUSIC) and charge -distribution (CD) MUSIC models were described as well. To avoid misuse or abuse, it must be emphasized that the applicability nd limitation for each model should be considered carefully when selecting the concerned model(s). In addition, some new powerful techniques for surface characterization and analysis applied to model establishment and modification were also briefly introduced.

  18. Nonequilibrium radiation and chemistry models for aerocapture vehicle flowfields, volume 1

    Science.gov (United States)

    Carlson, Leland A.

    1991-01-01

    The following subject areas are covered: the development of detailed nonequilibrium radiation models for molecules along with appropriate models for atoms; the inclusion of nongray radiation gasdynamic coupling in the VSL (Viscous Shock Layer) code; the development and evaluation of various electron-electronic energy models; and an examination of the effects of shock slip.

  19. Sensitivity of meteorological input and soil properties in simulating aerosols (dust, PM10, and BC) using CHIMERE chemistry transport model

    Indian Academy of Sciences (India)

    Nishi Srivastava; S K Satheesh; Nadège Blond

    2014-08-01

    The objective of this study is to evaluate the ability of a European chemistry transport model, ‘CHIMERE’ driven by the US meteorological model MM5, in simulating aerosol concentrations [dust, PM10 and black carbon (BC)] over the Indian region. An evaluation of a meteorological event (dust storm); impact of change in soil-related parameters and meteorological input grid resolution on these aerosol concentrations has been performed. Dust storm simulation over Indo-Gangetic basin indicates ability of the model to capture dust storm events. Measured (AERONET data) and simulated parameters such as aerosol optical depth (AOD) and Angstrom exponent are used to evaluate the performance of the model to capture the dust storm event. A sensitivity study is performed to investigate the impact of change in soil characteristics (thickness of the soil layer in contact with air, volumetric water, and air content of the soil) and meteorological input grid resolution on the aerosol (dust, PM10, BC) distribution. Results show that soil parameters and meteorological input grid resolution have an important impact on spatial distribution of aerosol (dust, PM10, BC) concentrations.

  20. Laboratory Studies of the Reactive Chemistry and Changing CCN Properties of Secondary Organic Aerosol, Including Model Development

    Energy Technology Data Exchange (ETDEWEB)

    Scot Martin

    2013-01-31

    The chemical evolution of secondary-organic-aerosol (SOA) particles and how this evolution alters their cloud-nucleating properties were studied. Simplified forms of full Koehler theory were targeted, specifically forms that contain only those aspects essential to describing the laboratory observations, because of the requirement to minimize computational burden for use in integrated climate and chemistry models. The associated data analysis and interpretation have therefore focused on model development in the framework of modified kappa-Koehler theory. Kappa is a single parameter describing effective hygroscopicity, grouping together several separate physicochemical parameters (e.g., molar volume, surface tension, and van't Hoff factor) that otherwise must be tracked and evaluated in an iterative full-Koehler equation in a large-scale model. A major finding of the project was that secondary organic materials produced by the oxidation of a range of biogenic volatile organic compounds for diverse conditions have kappa values bracketed in the range of 0.10 +/- 0.05. In these same experiments, somewhat incongruently there was significant chemical variation in the secondary organic material, especially oxidation state, as was indicated by changes in the particle mass spectra. Taken together, these findings then support the use of kappa as a simplified yet accurate general parameter to represent the CCN activation of secondary organic material in large-scale atmospheric and climate models, thereby greatly reducing the computational burden while simultaneously including the most recent mechanistic findings of laboratory studies.

  1. The description and validation of a computationally-Efficient CH4-CO-OH (ECCOHv1.01 chemistry module for 3-D model applications

    Directory of Open Access Journals (Sweden)

    Y. F. Elshorbany

    2015-11-01

    Full Text Available We present the Efficient CH4-CO-OH chemistry module (ECCOH that allows for the simulation of the methane, carbon monoxide and hydroxyl radical (CH4-CO-OH system, within a chemistry climate model, carbon cycle model, or earth system model. The computational efficiency of the module allows many multi-decadal sensitivity simulations of the CH4-CO-OH system, which primarily determines the global atmospheric oxidizing capacity. This capability is important for capturing the nonlinear feedbacks of the CH4-CO-OH system and understanding the perturbations to methane, CO and OH and the concomitant impacts on climate. We implemented the ECCOH chemistry module into the NASA GEOS-5 Atmospheric Global Circulation Model (AGCM, performed multiple sensitivity simulations of the CH4-CO-OH system over two decades, and evaluated the model output with surface and satellite datasets of methane and CO. The favorable comparison of output from the ECCOH chemistry module (as configured in the GEOS-5 AGCM with observations demonstrates the fidelity of the module for use in scientific research.

  2. Materials Chemistry

    CERN Document Server

    Fahlman, Bradley D

    2011-01-01

    The 2nd edition of Materials Chemistry builds on the strengths that were recognized by a 2008 Textbook Excellence Award from the Text and Academic Authors Association (TAA). Materials Chemistry addresses inorganic-, organic-, and nano-based materials from a structure vs. property treatment, providing a suitable breadth and depth coverage of the rapidly evolving materials field. The 2nd edition continues to offer innovative coverage and practical perspective throughout. After briefly defining materials chemistry and its history, seven chapters discuss solid-state chemistry, metals, semiconducting materials, organic "soft" materials, nanomaterials, and materials characterization. All chapters have been thoroughly updated and expanded with, for example, new sections on ‘soft lithographic’ patterning, ‘click chemistry’ polymerization, nanotoxicity, graphene, as well as many biomaterials applications. The polymer and ‘soft’ materials chapter represents the largest expansion for the 2nd edition. Each ch...

  3. Introductory Chemistry

    OpenAIRE

    Baron, Mark; Gonzalez-Rodriguez, Jose; Stevens, Gary; Gray, Nathan; Atherton, Thomas; Winn, Joss

    2010-01-01

    Teaching and Learning resources for the 1st Year Introductory Chemistry course (Forensic Science). 30 credits. These are Open Educational Resources (OER), made available for re-use under a Creative Commons license.

  4. Genetic algorithms and genetic programming for multiscale modeling: Applications in materials science and chemistry and advances in scalability

    Science.gov (United States)

    Sastry, Kumara Narasimha

    2007-03-01

    Effective and efficient rnultiscale modeling is essential to advance both the science and synthesis in a, wide array of fields such as physics, chemistry, materials science; biology, biotechnology and pharmacology. This study investigates the efficacy and potential of rising genetic algorithms for rnultiscale materials modeling and addresses some of the challenges involved in designing competent algorithms that solve hard problems quickly, reliably and accurately. In particular, this thesis demonstrates the use of genetic algorithms (GAs) and genetic programming (GP) in multiscale modeling with the help of two non-trivial case studies in materials science and chemistry. The first case study explores the utility of genetic programming (GP) in multi-timescaling alloy kinetics simulations. In essence, GP is used to bridge molecular dynamics and kinetic Monte Carlo methods to span orders-of-magnitude in simulation time. Specifically, GP is used to regress symbolically an inline barrier function from a limited set of molecular dynamics simulations to enable kinetic Monte Carlo that simulate seconds of real time. Results on a non-trivial example of vacancy-assisted migration on a surface of a face-centered cubic (fcc) Copper-Cobalt (CuxCo 1-x) alloy show that GP predicts all barriers with 0.1% error from calculations for less than 3% of active configurations, independent of type of potentials used to obtain the learning set of barriers via molecular dynamics. The resulting method enables 2--9 orders-of-magnitude increase in real-time dynamics simulations taking 4--7 orders-of-magnitude less CPU time. The second case study presents the application of multiobjective genetic algorithms (MOGAs) in multiscaling quantum chemistry simulations. Specifically, MOGAs are used to bridge high-level quantum chemistry and semiempirical methods to provide accurate representation of complex molecular excited-state and ground-state behavior. Results on ethylene and benzene---two common

  5. Analytical chemistry

    International Nuclear Information System (INIS)

    This book is comprised of nineteen chapters, which describes introduction of analytical chemistry, experimental error and statistics, chemistry equilibrium and solubility, gravimetric analysis with mechanism of precipitation, range and calculation of the result, volume analysis on general principle, sedimentation method on types and titration curve, acid base balance, acid base titration curve, complex and firing reaction, introduction of chemical electro analysis, acid-base titration curve, electrode and potentiometry, electrolysis and conductometry, voltammetry and polarographic spectrophotometry, atomic spectrometry, solvent extraction, chromatograph and experiments.

  6. Green Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Collison, Melanie

    2011-05-15

    Green chemistry is the science of chemistry used in a way that will not use or create hazardous substances. Dr. Rui Resendes is working in this field at GreenCentre Canada, an offshoot of PARTEQ Innovations in Kingston, Ontario. GreenCentre's preliminary findings suggest their licensed product {sup S}witchable Solutions{sup ,} featuring 3 classes of solvents and a surfactant, may be useful in bitumen oil sands extraction.

  7. Cluster Chemistry

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ Cansisting of eight scientists from the State Key Laboratory of Physical Chemistry of Solid Surfaces and Xiamen University, this creative research group is devoted to the research of cluster chemistry and creation of nanomaterials.After three-year hard work, the group scored a series of encouraging progresses in synthesis of clusters with special structures, including novel fullerenes, fullerene-like metal cluster compounds as well as other related nanomaterials, and their properties study.

  8. First implementation of secondary inorganic aerosols in the MOCAGE version R2.15.0 chemistry transport model

    Science.gov (United States)

    Guth, J.; Josse, B.; Marécal, V.; Joly, M.; Hamer, P.

    2016-01-01

    In this study we develop a secondary inorganic aerosol (SIA) module for the MOCAGE chemistry transport model developed at CNRM. The aim is to have a module suitable for running at different model resolutions and for operational applications with reasonable computing times. Based on the ISORROPIA II thermodynamic equilibrium module, the new version of the model is presented and evaluated at both the global and regional scales. The results show high concentrations of secondary inorganic aerosols in the most polluted regions: Europe, Asia and the eastern part of North America. Asia shows higher sulfate concentrations than other regions thanks to emission reductions in Europe and North America. Using two simulations, one with and the other without secondary inorganic aerosol formation, the global model outputs are compared to previous studies, to MODIS AOD retrievals, and also to in situ measurements from the HTAP database. The model shows a better agreement with MODIS AOD retrievals in all geographical regions after introducing the new SIA scheme. It also provides a good statistical agreement with in situ measurements of secondary inorganic aerosol composition: sulfate, nitrate and ammonium. In addition, the simulation with SIA generally gives a better agreement with observations for secondary inorganic aerosol precursors (nitric acid, sulfur dioxide, ammonia), in particular with a reduction of the modified normalized mean bias (MNMB). At the regional scale, over Europe, the model simulation with SIA is compared to the in situ measurements from the EMEP database and shows a good agreement with secondary inorganic aerosol composition. The results at the regional scale are consistent with those obtained from the global simulations. The AIRBASE database was used to compare the model to regulated air quality pollutants: particulate matter, ozone and nitrogen dioxide concentrations. Introduction of the SIA in MOCAGE provides a reduction in the PM2.5 MNMB of 0.44 on a

  9. Atmospheric transport and chemistry of trace gases in LMDz5B: evaluation and implications for inverse modelling

    Directory of Open Access Journals (Sweden)

    R. Locatelli

    2014-07-01

    Full Text Available Representation of atmospheric transport is a major source of error in the estimation of greenhouse gas sources and sinks by inverse modelling. Here we assess the impact on trace gas mole fractions of the new physical parameterisations recently implemented in the Atmospheric Global Climate Model LMDz to improve vertical diffusion, mesoscale mixing by thermal plumes in the planetary boundary layer (PBL, and deep convection in the troposphere. At the same time, the horizontal and vertical resolution of the model used in the inverse system has been increased. The aim of this paper is to evaluate the impact of these developments on the representation of trace gas transport and chemistry, and to anticipate the implications for inversions of greenhouse gas emissions using such an updated model. Comparison of a one-dimensional version of LMDz with large eddy simulations shows that the thermal scheme simulates shallow convective tracer transport in the PBL over land very efficiently, and much better than previous versions of the model. This result is confirmed in three dimensional simulations, by a much improved reproduction of the Radon-222 diurnal cycle. However, the enhanced dynamics of tracer concentrations induces a stronger sensitivity of the new LMDz configuration to external meteorological forcings. At larger scales, the inter-hemispheric exchange is slightly slower when using the new version of the model, bringing them closer to observations. The increase in the vertical resolution (from 19 to 39 layers significantly improves the representation of stratosphere/troposphere exchange. Furthermore, changes in atmospheric thermodynamic variables, such as temperature, due to changes in the PBL mixing, significantly modify chemical reaction rates and the equilibrium value of reactive trace gases. One implication of LMDz model developments for future inversions of greenhouse gas emissions is the ability of the updated system to assimilate a larger

  10. Interpreting the variability of CO2 columns over North America using a chemistry transport model: application to SCIAMACHY data

    Directory of Open Access Journals (Sweden)

    P. S. Monks

    2008-04-01

    Full Text Available We use the GEOS-Chem chemistry transport model to interpret variability of CO2 columns and associated column-averaged volume mixing ratios (CVMRs observed by the SCIAMACHY satellite instrument during the 2003 North American growing season, accounting for the instrument averaging kernel. Model and observed columns, largely determined by surface topography, averaged on a 2°×2.5° grid, are in excellent agreement (model bias=3%, r>0.9, as expected. Model and observed CVMRs, determined by scaling column CO2 by surface pressure data, are on average within 3% but are only weakly correlated, reflecting a large positive model bias (10–15 ppmv at 50–70° N during midsummer at the peak of biospheric uptake. GEOS-Chem generally reproduces the magnitude and seasonal cycle of observed CO2 surface VMRs across North America. During midsummer we find that model CVMRs and surface VMRs converge, reflecting the instrument vertical sensitivity and the strong influence of the land biosphere on lower tropospheric CO2 columns. We use model tagged tracers to show that local fluxes largely determine CVMR variability over North America, with the largest individual CVMR contributions (1.1% from the land biosphere. Fuel sources are relatively constant while biomass burning make a significant contribution only during midsummer. We also show that non-local sources contribute significantly to total CVMRs over North America, with the boreal Asian land biosphere contributing close to 1% in midsummer at high latitudes. We used the monthly-mean Jacobian matrix for North America to illustrate that: 1 North American CVMRs represent a superposition of many weak flux signatures, but differences in flux distributions should permit independent flux estimation; and 2 the atmospheric e-folding lifetimes for many of these flux signatures are 3–4 months, beyond which time they are too well-mixed to interpret.

  11. Solar cycle variations of stratospheric ozone and temperature in simulations of a coupled chemistry-climate model

    Directory of Open Access Journals (Sweden)

    J. Austin

    2007-01-01

    Full Text Available The results from three 45-year simulations of a coupled chemistry climate model are analysed for solar cycle influences on ozone and temperature. The simulations include UV forcing at the top of the atmosphere, which includes a generic 27-day solar rotation effect as well as the observed monthly values of the solar fluxes. The results are analysed for the 27-day and 11-year cycles in temperature and ozone. In accordance with previous results, the 27-day cycle results are in good qualitative agreement with observations, particularly for ozone. However, the results show significant variations, typically a factor of two or more in sensitivity to solar flux, depending on the solar cycle. In the lower and middle stratosphere we show good agreement also between the modelled and observed 11-year cycle results for the ozone vertical profile averaged over low latitudes. In particular, the minimum in solar response near 20 hPa is well simulated. In comparison, experiments of the model with fixed solar phase (solar maximum/solar mean and climatological sea surface temperatures lead to a poorer simulation of the solar response in the ozone vertical profile, indicating the need for variable phase simulations in solar sensitivity experiments. The role of sea surface temperatures and tropical upwelling in simulating the ozone minimum response are also discussed.

  12. Solar cycle variations of stratospheric ozone and temperature in simulations of a coupled chemistry-climate model

    Science.gov (United States)

    Austin, J.; Hood, L. L.; Soukharev, B. E.

    2007-03-01

    The results from three 45-year simulations of a coupled chemistry climate model are analysed for solar cycle influences on ozone and temperature. The simulations include UV forcing at the top of the atmosphere, which includes a generic 27-day solar rotation effect as well as the observed monthly values of the solar fluxes. The results are analysed for the 27-day and 11-year cycles in temperature and ozone. In accordance with previous results, the 27-day cycle results are in good qualitative agreement with observations, particularly for ozone. However, the results show significant variations, typically a factor of two or more in sensitivity to solar flux, depending on the solar cycle. In the lower and middle stratosphere we show good agreement also between the modelled and observed 11-year cycle results for the ozone vertical profile averaged over low latitudes. In particular, the minimum in solar response near 20 hPa is well simulated. In comparison, experiments of the model with fixed solar phase (solar maximum/solar mean) and climatological sea surface temperatures lead to a poorer simulation of the solar response in the ozone vertical profile, indicating the need for variable phase simulations in solar sensitivity experiments. The role of sea surface temperatures and tropical upwelling in simulating the ozone minimum response are also discussed.

  13. Water-Chemistry Evolution and Modeling of Radionuclide Sorption and Cation Exchange during Inundation of Frenchman Flat Playa

    Energy Technology Data Exchange (ETDEWEB)

    Hershey, Ronald; Cablk, Mary; LeFebre, Karen; Fenstermaker, Lynn; Decker, David

    2013-08-01

    valuable information about chemical processes occurring during inundation as the water disappeared. Important observations from water-chemistry analyses included: 1) total dissolved solids (TDS) and chloride ion (Cl-) concentrations were very low (TDS: < 200 mg/L and Cl-: < 3.0 mg/L, respectively) for all water samples regardless of time or areal extent; 2) all dissolved constituents were at concentrations well below what might be expected for evaporating shallow surface waters on a playa, even when 98 to 99 percent of the water had disappeared; 3) the amount of evaporation for the last water samples collected at the end of inundation, estimated with the stable isotopic ratios δ2H or δ18O, was approximately 60 percent; and 4) water samples analyzed by gamma spectroscopy did not show any man-made radioactivity; however, the short scanning time (24 hours) and relative chemical diluteness of the water samples (TDS ranged between 39 and 190 mg/L) may have contributed to none being detected. Additionally, any low-energy beta emitting radionuclides would not have been detected by gamma spectroscopy. From these observations, it was apparent that a significant portion of water on the playa did not evaporate, but rather infiltrated into the subsurface (approximately 40 percent). Consistent with this water chemistry-based conclusion is particle-size analysis of two archived Frenchman Flat playa soils samples, which showed low clay content in the near surface soil that also suggested infiltration. Infiltration of water from the playa during inundation into the subsurface does not necessarily imply that groundwater recharge is occurring, but it does provide a mechanism for moving residual radionuclides downward into the subsurface of Frenchman Flat playa. Water-mineral geochemical reactions were modeled so that changes in the water chemistry could be identified and the extent of reactions quantified. Geochemical modeling showed that evaporation; equilibrium with atmospheric carbon

  14. Dynamics of ozone and nitrogen oxides at Summit, Greenland. II. Simulating snowpack chemistry during a spring high ozone event with a 1-D process-scale model

    NARCIS (Netherlands)

    Murray, K.A.; Kramer, L.J.; Doskey, P.V.; Ganzeveld, L.N.; Seok, B.; Dam, van B.; Helmig, D.

    2015-01-01

    Observed depth profiles of nitric oxide (NO), nitrogen dioxide (NO2), and ozone (O3) in snowpack interstitial air at Summit, Greenland were best replicated by a 1-D process-scale model, which included (1) geometrical representation of snow grains as spheres, (2) aqueous-phase chemistry confined to a

  15. Introducing NMR to a General Chemistry Audience: A Structural-Based Instrumental Laboratory Relating Lewis Structures, Molecular Models, and [superscript 13]C NMR Data

    Science.gov (United States)

    Pulliam, Curtis R.; Pfeiffer, William F.; Thomas, Alyssa C.

    2015-01-01

    This paper describes a first-year general chemistry laboratory that uses NMR spectroscopy and model building to emphasize molecular shape and structure. It is appropriate for either a traditional or an atoms-first curriculum. Students learn the basis of structure and the use of NMR data through a cooperative learning hands-on laboratory…

  16. Modeling of meteorology, tracer transport and chemistry for the Uintah Basin Winter Ozone Studies 2012 and 2013

    Science.gov (United States)

    Ahmadov, R.; McKeen, S. A.; Angevine, W. M.; Frost, G. J.; Roberts, J. M.; De Gouw, J. A.; Warneke, C.; Peischl, J.; Brown, S. S.; Edwards, P. M.; Wild, R. J.; Pichugina, Y. L.; Banta, R. M.; Brewer, A.; Senff, C. J.; Langford, A. O.; Petron, G.; Karion, A.; Sweeney, C.; Schnell, R. C.; Johnson, B.; Zamora, R. J.; Helmig, D.; Park, J.; Evans, J.; Stephens, C. R.; Olson, J. B.; Trainer, M.

    2013-12-01

    The Uintah Basin Winter Ozone Studies (UBWOS) field campaigns took place during winter of 2012 and 2013 in the Uintah Basin, Utah. The studies were aimed at characterizing meteorology, emissions of atmospheric constituents and air chemistry in a region abundant with oil and gas production, with associated emissions of various volatile organic compounds (VOCs) and NOx. High ozone pollution events were observed throughout the Uintah Basin during the winter of 2013, but not during the winter of 2012. A clear understanding of the processes leading to high ozone events is still lacking. We present here high spatiotemporal resolution simulations of meteorology, tracer transport and gas chemistry over the basin during January-February, 2012 and 2013 using the WRF/Chem regional photochemical model. Correctly characterizing the meteorology poses unique challenges due to complex terrain, cold-pool conditions, and shallow inversion layers observed during the winter of 2013. We discuss the approach taken to adequately simulate the meteorology over the basin and present evaluations of the modeled meteorology using surface, lidar and tethersonde measurements. Initial simulations use a passive tracer within the model as a surrogate for CH4 released from oil and gas wells. These tracer transport simulations show that concentrations of inert, emitted species near the surface in 2013 were 4-8 times higher than 2012 due to much shallower boundary layers and reduced winds in 2013. This is supported by in-situ measurements of CH4 made at the Horse Pool surface station during the field campaigns. Full photochemical simulations are forced by VOC and NOx emissions that are determined in a top-down approach, using observed emission ratios of VOC and NOx relative to CH4, along with available information of active wells, compressors, and processing plants. We focus on differences in meteorology, temperature, and radiation between the two winters in determining ozone concentrations in the

  17. Structure, Raman spectra and defect chemistry modelling of conductive pyrochlore oxides

    DEFF Research Database (Denmark)

    Poulsen, F.W.; Glerup, M.; Holtappels, P.

    2000-01-01

    -O(x) and V-O on the O site, interstitial oxygens O-i", and delocalised electrons and electron holes. Four mass action law expressions govern such a model. The defect model can rationalise why home-valent doping, i.e. substitution of Zr(4+) by Ce(4+), can lead to an increase in ionic conductivity...

  18. Demystifying Introductory Chemistry. Part 2: Bonding and Molecular Geometry Without Orbitals--the Electron Domain Model.

    Science.gov (United States)

    Gillespie, Ronald J.; And Others

    1996-01-01

    Presents an alternative approach to bonding and geometry--the electron domain model--which avoids some of the problems with the conventional approach. Discusses difficulties with the orbital model at the introductory level, electron spin and the Pauli exclusion principle, electron pair domains, nonequivalent domains, multiple bonds, and origins…

  19. A modified RRSQRT-filter for assimilating data in atmospheric chemistry models

    NARCIS (Netherlands)

    Segers, A.J.; Heemink, A.W.; Verlaan, M.; Loon, M. van

    2000-01-01

    The RRSQRT-filter is a special formulation of the Kalman filter for assimilation of data in large scale models. In this formulation, the covariance matrix of the model state is expressed in a limited number of modes. Two modifications have been made to the filter such that it is more robust when app

  20. Can a coupled meteorology-chemistry model reproduce the historical trend in aerosol direct radiative effects over the Northern Hemisphere?

    Science.gov (United States)

    Xing, J.; Mathur, R.; Pleim, J.; Hogrefe, C.; Gan, C.-M.; Wong, D. C.; Wei, C.

    2015-09-01

    The ability of a coupled meteorology-chemistry model, i.e., Weather Research and Forecast and Community Multiscale Air Quality (WRF-CMAQ), to reproduce the historical trend in aerosol optical depth (AOD) and clear-sky shortwave radiation (SWR) over the Northern Hemisphere has been evaluated through a comparison of 21-year simulated results with observation-derived records from 1990 to 2010. Six satellite-retrieved AOD products including AVHRR, TOMS, SeaWiFS, MISR, MODIS-Terra and MODIS-Aqua as well as long-term historical records from 11 AERONET sites were used for the comparison of AOD trends. Clear-sky SWR products derived by CERES at both the top of atmosphere (TOA) and surface as well as surface SWR data derived from seven SURFRAD sites were used for the comparison of trends in SWR. The model successfully captured increasing AOD trends along with the corresponding increased TOA SWR (upwelling) and decreased surface SWR (downwelling) in both eastern China and the northern Pacific. The model also captured declining AOD trends along with the corresponding decreased TOA SWR (upwelling) and increased surface SWR (downwelling) in the eastern US, Europe and the northern Atlantic for the period of 2000-2010. However, the model underestimated the AOD over regions with substantial natural dust aerosol contributions, such as the Sahara Desert, Arabian Desert, central Atlantic and northern Indian Ocean. Estimates of the aerosol direct radiative effect (DRE) at TOA are comparable with those derived by measurements. Compared to global climate models (GCMs), the model exhibits better estimates of surface-aerosol direct radiative efficiency (Eτ). However, surface-DRE tends to be underestimated due to the underestimated AOD in land and dust regions. Further investigation of TOA-Eτ estimations as well as the dust module used for estimates of windblown-dust emissions is needed.

  1. Construction of a SORCE-based Solar Spectral Irradiance (SSI) Record for Input into Chemistry Climate Models

    Science.gov (United States)

    Harder, J. W.; Fontenla, J. M.

    2015-12-01

    We present a research program to produce a solar spectral irradiance (SSI) record suitable for whole atmosphere chemistry-climate model (CCM) transient studies over the 2001-2015 time period for Solar Cycle 23 and 24 (SC23-24). Climate simulations during this time period are particularly valuable because SC23-24 represents the best-observed solar cycle in history - both from the perspective of solar physics and in terms of Earth observation systems. This record will be based predominantly on the observed irradiance of the SORCE mission as measured by the SIM and SOLSTICE instruments from April of 2003 to the present time. The SSI data record for this proposed study requires very broad wavelength coverage (115-100000 nm), daily spectral coverage, compliance of the integrated SSI record with the TSI, and well-defined and documented uncertainty estimates. While the majority of the record will be derived from SORCE observations, extensions back to the SC23 maximum time period (early 2001) and closure of critical gaps in the SORCE record will be generated employing the Fontenla et al. (2015) Solar Radiation Physical Model (SRPMv2). Since SRPM is a physics-based model, estimates of the SSI for wavelengths outside the SORCE measurement range can be meaningfully included. This model now includes non-LTE contributions from metals in the atomic number range 22-28 (i.e. titanium through nickel) as well as important molecular photo-disassociation contributions from molecules such as NH, molecular hydrogen, CH, and OH led have led to greatly improved agreement between the model and the observed 0.1 nm SOLSTICE spectrum. Thus comparative studies of the SORCE observations with SRPMv2 provide meaningful insight into the nature of solar variability critical for subsequent Earth atmospheric modeling efforts.

  2. Quantum science in secondary chemistry: Influence of teachers' beliefs and knowledge on the use of interactive computer models

    Science.gov (United States)

    Robblee, Karen M.

    Current science education reform efforts promote inquiry-based learning, a goal that requires appropriate tools and instructional approaches. This study investigated the influence of the beliefs and knowledge of four experienced secondary chemistry teachers in their use of new instructional software that generates models of atoms and molecules based on quantum mechanics. The software, which was developed through a National Science Foundation funded project, Quantum Science Across Disciplines (QSAD), was designed to promote inquiry learning. Qualitative research methods were used for this multiple case study. Data from surveys, interviews, and extended classroom observations revealed a close correlation between a teacher's model of the learner and his or her model of teaching. Combined models of learner and teacher had the greatest influence on their decisions about implementing QSAD software. Teachers who espoused a constructivist model of learning and related models of teaching used the software to promote student investigations and inductive approaches to learning. Other factors that appeared to support the use of inquiry methods included sufficient time for students to investigate phenomena, the extent of the teacher's pedagogical content knowledge, and the amount of training using QSAD software. The Views-On-Science-Technology-Society (VOSTS) instrument was used to compare the informants' beliefs about the epistemology of science to their classroom practices. Data related to the role of teachers' beliefs about scientific knowledge were inconclusive, and VOSTS results were inconsistent with the informants' stated beliefs. All four cases revealed that the teachers acted as agents of the school culture. In schools that promoted development of critical thinking, questioning, and self-direction in students, teachers were more likely to use a variety of instructional methods and emphasize construction of knowledge. These findings suggest that educational reform

  3. Climate consequences of increasing ozone in the troposphere, studies with a coupled chemistry-general circulation model

    International Nuclear Information System (INIS)

    Anthropogenic activities have dramatically altered the chemical composition of the atmosphere. The focus of this study is on the composition of the troposphere, mainly associated with ozone which acts as a greenhouse gas, is damaging to living organisms, and co-determines the oxidative capacity of the atmosphere. A coupled tropospheric chemistry - general circulation model (ECHAM) has been applied to the simulation of tropospheric ozone distributions, using emissions of ozone precursors (NOx, CO, higher hydrocarbons) as boundary conditions. The model has been extended with detailed parameterizations for dry deposition of tract species, for the lower stratospheric ozone concentration which is used as boundary condition, and for the treatment of higher hydrocarbon species. The model has been extensively evaluated by comparison with observed long-term climatological data and with in-situ measurements from specific measurement campaigns. A proper representation of all ozone sources and sinks is prerequisite to an accurate estimate of the anthropogenic ozone increase in the troposphere. The representativity of stratosphere-troposphere exchange, which forms a major source for ozone in the troposphere, and its contribution to tropospheric ozone levels has been studied. Simulations have been performed using pre-industrial, present-day and future emission scenarios as boundary conditions, and the radiative forcing associated with the ozone increases has been estimated. The annually averaged global tropospheric ozone contents from these simulations are 190 Tg O3, 271 Tg O3, and 332 Tg O3 in 2025, corresponding to a global annual net radiative forcing at the tropopause of 0.42 W m-2 between the pre-industrial and the present-day simulations, and of 0.31 W m-2 between the present and future simulations. A second focus of the study is the simulation of the sulfur cycle. The model was part of a model intercomparison exercise, that aimed to document the present status of global

  4. Multi-model Mean Nitrogen and Sulfur Deposition from the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP): Evaluation Historical and Projected Changes

    Science.gov (United States)

    Lamarque, J.-F.; Dentener, F.; McConnell, J.; Ro, C.-U.; Shaw, M.; Vet, R.; Bergmann, D.; Cameron-Smith, P.; Doherty, R.; Faluvegi, G.; Ghan, S. J.; Josse, B.; Lee, Y. H.; MacKenzie, I. A.; Plummer, D.; Shindell, D. T.; Stevenson, D. S.; Strode, S.; Zeng, G.

    2013-01-01

    We present multi-model global datasets of nitrogen and sulfate deposition covering time periods from 1850 to 2100, calculated within the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP). The computed deposition fluxes are compared to surface wet deposition and ice-core measurements. We use a new dataset of wet deposition for 2000-2002 based on critical assessment of the quality of existing regional network data. We show that for present-day (year 2000 ACCMIP time-slice), the ACCMIP results perform similarly to previously published multi-model assessments. For this time slice, we find a multi-model mean deposition of 50 Tg(N) yr1 from nitrogen oxide emissions, 60 Tg(N) yr1 from ammonia emissions, and 83 Tg(S) yr1 from sulfur emissions. The analysis of changes between 1980 and 2000 indicates significant differences between model and measurements over the United States but less so over Europe. This difference points towards misrepresentation of 1980 NH3 emissions over North America. Based on ice-core records, the 1850 deposition fluxes agree well with Greenland ice cores but the change between 1850 and 2000 seems to be overestimated in the Northern Hemisphere for both nitrogen and sulfur species. Using the Representative Concentration Pathways to define the projected climate and atmospheric chemistry related emissions and concentrations, we find large regional nitrogen deposition increases in 2100 in Latin America, Africa and parts of Asia under some of the scenarios considered. Increases in South Asia are especially large, and are seen in all scenarios, with 2100 values more than double 2000 in some scenarios and reaching 1300 mg(N) m2 yr1 averaged over regional to continental scale regions in RCP 2.6 and 8.5, 3050 larger than the values in any region currently (2000). The new ACCMIP deposition dataset provides novel, consistent and evaluated global gridded deposition fields for use in a wide range of climate and ecological studies.

  5. Model development of dust emission and heterogeneous chemistry within the Community Multiscale Air Quality modeling system and its application over East Asia

    Science.gov (United States)

    Dong, Xinyi; Fu, Joshua S.; Huang, Kan; Tong, Daniel; Zhuang, Guoshun

    2016-07-01

    The Community Multiscale Air Quality (CMAQ) model has been further developed in terms of simulating natural wind-blown dust in this study, with a series of modifications aimed at improving the model's capability to predict the emission, transport, and chemical reactions of dust. The default parameterization of initial threshold friction velocity constants are revised to correct the double counting of the impact of soil moisture in CMAQ by the reanalysis of field experiment data; source-dependent speciation profiles for dust emission are derived based on local measurements for the Gobi and Taklamakan deserts in East Asia; and dust heterogeneous chemistry is also implemented. The improved dust module in the CMAQ is applied over East Asia for March and April from 2006 to 2010. The model evaluation result shows that the simulation bias of PM10 and aerosol optical depth (AOD) is reduced, respectively, from -55.42 and -31.97 % by the original CMAQ to -16.05 and -22.1 % by the revised CMAQ. Comparison with observations at the nearby Gobi stations of Duolun and Yulin indicates that applying a source-dependent profile helps reduce simulation bias for trace metals. Implementing heterogeneous chemistry also results in better agreement with observations for sulfur dioxide (SO2), sulfate (SO42-), nitric acid (HNO3), nitrous oxides (NOx), and nitrate (NO3-). The investigation of a severe dust storm episode from 19 to 21 March 2010 suggests that the revised CMAQ is capable of capturing the spatial distribution and temporal variation of dust. The model evaluation also indicates potential uncertainty within the excessive soil moisture used by meteorological simulation. The mass contribution of fine-mode particles in dust emission may be underestimated by 50 %. The revised CMAQ model provides a useful tool for future studies to investigate the emission, transport, and impact of wind-blown dust over East Asia and elsewhere.

  6. Modeling HCCI using CFD and Detailed Chemistry with Experimental Validation and a Focus on CO Emissions

    Energy Technology Data Exchange (ETDEWEB)

    Hessel, R; Foster, D; Aceves, S; Flowers, D; Pitz, B; Dec, J; Sjoberg, M; Babajimopoulos, A

    2007-04-23

    Multi-zone CFD simulations with detailed kinetics were used to model engine experiments performed on a diesel engine that was converted for single cylinder, HCCI operation, here using iso-octane as the fuel. The modeling goals were to validate the method (multi-zone combustion modeling) and the reaction mechanism (LLNL 857 species iso-octane), both of which performed very well. The purpose of this paper is to document the validation findings and to set the ground work for further analysis of the results by first looking at CO emissions characteristics with varying equivalence ratio.

  7. Perceived Autonomy-Support, Expectancy, Value, Metacognitive Strategies and Performance in Chemistry: A Structural Equation Model in Undergraduates

    Science.gov (United States)

    González, Antonio; Paoloni, Paola-Verónica

    2015-01-01

    Research in chemistry education has highlighted a number of variables that predict learning and performance, such as teacher-student interactions, academic motivation and metacognition. Most of this chemistry research has examined these variables by identifying dyadic relationships through bivariate correlations. The main purpose of this study was…

  8. Representativeness Errors in Comparing Chemistry Transport Models with Satellite UV/Vis Tropospheric Column Retrievals

    Science.gov (United States)

    Boersma, K. F.; Vinken, G. C.; Eskes, H.

    2015-12-01

    UV/Vis satellite retrievals of trace gas columns of nitrogen dioxide (NO2), sulphur dioxide (SO2), and formaldehyde (HCHO) are useful to test and improve models of atmospheric composition, for data assimilation, and to provide top-down constraints on emissions. However, because models and satellite measurements do not represent the exact same geophysical quantities, the process of confronting model fields with satellite measurements is complicated by representativeness errors, which degrade the quality of the comparison beyond contributions from modelling and measurement errors alone. Here we discuss representativeness errors that arise from the act of carrying out a model-satellite comparison: (1) horizontal representativeness errors due to imperfect collocation of the model grid cell and an ensemble of satellite pixels called superobservation, (2) temporal representativeness errors originating mostly from differences in cloud cover between the modelled and observed state, and (3) vertical representativeness errors because of reduced satellite sensitivity towards the surface. To minimize the impact of these representativeness errors, models and satellite measurements should be sampled as consistent as possible, and we provide recipes to do so. A practical confrontation of tropospheric NO2 columns simulated by the TM5 CTM with OMI tropospheric NO2 retrievals suggests that horizontal representativeness errors are random nature. These errors should be included along with the individual retrieval errors in the overall superobservation error. Temporal sampling errors from mismatches in cloud cover, and in photolysis rates, are on the order of 10% for NO2 and HCHO, and systematic, but partly avoidable. In the case of air pollution applications where sensitivity down to the ground is required, models should be sampled on the same mostly cloud-free days as the satellite retrievals. The most relevant representativeness error is associated with the vertical sensitivity of

  9. Can a coupled meteorology-chemistry model reproduce the historical trend in aerosol direct radiative effects over the Northern Hemisphere?

    Directory of Open Access Journals (Sweden)

    J. Xing

    2015-05-01

    Full Text Available The ability of a coupled meteorology-chemistry model, i.e., WRF-CMAQ, in reproducing the historical trend in AOD and clear-sky short-wave radiation (SWR over the Northern Hemisphere has been evaluated through a comparison of 21 year simulated results with observation-derived records from 1990–2010. Six satellite retrieved AOD products including AVHRR, TOMS, SeaWiFS, MISR, MODIS-terra and -aqua as well as long-term historical records from 11 AERONET sites were used for the comparison of AOD trends. Clear-sky SWR products derived by CERES at both TOA and surface as well as surface SWR data derived from seven SURFRAD sites were used for the comparison of trends in SWR. The model successfully captured increasing AOD trends along with the corresponding increased TOA SWR (upwelling and decreased surface SWR (downwelling in both eastern China and the northern Pacific. The model also captured declining AOD trends along with the corresponding decreased TOA SWR (upwelling and increased surface SWR (downwelling in eastern US, Europe and northern Atlantic for the period of 2000–2010. However, the model underestimated the AOD over regions with substantial natural dust aerosol contributions, such as the Sahara Desert, Arabian Desert, central Atlantic and north Indian Ocean. Estimates of aerosol direct radiative effect (DRE at TOA are comparable with those derived by measurements. Compared to GCMs, the model exhibits better estimates of surface- aerosol direct radiative efficiency (Eτ. However, surface-DRE tends to be underestimated due to the underestimated AOD in land and dust regions. Further investigation of TOA-Eτ estimations as well as the dust module used for estimates of windblown-dust emissions is needed.

  10. The Chemistry of Atmosphere-Forest Exchange (CAFE Model – Part 2: Application to BEARPEX-2007 observations

    Directory of Open Access Journals (Sweden)

    G. M. Wolfe

    2010-09-01

    Full Text Available In a companion paper, we have introduced the Chemistry of Atmosphere-Forest Exchange (CAFE model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. Here, we use CAFE to interpret noontime observations from the 2007 phase of the Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX-2007, conducted at a young Ponderosa pine plantation in the western Sierra Nevada. The model reproduces many features of the BEARPEX-2007 data and offers new insights into the forest-atmosphere exchange of reactive molecules at this location. Nitrogen oxide (NOx = NO + NO2 fluxes are driven by soil emissions of NO, while the partitioning between NO and NO2 fluxes is sensitive to in-canopy photochemical gradients. Enhanced thermolysis at the ground increases downward acyl peroxy nitrate (APN fluxes by as much as 50%, in general agreement with previous findings. APN fluxes are also influenced by in-canopy chemical production, especially when their formation is tied closely to oxidation of BVOC emissions. Gross dry N deposition is typically dominated by nitric acid, though other reactive nitrogen (NOy species can comprise up to 28% of the N deposition budget under cooler conditions. Upward NO2 fluxes cause the net above-canopy NOy flux to be ~30% lower than the gross depositional flux. Model-measurement comparison of hydrogen peroxide mixing ratios suggests this molecule deposits at the aerodynamic limit. CAFE under-predicts ozone fluxes by ~20%, which may indicate additional in-canopy chemical losses that are missing from the current model.

  11. Ferritin Protein Nanocages Use Ion Channels, Catalytic Sites, and Nucleation Channels To Manage Iron/Oxygen Chemistry: A review for: Current Opinion In Chemical Biology/Bioinorganic Chemistry: Iron Biochemistry

    OpenAIRE

    Theil, Elizabeth C.

    2011-01-01

    The ferritin superfamily is composed of ancient, nanocage proteins with an internal cavity, 60% of total volume, that reversibly synthesize solid minerals of hydrated ferric oxide; the minerals are iron concentrates for cell nutrition as well as antioxidants due to ferrous and oxygen consumption during mineralization. The cages have multiple iron entry/exit channels, oxidoreductase enzyme sites, and, in eukaryotes, Fe(III)O nucleation channels with clustered exits that extend protein activity...

  12. A Unified Monte Carlo Treatment of Gas-Grain Chemistry for Large Reaction Networks. II. A Multiphase Gas-Surface-Layered Bulk Model

    CERN Document Server

    Vasyunin, A I

    2012-01-01

    The observed gas-phase molecular inventory of hot cores is believed to be significantly impacted by the products of chemistry in interstellar ices. In this study, we report the construction of a full macroscopic Monte Carlo model of both the gas-phase chemistry and the chemistry occurring in the icy mantles of interstellar grains. Our model treats icy grain mantles in a layer-by-layer manner, which incorporates laboratory data on ice desorption correctly. The ice treatment includes a distinction between a reactive ice surface and an inert bulk. The treatment also distinguishes between zeroth and first order desorption, and includes the entrapment of volatile species in more refractory ice mantles. We apply the model to the investigation of the chemistry in hot cores, in which a thick ice mantle built up during the previous cold phase of protostellar evolution undergoes surface reactions and is eventually evaporated. For the first time, the impact of a detailed multilayer approach to grain mantle formation on ...

  13. Radiation Chemistry

    Science.gov (United States)

    Wojnárovits, L.

    Ionizing radiation causes chemical changes in the molecules of the interacting medium. The initial molecules change to new molecules, resulting in changes of the physical, chemical, and eventually biological properties of the material. For instance, water decomposes to its elements H2 and O2. In polymers, degradation and crosslinking take place. In biopolymers, e.g., DNS strand breaks and other alterations occur. Such changes are to be avoided in some cases (radiation protection), however, in other cases they are used for technological purposes (radiation processing). This chapter introduces radiation chemistry by discussing the sources of ionizing radiation (radionuclide sources, machine sources), absorption of radiation energy, techniques used in radiation chemistry research, and methods of absorbed energy (absorbed dose) measurements. Radiation chemistry of different classes of inorganic (water and aqueous solutions, inorganic solids, ionic liquids (ILs)) and organic substances (hydrocarbons, halogenated compounds, polymers, and biomolecules) is discussed in concise form together with theoretical and experimental backgrounds. An essential part of the chapter is the introduction of radiation processing technologies in the fields of polymer chemistry, food processing, and sterilization. The application of radiation chemistry to nuclear technology and to protection of environment (flue gas treatment, wastewater treatment) is also discussed.

  14. The impact of orbital sampling, monthly averaging and vertical resolution on climate chemistry model evaluation with satellite observations

    Directory of Open Access Journals (Sweden)

    A. M. Aghedo

    2011-07-01

    Full Text Available Ensemble climate model simulations used for the Intergovernmental Panel on Climate Change (IPCC assessments have become important tools for exploring the response of the Earth System to changes in anthropogenic and natural forcings. The systematic evaluation of these models through global satellite observations is a critical step in assessing the uncertainty of climate change projections. This paper presents the technical steps required for using nadir sun-synchronous infrared satellite observations for multi-model evaluation and the uncertainties associated with each step. This is motivated by need to use satellite observations to evaluate climate models. We quantified the implications of the effect of satellite orbit and spatial coverage, the effect of variations in vertical sensitivity as quantified by the observation operator and the impact of averaging the operators for use with monthly-mean model output. We calculated these biases in ozone, carbon monoxide, atmospheric temperature and water vapour by using the output from two global chemistry climate models (ECHAM5-MOZ and GISS-PUCCINI and the observations from the Tropospheric Emission Spectrometer (TES instrument on board the NASA-Aura satellite from January 2005 to December 2008.

    The results show that sampling and monthly averaging of the observation operators produce zonal-mean biases of less than ±3 % for ozone and carbon monoxide throughout the entire troposphere in both models. Water vapour sampling zonal-mean biases were also within the insignificant range of ±3 % (that is ±0.14 g kg−1 in both models. Sampling led to a temperature zonal-mean bias of ±0.3 K over the tropical and mid-latitudes in both models, and up to −1.4 K over the boundary layer in the higher latitudes. Using the monthly average of temperature and water vapour operators lead to large biases over the boundary layer in the southern-hemispheric higher latitudes and in the upper