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 func...... promising density functional for use and further development within the field of bioinorganic chemistry....

  3. Bioorganic and bioinorganic chemistry.

    Science.gov (United States)

    Constable, Edwin C; Housecroft, Catherine E; Creus, Marc; Gademann, Karl; Giese, Bernd; Ward, Thomas R; Woggon, Wolf D; Chougnet, Antoinette

    2010-01-01

    The interdisciplinary projects in bioinorganic and bioorganic chemistry of the Department of Chemistry, University of Basel led to the preparation of new systems that mimic biologically important processes and to the discovery of compounds from natural sources which are very promising with respect to medical applications. The advances in these areas are reported here.

  4. Structural and functional models in molybdenum and tungsten bioinorganic chemistry: description of selected model complexes, present scenario and possible future scopes.

    Science.gov (United States)

    Majumdar, Amit

    2014-06-28

    A brief description about some selected model complexes in molybdenum and tungsten bioinorganic chemistry is provided. The synthetic strategies involved and their limitations are discussed. Current status of molybdenum and tungsten bioinorganic modeling chemistry is presented briefly and synthetic problems associated therein are analyzed. Possible future directions which may expand the scope of modeling chemistry are suggested.

  5. An Undergraduate Laboratory Experiment in Bioinorganic Chemistry: Ligation States of Myoglobin

    Science.gov (United States)

    Bailey, James A.

    2011-01-01

    Although there are numerous inorganic model systems that are readily presented as undergraduate laboratory experiments in bioinorganic chemistry, there are few examples that explore the inorganic chemistry of actual biological molecules. We present a laboratory experiment using the oxygen-binding protein myoglobin that can be easily incorporated…

  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. 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)

  8. 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…

  9. 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.

  10. Catalytic Oxygen Evolution by a Bioinorganic Model of the Photosystem II Oxygen-Evolving Complex

    Science.gov (United States)

    Howard, Derrick L.; Tinoco, Arthur D.; Brudvig, Gary W.; Vrettos, John S.; Allen, Bertha Connie

    2005-01-01

    Bioinorganic models of the manganese Mn4 cluster are important not only as aids in understanding the structure and function of the oxygen-evolving complex (OEC), but also in developing artificial water-oxidation catalysts. The mechanism of water oxidation by photosystem II (PSII) is thought to involve the formation of a high-valent terminal Mn-oxo…

  11. 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

  12. 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.

  13. Bioinorganic chemistry of Parkinson's disease: structural determinants for the copper-mediated amyloid formation of alpha-synuclein.

    Science.gov (United States)

    Binolfi, Andrés; Rodriguez, Esaú E; Valensin, Daniela; D'Amelio, Nicola; Ippoliti, Emiliano; Obal, Gonzalo; Duran, Rosario; Magistrato, Alessandra; Pritsch, Otto; Zweckstetter, Markus; Valensin, Gianni; Carloni, Paolo; Quintanar, Liliana; Griesinger, Christian; Fernández, Claudio O

    2010-11-15

    The aggregation of alpha-synuclein (AS) is a critical step in the etiology of Parkinson's disease (PD). A central, unresolved question in the pathophysiology of PD relates to the role of AS-metal interactions in amyloid fibril formation and neurodegeneration. Our previous works established a hierarchy in alpha-synuclein-metal ion interactions, where Cu(II) binds specifically to the protein and triggers its aggregation under conditions that might be relevant for the development of PD. Two independent, non-interacting copper-binding sites were identified at the N-terminal region of AS, with significant difference in their affinities for the metal ion. In this work we have solved unknown details related to the structural binding specificity and aggregation enhancement mediated by Cu(II). The high-resolution structural characterization of the highest affinity N-terminus AS-Cu(II) complex is reported here. Through the measurement of AS aggregation kinetics we proved conclusively that the copper-enhanced AS amyloid formation is a direct consequence of the formation of the AS-Cu(II) complex at the highest affinity binding site. The kinetic behavior was not influenced by the His residue at position 50, arguing against an active role for this residue in the structural and biological events involved in the mechanism of copper-mediated AS aggregation. These new findings are central to elucidate the mechanism through which the metal ion participates in the fibrillization of AS and represent relevant progress in the understanding of the bioinorganic chemistry of PD.

  14. Invited award contribution for ACS Award in Inorganic Chemistry. Geometric and electronic structure contributions to function in bioinorganic chemistry: active sites in non-heme iron enzymes.

    Science.gov (United States)

    Solomon, E I

    2001-07-16

    Spectroscopy has played a major role in the definition of structure/function correlations in bioinorganic chemistry. The importance of spectroscopy combined with electronic structure calculations is clearly demonstrated by the non-heme iron enzymes. Many members of this large class of enzymes activate dioxygen using a ferrous active site that has generally been difficult to study with most spectroscopic methods. A new spectroscopic methodology has been developed utilizing variable temperature, variable field magnetic circular dichroism, which enables one to obtain detailed insight into the geometric and electronic structure of the non-heme ferrous active site and probe its reaction mechanism on a molecular level. This spectroscopic methodology is presented and applied to a number of key mononuclear non-heme iron enzymes leading to a general mechanistic strategy for O2 activation. These studies are then extended to consider the new features present in the binuclear non-heme iron enzymes and applied to understand (1) the mechanism of the two electron/coupled proton transfer to dioxygen binding to a single iron center in hemerythrin and (2) structure/function correlations over the oxygen-activating enzymes stearoyl-ACP Delta9-desaturase, ribonucleotide reductase, and methane monooxygenase. Electronic structure/reactivity correlations for O2 activation by non-heme relative to heme iron enzymes will also be developed.

  15. 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.

  16. 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

  17. 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.

  18. Science Update: Inorganic Chemistry

    Science.gov (United States)

    Rawls, Rebecca

    1978-01-01

    This first in a series of articles describing the state of the art of various branches of chemistry reviews inorganic chemistry, including bioinorganic, photochemistry, organometallic, and solid state chemistries. (SL)

  19. 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.

  20. 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.

  1. Copper dioxygen (bio)inorganic chemistry.

    Science.gov (United States)

    Solomon, Edward I; Ginsbach, Jake W; Heppner, David E; Kieber-Emmons, Matthew T; Kjaergaard, Christian H; Smeets, Pieter J; Tian, Li; Woertink, Julia S

    2011-01-01

    Cu/O2 intermediates in biological, homogeneous, and heterogeneous catalysts exhibit unique spectral features that reflect novel geometric and electronic structures that make significant contributions to reactivity. This review considers how the respective intermediate electronic structures overcome the spin-forbidden nature of O2 binding, activate O2 for electrophilic aromatic attack and H-atom abstraction, catalyze the 4 e- reduction of O2 to H2O, and discusses the role of exchange coupling between Cu ions in determining reactivity.

  2. Biological inorganic chemistry at the beginning of the 21st century.

    Science.gov (United States)

    Gray, Harry B

    2003-04-01

    Advances in bioinorganic chemistry since the 1970s have been driven by three factors: rapid determination of high-resolution structures of proteins and other biomolecules, utilization of powerful spectroscopic tools for studies of both structures and dynamics, and the widespread use of macromolecular engineering to create new biologically relevant structures. Today, very large molecules can be manipulated at will, with the result that certain proteins and nucleic acids themselves have become versatile model systems for elucidating biological function.

  3. 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...... or based on partial-equilibrium assumptions have limited predictive capabilities. Reburning models based on systematic reduction of a detailed chemical kinetic model offer a high accuracy but rely on input estimates of combustion intermediates, including free radicals. In the present work, an analytically...

  4. 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

  5. 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.

  6. 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.

  7. Application of isothermal titration calorimetry in bioinorganic chemistry.

    Science.gov (United States)

    Grossoehme, Nicholas E; Spuches, Anne M; Wilcox, Dean E

    2010-11-01

    The thermodynamics of metals ions binding to proteins and other biological molecules can be measured with isothermal titration calorimetry (ITC), which quantifies the binding enthalpy (ΔH°) and generates a binding isotherm. A fit of the isotherm provides the binding constant (K), thereby allowing the free energy (ΔG°) and ultimately the entropy (ΔS°) of binding to be determined. The temperature dependence of ΔH° can then provide the change in heat capacity (ΔC (p)°) upon binding. However, ITC measurements of metal binding can be compromised by undesired reactions (e.g., precipitation, hydrolysis, and redox), and generally involve competing equilibria with the buffer and protons, which contribute to the experimental values (K (ITC), ΔH (ITC)). Guidelines and factors that need to be considered for ITC measurements involving metal ions are outlined. A general analysis of the experimental ITC values that accounts for the contributions of metal-buffer speciation and proton competition and provides condition-independent thermodynamic values (K, ΔH°) for metal binding is developed and validated.

  8. Parallel computing in atmospheric chemistry models

    Energy Technology Data Exchange (ETDEWEB)

    Rotman, D. [Lawrence Livermore National Lab., CA (United States). Atmospheric Sciences Div.

    1996-02-01

    Studies of atmospheric chemistry are of high scientific interest, involve computations that are complex and intense, and require enormous amounts of I/O. Current supercomputer computational capabilities are limiting the studies of stratospheric and tropospheric chemistry and will certainly not be able to handle the upcoming coupled chemistry/climate models. To enable such calculations, the authors have developed a computing framework that allows computations on a wide range of computational platforms, including massively parallel machines. Because of the fast paced changes in this field, the modeling framework and scientific modules have been developed to be highly portable and efficient. Here, the authors present the important features of the framework and focus on the atmospheric chemistry module, named IMPACT, and its capabilities. Applications of IMPACT to aircraft studies will be presented.

  9. Predictive Modeling in Actinide Chemistry and Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Ping [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-16

    These are slides from a presentation on predictive modeling in actinide chemistry and catalysis. The following topics are covered in these slides: Structures, bonding, and reactivity (bonding can be quantified by optical probes and theory, and electronic structures and reaction mechanisms of actinide complexes); Magnetic resonance properties (transition metal catalysts with multi-nuclear centers, and NMR/EPR parameters); Moving to more complex systems (surface chemistry of nanomaterials, and interactions of ligands with nanoparticles); Path forward and conclusions.

  10. 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 result indicated…

  11. 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.

  12. 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).

  13. Water chemistry model development at Total EandP Canada: modeling uncertainty in ore chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Kaminsky, H.A.W.; Yoo, A.; Schaffer, M. [Total EandP Canada Ltd. (Canada)

    2011-07-01

    In oil sands mining operations, water chemistry is a key factor as it plays a role in the bitumen recovery and water discharge to the environment. Total Canada have developed a new water chemistry model combining the previous models developed by Rogers and Kasperski and making modifications to improve reliability of the results. Two challenges had to be addressed in the development of this model: making sure that the data used were appropriate, and accurately modeling uncertainty. The aim of this paper is to present the modifications made to the model and other water chemistry models. Laboratory tests were conducted using the double leach and the standard leach methods. Results showed that the standard leach method provides more accurate measurement on batch extraction tests. This paper outlined the challenges of developing a new prediction model; further tests are needed to determine the best method to use in describing ore chemistry.

  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. Applications of Density Functional Theory to Iron-Containing Molecules of Bioinorganic Interest

    Directory of Open Access Journals (Sweden)

    Hajime eHirao

    2014-04-01

    Full Text Available 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 mysterious 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 nonheme synthetic complexes, heme-type cytochrome P450 enzymes, and nonheme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.

  16. GEOS-5 Chemistry Transport Model User's Guide

    Science.gov (United States)

    Kouatchou, J.; Molod, A.; Nielsen, J. E.; Auer, B.; Putman, W.; Clune, T.

    2015-01-01

    The Goddard Earth Observing System version 5 (GEOS-5) General Circulation Model (GCM) makes use of the Earth System Modeling Framework (ESMF) to enable model configurations with many functions. One of the options of the GEOS-5 GCM is the GEOS-5 Chemistry Transport Model (GEOS-5 CTM), which is an offline simulation of chemistry and constituent transport driven by a specified meteorology and other model output fields. This document describes the basic components of the GEOS-5 CTM, and is a user's guide on to how to obtain and run simulations on the NCCS Discover platform. In addition, we provide information on how to change the model configuration input files to meet users' needs.

  17. Dilution physics modeling: Dissolution/precipitation chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Onishi, Y.; Reid, H.C.; Trent, D.S.

    1995-09-01

    This report documents progress made to date on integrating dilution/precipitation chemistry and new physical models into the TEMPEST thermal-hydraulics computer code. Implementation of dissolution/precipitation chemistry models is necessary for predicting nonhomogeneous, time-dependent, physical/chemical behavior of tank wastes with and without a variety of possible engineered remediation and mitigation activities. Such behavior includes chemical reactions, gas retention, solids resuspension, solids dissolution and generation, solids settling/rising, and convective motion of physical and chemical species. Thus this model development is important from the standpoint of predicting the consequences of various engineered activities, such as mitigation by dilution, retrieval, or pretreatment, that can affect safe operations. The integration of a dissolution/precipitation chemistry module allows the various phase species concentrations to enter into the physical calculations that affect the TEMPEST hydrodynamic flow calculations. The yield strength model of non-Newtonian sludge correlates yield to a power function of solids concentration. Likewise, shear stress is concentration-dependent, and the dissolution/precipitation chemistry calculations develop the species concentration evolution that produces fluid flow resistance changes. Dilution of waste with pure water, molar concentrations of sodium hydroxide, and other chemical streams can be analyzed for the reactive species changes and hydrodynamic flow characteristics.

  18. Modelling chemistry over the Dead Sea: bromine and ozone chemistry

    Directory of Open Access Journals (Sweden)

    R. von Glasow

    2009-07-01

    Full Text Available Measurements of O3 and BrO concentrations over the Dead Sea indicate that Ozone Depletion Events (ODEs, widely known to happen in polar regions, are also occuring over the Dead Sea due to the very high bromine content of the Dead Sea water. However, we show that BrO and O3 levels as they are detected cannot solely be explained by high Br levels in the Dead Sea water and the release of gas phase halogen species out of sea borne aerosol particles and their conversion to reactive halogen species. It is likely that other sources for reactive halogen compounds are needed to explain the observed concentrations for BrO and O3. To explain the chemical mechanism taking place over the Dead Sea leading to BrO levels of several pmol/mol we used the one-dimensional model MISTRA which calculates microphysics, meteorology, gas and aerosol phase chemistry. We performed pseudo Lagrangian studies by letting the model column first move over the desert which surrounds the Dead Sea region and then let it move over the Dead Sea itself. To include an additional source for gas phase halogen compounds, gas exchange between the Dead Sea water and the atmosphere is treated explicitly. Model calculations indicate that this process has to be included to explain the measurements.

  19. Chemistry Teacher Education Coalition: Extending the PhysTEC Model to Chemistry

    Science.gov (United States)

    Kirchhoff, Mary

    2012-02-01

    The American Association of Employment in Education reports that chemistry, like physics, faces ``some shortage'' of educators. Inspired by the success of the Physics Teacher Education Coalition (PhysTEC), the American Chemical Society (ACS) is developing the Chemistry Teacher Education Coalition (CTEC) to actively engage chemistry departments in the preparation of future chemistry teachers. Engaging chemistry departments in teacher preparation would increase the number and diversity of well-prepared high school chemistry teachers while catalyzing cultural change within chemistry departments. Many features of PhysTEC, such as a grant competition to create model teacher preparation programs and regular conferences, are directly applicable to chemistry. This presentation will provide an overview of ACS efforts to launch a successful CTEC initiative.

  20. Teaching Chemistry with Electron Density Models

    Science.gov (United States)

    Shusterman, Gwendolyn P.; Shusterman, Alan J.

    1997-07-01

    Linus Pauling once said that a topic must satisfy two criteria before it can be taught to students. First, students must be able to assimilate the topic within a reasonable amount of time. Second, the topic must be relevant to the educational needs and interests of the students. Unfortunately, the standard general chemistry textbook presentation of "electronic structure theory", set as it is in the language of molecular orbitals, has a difficult time satisfying either criterion. Many of the quantum mechanical aspects of molecular orbitals are too difficult for most beginning students to appreciate, much less master, and the few applications that are presented in the typical textbook are too limited in scope to excite much student interest. This article describes a powerful new method for teaching students about electronic structure and its relevance to chemical phenomena. This method, which we have developed and used for several years in general chemistry (G.P.S.) and organic chemistry (A.J.S.) courses, relies on computer-generated three-dimensional models of electron density distributions, and largely satisfies Pauling's two criteria. Students find electron density models easy to understand and use, and because these models are easily applied to a broad range of topics, they successfully convey to students the importance of electronic structure. In addition, when students finally learn about orbital concepts they are better prepared because they already have a well-developed three-dimensional picture of electronic structure to fall back on. We note in this regard that the types of models we use have found widespread, rigorous application in chemical research (1, 2), so students who understand and use electron density models do not need to "unlearn" anything before progressing to more advanced theories.

  1. 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.

  2. 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.

  3. Halogen Chemistry in the CMAQ Model

    Science.gov (United States)

    Halogens (iodine and bromine) emitted from oceans alter atmospheric chemistry and influence atmospheric ozone mixing ratio. We previously incorporated a representation of detailed halogen chemistry and emissions of organic and inorganic halogen species into the hemispheric Commun...

  4. 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.

  5. Estimating numerical errors due to operator splitting in global atmospheric chemistry models: Transport and chemistry

    Science.gov (United States)

    Santillana, Mauricio; Zhang, Lin; Yantosca, Robert

    2016-01-01

    We present upper bounds for the numerical errors introduced when using operator splitting methods to integrate transport and non-linear chemistry processes in global chemical transport models (CTM). We show that (a) operator splitting strategies that evaluate the stiff non-linear chemistry operator at the end of the time step are more accurate, and (b) the results of numerical simulations that use different operator splitting strategies differ by at most 10%, in a prototype one-dimensional non-linear chemistry-transport model. We find similar upper bounds in operator splitting numerical errors in global CTM simulations.

  6. A New Definition of Models and Modeling in Chemistry's Teaching

    Science.gov (United States)

    Chamizo, José A.

    2013-07-01

    The synthesis of new chemical compounds makes it the most productive science. Unfortunately chemistry education practice has not been driven to any great extent by research findings, philosophical positions or advances in new ways of approaching knowledge. The changes that have occurred in textbooks during the past three decades do not show any real recognition of these. Despite previously reported different types of models in this paper, from an `empirical reliability with minimal realism' approach to realism, a new simple and broad definition, a typology of models and their relation with modeling is presented.

  7. 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…

  8. 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…

  9. Thole's interacting polarizability model in computational chemistry practice

    NARCIS (Netherlands)

    deVries, AH; vanDuijnen, PT; Zijlstra, RWJ; Swart, M

    1997-01-01

    Thole's interacting polarizability model to calculate molecular polarizabilities from interacting atomic polarizabilities is reviewed and its major applications in computational chemistry are illustrated. The applications include prediction of molecular polarizabilities, use in classical expressions

  10. Nuclear chemistry model of borated fuel crud

    Energy Technology Data Exchange (ETDEWEB)

    Sawicki, J.A. [Atomic Energy of Canada Ltd., Chalk River, ON (Canada)

    2002-07-01

    Fuel crud deposits on Callaway Cycle 9 once-burnt high-axial offset anomaly (AOA {approx} -15%) feed assemblies revealed a complex 4-phase matted-layered morphology of a new type that is uncommon in pressurized water reactors [1-3]. The up to 140-{open_square}m-thick crud flakes consisted predominantly of insoluble needle-like particles of Ni-Fe oxy-borate Ni{sub 2}FeBO{sub 5} (bonaccordite) and granular precipitates of m-ZrO{sub 2} (baddeleyite), along with nickel oxide NiO (bunsenite) and minor amount of nickel ferrite NiFe{sub 2}O{sub 4} (trevorite). Furthermore, boron in crud flakes showed that the concentration of {sup 10}B had depleted to 10.2{+-}0.2%, as compared to its 20% natural isotopic abundance and its 17% end-of-cycle abundance in bulk coolant. The form and depth distribution of Ni{sub 2}FeBO{sub 5} and m-ZrO{sub 2} precipitates, as well as substantial {sup 10}B burn-up, point to a strongly alkaline environment at the clad surface of the high-duty fuel rods. This paper extends a nuclear chemistry model of heavily borated fuel crud deposits. The paper shows that the local nuclear heat and lithium buildup from {sup 10}B(n,{open_square}){sup 7}Li reactions may help to create hydrothermal and chemical conditions within the crud layer in favor of Ni{sub 2}FeBO{sub 5} formation and a ZrO{sub 2} dissolution-reprecipitation mechanism. Consistent with the model, the hydrothermal formation of Ni{sub 2}FeBO{sub 5} needles was recently proved to be possible in laboratory tests with aqueous NiO-Fe{sub 2}O{sub 3}-H{sub 3}BO{sub 3}-LiOH slurries, at temperatures only slightly exceeding 400 C. (author)

  11. 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.

  12. 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.

  13. Oxovanadium(IV complexes of bioinorganic and medicinal relevance: Synthesis, characterization and 3D molecular modeling of some oxovanadium(IV complexes involving O, N-donor environment of salicylaldehyde-based sulfa drug Schiff bases

    Directory of Open Access Journals (Sweden)

    R.C. Maurya

    2016-11-01

    Full Text Available The present paper reports the synthesis and characterization of some new sulfa drug based Schiff base oxovanadium(IV complexes of composition, [VO(sal-sdz2(H2O]·H2O, [VO(sal-sgn2(H2O]·H2O, [VO(sal-snm(H2O]·H2O, [VO(sal-smr2(H2O]·H2O and [VO(dadps(H2O]2·2H2O, where sal-sdzH = N-(salicylidenesulfadizine, sal-sgnH = N-(salicylidenesulfaguanidine, sal-snmH = N-(salicylidenesulfanilamide, sal-smrH = N-(salicylidenesulfamerizine, sal-dadpsH2 = N,N′-bis(salicylidene-4,4′-diaminodiphenylsulfone, respectively. Complexes, (1–(4 were prepared by the reaction of VOSO4·5H2O with the Schiff bases in 1:2 metal-ligand ratio while complex (5 in 2:2 metal-ligand ratio in DMF-ethanol medium. The compounds so obtained were characterized by different physico-chemical studies, such as, elemental analysis, molar conductance and magnetic measurements, infrared, ESR, thermogravimetric studies, mass and electronic spectral studies. The overall IR studies conclude that the ligand in complex (1–(4 behave as monobasic bidentate ON donor, while the ligand in the complex (5 behaves as dibasic tetradentate O2N2 donor. The 3D-molecular modeling and analysis for bond lengths and bond angles have also been carried out for two representative compounds, [VO(sal-snm2(H2O]·H2O (3 and [VO(dadps(H2O]2·2H2O (5 to substantiate the proposed structures. Based on these studies suitable octahedral structures have been proposed for these complexes.

  14. 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.

  15. 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…

  16. 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…

  17. Disciplines, models, and computers: the path to computational quantum chemistry.

    Science.gov (United States)

    Lenhard, Johannes

    2014-12-01

    Many disciplines and scientific fields have undergone a computational turn in the past several decades. This paper analyzes this sort of turn by investigating the case of computational quantum chemistry. The main claim is that the transformation from quantum to computational quantum chemistry involved changes in three dimensions. First, on the side of instrumentation, small computers and a networked infrastructure took over the lead from centralized mainframe architecture. Second, a new conception of computational modeling became feasible and assumed a crucial role. And third, the field of computa- tional quantum chemistry became organized in a market-like fashion and this market is much bigger than the number of quantum theory experts. These claims will be substantiated by an investigation of the so-called density functional theory (DFT), the arguably pivotal theory in the turn to computational quantum chemistry around 1990.

  18. 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

  19. Theory and modeling in combustion chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J.A.

    1996-10-01

    This paper discusses four important problems in combustion chemistry. In each case, resolution of the problem focuses on a single elementary reaction. Theoretical analysis of this reaction is discussed in some depth, with emphasis on its unusual features. The four combustion problems and their elementary reactions are: (1) Burning velocities, extinction limits, and flammability limits: H+O{sub 2}{leftrightarrow}OH+O, (2) Prompt NO: CH+N{sub 2}{leftrightarrow}HCN+N, (3) the Thermal De-NO{sub x} Process: NH{sub 2}+NO{leftrightarrow}products, and (4) ``Ring`` formation in flames of aliphatic fuels and the importance of resonantly stabilized free radicals: C{sub 3}H{sub 3}{leftrightarrow}products.

  20. 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.

  1. Computational quantum chemistry and adaptive ligand modeling in mechanistic QSAR.

    Science.gov (United States)

    De Benedetti, Pier G; Fanelli, Francesca

    2010-10-01

    Drugs are adaptive molecules. They realize this peculiarity by generating different ensembles of prototropic forms and conformers that depend on the environment. Among the impressive amount of available computational drug discovery technologies, quantitative structure-activity relationship approaches that rely on computational quantum chemistry descriptors are the most appropriate to model adaptive drugs. Indeed, computational quantum chemistry descriptors are able to account for the variation of the intramolecular interactions of the training compounds, which reflect their adaptive intermolecular interaction propensities. This enables the development of causative, interpretive and reasonably predictive quantitative structure-activity relationship models, and, hence, sound chemical information finalized to drug design and discovery.

  2. The global chemistry transport model TM5: description and evaluation of the tropospheric chemistry version 3.0

    NARCIS (Netherlands)

    Huijnen, V.; Williams, J.; van Weele, M.; van Noije, T.; Krol, M.; Dentener, F.; Segers, A.; Houweling, S.; Peters, W.; de Laat, J.; Boersma, F.; Bergamaschi, P.; van Velthoven, P.; Le Sager, P.; Eskes, H.; Alkemade, F.; Scheele, R.; Nédélec, P.; Pätz, H.-W.

    2010-01-01

    We present a comprehensive description and benchmark evaluation of the tropospheric chemistry version of the global chemistry transport model TM5 (Tracer Model 5, version TM5-chem-v3.0). A full description is given concerning the photochemical mechanism, the interaction with aerosol, the treatment o

  3. 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…

  4. Promoting Representational Competence with Molecular Models in Organic Chemistry

    Science.gov (United States)

    Stull, Andrew T.; Gainer, Morgan; Padalkar, Shamin; Hegarty, Mary

    2016-01-01

    Mastering the many different diagrammatic representations of molecules used in organic chemistry is challenging for students. This article summarizes recent research showing that manipulating 3-D molecular models can facilitate the understanding and use of these representations. Results indicate that students are more successful in translating…

  5. Model inter-comparison on transport and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Bergamaschi, P. [European Commission, DG Joint Research Centre, Institute for Environment and Sustainability, Ispra (Italy); Meirink, J.F. [Royal Netherlands Meteorological Institute KNMI, De Bilt (Netherlands); Mueller, J.F. [Belgian Institute for Space Aeronomy, Brussels (Belgium); Koerner, S.; Heimann, M. [Max Planck Institute for Biogeochemie, Jena (Germany); Bousquet, P.; Ramonet, M. [Laboratoire des Sciences du Climat et de l' Environment LSCE, Gif sur Yvette (France); Dlugokencky, E.J. [NOAA Earth Science Research Laboratory, Global Monitoring Division, Boulder, CO (United States); Kaminski, U. [Deutscher Wetterdienst, Meteorologisches Observatorium Hohenpeissenberg (Germany); Vecchi, R.; Marcazzan, G. [Istituto di Fisica Generale Applicata, Universita' degli Studi di Milano, Milan (Italy); Meinhardt, F. [Umweltbundesamt, Messstelle Schauinsland, Kirchzarten (Germany); Sartorius, H. [Bundesamt fuer Strahlenschutz, Freiburg (Germany); Zahorowski, W. [Australian Nuclear Science and Technology Organisation, Menai (Australia)

    2006-07-01

    A comprehensive inter-comparison of 5 atmospheric chemistry transport models (TM5, TM4, TM3, IMAGES, and LMDZ) has been performed. The main objective was to analyze differences in model transport, in particular vertical mixing (boundary layer and convective transport), synoptic variations, and large scale global circulation (including inter-hemispheric exchange and stratospheric tropospheric exchange (STE)). For this purpose simulations of various tracers with very different atmospheric lifetimes {tau} have been carried out: 222Rn ({tau} = 3.8 days), SF6 ({tau} {approx}3000 years), and CH4 ({tau} = {approx}9 years), using prescribed boundary conditions for all models. Furthermore, OH fields from various model simulations with full chemistry have been compared.

  6. Analyzing Students' Understanding of Models and Modeling Referring to the Disciplines Biology, Chemistry, and Physics

    Science.gov (United States)

    Krell, Moritz; Reinisch, Bianca; Krüger, Dirk

    2015-01-01

    In this study, secondary school students' (N?=?617; grades 7 to 10) understanding of models and modeling was assessed using tasks which explicitly refer to the scientific disciplines of biology, chemistry, and physics and, as a control, to no scientific discipline. The students' responses are interpreted as their biology-, chemistry-, and…

  7. Accounting for non-linear chemistry of ship plumes in the GEOS-Chem global chemistry transport model

    NARCIS (Netherlands)

    Vinken, G.C.M.; Boersma, K.F.; Jacob, D.J.; Meijer, E.W.

    2011-01-01

    We present a computationally efficient approach to account for the non-linear chemistry occurring during the dispersion of ship exhaust plumes in a global 3-D model of atmospheric chemistry (GEOS-Chem). We use a plume-in-grid formulation where ship emissions age chemically for 5 h before being relea

  8. Accounting for non-linear chemistry of ship plumes in the GEOS-Chem global chemistry transport model

    NARCIS (Netherlands)

    Meijer, E.W.; Vinken, G.C.M.; Boersma, K.F.; Jacob, D.J.

    2011-01-01

    Abstract. We present a computationally efficient approach to account for the non-linear chemistry occurring during the dispersion of ship exhaust plumes in a global 3-D model of atmospheric chemistry (GEOS-Chem). We use a plume-ingrid formulation where ship emissions age chemically for 5 h before be

  9. 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.

  10. 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

  11. 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.

  12. A Global PLASIMO Model for H2O Chemistry

    Science.gov (United States)

    Tadayon Mousavi, Samaneh; Koelman, Peter; Graef, Wouter; Mihailova, Diana; van Dijk, Jan; EPG/ Applied Physics/ Eindhoven University of Technology Team; Plasma Matters B. V. Team

    2016-09-01

    Global warming is one of the critical contemporary problems for mankind. Transformation of CO2 into fuels, like CH4, that are transportable with the current infrastructure seems a promising idea to solve this threatening issue. The final aim of this research is to produce CH4 by using microwave plasma in CO2 -H2 O mixture and follow-up catalytic processes. In this contribution we present a global model for H2 O chemistry that is based on the PLASIMO plasma modeling toolkit. The time variation of the electron energy and the species' densities are calculated based on the source and loss terms in plasma due to chemical reactions. The short simulation times of such models allow an efficient assessment and chemical reduction of the H2O chemistry, which is required for full spatially resolved simulations.

  13. Better Galactic mass models through chemistry

    Science.gov (United States)

    Sanderson, Robyn Ellyn; Wetzel, Andrew; Hopkins, Philip F.; Sharma, Sanjib

    2017-01-01

    With the upcoming release of the Gaia catalog and the many multiplexed spectroscopic surveys on the horizon, we are rapidly moving into a new data-driven era in the study of the Milky Way's stellar halo. When combined, these data sets will give us a many-dimensional view of stars in accreted structures in the halo that includes both dynamical information about their orbits and chemical information about their formation histories. Using simulated data from the state-of-the-art Latte simulations of Milky-Way-like galaxies, which include hydrodynamics, feedback, and chemical evolution in a cosmological setting using the FIRE physics model, we demonstrate that while dynamical information alone can be used to constrain models of the Galactic mass distribution in the halo, including the extra dimensions provided by chemical abundances can improve these constraints as well as assist in untangling different accreted components.

  14. 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...

  15. The effects of atmospheric chemistry on radiation budget in the Community Earth Systems Model

    Science.gov (United States)

    Choi, Y.; Czader, B.; Diao, L.; Rodriguez, J.; Jeong, G.

    2013-12-01

    The Community Earth Systems Model (CESM)-Whole Atmosphere Community Climate Model (WACCM) simulations were performed to study the impact of atmospheric chemistry on the radiation budget over the surface within a weather prediction time scale. The secondary goal is to get a simplified and optimized chemistry module for the short time period. Three different chemistry modules were utilized to represent tropospheric and stratospheric chemistry, which differ in how their reactions and species are represented: (1) simplified tropospheric and stratospheric chemistry (approximately 30 species), (2) simplified tropospheric chemistry and comprehensive stratospheric chemistry from the Model of Ozone and Related Chemical Tracers, version 3 (MOZART-3, approximately 60 species), and (3) comprehensive tropospheric and stratospheric chemistry (MOZART-4, approximately 120 species). Our results indicate the different details in chemistry treatment from these model components affect the surface temperature and impact the radiation budget.

  16. 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

  17. 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.

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. Silicateins--a novel paradigm in bioinorganic chemistry: enzymatic synthesis of inorganic polymeric silica.

    Science.gov (United States)

    Müller, Werner E G; Schröder, Heinz C; Burghard, Zaklina; Pisignano, Dario; Wang, Xiaohong

    2013-05-03

    The inorganic matrix of the siliceous skeletal elements of sponges, that is, spicules, is formed of amorphous biosilica. Until a decade ago, it remained unclear how the hard biosilica monoliths of the spicules are formed in sponges that live in a silica-poor (<50 μM) aquatic environment. The following two discoveries caused a paradigm shift and allowed an elucidation of the processes underlying spicule formation; first the discovery that in the spicules only one major protein, silicatein, exists and second, that this protein displays a bio-catalytical, enzymatic function. These findings caused a paradigm shift, since silicatein is the first enzyme that catalyzes the formation of an inorganic polymer from an inorganic monomeric substrate. In the present review the successive steps, following the synthesis of the silicatein product, biosilica, and resulting in the formation of the hard monolithic spicules is given. The new insight is assumed to open new horizons in the field of biotechnology and also in biomedicine.

  3. Marine Bioinorganic Chemistry Workshop Held in Heron Island on 28 June - 2nd July 1989

    Science.gov (United States)

    1990-02-09

    of Japan for the Protection of Migratory Birds and Birds in Danger of Extinction and their Environment. Schedule 2: * Appendix II to CITES - except...pictured) have up to fortymay cement the cay sands into a species including rainforest trees. hard pan known as cay sandstone. Some cays of the

  4. 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.

  5. Bioinorganic chemistry of copper coordination to alpha-synuclein: relevance to Parkinson's disease.

    OpenAIRE

    Binolfi, A.; L. Quintanar; Bertoncini, C.; Griesinger, C.; FERNANDEZ, C., LEOZ, J.

    2012-01-01

    Alpha-synuclein (AS) aggregation is associated with neurodegeneration in Parkinson'sdisease (PD). At the same time, alterations in metal ion homeostasis may play a pivotal role in the progression of AS amyloid assembly and the onset of PD. Elucidation of the structural basis directing AS–metal interactions and their effect on AS aggregation constitutes a key step toward understanding the role of metal ions in AS amyloid formation and neurodegeneration. This work provides a comprehensive revie...

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. SWIFT: Semi-empirical and numerically efficient stratospheric ozone chemistry for global climate models

    OpenAIRE

    Kreyling, Daniel; Wohltmann, Ingo; Lehmann, Ralph; Rex, Markus

    2015-01-01

    The SWIFT model is a fast yet accurate chemistry scheme for calculating the chemistry of stratospheric ozone. It is mainly intended for use in Global Climate Models (GCMs), Chemistry Climate Models (CCMs) and Earth System Models (ESMs). For computing time reasons these models often do not employ full stratospheric chem- istry modules, but use prescribed ozone instead. This can lead to insufficient representation between stratosphere and troposphere. The SWIFT stratospheric ozone chem...

  12. 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.

  13. Acoustic Gravity Wave Chemistry Model for the RAYTRACE Code.

    Science.gov (United States)

    2014-09-26

    AU)-AI56 850 ACOlUSTIC GRAVITY WAVE CHEMISTRY MODEL FOR THE IAYTRACE I/~ CODE(U) MISSION RESEARCH CORP SANTA BARBIARA CA T E OLD Of MAN 84 MC-N-SlS...DNA-TN-S4-127 ONAOOI-BO-C-0022 UNLSSIFIlED F/O 20/14 NL 1-0 2-8 1111 po 312.2 1--I 11111* i •. AD-A 156 850 DNA-TR-84-127 ACOUSTIC GRAVITY WAVE...Hicih Frequency Radio Propaoation Acoustic Gravity Waves 20. ABSTRACT (Continue en reveree mide if tteceeemr and Identify by block number) This

  14. 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…

  15. 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.

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

    Science.gov (United States)

    Bonten, Luc T C; Groenenberg, Jan E; Meesenburg, Henning; de Vries, Wim

    2011-10-01

    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.

  17. Sulfur chemistry: 1D modeling in massive dense cores

    CERN Document Server

    Wakelam, V; Herpin, F

    2011-01-01

    The main sulfur-bearing molecules OCS, H2S, SO, SO2, and CS have been observed in four high mass dense cores (W43-MM1, IRAS 18264, IRAS 05358, and IRAS 18162). Our goal is to put some constraints on the relative evolutionary stage of these sources by comparing these observations with time-dependent chemical modeling. We used the chemical model Nahoon, which computes the gas-phase chemistry and gas-grain interactions of depletion and evaporation. Mixing of the different chemical compositions shells in a 1D structure through protostellar envelope has been included since observed lines suggest nonthermal supersonic broadening. Observed radial profiles of the temperature and density are used to compute the chemistry as a function of time. With our model, we underproduce CS by several orders of magnitude compared to the other S-bearing molecules, which seems to contradict observations, although some uncertainties in the CS abundance observed at high temperature remain. The OCS/SO2, SO/SO2, and H2S/SO2 abundance ra...

  18. The chemical bond in inorganic chemistry the bond valence model

    CERN Document Server

    Brown, I David

    2016-01-01

    The bond valence model is a version of the ionic model in which the chemical constraints are expressed in terms of localized chemical bonds formed by the valence charge of the atoms. Theorems derived from the properties of the electrostatic flux predict the rules obeyed by both ionic and covalent bonds. They make quantitative predictions of coordination number, crystal structure, bond lengths and bond angles. Bond stability depends on the matching of the bonding strengths of the atoms, while the conflicting requirements of chemistry and space lead to the structural instabilities responsible for the unusual physical properties displayed by some materials. The model has applications in many fields ranging from mineralogy to molecular biology.

  19. 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

  20. Model for acid-base chemistry in nanoparticle growth (MABNAG)

    Science.gov (United States)

    Yli-Juuti, T.; Barsanti, K.; Hildebrandt Ruiz, L.; Kieloaho, A.-J.; Makkonen, U.; Petäjä, T.; Ruuskanen, T.; Kulmala, M.; Riipinen, I.

    2013-12-01

    Climatic effects of newly-formed atmospheric secondary aerosol particles are to a large extent determined by their condensational growth rates. However, all the vapours condensing on atmospheric nanoparticles and growing them to climatically relevant sizes are not identified yet and the effects of particle phase processes on particle growth rates are poorly known. Besides sulfuric acid, organic compounds are known to contribute significantly to atmospheric nanoparticle growth. In this study a particle growth model MABNAG (Model for Acid-Base chemistry in NAnoparticle Growth) was developed to study the effect of salt formation on nanoparticle growth, which has been proposed as a potential mechanism lowering the equilibrium vapour pressures of organic compounds through dissociation in the particle phase and thus preventing their evaporation. MABNAG is a model for monodisperse aqueous particles and it couples dynamics of condensation to particle phase chemistry. Non-zero equilibrium vapour pressures, with both size and composition dependence, are considered for condensation. The model was applied for atmospherically relevant systems with sulfuric acid, one organic acid, ammonia, one amine and water in the gas phase allowed to condense on 3-20 nm particles. The effect of dissociation of the organic acid was found to be small under ambient conditions typical for a boreal forest site, but considerable for base-rich environments (gas phase concentrations of about 1010 cm-3 for the sum of the bases). The contribution of the bases to particle mass decreased as particle size increased, except at very high gas phase concentrations of the bases. The relative importance of amine versus ammonia did not change significantly as a function of particle size. While our results give a reasonable first estimate on the maximum contribution of salt formation to nanoparticle growth, further studies on, e.g. the thermodynamic properties of the atmospheric organics, concentrations of low

  1. Model for acid-base chemistry in nanoparticle growth (MABNAG

    Directory of Open Access Journals (Sweden)

    T. Yli-Juuti

    2013-03-01

    Full Text Available Climatic effects of newly-formed atmospheric secondary aerosol particles are to a large extent determined by their condensational growth rates. However, all the vapors condensing on atmospheric nanoparticles and growing them to climatically relevant sizes are not identified yet and the effects of particle phase processes on particle growth rates are poorly known. Besides sulfuric acid, organic compounds are known to contribute significantly to atmospheric nanoparticle growth. In this study a particle growth model MABNAG (Model for Acid-Base chemistry in NAnoparticle Growth was developed to study the effect of salt formation on nanoparticle growth, which has been proposed as a potential mechanism lowering the equilibrium vapor pressures of organic compounds through dissociation in the particle phase and thus preventing their evaporation. MABNAG is a model for monodisperse aqueous particles and it couples dynamics of condensation to particle phase chemistry. Non-zero equilibrium vapor pressures, with both size and composition dependence, are considered for condensation. The model was applied for atmospherically relevant systems with sulfuric acid, one organic acid, ammonia, one amine and water in the gas phase allowed to condense on 3–20 nm particles. The effect of dissociation of the organic acid was found to be small under ambient conditions typical for a boreal forest site, but considerable for base-rich environments (gas phase concentrations of about 1010 cm−3 for the sum of the bases. The contribution of the bases to particle mass decreased as particle size increased, except at very high gas phase concentrations of the bases. The relative importance of amine versus ammonia did not change significantly as a function of particle size. While our results give a reasonable first estimate on the maximum contribution of salt formation to nanoparticle growth, further studies on, e.g. the thermodynamic properties of the atmospheric organics

  2. 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.

  3. 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.

  4. 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

  5. Chemistry and Climate in Asia - An Earth System Modeling Project

    Science.gov (United States)

    Barth, M. C.; Emmons, L. K.; Massie, S. T.; Pfister, G.; Romero Lankao, P.; Lamarque, J.; Carmichael, G. R.

    2011-12-01

    Asia is one of the most highly populated and economically dynamic regions in the world, with much of the population located in growing mega-cities. It is a region with significant emissions of greenhouse gases, aerosols and other pollutants, which pose high health risks to urban populations. Emissions of these aerosols and gases increased drastically over the last decade due to economic growth and urbanization and are expected to rise further in the near future. As such, the continent plays a role in influencing climate change via its effluent of aerosols and gaseous pollutants. Asia is also susceptible to adverse climate change through interactions between aerosols and clouds, which potentially can have serious implications for freshwater resources. We are developing an integrated inter-disciplinary program to focus on Asia, its climate, air quality, and impact on humans that will include connections with hydrology, ecosystems, extreme weather events, and human health. The primary goal of this project is to create a team to identify key scientific questions and establish networks of specialists to create a plan for future studies to address these questions. A second goal is to establish research facilities and a framework for investigating chemistry and climate over Asia. These facilities include producing high resolution Earth System Model simulations that have been evaluated with meteorological and chemical measurements, producing high-resolution emission inventories, analyzing satellite data, and analyzing the vulnerability of humans to air quality and extreme natural events. In this presentation we will describe in more detail these activities and discuss a future workshop on the impact of chemistry in climate on air quality and human health.

  6. Air chemistry over the Dead Sea: Observations and Model Simulations

    Science.gov (United States)

    Luria, M.; Tas, E.; Obrist, D.; Marveev, V.; Peleg, M.

    2011-12-01

    The Dead Sea which lies between Israel and Jordan is the deepest place on the planet with a negative elevation of 424 m below sea level. Because it is situated in isolated water shed with much higher evaporation rates relative to water inflow, its salinity is 10 times greater (numbers??) than normal ocean water. Emissions of bromine into the air in the form of reactive bromine species (RBS) are responsible for unique chemistry found only during the spring season over the Arctic Ocean and the stratosphere over Antarctica. Measurements of chemical and meteorological parameters took place at the Dead Sea during a series of studies between 1997 and 2010. Initially, the sensitivity of RBS formation to both meteorological and anthropogenic parameters was investigated using measurement-based simulations. The results show that RBS formation at the Dead Sea occurs efficiently via both aerosol-induced chemistry and direct bromine release from the Dead Sea water. Aerosol-induced RBS formation was found to be active when the measured relative humidity (RH) was higher than ~30%. Direct release of bromine from the seawater appears to occur efficiently only when wind speeds are below ~2m/s. Anthropogenic NO2 and sulfate aerosols significantly enhance RBS formation at the Dead Sea at times when aerosol chemistry is active. This appears to occur via the heterogeneous decomposition of BrONO2 on sulfate aerosols. However, above a threshold level of NO2, inhibition of RBS production can occur. This threshold NO2 level is highly dependent on several variables, including RBS levels and concentrations of sulfate aerosols. Overall, direct bromine release from the seawater appears to be more efficient than aerosol-induced RBS formation, but at times when measured RH exceed ~30%, extremely high BrO formation can occur via aerosol-induced chemistry. The second part of the study included simulations to examine the effects of RBS on atmospheric mercury depletion events (AMDEs) that occur in

  7. 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

  8. A dynamic model reduction algorithm for atmospheric chemistry models

    Science.gov (United States)

    Santillana, Mauricio; Le Sager, Philippe; Jacob, Daniel J.; Brenner, Michael

    2010-05-01

    Understanding the dynamics of the chemical composition of our atmosphere is essential to address a wide range of environmental issues from air quality to climate change. Current models solve a very large and stiff system of nonlinear advection-reaction coupled partial differential equations in order to calculate the time evolution of the concentration of over a hundred chemical species. The numerical solution of this system of equations is difficult and the development of efficient and accurate techniques to achieve this has inspired research for the past four decades. In this work, we propose an adaptive method that dynamically adjusts the chemical mechanism to be solved to the local environment and we show that the use of our approach leads to accurate results and considerable computational savings. Our strategy consists of partitioning the computational domain in active and inactive regions for each chemical species at every time step. In a given grid-box, the concentration of active species is calculated using an accurate numerical scheme, whereas the concentration of inactive species is calculated using a simple and computationally inexpensive formula. We demonstrate the performance of the method by application to the GEOS-Chem global chemical transport model.

  9. 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

  10. 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

  11. 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

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

    OpenAIRE

    Hashemi, Hamid; Hansen, Stine; Toftegaard, Maja Bøg; Pedersen, Kim Hougaard; Jensen, Anker Degn; Dam-Johansen, Kim; Glarborg, Peter

    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, heating and devolatilization of particles, and gas–solid reactions. The model is validated by comparison with entrained flow reactor results from the present work and from the literature on pulver...

  13. 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.

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

    OpenAIRE

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

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

    OpenAIRE

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

    2006-01-01

    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 ...

  16. Controlling Multivalent Binding through Surface Chemistry: Model Study on Streptavidin

    Science.gov (United States)

    2017-01-01

    Although multivalent binding to surfaces is an important tool in nanotechnology, quantitative information about the residual valency and orientation of surface-bound molecules is missing. To address these questions, we study streptavidin (SAv) binding to commonly used biotinylated surfaces such as supported lipid bilayers (SLBs) and self-assembled monolayers (SAMs). Stability and kinetics of SAv binding are characterized by quartz crystal microbalance with dissipation monitoring, while the residual valency of immobilized SAv is quantified using spectroscopic ellipsometry by monitoring binding of biotinylated probes. Purpose-designed SAv constructs having controlled valencies (mono-, di-, trivalent in terms of biotin-binding sites) are studied to rationalize the results obtained on regular (tetravalent) SAv. We find that divalent interaction of SAv with biotinylated surfaces is a strict requirement for stable immobilization, while monovalent attachment is reversible and, in the case of SLBs, leads to the extraction of biotinylated lipids from the bilayer. The surface density and lateral mobility of biotin, and the SAv surface coverage are all found to influence the average orientation and residual valency of SAv on a biotinylated surface. We demonstrate how the residual valency can be adjusted to one or two biotin binding sites per immobilized SAv by choosing appropriate surface chemistry. The obtained results provide means for the rational design of surface-confined supramolecular architectures involving specific biointeractions at tunable valency. This knowledge can be used for the development of well-defined bioactive coatings, biosensors and biomimetic model systems. PMID:28234007

  17. Modeling the chemistry of plasma polymerization using mass spectrometry.

    Science.gov (United States)

    Ihrig, D F; Stockhaus, J; Scheide, F; Winkelhake, Oliver; Streuber, Oliver

    2003-04-01

    The goal of the project is a solvent free painting shop. The environmental technologies laboratory is developing processes of plasma etching and polymerization. Polymerized thin films are first-order corrosion protection and primer for painting. Using pure acetylene we get very nice thin films which were not bonded very well. By using air as bulk gas it is possible to polymerize, in an acetylene plasma, well bonded thin films which are stable first-order corrosion protections and good primers. UV/Vis spectroscopy shows nitrogen oxide radicals in the emission spectra of pure nitrogen and air. But nitrogen oxide is fully suppressed in the presence of acetylene. IR spectroscopy shows only C=O, CH(2) and CH(3) groups but no nitrogen species. With the aid of UV/Vis spectra and the chemistry of ozone formation it is possible to define reactive traps and steps, molecule depletion and processes of proton scavenging and proton loss. Using a numerical model it is possible to evaluate these processes and to calculate theoretical mass spectra. Adjustment of theoretical mass spectra to real measurements leads to specific channels of polymerization which are driven by radicals especially the acetyl radical. The estimated theoretical mass spectra show the specific channels of these chemical processes. It is possible to quantify these channels. This quantification represents the mass flow through this chemical system. With respect to these chemical processes it is possible to have an idea of pollutant production processes.

  18. 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…

  19. Accounting for non-linear chemistry of ship plumes in the GEOS-Chem global chemistry transport model

    Directory of Open Access Journals (Sweden)

    G. C. M. Vinken

    2011-11-01

    Full Text Available We present a computationally efficient approach to account for the non-linear chemistry occurring during the dispersion of ship exhaust plumes in a global 3-D model of atmospheric chemistry (GEOS-Chem. We use a plume-in-grid formulation where ship emissions age chemically for 5 h before being released in the global model grid. Besides reducing the original ship NOx emissions in GEOS-Chem, our approach also releases the secondary compounds ozone and HNO3, produced during the 5 h after the original emissions, into the model. We applied our improved method and also the widely used "instant dilution" approach to a 1-yr GEOS-Chem simulation of global tropospheric ozone-NOx-VOC-aerosol chemistry. We also ran simulations with the standard model (emitting 10 molecules O3 and 1 molecule HNO3 per ship NOx molecule, and a model without any ship emissions at all. The model without any ship emissions simulates up to 0.1 ppbv (or 50% lower NOx concentrations over the North Atlantic in July than our improved GEOS-Chem model. "Instant dilution" overestimates NOx concentrations by 0.1 ppbv (50% and ozone by 3–5 ppbv (10–25%, compared to our improved model over this region. These conclusions are supported by comparing simulated and observed NOx and ozone concentrations in the lower troposphere over the Pacific Ocean. The comparisons show that the improved GEOS-Chem model simulates NOx concentrations in between the instant dilution model and the model without ship emissions, which results in lower O3 concentrations than the instant dilution model. The relative differences in simulated NOx and ozone between our improved approach and instant dilution are smallest over strongly polluted seas (e.g. North Sea, suggesting that accounting for in-plume chemistry is most relevant for pristine marine areas.

  20. 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.

  1. Accounting for non-linear chemistry of ship plumes in the GEOS-Chem global chemistry transport model

    Directory of Open Access Journals (Sweden)

    G. C. M. Vinken

    2011-06-01

    Full Text Available We present a computationally efficient approach to account for the non-linear chemistry occurring during the dispersion of ship exhaust plumes in a global 3-D model of atmospheric chemistry (GEOS-Chem. We use a plume-in-grid formulation where ship emissions age chemically for 5 h before being released in the global model grid. Besides reducing the original ship NOx emissions in GEOS-Chem, our approach also releases the secondary compounds ozone and HNO3, produced in the 5 h after the original emissions, into the model. We applied our improved method and also the widely used "instant dilution" approach to a 1-yr GEOS-Chem simulation of global tropospheric ozone-NOx-VOC-aerosol chemistry. We also ran simulations with the standard model, and a model without any ship emissions at all. Our improved GEOS-Chem model simulates up to 0.1 ppbv (or 90 % more NOx over the North Atlantic in July than GEOS-Chem versions without any ship NOx emissions at all. "Instant dilution" overestimates NOx concentrations by 50 % (0.1 ppbv and ozone by 10–25 % (3–5 ppbv over this region. These conclusions are supported by comparing simulated and observed NOx and ozone concentrations in the lower troposphere over the Pacific Ocean. The comparisons show that the improved GEOS-Chem model simulates NOx concentrations in between the instant diluting model and the model with no ship emissions, and results in lower O3 concentrations than the instant diluting model. The relative differences in simulated NOx and ozone between our improved approach and instant dilution are smallest over strongly polluted seas (e.g. North Sea, suggesting that accounting for in-plume chemistry is most relevant for pristine marine areas.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Multiscale Modeling of Chemistry in Water: Are We There Yet?

    Science.gov (United States)

    Bulo, Rosa E; Michel, Carine; Fleurat-Lessard, Paul; Sautet, Philippe

    2013-12-10

    This paper critically evaluates the state of the art in combined quantum mechanical/molecular mechanical (QM/MM) approaches to the computational description of chemistry in water and supplies guidelines for the setup of customized multiscale simulations of aqueous processes. We differentiate between structural and dynamic performance, since some tasks, e.g., the reproduction of NMR or UV-vis spectra, require only structural accuracy, while others, i.e., reaction mechanisms, require accurate dynamic data as well. As a model system for aqueous solutions in general, the approaches were tested on a QM water cluster in an environment of MM water molecules. The key difficulty is the description of the possible diffusion of QM molecules into the MM region and vice versa. The flexible inner region ensemble separator (FIRES) approach constrains QM solvent molecules within an active (QM) region. Sorted adaptive partitioning (SAP), difference-based adaptive solvation (DAS), and buffered-force (BF) are all adaptive approaches that use a buffer zone in which solvent molecules gradually adapt from QM to MM (or vice versa). The costs of SAP and DAS are relatively high, while BF is fast but sacrifices conservation of both energy and momentum. Simulations in the limit of an infinitely small buffer zone, where DAS and SAP become equivalent, are discussed as well and referred to as ABRUPT. The best structural accuracy is obtained with DAS, BF, and ABRUPT, all three of similar quality. FIRES performs very well for dynamic properties localized deep within the QM region. By means of elimination DAS emerges as the best overall compromise between structural and dynamic performance. Eliminating the buffer zone (ABRUPT) improves efficiency and still leads to surprisingly good results. While none of the many new flavors are perfect, all together this new field already allows accurate description of a wide range of structural and dynamic properties of aqueous solutions.

  7. 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.

  8. Understanding Differences in Chemistry Climate Model Projections 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 project future evolution of stratospheric ozone as concentrations of ozone-depleting substances (ODSs) decrease and greenhouse gases increase, cooling the stratosphere. CCM projections exhibit not only 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 ODS concentration change from that due to climate change. We show that the sensitivity of lower stratospheric ozone to chlorine change Delta Ozone/Delta inorganic chlorine is a near-linear function of partitioning of total inorganic chlorine into its reservoirs; both inorganic chlorine and its partitioning are largely controlled by lower stratospheric transport. CCMs with best performance on transport diagnostics agree with observations for chlorine reservoirs and produce similar ozone responses to chlorine change. After 2035, differences in Delta Ozone/Delta inorganic chlorine contribute little to the spread in CCM projections as the anthropogenic contribution to inorganic chlorine becomes unimportant. Differences among upper stratospheric ozone increases due to temperature decreases are explained by differences in ozone sensitivity to temperature change Delta Ozone/Delta T due to different contributions from various ozone loss processes, each with its own temperature dependence. Ozone decrease in the tropical lower stratosphere caused by a projected speedup in the Brewer-Dobson circulation may or may not be balanced by ozone increases in the middle- and high-latitude lower stratosphere and upper troposphere. This balance, or lack thereof, contributes most to the spread in late 21st century projections.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    Science.gov (United States)

    Knote, C.; Brunner, D.

    2012-10-01

    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 contribute up to 50% of total evaporated mass near the surface.

  15. 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

  16. Modeling SOAaq Formation: Explicit Organic Chemistry in Cloud Droplets with CMAQ

    Science.gov (United States)

    Carlton, A. G.; Sareen, N.; Fahey, K.; Hutzell, W. T.

    2013-12-01

    Aqueous multiphase chemistry in the atmosphere has a substantial impact on climate and can lead to air quality changes that adversely impact human health and the environment. The chemistry is complex because of the variety of compounds present in the atmosphere and the phase transitions associated with multiphase reactions. These reactions can lead to the formation of secondary organic aerosols (SOAAQ) in the atmosphere. When included, current photochemical models typically use a simple parameterization to describe SOAAQ formation. Here, we discuss the implementation of explicit aqueous SOA chemistry in a box model of the CMAQ 5.0.1 aqueous phase chemistry mechanism using the Kinetic PreProcessor (KPP). The expanded chemistry model includes reactions of glyoxal, methylglyoxal, and glycolaldehyde as precursors to form SOAAQ and is based on the mechanism from Lim et. al. 2010. The current aqueous phase chemistry module in CMAQ uses a forward Euler method to solve the system of oxidation equations, estimating the pH with a bisection method assuming electroneutrality, and multiphase processes are solved sequentially. This is not robust for systems with large dynamic range (e.g., multiphase systems), and inhibits expansion of the aqueous phase chemical mechanism to adequately incorporate the growing body of literature that describes multiphase organic chemistry. The KPP solver allows for all processes to be solved simultaneously and facilitates expansion of the current mechanism. Addition of explicit organic reactions and H2O2 photolysis in the KPP box model results in increased mass of organic aerosol and more realistic predictions. For particulate matter focused air quality management strategies to be effective, it is important that models move away from the yield-based approach currently used and expand to include more explicit organic chemistry.

  17. 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…

  18. Lessons from a low-order coupled chemistry meteorology model and applications to a high-dimensional chemical transport model

    Science.gov (United States)

    Haussaire, Jean-Matthieu; Bocquet, Marc

    2016-04-01

    Atmospheric chemistry models are becoming increasingly complex, with multiphasic chemistry, size-resolved particulate matter, and possibly coupled to numerical weather prediction models. In the meantime, data assimilation methods have also become more sophisticated. Hence, it will become increasingly difficult to disentangle the merits of data assimilation schemes, of models, and of their numerical implementation in a successful high-dimensional data assimilation study. That is why we believe that the increasing variety of problems encountered in the field of atmospheric chemistry data assimilation puts forward the need for simple low-order models, albeit complex enough to capture the relevant dynamics, physics and chemistry that could impact the performance of data assimilation schemes. Following this analysis, we developped a low-order coupled chemistry meteorology model named L95-GRS [1]. The advective wind is simulated by the Lorenz-95 model, while the chemistry is made of 6 reactive species and simulates ozone concentrations. With this model, we carried out data assimilation experiments to estimate the state of the system as well as the forcing parameter of the wind and the emissions of chemical compounds. This model proved to be a powerful playground giving insights on the hardships of online and offline estimation of atmospheric pollution. Building on the results on this low-order model, we test advanced data assimilation methods on a state-of-the-art chemical transport model to check if the conclusions obtained with our low-order model still stand. References [1] Haussaire, J.-M. and Bocquet, M.: A low-order coupled chemistry meteorology model for testing online and offline data assimilation schemes, Geosci. Model Dev. Discuss., 8, 7347-7394, doi:10.5194/gmdd-8-7347-2015, 2015.

  19. 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…

  20. Secondary Students' Mental Models of Atoms and Molecules: Implications for Teaching Chemistry.

    Science.gov (United States)

    Harrison, Allan G.; Treagust, David F.

    1996-01-01

    Examines the reasoning behind views of atoms and molecules held by students (n=48) and investigates how mental models may assist or hamper further instruction in chemistry. Reports that students prefer models of atoms and molecules that depict them as discrete, concrete structures. Recommends that teachers develop student modeling skills and…

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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…

  12. Redox Models in Chemistry Textbooks for the Upper Secondary School: Friend or Foe?

    Science.gov (United States)

    Osterlund, Lise-Lotte; Berg, Anders; Ekborg, Margareta

    2010-01-01

    We have investigated how chemistry textbooks use models of redox reactions in different subject areas, how they change models between and within the topics, and how they deal with specific learning difficulties identified in the literature. The textbooks examined were published for use in the natural science programme in Swedish upper secondary…

  13. 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…

  14. Development and Validation of a Path Analytic Model of Students' Performance in Chemistry.

    Science.gov (United States)

    Anamuah-Mensah, Jophus; And Others

    1987-01-01

    Reported the development and validation of an integrated model of performance on chemical concept-volumetric analysis. Model was tested on 265 chemistry students in eight schools.Results indicated that for subjects using algorithms without understanding, performance on volumetric analysis problems was not influenced by proportional reasoning…

  15. 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.

  16. 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.

    2009-06-01

    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 (lateral salt patterns in WA lakes. The WA playa lakes display significant lateral variations in mineralogy and water chemistry over short distances, reflecting the interaction of acid ground waters with neutral to alkaline lake waters derived from ponded surface runoff. Meridiani Planum observations indicate that such lateral variations are much less pronounced, pointing to the dominant influence of ground water chemistry, vertical ground water movements, and aeolian processes on the Martian surface mineralogy.

  17. 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…

  18. Adapting authentic science practices into contexts for learning: The case of models and modelling in pre-university chemistry education

    NARCIS (Netherlands)

    Prins, G.T.; Pilot, A.

    2013-01-01

    This research study explores the potential benefits of using authentic modelling practices as contexts for learning in chemistry education. An authentic modelling practice is characterized as professionals sharing common purposes, working to a similar type of modelling procedure, while applying rele

  19. Implementation of a PETN failure model using ARIA's general chemistry framework

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, Michael L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-01-01

    We previously developed a PETN thermal decomposition model that accurately predicts thermal ignition and detonator failure [1]. This model was originally developed for CALORE [2] and required several complex user subroutines. Recently, a simplified version of the PETN decomposition model was implemented into ARIA [3] using a general chemistry framework without need for user subroutines. Detonator failure was also predicted with this new model using ENCORE. The model was simplified by 1) basing the model on moles rather than mass, 2) simplifying the thermal conductivity model, and 3) implementing ARIA’s new phase change model. This memo briefly describes the model, implementation, and validation.

  20. Structural characterization of copper(II) binding to alpha-synuclein: Insights into the bioinorganic chemistry of Parkinson's disease.

    Science.gov (United States)

    Rasia, Rodolfo M; Bertoncini, Carlos W; Marsh, Derek; Hoyer, Wolfgang; Cherny, Dmitry; Zweckstetter, Markus; Griesinger, Christian; Jovin, Thomas M; Fernández, Claudio O

    2005-03-22

    The aggregation of alpha-synuclein (AS) is characteristic of Parkinson's disease and other neurodegenerative synucleinopathies. We demonstrate here that Cu(II) ions are effective in accelerating AS aggregation at physiologically relevant concentrations without altering the resultant fibrillar structures. By using numerous spectroscopic techniques (absorption, CD, EPR, and NMR), we have located the primary binding for Cu(II) to a specific site in the N terminus, involving His-50 as the anchoring residue and other nitrogen/oxygen donor atoms in a square planar or distorted tetragonal geometry. The carboxylate-rich C terminus, originally thought to drive copper binding, is able to coordinate a second Cu(II) equivalent, albeit with a 300-fold reduced affinity. The NMR analysis of AS-Cu(II) complexes reveals the existence of conformational restrictions in the native state of the protein. The metallobiology of Cu(II) in Parkinson's disease is discussed by a comparative analysis with other Cu(II)-binding proteins involved in neurodegenerative disorders.

  1. 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.

  2. 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.

  3. Structural characterization of copper(II) binding to α-synuclein: Insights into the bioinorganic chemistry of Parkinson's disease

    OpenAIRE

    Rasia, Rodolfo M.; Carlos W Bertoncini; Marsh, Derek; Hoyer, Wolfgang; Cherny, Dmitry; Zweckstetter, Markus; Griesinger, Christian; Jovin, Thomas M.; Fernández, Claudio O

    2005-01-01

    The aggregation of α-synuclein (AS) is characteristic of Parkinson's disease and other neurodegenerative synucleinopathies. We demonstrate here that Cu(II) ions are effective in accelerating AS aggregation at physiologically relevant concentrations without altering the resultant fibrillar structures. By using numerous spectroscopic techniques (absorption, CD, EPR, and NMR), we have located the primary binding for Cu(II) to a specific site in the N terminus, involving His-50 as the anchoring r...

  4. Structural characterization of copper(II) binding to α-Synuclein: Insights into the bioinorganic chemistry of Parkinson's disease

    OpenAIRE

    Rasia, R.; BERTONCINI, C; Marsh, D; Hoyer, W.; Cherny, D; Zweckstetter, M.; Griesinger, C; Jovin, T.; Fernandez, C.

    2005-01-01

    The aggregation of α -synuclein (AS) is characteristic of Parkinson’s disease and other neurodegenerative synucleinopathies. We demonstrate here that Cu(II) ions are effective in accelerating AS aggregation at physiologically relevant concentrations without altering the resultant fibrillar structures. By using numerous spectroscopic techniques (absorption, CD, EPR, and NMR), we have located the primary binding for Cu(II) to a specific site in the N terminus, involving His-50 as the anchoring ...

  5. 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.

  6. 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.

  7. Study and modeling of finite rate chemistry effects in turbulent non-premixed flames

    Science.gov (United States)

    Vervisch, Luc

    1993-01-01

    The development of numerical models that reflect some of the most important features of turbulent reacting flows requires information about the behavior of key quantities in well defined combustion regimes. In turbulent flames, the coupling between turbulent and chemical processes is so strong that it is extremely difficult to isolate the role played by one individual physical phenomenon. Direct numerical simulation (hereafter DNS) allows us to study in detail the turbulence-chemistry interaction in some restricted but completely defined situations. Globally, non-premixed flames are controlled by two limiting regimes: the fast chemistry case, where the turbulent flame can be pictured as a random distribution of local chemical equilibrium problems; and the slow chemistry case, where the chemistry integrates in time the turbulent fluctuations. The Damkoehler number, ratio of a mechanical time scale to chemical time scale, is used to distinguish between these regimes. Today most of the industrial computer codes are able to perform predictions in the hypothesis of local equilibrium chemistry using a presumed shape for the probability density function (pdt) of the conserved scalar. However, the finite rate chemistry situation is of great interest because industrial burners usually generate regimes in which, at some points, the flame is undergoing local extinction or at least non-equilibrium situations. Moreover, this variety of situations strongly influences the production of pollutants. To quantify finite rate chemistry effect, the interaction between a non-premixed flame and a free decaying turbulence is studied using DNS. The attention is focused on the dynamic of extinction, and an attempt is made to quantify the effect of the reaction on the small scale mixing process. The unequal diffusivity effect is also addressed. Finally, a simple turbulent combustion model based on the DNS observations and tractable in real flow configurations is proposed.

  8. 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

  9. 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.

  10. 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...

  11. 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.)

  12. 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.

  13. 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.

  14. 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…

  15. 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

    , heating and devolatilization of particles, and gas–solid reactions. The model is validated by comparison with entrained flow reactor results from the present work and from the literature on pulverized coal combustion in O2/CO2 and air, covering the effects of fuel, mixing conditions, temperature......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...

  16. 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...

  17. 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.

  18. 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

  19. 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

  20. Examination of Bond Properties through Infrared Spectroscopy and Molecular Modeling in the General Chemistry Laboratory

    Science.gov (United States)

    Csizmar, Clifford M.; Force, Dee Ann; Warner, Don L.

    2012-01-01

    A concerted effort has been made to increase the opportunities for undergraduate students to address scientific problems employing the processes used by practicing chemists. As part of this effort, an infrared (IR) spectroscopy and molecular modeling experiment was developed for the first-year general chemistry laboratory course. In the…

  1. 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…

  2. 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.

  3. 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.

  4. 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

  5. An advanced modeling study on the impacts and atmospheric implications of multiphase dimethyl sulfide chemistry.

    Science.gov (United States)

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

    2016-10-18

    Oceans dominate emissions of dimethyl sulfide (DMS), the major natural sulfur source. DMS is important for the formation of non-sea salt sulfate (nss-SO4(2-)) aerosols and secondary particulate matter over oceans and thus, significantly influence global climate. The mechanism of DMS oxidation has accordingly been investigated in several different model studies in the past. However, these studies had restricted oxidation mechanisms that mostly underrepresented important aqueous-phase chemical processes. These neglected but highly effective processes strongly impact direct product yields of DMS oxidation, thereby affecting the climatic influence of aerosols. To address these shortfalls, an extensive multiphase DMS chemistry mechanism, the Chemical Aqueous Phase Radical Mechanism DMS Module 1.0, was developed and used in detailed model investigations of multiphase DMS chemistry in the marine boundary layer. The performed model studies confirmed the importance of aqueous-phase chemistry for the fate of DMS and its oxidation products. Aqueous-phase processes significantly reduce the yield of sulfur dioxide and increase that of methyl sulfonic acid (MSA), which is needed to close the gap between modeled and measured MSA concentrations. Finally, the simulations imply that multiphase DMS oxidation produces equal amounts of MSA and sulfate, a result that has significant implications for nss-SO4(2-) aerosol formation, cloud condensation nuclei concentration, and cloud albedo over oceans. Our findings show the deficiencies of parameterizations currently used in higher-scale models, which only treat gas-phase chemistry. Overall, this study shows that treatment of DMS chemistry in both gas and aqueous phases is essential to improve the accuracy of model predictions.

  6. 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.

  7. Manganese(II chelates of bioinorganic and medicinal relevance: Synthesis, characterization, antibacterial activity and 3D-molecular modeling of some penta-coordinated manganese(II chelates in O,N-donor coordination matrix of β-diketoenolates and picolinate

    Directory of Open Access Journals (Sweden)

    R.C. Maurya

    2016-09-01

    Full Text Available Four new mixed-ligand complexes of manganese(II of the composition [Mn(pa(L(H2O], where paH = picolinic acid and LH = acetoacetanilide (aaH, o-acetoacetanisidide (o-aansH, o-acetoacetotoluidide (o-aatdH or ethylacetoacetate (eacacH, have been synthesized by the interaction of MnCl2·4H2O with the said ligands in aqueous-ethanol medium. The complexes so obtained have been characterized on the basis of elemental analyses, molar conductance and magnetic measurements, thermogravimetric analyses, mass, EPR, infrared and electronic spectral studies. Synthesized complexes have shown significantly greater antibacterial activity against Escherichia coli and Vibrio cholera than ligands. The 3D-molecular modeling and analysis for bond lengths and bond angles have also been carried out for one of the representative compound [Mn(pa(aa(H2O] (1 to substantiate the proposed structures.

  8. 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.

  9. 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

  10. 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

  11. Description and evaluation of the Multiscale Online Nonhydrostatic AtmospheRe CHemistry model (NMMB-MONARCH) version 1.0: gas-phase chemistry at global scale

    Science.gov (United States)

    Badia, Alba; Jorba, Oriol; Voulgarakis, Apostolos; Dabdub, Donald; Pérez García-Pando, Carlos; Hilboll, Andreas; Gonçalves, María; Janjic, Zavisa

    2017-02-01

    This paper presents a comprehensive description and benchmark evaluation of the tropospheric gas-phase chemistry component of the Multiscale Online Nonhydrostatic AtmospheRe CHemistry model (NMMB-MONARCH), formerly known as NMMB/BSC-CTM, that can be run on both regional and global domains. Here, 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 campaigns), and satellite observations (SCIAMACHY and MOPITT). We also include an extensive discussion of our results in comparison to other state-of-the-art models. We note that in this study, we omitted aerosol processes and some natural emissions (lightning and volcano emissions). The model shows a realistic oxidative capacity across the globe. The seasonal cycle for CO is fairly well represented at different locations (correlations around 0.3-0.7 in surface concentrations), although concentrations are underestimated in spring and winter in the Northern Hemisphere, and are overestimated throughout the year at 800 and 500 hPa in the Southern Hemisphere. Nitrogen species are well represented in almost all locations, particularly NO2 in Europe (root mean square error - RMSE - below 5 ppb). The modeled vertical distributions of NOx and HNO3 are in excellent agreement with the observed values and the spatial and seasonal trends of tropospheric NO2 columns correspond well to observations from SCIAMACHY, capturing the highly polluted areas and the biomass burning cycle throughout the year. Over Asia, the model underestimates NOx from March to August, probably due to an underestimation of NOx emissions in the region. Overall, the comparison of the modeled CO and NO2 with MOPITT and SCIAMACHY observations emphasizes the need for more accurate emission rates from anthropogenic and biomass burning sources (i.e., specification of temporal variability). The resulting

  12. 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.

  13. 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...

  14. The Use of Molecular Modeling Programs in Medicinal Chemistry Instruction.

    Science.gov (United States)

    Harrold, Marc W.

    1992-01-01

    This paper describes and evaluates the use of a molecular modeling computer program (Alchemy II) in a pharmaceutical education program. Provided are the hardware requirements and basic program features as well as several examples of how this program and its features have been applied in the classroom. (GLR)

  15. Teaching “Chemistry in Our Lives” Unit in the 9th Grade Chemistry Course through Context-Based ARCS Instructional Model

    Directory of Open Access Journals (Sweden)

    Hülya KUTU

    2011-03-01

    Full Text Available The purpose of this study is to examine the usability of Context-based ARCS Instructional Model on secondary school chemistry teaching. For this purpose the effects of learning through Context-based ARCS Instructional Model on the retention of knowledge, students’ motivation and attitude towards chemistry have been investigated. An instrumental case study has been utilized as the research method to teach the unit “Chemistry in Our Lives” in the 9th grade high school chemistry curriculum through Context-based ARCS Instructional Model. The sample of the study is composed of totally 60 ninth grade students from two different classes in a high school in Erzurum. The sample has been selected by convenience sampling method. Data have been collected through “Attitude Towards Chemistry Scale [ATCS]”; “Instructional Materials Motivation Survey [IMMS]”, “Constructivist Learning Environment Survey [CLES]”, “Achievement Test [AT]” have been developed by the researchers and semi-structured interviews. The data for IMMS, CLES and AT have been analyzed through descriptive statistics and results were presented as mean, standard deviation and charts. ATCS test has been analyzed by dependent sample t-test to see whether there is a significant difference between pre and post-tests scores. Semi-structured interviews have been subjected to content analysis and the results are presented as descriptively. The results show that the method used has increased the retention of learning and students’ motivation but has not had a statistically significant impact on students’ attitudes towards chemistry. In addition, it has been seen that students perceive classroom milieu as a constructivist learning environment.

  16. 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.

  17. 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.

  18. Interactive computer modeling of combustion chemistry and coalescence-dispersion modeling of turbulent combustion

    Science.gov (United States)

    Pratt, D. T.

    1984-01-01

    An interactive computer code for simulation of a high-intensity turbulent combustor as a single point inhomogeneous stirred reactor was developed from an existing batch processing computer code CDPSR. The interactive CDPSR code was used as a guide for interpretation and direction of DOE-sponsored companion experiments utilizing Xenon tracer with optical laser diagnostic techniques to experimentally determine the appropriate mixing frequency, and for validation of CDPSR as a mixing-chemistry model for a laboratory jet-stirred reactor. The coalescence-dispersion model for finite rate mixing was incorporated into an existing interactive code AVCO-MARK I, to enable simulation of a combustor as a modular array of stirred flow and plug flow elements, each having a prescribed finite mixing frequency, or axial distribution of mixing frequency, as appropriate. Further increase the speed and reliability of the batch kinetics integrator code CREKID was increased by rewriting in vectorized form for execution on a vector or parallel processor, and by incorporating numerical techniques which enhance execution speed by permitting specification of a very low accuracy tolerance.

  19. 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.

  20. 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.

  1. The Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP): Overview and Description of Models, Simulations and Climate Diagnostics

    Science.gov (United States)

    Lamarque, J.-F.; Shindell, D. T.; Naik, V.; Plummer, D.; Josse, B.; Righi, M.; Rumbold, S. T.; Schulz, M.; Skeie, R. B.; Strode, S.; Young, P. J.; Cionni, I.; Dalsoren, S.; Eyring, V.; Bergmann, D.; Cameron-Smith, P.; Collins, W. J.; Doherty, R.; Faluvegi, G.; Folberth, G.; Ghan, S. J.; Horowitz, L. W.; Lee, Y. H.; MacKenzie, I. A.; Nagashima, T.

    2013-01-01

    The Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP) consists of a series of time slice experiments targeting the long-term changes in atmospheric composition between 1850 and 2100, with the goal of documenting composition changes and the associated radiative forcing. In this overview paper, we introduce the ACCMIP activity, the various simulations performed (with a requested set of 14) and the associated model output. The 16 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 are responsible for a significant range across models, mostly in the case of 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. However, models that are clear outliers are different enough from the other models to significantly affect their simulation of atmospheric chemistry.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Modeling calcium sulfate chemistries with applications to Mars

    Science.gov (United States)

    Marion, G. M.; Catling, D. C.; Kargel, J. S.; Crowley, J. K.

    2016-11-01

    On Mars, evidence indicates widespread calcium sulfate minerals. Gypsum (CaSO4ṡ2H2O) seems to be the dominant calcium sulfate mineral in the north polar region of Mars. On the other hand, anhydrite (CaSO4) and bassanite (CaSO4ṡ0.5H2O) appear to be more common in large sedimentary deposits in the lower latitudes. The tropics are generally warmer and drier, and at least locally show evidence of acidic environments in the past. FREZCHEM is a thermodynamic modeling tool used for assessment of equilibrium involving high salinity solutions and salts, designed especially for low temperatures below 298 K (with one version adapted for temperatures up to 373 K), and we have used it to investigate many Earth, Mars, and other planetary science problems. Gypsum and anhydrite were included in earlier versions of FREZCHEM and our model Mars applications, but bassanite (the CaSO4 hemihydrate) has not previously been included. The objectives of this work are to (1) add bassanite to the FREZCHEM model, (2) examine the environments in which thermodynamic equilibrium precipitation of calcium sulfate minerals would be favored on Mars, and (3) use FREZCHEM to model situations where metastable equilibrium might be favored and promote the formation or persistence of one of these phases over the others in violation of an idealized equilibrium state. We added a bassanite equation based on high temperatures (343-373 K). A Mars simulation was based on a previously published Nasbnd Casbnd Mgsbnd Clsbnd SO4 system over the temperature range of 273 to 373 K. With declining temperatures, the first solid phase under equilibrium precipitation is anhydrite at 373 K, then gypsum forms at 319 K (46 °C), and epsomite (MgSO4ṡ7H2O) at 277 K. This sequence could reflect, for example, the precipitation sequence in a saturated solution that is slowly cooled in a deep, warm aquifer. Because FREZCHEM is based on thermodynamic equilibrium, a crude approach to problems involving metastable equilibria is

  7. Representation of the Community Earth System Model (CESM1) CAM4-chem within the Chemistry-Climate Model Initiative (CCMI)

    Science.gov (United States)

    Tilmes, Simone; Lamarque, Jean-Francois; Emmons, Louisa K.; Kinnison, Doug E.; Marsh, Dan; Garcia, Rolando R.; Smith, Anne K.; Neely, Ryan R.; Conley, Andrew; Vitt, Francis; Martin, Maria Val; Tanimoto, Hiroshi; Simpson, Isobel; Blake, Don R.; Blake, Nicola

    2016-05-01

    The Community Earth System Model (CESM1) CAM4-chem has been used to perform the Chemistry Climate Model Initiative (CCMI) reference and sensitivity simulations. In this model, the Community Atmospheric Model version 4 (CAM4) is fully coupled to tropospheric and stratospheric chemistry. Details and specifics of each configuration, including new developments and improvements are described. CESM1 CAM4-chem is a low-top model that reaches up to approximately 40 km and uses a horizontal resolution of 1.9° latitude and 2.5° longitude. For the specified dynamics experiments, the model is nudged to Modern-Era Retrospective Analysis for Research and Applications (MERRA) reanalysis. We summarize the performance of the three reference simulations suggested by CCMI, with a focus on the last 15 years of the simulation when most observations are available. Comparisons with selected data sets are employed to demonstrate the general performance of the model. We highlight new data sets that are suited for multi-model evaluation studies. Most important improvements of the model are the treatment of stratospheric aerosols and the corresponding adjustments for radiation and optics, the updated chemistry scheme including improved polar chemistry and stratospheric dynamics and improved dry deposition rates. These updates lead to a very good representation of tropospheric ozone within 20 % of values from available observations for most regions. In particular, the trend and magnitude of surface ozone is much improved compared to earlier versions of the model. Furthermore, stratospheric column ozone of the Southern Hemisphere in winter and spring is reasonably well represented. All experiments still underestimate CO most significantly in Northern Hemisphere spring and show a significant underestimation of hydrocarbons based on surface observations.

  8. Review of the global models used within phase 1 of the Chemistry-Climate Model Initiative (CCMI)

    Science.gov (United States)

    Morgenstern, Olaf; Hegglin, Michaela I.; Rozanov, Eugene; O'Connor, Fiona M.; Abraham, N. Luke; Akiyoshi, Hideharu; Archibald, Alexander T.; Bekki, Slimane; Butchart, Neal; Chipperfield, Martyn P.; Deushi, Makoto; Dhomse, Sandip S.; Garcia, Rolando R.; Hardiman, Steven C.; Horowitz, Larry W.; Jöckel, Patrick; Josse, Beatrice; Kinnison, Douglas; Lin, Meiyun; Mancini, Eva; Manyin, Michael E.; Marchand, Marion; Marécal, Virginie; Michou, Martine; Oman, Luke D.; Pitari, Giovanni; Plummer, David A.; Revell, Laura E.; Saint-Martin, David; Schofield, Robyn; Stenke, Andrea; Stone, Kane; Sudo, Kengo; Tanaka, Taichu Y.; Tilmes, Simone; Yamashita, Yousuke; Yoshida, Kohei; Zeng, Guang

    2017-02-01

    We present an overview of state-of-the-art chemistry-climate and chemistry transport models that are used within phase 1 of the Chemistry-Climate Model Initiative (CCMI-1). The CCMI aims to conduct a detailed evaluation of participating models using process-oriented diagnostics derived from observations in order to gain confidence in the models' projections of the stratospheric ozone layer, tropospheric composition, air quality, where applicable global climate change, and the interactions between them. Interpretation of these diagnostics requires detailed knowledge of the radiative, chemical, dynamical, and physical processes incorporated in the models. Also an understanding of the degree to which CCMI-1 recommendations for simulations have been followed is necessary to understand model responses to anthropogenic and natural forcing and also to explain inter-model differences. This becomes even more important given the ongoing development and the ever-growing complexity of these models. This paper also provides an overview of the available CCMI-1 simulations with the aim of informing CCMI data users.

  9. A Novel Lattice Boltzmann Model For Reactive Flows with Fast Chemistry

    Institute of Scientific and Technical Information of China (English)

    CHEN Sheng; LIU Zhao-Hui; HE Zhu; ZHANG Chao; TIAN Zhi-Wei; SHI Bao-Chang; ZHENG Chu-Guang

    2006-01-01

    @@ A novel lattice Boltzmann model, in which we take the ratio of temperature difference in the temperature field to the environment one to be more than one order of magnitude than before, is developed to simulate two dimensional reactive flows with fast chemistry. Different from the hybrid scheme for reactive flows [Comput.Phys. Commun. 129 (2000)267], this scheme is strictly in a pure lattice Boltzmann style (i.e., we solve the flow, temperature, and concentration fields using the lattice Boltzmann method only). Different from the recent non-coupled lattice Boltzmann scheme [Int. J. Mod. Phys. B 17(2003) 197], the fluid density in our model is coupled directly with the temperature. Excellent agreement between the present results and other numerical data shows that this scheme is an efficient numerical method for practical reactive flows with fast chemistry.

  10. 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.

  11. 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.

  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. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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).

  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. Activity and property landscape modeling is at the interface of chemoinformatics and medicinal chemistry.

    Science.gov (United States)

    Medina-Franco, José L; Navarrete-Vázquez, Gabriel; Méndez-Lucio, Oscar

    2015-01-01

    Property landscape modeling (PLM) methods are at the interface of experimental sciences and computational chemistry. PLM are becoming a common strategy to describe systematically structure-property relationships of datasets. Thus far, PLM have been used mainly in medicinal chemistry and drug discovery. Herein, we survey advances on key topics on PLM with emphasis on questions often raised regarding the outcomes of the property landscape studies. We also emphasize on concepts of PLM that are being extended to other experimental areas beyond drug discovery. Topics discussed in this paper include applications of PLM to further characterize protein-ligand interactions, the utility of PLM as a quantitative and descriptive approach, and the statistical validation of property cliffs.

  2. 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.

  3. 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.

  4. 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.

  5. Numerical Modeling of Climate-Chemistry Connections: Recent Developments and Future Challenges

    Directory of Open Access Journals (Sweden)

    Patrick Jöckel

    2013-05-01

    Full Text Available This paper reviews the current state and development of different numerical model classes that are used to simulate the global atmospheric system, particularly Earth’s climate and climate-chemistry connections. The focus is on Chemistry-Climate Models. In general, these serve to examine dynamical and chemical processes in the Earth atmosphere, their feedback, and interaction with climate. Such models have been established as helpful tools in addition to analyses of observational data. Definitions of the global model classes are given and their capabilities as well as weaknesses are discussed. Examples of scientific studies indicate how numerical exercises contribute to an improved understanding of atmospheric behavior. There, the focus is on synergistic investigations combining observations and model results. The possible future developments and challenges are presented, not only from the scientific point of view but also regarding the computer technology and respective consequences for numerical modeling of atmospheric processes. In the future, a stronger cross-linkage of subject-specific scientists is necessary, to tackle the looming challenges. It should link the specialist discipline and applied computer science.

  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. 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.

  8. 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

  9. 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

  10. Trends in Mesospheric Dynamics and Chemistry: Simulations With a Model of the Entire Atmosphere

    Science.gov (United States)

    Brasseur, G. P.

    2005-05-01

    The cooling resulting from infrared CO2 radiative transfer is a major contribution to the energy budget of the middle atmosphere and thermosphere. The rapid increase of the atmospheric CO2 concentration resulting from anthropogenic emissions is therefore expected to lead, in general, to a substantial cooling in this height range. This can potentially be counteracted by heating due to absorption of near infrared radiation by CO2. Changes in ozone as a consequence of increasing methane and water vapor may also have an impact on the energy budget as dynamical changes caused by increased tropospheric temperatures. By means of numerical simulations with a general circulation and chemistry model of the entire atmosphere we will address the following questions: 1.) Can state-of-the-art atmospheric modeling explain the mesospheric temperature trends observed during the last decades? 2.)Which part of the temperature changes resulting from an increase of atmospheric CO2 is caused by local changes in the radiative budget and which part is influenced by remote dynamical effects? The model used is the newly developed Hamburg Model of the Neutral and Ionized Atmosphere (HAMMONIA) that resolves the atmosphere from the Earth's surface up to about 250 km altitude, and is based on the 3-D dynamics from the ECHAM5 general circulation model and the chemistry scheme from MOZART-3. Results from different time slice experiment representative of years 1970 and 2000, and for a doubling of CO2 will be presented.

  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 New Definition of Models and Modeling in Chemistry's Teaching

    Science.gov (United States)

    Chamizo, José A.

    2013-01-01

    The synthesis of new chemical compounds makes it the most productive science. Unfortunately chemistry education practice has not been driven to any great extent by research findings, philosophical positions or advances in new ways of approaching knowledge. The changes that have occurred in textbooks during the past three decades do not show any…

  13. Chemistry in Disks. IV. Benchmarking gas-grain chemical models with surface reactions

    CERN Document Server

    Semenov, D; Wakelam, V; Dutrey, A; Chapillon, E; Guilloteau, St; Henning, Th; Launhardt, R; Pietu, V; Schreyer, K

    2010-01-01

    Abridged: We detail and benchmark two sophisticated chemical models developed by the Heidelberg and Bordeaux astrochemistry groups. The main goal of this study is to elaborate on a few well-described tests for state-of-the-art astrochemical codes covering a range of physical conditions and chemical processes, in particular those aimed at constraining current and future interferometric observations of protoplanetary disks. We consider three physical models: a cold molecular cloud core, a hot core, and an outer region of a T Tauri disk. Our chemical network (for both models) is based on the original gas-phase osu_03_2008 ratefile and includes gas-grain interactions and a set of surface reactions for the H-, O-, C-, S-, and N-bearing molecules. The benchmarking is performed with the increasing complexity of the considered processes: (1) the pure gas-phase chemistry, (2) the gas-phase chemistry with accretion and desorption, and (3) the full gas-grain model with surface reactions. Using atomic initial abundances ...

  14. 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.

  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. Hydroxyl and Hydroperoxy Radical Chemistry during the MCMA-2006 Field Campaign: Measurement and Model Comparison

    Science.gov (United States)

    Dusanter, S.; Vimal, D.; Stevens, P. S.; Volkamer, R.; Molina, L. T.

    2007-12-01

    The Mexico City Metropolitan Area (MCMA) field campaign, held in March 2006, was a unique opportunity to collect data in one of the most polluted megacities in the world. Such environments exhibit a complex oxidation chemistry involving a strong coupling between odd hydrogen radicals (HOX=OH+HO2) and nitrogen oxides species (NOX=NO+NO2). High levels of volatile organic compounds (VOCs) and NOX control the HOX budget and lead to elevated tropospheric ozone formation. The HOX-NOX coupling can be investigated by comparing measured and model-predicted HOx concentrations. Atmospheric HOX concentrations were measured by the Indiana University laser-induced fluorescence instrument and data were collected at the Instituto Mexicano del Petroleo between 14 and 31 March. Measured hydroxyl radical (OH) concentrations are comparable to that measured in less polluted urban environments and suggest that the OH concentrations are highly buffered under high NOX conditions. In contrast, hydroperoxy radical (HO2) concentrations are more sensitive to the NOX levels and are highly variable between different urban sites. Enhanced levels of OH and HO2 radicals were observed on several days between 9h30-11h00 AM and suggest an additional HOX source for the morning hours and/or a fast HOX cycling under the high NOX conditions of the MCMA. A preliminary investigation of the HOX chemistry occurring in the MCMA urban atmosphere was performed using a photochemical box model based on the Regional Atmospheric Chemistry Mechanism (RACM). Model comparisons will be presented and the agreement between measured and predicted HOX concentrations will be discussed.

  17. 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.

  18. 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.

  19. Influence of Constructivist Professional Development on Chemistry Content Knowledge and Scientific Model Development

    Science.gov (United States)

    Khourey-Bowers, Claudia; Fenk, Christopher

    2009-10-01

    The purpose of this study was to explore the relationship between teachers’ ( N = 69) participation in constructivist chemistry professional development (PD) and enhancement of content (CK) and pedagogical content knowledge (PCK) (representational thinking and conceptual change strategies) and self-efficacy (PSTE). Quantitative measures assessed CK, PCK, and PSTE. Document analysis focused on PCK. Elementary teachers gained CK, PCK, PSTE, and designed lessons to advance thinking from macroscopic to abstract models. Middle/secondary teachers gained PSTE, PCK, and introduced macroscopic models to develop understanding of previously taught abstract models. All implemented representational thinking and conceptual change strategies. Results suggest that: (1) constructivist PD meets the needs of teachers of varying CK, and (2) instruction should connect representational models with alternative conceptions, integrating radical and social constructivism.

  20. Redox Chemistry in Radiation Induced Dissolution of Spent Nuclear Fuel : from Elementary Reactions to Predictive Modeling

    OpenAIRE

    Roth, Olivia

    2008-01-01

    The focus of this doctoral thesis is the redox chemistry involved in radiation induced oxidative dissolution of spent nuclear fuel and UO2 (as a model substance for spent nuclear fuel). It is shown that two electron oxidants are more efficient than one electron oxidants in oxidative dissolution of UO2 at low oxidant concentrations. Furthermore, it is shown that H2O2 is the only oxidant that has to be taken into account in radiation induced dissolution of UO2 under deep repository conditions (...

  1. 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.

  2. Expertise in soccer teams: A thematic inquiry into the role of shared mental models within team chemistry

    OpenAIRE

    Gershgoren, Lael; Basevitch, Itay; Filho, Edson; Gershgoren, Aaron; Brill, Yaron S.; Robert J. Schinke; Tenenbaum, Gershon

    2015-01-01

    Aims. The purpose of the current study was to establish a conceptual framework of team chemistry components in sport with an emphasis on Shared Mental Models (SMM).\\ud Method. Elite soccer coaches (n = 6) and players (n = 3) were interviewed using a semi-structured interview guide. An inductive thematic analysis was employed to analyze the data. Results. Four themes related to team chemistry components were identified: (1) members' characteristics (i.e., demographic data, on-field characteris...

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

    Science.gov (United States)

    Turi, László

    2016-04-21

    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 cavitystructure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

  5. Uncertainties in modeling heterogeneous chemistry and Arctic ozone depletion in the winter 2009/2010

    Directory of Open Access Journals (Sweden)

    I. Wohltmann

    2012-10-01

    Full Text Available Stratospheric chemistry and denitrification are simulated for the Arctic winter 2009/2010 with the Lagrangian Chemistry and Transport Model ATLAS. A number of sensitivity runs is used to explore the impact of uncertainties in chlorine activation and denitrification on the model results. In particular, the efficiency of chlorine activation on different types of liquid aerosol versus activation on nitric acid trihydrate clouds is examined. Additionally, the impact of changes in reaction rate coefficients, in the particle number density of polar stratospheric clouds, in supersaturation, temperature or the extent of denitrification is investigated. Results are compared to satellite measurements of MLS and ACE-FTS and to in-situ measurements onboard the Geophysica aircraft during the RECONCILE measurement campaign. It is shown that even large changes in the underlying assumptions have only a small impact on the modeled ozone loss, even though they can cause considerable differences in chemical evolution and denitrification. In addition, it is shown that chlorine activation on liquid aerosols alone is able to explain the observed magnitude and morphology of the mixing ratios of active chlorine, reservoir gases and ozone.

  6. Uncertainties in modeling heterogeneous chemistry and Arctic ozone depletion in the winter 2009/2010

    Science.gov (United States)

    Wohltmann, I.; Wegner, T.; Müller, R.; Lehmann, R.; Rex, M.; Manney, G. L.; Santee, M. L.; Bernath, P.; Sumińska-Ebersoldt, O.; Stroh, F.; von Hobe, M.; Volk, C. M.; Hösen, E.; Ravegnani, F.; Ulanovsky, A.; Yushkov, V.

    2012-10-01

    Stratospheric chemistry and denitrification are simulated for the Arctic winter 2009/2010 with the Lagrangian Chemistry and Transport Model ATLAS. A number of sensitivity runs is used to explore the impact of uncertainties in chlorine activation and denitrification on the model results. In particular, the efficiency of chlorine activation on different types of liquid aerosol versus activation on nitric acid trihydrate clouds is examined. Additionally, the impact of changes in reaction rate coefficients, in the particle number density of polar stratospheric clouds, in supersaturation, temperature or the extent of denitrification is investigated. Results are compared to satellite measurements of MLS and ACE-FTS and to in-situ measurements onboard the Geophysica aircraft during the RECONCILE measurement campaign. It is shown that even large changes in the underlying assumptions have only a small impact on the modeled ozone loss, even though they can cause considerable differences in chemical evolution and denitrification. In addition, it is shown that chlorine activation on liquid aerosols alone is able to explain the observed magnitude and morphology of the mixing ratios of active chlorine, reservoir gases and ozone.

  7. 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.

  8. 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

  9. The importance of high spatial resolution for the performance of atmospheric chemistry-transport models

    Science.gov (United States)

    Mantzius Hansen, Kaj

    2010-05-01

    We have investigated the importance of spatial resolution for the performance of the Danish Eulerian Hemispheric Model (DEHM), a state-of-the-art atmospheric chemistry-transport model covering the majority of the Northern Hemisphere with a horizontal grid resolution of 150 km X 150 km. DEHM has 29 vertical layers in terrain-following sigma-coordinates extending up to a height of 100 hPa. Two-way nesting options with a nesting factor of three can be applied with higher resolution over a limited area of the model. At present the model can be run without nests or with one, two or three nests, each with resolutions of 50 km X 50 km, 16.7 km X 16.7 km, and 5.6 km X 5.6 km, respectively. The model includes a comprehensive chemistry scheme with more than 100 reactions and 67 atmospheric constituents, of which 4 relate to primary particulates (PM2.5, PM10, TSP and sea salt), other species are SOx, NOx, NHx, VOCs, and secondary inorganic particulates. DEHM is driven by meteorological data from the numerical weather prediction model MM5v3. Three simulations were performed with DEHM: one simulation with only the mother domain, one simulation with one nest over Europe, and one simulation with an additional nest covering Denmark and surrounding countries. All three simulations cover the period from 1989 to 2006. The predicted concentrations were evaluated against measurements from the EMEP monitoring network. Only sites within the innermost nest were included in the evaluation and the evaluations of the three simulations were compared to test the influence of spatial resolution on the performance of the model.

  10. Evaluation of Convective Transport in the GEOS-5 Chemistry and Climate Model

    Science.gov (United States)

    Pickering, Kenneth E.; Ott, Lesley E.; Shi, Jainn J.; Tao. Wei-Kuo; Mari, Celine; Schlager, Hans

    2011-01-01

    The NASA Goddard Earth Observing System (GEOS-5) Chemistry and Climate Model (CCM) consists of a global atmospheric general circulation model and the combined stratospheric and tropospheric chemistry package from the NASA Global Modeling Initiative (GMI) chemical transport model. The subgrid process of convective tracer transport is represented through the Relaxed Arakawa-Schubert parameterization in the GEOS-5 CCM. However, substantial uncertainty for tracer transport is associated with this parameterization, as is the case with all global and regional models. We have designed a project to comprehensively evaluate this parameterization from the point of view of tracer transport, and determine the most appropriate improvements that can be made to the GEOS-5 convection algorithm, allowing improvement in our understanding of the role of convective processes in determining atmospheric composition. We first simulate tracer transport in individual observed convective events with a cloud-resolving model (WRF). Initial condition tracer profiles (CO, CO2, O3) are constructed from aircraft data collected in undisturbed air, and the simulations are evaluated using aircraft data taken in the convective anvils. A single-column (SCM) version of the GEOS-5 GCM with online tracers is then run for the same convective events. SCM output is evaluated based on averaged tracer fields from the cloud-resolving model. Sensitivity simulations with adjusted parameters will be run in the SCM to determine improvements in the representation of convective transport. The focus of the work to date is on tropical continental convective events from the African Monsoon Multidisciplinary Analyses (AMMA) field mission in August 2006 that were extensively sampled by multiple research aircraft.

  11. 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.

  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. 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.

  14. 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...

  15. Antarctic ozone depletion between 1960 and 1980 in observations and chemistry-climate model simulations

    Science.gov (United States)

    Langematz, Ulrike; Schmidt, Franziska; Kunze, Markus; Bodeker, Gregory E.; Braesicke, Peter

    2016-12-01

    The year 1980 has often been used as a benchmark for the return of Antarctic ozone to conditions assumed to be unaffected by emissions of ozone-depleting substances (ODSs), implying that anthropogenic ozone depletion in Antarctica started around 1980. Here, the extent of anthropogenically driven Antarctic ozone depletion prior to 1980 is examined using output from transient chemistry-climate model (CCM) simulations from 1960 to 2000 with prescribed changes of ozone-depleting substance concentrations in conjunction with observations. A regression model is used to attribute CCM modelled and observed changes in Antarctic total column ozone to halogen-driven chemistry prior to 1980. Wintertime Antarctic ozone is strongly affected by dynamical processes that vary in amplitude from year to year and from model to model. However, when the dynamical and chemical impacts on ozone are separated, all models consistently show a long-term, halogen-induced negative trend in Antarctic ozone from 1960 to 1980. The anthropogenically driven ozone loss from 1960 to 1980 ranges between 26.4 ± 3.4 and 49.8 ± 6.2 % of the total anthropogenic ozone depletion from 1960 to 2000. An even stronger ozone decline of 56.4 ± 6.8 % was estimated from ozone observations. This analysis of the observations and simulations from 17 CCMs clarifies that while the return of Antarctic ozone to 1980 values remains a valid milestone, achieving that milestone is not indicative of full recovery of the Antarctic ozone layer from the effects of ODSs.

  16. One-Dimensional Transport with Equilibrium Chemistry (OTEQ) - A Reactive Transport Model for Streams and Rivers

    Science.gov (United States)

    Runkel, Robert L.

    2010-01-01

    OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption. Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale. This report details the development and application of OTEQ. Sections of the report describe model theory, input/output specifications, model applications, and installation instructions. OTEQ may be obtained over the Internet at http://water.usgs.gov/software/OTEQ.

  17. 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.

  18. An adaptive reduction algorithm for efficient chemical calculations in global atmospheric chemistry models

    Science.gov (United States)

    Santillana, Mauricio; Le Sager, Philippe; Jacob, Daniel J.; Brenner, Michael P.

    2010-11-01

    We present a computationally efficient adaptive method for calculating the time evolution of the concentrations of chemical species in global 3-D models of atmospheric chemistry. Our strategy consists of partitioning the computational domain into fast and slow regions for each chemical species at every time step. In each grid box, we group the fast species and solve for their concentration in a coupled fashion. Concentrations of the slow species are calculated using a simple semi-implicit formula. Separation of species between fast and slow is done on the fly based on their local production and loss rates. This allows for example to exclude short-lived volatile organic compounds (VOCs) and their oxidation products from chemical calculations in the remote troposphere where their concentrations are negligible, letting the simulation determine the exclusion domain and allowing species to drop out individually from the coupled chemical calculation as their production/loss rates decline. We applied our method to a 1-year simulation of global tropospheric ozone-NO x-VOC-aerosol chemistry using the GEOS-Chem model. Results show a 50% improvement in computational performance for the chemical solver, with no significant added error.

  19. Development and evaluation of the aerosol dynamic and gas phase chemistry model ADCHEM

    Directory of Open Access Journals (Sweden)

    P. Roldin

    2010-08-01

    Full Text Available The aim of this work was to develop a model ideally suited for detailed studies on aerosol dynamics, gas and particle phase chemistry within urban plumes, from local scale (1×1 km2 to regional or global scale. This article describes and evaluates the trajectory model for Aerosol Dynamics, gas and particle phase CHEMistry and radiative transfer (ADCHEM, which has been developed and used at Lund University since 2007. The model treats both vertical and horizontal dispersion perpendicular to an air mass trajectory (2-space dimensions, which is not treated in Lagrangian box-models (0-space dimensions. The Lagrangian approach enables a more detailed representation of the aerosol dynamics, gas and particle phase chemistry and a finer spatial and temporal resolution compared to that of available regional 3D-CTMs. These features make it among others ideally suited for urban plume studies. The aerosol dynamics model includes Brownian coagulation, dry deposition, wet deposition, in-cloud processing, condensation, evaporation, primary particle emissions and homogeneous nucleation. The gas phase chemistry model calculates the gas phase concentrations of 63 different species, using 119 different chemical reactions. Daily isoprene and monoterpene emissions from European forests were simulated separately with the vegetation model LPJ-GUESS, and included as input to ADCHEM. ADCHEM was used to simulate the ageing of the urban plumes from the city of Malmö in Southern Sweden (280 000 inhabitants. Several sensitivity tests were performed concerning the number of size bins, size structure method, coupled or uncoupled condensation, the volatility basis set (VBS or traditional 2-product model for secondary organic aerosol formation, different aerosol dynamic processes and vertical and horizontal mixing. The simulations show that the full-stationary size structure gives accurate results with little numerical diffusion when more than 50 size bins are used

  20. The Effects of a Flipped Classroom Model of Instruction on Students' Performance and Attitudes Towards Chemistry

    Science.gov (United States)

    Olakanmi, Eunice Eyitayo

    2017-02-01

    This study establishes the effects of a flipped classroom model of instruction on academic performance and attitudes of 66 first-year secondary school students towards chemistry. A pre-test and post-test experimental design was employed to assign students randomly into either the experimental or control group. In order to assess the suitability of using flipped model of instruction, students were divided in two groups. For the first group called the experimental group, a "flipped classroom" was used in which the students were given video lessons and reading materials, before the class to be revised at home. On the other hand, the second group followed traditional methodology, and it was used as control. The rate of reaction knowledge test and the chemistry attitude scale were administered. In addition, the researcher documented classroom observations, experiences, thoughts and insights regarding the intervention in a journal on a daily basis in order to enrich the data. Students were interviewed at the end of the research in order to enrich the qualitative data also. Findings from this study reveal that the flipped instruction model facilitates a shift in students' conceptual understanding of the rate of chemical reaction significantly more than the control condition. Positive significant differences were found on all assessments with the flipped class students performing higher on average. Students in the flipped classroom model condition benefited by preparing for the lesson before the classes and had the opportunity to interact with peers and the teacher during the learning processes in the classroom. The findings support the notion that teachers should be trained or retrained on how to incorporate the flipped classroom model into their teaching and learning processes because it encourages students to be directly involved and active in the learning.

  1. The Effects of a Flipped Classroom Model of Instruction on Students' Performance and Attitudes Towards Chemistry

    Science.gov (United States)

    Olakanmi, Eunice Eyitayo

    2016-10-01

    This study establishes the effects of a flipped classroom model of instruction on academic performance and attitudes of 66 first-year secondary school students towards chemistry. A pre-test and post-test experimental design was employed to assign students randomly into either the experimental or control group. In order to assess the suitability of using flipped model of instruction, students were divided in two groups. For the first group called the experimental group, a "flipped classroom" was used in which the students were given video lessons and reading materials, before the class to be revised at home. On the other hand, the second group followed traditional methodology, and it was used as control. The rate of reaction knowledge test and the chemistry attitude scale were administered. In addition, the researcher documented classroom observations, experiences, thoughts and insights regarding the intervention in a journal on a daily basis in order to enrich the data. Students were interviewed at the end of the research in order to enrich the qualitative data also. Findings from this study reveal that the flipped instruction model facilitates a shift in students' conceptual understanding of the rate of chemical reaction significantly more than the control condition. Positive significant differences were found on all assessments with the flipped class students performing higher on average. Students in the flipped classroom model condition benefited by preparing for the lesson before the classes and had the opportunity to interact with peers and the teacher during the learning processes in the classroom. The findings support the notion that teachers should be trained or retrained on how to incorporate the flipped classroom model into their teaching and learning processes because it encourages students to be directly involved and active in the learning.

  2. Approximations for modelling CO chemistry in GMCs: a comparison of approaches

    CERN Document Server

    Glover, S C O

    2011-01-01

    We examine several different simplified approaches for modelling the chemistry of CO in three-dimensional numerical simulations of turbulent molecular clouds. We compare the different models both by looking at the behaviour of integrated quantities such as the mean CO fraction or the cloud-averaged CO-to-H2 conversion factor, and also by studying the detailed distribution of CO as a function of gas density and visual extinction. In addition, we examine the extent to which the density and temperature distributions depend on our choice of chemical model. We find that the two most complex models that we examine in this study, taken from work by Nelson & Langer (1999) and Glover et al. (2010), produce very similar results in all of our comparisons. However, the Nelson & Langer model is roughly a factor of three faster than the Glover et al. model, and thus will be the better choice for many applications. The simpler models examined in this study are even faster than the Nelson & Langer (1999) model, b...

  3. A Model for Incorporating Research into the First-Year Chemistry Curriculum

    Science.gov (United States)

    Ford, James R.; Prudente, Caryn; Newton, Thomas A.

    2008-01-01

    The development, implementation, and evaluation of a research-based program of laboratory instruction for first-year chemistry students is described. The new approach engages students in interdisciplinary, chemistry-centered research projects during the second semester of their general chemistry course. (Contains 1 figure and 1 table.)

  4. 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

  5. Computational Material Modeling of Hydrated Cement Paste Calcium Silicate Hydrate (C-S-H) Chemistry Structure - Influence of Magnesium Exchange on Mechanical Stiffness: C-S-H Jennite

    Science.gov (United States)

    2015-04-27

    material chemistry structure are studied following a molecular dynamics (MD) computational modeling methodology. Calcium ions are replaced with... chemistry structure. Conference Name: 1st Pan-American Conference on Computational Mechanics Conference Date: April 27, 2015 1st Pan-American Congress on...MODELING OF C-S-H Material chemistry level modeling following the principles and techniques commonly grouped under Computational Material Science is

  6. 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.

  7. On determining important aspects of mathematical models: Application to problems in physics and chemistry

    Science.gov (United States)

    Rabitz, Herschel

    1987-01-01

    The use of parametric and functional gradient sensitivity analysis techniques is considered for models described by partial differential equations. By interchanging appropriate dependent and independent variables, questions of inverse sensitivity may be addressed to gain insight into the inversion of observational data for parameter and function identification in mathematical models. It may be argued that the presence of a subset of dominantly strong coupled dependent variables will result in the overall system sensitivity behavior collapsing into a simple set of scaling and self similarity relations amongst elements of the entire matrix of sensitivity coefficients. These general tools are generic in nature, but herein their application to problems arising in selected areas of physics and chemistry is presented.

  8. 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...

  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. Consistent descriptions of metal–ligand bonds and spin-crossover in inorganic chemistry

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2013-01-01

    Density functional theory (DFT) is today the unchallenged tool for routinely obtaining molecular information on chemical stability, reactivity, and electronic structure across the Periodic Table. The chemical bond is the fundamental unit of molecular structure and reactivity, and thus, large-scal......-blocks. Physical effects and ingredients in functionals, their systematic errors, and approaches to deal with them are discussed, in order to identify broadly applicable methods for inorganic chemistry.......-scale DFT studies of inorganic systems in catalysis and bioinorganic chemistry rely directly on the ability to balance correlation effects in the involved bonds across the s-, p-, and d-blocks. This review concerns recent efforts to describe such bonds accurately and consistently across the s-, p-, and d...

  11. Uncertainties in modelling heterogeneous chemistry and Arctic ozone depletion in the winter 2009/2010

    Directory of Open Access Journals (Sweden)

    I. Wohltmann

    2013-04-01

    Full Text Available Stratospheric chemistry and denitrification are simulated for the Arctic winter 2009/2010 with the Lagrangian Chemistry and Transport Model ATLAS. A number of sensitivity runs is used to explore the impact of uncertainties in chlorine activation and denitrification on the model results. In particular, the efficiency of chlorine activation on different types of liquid aerosol versus activation on nitric acid trihydrate clouds is examined. Additionally, the impact of changes in reaction rate coefficients, in the particle number density of polar stratospheric clouds, in supersaturation, temperature or the extent of denitrification is investigated. Results are compared to satellite measurements of MLS and ACE-FTS and to in-situ measurements onboard the Geophysica aircraft during the RECONCILE measurement campaign. It is shown that even large changes in the underlying assumptions have only a small impact on the modelled ozone loss, even though they can cause considerable differences in chemical evolution of other species and in denitrification. Differences in column ozone between the sensitivity runs stay below 10% at the end of the winter. Chlorine activation on liquid aerosols alone is able to explain the observed magnitude and morphology of the mixing ratios of active chlorine, reservoir gases and ozone. This is even true for binary aerosols (no uptake of HNO3 from the gas-phase allowed in the model. Differences in chlorine activation between sensitivity runs are within 30%. Current estimates of nitric acid trihydrate (NAT number density and supersaturation imply that, at least for this winter, NAT clouds play a relatively small role compared to liquid clouds in chlorine activation. The change between different reaction rate coefficients for liquid or solid clouds has only a minor impact on ozone loss and chlorine activation in our sensitivity runs.

  12. Uncertainties in modelling heterogeneous chemistry and Arctic ozone depletion in the winter 2009/2010

    Science.gov (United States)

    Wohltmann, I.; Wegner, T.; Müller, R.; Lehmann, R.; Rex, M.; Manney, G. L.; Santee, M. L.; Bernath, P.; Sumińska-Ebersoldt, O.; Stroh, F.; von Hobe, M.; Volk, C. M.; Hösen, E.; Ravegnani, F.; Ulanovsky, A.; Yushkov, V.

    2013-04-01

    Stratospheric chemistry and denitrification are simulated for the Arctic winter 2009/2010 with the Lagrangian Chemistry and Transport Model ATLAS. A number of sensitivity runs is used to explore the impact of uncertainties in chlorine activation and denitrification on the model results. In particular, the efficiency of chlorine activation on different types of liquid aerosol versus activation on nitric acid trihydrate clouds is examined. Additionally, the impact of changes in reaction rate coefficients, in the particle number density of polar stratospheric clouds, in supersaturation, temperature or the extent of denitrification is investigated. Results are compared to satellite measurements of MLS and ACE-FTS and to in-situ measurements onboard the Geophysica aircraft during the RECONCILE measurement campaign. It is shown that even large changes in the underlying assumptions have only a small impact on the modelled ozone loss, even though they can cause considerable differences in chemical evolution of other species and in denitrification. Differences in column ozone between the sensitivity runs stay below 10% at the end of the winter. Chlorine activation on liquid aerosols alone is able to explain the observed magnitude and morphology of the mixing ratios of active chlorine, reservoir gases and ozone. This is even true for binary aerosols (no uptake of HNO3 from the gas-phase allowed in the model). Differences in chlorine activation between sensitivity runs are within 30%. Current estimates of nitric acid trihydrate (NAT) number density and supersaturation imply that, at least for this winter, NAT clouds play a relatively small role compared to liquid clouds in chlorine activation. The change between different reaction rate coefficients for liquid or solid clouds has only a minor impact on ozone loss and chlorine activation in our sensitivity runs.

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

    Science.gov (United States)

    Arnold, J.; Kosson, D. S.; Brown, K. G.; Garrabrants, A. C.; Meeussen, J. C. L.; van der Sloot, H. A.

    2013-07-01

    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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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

  1. Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface

    Science.gov (United States)

    Hoekstra, Alfons G.; Alowayyed, Saad; Lorenz, Eric; Melnikova, Natalia; Mountrakis, Lampros; van Rooij, Britt; Svitenkov, Andrew; Závodszky, Gábor; Zun, Pavel

    2016-11-01

    This discussion paper introduces the concept of the Virtual Artery as a multiscale model for arterial physiology and pathologies at the physics-chemistry-biology (PCB) interface. The cellular level is identified as the mesoscopic level, and we argue that by coupling cell-based models with other relevant models on the macro- and microscale, a versatile model of arterial health and disease can be composed. We review the necessary ingredients, both models of arteries at many different scales, as well as generic methods to compose multiscale models. Next, we discuss how this can be combined into the virtual artery. Finally, we argue that the concept of models at the PCB interface could or perhaps should become a powerful paradigm, not only as in our case for studying physiology, but also for many other systems that have such PCB interfaces. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

  2. The Strengths and Limitations of Satellite Data for Evaluating Tropospheric Processes in Chemistry-Climate Models

    Science.gov (United States)

    Duncan, Bryan

    2012-01-01

    There is now a wealth of satellite data products available with which to evaluate a model fs simulation of tropospheric composition and other model processes. All of these data products have their strengths and limitations that need to be considered for this purpose. For example, uncertainties are introduced into a data product when 1) converting a slant column to a vertical column and 2) estimating the amount of a total column of a trace gas (e.g., ozone, nitrogen dioxide) that resides in the troposphere. Oftentimes, these uncertainties are not well quantified and the satellite data products are not well evaluated against in situ observations. However, these limitations do not preclude us from using these data products to evaluate our model processes if we understand these strengths and limitations when developing diagnostics. I will show several examples of how satellite data products are being used to evaluate particular model processes with a focus on the strengths and limitations of these data products. In addition, I will introduce the goals of a newly formed team to address issues on the topic of "satellite data for improved model evaluation and process studies" that is established in support of the IGAC/SPARC Global Chemistry ]Climate Modeling and Evaluation Workshop.

  3. 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…

  4. Modelling the effects of (short-term solar variability on stratospheric chemistry

    Directory of Open Access Journals (Sweden)

    R. Muncaster

    2011-12-01

    lower than 1% and 15% of the ozone response, respectively. The results are found to be insensitive to an increase in the magnitude of the solar variability by a factor three, when this increase is applied uniformly throughout the solar spectrum. These statistical models offer accurate, computationally inexpensive parameterisations of the effect of solar variability in the stratosphere for climate-chemistry models with simplified chemistry that can be driven by any solar variability index. Finally, the statistical approach introduced here, based on ensemble photochemical simulations, provides an effective gauge to measure the effects of using more realistic solar variability spectra on the ozone response.

  5. Description and Evaluation of the Multiscale Online Nonhydrostatic AtmospheRe CHemistry Model (NMMB-MONARCH) Version 1.0: Gas-Phase Chemistry at Global Scale

    Science.gov (United States)

    Badia, Alba; Jorba, Oriol; Voulgarakis, Apostolos; Dabdub, Donald; Garcia-Pando, Carlos Perez; Hilboll, Andreas; Goncalves, Maria; Janjic, Zavisa

    2017-01-01

    This paper presents a comprehensive description and benchmark evaluation of the tropospheric gas-phase chemistry component of the Multiscale Online Nonhydrostatic AtmospheRe CHemistry model (NMMBMONARCH), formerly known as NMMB/BSC-CTM, that can be run on both regional and global domains. Here, 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 campaigns), and satellite observations (SCIAMACHY and MOPITT).We also include an extensive discussion of our results in comparison to other state-of-the-art models. We note that in this study, we omitted aerosol processes and some natural emissions (lightning and volcano emissions). The model shows a realistic oxidative capacity across the globe. The seasonal cycle for CO is fairly well represented at different locations (correlations around 0.3-0.7 in surface concentrations), although concentrations are underestimated in spring and winter in the Northern Hemisphere, and are overestimated throughout the year at 800 and 500 hPa in the Southern Hemisphere. Nitrogen species are well represented in almost all locations, particularly NO2 in Europe (root mean square error - RMSE - below 5 ppb). The modeled vertical distributions of NOx and HNO3 are in excellent agreement with the observed values and the spatial and seasonal trends of tropospheric NO2 columns correspond well to observations from SCIAMACHY, capturing the highly polluted areas and the biomass burning cycle throughout the year. Over Asia, the model underestimates NOx from March to August, probably due to an underestimation of NOx emissions in the region. Overall, the comparison of the modeled CO and NO2 with MOPITT and SCIAMACHY observations emphasizes the need for more accurate emission rates from anthropogenic and biomass burning sources (i.e., specification of temporal variability).

  6. Modeling Feedbacks between Biogenic Emissions and Air Chemistry from Site to Globe

    Science.gov (United States)

    Butler, T. M.; Grote, R.

    2014-12-01

    We present the implementation of a new model describing light dependent emission of volatile organic compounds (BVOC) that derives isoprenoid production directly from the electron transport potential and consumption from photosynthesis. Photosynthesis information requirements are designed to be met by many recent land-surface models that apply the Farquhar assimilation scheme, e.g. JULES or CLM. The new approach has the advantages that 1) the commonly observed decrease of (isoprene) emission with increasing CO2 air concentration is considered by the competition on energy between photosynthesis and emission processes, and 2) air pollution impacts may be considered as inducing emissions by activating emission enzymes as well as decreasing substrate supply from photosynthesis, and 3) many environmental drivers of BVOC emissions are implicitly considered in the description of plant photosynthesis and phenology, reducing the demand for species-specific emission parameters. We investigate the parameter sensitivity of the suggested model as well as the sensitivity of emissions to a range of environmental conditions with a particular focus on CO2 responses. We present evaluation at the site level and compare the model with other approaches. Finally, we demonstrate the implementation into a coupled global-air chemistry model and discuss the requirements to appropriately parameterize plant functional types.

  7. A new self-consistent hybrid chemistry model for Mars and cometary environments

    Science.gov (United States)

    Wedlund, Cyril Simon; Kallio, Esa; Jarvinen, Riku; Dyadechkin, Sergey; Alho, Markku

    2014-05-01

    Over the last 15 years, a 3-D hybrid-PIC planetary plasma interaction modelling platform, named HYB, has been developed, which was applied to several planetary environment such as those of Mars, Venus, Mercury, and more recently, the Moon. We present here another evolution of HYB including a fully consistent ionospheric-chemistry package designed to reproduce the main ions in the lower boundary of the model. This evolution, also permitted by the increase in computing power and the switch to spherical coordinates for higher spatial resolution (Dyadechkin et al., 2013), is motivated by the imminent arrival of the Rosetta spacecraft in the vicinity of comet 67P/Churyumov-Gerasimenko. In this presentation we show the application of the new HYB-ionosphere model to 1D and 2D hybrid simulations at Mars above 100 km altitude and demonstrate that with a limited number of chemical reactions, good agreement with 1D kinetic models may be found. This is a first validation step before applying the model to the 67P/CG comet environment, which, like Mars, is expected be rich in carbon oxide compounds.

  8. Impact of nitrous acid chemistry on air quality modeling results over the Pearl River Delta region

    Directory of Open Access Journals (Sweden)

    R. Zhang

    2011-05-01

    Full Text Available The impact of nitrous acid chemistry on regional ozone and particulate matter in Pearl River Delta region was investigated using the Community Mutilscale Air Quality modeling system and the CB05 mechanism. Model simulations were conducted for a ten-day period in October 2004. Compared with available observed data, the model performance for NOx, SO2, PM10, and sulfate is reasonably good; however, predictions of HONO are an order of magnitude lower than observed data. The CB05 mechanism contains several homogenous reactions related to nitrous acid. To improve the model performance for nitrous acid, direct emissions, two heterogeneous reactions, and two surface photolysis reactions were incorporated into the model. The inclusion of the additional formation pathways significantly improved simulated nitrous acid compared with observed data. The addition of nitrous acid sources enhance daily maximum 8-h ozone by up to 6 ppb V (8 % and daily mean PM2.5 by up to 17 μg m−3 (12 %. They also affected ozone control strategy in Pearl River Delta region.

  9. 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.

  10. Assimilation Experiments using Geodetic Observations to Diagnose AAM in a Chemistry-Climate Model

    Science.gov (United States)

    Neef, Lisa; Matthes, Katja

    2010-05-01

    Variation of the global angular momentum of the atmosphere (AAM) results from fluctuations in the mass-distribution and large-scale wind patterns of the atmosphere. It has moreoever been known for some time that global-scale natural modes of variability (such as ENSO) have clear footprints in the AAM history. Due to exchange of angular momentum between the atmosphere and the solid earth, fluctuations in AAM are reflected in observations of the Earth Rotation Parameters(ERPs). ERPs therefore provide an observational constraint for global climate models, via the simulated AAM. We are planning to assimilate ERPs into the chemistry-climate model ECHAM5/MESSy, to not only improve the agreement with observations but also to better diagnose model deficiencies. As a step toward developing such an assimilation system, we present a comparison between modeled AAM, and the AAM implied by ERP observations. We also illustrate and discuss the problem of extracting information about individual components of a model state from observations of a global integral quantity. This is done via data assimilation experiments in a highly simplified (Lorenz) dynamical system.

  11. 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

  12. Partial Overhaul and Initial Parallel Optimization of KINETICS, a Coupled Dynamics and Chemistry Atmosphere Model

    Science.gov (United States)

    Nguyen, Howard; Willacy, Karen; Allen, Mark

    2012-01-01

    KINETICS is a coupled dynamics and chemistry atmosphere model that is data intensive and computationally demanding. The potential performance gain from using a supercomputer motivates the adaptation from a serial version to a parallelized one. Although the initial parallelization had been done, bottlenecks caused by an abundance of communication calls between processors led to an unfavorable drop in performance. Before starting on the parallel optimization process, a partial overhaul was required because a large emphasis was placed on streamlining the code for user convenience and revising the program to accommodate the new supercomputers at Caltech and JPL. After the first round of optimizations, the partial runtime was reduced by a factor of 23; however, performance gains are dependent on the size of the data, the number of processors requested, and the computer used.

  13. Multigrid Method for Modeling Multi-Dimensional Combustion with Detailed Chemistry

    Science.gov (United States)

    Zheng, Xiaoqing; Liu, Chaoqun; Liao, Changming; Liu, Zhining; McCormick, Steve

    1996-01-01

    A highly accurate and efficient numerical method is developed for modeling 3-D reacting flows with detailed chemistry. A contravariant velocity-based governing system is developed for general curvilinear coordinates to maintain simplicity of the continuity equation and compactness of the discretization stencil. A fully-implicit backward Euler technique and a third-order monotone upwind-biased scheme on a staggered grid are used for the respective temporal and spatial terms. An efficient semi-coarsening multigrid method based on line-distributive relaxation is used as the flow solver. The species equations are solved in a fully coupled way and the chemical reaction source terms are treated implicitly. Example results are shown for a 3-D gas turbine combustor with strong swirling inflows.

  14. 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.

  15. 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.

  16. Evaluation of connectedness between the University courses of Physics and Chemistry basing on the graph model of intersubject links

    Science.gov (United States)

    Gnitetskaya, Tatyana; Ivanova, Elena

    2016-08-01

    An application of the graph model of inter-subject links to University courses of Physics and Chemistry is presented in this article. A part of inter-subject space with directions of inter-subject links from Physics to Chemistry in the group of physical concepts has been shown. The graph model of inter-subject links includes quantitative indicators. Its numerical values are given in the article. The degree of connectedness between the data of Physics and Chemistry courses is discussed for the courses considered. The effect of the courses placement within a curriculum on the value of their connectedness is shown. The placement of courses within a curriculum can provide the study of the courses at the same time or consecutive study, when one course precedes another.

  17. Titan Tholin Production Through Ion-Neutral Chemistry: Data and Model

    Science.gov (United States)

    Westlake, J. H.; Waite, J. H.; Crary, F. J.; Magee, B. A.; Mandt, K. E.; Young, D. T.

    2009-12-01

    Ion-neutral chemistry in Titan’s upper atmosphere produces a plethora of positive ions with masses up to about 350 amu and negative ions with much larger masses. The Cassini Plasma Spectrometer Ion Beam Spectrometer (CAPS-IBS), the Ion and Neutral Mass Spectrometer (INMS), and the CAPS Electron Spectrometer (CAPS-ELS) measure positive ions up to ~350 amu, positive ions and neutrals up to 100 amu, and negative ions to greater than 10,000 amu respectively. High-mass (greater than 100 Da.) spectral peaks lie in the region expected for polycyclic aromatic hydrocarbons and heterocyclic compounds. Coupled CAPS-IBS and INMS measurements provide ion densities through an iterative fitting process that are consistent with those measured by the Langmuir probe on Cassini. General properties of the high-mass positive ions are presented including scale height and day-night distribution. An ion-neutral model is presented which replicates the structure, primary peaks, and densities of the high mass ions observed. This model utilizes reactions studied within the context of Titan’s ionosphere, cold interstellar environments, and sooting flames as well as calculated reaction rates based on theoretical pathways. The primary ion-neutral reaction pathways are found to be acetylene addition, hydrogen cyanide insertion, and protonation. These processes are shown to reproduce the CAPS-IBS spectral peaks with good accuracy. We assess the possibility of heterocyclic compound production through ion-neutral chemistry in which nitrogen substituted aromatics, produced through reactions with HCN and HC3N, participate in associative reactions. Heterocyclic compounds, such as purine and pyrimidine, form the basic structural units of nucleotides.

  18. 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

  19. 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

  20. 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

  1. Modeling physical chemistry of the Io plasma torus in two dimensions

    Science.gov (United States)

    Copper, M.; Delamere, P. A.; Overcast-Howe, K.

    2016-07-01

    Periodicities in the Io plasma illustrate the rich complexity of magnetosphere-ionosphere coupling in space plasmas. The confounding System IV period (slower than the rotation of Jupiter's magnetic field ≡ System III) remains a mystery of the torus. Common to both System III and IV are modulations of the superthermal electron population. The small fraction (<1%) of hot electrons plays a vital role in torus physical and chemical properties, modulating the abundance and temperature of ion species. Building on previous models of torus physical chemistry, we have developed a two-dimensional model that includes azimuthal and radial transport (diffusion equation) while averaging chemical processes in latitude. This paper presents initial results of the model, demonstrating the role of hot electrons in forming a single-peaked torus structure. The effect of azimuthal shear is investigated as plasma is transported radially outward, showing how the torus properties evolve during transport from a chemically dominated regime (inner torus) to a transport dominated regime (outer torus). Surprisingly, we find that hot electron populations influence torus properties at all radial distances. While many of our results are preliminary, suggestions for future modeling experiments are suggested to provide additional insight into the origin of the ubiquitous superthermal electrons.

  2. 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.

  3. 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.

  4. Development and validation of a path analytic model of students' performance in chemistry

    Science.gov (United States)

    Anamuah-Mensah, Jophus; Erickson, Gaalen; Gaskell, Jim

    This article reports the development and validation of an integrated model of performance on a chemical concept - volumetric analysis. From the chemical literature a path-analytic model of performance on volumetric analysis calculation was postulated based on studies utilizing the proportional reasoning schema of Piaget and the Cumulative learning theory of Gagne. This integrated model hypothesized some relationships among the variables: direct proportional reasoning, inverse proportional reasoning, prerequisite concepts (content) and performance on volumetric analysis calculations. This model was postulated for the two groups of students involved in the study - that is those who use algorithms with understanding and those who use algorithms without understanding. Two hundred and sixty-five grade twelve chemistry students in eight schools (14 classes) in the lower mainland of British Columbia, Canada participated fully in the study. With the exception of the test on volumetric analysis calculations all the other tests were administered prior to the teaching of the unit on volumetric analysis. The results of the study indicate that for subjects using algorithms without understanding, their performance on VA problems is not influenced by proportional reasoning strategies while for those who use algorithms with understanding, their performance is influenced by proportional reasoning strategies.

  5. A kinetic chemistry tagging technique and its application to modelling the stable isotopic composition of atmospheric trace gases

    Directory of Open Access Journals (Sweden)

    S. Gromov

    2010-08-01

    Full Text Available Isotope composition, in many cases, holds unique information on the sources, chemical modification and sinks of atmospheric trace gases. Vital to the interpretation and use of an increasing number of isotope analyses is appropriate modelling. However, the exact implementation of isotopic information in chemistry-climate models is a challenge, and often studies use simplifications which limit their applicability. Here we implement a thorough isotopic extension in MECCA, a comprehensive kinetic chemistry sub-model. To this end, we devise a generic tagging technique for the kinetic chemistry mechanisms implemented as the sub-submodel MECCA-TAG. The technique is diagnostic and numerically efficient and supports the investigation of various aspects of kinetic chemistry schemes. We focus specifically on the application to the modelling of stable isotopic composition. The results of MECCA-TAG are evaluated against the reference sub-submodel MECCA-DBL, which is implicitly full-detailed, but computationally expensive and thus sub-optimal in practical applications. Furthermore, we evaluate the elaborate carbon and oxygen isotopic mechanism by simulating the multi-isotope composition of CO and other trace gases in the CAABA/MECCA box-model. The mechanism realistically simulates the oxygen isotope composition of key species, as well as the carbon isotope signature transfer. The model adequately reproduces the isotope chemistry features for CO, taking into account the limits of the modelling domain. In particular, the mass-independently fractionated (MIF composition of CO due to reactions of ozone with unsaturated hydrocarbons (a source effect versus its intrinsic MIF enrichment induced in the removal reaction via oxidation by OH is assessed. The simulated ozone source effect was up to +1‰ in Δ17O(CO. The versatile modelling framework we employ (the Modular Earth Submodel System, MESSy opens the way for implementation of the novel detailed

  6. 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.

  7. 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.

  8. 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.

  9. 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…

  10. 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…

  11. 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…

  12. 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...

  13. 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…

  14. 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…

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Addressing the complexity of water chemistry in environmental fate modeling for engineered nanoparticles.

    Science.gov (United States)

    Sani-Kast, Nicole; Scheringer, Martin; Slomberg, Danielle; Labille, Jérôme; Praetorius, Antonia; Ollivier, Patrick; Hungerbühler, Konrad

    2015-12-01

    Engineered nanoparticle (ENP) fate models developed to date - aimed at predicting ENP concentration in the aqueous environment - have limited applicability because they employ constant environmental conditions along the modeled system or a highly specific environmental representation; both approaches do not show the effects of spatial and/or temporal variability. To address this conceptual gap, we developed a novel modeling strategy that: 1) incorporates spatial variability in environmental conditions in an existing ENP fate model; and 2) analyzes the effect of a wide range of randomly sampled environmental conditions (representing variations in water chemistry). This approach was employed to investigate the transport of nano-TiO2 in the Lower Rhône River (France) under numerous sets of environmental conditions. The predicted spatial concentration profiles of nano-TiO2 were then grouped according to their similarity by using cluster analysis. The analysis resulted in a small number of clusters representing groups of spatial concentration profiles. All clusters show nano-TiO2 accumulation in the sediment layer, supporting results from previous studies. Analysis of the characteristic features of each cluster demonstrated a strong association between the water conditions in regions close to the ENP emission source and the cluster membership of the corresponding spatial concentration profiles. In particular, water compositions favoring heteroaggregation between the ENPs and suspended particulate matter resulted in clusters of low variability. These conditions are, therefore, reliable predictors of the eventual fate of the modeled ENPs. The conclusions from this study are also valid for ENP fate in other large river systems. Our results, therefore, shift the focus of future modeling and experimental research of ENP environmental fate to the water characteristic in regions near the expected ENP emission sources. Under conditions favoring heteroaggregation in these

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

    NARCIS (Netherlands)

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

    2016-01-01

    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, a

  1. Sensitivity of Global Modeling Initiative chemistry and transport model simulations of radon-222 and lead-210 to input meteorological data

    Directory of Open Access Journals (Sweden)

    D. B. Considine

    2005-01-01

    Full Text Available We have used the Global Modeling Initiative chemistry and transport model to simulate the radionuclides radon-222 and lead-210 using three different sets of input meteorological information: 1. Output from the Goddard Space Flight Center Global Modeling and Assimilation Office GEOS-STRAT assimilation; 2. Output from the Goddard Institute for Space Studies GISS II' general circulation model; and 3. Output from the National Center for Atmospheric Research MACCM3 general circulation model. We intercompare these simulations with observations to determine the variability resulting from the different meteorological data used to drive the model, and to assess the agreement of the simulations with observations at the surface and in the upper troposphere/lower stratosphere region. The observational datasets we use are primarily climatologies developed from multiple years of observations. In the upper troposphere/lower stratosphere region, climatological distributions of lead-210 were constructed from ~25 years of aircraft and balloon observations compiled into the US Environmental Measurements Laboratory RANDAB database. Taken as a whole, no simulation stands out as superior to the others. However, the simulation driven by the NCAR MACCM3 meteorological data compares better with lead-210 observations in the upper troposphere/lower stratosphere region. Comparisons of simulations made with and without convection show that the role played by convective transport and scavenging in the three simulations differs substantially. These differences may have implications for evaluation of the importance of very short-lived halogen-containing species on stratospheric halogen budgets.

  2. 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

  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. Impact of Improvements in Volcanic Implementation on Atmospheric Chemistry and Climate in the GISS-E2 Model

    Science.gov (United States)

    Tsigaridis, Kostas; LeGrande, Allegra; Bauer, Susanne

    2015-01-01

    The representation of volcanic eruptions in climate models introduces some of the largest errors when evaluating historical simulations, partly due to the crude model parameterizations. We will show preliminary results from the Goddard Institute for Space Studies (GISS)-E2 model comparing traditional highly parameterized volcanic implementation (specified Aerosol Optical Depth, Effective Radius) to deploying the full aerosol microphysics module MATRIX and directly emitting SO2 allowing us the prognosically determine the chemistry and climate impact. We show a reasonable match in aerosol optical depth, effective radius, and forcing between the full aerosol implementation and reconstructions/observations of the Mt. Pinatubo 1991 eruption, with a few areas as targets for future improvement. This allows us to investigate not only the climate impact of the injection of volcanic aerosols, but also influences on regional water vapor, O3, and OH distributions. With the skill of the MATRIX volcano implementation established, we explore (1) how the height of the injection column of SO2 influence atmospheric chemistry and climate response, (2) how the initial condition of the atmosphere influences the climate and chemistry impact of the eruption with a particular focus on how ENSO and QBO and (3) how the coupled chemistry could mitigate the climate signal for much larger eruptions (i.e. the 1258 eruption, reconstructed to be approximately 10x Pinatubo). During each sensitivity experiment we assess the impact on profiles of water vapor, O3, and OH, and assess how the eruption impacts the budget of each.

  5. 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

  6. Variational assimilation of stratospheric remote sounding data by an adjoint chemistry-transport-model

    Energy Technology Data Exchange (ETDEWEB)

    Klasen, D.

    2003-07-01

    In recent years high resolution data have become available due to the deployment of satellite born instruments observing the state of a large number of stratospheric constituents with unprecedentedly high horizontal and vertical resolution. These measurements are valuable for accessing the state of the atmosphere and for helping to develop guidelines for its preservation as a protection layer for terrestrial life. Nevertheless, the measurements alone offer limited direct information. They require interpretation and combination with other information sources to accurately describe the state of the atmosphere. By combining measurements with atmospheric models, the measurements' scatter in time and space can be mitigated and their interpretation improved. A chemistry-transport model (CTM) version of the Cologne model of the middle atmosphere (COMMA) has been developed to model transport and chemical transformation of atmospheric trace gases. In this thesis, the method of four-dimensional variational data assimilation is used to realize the above-mentioned combination in a mathematically rigorous way. The goal is to identify the most probable chemical state of the atmosphere using all available information. As chemistry-transport modelling is an initial value problem, those initial conditions are sought which result in best compliance of the model state with available information during the time period considered. As a measure of compliance, a cost function is specified, whose gradient is needed for minimising the cost function, and which can be obtained by means of an adjoint model. To this end, the adjoint code to the CTM was developed. As a last building block of the data assimilation system, the L-BFGS algorithm for the minimization of the cost function was added. The adjoint model of the middle atmosphere of Cologne CTM (AMMOC-CTM) data-assimilation system thereby developed was tested by applying it to data measured by the cryogenic infrared spectrometer and

  7. A pebbles accretion model with chemistry and implications for the Solar system

    Science.gov (United States)

    Ali-Dib, Mohamad

    2017-02-01

    We investigate the chemical composition of the Solar system's giant planets atmospheres using a physical formation model with chemistry. The model incorporate disc evolution, pebbles and gas accretion, type I and II migration, simplified disc 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 disc chemical enrichment via photoevaporation (PE). 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 disc 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 us to easily reproduce Jupiter's nitrogen observations. In the case with disc PE, less core erosion is needed to reproduce the chemical composition of the atmospheres, so both planets will end up with possibly more massive residual cores and higher total mass of heavy elements. It is also significantly easier to reproduce Jupiter's nitrogen abundance. No single disc was found to form both Jupiter and Saturn with all their constraints in the case without photoevaporation. No model was able to fit the constraints on Uranus and Neptune, hinting towards a more complicated formation mechanism for these planets. The predictions of these models should be compared to the upcoming Juno measurements to better understand the origins of the Solar system giant planets.

  8. Modeling aerosol surface chemistry and gas-particle interaction kinetics with K2-SURF: PAH oxidation

    Science.gov (United States)

    Shiraiwa, M.; Garland, R.; Pöschl, U.

    2009-04-01

    Atmospheric aerosols are ubiquitous in the atmosphere. They have the ability to impact cloud properties, radiative balance and provide surfaces for heterogeneous reactions. The uptake of gaseous species on aerosol surfaces impacts both the aerosol particles and the atmospheric budget of trace gases. These subsequent changes to the aerosol can in turn impact the aerosol chemical and physical properties. However, this uptake, as well as the impact on the aerosol, is not fully understood. This uncertainty is due not only to limited measurement data, but also a dearth of comprehensive and applicable modeling formalizations used for the analysis, interpretation and description of these heterogeneous processes. Without a common model framework, comparing and extrapolating experimental data is difficult. In this study, a novel kinetic surface model (K2-SURF) [Ammann & Pöschl, 2007; Pöschl et al., 2007] was used to describe the oxidation of a variety of polycyclic aromatic hydrocarbons (PAHs). Integrated into this consistent and universally applicable kinetic and thermodynamic process model are the concepts, terminologies and mathematical formalizations essential to the description of atmospherically relevant physicochemical processes involving organic and mixed organic-inorganic aerosols. Within this process model framework, a detailed master mechanism, simplified mechanism and parameterizations of atmospheric aerosol chemistry are being developed and integrated in analogy to existing mechanisms and parameterizations of atmospheric gas-phase chemistry. One of the key aspects to this model is the defining of a clear distinction between various layers of the particle and surrounding gas phase. The processes occurring at each layer can be fully described using known fluxes and kinetic parameters. Using this system there is a clear separation of gas phase, gas-surface and surface bulk transport and reactions. The partitioning of compounds can be calculated using the flux

  9. A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences.

    Science.gov (United States)

    Eid, Sameh; Zalewski, Adam; Smieško, Martin; Ernst, Beat; Vedani, Angelo

    2013-01-04

    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.

  10. Contributions to Future Stratospheric Climate Change: An Idealized Chemistry-Climate Model Sensitivity Study

    Science.gov (United States)

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

    2010-01-01

    Within the framework of an idealized model sensitivity study, three of the main contributors to future stratospheric climate change are evaluated: increases in greenhouse gas concentrations, ozone recovery, and changing sea surface temperatures (SSTs). These three contributors are explored in combination and separately, to test the interactions between ozone and climate; the linearity of their contributions to stratospheric climate change is also assessed. In a simplified chemistry-climate model, stratospheric global mean temperature is most sensitive to CO2 doubling, followed by ozone depletion, then by increased SSTs. At polar latitudes, the Northern Hemisphere (NH) stratosphere is more sensitive to changes in CO2, SSTs and O3 than is the Southern Hemisphere (SH); the opposing responses to ozone depletion under low or high background CO2 concentrations, as seen with present-day SSTs, are much weaker and are not statistically significant under enhanced SSTs. Consistent with previous studies, the strength of the Brewer-Dobson circulation is found to increase in an idealized future climate; SSTs contribute most to this increase in the upper troposphere/lower stratosphere (UT/LS) region, while CO2 and ozone changes contribute most in the stratosphere and mesosphere.

  11. 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.

  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. 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.

  14. 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.

  15. Glyoxal as a tracer of VOC oxidation chemistry: Comparison of measurements with model results for Blodgett Forest, California

    Science.gov (United States)

    Huisman, Andrew; Carlton, Annmarie; Keutsch, Frank

    2010-05-01

    We present a study investigating Volatile Organic Compound (VOC) oxidation chemistry in the context of regional ozone (O3) production during the BEARPEX 2007 and 2009 campaigns at Blodgett Forest Research Station (BFRS) in the Sierra Nevada mountains, CA. Measurements are compared with results from a regional model (US EPA CMAQ) and a zero dimensional (0-D) box model based on the Master Chemical Mechanism (MCM). We use glyoxal (CHOCHO) and formaldehyde (HCHO) as tracers for generalized oxidation processes and employ ratios of compounds (e.g. CHOCHO / HCHO, CHOCHO / MPAN) to study plume evolution as doing so attenuates the influence of meteorology. One of the goals of this study is to investigate the utility of glyoxal as a tracer of VOC oxidation chemistry for measurement/model comparisons, for which formaldehyde has served in the past. In this context, we investigate the discrepancies between models and measurements, and the degree to which these can be attributed to the representation of glyoxal chemistry (e.g. yields) or whether these discrepancies reflect VOC-HOx-NOx oxidation more generally, which has implications for ozone and secondary organic aerosol formation. Model results from CMAQ and the 0-D box model substantially overestimate the absolute measured concentration of CHOCHO at BFRS, and the CMAQ model also shows poor agreement with the diurnal profile. The 0-D box model also overestimates CHOCHO in data taken at the Caltech Indoor Air Chambers, suggesting that 2nd- and/or higher-generation yields of CHOCHO from isoprene are substantially overestimated in the MCM. 0-D model results that use attenuated 2nd- and higher-generation production of CHOCHO from isoprene show enhanced agreement with chamber results. We will present model results of the 0-D Box Model from BFRS employing these reduced yields that show improved agreement with measurements and also compare these results with the other models. We also present results obtained with two modifications of

  16. 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.

  17. Role of climate feedback on methane and ozone studied with a coupled ocean-atmosphere-chemistry model.

    OpenAIRE

    Johnson, C E; D. S. Stevenson; Collins, W. J.; R. G. Derwent

    2001-01-01

    We present results from two experiments carried out with a coupled ocean-atmosphere-tropospheric chemistry model run continously over the period 1990 to 2100. In the control experiment, climate is unforced, but emissions of trace gases to the chemical model increase in line with an illustrative scenario for future trace gas emissions with medium high growth. In the climate change experiment trace gas emissions are identical to the control, but climate is also forced using greenhouse gas conce...

  18. Mass balance inverse modelling of methane in the 1990s using a Chemistry Transport Model

    OpenAIRE

    T. M. Butler; Simmonds, I.; Rayner, P. J.

    2004-01-01

    International audience; A mass balance inverse modelling procedure is applied with a time-dependent methane concentration boundary condition and a chemical transport model to relate observed changes in the surface distribution of methane mixing ratios during the 1990s to changes in its surface sources. The model reproduces essential features of the global methane cycle, such as the latitudinal distribution and seasonal cycle of fluxes, without using a priori knowledge of methane fluxes. A det...

  19. A kinetic chemistry tagging technique and its application to modelling the stable isotopic composition of atmospheric trace gases

    Directory of Open Access Journals (Sweden)

    S. Gromov

    2010-02-01

    Full Text Available Isotope composition, in many cases, holds unique information on sources, chemical modification and sinks of atmospheric trace gases. Vital to the interpretation and use of an increasing number of isotope analyses is appropriate modelling. However, the exact implementation of isotopic information is a challenge, and often studies use simplifications which limit their applicability. Here we confer a thorough isotopic extension to MECCA, a comprehensive kinetic chemistry sub-model. To this end, we devise a generic tagging technique for the kinetic chemistry mechanisms implemented as the sub-submodel MECCA-TAG. The technique constitutes a diagnostic tool that can benefit the investigation of various aspects of kinetic chemistry schemes; at the same time, the designed numerical optimisation reduces the computational effort while keeping important details unaffected. We further focus specifically on the modelling of stable isotopic composition, including the required extensions of the approach. The results of MECCA-TAG are evaluated against the reference sub-submodel MECCA-DBL, which is implicitly full-detailed, but necessarily is sub-optimal in practical applications due to its high computational demands. Furthermore, we evaluate the elaborate carbon and oxygen isotopic mechanism by simulating the multi-isotope composition of CO and other trace gases in the CAABA/MECCA box-model. The mechanism realistically simulates the oxygen isotope composition of key species resulting from the interchange with ozone and main atmospheric reservoirs, as well as the carbon isotope signature transfer. The model adequately reproduces the isotope chemistry features for CO under the limitation of the modelling domain. In particular, the mass-independently fractionated (MIF composition of CO due to reactions of ozone with unsaturated hydrocarbons (a source effect versus its intrinsic MIF enrichment induced in the removal reaction via oxidation by OH is assessed. As for

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Recent insights on the medicinal chemistry of metal-based compounds: hints for the successful drug design.

    Science.gov (United States)

    Hernandes, M Z; de S Pontes, F J; Coelho, L C D; Moreira, D R M; Pereira, V R A; Leite, A C L

    2010-01-01

    Although more complex than usually described, the anticancer action mechanism of cisplatin is based on binding to DNA. Following this line of reasoning, most the metal-based compounds discovered soon after cisplatin were designed to acting as DNA-binding agents and their pharmacological properties were thought to be correlated with this mechanism. Apart from the DNA structure, a significant number of proteins and biochemical pathways have been described as drug targets for metal-based compounds. This paper is therefore aimed at discussing the most recent findings on the medicinal chemistry of metal-based drugs. It starts illustrating the design concept behind the bioinorganic chemistry of anticancer complexes. Anticancer metallic compounds that inhibit the protein kinases are concisely discussed as a case study. The accuracy and limitations of molecular docking programs currently available to predict the binding mode of metallic complexes in molecular targets are further discussed. Finally, the advantages and disadvantages of different in vitro screenings are briefly commented.

  5. Parameterization of gaseous dry deposition in atmospheric chemistry models: Sensitivity to aerodynamic resistance formulations under statically stable conditions

    Science.gov (United States)

    Toyota, Kenjiro; Dastoor, Ashu P.; Ryzhkov, Andrei

    2016-12-01

    Turbulence controls the vertical transfer of momentum, heat and trace constituents in the atmospheric boundary layer. In the lowest 10% of this layer lies the surface boundary layer (SBL) where the vertical fluxes of transferred quantities have been successfully parameterized using the Monin-Obukhov similarity theory in weather forecast, climate and atmospheric chemistry models. However, there is a large degree of empiricism in the stability-correction parameterizations used to formulate eddy diffusivity and aerodynamic resistance particularly under strongly stable ambient conditions. Although the influence of uncertainties in stability-correction parameterizations on eddy diffusivity is actively studied in boundary-layer meteorological modeling, its impact on dry deposition in atmospheric chemistry modeling is not well characterized. In this study, we address this gap by providing the mathematical basis for the relationship between the formulations of vertical surface flux used in meteorological and atmospheric chemistry modeling communities, and by examining the sensitivity of the modeled dry deposition velocities in statically stable SBL to the choice of stability-correction parameterizations used in three operational and/or research environmental models (GEM/GEM-MACH, ECMWF IFS and CMAQ-MM5). Aerodynamic resistances (ra) calculated by the three sets of parameterizations are notably different from each other and are also different from those calculated by a "z-less" scaling formulation under strongly stable conditions (the bulk Richardson number > 0.2). Furthermore, we show that many atmospheric chemistry models calculate ra using formulations which are inconsistent with the derivation of micro-meteorological parameters. Finally, practical implications of the differences in stability-correction algorithms are discussed for the computations of dry deposition velocities of SO2, O3 and reactive bromine compounds for specific cases of stable SBL.

  6. OCEANFILMS-2: Representing coadsorption of saccharides in marine films and potential impacts on modeled marine aerosol chemistry

    Science.gov (United States)

    Burrows, Susannah M.; Gobrogge, Eric; Fu, Li; Link, Katie; Elliott, Scott M.; Wang, Hongfei; Walker, Rob

    2016-08-01

    Here we show that the addition of chemical interactions between soluble monosaccharides and an insoluble lipid surfactant monolayer improves agreement of modeled sea spray chemistry with observed marine aerosol chemistry. In particular, the alkane:hydroxyl mass ratio in modeled sea spray organic matter is reduced from a median of 2.73 to a range of 0.41-0.69, reducing the discrepancy with previous Fourier transform infrared spectroscopy (FTIR) observations of clean marine aerosol (ratio: 0.24-0.38). The overall organic fraction of submicron sea spray also increases, allowing organic mass fractions in the range 0.5-0.7 for submicron sea spray particles over highly active phytoplankton blooms. Sum frequency generation experiments support the modeling approach by demonstrating that soluble monosaccharides can strongly adsorb to a lipid monolayer likely via Coulomb interactions under appropriate conditions. These laboratory findings motivate further research to determine the relevance of coadsorption mechanisms for real-world, sea spray aerosol production.

  7. OCEANFILMS-2: Representing coadsorption of saccharides in marine films and potential impacts on modeled marine aerosol chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Burrows, Susannah M. [Atmospheric Science and Global Change Division, Pacific Northwest National Laboratory, Richland Washington USA; Gobrogge, Eric [Department of Chemistry and Biochemistry, Montana State University, Bozeman Montana USA; Fu, Li [Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington USA; Link, Katie [Department of Chemistry and Biochemistry, Montana State University, Bozeman Montana USA; Elliott, Scott M. [Climate, Ocean, and Sea Ice Modelling Group, Los Alamos National Laboratory, Los Alamos New Mexico USA; Wang, Hongfei [Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington USA; Walker, Rob [Department of Chemistry and Biochemistry, Montana State University, Bozeman Montana USA

    2016-08-10

    Here we show that the addition of chemical interactions of soluble polysaccharides with a surfactant monolayer improves agreement of modeled sea spray chemistry with observed marine aerosol chemistry. In particular, the fraction of hydroxyl functional groups in modeled sea spray organic matter is increased, improving agreement with FTIR observations of marine aerosol composition. The overall organic fraction of submicron sea spray also increases, allowing organic mass fractions in the range 0.5 – 0.7 for submicron sea spray particles over highly active phytoplankton blooms. We show results from Sum Frequency Generation (SFG) experiments that support the modeling approach, by demonstrating that soluble polysaccharides can strongly adsorb to a lipid monolayer via columbic interactions under appropriate conditions.

  8. THE DEVELOPMENT OF LECTURE MODEL OF CHEMICAL EDUCATION MANAGEMENT BASED ON LESSON STUDY TO IMPROVE CHEMISTRY TEACHER CANDIDATES’ PROFESIONALISM

    Directory of Open Access Journals (Sweden)

    S.S. Sumarti

    2015-04-01

    Full Text Available The purpose of this research is to produce a lecture model of chemical education management based on lesson study as an effort to improve chemistry teacher candidates’ professionalism. This study used a model of ADDIE (Analysis-Design-Implement-Develop-Evaluate. Based on the results of the reflection, lecturer and team can arrange the post-presentation activities (discussing material theoretically with a variety of management practices in the field. Activities will be carried out by presenting a real problem in the field to find the solution, thus the students’ curiosity about management implementation will be fulfilled. Lecture Model of Chemical Education Management Based on Lesson Study can improve the chemistry teacher candidates’ professionalism, primarily in preparing, presenting and being responsible of their work by learning from their learning experience.

  9. 3-D evaluation of tropospheric ozone simulations by an ensemble of regional Chemistry Transport Model

    Directory of Open Access Journals (Sweden)

    D. Zyryanov

    2012-04-01

    Full Text Available A detailed 3-D evaluation of an ensemble of five regional Chemistry Transport Models (RCTM and one global CTM with focus on free tropospheric ozone over Europe is presented. It is performed over a summer period (June to August 2008 in the context of the GEMS-RAQ project. A data set of about 400 vertical ozone profiles from balloon soundings and commercial aircraft at 11 different locations is used for model evaluation, in addition to satellite measurements with the infrared nadir sounder (IASI showing largest sensitivity to free tropospheric ozone. In the middle troposphere, the four regional models using the same top and boundary conditions from IFS-MOZART exhibit a systematic negative bias with respect to observed profiles of about −20%. Root Mean Square Error (RMSE values are constantly growing with altitude, from 22% to 32% to 53%, respectively for 0–2 km, 2–8 km and 8–10 km height ranges. Lowest correlation is found in the middle troposphere, with minimum coefficients (R between 0.2 to 0.45 near 8 km, as compared to 0.7 near the surface and similar values around 10 km. A sensitivity test made with the CHIMERE mode also shows that using hourly instead of monthly chemical boundary conditions generally improves the model skill (i.e. improve RMSE and correlation. Lower tropospheric 0–6 km partial ozone columns derived from IASI show a clear North-South gradient over Europe, which is qualitatively reproduced by the models. Also the temporal variability showing decreasing ozone concentrations in the lower troposphere (0–6 km columns during summer is well reproduced by models even if systematic bias remains (the value of the bias being also controlled by the type of used boundary conditions. A multi-day case study of a trough with low tropopause was conducted and showed that both IASI and models were able to resolve strong horizontal gradients of middle and upper tropospheric ozone occurring in the vicinity of an upper

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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 ...

  15. Inter-comparison and performance evaluation of chemistry transport models over Indian region

    Science.gov (United States)

    Govardhan, Gaurav R.; Nanjundiah, Ravi S.; Satheesh, S. K.; Moorthy, K. Krishna; Takemura, Toshihiko

    2016-01-01

    Aerosol loading over the South Asian region has the potential to affect the monsoon rainfall, Himalayan glaciers and regional air-quality, with implications for the billions in this region. While field campaigns and network observations provide primary data, they tend to be location/season specific. Numerical models are useful to regionalize such location-specific data. Studies have shown that numerical models underestimate the aerosol scenario over the Indian region, mainly due to shortcomings related to meteorology and the emission inventories used. In this context, we have evaluated the performance of two such chemistry-transport models: WRF-Chem and SPRINTARS over an India-centric domain. The models differ in many aspects including physical domain, horizontal resolution, meteorological forcing and so on etc. Despite these differences, both the models simulated similar spatial patterns of Black Carbon (BC) mass concentration, (with a spatial correlation of 0.9 with each other), and a reasonable estimates of its concentration, though both of them under-estimated vis-a-vis the observations. While the emissions are lower (higher) in SPRINTARS (WRF-Chem), overestimation of wind parameters in WRF-Chem caused the concentration to be similar in both models. Additionally, we quantified the underestimations of anthropogenic BC emissions in the inventories used these two models and three other widely used emission inventories. Our analysis indicates that all these emission inventories underestimate the emissions of BC over India by a factor that ranges from 1.5 to 2.9. We have also studied the model simulations of aerosol optical depth over the Indian region. The models differ significantly in simulations of AOD, with WRF-Chem having a better agreement with satellite observations of AOD as far as the spatial pattern is concerned. It is important to note that in addition to BC, dust can also contribute significantly to AOD. The models differ in simulations of the spatial

  16. 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.

  17. A Course in Early Chemistry for Undergraduates. A Speculative Experiment in Historical Modeling at the Donetsk State University

    Science.gov (United States)

    Rodygin, Mikhail Yu.; Rodygina, Irene V.

    1998-10-01

    Analysis of the world's teaching practices in the history of chemistry shows us that, despite the common time shortage for general educational courses, serious attention should be focused on the early stages of science development. Studies on the history of early chemistry allow students to trace the origins and development of fundamental chemical principles and concepts, to recognize tight relationships between the past and present of human society, and, at last, to obtain broader professional knowledge. An advanced course in the history of early chemistry was taught for senior students at the Donetsk State University, Ukraine. The important constituents of the course were studies on the original works of ancient authors as well as development of the students' ability to absorb and interpret the material adequately. Discussion of general problems in natural history was considered an important part of the education. Thus, the course was based on discussions of selected topics. Throughout the course, the history of chemistry was considered mostly from Biblical and Aristotelian standpoints. This peculiarity makes the teaching approach quite close to approaches used at medieval European universities. It allows us to consider the course as an experiment in speculative historical modeling. Reconstruction of medieval scholastic approaches may reveal original and new pathways to the unveiling of numerous mysteries still remaining in the history of natural science.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hume, Stephanie L.; Jeerage, Kavita M., E-mail: jeerage@boulder.nist.gov [National Institute of Standards and Technology (NIST), Applied Chemicals and Materials Division, Material Measurement Laboratory (United States)

    2013-05-15

    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 {approx}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.

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

    Science.gov (United States)

    Hume, Stephanie L.; Jeerage, Kavita M.

    2013-05-01

    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. Bioinorganic Drugs-2

    Science.gov (United States)

    Williams, David R.

    1974-01-01

    Discusses the metallotherapy approach to viral infection, cadmium poisoning and Wilson's disease. Presents a plan for progress in metallotherapy through more education, more basic research, and more epidemiological studies. (GS)

  1. 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...

  2. Numerical simulation for regional ozone concentrations: A case study by weather research and forecasting/chemistry (WRF/Chem) model

    OpenAIRE

    Khandakar Md Habib Al Razi, Moritomi Hiroshi

    2013-01-01

    The objective of this research is to better understand and predict the atmospheric concentration distribution of ozone and its precursor (in particular, within the Planetary Boundary Layer (Within 110 km to 12 km) over Kasaki City and the Greater Tokyo Area using fully coupled online WRF/Chem (Weather Research and Forecasting/Chemistry) model. In this research, a serious and continuous high ozone episode in the Greater Tokyo Area (GTA) during the summer of 14–18 August 2010 was investigated u...

  3. 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

  4. 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.

    2015-01-01

    The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been re-engineered to also serve as an atmospheric chemistry module for Earth system models (ESMs). This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of the GEOSChem scientific code, permitting the exact same GEOSChem code to be used as an ESM module or as a standalone CTM. In this manner, the continual stream of updates contributed by the CTM user community is automatically passed on to the ESM module, which remains state of science and referenced to the latest version of the standard GEOS-Chem CTM. A major step in this re-engineering was to make GEOS-Chem grid independent, i.e., capable of using any geophysical grid specified at run time. GEOS-Chem data sockets were also created for communication between modules and with external ESM code. The grid-independent, ESMF-compatible GEOS-Chem is now the standard version of the GEOS-Chem CTM. It has been implemented as an atmospheric chemistry module into the NASA GEOS- 5 ESM. The coupled GEOS-5-GEOS-Chem system was tested for scalability and performance with a tropospheric oxidant-aerosol simulation (120 coupled species, 66 transported tracers) using 48-240 cores and message-passing interface (MPI) distributed-memory parallelization. Numerical experiments demonstrate that the GEOS-Chem chemistry module scales efficiently for the number of cores tested, with no degradation as the number of cores increases. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemistry module means that the relative cost goes down with increasing number of cores in a massively parallel environment.

  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. 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.

  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. 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.

  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. 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.

  11. 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

  12. 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.

  13. Final Report for LDRD Project 05-ERD-050: "Developing a Reactive Chemistry Capability for the NARAC Operational Model (LODI)"

    Energy Technology Data Exchange (ETDEWEB)

    Cameron-Smith, P; Grant, K; Connell, P

    2008-02-11

    In support of the National Security efforts of LLNL, this project addressed the existing imbalance between dispersion and chemical capabilities of LODI (Lagrangian Operational Dispersion Integrator--the NARAC operational dispersion model). We have demonstrated potentially large effects of atmospheric chemistry on the impact of chemical releases (e.g., industrial chemicals and nerve agents). Prior to our work, LODI could only handle chains of first-order losses (exponential decays) that were independent of time and space, limiting NARAC's capability to respond when reactive chemistry is important. We significantly upgraded the chemistry and aerosol capability of LODI to handle (1) arbitrary networks of chemical reactions, (2) mixing and reactions with ambient species, (3) evaporation and condensation of aerosols, and (4) heat liberated from chemical reactions and aerosol condensation (which can cause a cold and dense plume hugging the ground to rise into the atmosphere, then descend to the ground again as droplets). When this is made operational, it will significantly improve NARAC's ability to respond to terrorist attacks and industrial accidents that involve reactive chemistry, including many chemical agents and toxic industrial chemicals (TICS). As a dual-use, the resulting model also has the potential to be a state-of-the-art air-quality model. Chemical releases are the most common type of airborne hazardous release and many operational applications involve such scenarios. The new capability we developed is therefore relevant to the needs of the Department of Energy (DOE), Department of Homeland Security (DHS) and Department of Defense (DoD).

  14. 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

  15. 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.

  16. Modelling the chemistry and transport of bromoform within a sea breeze driven convective system during the SHIVA Campaign

    Science.gov (United States)

    Hamer, P. D.; Marécal, V.; Hossaini, R.; Pirre, M.; Warwick, N.; Chipperfield, M.; Samah, A. A.; Harris, N.; Robinson, A.; Quack, B.; Engel, A.; Krüger, K.; Atlas, E.; Subramaniam, K.; Oram, D.; Leedham, E.; Mills, G.; Pfeilsticker, K.; Sala, S.; Keber, T.; Bönisch, H.; Peng, L. K.; Nadzir, M. S. M.; Lim, P. T.; Mujahid, A.; Anton, A.; Schlager, H.; Catoire, V.; Krysztofiak, G.; Fühlbrügge, S.; Dorf, M.; Sturges, W. T.

    2013-08-01

    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 the physical and

  17. 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

  18. 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...

  19. Modeling the observed tropospheric BrO background: Importance of multiphase chemistry and implications for ozone, OH, and mercury

    Science.gov (United States)

    Schmidt, J. A.; Jacob, D. J.; Horowitz, H. M.; Hu, L.; Sherwen, T.; Evans, M. J.; Liang, Q.; Suleiman, R. M.; Oram, D. E.; Le Breton, M.; Percival, C. J.; Wang, S.; Dix, B.; Volkamer, R.

    2016-10-01

    Aircraft and satellite observations indicate the presence of ppt (ppt ≡ pmol/mol) levels of BrO in the free troposphere with important implications for the tropospheric budgets of ozone, OH, and mercury. We can reproduce these observations with the GEOS-Chem global tropospheric chemistry model by including a broader consideration of multiphase halogen (Br-Cl) chemistry than has been done in the past. Important reactions for regenerating BrO from its nonradical reservoirs include HOBr + Br-/Cl- in both aerosols and clouds, and oxidation of Br- by ClNO3 and ozone. Most tropospheric BrO in the model is in the free troposphere, consistent with observations and originates mainly from the photolysis and oxidation of ocean-emitted CHBr3. Stratospheric input is also important in the upper troposphere. Including production of gas phase inorganic bromine from debromination of acidified sea salt aerosol increases free tropospheric Bry by about 30%. We find HOBr to be the dominant gas-phase reservoir of inorganic bromine. Halogen (Br-Cl) radical chemistry as implemented here in GEOS-Chem drives 14% and 11% decreases in the global burdens of tropospheric ozone and OH, respectively, a 16% increase in the atmospheric lifetime of methane, and an atmospheric lifetime of 6 months for elemental mercury. The dominant mechanism for the Br-Cl driven tropospheric ozone decrease is oxidation of NOx by formation and hydrolysis of BrNO3 and ClNO3.

  20. 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

  1. Multi-model mean nitrogen and sulfur deposition from the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP): evaluation historical and projected changes

    OpenAIRE

    J.-F. Lamarque; Dentener, F.; Mcconnell, J.; C.-U. Ro; M. Shaw; Vet, R.; D. Bergmann; Cameron-Smith, P.; Doherty, R.; Faluvegi, G.; Ghan, S. J.; B. Josse; Lee, Y. H.; I. A. MacKenzie; Plummer, D.

    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...

  2. Multi-model mean nitrogen and sulfur deposition from the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP): evaluation of historical and projected future changes

    OpenAIRE

    Lamarque, J.-F.; Dentener, F.; Mcconnell, J.; Ro, C.-U.; M. Shaw; Vet, R.; D. Bergmann; Cameron-Smith, P.; Dalsoren, S.; Doherty, R.; Faluvegi, G.; Ghan, S. J.; B. Josse; Lee, Y. H.; I. A. MacKenzie

    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...

  3. 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)

  4. Chemistry Dashboard

    Science.gov (United States)

    The Chemistry Dashboard is part of a suite of dashboards developed by EPA to help evaluate the safety of chemicals. The Chemistry Dashboard provides access to a variety of information on over 700,000 chemicals currently in use.

  5. 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)

  6. Biophysical chemistry.

    Science.gov (United States)

    Häussinger, Daniel; Pfohl, Thomas

    2010-01-01

    Biophysical chemistry at the Department of Chemistry, University of Basel, covers the NMR analysis of protein-protein interaction using paramagnetic tags and sophisticated microscopy techniques investigating the dynamics of biological matter.

  7. Heterocyclic chemistry

    OpenAIRE

    Hemming, Karl

    2011-01-01

    Recent progress in the synthesis of heterocyclic compounds is presented\\ud 2010 offered highlights in pericyclic chemistry, particularly 1,3-dipolar cycloaddition chemistry, asymmetric synthesis, gold catalysis, organocatalysis, hydroamination, C–H activation and multicomponent reactions.

  8. Exploring the Gas Chemistry of Old Submarine Technologies Using Plastic Bottles as Reaction Vessels and Models

    Science.gov (United States)

    Horikoshi, Ryo; Takeiri, Fumitaka; Kobayashi, Yoji; Kageyama, Hiroshi

    2016-01-01

    We describe an activity that is suitable for high school students and makes use of plastic bottles. This activity allows students to familiarize themselves with gas chemistry by introducing technologies that were applied in old submarine systems. Plastic bottles, which are representative of submarines, are used as reaction vessels. Three simple…

  9. How the Chemistry Modeling Curriculum Engages Students in Seven Science Practices Outlined by the College Board

    Science.gov (United States)

    Posthuma-Adams, Erica

    2014-01-01

    As advanced placement (AP) teachers strive to implement the changes outlined in the AP chemistry redesign, they will have the opportunity to reflect on and evaluate their current practices. For many AP teachers, the new focus on conceptual understanding, reasoning, inquiry, and critical thinking over memorization and algorithmic problem solving…

  10. 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…

  11. New framework for extending cloud chemistry in the Community Multiscale Air Quality (CMAQ) modeling

    Science.gov (United States)

    Clouds and fogs significantly impact the amount, composition, and spatial distribution of gas and particulate atmospheric species, not least of which through the chemistry that occurs in cloud droplets. Atmospheric sulfate is an important component of fine aerosol mass and in an...

  12. Students' Levels of Explanations, Models, and Misconceptions in Basic Quantum Chemistry: A Phenomenographic Study

    Science.gov (United States)

    Stefani, Christina; Tsaparlis, Georgios

    2009-01-01

    We investigated students' knowledge constructions of basic quantum chemistry concepts, namely atomic orbitals, the Schrodinger equation, molecular orbitals, hybridization, and chemical bonding. Ausubel's theory of meaningful learning provided the theoretical framework and phenomenography the method of analysis. The semi-structured interview with…

  13. High-resolution air quality simulation over Europe with the chemistry transport model CHIMERE

    Directory of Open Access Journals (Sweden)

    E. Terrenoire

    2015-01-01

    The results suggest that future work should focus on the development of national bottom-up emission inventories including a better account for semi-volatile organic compounds and their conversion to SOA, the improvement of the CHIMERE urban parameterization, the introduction into CHIMERE of the coarse nitrate chemistry and an advanced parameterization accounting for windblown dust emissions.

  14. Extending atomistic scale chemistry to mesoscale model of condensed-phase deflagration

    Science.gov (United States)

    Joshi, Kaushik; Chaudhuri, Santanu

    2017-01-01

    Predictive simulations connecting chemistry that follow the shock or thermal initiation of energetic materials to subsequent deflagration or detonation events is currently outside the realm of possibilities. Molecular dynamics and first-principles based dynamics have made progress in understanding reactions in picosecond to nanosecond time scale. Results from thermal ignition of different phases of RDX show a complex reaction network and emergence of a deterministic behavior for critical temperature before ignition and hot spot growth rates. The kinetics observed is dependent on the hot spot temperature, system size and thermal conductivity. For cases where ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. The gradual temperature and pressure increase in the incubation period is accompanied by accumulation of heavier polyradicals. The challenge of connecting such chemistry in mesoscale simulations remain in reducing the complexity of chemistry. The hot spot growth kinetics in RDX grains and interfaces is an important challenge for reactive simulations aiming to fill in the gaps in our knowledge in the nanoseconds to microseconds time scale. The results discussed indicate that the mesoscale chemistry may include large polyradical molecules in dense reactive mix reaching an instability point at certain temperatures and pressures.

  15. 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....

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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).

  1. Skin cancer risks avoided by the Montreal Protocol--worldwide modeling integrating coupled climate-chemistry models with a risk model for UV.

    Science.gov (United States)

    van Dijk, Arjan; Slaper, Harry; den Outer, Peter N; Morgenstern, Olaf; Braesicke, Peter; Pyle, John A; Garny, Hella; Stenke, Andrea; Dameris, Martin; Kazantzidis, Andreas; Tourpali, Kleareti; Bais, Alkiviadis F

    2013-01-01

    The assessment model for ultraviolet radiation and risk "AMOUR" is applied to output from two chemistry-climate models (CCMs). Results from the UK Chemistry and Aerosols CCM are used to quantify the worldwide skin cancer risk avoided by the Montreal Protocol and its amendments: by the year 2030, two million cases of skin cancer have been prevented yearly, which is 14% fewer skin cancer cases per year. In the "World Avoided," excess skin cancer incidence will continue to grow dramatically after 2030. Results from the CCM E39C-A are used to estimate skin cancer risk that had already been inevitably committed once ozone depletion was recognized: excess incidence will peak mid 21st century and then recover or even super-recover at the end of the century. When compared with a "No Depletion" scenario, with ozone undepleted and cloud characteristics as in the 1960s throughout, excess incidence (extra yearly cases skin cancer per million people) of the "Full Compliance with Montreal Protocol" scenario is in the ranges: New Zealand: 100-150, Congo: -10-0, Patagonia: 20-50, Western Europe: 30-40, China: 90-120, South-West USA: 80-110, Mediterranean: 90-100 and North-East Australia: 170-200. This is up to 4% of total local incidence in the Full Compliance scenario in the peak year.

  2. Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations.

    Science.gov (United States)

    Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad

    2015-02-15

    The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported.

  3. 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

  4. Forensic chemistry.

    Science.gov (United States)

    Bell, Suzanne

    2009-01-01

    Forensic chemistry is unique among chemical sciences in that its research, practice, and presentation must meet the needs of both the scientific and the legal communities. As such, forensic chemistry research is applied and derivative by nature and design, and it emphasizes metrology (the science of measurement) and validation. Forensic chemistry has moved away from its analytical roots and is incorporating a broader spectrum of chemical sciences. Existing forensic practices are being revisited as the purview of forensic chemistry extends outward from drug analysis and toxicology into such diverse areas as combustion chemistry, materials science, and pattern evidence.

  5. 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

  6. 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.

  7. 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.

  8. 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...

  9. 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.

  10. 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

  11. 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

  12. Biosynthetic inorganic chemistry.

    Science.gov (United States)

    Lu, Yi

    2006-08-25

    Inorganic chemistry and biology can benefit greatly from each other. Although synthetic and physical inorganic chemistry have been greatly successful in clarifying the role of metal ions in biological systems, the time may now be right to utilize biological systems to advance coordination chemistry. One such example is the use of small, stable, easy-to-make, and well-characterized proteins as ligands to synthesize novel inorganic compounds. This biosynthetic inorganic chemistry is possible thanks to a number of developments in biology. This review summarizes the progress in the synthesis of close models of complex metalloproteins, followed by a description of recent advances in using the approach for making novel compounds that are unprecedented in either inorganic chemistry or biology. The focus is mainly on synthetic "tricks" learned from biology, as well as novel structures and insights obtained. The advantages and disadvantages of this biosynthetic approach are discussed.

  13. Uncertainty in a chemistry-transport model due to physical parameterizations and numerical approximations: An ensemble approach applied to ozone modeling

    OpenAIRE

    Mallet, Vivien; Sportisse, Bruno

    2006-01-01

    International audience; This paper estimates the uncertainty in the outputs of a chemistry-transport model due to physical parameterizations and numerical approximations. An ensemble of 20 simulations is generated from a reference simulation in which one key parameterization (chemical mechanism, dry deposition parameterization, turbulent closure, etc.) or one numerical approximation (grid size, splitting method, etc.) is changed at a time. Intercomparisons of the simulations and comparisons w...

  14. 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.

  15. Astronomical chemistry.

    Science.gov (United States)

    Klemperer, William

    2011-01-01

    The discovery of polar polyatomic molecules in higher-density regions of the interstellar medium by means of their rotational emission detected by radioastronomy has changed our conception of the universe from essentially atomic to highly molecular. We discuss models for molecule formation, emphasizing the general lack of thermodynamic equilibrium. Detailed chemical kinetics is needed to understand molecule formation as well as destruction. Ion molecule reactions appear to be an important class for the generally low temperatures of the interstellar medium. The need for the intrinsically high-quality factor of rotational transitions to definitively pin down molecular emitters has been well established by radioastronomy. The observation of abundant molecular ions both positive and, as recently observed, negative provides benchmarks for chemical kinetic schemes. Of considerable importance in guiding our understanding of astronomical chemistry is the fact that the larger molecules (with more than five atoms) are all organic.

  16. Promoting Student Development of Models and Scientific Inquiry Skills in Acid-Base Chemistry: An Important Skill Development in Preparation for AP Chemistry

    Science.gov (United States)

    Hale-Hanes, Cara

    2015-01-01

    In this study, two groups of 11th grade chemistry students (n = 210) performed a sequence of hands-on and virtual laboratories that were progressively more inquiry-based. One-half of the students did the laboratory sequence with the addition of a teacher-led discussion connecting student data to student-generated visual representations of…

  17. 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

  18. 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

  19. 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

  20. Computational chemistry

    OpenAIRE

    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 ...

  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. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Chemistry Technology

    Data.gov (United States)

    Federal Laboratory Consortium — Chemistry technology experts at NCATS engage in a variety of innovative translational research activities, including:Design of bioactive small molecules.Development...

  7. 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

  8. 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

  9. 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.

  10. Global transcriptomic analysis of model human cell lines exposed to surface-modified gold nanoparticles: the effect of surface chemistry

    Science.gov (United States)

    Grzincic, E. M.; Yang, J. A.; Drnevich, J.; Falagan-Lotsch, P.; Murphy, C. J.

    2015-01-01

    Gold nanoparticles (Au NPs) are attractive for biomedical applications not only for their remarkable physical properties, but also for the ease of which their surface chemistry can be manipulated. Many applications involve functionalization of the Au NP surface in order to improve biocompatibility, attach targeting ligands or carry drugs. However, changes in cells exposed to Au NPs of different surface chemistries have been observed, and little is known about how Au NPs and their surface coatings may impact cellular gene expression. The gene expression of two model human cell lines, human dermal fibroblasts (HDF) and prostate cancer cells (PC3) was interrogated by microarray analysis of over 14 000 human genes. The cell lines were exposed to four differently functionalized Au NPs: citrate, poly(allylamine hydrochloride) (PAH), and lipid coatings combined with alkanethiols or PAH. Gene functional annotation categories and weighted gene correlation network analysis were used in order to connect gene expression changes to common cellular functions and to elucidate expression patterns between Au NP samples. Coated Au NPs affect genes implicated in proliferation, angiogenesis, and metabolism in HDF cells, and inflammation, angiogenesis, proliferation apoptosis regulation, survival and invasion in PC3 cells. Subtle changes in surface chemistry, such as the initial net charge, lability of the ligand, and underlying layers greatly influence the degree of expression change and the type of cellular pathway affected.Gold nanoparticles (Au NPs) are attractive for biomedical applications not only for their remarkable physical properties, but also for the ease of which their surface chemistry can be manipulated. Many applications involve functionalization of the Au NP surface in order to improve biocompatibility, attach targeting ligands or carry drugs. However, changes in cells exposed to Au NPs of different surface chemistries have been observed, and little is known about how

  11. 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...

  12. Analytical Models of Exoplanetary Atmospheres. III. Gaseous C-H-O-N Chemistry with Nine Molecules

    Science.gov (United States)

    Heng, Kevin; Tsai, Shang-Min

    2016-10-01

    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 (C2H2), ammonia (NH3), carbon dioxide (CO2), carbon monoxide (CO), ethylene (C2H4), hydrogen cyanide (HCN), methane (CH4), molecular nitrogen (N2), and water (H2O). By considering only the gas phase, we prove that the mixing ratio of carbon monoxide is governed by a decic equation (polynomial equation of 10 degrees). We validate our solutions against numerical calculations of equilibrium chemistry that perform Gibbs free energy minimization and demonstrate that they are accurate at the ˜ 1 % level for temperatures from 500 to 3000 K. In hydrogen-dominated atmospheres, the ratio of abundances of HCN to CH4 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 for the convenient benchmarking of chemical kinetics codes and provide an efficient way of enforcing chemical equilibrium in atmospheric retrieval calculations.

  13. Yields of AGB and SAGB models with chemistry of low- and high-metallicity Globular Clusters

    CERN Document Server

    Ventura, P; Carini, R; D'Antona, F

    2013-01-01

    We present yields from stars of mass in the range Mochemistry of low- and high-Z Globular Clusters. The yields are based on full evolutionary computations, following the evolution of the stars from the pre-Main Sequence through the Asymptotic Giant Branch phase, until the external envelope is lost. Independently of metallicity, stars with M<3Mo are dominated by Third Dredge-Up, thus ejecting into their surroundings gas enriched in carbon and nitrogen. Conversely, Hot Bottom Burning is the main responsible for the modification of the surface chemistry of more massive stars, whose mass exceeds 3Mo: their gas shows traces of proton-capture nucleosynthesis. The extent of Hot Bottom Burning turns out to be strongly dependent on metallicity. In this paper we analyze the consequences of this fact. These results can be used to understand the role played by intermediate mass stars in the self-enrichment scenario of globular clusters: the resu...

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Evaluation of Present-day Aerosols over China Simulated from the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP)

    Science.gov (United States)

    Liao, H.; Chang, W.

    2014-12-01

    High concentrations of aerosols over China lead to strong radiative forcing that is important for both regional and global climate. To understand the representation of aerosols in China in current global climate models, we evaluate extensively the simulated present-day aerosol concentrations and aerosol optical depth (AOD) over China from the 12 models that participated in Atmospheric Chemistry & Climate Model Intercomparison Project (ACCMIP), by using ground-based measurements and satellite remote sensing. Ground-based measurements of aerosol concentrations used in this work include those from the China Meteorological Administration (CMA) Atmosphere Watch Network (CAWNET) and the observed fine-mode aerosol concentrations collected from the literature. The ground-based measurements of AOD in China are taken from the AErosol RObotic NETwork (AERONET), the sites with CIMEL sun photometer operated by Institute of Atmospheric Physics, Chinese Academy of Sciences, and from Chinese Sun Hazemeter Network (CSHNET). We find that the ACCMIP models generally underestimate concentrations of all major aerosol species in China. On an annual mean basis, the multi-model mean concentrations of sulfate, nitrate, ammonium, black carbon, and organic carbon are underestimated by 63%, 73%, 54%, 53%, and 59%, respectively. The multi-model mean AOD values show low biases of 20-40% at studied sites in China. The ACCMIP models can reproduce seasonal variation of nitrate but cannot capture well the seasonal variations of other aerosol species. Our analyses indicate that current global models generally underestimate the role of aerosols in China in climate simulations.

  19. 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

  20. Modelling the response of soil and runoff chemistry to forest harvesting in a low deposition area (Kangasvaara, eastern Finland

    Directory of Open Access Journals (Sweden)

    J. Kämäri

    1998-01-01

    Full Text Available A simple dynamic soil model developed to analyse the effects of atmospheric deposition and nutrient cycling on terrestrial ecosystems, SMART 2, was applied to the Kangasvaara catchment in eastern Finland. Given the historical deposition and forest growth patterns and reasonable values for the input parameters, SMART 2 was calibrated successfully to reproduce present-day soil and Kangasvaara catchment on the soil and runoff water chemistry under a future deposition scenario (GRP scenario. These impacts were also compared to the effects of further reducing the deposition of sulphur and nitrate under the maximum feasible reduction (MFR scenario. The model demonstrates the consequences of breaking the nutrient cycle, and predicts that final cutting results in increased leaching of inorganic nitrogen and base cations from the cut part of the catchment for about 10 years. The resulting concentrations in the stream will depend on the ability of the buffer zones surrounding the stream to capture and utilize these nutrients.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Computational chemistry modeling and design of photoswitchable alignment materials for optically addressable liquid crystal devices

    Science.gov (United States)

    Marshall, K. L.; Sekera, E. R.; Xiao, K.

    2015-09-01

    Photoalignment technology based on optically switchable "command surfaces" has been receiving increasing interest for liquid crystal optics and photonics device applications. Azobenzene compounds in the form of low-molar-mass, watersoluble salts deposited either directly on the substrate surface or after dispersion in a polymer binder have been almost exclusively employed for these applications, and ongoing research in the area follows a largely empirical materials design and development approach. Recent computational chemistry advances now afford unprecedented opportunities to develop predictive capabilities that will lead to new photoswitchable alignment layer materials with low switching energies, enhanced bistability, write/erase fatigue resistance, and high laser-damage thresholds. In the work described here, computational methods based on the density functional theory and time-dependent density functional theory were employed to study the impact of molecular structure on optical switching properties in photoswitchable methacrylate and acrylamide polymers functionalized with azobenzene and spiropyran pendants.

  6. 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.

  7. 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.

  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. 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,

  11. 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.

  12. A comprehensive review on biosorption of heavy metals by algal biomass: materials, performances, chemistry, and modeling simulation tools.

    Science.gov (United States)

    He, Jinsong; Chen, J Paul

    2014-05-01

    Heavy metals contamination has become a global issue of concern due to their higher toxicities, nature of non-biodegradability, high capabilities in bioaccumulation in human body and food chain, and carcinogenicities to humans. A series of researches demonstrate that biosorption is a promising technology for removal of heavy metals from aqueous solutions. Algae serve as good biosorbents due to their abundance in seawater and fresh water, cost-effectiveness, reusability and high metal sorption capacities. This article provides a comprehensive review of recent findings on performances, applications and chemistry of algae (e.g., brown, green and red algae, modified algae and the derivatives) for sequestration of heavy metals. Biosorption kinetics and equilibrium models are reviewed. The mechanisms for biosorption are presented. Biosorption is a complicated process involving ion-exchange, complexation and coordination. Finally the theoretical simulation tools for biosorption equilibrium and kinetics are presented so that the readers can use them for further studies.

  13. 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.

  14. 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}.

  15. 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.

  16. 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...

  17. Glassy state on the undergraduate course in chemistry (physical chemistry).

    OpenAIRE

    Yamaki, SB; Pedroso, AG; ATVARS, TDZ

    2002-01-01

    We consider the relevance of the study of the glassy state properties and the glass transition as important topics of the physical chemistry for undergraduate courses of Chemistry. Two of the most important theoretical approaches for the description of the glassy state, the thermodynamic and the kinetic models, are summarized with emphasis on the physical chemistry aspects. Examples illustrating the glass transition of some materials are also presented.

  18. 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.

  19. Nuclear Chemistry.

    Science.gov (United States)

    Chemical and Engineering News, 1979

    1979-01-01

    Provides a brief review of the latest developments in nuclear chemistry. Nuclear research today is directed toward increased activity in radiopharmaceuticals and formation of new isotopes by high-energy, heavy-ion collisions. (Author/BB)

  20. 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...

  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. First principles pKa calculations on carboxylic acids using the SMD solvation model: effect of thermodynamic cycle, model chemistry, and explicit solvent molecules.

    Science.gov (United States)

    Sutton, Catherine C R; Franks, George V; da Silva, Gabriel

    2012-10-04

    Aqueous pK(a) values are calculated from first principles for a set of carboxylic acids using the SMD solvation model with various model chemistries, thermodynamic cycles, and treatments of explicit solvation. In all, 108 unique theoretical protocols are examined. The direct (D) and water proton exchange (PX) cycles are trialled along with a new approach, termed the semidirect (SD) cycle. The SD thermodynamic cycle offers some improvements over the D and PX schemes, as it bypasses the gas-phase heterolytic bond dissociation calculation required in the conventional D approach while also avoiding an aqueous OH(-) calculation required by the PX method when using water as the reference acid. With all three cycles, the recommended model chemistry employs M05-2X/cc-pVTZ Gibbs energies of solvation with a single discrete water molecule and a high-level composite method for the gas-phase reaction energies. With the SD cycle, these calculations result in a mean unsigned error of less than 1 pK(a) units, with respective mean signed error and maximum unsigned error of less than 0.5 and 2 pK(a) units. Similar results are obtained with the D and PX cycles, and further improvement is required in both the gas and aqueous phase ab initio energy calculations before we can truly discriminate between the thermodynamic cycles investigated here.

  3. 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.

  4. 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.

  5. Interpretation of NO(x)/NO(y) observations from AASE-2 using a model of chemistry along trajectories

    Science.gov (United States)

    Kawa, S. R.; Fahey, D. W.; Wilson, J. C.; Schoeberl, M. R.; Douglass, A. R.; Stolarski, R. S.; Woodbridge, E. L.; Jonsson, H.; Lait, L. R.; Newman, P. A.

    1993-01-01

    In situ measurements of NO and NO(y) are used to derive the ratio NO(x)/NO(y) along the flight track of the NASA ER-2 aircraft. Data are presented for two flights at midlatitudes in October 1991 during the Airborne Arctic Stratospheric Expedition-2 (AASE-2). Aerosol particle surface area was concurrently measured. The observations are compared with a photochemical model integrated along back trajectories from the aircraft flight track. Comparison of observations with the model run along trajectories and at a fixed position clearly and quantitatively demonstrates the importance of an air parcel's dynamic history in interpretation of local chemical observations. Comparison of the data with model runs under different assumptions regarding heterogeneous chemistry further reinforces the case for occurrence of the reaction of N2O5 + H2O on sulfate aerosol surfaces in the atmosphere. Finally, comparisons for which relative changes in the model and the data are not consistent caution that our ability to resolve all the observations is not yet complete.

  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. 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.

  9. 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

  10. Phase chemistry in process models for cement clinker and lime production

    OpenAIRE

    2014-01-01

    The goal of the thesis is to evaluate if developed phase chemical process models for cement clinker and lime production processes are reliable to use as predictive tools in understanding the changes when introducing sustainability measures. The thesis describes the development of process simulation models in the application of sustainability measures as well as the evaluation of these models. The motivation for developing these types of models arises from the need to predict the chemical and ...

  11. Predicting Radiative Heat Transfer in Oxy-Methane Flame Simulations: An Examination of Its Sensitivities to Chemistry and Radiative Property Models

    Directory of Open Access Journals (Sweden)

    Hassan Abdul-Sater

    2015-01-01

    Full Text Available Measurements from confined, laminar oxy-methane flames at different O2/CO2 dilution ratios in the oxidizer are first reported with measurements from methane-air flames included for comparison. Simulations of these flames employing appropriate chemistry and radiative property modeling options were performed to garner insights into the experimental trends and assess prediction sensitivities to the choice of modeling options. The chemistry was modeled employing a mixture-fraction based approach, Eddy dissipation concept (EDC, and refined global finite rate (FR models. Radiative properties were estimated employing four weighted-sum-of-gray-gases (WSGG models formulated from different spectroscopic/model databases. The mixture fraction and EDC models correctly predicted the trends in flame length and OH concentration variations, and the O2, CO2, and temperature measurements outside the flames. The refined FR chemistry model predictions of CO2 and O2 deviated from their measured values in the flame with 50% O2 in the oxidizer. Flame radiant power estimates varied by less than 10% between the mixture fraction and EDC models but more than 60% between the different WSGG models. The largest variations were attributed to the postcombustion gases in the temperature range 500 K–800 K in the upper sections of the furnace which also contributed significantly to the overall radiative transfer.

  12. The mineral dissolution rate conundrum: Insights from reactive transport modeling of U isotopes and pore fluid chemistry in marine sediments

    Science.gov (United States)

    Maher, Kate; Steefel, Carl I.; DePaolo, Donald J.; Viani, Brian E.

    2006-01-01

    Pore water chemistry and 234U/ 238U activity ratios from fine-grained sediment cored by the Ocean Drilling Project at Site 984 in the North Atlantic were used as constraints in modeling in situ rates of plagioclase dissolution with the multicomponent reactive transport code Crunch. The reactive transport model includes a solid-solution formulation to enable the use of the 234U/ 238U activity ratios in the solid and fluid as a tracer of mineral dissolution. The isotopic profiles are combined with profiles of the major element chemistry (especially alkalinity and calcium) to determine whether the apparent discrepancy between laboratory and field dissolution rates still exists when a mechanistic reactive transport model is used to interpret rates in a natural system. A suite of reactions, including sulfate reduction and methane production, anaerobic methane oxidation, CaCO 3 precipitation, dissolution of plagioclase, and precipitation of secondary clay minerals, along with diffusive transport and fluid and solid burial, control the pore fluid chemistry in Site 984 sediments. The surface area of plagioclase in intimate contact with the pore fluid is estimated to be 6.9 m 2/g based on both grain geometry and on the depletion of 234U/ 238U in the sediment via α-recoil loss. Various rate laws for plagioclase dissolution are considered in the modeling, including those based on (1) a linear transition state theory (TST) model, (2) a nonlinear dependence on the undersaturation of the pore water with respect to plagioclase, and (3) the effect of inhibition by dissolved aluminum. The major element and isotopic methods predict similar dissolution rate constants if additional lowering of the pore water 234U/ 238U activity ratio is attributed to isotopic exchange via recrystallization of marine calcite, which makes up about 10-20% of the Site 984 sediment. The calculated dissolution rate for plagioclase corresponds to a rate constant that is about 10 2 to 10 5 times smaller than

  13. 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

  14. 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.

  15. 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

  16. 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......, require a major, but unavoidable, additional degree of complexity when representing cationic/anionic behaviour in Activated Sludge (AS)/Anaerobic Digestion (AD) systems (Ikumi et al., 2014). In this paper, a plant-wide aqueous phase chemistry module describing pH variations plus ion speciation......). Simulation results show pH predictions when describing Biological Nutrient Removal (BNR) by the activated sludge models (ASM) 1, 2d and 3 (Henze et al., 2000) comparing the performance of a nitrogen removal (WWTP1) and a combined nitrogen and phosphorus removal (WWTP2) treatment plant configuration under...

  17. 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…

  18. 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

  19. Model analysis of secondary organic aerosol formation by glyoxal in laboratory studies: the case for photoenhanced chemistry.

    Science.gov (United States)

    Sumner, Andrew J; Woo, Joseph L; McNeill, V Faye

    2014-10-21

    The reactive uptake of glyoxal by atmospheric aerosols is believed to be a significant source of secondary organic aerosol (SOA). Several recent laboratory studies have been performed with the goal of characterizing this process, but questions remain regarding the effects of photochemistry on SOA growth. We applied GAMMA (McNeill et al. Environ. Sci. Technol. 2012, 46, 8075-8081), a photochemical box model with coupled gas-phase and detailed aqueous aerosol-phase chemistry, to simulate aerosol chamber studies of SOA formation by the uptake of glyoxal by wet aerosol under dark and irradiated conditions (Kroll et al. J. Geophys. Res. 2005, 110 (D23), 1-10; Volkamer et al. Atmos. Chem. Phys. 2009, 9, 1907-1928; Galloway et al. Atmos. Chem. Phys. 2009, 9, 3331- 306 3345 and Geophys. Res. Lett. 2011, 38, L17811). We find close agreement between simulated SOA growth and the results of experiments conducted under dark conditions using values of the effective Henry's Law constant of 1.3-5.5 × 10(7) M atm(-1). While irradiated conditions led to the production of some organic acids, organosulfates, and other oxidation products via well-established photochemical mechanisms, these additional product species contribute negligible aerosol mass compared to the dark uptake of glyoxal. Simulated results for irradiated experiments therefore fell short of the reported SOA mass yield by up to 92%. This suggests a significant light-dependent SOA formation mechanism that is not currently accounted for by known bulk photochemistry, consistent with recent laboratory observations of SOA production via photosensitizer chemistry.

  20. NASA's Upper Atmosphere Research Program (UARP) and Atmospheric Chemistry Modeling and Analysis Program (ACMAP): Research Summaries 1997-1999

    Science.gov (United States)

    Kurylo, M. J.; DeCola, P. L.; Kaye, J. A.

    2000-01-01

    Under the mandate contained in the FY 1976 NASA Authorization Act, the National Aeronautics and Space Administration (NASA) has developed and is implementing a comprehensive program of research, technology development, and monitoring of the Earth's upper atmosphere, with emphasis on the upper troposphere and stratosphere. This program aims at expanding our chemical and physical understanding to permit both the quantitative analysis of current perturbations as well as the assessment of possible future changes in this important region of our environment. It is carried out jointly by the Upper Atmosphere Research Program (UARP) and the Atmospheric Chemistry Modeling and Analysis Program (ACMAP), both managed within the Research Division in the Office of Earth Science at NASA. Significant contributions to this effort have also been provided by the Atmospheric Effects of Aviation Project (AEAP) of NASA's Office of Aero-Space Technology. The long-term objectives of the present program are to perform research to: understand the physics, chemistry, and transport processes of the upper troposphere and the stratosphere and their control on the distribution of atmospheric chemical species such as ozone; assess possible perturbations to the composition of the atmosphere caused by human activities and natural phenomena (with a specific emphasis on trace gas geographical distributions, sources, and sinks and the role of trace gases in defining the chemical composition of the upper atmosphere); understand the processes affecting the distributions of radiatively active species in the atmosphere, and the importance of chemical-radiative-dynamical feedbacks on the meteorology and climatology of the stratosphere and troposphere; and understand ozone production, loss, and recovery in an atmosphere with increasing abundances of greenhouse gases. The current report is composed of two parts. Part 1 summarizes the objectives, status, and accomplishments of the research tasks supported

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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-Technolo