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Sample records for dynamic combinatorial chemistry

  1. UNC Center for Dynamic Combinatorial Chemistry

    DTIC Science & Technology

    2014-04-09

    Waters). 9) “Developing small molecules for anion binding using dynamic combinatorial chemistry”, Oct. 26, 2010, group meeting (J. Beaver /Waters...combinatorial chemistry-update”, Jan. 10, 2011, group meeting (J. Beaver /Waters). 12) “Developmen of DCC assay for protein-protein interaction inhibitors...dynamic combinatorial chemistry-update”, Aug. 4, 2011, DCC intergroup meeting (J. Beaver /Gagné/Waters). 15) “Development various peptides for G

  2. Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.

    PubMed

    Orrillo, A Gastón; Escalante, Andrea M; Furlan, Ricardo L E

    2016-05-10

    Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks.

  3. Introducing Dynamic Combinatorial Chemistry: Probing the Substrate Selectivity of Acetylcholinesterase

    ERIC Educational Resources Information Center

    Angelin, Marcus; Larsson, Rikard; Vongvilai, Pornrapee; Ramstrom, Olof

    2010-01-01

    In this laboratory experiment, college students are introduced to dynamic combinatorial chemistry (DCC) and apply it to determine the substrate selectivity of acetylcholinesterase (AChE). Initially, the students construct a chemical library of dynamically interchanging thioesters and thiols. Then, AChE is added and allowed to select and hydrolyze…

  4. Protein-Directed Dynamic Combinatorial Chemistry: A Guide to Protein Ligand and Inhibitor Discovery.

    PubMed

    Huang, Renjie; Leung, Ivanhoe K H

    2016-07-16

    Protein-directed dynamic combinatorial chemistry is an emerging technique for efficient discovery of novel chemical structures for binding to a target protein. Typically, this method relies on a library of small molecules that react reversibly with each other to generate a combinatorial library. The components in the combinatorial library are at equilibrium with each other under thermodynamic control. When a protein is added to the equilibrium mixture, and if the protein interacts with any components of the combinatorial library, the position of the equilibrium will shift and those components that interact with the protein will be amplified, which can then be identified by a suitable biophysical technique. Such information is useful as a starting point to guide further organic synthesis of novel protein ligands and enzyme inhibitors. This review uses literature examples to discuss the practicalities of applying this method to inhibitor discovery, in particular, the set-up of the combinatorial library, the reversible reactions that may be employed, and the choice of detection methods to screen protein ligands from a mixture of reversibly forming molecules.

  5. Combinatorial chemistry in drug discovery.

    PubMed

    Liu, Ruiwu; Li, Xiaocen; Lam, Kit S

    2017-06-01

    Several combinatorial methods have been developed to create focused or diverse chemical libraries with a wide range of linear or macrocyclic chemical molecules: peptides, non-peptide oligomers, peptidomimetics, small-molecules, and natural product-like organic molecules. Each combinatorial approach has its own unique high-throughput screening and encoding strategy. In this article, we provide a brief overview of combinatorial chemistry in drug discovery with emphasis on recently developed new technologies for design, synthesis, screening and decoding of combinatorial library. Examples of successful application of combinatorial chemistry in hit discovery and lead optimization are given. The limitations and strengths of combinatorial chemistry are also briefly discussed. We are now in a better position to truly leverage the power of combinatorial technologies for the discovery and development of next-generation drugs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Generation of a Multicomponent Library of Disulfide Donor-Acceptor Architectures Using Dynamic Combinatorial Chemistry

    PubMed Central

    Drożdż, Wojciech; Kołodziejski, Michał; Markiewicz, Grzegorz; Jenczak, Anna; Stefankiewicz, Artur R.

    2015-01-01

    We describe here the generation of new donor-acceptor disulfide architectures obtained in aqueous solution at physiological pH. The application of a dynamic combinatorial chemistry approach allowed us to generate a large number of new disulfide macrocyclic architectures together with a new type of [2]catenanes consisting of four distinct components. Up to fifteen types of structurally-distinct dynamic architectures have been generated through one-pot disulfide exchange reactions between four thiol-functionalized aqueous components. The distribution of disulfide products formed was found to be strongly dependent on the structural features of the thiol components employed. This work not only constitutes a success in the synthesis of topologically- and morphologically-complex targets, but it may also open new horizons for the use of this methodology in the construction of molecular machines. PMID:26193265

  7. Applications of dynamic combinatorial chemistry for the determination of effective molarity.

    PubMed

    Ciaccia, Maria; Tosi, Irene; Baldini, Laura; Cacciapaglia, Roberta; Mandolini, Luigi; Di Stefano, Stefano; Hunter, Christopher A

    2015-01-01

    A new strategy for determining thermodynamic effective molarities (EM) for macrocylisation reactions using dynamic combinatorial chemistry under dilute conditions is presented. At low concentrations, below the critical value, Dynamic Libraries (DLs) of bifunctional building blocks contain only cyclic species, so it is not possible to quantify the equilibria between linear and cyclic species. However, addition of a monofunctional chain stopper can be used to promote the formation of linear oligomers allowing measurement of EM for all cyclic species present in the DL. The effectiveness of this approach was demonstrated for DLs generated from mixtures of 1,3-diimine calix[4]arenes, linear diaminoalkanes and monoaminoalkanes. For macrocycles deriving from one bifunctional calixarene and one diamine, there is an alternating pattern of EM values with the number of methylene units in the diamine: odd numbers give significantly higher EMs than even numbers. For odd numbers of methylene units, the alkyl chain can adopt an extended all anti conformation, whereas for even numbers of methylene units, gauche conformations are required for cyclisation, and the associated strain reduces EM. The value of EM for the five-carbon linker indicates that this macrocycle is a strainless ring.

  8. Identification of inhibitors for vascular endothelial growth factor receptor by using dynamic combinatorial chemistry.

    PubMed

    Yang, Zhao; Fang, Zheng; He, Wei; Wang, Zhixiang; Gan, Haifeng; Tian, Qitao; Guo, Kai

    2016-04-01

    The novel analysis method consisting of size-exclusion chromatography (SEC) and HRMS analysis was firstly applied in the discovery of potential inhibitors towards cancer drug targets. With vascular endothelial growth factor receptor (VEGFR-2) as a target, dynamic combinatorial libraries (DCLs) were prepared by reacting aldehydes with amines. Four sensitive binders targeted VEGFR-2 were directly isolated from the library. Antitumor activity test in vitro and inhibition experiments toward angiogenesis were also carried out.

  9. From Dynamic Combinatorial Chemistry to in Vivo Evaluation of Reversible and Irreversible Myeloperoxidase Inhibitors.

    PubMed

    Soubhye, Jalal; Gelbcke, Michel; Van Antwerpen, Pierre; Dufrasne, François; Boufadi, Mokhtaria Yasmina; Nève, Jean; Furtmüller, Paul G; Obinger, Christian; Zouaoui Boudjeltia, Karim; Meyer, Franck

    2017-02-09

    The implementation of dynamic combinatorial libraries allowed the determination of highly active reversible and irreversible inhibitors of myeloperoxidase (MPO) at the nanomolar level. Docking experiments highlighted the interaction between the most active ligands and MPO, and further kinetic studies defined the mode of inhibition of these compounds. Finally, in vivo evaluation showed that one dose of irreversible inhibitors is able to suppress the activity of MPO after inducing inflammation.

  10. Mass spectrometry in combinatorial chemistry.

    PubMed

    Enjalbal, C; Martinez, J; Aubagnac, J L

    2000-01-01

    In the fast expanding field of combinatorial chemistry, profiling libraries has always been a matter of concern--as illustrated by the buoyant literature over the past seven years. Spectroscopic methods, including especially mass spectrometry and to a lesser extent IR and NMR, have been applied at different levels of combinatorial library synthesis: in the rehearsal phase to optimize the chemistry prior to library generation, to confirm library composition, and to characterize after screening each structure that exhibits positive response. Most of the efforts have been concentrated on library composition assessment. The difficulties of such analyses have evolved from the infancy of the combinatorial concept, where large mixtures were prepared, to the recent parallel syntheses of collections of discrete compounds. Whereas the complexity of the analyses has diminished, an increased degree of automation was simultaneously required to achieve efficient library component identification and quantification. In this respect, mass spectrometry has been found to be the method of choice, providing rapid, sensitive, and informative analyses, especially when coupled to chromatographic separation. Fully automated workstations able to cope with several hundreds of compounds per day have been designed. After a brief introduction to describe the combinatorial approach, library characterization will be discussed in detail, considering first the solution-based methodologies and secondly the support-bound material analyses.

  11. Target-directed Dynamic Combinatorial Chemistry: A Study on Potentials and Pitfalls as Exemplified on a Bacterial Target.

    PubMed

    Frei, Priska; Pang, Lijuan; Silbermann, Marleen; Eriş, Deniz; Mühlethaler, Tobias; Schwardt, Oliver; Ernst, Beat

    2017-08-25

    Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures.

    PubMed

    Herrmann, Andreas

    2014-03-21

    Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

  13. Combinatorial Chemistry for Optical Sensing Applications

    NASA Astrophysics Data System (ADS)

    Díaz-García, M. E.; Luis, G. Pina; Rivero-Espejel, I. A.

    The recent interest in combinatorial chemistry for the synthesis of selective recognition materials for optical sensing applications is presented. The preparation, screening, and applications of libraries of ligands and chemosensors against molecular species and metal ions are first considered. Included in this chapter are also the developments involving applications of combinatorial approaches to the discovery of sol-gel and acrylic-based imprinted materials for optical sensing of antibiotics and pesticides, as well as libraries of doped sol-gels for high-throughput optical sensing of oxygen. The potential of combinatorial chemistry applied to the discovery of new sensing materials is highlighted.

  14. Similarity searching in large combinatorial chemistry spaces

    NASA Astrophysics Data System (ADS)

    Rarey, Matthias; Stahl, Martin

    2001-06-01

    We present a novel algorithm, called Ftrees-FS, for similarity searching in large chemistry spaces based on dynamic programming. Given a query compound, the algorithm generates sets of compounds from a given chemistry space that are similar to the query. The similarity search is based on the feature tree similarity measure representing molecules by tree structures. This descriptor allows handling combinatorial chemistry spaces as a whole instead of looking at subsets of enumerated compounds. Within few minutes of computing time, the algorithm is able to find the most similar compound in very large spaces as well as sets of compounds at an arbitrary similarity level. In addition, the diversity among the generated compounds can be controlled. A set of 17 000 fragments of known drugs, generated by the RECAP procedure from the World Drug Index, was used as the search chemistry space. These fragments can be combined to more than 1018 compounds of reasonable size. For validation, known antagonists/inhibitors of several targets including dopamine D4, histamine H1, and COX2 are used as queries. Comparison of the compounds created by Ftrees-FS to other known actives demonstrates the ability of the method to jump between structurally unrelated molecule classes.

  15. Dynamic combinatorial self-replicating systems.

    PubMed

    Moulin, Emilie; Giuseppone, Nicolas

    2012-01-01

    Thanks to their intrinsic network topologies, dynamic combinatorial libraries (DCLs) represent new tools for investigating fundamental aspects related to self-organization and adaptation processes. Very recently the first examples integrating self-replication features within DCLs have pushed even further the idea of implementing dynamic combinatorial chemistry (DCC) towards minimal systems capable of self-construction and/or evolution. Indeed, feedback loop processes - in particular in the form of autocatalytic reactions - are keystones to build dynamic supersystems which could possibly approach the roots of "Darwinian" evolvability at mesoscale. This topic of current interest also shows significant potentialities beyond its fundamental character, because truly smart and autonomous materials for the future will have to respond to changes of their environment by selecting and by exponentially amplifying their fittest constituents.

  16. Integrating virtual screening and combinatorial chemistry for accelerated drug discovery.

    PubMed

    López-Vallejo, Fabian; Caulfield, Thomas; Martínez-Mayorga, Karina; Giulianotti, Marc A; Nefzi, Adel; Houghten, Richard A; Medina-Franco, Jose L

    2011-07-01

    Virtual screening is increasingly being used in drug discovery programs with a growing number of successful applications. Experimental methodologies developed to speed up the drug discovery processes include high-throughput screening and combinatorial chemistry. The complementarities between computational and experimental screenings have been recognized and reviewed in the literature. Computational methods have also been used in the combinatorial chemistry field, in particular in library design. However, the integration of computational and combinatorial chemistry screenings has been attempted only recently. Combinatorial libraries (experimental or virtual) represent a notable source of chemically related compounds. Advances in combinatorial chemistry and deconvolution strategies, have enabled the rapid exploration of novel and dense regions in the chemical space. The present review is focused on the integration of virtual and experimental screening of combinatorial libraries. Applications of virtual screening to discover novel anticancer agents and our ongoing efforts towards the integration of virtual screening and combinatorial chemistry are also discussed.

  17. Dynamic mixtures and combinatorial libraries: imines as probes for molecular evolution at the interface between chemistry and biology.

    PubMed

    Herrmann, Andreas

    2009-08-21

    In analogy to evolution in biological processes, "molecular evolution", based on the reversible formation of imines, has successfully been explored for drug discovery, receptor design and as a controlled-release vehicle. Multicomponent systems composed of amines and carbonyl compounds generate structural diversity by reversible reaction of the different components to form equilibrated dynamic mixtures or combinatorial libraries (DCLs). Under thermodynamic control and in the presence of an external factor which influences the equilibrium, these systems evolve by selective adaptation to the changing external conditions. This concept allows the casting of biologically or catalytically active substrates and the molding of receptors from DCLs which are composed of smaller non-active amine and carbonyl moieties. Similarly, if the amine or carbonyl compounds are the biologically active compounds of interest, the corresponding dynamic mixtures are found to be efficient delivery systems, allowing their controlled release over time.

  18. DNA-Encoded Dynamic Combinatorial Chemical Libraries.

    PubMed

    Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin

    2015-06-26

    Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions.

  19. Generalized topological spaces in evolutionary theory and combinatorial chemistry.

    PubMed

    Stadler, Bärbel M R; Stadler, Peter F

    2002-01-01

    The search spaces in combinatorial chemistry as well as the sequence spaces underlying (molecular) evolution are conventionally thought of as graphs. Recombination, however, implies a nongraphical structure of the combinatorial search spaces. These structures, and their implications for search process itself, are heretofore not well understood in general. In this contribution we review a very general formalism from point set topology and discuss its application to combinatorial search spaces, fitness landscapes, evolutionary trajectories, and artificial chemistries.

  20. MCR XVI. Mathematical support for combinatorial chemistry

    PubMed

    Gruber

    2000-05-01

    The algebra of the s- and r-vectors is an adequate formal tool to describe chemical objects in an abstract way. Compounds as well as reactions are represented, including all constitutional and configurational aspects. The stereochemistry of simple organic molecules as well as those of metal-organic compounds may be described in a unique way. Ionic bonds, covalent bonds, aromatics, and electron-deficiency compounds can formally be described without loss of information. Even reaction types and the flow of electrons can be described by this algebra. The biggest benefit of this approach is its intrinsic group theoretical structure. This does not bother the chemist for its use but allows a computer to handle and structure huge amounts of chemical data. This is especially important for combinatorial chemistry, which deals with huge sets of chemically distinct molecules, the so-called molecular libraries.

  1. Method and apparatus for combinatorial chemistry

    SciTech Connect

    Foote, Robert S.

    2009-06-23

    A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.

  2. Method and apparatus for combinatorial chemistry

    DOEpatents

    Foote, Robert S [Oak Ridge, TN

    2012-06-05

    A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.

  3. Method and apparatus for combinatorial chemistry

    DOEpatents

    Foote, Robert S.

    2007-02-20

    A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.

  4. Natural products and combinatorial chemistry: back to the future.

    PubMed

    Ortholand, Jean-Yves; Ganesan, A

    2004-06-01

    The introduction of high-throughput synthesis and combinatorial chemistry has precipitated a global decline in the screening of natural products by the pharmaceutical industry. Some companies terminated their natural products program, despite the unproven success of the new technologies. This was a premature decision, as natural products have a long history of providing important medicinal agents. Furthermore, they occupy a complementary region of chemical space compared with the typical synthetic compound library. For these reasons, the interest in natural products has been rekindled. Various approaches have evolved that combine the power of natural products and organic chemistry, ranging from the combinatorial total synthesis of analogues to the exploration of natural product scaffolds and the design of completely unnatural molecules that resemble natural products in their molecular characteristics.

  5. From combinatorial chemistry to cancer targeting nanotherapeutics

    NASA Astrophysics Data System (ADS)

    Xiao, Kai; Luo, Juntao; Li, Yuanpei; Xiao, Wenwu; Lee, Joyce S.; Gonik, Abby M.; Lam, Kit S.

    2010-04-01

    We have developed a number of amphiphilic polymers, comprised of a cluster of cholic acids (4 to 10) linked by a series of lysines and attached to one end of a linear polyethylene glycol chain (PEG, 2000-5000 Dalton). Under aqueous condition, such telodendrimers can self-assemble together with hydrophobic payloads to form highly stable micelles (15-150 nm diameter, size tunable). We used near infrared fluorescence (NIRF) optical imaging technique to study the in vivo passive accumulation of our nanocarriers (via EPR effect) in different types and stages of tumors. The results demonstrated that the micelle could preferentially accumulate in many types of tumor xenografts or synografts implanted in mice. Nanoparticle uptake in solid tumors was found to be much higher than that of lymphoma, which could be attributed to the relatively low microvascular density in the latter. We have also demonstrated that micelles smaller than 64 nm preferentially targeted xenografts with high efficiency and with low liver and lung uptake, whereas those micelles at 154 nm targeted the tumor poorly but with very high liver and lung uptake. Telodendrimers decorated with oligolysine or oligoaspartic acid resulted in high uptake of the nanoparticles into the liver. When decorated with cancer targeting ligands identified from the one-bead-one-compound (OBOC) combinatorial library methods, the drug-loaded nanoparticles were rapidly taken up by the target cultured tumor cells causing cell death. In vivo near infra-red optical imaging studies with hydrophobic fluorescent dye demonstrated that xenograft uptake of the micelles was greatly enhanced by the cancer targeting peptide.

  6. Automated Combinatorial Chemistry in the Organic Chemistry Majors Laboratory

    ERIC Educational Resources Information Center

    Nichols, Christopher J.; Hanne, Larry F.

    2010-01-01

    A multidisciplinary experiment has been developed in which students each synthesize a combinatorial library of 48 hydrazones with the aid of a liquid-handling robot. Each product is then subjected to a Kirby-Bauer disk diffusion assay to assess its antibacterial activity. Students gain experience working with automation and at the…

  7. Automated Combinatorial Chemistry in the Organic Chemistry Majors Laboratory

    ERIC Educational Resources Information Center

    Nichols, Christopher J.; Hanne, Larry F.

    2010-01-01

    A multidisciplinary experiment has been developed in which students each synthesize a combinatorial library of 48 hydrazones with the aid of a liquid-handling robot. Each product is then subjected to a Kirby-Bauer disk diffusion assay to assess its antibacterial activity. Students gain experience working with automation and at the…

  8. Discovery of New Luminescent Oxides by Combinatorial Solid State Chemistry

    NASA Astrophysics Data System (ADS)

    McFarland, Eric

    1998-03-01

    Combinatorial synthesis and screening of extraordinarily large numbers of different organic compounds has been widely applied in the pharmaceutical industry for drug discovery. Combinatorial chemistry is particularly well suited for ternary and higher order inorganic materials discovery where efforts to predict basic properties have been unsuccessful. New compounds for ultraviolet excited phosphors are important for flat panel displays and for lighting applications. Utilizing automated thin film synthesis and parallel screening techniques, combinatorial libraries with up to 25,000 compositions have been investigated for photoluminescence. Screening of the libraries identified Y_0.845Al_0.070La_0.060Eu_0.025VO4 as a new red phosphor which, when synthesized in bulk, has an intrinsic quantum efficiency under 254 nm excitation of 0.83 ± 0.06 (A COMBINATORIAL APPROACH TO THE DISCOVERY AND OPTIMIZATION OF LUMINESCENT MATERIALS, Earl Danielson, Josh Golden, Eric W. McFarland, Casper M. Reaves, W. Henry Weinberg, and Xin Di Wu, Nature), Vol. 389, (1997). In addition, the first one-dimensional (1-D) luminescent inorganic oxide, Sr_2CeO_4, has been discovered using combinatorial solid state chemistry. The elemental ratios from a diverse discovery library led to the synthesis of a bulk sample of single phase Sr_2CeO4 that was structurally characterized by Rietveld refinement of the powder X-ray data to possess a new structure type for a luminescent oxide built up from 1-D chains of edge sharing CeO6 octahedra, with two terminal O atoms per Ce center isolated from one another by Sr^2+ cations. The cerate shows broad excitation and emission maxima at 310 and 485 nm. The lifetime of the excited state, epr data, crystallographic structure, and magnetic susceptibility all suggest that the mechanism of luminescence originates from a ligand to metal Ce^4+ charge transfer. We speculate that the relatively electron rich terminal O atoms bonded to Ce^4+ in Sr_2CeO_4, which give rise

  9. Sponge derived bromotyrosines: structural diversity through natural combinatorial chemistry.

    PubMed

    Niemann, Hendrik; Marmann, Andreas; Lin, Wenhan; Proksch, Peter

    2015-01-01

    Sponge derived bromotyrosines are a multifaceted class of marine bioactive compounds that are important for the chemical defense of sponges but also for drug discovery programs as well as for technical applications in the field of antifouling constituents. These compounds, which are mainly accumulated by Verongid sponges, exhibit a diverse range of bioactivities including antibiotic, cytotoxic and antifouling effects. In spite of the simple biogenetic building blocks, which consist only of brominated tyrosine and tyramine units, an impressive diversity of different compounds is obtained through different linkages between these precursors and through structural modifications of the side chains and/or aromatic rings resembling strategies that are known from combinatorial chemistry. As examples for bioactive, structurally divergent bromotyrosines psammaplin A, Aplysina alkaloids featuring aerothionin, aeroplysinin-1 and the dienone, and the bastadins, including the synthetically derived hemibastadin congeners, have been selected for this review. Whereas all of these natural products are believed to be involved in the chemical defense of sponges, some of them may also be of particular relevance to drug discovery due to their interaction with specific molecular targets in eukaryotic cells. These targets involve important enzymes and receptors, such as histone deacetylases (HDAC) and DNA methyltransferases (DNMT), which are inhibited by psammaplin A, as well as ryanodine receptors that are targeted by bastadine type compounds. The hemibastadins such as the synthetically derived dibromohemibastadin are of particular interest due to their antifouling activity. For the latter, a phenoloxidase which catalyzes the bioglue formation needed for firm attachment of fouling organisms to a given substrate was identified as a molecular target. The Aplysina alkaloids finally provide a vivid example for dynamic wound induced bioconversions of natural products that generate highly

  10. The Lock is the Key: Development of Novel Drugs through Receptor Based Combinatorial Chemistry.

    PubMed

    Maraković, Nikola; Šinko, Goran

    2017-01-01

    Modern drug discovery is mainly based on the de novo synthesis of a large number of compounds with a diversity of chemical functionalities. Though the introduction of combinatorial chemistry enabled the preparation of large libraries of compounds from so-called building blocks, the problem of successfully identifying leads remains. The introduction of a dynamic combinatorial chemistry method served as a step forward due to the involvement of biological macromolecular targets (receptors) in the synthesis of high affinity products. The major breakthrough was a synthetic method in which building blocks are irreversibly combined due to the presence of a receptor. Here we present various receptor-based combinatorial chemistry approaches. Huisgen's cycloaddition (1,3-dipolar cycloaddition of azides and alkynes) forms stabile 1,2,3-triazoles with very high receptor affinity that can reach femtomolar levels, as the case with acetylcholinesterase inhibitors shows. Huisgen's cycloaddition can be applied to various receptors including acetylcholinesterase, acetylcholine binding protein, carbonic anhydrase-II, serine/threonine-protein kinase and minor groove of DNA.

  11. Intrinsic information carriers in combinatorial dynamical systems

    NASA Astrophysics Data System (ADS)

    Harmer, Russ; Danos, Vincent; Feret, Jérôme; Krivine, Jean; Fontana, Walter

    2010-09-01

    Many proteins are composed of structural and chemical features—"sites" for short—characterized by definite interaction capabilities, such as noncovalent binding or covalent modification of other proteins. This modularity allows for varying degrees of independence, as the behavior of a site might be controlled by the state of some but not all sites of the ambient protein. Independence quickly generates a startling combinatorial complexity that shapes most biological networks, such as mammalian signaling systems, and effectively prevents their study in terms of kinetic equations—unless the complexity is radically trimmed. Yet, if combinatorial complexity is key to the system's behavior, eliminating it will prevent, not facilitate, understanding. A more adequate representation of a combinatorial system is provided by a graph-based framework of rewrite rules where each rule specifies only the information that an interaction mechanism depends on. Unlike reactions, which deal with molecular species, rules deal with patterns, i.e., multisets of molecular species. Although the stochastic dynamics induced by a collection of rules on a mixture of molecules can be simulated, it appears useful to capture the system's average or deterministic behavior by means of differential equations. However, expansion of the rules into kinetic equations at the level of molecular species is not only impractical, but conceptually indefensible. If rules describe bona fide patterns of interaction, molecular species are unlikely to constitute appropriate units of dynamics. Rather, we must seek aggregate variables reflective of the causal structure laid down by the rules. We call these variables "fragments" and the process of identifying them "fragmentation." Ideally, fragments are aspects of the system's microscopic population that the set of rules can actually distinguish on average; in practice, it may only be feasible to identify an approximation to this. Most importantly, fragments are

  12. Dynamic combinatorial libraries of artificial repeat proteins.

    PubMed

    Eisenberg, Margarita; Shumacher, Inbal; Cohen-Luria, Rivka; Ashkenasy, Gonen

    2013-06-15

    Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (~14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.

  13. Dynamic chemistry of anion recognition

    SciTech Connect

    Custelcean, Radu

    2012-01-01

    In the past 40 years, anion recognition by synthetic receptors has grown into a rich and vibrant research topic, developing into a distinct branch of Supramolecular Chemistry. Traditional anion receptors comprise organic scaffolds functionalized with complementary binding groups that are assembled by multistep organic synthesis. Recently, a new approach to anion receptors has emerged, in which the host is dynamically self-assembled in the presence of the anionic guest, via reversible bond formation between functional building units. While coordination bonds were initially employed for the self-assembly of the anion hosts, more recent studies demonstrated that reversible covalent bonds can serve the same purpose. In both cases, due to their labile connections, the molecular constituents have the ability to assemble, dissociate, and recombine continuously, thereby creating a dynamic combinatorial library (DCL) of receptors. The anionic guests, through specific molecular recognition, may then amplify (express) the formation of a particular structure among all possible combinations (real or virtual) by shifting the equilibria involved towards the most optimal receptor. This approach is not limited to solution self-assembly, but is equally applicable to crystallization, where the fittest anion-binding crystal may be selected. Finally, the pros and cons of employing dynamic combinatorial chemistry (DCC) vs molecular design for developing anion receptors, and the implications of both approaches to selective anion separations, will be discussed.

  14. Photoelectrochemical Hydrogen Production Using New Combinatorial Chemistry Derived Materials

    SciTech Connect

    Jaramillo, Thomas F.; Baeck, Sung-Hyeon; Kleiman-Shwarsctein, Alan; Stucky, Galen D.; McFarland, Eric W.

    2004-10-25

    Solar photoelectrochemical water-splitting has long been viewed as one of the “holy grails” of chemistry because of its potential impact as a clean, renewable method of fuel production. Several known photocatalytic semiconductors can be used; however, the fundamental mechanisms of the process remain poorly understood and no known material has the required properties for cost effective hydrogen production. In order to investigate morphological and compositional variations in metal oxides as they relate to opto-electrochemical properties, we have employed a combinatorial methodology using automated, high-throughput, electrochemical synthesis and screening together with conventional solid-state methods. This report discusses a number of novel, high-throughput instruments developed during this project for the expeditious discovery of improved materials for photoelectrochemical hydrogen production. Also described within this report are results from a variety of materials (primarily tungsten oxide, zinc oxide, molybdenum oxide, copper oxide and titanium dioxide) whose properties were modified and improved by either layering, inter-mixing, or doping with one or more transition metals. Furthermore, the morphologies of certain materials were also modified through the use of structure directing agents (SDA) during synthesis to create mesostructures (features 2-50 nm) that increased surface area and improved rates of hydrogen production.

  15. Advances in microwave-assisted combinatorial chemistry without polymer-supported reagents.

    PubMed

    Martínez-Palou, Rafael

    2006-08-01

    Combinatorial methodologies have dramatically changed the chemical research and discovery process, offering an unlimited source of new molecule entities to be screened for activity. The application of microwave irradiation in Combinatorial Chemistry and high-throughput synthesis has become increasingly popular. By taking advantage of this energy source, compound libraries for lead generation can be assembled in a fraction of time required by conventional thermal heating. This review focuses on the advances in developing synthetic methodologies in microwave without polymer-supported reagents suitable for combinatorial chemistry, including the advances in microwave-assisted fluorous synthesis technology.

  16. Combinatorial chemistry, automation and molecular diversity: new trends in the pharmaceutical industry.

    PubMed

    Van Hijfte, L; Marciniak, G; Froloff, N

    1999-04-02

    Combinatorial chemistry has emerged as a set of novel strategies for the synthesis of large sets of compounds (combinatorial libraries) for biological evaluation. Within a few years combinatorial chemistry has undergone a series of changes in trends, which are closely related to two important factors in libraries: numbers and quality. While the number of compounds in a library may be easily expressed, it is a lot more difficult to indicate the degree of quality of a library. This degree of quality can be split into two aspects: purity and diversity. The changing trends in combinatorial chemistry with respect to the strategies, the technologies, the libraries themselves (numbers and purity aspects) and the molecular diversity are outlined in this paper.

  17. Application of computer assisted combinatorial chemistry in antivirial, antimalarial and anticancer agents design

    NASA Astrophysics Data System (ADS)

    Burello, E.; Bologa, C.; Frecer, V.; Miertus, S.

    Combinatorial chemistry and technologies have been developed to a stage where synthetic schemes are available for generation of a large variety of organic molecules. The innovative concept of combinatorial design assumes that screening of a large and diverse library of compounds will increase the probability of finding an active analogue among the compounds tested. Since the rate at which libraries are screened for activity currently constitutes a limitation to the use of combinatorial technologies, it is important to be selective about the number of compounds to be synthesized. Early experience with combinatorial chemistry indicated that chemical diversity alone did not result in a significant increase in the number of generated lead compounds. Emphasis has therefore been increasingly put on the use of computer assisted combinatorial chemical techniques. Computational methods are valuable in the design of virtual libraries of molecular models. Selection strategies based on computed physicochemical properties of the models or of a target compound are introduced to reduce the time and costs of library synthesis and screening. In addition, computational structure-based library focusing methods can be used to perform in silico screening of the activity of compounds against a target receptor by docking the ligands into the receptor model. Three case studies are discussed dealing with the design of targeted combinatorial libraries of inhibitors of HIV-1 protease, P. falciparum plasmepsin and human urokinase as potential antivirial, antimalarial and anticancer drugs. These illustrate library focusing strategies.

  18. Discovery of bioactive molecules from CuAAC click-chemistry-based combinatorial libraries.

    PubMed

    Wang, Xueshun; Huang, Boshi; Liu, Xinyong; Zhan, Peng

    2016-01-01

    The rapid assembly and in situ screening of focused combinatorial fragment libraries using CuAAC click chemistry is a highly robust and efficient strategy for establishing SAR and for discovering bioactive molecules. This review outlines the current status of this methodology in drug discovery application. The inherent limitations, challenges and prospects are critically discussed.

  19. [New methods in pharmaceutical research: combinatorial chemistry and high throughput screening].

    PubMed

    Schirlin, Daniel; Galvan, Martin; Le Fur, Gérard

    2007-01-01

    New lead-identification methodologies such as high-throughput screening and combinatorial chemistry have been integrated into pharmaceutical research over the past 5-10 years. More rational use in the selection of potential preclinical candidates for some difficult targets has increased the chances of success.

  20. Carbonic anhydrase II-induced selection of inhibitors from a dynamic combinatorial library of Schiff's bases.

    PubMed

    Nasr, Gihane; Petit, Eddy; Supuran, Claudiu T; Winum, Jean-Yves; Barboiu, Mihail

    2009-11-01

    A dynamic combinatorial library (DCL) has been generated under thermodynamic control by using the aminocarbonyl/imine interconversion as reversible chemistry, combined with non-covalent binding within the active site of the metalloenzyme human carbonic anhydrase II (hCA II, EC 4.2.1.1). The high affinity of hCA II isozyme towards some sulfonamide inhibitors obtained here was used to select from the dynamic library specific inhibitors of this isoform. These results point out to the possibility of identifying sulfonamide amplified compounds presenting potent inhibition and high yield of formation in the presence of the isoform(s) towards which the inhibitors were designed.

  1. A new combinatorial method for synthesizing, screening, and discovering antifouling surface chemistries.

    PubMed

    Imbrogno, Joseph; Williams, Matthew D; Belfort, Georges

    2015-02-04

    A set of diverse monomers were synthesized using combinatorial chemistry and tested using our unique high-throughput screening platform. The versatility of our platform is exemplified by possible applications in reducing biological fouling on ship hulls, filtration membranes, and surgical instruments, to name a few. To demonstrate its efficacy, the novel monomers were graft-polymerized onto light sensitive poly(ether sulfone) (PES) membranes via atmospheric-pressure plasma polymerization. A diverse library was synthesized by reacting a common vinyl ester linker with a library of maleimides containing various different functional groups. This allowed us to produce a library of many different surfaces and graft them all using the same linker chemistry. The modified surfaces were then tested and screened for the best antiprotein adsorption (nonfouling) properties. Membranes, functionalized with carboxylic acid, zwitterionic, and ester groups, had the lowest protein adhesion compared with that of an unmodified control PES membrane after a static fouling test. After dynamic fouling, these same functionalities as well as a hydroxyl group exhibited the highest permeability. These monomers performed better than our best previously synthesized amide monomers as well as our best poly(ethylene glycol) monomers, which are known to have very high protein resistance. Hansen solubility parameters qualitatively predicted which monomers performed best, indicating favorable interactions with water molecules.

  2. Combinatorial chemistry: polymer supported synthesis of peptide and non-peptide libraries.

    PubMed

    Kundu, B; Khare, S K; Rastogi, S K

    1999-01-01

    In recent years, combinatorial chemistry has emerged as a powerful tool for accelerating drug discovery. While industry is rapidly embracing the technology, researchers continue to develop novel library methods including resins, linkers, tagging and deconvolution techniques. Newer strategies involving computer-customized combinatorial libraries offer enormous potential for the design of more "focused" and "smart" chemical libraries with maximal diversity. In addition, miniaturized systems for synthesizing chemical libraries are also being developed, which has made it possible to carry out reactions at submicroliter volumes.

  3. Combinatorial computational chemistry approach for materials design: applications in deNOx catalysis, Fischer-Tropsch synthesis, lanthanoid complex, and lithium ion secondary battery.

    PubMed

    Koyama, Michihisa; Tsuboi, Hideyuki; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A; Miyamoto, Akira

    2007-02-01

    Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational chemistry, a new concept "combinatorial computational chemistry" has been proposed by introducing the concept of combinatorial chemistry to computational chemistry. This combinatorial computational chemistry approach enables theoretical high-throughput screening for materials design. In this manuscript, we review the successful applications of combinatorial computational chemistry to deNO(x) catalysts, Fischer-Tropsch catalysts, lanthanoid complex catalysts, and cathodes of the lithium ion secondary battery.

  4. Transfer RNA modifications: Nature’s combinatorial chemistry playground

    PubMed Central

    Jackman, Jane E.; Alfonzo, Juan D.

    2012-01-01

    Following synthesis, tRNAs are peppered by numerous chemical modifications which may differentially affect a tRNA’s structure and function. Although modifications affecting the business ends of a tRNA are predictably important for cell viability, a majority of modifications play more subtle structural roles that can affect tRNA stability and folding. The current trend is that modifications act in concert and it is in the context of the specific sequence of a given tRNA that they impart their differing effects. Recent developments in the modification field have highlighted the diversity of modifications in tRNA. From these the combinatorial nature of modifications in explaining previously described phenotypes derived from their absence has emerged as a growing theme. PMID:23139145

  5. Combinatorial chemistry approach to chiral catalyst engineering and screening: rational design and serendipity.

    PubMed

    Ding, Kuiling; Du, Haifeng; Yuan, Yu; Long, Jiang

    2004-06-21

    An efficient asymmetric catalyst relies on the successful combination of a large number of interrelated variables, including rational design, intuition, persistence, and good fortune-not all of which are necessarily well-understood; this renders such practice largely empirical. As a result, the possibility of using combinatorial chemistry methods in asymmetric catalysis research has been widely recognized to be highly desirable. In this account, we attempt to show the principle and application of combinatorial approach in the discovery of chiral catalysts for enantioselective reactions. The concept focuses on the strategy for the creation of a modular chiral catalyst library by two-component ligand modification of metal ions on the basis of molecular recognition and assembly. The self-assembled chiral catalyst with two different ligands indeed exhibited synergistic effects in terms of both enantioselectivity and activity in comparison with its corresponding homocombinations in many reactions. The examples described in this paper demonstrated the powerfulness of combinatorial approach for the discovery of novel chiral catalyst systems, particularly for the development of highly efficient, enantioselective, and practical catalysts for enantioselective reactions. We hope this concept will stimulate further work on the discovery of more highly efficient and enantioselective catalysts, as well as unexpected classes of catalysts or catalytic enantioselective reactions in the future with the help of a combinatorial chemistry approach.

  6. DNA functionalization by dynamic chemistry

    PubMed Central

    Kanlidere, Zeynep; Jochim, Oleg; Cal, Marta

    2016-01-01

    Summary Dynamic combinatorial chemistry (DCC) is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80%) was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue. PMID:27829920

  7. Mass spectrometry and combinatorial chemistry: new approaches for direct support-bound compound identification.

    PubMed

    Enjalbal, C; Maux, D; Martinez, J; Combarieu, R; Aubagnac, J L

    2001-06-01

    Mass spectrometry is a powerful analytical tool allowing rapid and sensitive structural elucidation of a wide range of molecules issued from solution-, solid- and liquid-phase syntheses. Therefore, mass spectrometry has become the most widely used tool to probe combinatorial libraries. A significant portion of the reported combinatorial data are being produced using solid phase organic synthesis. In contrast to indirect strategies where the tethered structures were released from the support into solution to undergo standard mass spectrometric analyses, static - secondary ion mass spectrometry (S-SIMS) has enabled the identification of support-bound molecules without any chemical treatment of the resin bead. Such non-destructive characterization was applied at the bead level and facilitated the step-by-step monitoring of solid-phase peptide syntheses. Side-reactions were also detected. The relevance of S-SIMS in the rehearsal phase of combinatorial chemistry is demonstrated by comparison with infrared and nuclear magnetic resonance (NMR) spectroscopies, the two other techniques investigated in that field. An alternative to solid-phase synthesis consists of assembling molecules on a soluble polymer. This methodology is termed liquid-phase synthesis. Compound characterization is facilitated since the derivatized support is soluble in spectroscopic solvents used in NMR or in electrospray ionization mass spectrometry. The advantages and drawbacks of this approach will be discussed in terms of the direct monitoring of supported reactions during chemistry optimization and rehearsal library validation.

  8. Synthesis of Chemiluminescent Esters: A Combinatorial Synthesis Experiment for Organic Chemistry Students

    ERIC Educational Resources Information Center

    Duarte, Robert; Nielson, Janne T.; Dragojlovic, Veljko

    2004-01-01

    A group of techniques aimed at synthesizing a large number of structurally diverse compounds is called combinatorial synthesis. Synthesis of chemiluminescence esters using parallel combinatorial synthesis and mix-and-split combinatorial synthesis is experimented.

  9. Synthesis of Chemiluminescent Esters: A Combinatorial Synthesis Experiment for Organic Chemistry Students

    ERIC Educational Resources Information Center

    Duarte, Robert; Nielson, Janne T.; Dragojlovic, Veljko

    2004-01-01

    A group of techniques aimed at synthesizing a large number of structurally diverse compounds is called combinatorial synthesis. Synthesis of chemiluminescence esters using parallel combinatorial synthesis and mix-and-split combinatorial synthesis is experimented.

  10. WORKSHOP ON NEW DEVELOPMENTS IN CHEMICAL SEPARATIONS FROM COMBINATORIAL CHEMISTRY AND RELATED SYNTHETIC STRATEGIES

    SciTech Connect

    Weber, Stephen G.

    1998-08-22

    The power of combinatorial chemistry and related high throughput synthetic strategies is currently being pursued as a fruitful way to develop molecules and materials with new properties. The strategy is motivated, for example in the pharmaceutical industry, by the difficulty of designing molecules to bind to specific sites on target biomolecules. By synthesizing a variety of similar structures, and then finding the one that has the most potent activity, new so-called lead structures will be found rapidly. Existing lead structures can be optimized. This relatively new approach has many implications for separation science. The most obvious is the call for more separations power: higher resolution, lower concentrations, higher speed. This pressure butresses the traditional directions of research into the development of more useful separations. The advent of chip-based, electroosmotically pumped systems1 will certainly accelerate progress in this traditional direction. The progress in combinatorial chemistry and related synthetic strategies gives rise to two other, broadly significant possibilities for large changes in separation science. One possibility results from the unique requirements of the synthesis of a huge number of products simultaneously. Can syntheses and separations be designed to work together to create strategies that lead to mixtures containing only desired products but without side products? The other possibility results from the need for molecular selectivity in separations. Can combinatorial syntheses and related strategies be used in the development of better separations media? A workshop in two parts was held. In one half-day session, pedagogical presentations educated across the barriers of discipline and scale. In the second half-day session, the participants broke into small groups to flesh out new ideas. A panel summarized the breakout discussions.

  11. Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.

    PubMed

    Lehn, Jean-Marie

    2012-01-01

    Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation.The merging of the features: -information and programmability, -dynamics and reversibility, -constitution and structural diversity, points to the emergence of adaptive and evolutive chemistry, towards a chemistry of complex matter.

  12. Dynamic imine chemistry.

    PubMed

    Belowich, Matthew E; Stoddart, J Fraser

    2012-03-21

    Formation of an imine--from an amine and an aldehyde--is a reversible reaction which operates under thermodynamic control such that the formation of kinetically competitive intermediates are, in the fullness of time, replaced by the thermodynamically most stable product(s). For this fundamental reason, the imine bond has emerged as an extraordinarily diverse and useful one in the hands of synthetic chemists. Imine bond formation is one of a handful of reactions which define a discipline known as dynamic covalent chemistry (DCC), which is now employed widely in the construction of exotic molecules and extended structures on account of the inherent 'proof-reading' and 'error-checking' associated with these reversible reactions. While both supramolecular chemistry and DCC operate under the regime of reversibility, DCC has the added advantage of constructing robust molecules on account of the formation of covalent bonds rather than fragile supermolecules resulting from noncovalent bonding interactions. On the other hand, these products tend to require more time to form--sometimes days or even months--but their formation can often be catalysed. In this manner, highly symmetrical molecules and extended structures can be prepared from relatively simple precursors. When DCC is utilised in conjunction with template-directed protocols--which rely on the use of noncovalent bonding interactions between molecular building blocks in order to preorganise them into certain relative geometries as a prelude to the formation of covalent bonds under equilibrium control--an additional level of control of structure and topology arises which offers a disarmingly simple way of constructing mechanically-interlocked molecules, such as rotaxanes, catenanes, Borromean rings, and Solomon knots. This tutorial review focuses on the use of dynamic imine bonds in the construction of compounds and products formed with and without the aid of additional templates. While synthesis under thermodynamic

  13. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery.

    PubMed

    Therrien, Eric; Englebienne, Pablo; Arrowsmith, Andrew G; Mendoza-Sanchez, Rodrigo; Corbeil, Christopher R; Weill, Nathanael; Campagna-Slater, Valérie; Moitessier, Nicolas

    2012-01-23

    As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.

  14. Selective host molecules obtained by dynamic adaptive chemistry.

    PubMed

    Matache, Mihaela; Bogdan, Elena; Hădade, Niculina D

    2014-02-17

    Up till 20 years ago, in order to endow molecules with function there were two mainstream lines of thought. One was to rationally design the positioning of chemical functionalities within candidate molecules, followed by an iterative synthesis-optimization process. The second was the use of a "brutal force" approach of combinatorial chemistry coupled with advanced screening for function. Although both methods provided important results, "rational design" often resulted in time-consuming efforts of modeling and synthesis only to find that the candidate molecule was not performing the designed job. "Combinatorial chemistry" suffered from a fundamental limitation related to the focusing of the libraries employed, often using lead compounds that limit its scope. Dynamic constitutional chemistry has developed as a combination of the two approaches above. Through the rational use of reversible chemical bonds together with a large plethora of precursor libraries, one is now able to build functional structures, ranging from quite simple molecules up to large polymeric structures. Thus, by introduction of the dynamic component within the molecular recognition processes, a new perspective of deciphering the world of the molecular events has aroused together with a new field of chemistry. Since its birth dynamic constitutional chemistry has continuously gained attention, in particular due to its ability to easily create from scratch outstanding molecular structures as well as the addition of adaptive features. The fundamental concepts defining the dynamic constitutional chemistry have been continuously extended to currently place it at the intersection between the supramolecular chemistry and newly defined adaptive chemistry, a pivotal feature towards evolutive chemistry. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Combinatorial and automated synthesis of phosphodiester galactosyl cluster on solid support by click chemistry assisted by microwaves.

    PubMed

    Pourceau, Gwladys; Meyer, Albert; Vasseur, Jean-Jacques; Morvan, François

    2008-08-01

    Small libraries of di-, tri-, and tetragalactosyl clusters were efficiently synthesized using combinatorial methodology, on solid support, by click chemistry assisted by microwaves, starting from different poly alkyne DNA-based scaffolds and two galactosyl azide derivatives. The scaffold was synthesized by standard DNA solid-supported phosphoramidite chemistry using a novel alkyne phosphoramidite and an alkyne solid support. The proportion of each glycocluster in a library was modulated using different molar ratios of both galactose azides.

  16. Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry

    PubMed Central

    Bhat, Venugopal T.; Caniard, Anne M.; Luksch, Torsten; Brenk, Ruth; Campopiano, Dominic J.; Greaney, Michael F.

    2010-01-01

    Dynamic covalent chemistry uses reversible chemical reactions to set up an equilibrating network of molecules at thermodynamic equilibrium, which can adjust its composition in response to any agent capable of altering the free energy of the system. When the target is a biological macromolecule, such as a protein, the process corresponds to the protein directing the synthesis of its own best ligand. Here, we demonstrate that reversible acylhydrazone formation is an effective chemistry for biological dynamic combinatorial library formation. In the presence of aniline as a nucleophilic catalyst, dynamic combinatorial libraries equilibrate rapidly at pH 6.2, are fully reversible, and may be switched on or off by means of a change in pH. We have interfaced these hydrazone dynamic combinatorial libraries with two isozymes from the glutathione S-transferase class of enzyme, and observed divergent amplification effects, where each protein selects the best-fitting hydrazone for the hydrophobic region of its active site. PMID:20489719

  17. Salt-induced adaptation of a dynamic combinatorial library of pseudopeptidic macrocycles: unraveling the electrostatic effects in mixed aqueous media.

    PubMed

    Atcher, Joan; Moure, Alejandra; Bujons, Jordi; Alfonso, Ignacio

    2015-04-27

    Dynamic combinatorial libraries are powerful systems for studying adaptive behaviors and relationships, as models of more complex molecular networks. With this aim, we set up a chemically diverse dynamic library of pseudopeptidic macrocycles containing amino-acid side chains with differently charged residues (negative, positive, and neutral). The responsive ability of this complex library upon the increase of the ionic strength has been thoroughly studied. The families of the macrocyclic members concentrating charges of the same sign showed a large increase in its proportion as the ionic strength increases, whereas those with residues of opposite charges showed the reverse behavior. This observation suggested an electrostatic shielding effect of the salt within the library of macrocycles. The top-down deconvolution of the library allowed us to obtain the fundamental thermodynamic information connecting the library members (exchange equilibrium constants), as well as to parameterize the adaptation to the external stimulus. We also visualized the physicochemical driving forces for the process by structural analysis using NMR spectroscopy and molecular modeling. This knowledge permitted the full understanding of the whole dynamic library and also the de novo design of dynamic chemical systems with tailored co-adaptive relationships, containing competing or cooperating species. This study highlights the utility of dynamic combinatorial libraries in the emerging field of systems chemistry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Modulating weak interactions for molecular recognition: a dynamic combinatorial analysis for assessing the contribution of electrostatics to the stability of CH-π bonds in water.

    PubMed

    Jiménez-Moreno, Ester; Gómez, Ana M; Bastida, Agatha; Corzana, Francisco; Jiménez-Oses, Gonzalo; Jiménez-Barbero, Jesús; Asensio, Juan Luis

    2015-03-27

    Electrostatic and charge-transfer contributions to CH-π complexes can be modulated by attaching electron-withdrawing substituents to the carbon atom. While clearly stabilizing in the gas phase, the outcome of this chemical modification in water is more difficult to predict. Herein we provide a definitive and quantitative answer to this question employing a simple strategy based on dynamic combinatorial chemistry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Fuzzy electron density fragments in macromolecular quantum chemistry, combinatorial quantum chemistry, functional group analysis, and shape-activity relations.

    PubMed

    Mezey, Paul G

    2014-09-16

    example, in medicinal drug design, and (g) tools for combinatorial quantum chemistry approaches using fuzzy fragment databanks and rapid construction of a large number of approximate electron densities for large sets of related molecules, relevant in theoretical molecular and nanostructure design.

  20. A combinatorial chemistry method for fast screening of perovskite-based NO oxidation catalyst.

    PubMed

    Yoon, Dal Young; Lim, Eunho; Kim, Young Jin; Cho, Byong K; Nam, In-Sik; Choung, Jin Woo; Yoo, Seungbeom

    2014-11-10

    A fast parallel screening method based on combinatorial chemistry (combichem) has been developed and applied in the screening tests of perovskite-based oxide (PBO) catalysts for NO oxidation to hit a promising PBO formulation for the oxidation of NO to NO2. This new method involves three consecutive steps: oxidation of NO to NO2 over a PBO catalyst, adsorption of NOx onto the PBO and K2O/Al2O3, and colorimetric assay of the NOx adsorbed thereon. The combichem experimental data have been used for determining the oxidation activity of NO over PBO catalysts as well as three critical parameters, such as the adsorption efficiency of K2O/Al2O3 for NO2 (α) and NO (β), and the time-average fraction of NO included in the NOx feed stream (ξ). The results demonstrated that the amounts of NO2 produced over PBO catalysts by the combichem method under transient conditions correlate well with those from a conventional packed-bed reactor under steady-state conditions. Among the PBO formulations examined, La0.5Ag0.5MnO3 has been identified as the best chemical formulation for oxidation of NO to NO2 by the present combichem method and also confirmed by the conventional packed-bed reactor tests. The superior efficiency of the combichem method for high-throughput catalyst screening test validated in this study is particularly suitable for saving the time and resources required in developing a new formulation of PBO catalyst whose chemical composition may have an enormous number of possible variations.

  1. Heuristic Implementation of Dynamic Programming for Matrix Permutation Problems in Combinatorial Data Analysis

    ERIC Educational Resources Information Center

    Brusco, Michael J.; Kohn, Hans-Friedrich; Stahl, Stephanie

    2008-01-01

    Dynamic programming methods for matrix permutation problems in combinatorial data analysis can produce globally-optimal solutions for matrices up to size 30x30, but are computationally infeasible for larger matrices because of enormous computer memory requirements. Branch-and-bound methods also guarantee globally-optimal solutions, but computation…

  2. Heuristic Implementation of Dynamic Programming for Matrix Permutation Problems in Combinatorial Data Analysis

    ERIC Educational Resources Information Center

    Brusco, Michael J.; Kohn, Hans-Friedrich; Stahl, Stephanie

    2008-01-01

    Dynamic programming methods for matrix permutation problems in combinatorial data analysis can produce globally-optimal solutions for matrices up to size 30x30, but are computationally infeasible for larger matrices because of enormous computer memory requirements. Branch-and-bound methods also guarantee globally-optimal solutions, but computation…

  3. Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting

    DTIC Science & Technology

    2006-08-01

    inhibitor against an enzyme found in bacteria .26 Scheme 2-3. Retrosynthethic analysis of 2-6...potential HIV protease inhibitors by grafting pharmacophoric groups on a azasugar scaffold (Figure 1-4),46 but a rather lengthy synthetic scheme starting...macrocyclic lactams is shown in Scheme 2- 2, in which Pei et al. discovered that 15-17 membered rings provided the best inhibitor properties against an

  4. Estimating equilibrium constants for aggregation from the product distribution of a dynamic combinatorial library.

    PubMed

    Hunt, Rosemary A R; Ludlow, R Frederick; Otto, Sijbren

    2009-11-19

    Multicomponent chemical systems that exhibit a network of covalent and intermolecular interactions may produce interesting and often unexpected chemical or physical behavior. The formation of aggregates is a well-recognized example and presents a particular analytical challenge. We now report the development of a numerical fitting method capable of estimating equilibrium constants for the formation of aggregates from the product distribution of a dynamic combinatorial library containing self-recognizing library members.

  5. The identification and characterization of hydrazinyl urea-based antibacterial agents through combinatorial chemistry.

    PubMed

    Wilson, L J; Morris, T W; Wu, Q; Renick, P J; Parker, C N; Davis, M C; McKeever, H D; Hershberger, P M; Switzer, A G; Shrum, G; Sunder, S; Jones, D R; Soper, S S; Dobson, R L; Burt, T; Morand, K L; Stella, M

    2001-05-07

    An effort to identify novel inhibitors of peptidoglycan synthesis with antibacterial activity resulted in the discovery of a series of biaryl urea-based antibacterial agents through isolation of a by-product from a mixture-based combinatorial library of semi-carbazones and subsequent parallel synthesis efforts. The compounds were shown to possess broad spectrum antibacterial activity against gram-positive drug resistant pathogens, and showed apparent specificity for disruption of the bacterial cell wall biosynthesis pathway.

  6. Dynamic Hierarchical Energy-Efficient Method Based on Combinatorial Optimization for Wireless Sensor Networks.

    PubMed

    Chang, Yuchao; Tang, Hongying; Cheng, Yongbo; Zhao, Qin; Yuan, Baoqing Li andXiaobing

    2017-07-19

    Routing protocols based on topology control are significantly important for improving network longevity in wireless sensor networks (WSNs). Traditionally, some WSN routing protocols distribute uneven network traffic load to sensor nodes, which is not optimal for improving network longevity. Differently to conventional WSN routing protocols, we propose a dynamic hierarchical protocol based on combinatorial optimization (DHCO) to balance energy consumption of sensor nodes and to improve WSN longevity. For each sensor node, the DHCO algorithm obtains the optimal route by establishing a feasible routing set instead of selecting the cluster head or the next hop node. The process of obtaining the optimal route can be formulated as a combinatorial optimization problem. Specifically, the DHCO algorithm is carried out by the following procedures. It employs a hierarchy-based connection mechanism to construct a hierarchical network structure in which each sensor node is assigned to a special hierarchical subset; it utilizes the combinatorial optimization theory to establish the feasible routing set for each sensor node, and takes advantage of the maximum-minimum criterion to obtain their optimal routes to the base station. Various results of simulation experiments show effectiveness and superiority of the DHCO algorithm in comparison with state-of-the-art WSN routing algorithms, including low-energy adaptive clustering hierarchy (LEACH), hybrid energy-efficient distributed clustering (HEED), genetic protocol-based self-organizing network clustering (GASONeC), and double cost function-based routing (DCFR) algorithms.

  7. Dynamic Hierarchical Energy-Efficient Method Based on Combinatorial Optimization for Wireless Sensor Networks

    PubMed Central

    Tang, Hongying; Cheng, Yongbo; Zhao, Qin; Li, Baoqing; Yuan, Xiaobing

    2017-01-01

    Routing protocols based on topology control are significantly important for improving network longevity in wireless sensor networks (WSNs). Traditionally, some WSN routing protocols distribute uneven network traffic load to sensor nodes, which is not optimal for improving network longevity. Differently to conventional WSN routing protocols, we propose a dynamic hierarchical protocol based on combinatorial optimization (DHCO) to balance energy consumption of sensor nodes and to improve WSN longevity. For each sensor node, the DHCO algorithm obtains the optimal route by establishing a feasible routing set instead of selecting the cluster head or the next hop node. The process of obtaining the optimal route can be formulated as a combinatorial optimization problem. Specifically, the DHCO algorithm is carried out by the following procedures. It employs a hierarchy-based connection mechanism to construct a hierarchical network structure in which each sensor node is assigned to a special hierarchical subset; it utilizes the combinatorial optimization theory to establish the feasible routing set for each sensor node, and takes advantage of the maximum–minimum criterion to obtain their optimal routes to the base station. Various results of simulation experiments show effectiveness and superiority of the DHCO algorithm in comparison with state-of-the-art WSN routing algorithms, including low-energy adaptive clustering hierarchy (LEACH), hybrid energy-efficient distributed clustering (HEED), genetic protocol-based self-organizing network clustering (GASONeC), and double cost function-based routing (DCFR) algorithms. PMID:28753962

  8. Combinatorial optimization using dynamical phase transitions in driven-dissipative systems.

    PubMed

    Leleu, Timothée; Yamamoto, Yoshihisa; Utsunomiya, Shoko; Aihara, Kazuyuki

    2017-02-01

    The dynamics of driven-dissipative systems is shown to be well-fitted for achieving efficient combinatorial optimization. The proposed method can be applied to solve any combinatorial optimization problem that is equivalent to minimizing an Ising Hamiltonian. Moreover, the dynamics considered can be implemented using various physical systems as it is based on generic dynamics-the normal form of the supercritical pitchfork bifurcation. The computational principle of the proposed method relies on an hybrid analog-digital representation of the binary Ising spins by considering the gradient descent of a Lyapunov function that is the sum of an analog Ising Hamiltonian and archetypal single or double-well potentials. By gradually changing the shape of the latter potentials from a single to double well shape, it can be shown that the first nonzero steady states to become stable are associated with global minima of the Ising Hamiltonian, under the approximation that all analog spins have the same amplitude. In the more general case, the heterogeneity in amplitude between analog spins induces the stabilization of local minima, which reduces the quality of solutions to combinatorial optimization problems. However, we show that the heterogeneity in amplitude can be reduced by setting the parameters of the driving signal near a regime, called the dynamic phase transition, where the analog spins' DC components map more accurately the global minima of the Ising Hamiltonian which, in turn, increases the quality of solutions found. Last, we discuss the possibility of a physical implementation of the proposed method using networks of degenerate optical parametric oscillators.

  9. Combinatorial optimization using dynamical phase transitions in driven-dissipative systems

    NASA Astrophysics Data System (ADS)

    Leleu, Timothée; Yamamoto, Yoshihisa; Utsunomiya, Shoko; Aihara, Kazuyuki

    2017-02-01

    The dynamics of driven-dissipative systems is shown to be well-fitted for achieving efficient combinatorial optimization. The proposed method can be applied to solve any combinatorial optimization problem that is equivalent to minimizing an Ising Hamiltonian. Moreover, the dynamics considered can be implemented using various physical systems as it is based on generic dynamics—the normal form of the supercritical pitchfork bifurcation. The computational principle of the proposed method relies on an hybrid analog-digital representation of the binary Ising spins by considering the gradient descent of a Lyapunov function that is the sum of an analog Ising Hamiltonian and archetypal single or double-well potentials. By gradually changing the shape of the latter potentials from a single to double well shape, it can be shown that the first nonzero steady states to become stable are associated with global minima of the Ising Hamiltonian, under the approximation that all analog spins have the same amplitude. In the more general case, the heterogeneity in amplitude between analog spins induces the stabilization of local minima, which reduces the quality of solutions to combinatorial optimization problems. However, we show that the heterogeneity in amplitude can be reduced by setting the parameters of the driving signal near a regime, called the dynamic phase transition, where the analog spins' DC components map more accurately the global minima of the Ising Hamiltonian which, in turn, increases the quality of solutions found. Last, we discuss the possibility of a physical implementation of the proposed method using networks of degenerate optical parametric oscillators.

  10. Synthesis of new water-soluble metal-binding polymers: Combinatorial chemistry approach. 1997 mid-year progress report

    SciTech Connect

    Smith, B.F.

    1997-06-01

    'The first objective of this research is to develop rapid discovery and optimization approaches to new water-soluble chelating polymers. A byproduct of the development approach will be the new, selective, and efficient metal-binding agents. The second objective is to evaluate the concept of using water and organic soluble polymers as new solid supports for combinatorial synthesis. The technology under development, Polymer Filtration (PF), is a technique to selectively remove or recover hazardous and valuable metal ions and radionuclides from various dilute aqueous streams. Not only can this technology be used to remediate contaminated soils and solid surfaces and treat aqueous wastes, it can also be incorporated into facilities as a pollution prevention and waste minimization technology. Polymer Filtration uses water-soluble metal-binding polymers to sequester metal ions in dilute solution. The water-soluble polymers have a sufficiently large molecular size that they can be separated and concentrated using commercial ultrafiltration technology. Water, small organic molecules, and unbound metals pass freely through the ultrafiltration membrane while concentrating the metal-binding polymer. The polymers can then be reused by changing the solution conditions to release the metal ions. The metal-ions are recovered in concentrated form for recycle or disposal using a diafiltration process. The water-soluble polymer can be recycled for further aqueous-stream processing. To advance Polymer Filtration technology to the selectivity levels required for DOE needs. fixture directions in Polymer Filtration must include rapid development, testing, and characterization of new metal-binding polymers. The development of new chelating molecules can be equated to the process of new drugs or new materials discovery. Thus, the authors want to build upon and adapt the combinatorial chemistry approaches developed for rapid molecule generation for the drug industry to the rapid

  11. Chemistry in dynamically evolving clouds

    NASA Technical Reports Server (NTRS)

    Tarafdar, S. P.; Prasad, S. S.; Huntress, W. T., Jr.; Villere, K. R.; Black, D. C.

    1985-01-01

    A unified model of chemical and dynamical evolution of isolated, initially diffuse and quiescent interstellar clouds is presented. The model uses a semiempirically derived dependence of the observed cloud temperatures on the visual extinction and density. Even low-mass, low-density, diffuse clouds can collapse in this model, because the inward pressure gradient force assists gravitational contraction. In contrast, previous isothermal collapse models required the low-mass diffuse clouds to be unrealistically cold before gravitational contraction could start. Theoretically predicted dependences of the column densities of various atoms and molecules, such as C and CO, on visual extinction in diffuse clouds are in accord with observations. Similarly, the predicted dependences of the fractional abundances of various chemical species (e.g., CO, H2CO, HCN, HCO(+)) on the total hydrogen density in the core of the dense clouds also agree with observations reported to date in the literature. Compared with previous models of interstellar chemistry, the present model has the potential to explain the wide spectrum of chemical and physical properties of both diffuse and dense clouds with a common formalism employing only a few simple initial conditions.

  12. Chemistry in dynamically evolving clouds

    NASA Technical Reports Server (NTRS)

    Tarafdar, S. P.; Prasad, S. S.; Huntress, W. T., Jr.; Villere, K. R.; Black, D. C.

    1985-01-01

    A unified model of chemical and dynamical evolution of isolated, initially diffuse and quiescent interstellar clouds is presented. The model uses a semiempirically derived dependence of the observed cloud temperatures on the visual extinction and density. Even low-mass, low-density, diffuse clouds can collapse in this model, because the inward pressure gradient force assists gravitational contraction. In contrast, previous isothermal collapse models required the low-mass diffuse clouds to be unrealistically cold before gravitational contraction could start. Theoretically predicted dependences of the column densities of various atoms and molecules, such as C and CO, on visual extinction in diffuse clouds are in accord with observations. Similarly, the predicted dependences of the fractional abundances of various chemical species (e.g., CO, H2CO, HCN, HCO(+)) on the total hydrogen density in the core of the dense clouds also agree with observations reported to date in the literature. Compared with previous models of interstellar chemistry, the present model has the potential to explain the wide spectrum of chemical and physical properties of both diffuse and dense clouds with a common formalism employing only a few simple initial conditions.

  13. A hybrid approach using chaotic dynamics and global search algorithms for combinatorial optimization problems

    NASA Astrophysics Data System (ADS)

    Igeta, Hideki; Hasegawa, Mikio

    Chaotic dynamics have been effectively applied to improve various heuristic algorithms for combinatorial optimization problems in many studies. Currently, the most used chaotic optimization scheme is to drive heuristic solution search algorithms applicable to large-scale problems by chaotic neurodynamics including the tabu effect of the tabu search. Alternatively, meta-heuristic algorithms are used for combinatorial optimization by combining a neighboring solution search algorithm, such as tabu, gradient, or other search method, with a global search algorithm, such as genetic algorithms (GA), ant colony optimization (ACO), or others. In these hybrid approaches, the ACO has effectively optimized the solution of many benchmark problems in the quadratic assignment problem library. In this paper, we propose a novel hybrid method that combines the effective chaotic search algorithm that has better performance than the tabu search and global search algorithms such as ACO and GA. Our results show that the proposed chaotic hybrid algorithm has better performance than the conventional chaotic search and conventional hybrid algorithms. In addition, we show that chaotic search algorithm combined with ACO has better performance than when combined with GA.

  14. Characterization of small combinatorial chemistry libraries by (1)H NMR. Quantitation with a convenient and novel internal standard.

    PubMed

    Pinciroli, V; Biancardi, R; Colombo, N; Colombo, M; Rizzo, V

    2001-01-01

    A novel silane standard, 1,4-bis(trimethylsilyl)benzene (BTMSB), is introduced for the generic quantitation of small organic molecules in DMSO-d(6) solution by (1)H NMR. This standard is an easily weighable solid and is stable for at least 1 month in DMSO solution, and its (1)H NMR spectrum contains a strong singlet in a region usually free of signals. With a set of certified standards, concentration determination with about 2% precision and accuracy is verified after solution preparation with fully automated procedures, thus making very effective the characterization of small combinatorial chemistry libraries for identity and purity when combined with other physicochemical or biochemical tests. As an example, for a set of about 400 compounds, results of (1)H NMR characterization are compared to the more customary LC-UV-MS method. NMR and MS data agree for identity on the vast majority of cases (84% positive and 5% negative), whereas the remaining cases (11%) are marked as highly impure only after NMR spectra analysis. Most importantly, determination of concentration rather than that of relative purity appears the right choice for a correct evaluation of biochemical potency.

  15. A noisy self-organizing neural network with bifurcation dynamics for combinatorial optimization.

    PubMed

    Kwok, Terence; Smith, Kate A

    2004-01-01

    The self-organizing neural network (SONN) for solving general "0-1" combinatorial optimization problems (COPs) is studied in this paper, with the aim of overcoming existing limitations in convergence and solution quality. This is achieved by incorporating two main features: an efficient weight normalization process exhibiting bifurcation dynamics, and neurons with additive noise. The SONN is studied both theoretically and experimentally by using the N-queen problem as an example to demonstrate and explain the dependence of optimization performance on annealing schedules and other system parameters. An equilibrium model of the SONN with neuronal weight normalization is derived, which explains observed bands of high feasibility in the normalization parameter space in terms of bifurcation dynamics of the normalization process, and provides insights into the roles of different parameters in the optimization process. Under certain conditions, this dynamical systems view of the SONN reveals cascades of period-doubling bifurcations to chaos occurring in multidimensional space with the annealing temperature as the bifurcation parameter. A strange attractor in the two-dimensional (2-D) case is also presented. Furthermore, by adding random noise to the cost potentials of the network nodes, it is demonstrated that unwanted oscillations between symmetrical and "greedy" nodes can be sufficiently reduced, resulting in higher solution quality and feasibility.

  16. Combinatorial Spacetimes

    NASA Astrophysics Data System (ADS)

    Hillman, David

    1995-11-01

    Combinatorial spacetimes are a class of dynamical systems in which finite pieces of spacetime contain finite amounts of information. Most of the guiding principles for designing these systems are drawn from general relativity: the systems are deterministic; spacetime may be foliated into Cauchy surfaces; the law of evolution is local (there is a light-cone structure); and the geometry evolves locally (curvature may be present; big bangs are possible). However, the systems differ from general relativity in that spacetime is a combinatorial object, constructed by piecing together copies of finitely many types of allowed neighborhoods in a prescribed manner. Hence at least initially there is no metric, no concept of continuity or diffeomorphism. The role of diffeomorphism, however, is played by something called a "local equivalence map.". Here I attempt to begin to lay the mathematical foundations for the study of these systems. (Examples of such systems already exist in the literature. The most obvious is reversible cellular automata, which are flat combinatorial spacetimes. Other related systems are structurally dynamic cellular automata, L systems and parallel graph grammars.) In the 1+1-dimensional oriented case, sets of spaces may be described equivalently by matrices of nonnegative integers, directed graphs, or symmetric tensors; local equivalences between space sets are generated by simple matrix transformations. These equivalence maps turn out to be closely related to the flow equivalence maps between subshifts of finite type studied in symbolic dynamics. Also, the symmetric tensor algebra generated by equivalence transformations turns out to be isomorphic to the abstract tensor algebra generated by commutative cocommutative bialgebras. In higher dimensions I attempt to follow the same basic model, which is to define the class of n-dimensional space set descriptions and then generate local equivalences between these descriptions using elementary

  17. Dynamic Mechanical and Nanofibrous Topological Combinatory Cues Designed for Periodontal Ligament Engineering

    PubMed Central

    Kim, Joong-Hyun; Kang, Min Sil; Eltohamy, Mohamed; Kim, Tae-Hyun; Kim, Hae-Won

    2016-01-01

    Complete reconstruction of damaged periodontal pockets, particularly regeneration of periodontal ligament (PDL) has been a significant challenge in dentistry. Tissue engineering approach utilizing PDL stem cells and scaffolding matrices offers great opportunity to this, and applying physical and mechanical cues mimicking native tissue conditions are of special importance. Here we approach to regenerate periodontal tissues by engineering PDL cells supported on a nanofibrous scaffold under a mechanical-stressed condition. PDL stem cells isolated from rats were seeded on an electrospun polycaprolactone/gelatin directionally-oriented nanofiber membrane and dynamic mechanical stress was applied to the cell/nanofiber construct, providing nanotopological and mechanical combined cues. Cells recognized the nanofiber orientation, aligning in parallel, and the mechanical stress increased the cell alignment. Importantly, the cells cultured on the oriented nanofiber combined with the mechanical stress produced significantly stimulated PDL specific markers, including periostin and tenascin with simultaneous down-regulation of osteogenesis, demonstrating the roles of topological and mechanical cues in altering phenotypic change in PDL cells. Tissue compatibility of the tissue-engineered constructs was confirmed in rat subcutaneous sites. Furthermore, in vivo regeneration of PDL and alveolar bone tissues was examined under the rat premaxillary periodontal defect models. The cell/nanofiber constructs engineered under mechanical stress showed sound integration into tissue defects and the regenerated bone volume and area were significantly improved. This study provides an effective tissue engineering approach for periodontal regeneration—culturing PDL stem cells with combinatory cues of oriented nanotopology and dynamic mechanical stretch. PMID:26989897

  18. Dynamic Mechanical and Nanofibrous Topological Combinatory Cues Designed for Periodontal Ligament Engineering.

    PubMed

    Kim, Joong-Hyun; Kang, Min Sil; Eltohamy, Mohamed; Kim, Tae-Hyun; Kim, Hae-Won

    2016-01-01

    Complete reconstruction of damaged periodontal pockets, particularly regeneration of periodontal ligament (PDL) has been a significant challenge in dentistry. Tissue engineering approach utilizing PDL stem cells and scaffolding matrices offers great opportunity to this, and applying physical and mechanical cues mimicking native tissue conditions are of special importance. Here we approach to regenerate periodontal tissues by engineering PDL cells supported on a nanofibrous scaffold under a mechanical-stressed condition. PDL stem cells isolated from rats were seeded on an electrospun polycaprolactone/gelatin directionally-oriented nanofiber membrane and dynamic mechanical stress was applied to the cell/nanofiber construct, providing nanotopological and mechanical combined cues. Cells recognized the nanofiber orientation, aligning in parallel, and the mechanical stress increased the cell alignment. Importantly, the cells cultured on the oriented nanofiber combined with the mechanical stress produced significantly stimulated PDL specific markers, including periostin and tenascin with simultaneous down-regulation of osteogenesis, demonstrating the roles of topological and mechanical cues in altering phenotypic change in PDL cells. Tissue compatibility of the tissue-engineered constructs was confirmed in rat subcutaneous sites. Furthermore, in vivo regeneration of PDL and alveolar bone tissues was examined under the rat premaxillary periodontal defect models. The cell/nanofiber constructs engineered under mechanical stress showed sound integration into tissue defects and the regenerated bone volume and area were significantly improved. This study provides an effective tissue engineering approach for periodontal regeneration-culturing PDL stem cells with combinatory cues of oriented nanotopology and dynamic mechanical stretch.

  19. Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models.

    PubMed

    Pencovich, Niv; Jaschek, Ram; Tanay, Amos; Groner, Yoram

    2011-01-06

    Specific interactions of transcription factors (TFs) with their targets are crucial for specifying gene expression programs during cell differentiation. How specificity is maintained despite limited selectivity of individual TF-DNA interactions is not fully understood. RUNX1 TF is among the most frequently mutated genes in human leukemia and an important regulator of megakaryopoiesis. We used megakaryocytic cell lines to characterize the network of RUNX1 targets and cooperating TFs in differentiating megakaryocytes and demonstrated how dynamic partnerships between RUNX1 and cooperating TFs facilitated regulatory plasticity and specificity during this process. After differentiation onset, RUNX1 directly activated a large number of genes through interaction with preexisting and de novo binding sites. Recruitment of RUNX1 to de novo occupied sites occurred at H3K4me1-marked preprogrammed enhancers. A significant number of these de novo bound sites lacked RUNX motif but were occupied by AP-1 TFs. Reciprocally, AP-1 TFs were up-regulated by RUNX1 after 12-O-tetradecanoylphorbol-13-acetate induction and recruited to RUNX1-occupied sites lacking AP-1 motifs. At other differentiation stages, additional combinatorial interactions occurred between RUNX1 and its coregulators, GATA1 and ETS. The findings suggest that in differentiating megakaryocytic cell lines, RUNX1 cooperates with GATA1, AP-1, and ETS to orchestrate cell-specific transcription programs through dynamic TF partnerships.

  20. Combinatorial synthesis in micro reactors.

    PubMed

    Watts, P; Haswell, S J

    2004-08-01

    This article reviews the current and future applications of micro reactors in the field of combinatorial chemistry and drug discovery. Liquid phase reactions have been used to illustrate the advantages of performing chemical reactions in micro reactors which illustrate that reactions can be performed very rapidly in high yield to enable the preparation of combinatorial libraries of structurally related compounds.

  1. Photodissociation dynamics and atmospheric chemistry

    NASA Astrophysics Data System (ADS)

    Wayne, R. P.

    1993-07-01

    The paper uses data from the literature to explore photodissociation dynamics of molecules possessing three, four, and five atoms, as represented by O3 and CO2, NH3 and C2H2, and CH4, respectively. The results yield many details, even in regard to the disposal of energy into rotation, which have applications to atmospheric problems. For instance, experiments probing the translational energies of the O and the vibrational and rotational distributions in the CO suggest that a spin-forbidden channel operates as it does in ozone photolysis. The data for both O3 and CO2 suggest a relationship between the structure of the parent molecule and the dynamics of dissociation.

  2. A dynamic multiarmed bandit-gene expression programming hyper-heuristic for combinatorial optimization problems.

    PubMed

    Sabar, Nasser R; Ayob, Masri; Kendall, Graham; Qu, Rong

    2015-02-01

    Hyper-heuristics are search methodologies that aim to provide high-quality solutions across a wide variety of problem domains, rather than developing tailor-made methodologies for each problem instance/domain. A traditional hyper-heuristic framework has two levels, namely, the high level strategy (heuristic selection mechanism and the acceptance criterion) and low level heuristics (a set of problem specific heuristics). Due to the different landscape structures of different problem instances, the high level strategy plays an important role in the design of a hyper-heuristic framework. In this paper, we propose a new high level strategy for a hyper-heuristic framework. The proposed high-level strategy utilizes a dynamic multiarmed bandit-extreme value-based reward as an online heuristic selection mechanism to select the appropriate heuristic to be applied at each iteration. In addition, we propose a gene expression programming framework to automatically generate the acceptance criterion for each problem instance, instead of using human-designed criteria. Two well-known, and very different, combinatorial optimization problems, one static (exam timetabling) and one dynamic (dynamic vehicle routing) are used to demonstrate the generality of the proposed framework. Compared with state-of-the-art hyper-heuristics and other bespoke methods, empirical results demonstrate that the proposed framework is able to generalize well across both domains. We obtain competitive, if not better results, when compared to the best known results obtained from other methods that have been presented in the scientific literature. We also compare our approach against the recently released hyper-heuristic competition test suite. We again demonstrate the generality of our approach when we compare against other methods that have utilized the same six benchmark datasets from this test suite.

  3. Overview on the current status on virtual high-throughput screening and combinatorial chemistry approaches in multi-target anticancer drug discovery; Part II.

    PubMed

    Geromichalos, George D; Alifieris, Constantinos E; Geromichalou, Elena G; Trafalis, Dimitrios T

    2016-01-01

    Conventional drug design embraces the "one gene, one drug, one disease" philosophy. Nowadays, new generation of anticancer drugs, able to inhibit more than one pathway, is believed to play a major role in contemporary anticancer drug research. In this way, polypharmacology, focusing on multi-target drugs, has emerged as a new paradigm in drug discovery. A number of recent successful drugs have in part or in whole emerged from a structure-based research approach. Many advances including crystallography and informatics are behind these successes. In this part II we will review the role and methodology of ligand-, structure- and fragment-based computer-aided drug design computer aided drug desing (CADD), virtual high throughput screening (vHTS), de novo drug design, fragment-based design and structure-based molecular docking, homology modeling, combinatorial chemistry and library design, pharmacophore model chemistry and informatics in modern drug discovery.

  4. Combinatorial Solid-Phase Synthesis of Aromatic Oligoamides: A Research-Based Laboratory Module for Undergraduate Organic Chemistry

    ERIC Educational Resources Information Center

    Fuller, Amelia A.

    2016-01-01

    A five-week, research-based experiment suitable for second-semester introductory organic laboratory students is described. Each student designs, prepares, and analyzes a combinatorial array of six aromatic oligoamides. Molecules are prepared on solid phase via a six-step synthetic sequence, and purities and identities are determined by analysis of…

  5. Combinatorial Solid-Phase Synthesis of Aromatic Oligoamides: A Research-Based Laboratory Module for Undergraduate Organic Chemistry

    ERIC Educational Resources Information Center

    Fuller, Amelia A.

    2016-01-01

    A five-week, research-based experiment suitable for second-semester introductory organic laboratory students is described. Each student designs, prepares, and analyzes a combinatorial array of six aromatic oligoamides. Molecules are prepared on solid phase via a six-step synthetic sequence, and purities and identities are determined by analysis of…

  6. Dynamic adaptive chemistry for turbulent flame simulations

    NASA Astrophysics Data System (ADS)

    Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.

    2013-02-01

    The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.

  7. A review of mesospheric dynamics and chemistry

    SciTech Connect

    Viereck, R.A. )

    1991-01-01

    Advances made in understanding the chemistry and dynamics of the atmosphere in the approximate altitude range of 50 to 90 km are addressed. Attention is given to mesospheric structure and seasonal variations, gravity waves and gravity wave saturation, the effects of gravity waves on thermal, momentum and constituent fluxes, and the effect of gravity waves on airglow emissions. A review of research on tides and planetary waves and their effects on the mesosphere are presented as well as discussions on ozone hydroxyl, water vapor, and noctilucent cloud research. 217 refs.

  8. Dynamic expression of combinatorial replication-dependent histone variant genes during mouse spermatogenesis.

    PubMed

    Sun, Rongfang; Qi, Huayu

    2014-01-01

    Nucleosomes are basic chromatin structural units that are formed by DNA sequences wrapping around histones. Global chromatin states in different cell types are specified by combinatorial effects of post-translational modifications of histones and the expression of histone variants. During mouse spermatogenesis, spermatogonial stem cells (SSCs) self-renew while undergo differentiation, events that occur in the company of constant re-modeling of chromatin structures. Previous studies have shown that testes contain highly expressed or specific histone variants to facilitate these epigenetic modifications. However, mechanisms of regulating the epigenetic changes and the specific histone compositions of spermatogenic cells are not fully understood. Using real time quantitative RT-PCR, we examined the dynamic expression of replication-dependent histone genes in post-natal mouse testes. It was found that distinct sets of histone genes are expressed in various spermatogenic cells at different stages during spermatogenesis. While gonocyte-enriched testes from mice at 2-dpp (days post partum) express pre-dominantly thirteen histone variant genes, SSC-stage testes at 9-dpp highly express a different set of eight histone genes. During differentiation stage when testes are occupied mostly by spermatocytes and spermatids, another twenty-two histone genes are expressed much higher than the rest, including previously known testis-specific hist1h1t, hist1h2ba and hist1h4c. In addition, histone genes that are pre-dominantly expressed in gonocytes and SSCs are also highly expressed in embryonic stem cells. Several of them were changed when embryoid bodies were formed from ES cells, suggesting their roles in regulating pluripotency of the cells. Further more, differentially expressed histone genes are specifically localized in either SSCs or spermatocytes and spermatids, as demonstrated by in situ hybridization using gene specific probes. Taken together, results presented here

  9. Dynamic covalent chemistry of bisimines at the solid/liquid interface monitored by scanning tunnelling microscopy.

    PubMed

    Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo

    2014-11-01

    Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.

  10. Dynamic covalent chemistry of bisimines at the solid/liquid interface monitored by scanning tunnelling microscopy

    NASA Astrophysics Data System (ADS)

    Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo

    2014-11-01

    Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.

  11. Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.

    PubMed

    Luk, Hoi Ling; Feist, Johannes; Toppari, J Jussi; Groenhof, Gerrit

    2017-09-12

    When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model with which the effect of the light-matter coupling on the molecular dynamics can be predicted accurately. Here we present a multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons. Using this model we have performed simulations with up to 1600 Rhodamine molecules in a cavity. The results of these simulations reveal that the contributions of the molecules to the polariton are time-dependent due to thermal fluctuations that break symmetry. Furthermore, the simulations suggest that in addition to the cavity quality factor, also the Stokes shift and number of molecules control the lifetime of the polariton. Because large numbers of molecules interacting with confined light can now be simulated in atomic detail, we anticipate that our method will lead to a better understanding of the effects of strong coupling on chemical reactivity. Ultimately the method may even be used to systematically design cavities to control photochemistry.

  12. Development of the first potent and selective inhibitor of the zinc endopeptidase neurolysin using a systematic approach based on combinatorial chemistry of phosphinic peptides.

    PubMed

    Jirácek, J; Yiotakis, A; Vincent, B; Checler, F; Dive, V

    1996-08-09

    A new systematic approach, based on combinatorial chemistry of phosphinic peptides, is proposed for rapid development of highly potent and selective inhibitors of zinc metalloproteases. This strategy first evaluates the effects on the inhibitory potency and selectivity of the following parameters: 1) size of the phosphinic peptides, 2) position of the phosphinic bond in the sequence, and 3) the state (free or blocked) of the peptide extremities. After this selection step, the influence of the inhibitor sequence is analyzed in order to determine the identity of the residues that optimized both the potency and the selectivity. We demonstrate the efficiency of this novel approach in rapid identification of the first potent inhibitor of the mammalian zinc endopeptidase neurolysin(24-16), able to discriminate between this enzyme and the related zinc endopeptidase thimet oligopeptidase(24-15). The most potent and selective inhibitor developed in this study, Pro-LPhePsi(PO2CH2)Gly-Pro, displays a Ki value of 4 nM for 24-16 and is 2000 times less potent on 24-15. The specific recognition of such a free phosphinic tetrapeptide by 24-16, as well as the unique specificity of the 24-16 S2 and S2' subsites for proline, unveiled by this study, are discussed in terms of their possible significance for the function of this enzyme and its related zinc endopeptidase activities.

  13. Probing the dynamic reversibility and generation of dynamic combinatorial libraries in the presence of bacterial model oligopeptides as templating guests of tetra-carbohydrazide macrocycles using electrospray mass spectrometry.

    PubMed

    Nour, Hany F; Islam, Tuhidul; Fernández-Lahore, Marcelo; Kuhnert, Nikolai

    2012-12-30

    Over the past few decades, bacterial resistance to antibiotics has emerged as a real threat to human health. Accordingly, there is an urgent demand for the development of innovative strategies for discovering new antibiotics. We present the first use of tetra-carbohydrazide cyclophane macrocycles in dynamic combinatorial chemistry (DCC) and molecular recognition as chiral hosts binding oligopeptides, which mimic bacterial cell wall. This study introduces an innovative application of electrospray ionisation time-of-flight mass spectrometry (ESI-TOF MS) to oligopeptides recognition using DCC. A small dynamic library composed of eight functionalised macrocycles has been generated in solution and all members were characterised by ESI-TOF MS. We also probed the dynamic reversibility and mechanism of formation of tetra-carbohydrazide cyclophanes in real-time using ESI-TOF MS. Dynamic reversibility of tetra-carbohydrazide cyclophanes is favored under thermodynamic control. The mechanism of formation of tetra-carbohydrazide cyclophanes involves key dialdehyde intermediates, which have been detected and assigned according to their high-resolution m/z values. Three members of the dynamic library bind efficiently in the gas phase to a selection of oligopeptides, unique to bacteria, allowing observation of host/guest complex ions in the gas phase. We probed the mechanism of the [2+2]-cyclocondensation reaction forming library members, proved dynamic reversibility of tetra-carbohydrazide cyclophanes and showed that complex ions formed between library members and hosts can be observed in the gas phase, allowing the solution of an important problem of biological interest. Copyright © 2012 John Wiley & Sons, Ltd.

  14. Combinatorial Origami

    NASA Astrophysics Data System (ADS)

    Dieleman, Peter; Waitukaitis, Scott; van Hecke, Martin

    To design rigidly foldable quadrilateral meshes one generally needs to solve a complicated set of constraints. Here we present a systematic, combinatorial approach to create rigidly foldable quadrilateral meshes with a limited number of different vertices. The number of discrete, 1 degree-of-freedom folding branches for some of these meshes scales exponentially with the number of vertices on the edge, whilst other meshes generated this way only have two discrete folding branches, regardless of mesh size. We show how these two different behaviours both emerge from the two folding branches present in a single generic 4-vertex. Furthermore, we model generic 4-vertices as a spherical linkage and exploit a previously overlooked symmetry to create non-developable origami patterns using the same combinatorial framework.

  15. Chemogenomics: a discipline at the crossroad of high throughput technologies, biomarker research, combinatorial chemistry, genomics, cheminformatics, bioinformatics and artificial intelligence.

    PubMed

    Maréchal, Eric

    2008-09-01

    Chemogenomics is the study of the interaction of functional biological systems with exogenous small molecules, or in broader sense the study of the intersection of biological and chemical spaces. Chemogenomics requires expertises in biology, chemistry and computational sciences (bioinformatics, cheminformatics, large scale statistics and machine learning methods) but it is more than the simple apposition of each of these disciplines. Biological entities interacting with small molecules can be isolated proteins or more elaborate systems, from single cells to complete organisms. The biological space is therefore analyzed at various postgenomic levels (genomic, transcriptomic, proteomic or any phenotypic level). The space of small molecules is partially real, corresponding to commercial and academic collections of compounds, and partially virtual, corresponding to the chemical space possibly synthesizable. Synthetic chemistry has developed novel strategies allowing a physical exploration of this universe of possibilities. A major challenge of cheminformatics is to charter the virtual space of small molecules using realistic biological constraints (bioavailability, druggability, structural biological information). Chemogenomics is a descendent of conventional pharmaceutical approaches, since it involves the screening of chemolibraries for their effect on biological targets, and benefits from the advances in the corresponding enabling technologies and the introduction of new biological markers. Screening was originally motivated by the rigorous discovery of new drugs, neglecting and throwing away any molecule that would fail to meet the standards required for a therapeutic treatment. It is now the basis for the discovery of small molecules that might or might not be directly used as drugs, but which have an immense potential for basic research, as probes to explore an increasing number of biological phenomena. Concerns about the environmental impact of chemical industry

  16. Scent Transmutation: A New Way to Teach on Chemical Equilibrium, Distillation, and Dynamic Combinatorial Chemistry

    ERIC Educational Resources Information Center

    Ji, Qing; El-Hamdi, Nadia S.; Miljanic´, Ognjen S?.

    2014-01-01

    Esters are volatile and pleasantly smelling compounds, commonly used as food additives. Using Ti(OBu)[subscript 4]-catalyzed acyl exchange, we demonstrate a scent transmutation experiment, in which two fragrant esters swap their acyl and alkoxy substituents and are, during the course of a reactive distillation, quantitatively converted into two…

  17. Scent Transmutation: A New Way to Teach on Chemical Equilibrium, Distillation, and Dynamic Combinatorial Chemistry

    ERIC Educational Resources Information Center

    Ji, Qing; El-Hamdi, Nadia S.; Miljanic´, Ognjen S?.

    2014-01-01

    Esters are volatile and pleasantly smelling compounds, commonly used as food additives. Using Ti(OBu)[subscript 4]-catalyzed acyl exchange, we demonstrate a scent transmutation experiment, in which two fragrant esters swap their acyl and alkoxy substituents and are, during the course of a reactive distillation, quantitatively converted into two…

  18. Combinatorial chemistry: libraries from libraries, the art of the diversity-oriented transformation of resin-bound peptides and chiral polyamides to low molecular weight acyclic and heterocyclic compounds.

    PubMed

    Nefzi, Adel; Ostresh, John M; Yu, Yongping; Yu, Jongping; Houghten, Richard A

    2004-05-28

    Combinatorial chemistry has deeply impacted the drug discovery process by accelerating the synthesis and screening of large numbers of compounds having therapeutic and/or diagnostic potential. These techniques offer unique enhancement in the potential identification of new and/or therapeutic candidates. Our efforts over the past 10 years in the design and diversity-oriented synthesis of low molecular weight acyclic and heterocyclic combinatorial libraries derived from amino acids, peptides, and/or peptidomimetics are described. Employing a "toolbox" of various chemical transformations, including alkylation, oxidation, reduction, acylation, and the use of a variety of multifunctional reagents, the "libraries from libraries" concept has enabled the continued development of an ever-expanding, structurally varied series of organic chemical libraries.

  19. Dynamics and Chemistry of Planet Construction

    NASA Astrophysics Data System (ADS)

    Taylor, G. J.

    2010-03-01

    Sophisticated calculations of how planetesimals assembled into the terrestrial planets can be tested by using models of the chemistry of the solar nebula. Jade Bond (previously at University of Arizona and now at the Planetary Science Institute, Tucson, AZ), Dante Lauretta (University of Arizona) and Dave O'Brien (Planetary Sciences Institute) combined planetary accretion simulations done by O'Brien, Alessandro Morbidelli (Observatoire de Nice, France), and Hal Levison (Southwest Research Institute, Boulder) with calculations of the solar nebula chemistry as a function of time and distance from the Sun to determine the overall chemical composition of the planets formed in the simulations. They then compared the simulated planets with the compositions of Earth and Mars. The simulated planets have chemical compositions similar to real planets, indicating that the accretion calculations are reasonable. Questions remain about the accretion of water and other highly volatile compounds, including C and N, which are essential for life.

  20. Organoactinide chemistry: synthesis, structure, and solution dynamics

    SciTech Connect

    Brennan, J.G.

    1985-12-01

    This thesis considers three aspects of organoactinide chemistry. In chapter one, a bidentate phosphine ligand was used to kinetically stabilize complexes of the type Cp/sub 2/MX/sub 2/. Ligand redistribution processes are present throughout the synthetic work, as has often been observed in uranium cyclopentadienyl chemistry. The effects of covalent M-L bonding on the solution and solid state properties of U(III) coordination complexes are considered. In particular, the nature of the more subtle interaction between the metal and the neutral ligand are examined. Using relative basicity data obtained in solution, and solid state structural data (and supplemented by gas phase photoelectron measurements), it is demonstrated that the more electron rich U(III) centers engage in significant U ..-->.. L ..pi..-donation. Trivalent uranium is shown to be capable of acting either as a one- or two-electron reducing agent toward a wide variety of unsaturated organic and inorganic molecules, generating molecular classes unobtainable via traditional synthetic approaches, as well as offering an alternative synthetic approach to molecules accessible via metathesis reactions. Ligand redistribution processes are again observed, but given the information concerning ligand lability, this reactivity pattern is applied to the synthesis of pure materials inaccessible from redox chemistry. 214 refs., 33 figs., 10 tabs.

  1. Dynamic covalent chemistry approaches toward macrocycles, molecular cages, and polymers.

    PubMed

    Jin, Yinghua; Wang, Qi; Taynton, Philip; Zhang, Wei

    2014-05-20

    The current research in the field of dynamic covalent chemistry includes the study of dynamic covalent reactions, catalysts, and their applications. Unlike noncovalent interactions utilized in supramolecular chemistry, the formation/breakage of covalent bonding has slower kinetics and usually requires the aid of a catalyst. Catalytic systems that enable efficient thermodynamic equilibrium are thus essential. In this Account, we describe the development of efficient catalysts for alkyne metathesis, and discuss the application of dynamic covalent reactions (mainly imine, olefin, and alkyne metathesis) in the development of organic functional materials. Alkyne metathesis is an emerging dynamic covalent reaction that offers robust and linear acetylene linkages. By introducing a podand motif into the catalyst ligand design, we have developed a series of highly active and robust alkyne metathesis catalysts, which, for the first time, enabled the one-step covalent assembly of ethynylene-linked functional molecular cages. Imine chemistry and olefin metathesis are among the most well-established reversible reactions, and have also been our main synthetic tools. Various shape-persistent macrocycles and covalent organic polyhedrons have been efficiently constructed in one-step through dynamic imine chemistry and olefin metathesis. The geometrical features and solubilizing groups of the building blocks as well as the reaction kinetics have significant effect on the outcome of a covalent assembly process. More recently, we explored the orthogonality of imine and olefin metatheses, and successfully synthesized heterosequenced macrocycles and molecular cages through one-pot orthogonal dynamic covalent chemistry. In addition to discrete molecular architectures, functional polymeric materials can also be accessed through dynamic covalent reactions. Defect-free solution-processable conjugated polyaryleneethynylenes and polydiacetylenes have been prepared through alkyne metathesis

  2. Combinatorial Optimization Algorithms for Dynamic Multiple Fault Diagnosis in Automotive and Aerospace Applications

    NASA Astrophysics Data System (ADS)

    Kodali, Anuradha

    In this thesis, we develop dynamic multiple fault diagnosis (DMFD) algorithms to diagnose faults that are sporadic and coupled. Firstly, we formulate a coupled factorial hidden Markov model-based (CFHMM) framework to diagnose dependent faults occurring over time (dynamic case). Here, we implement a mixed memory Markov coupling model to determine the most likely sequence of (dependent) fault states, the one that best explains the observed test outcomes over time. An iterative Gauss-Seidel coordinate ascent optimization method is proposed for solving the problem. A soft Viterbi algorithm is also implemented within the framework for decoding dependent fault states over time. We demonstrate the algorithm on simulated and real-world systems with coupled faults; the results show that this approach improves the correct isolation rate as compared to the formulation where independent fault states are assumed. Secondly, we formulate a generalization of set-covering, termed dynamic set-covering (DSC), which involves a series of coupled set-covering problems over time. The objective of the DSC problem is to infer the most probable time sequence of a parsimonious set of failure sources that explains the observed test outcomes over time. The DSC problem is NP-hard and intractable due to the fault-test dependency matrix that couples the failed tests and faults via the constraint matrix, and the temporal dependence of failure sources over time. Here, the DSC problem is motivated from the viewpoint of a dynamic multiple fault diagnosis problem, but it has wide applications in operations research, for e.g., facility location problem. Thus, we also formulated the DSC problem in the context of a dynamically evolving facility location problem. Here, a facility can be opened, closed, or can be temporarily unavailable at any time for a given requirement of demand points. These activities are associated with costs or penalties, viz., phase-in or phase-out for the opening or closing of a

  3. Combinatorial structures to modeling simple games and applications

    NASA Astrophysics Data System (ADS)

    Molinero, Xavier

    2017-09-01

    We connect three different topics: combinatorial structures, game theory and chemistry. In particular, we establish the bases to represent some simple games, defined as influence games, and molecules, defined from atoms, by using combinatorial structures. First, we characterize simple games as influence games using influence graphs. It let us to modeling simple games as combinatorial structures (from the viewpoint of structures or graphs). Second, we formally define molecules as combinations of atoms. It let us to modeling molecules as combinatorial structures (from the viewpoint of combinations). It is open to generate such combinatorial structures using some specific techniques as genetic algorithms, (meta-)heuristics algorithms and parallel programming, among others.

  4. Designing a new Diels-Alderase: a combinatorial, semirational approach including dynamic optimization.

    PubMed

    Linder, Mats; Johansson, Adam Johannes; Olsson, Tjelvar S G; Liebeschuetz, John; Brinck, Tore

    2011-08-22

    A computationally inexpensive design strategy involving 'semirational' screening for enzymatic catalysis is presented. The protocol is based on well-established computational methods and represents a holistic approach to the catalytic process. The model reaction studied here is the Diels-Alder, for which a successful computational design has recently been published (Siegel, J. B. et al. Science 2010, 329, 309-313). While it is a leap forward in the field of computational design, the focus on designing only a small fraction of the active site gives little control over dynamics. Our approach explicitly incorporates mutagenesis and the analysis of binding events and transition states, and a promising enzyme-substrate candidate is generated with relatively little effort. We estimate catalytic rate accelerations of up to 10⁵.

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

    NASA Astrophysics Data System (ADS)

    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

  6. Complex Dynamics in Nonequilibrium Economics and Chemistry

    NASA Astrophysics Data System (ADS)

    Wen, Kehong

    Complex dynamics provides a new approach in dealing with economic complexity. We study interactively the empirical and theoretical aspects of business cycles. The way of exploring complexity is similar to that in the study of an oscillatory chemical system (BZ system)--a model for modeling complex behavior. We contribute in simulating qualitatively the complex periodic patterns observed from the controlled BZ experiments to narrow the gap between modeling and experiment. The gap between theory and reality is much wider in economics, which involves studies of human expectations and decisions, the essential difference from natural sciences. Our empirical and theoretical studies make substantial progress in closing this gap. With the help from the new development in nonequilibrium physics, i.e., the complex spectral theory, we advance our technique in detecting characteristic time scales from empirical economic data. We obtain correlation resonances, which give oscillating modes with decays for correlation decomposition, from different time series including S&P 500, M2, crude oil spot prices, and GNP. The time scales found are strikingly compatible with business experiences and other studies in business cycles. They reveal the non-Markovian nature of coherent markets. The resonances enhance the evidence of economic chaos obtained by using other tests. The evolving multi-humped distributions produced by the moving-time -window technique reveal the nonequilibrium nature of economic behavior. They reproduce the American economic history of booms and busts. The studies seem to provide a way out of the debate on chaos versus noise and unify the cyclical and stochastic approaches in explaining business fluctuations. Based on these findings and new expectation formulation, we construct a business cycle model which gives qualitatively compatible patterns to those found empirically. The soft-bouncing oscillator model provides a better alternative than the harmonic oscillator

  7. Forcing of stratospheric chemistry and dynamics during the Dalton Minimum

    NASA Astrophysics Data System (ADS)

    Anet, J. G.; Muthers, S.; Rozanov, E.; Raible, C. C.; Peter, T.; Stenke, A.; Shapiro, A. I.; Beer, J.; Steinhilber, F.; Brönnimann, S.; Arfeuille, F.; Brugnara, Y.; Schmutz, W.

    2013-11-01

    The response of atmospheric chemistry and dynamics to volcanic eruptions and to a decrease in solar activity during the Dalton Minimum is investigated with the fully coupled atmosphere-ocean chemistry general circulation model SOCOL-MPIOM (modeling tools for studies of SOlar Climate Ozone Links-Max Planck Institute Ocean Model) covering the time period 1780 to 1840 AD. We carried out several sensitivity ensemble experiments to separate the effects of (i) reduced solar ultra-violet (UV) irradiance, (ii) reduced solar visible and near infrared irradiance, (iii) enhanced galactic cosmic ray intensity as well as less intensive solar energetic proton events and auroral electron precipitation, and (iv) volcanic aerosols. The introduced changes of UV irradiance and volcanic aerosols significantly influence stratospheric dynamics in the early 19th century, whereas changes in the visible part of the spectrum and energetic particles have smaller effects. A reduction of UV irradiance by 15%, which represents the presently discussed highest estimate of UV irradiance change caused by solar activity changes, causes global ozone decrease below the stratopause reaching as much as 8% in the midlatitudes at 5 hPa and a significant stratospheric cooling of up to 2 °C in the mid-stratosphere and to 6 °C in the lower mesosphere. Changes in energetic particle precipitation lead only to minor changes in the yearly averaged temperature fields in the stratosphere. Volcanic aerosols heat the tropical lower stratosphere, allowing more water vapour to enter the tropical stratosphere, which, via HOx reactions, decreases upper stratospheric and mesospheric ozone by roughly 4%. Conversely, heterogeneous chemistry on aerosols reduces stratospheric NOx, leading to a 12% ozone increase in the tropics, whereas a decrease in ozone of up to 5% is found over Antarctica in boreal winter. The linear superposition of the different contributions is not equivalent to the response obtained in a simulation

  8. Interactions between dynamics and chemistry by COMMA modeling

    NASA Astrophysics Data System (ADS)

    Berger, U.; Koerner, U.; Sonnemann, G.

    Much of our current knowledge of the chemistry and circulation of the middle atmosphere derives from the spacecraft instruments since the the late 1970s (LIMS, SAGE II, ATMOS) and in particular the 1990s (HALOE, MLS, MAS, ILAS POAM III). In parallel , knowledge of the global circulation has continued to advance thanks to rapid developments in theoretical studies performed using numerical general circulation models (GCMs). This paper will focus on the upper atmosphere at polar latitudes because this region is of special importance for climate studies where trace gases like carbon dioxide, water vapor, ozone, etc. are key ingredients in determing the thermal structure of the summer high latitude mesopause region. Both processes, chemistry as well as dynamical induced transports, and their numerical description define the quality criterions of Middle Atmosphere GCMs. Due to comparisons of modeled and observed trace gas distributions (time scale season down to hours) we will discuss recent advance in numerical modeling of the MLT region.

  9. Ionic Liquids: Radiation Chemistry, Solvation Dynamics and Reactivity Patterns

    SciTech Connect

    Wishart, J.F.

    2011-06-12

    Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs generally have low volatilities and are combustion-resistant, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of primary radiation chemistry, charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of reactions and product distributions. We study these issues by characterization of primary radiolysis products and measurements of their yields and reactivity, quantification of electron solvation dynamics and scavenging of electrons in different states of solvation. From this knowledge we wish to learn how to predict radiolytic mechanisms and control them or mitigate their effects on the properties of materials used in nuclear fuel processing, for example, and to apply IL radiation chemistry to answer questions about general chemical reactivity in ionic liquids that will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that the slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increase the importance of pre-solvated electron reactivity and consequently alter product distributions and subsequent chemistry. This difference from conventional solvents has profound effects on predicting and controlling radiolytic yields

  10. Interstellar clouds - From a dynamical perspective on their chemistry

    NASA Technical Reports Server (NTRS)

    Prasad, S. S.

    1985-01-01

    The possibility is examined that in the course of its dynamical evolution, a single mass of interstellar gas would exhibit properties of diffuse clouds, dense clouds and finally also of clouds perturbed by shocks or intense UV or X-ray radiation generated by a star of its own creation. This concept provides a common thread through the bewildering diversity of physical and chemical compositional properties shown by interstellar clouds. From this perspective, instead of being static objects, interstellar clouds are possibly incessantly evolving from initially diffuse to later dense state and then to star formation which ultimately restructures or disperses the remaining cloud material to begin the whole evolutionary process once again. Based on a simplified study of interstellar chemistry from a dynamical perspective, the ideas are presented as an heuristic: to encourage thought on the future direction of molecular astrophysics and the need to consider the chemical behavior of interstellar clouds in conjunction with, rather than in isolation from, their dynamical behavior. A physical basis must be sought for the semiempirical temperature formula which has been given a critical role in the collapse of diffuse clouds. Self-shielding effects in the chemistry of CO were neglected and this drawback should be removed; the ability of the model to explain the fractional abundances of more complex molecules, such as cyanopolyynes, should be examined.

  11. Combinatorial synthesis of deuterium-enriched atorvastatin.

    PubMed

    Li, Feng; Jiang, Wenfeng; Czarnik, Anthony W; Li, Wenbao

    2016-05-01

    It becomes more and more difficult to discover a new drug by existing models. The concept of deuteration has gained attention due to its advantages in the study of clinical pharmacokinetics and metabolic profiles. Herein we built a library of deuterated atorvastatins using combinatorial chemistry, and all 16 D-compounds were characterized by 1H NMR, 13C NMR, MS, and elemental analysis.

  12. Forcing of stratospheric chemistry and dynamics during the Dalton Minimum

    NASA Astrophysics Data System (ADS)

    Anet, J. G.; Muthers, S.; Rozanov, E.; Raible, C. C.; Peter, T.; Stenke, A.; Shapiro, A. I.; Beer, J.; Steinhilber, F.; Brönnimann, S.; Arfeuille, F.; Brugnara, Y.; Schmutz, W.

    2013-06-01

    especially UV and volcanic eruptions dominate the changes in the ozone, temperature and dynamics while the NOx field is dominated by the EPP. Visible radiation changes have only very minor effects on both stratospheric dynamics and chemistry.

  13. Combinatorial methods in sol-gel technology

    NASA Astrophysics Data System (ADS)

    Rantala, Juha T.; Kololuoma, Terho K.; Kivimaki, L.

    2000-05-01

    Sol-gel processing consists several variable parameters during materials synthesis and post processing steps. The sol-gel synthesis is rather sensitive for the parameters such as pH, temperature, type of catalyst, reaction time etc. However, this sensitivity can be taken as an advantage when developing and studying new materials and their properties. Furthermore, since the sol-gel technology mainly describes the fabrication of solid state materials from a liquid phase by applying metal alkoxides or metal salts as precursors, the post processing such as sintering has critical effects on the final form and properties of the solid material. Combinatorial chemistry and methods are valuable tools to estimate the effects of different variables and to build-up combinatorial libraries for the sol-gel technique. This paper generally describes potentials and the usage motivation of combinatorial chemistry in the sol-gel technology by taking into account some major steps in the synthesis and processing which are valuable for the estimation of the final product properties. Different kind of post processing steps in the combinatorial manner are studied in details. As an example the post processing of sol-gel derived semiconductor oxides and photosensitivity of hybrid sol-gel glasses are presented. The combinatorial treatment and measurement methods for these materials are explained.

  14. Monitoring Dynamic Glycosylation in Vivo Using Supersensitive Click Chemistry

    PubMed Central

    2015-01-01

    To monitor the kinetics of biological processes that take place within the minute time scale, simple and fast analytical methods are required. In this article, we present our discovery of an azide with an internal Cu(I)-chelating motif that enabled the development of the fastest protocol for Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) to date, and its application toward following the dynamic process of glycan biosynthesis. We discovered that an electron-donating picolyl azide boosted the efficiency of the ligand-accelerated CuAAC 20–38-fold in living systems with no apparent toxicity. With a combination of this azide and BTTPS, a tris(triazolylmethyl)amine-based ligand for Cu(I), we were able to detect newly synthesized cell-surface glycans by flow cytometry using as low as 1 nM of a metabolic precursor. This supersensitive chemistry enabled us to monitor the dynamic glycan biosynthesis in mammalian cells and in early zebrafish embryogenesis. In live mammalian cells, we discovered that it takes approximately 30–45 min for a monosaccharide building block to be metabolized and incorporated into cell-surface glycoconjugates. In zebrafish embryos, the labeled glycans could be detected as early as the two-cell stage. To our knowledge, this was the first time that newly synthesized glycans were detected at the cleavage period (0.75–2 hpf) in an animal model using bioorthogonal chemistry. PMID:24499412

  15. Future Arctic ozone recovery: the importance of chemistry and dynamics

    NASA Astrophysics Data System (ADS)

    Bednarz, Ewa; Maycock, Amanda; Abraham, Luke; Braesicke, Peter; Dessens, Olivier; Pyle, John

    2016-04-01

    Future trends in Arctic springtime total column ozone, and its chemical and dynamical drivers, are assessed using a 7 member ensemble from the Met Office Unified Model with United Kingdom Chemistry and Aerosols (UM-UKCA) simulating the period 1960-2100. The Arctic mean March total column ozone increases throughout the 21st century at a rate of ~11.5 DU/decade, and is projected to return to the 1980 level in the late 2030s. However, the integrations show that even past 2060 springtime Arctic ozone can episodically drop by ~50-100 DU below the long-term mean to near present day values. Consistent with the global decline in inorganic chlorine over the century, the estimated mean halogen induced chemical ozone loss in the Arctic lower atmosphere in spring decreases by around a factor of two between 1981-2000 and 2061-2080. However, in the presence of a cold and strong polar vortex elevated halogen losses well above the long-term mean continue to occur in the simulations into the second part of the century. The ensemble shows a radiatively-driven cooling trend modelled in the Arctic winter mid- and upper stratosphere, but there is less consistency across the seven ensemble members in the lower stratosphere. This is partly due to an increase in downwelling over the Arctic polar cap in winter, which increases transport of ozone into the polar region as well as drives adiabatic warming that partly offsets the radiatively-driven stratospheric cooling. However, individual years characterised by significantly suppressed downwelling, reduced transport and low temperatures continue into the future. We conclude that despite the future long-term recovery of Arctic ozone, the large interannual dynamical variability is expected to continue thereby facilitating episodic reductions in springtime ozone columns. Whilst our results suggest that the relative role of dynamical processes for determining Arctic springtime ozone will increase in the future, halogen chemistry will remain a

  16. Combinatorial enzyme technology for the conversion of agricultural fibers to functional properties

    USDA-ARS?s Scientific Manuscript database

    The concept of combinatorial chemistry has received little attention in agriculture and food research, although its applications in this area were described more than fifteen years ago (1, 2). More recently, interest in the use of combinatorial chemistry in agrochemical discovery has been revitalize...

  17. Combinatorial enzyme technology for the conversion of agricultural fibers to functional properties

    USDA-ARS?s Scientific Manuscript database

    The concept of combinatorial chemistry has received little attention in agriculture and food research, although its applications in this area were described more than fifteen years ago (1, 2). More recently, interest in the use of combinatorial chemistry in agrochemical discovery has been revitalize...

  18. Dynamics and Chemistry of Marine Stratocumulus (DYCOMS) Experiment.

    NASA Astrophysics Data System (ADS)

    Lenschow, D. H.; Paluch, I. R.; Bandy, A. R.; Pearson, R., Jr.; Kawa, S. R.; Weaver, C. J.; Huebert, B. J.; Kay, J. G.; Thornton, D. C.; Driedger, A. R., III

    1988-09-01

    A combined atmospheric chemistry-meteorology experiment, the Dynamics and Chemistry of the Marine Stratocumulus (DYCOMS), was carried out during the summer of 1985 over the eastern Pacific Ocean using the NCAR Electra aircraft. The objectives were to 1) study the budgets of several trace reactive species in a relatively pristine, steady-state, horizontally homogeneous, well-mixed boundary layer capped by a strong inversion and 2) study the formation. maintenance and dissipation of marine stratocumulus that persists off the California coast (as well as similar regions elsewhere) in summer. We obtained both mean and turbulence measurements of meteorological variables within and above the cloud-capped boundary layer that is typical of this region. Ozone was used successfully as a tracer for estimating entrainment rate. We found, however, that horizontal variability was large enough for ozone that a correction needs to be included in the ozone budget for the horizontal displacement due to turns even though the airplane was allowed to drift with the wind. The time rate-of-change term was significant in both the ozone and radon budgets; as a result, a considerably longer time interval than the two hours used between sets of flight legs would be desirable to improve the measurement accuracy of this tern.

  19. Influence of chemistry on wetting dynamics of nanotextured hydrophobic surfaces.

    PubMed

    Di Mundo, Rosa; Palumbo, Fabio; d'Agostino, Riccardo

    2010-04-06

    In this work, the role of a chemical parameter, such as the degree of fluorination, on the wetting behavior of nanotextured hydrophobic surfaces is investigated. Texture and chemistry tuning of the surfaces has been accomplished with single batch radiofrequency low-pressure plasma processes. Polystyrene substrates have been textured by CF(4) plasma etching and subsequently covered by thin films with a tunable F-to-C ratio, obtained in discharges fed with C(4)F(8)-C(2)H(4). Measurements of wetting dynamics reveal a regime transition from adhesive-hydrophobic to slippery-superhydrophobic, i.e., from wet to non wet states, as the F-to-C rises at constant topography. Such achievements are strengthened by calculation of the solid fraction of surface water contact area applying Cassie-Baxter advancing and receding equations to water contact angle data of textured and flat reference surfaces.

  20. Fast combinatorial vector field topology.

    PubMed

    Reininghaus, Jan; Löwen, Christian; Hotz, Ingrid

    2011-10-01

    This paper introduces a novel approximation algorithm for the fundamental graph problem of combinatorial vector field topology (CVT). CVT is a combinatorial approach based on a sound theoretical basis given by Forman's work on a discrete Morse theory for dynamical systems. A computational framework for this mathematical model of vector field topology has been developed recently. The applicability of this framework is however severely limited by the quadratic complexity of its main computational kernel. In this work, we present an approximation algorithm for CVT with a significantly lower complexity. This new algorithm reduces the runtime by several orders of magnitude and maintains the main advantages of CVT over the continuous approach. Due to the simplicity of our algorithm it can be easily parallelized to improve the runtime further. © 2011 IEEE

  1. Dynamical variability in the modelling of chemistry-climate interactions.

    PubMed

    Pyle, J A; Braesicke, P; Zeng, G

    2005-01-01

    We have used a version of the Met Office's climate model, into which we have introduced schemes for atmospheric chemistry, to study chemistry-dynamics-climate interactions. We have considered the variability of the stratospheric polar vortex, whose behaviour influences stratospheric ozone loss and will affect ozone recovery. In particular, we analyse the dynamical control of high latitude ozone in a model version which includes an assimilation of the equatorial quasi-biennial oscillation (QBO), demonstrating the stability of the linear relation between vortex strength and high latitude ozone. We discuss the effect of interactive model ozone on polar stratospheric cloud (PSC) area/volume and winter-spring stratospheric ozone loss in the northern hemisphere. In general we find larger polar ozone losses calculated in those model integrations in which modelled ozone is used interactively in the radiation scheme, even though we underestimate the slope of the ozone loss per PSC volume relation derived from observations. We have also looked at the influence of changing stratosphere-to-troposphere exchange on the tropospheric oxidizing capacity and, in particular, have considered the variability of tropospheric composition under different climate regimes (El Niño/La Niña, etc.). Focusing on the UT/LS, we show the response of ozone to El Niño in two different model set-ups (tropospheric/ stratospheric). In the stratospheric model set-up we find a distinct signal in the lower tropical stratosphere, which shows an anti-correlation between the Niño 3 index and the ozone column amount. In contrast ozone generally increases in the upper troposphere of the tropospheric model set-up after an El Niño. Understanding future trends in stratospheric ozone and tropospheric oxidizing capacity requires an understanding of natural variability, which we explore here.

  2. Ionic Liquids: Radiation Chemistry, Solvation Dynamics and Reactivity Patterns

    SciTech Connect

    Wishart,J.F.

    2008-09-29

    Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are generally nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increases the importance of pre-solvated electron reactivity and consequently alters product distributions. Parallel studies of IL solvation phenomena using coumarin-153 dynamic Stokes shifts and polarization anisotropy decay rates are done to compare with electron solvation studies and to evaluate

  3. IONIC LIQUIDS: RADIATION CHEMISTRY, SOLVATION DYNAMICS AND REACTIVITY PATTERNS.

    SciTech Connect

    WISHART,J.F.

    2007-10-01

    energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are generally nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increases the importance of pre-solvated electron reactivity and consequently alters product distributions. Parallel studies of IL solvation phenomena using coumarin-153 dynamic Stokes shifts and polarization anisotropy decay rates are done to compare with electron solvation studies and to evaluate the influence of ILs on charge transport processes. Methods. Picosecond pulse radiolysis studies at BNL

  4. Neural Meta-Memes Framework for Combinatorial Optimization

    NASA Astrophysics Data System (ADS)

    Song, Li Qin; Lim, Meng Hiot; Ong, Yew Soon

    In this paper, we present a Neural Meta-Memes Framework (NMMF) for combinatorial optimization. NMMF is a framework which models basic optimization algorithms as memes and manages them dynamically when solving combinatorial problems. NMMF encompasses neural networks which serve as the overall planner/coordinator to balance the workload between memes. We show the efficacy of the proposed NMMF through empirical study on a class of combinatorial problem, the quadratic assignment problem (QAP).

  5. Vesper - Venus Chemistry and Dynamics Orbiter - A NASA Discovery Mission Proposal: Submillimeter Investigation of Atmospheric Chemistry and Dynamics

    NASA Technical Reports Server (NTRS)

    Chin, Gordon

    2011-01-01

    Vesper conducts a focused investigation of the chemistry and dynamics of the middle atmosphere of our sister planet- from the base of the global cloud cover to the lower thermosphere. The middle atmosphere controls the stability of the Venus climate system. Vesper determines what processes maintain the atmospheric chemical stability, cause observed variability of chemical composition, control the escape of water, and drive the extreme super-rotation. The Vesper science investigation provides a unique perspective on the Earth environment due to the similarities in the middle atmosphere processes of both Venus and the Earth. Understanding key distinctions and similarities between Venus and Earth will increase our knowledge of how terrestrial planets evolve along different paths from nearly identical initial conditions.

  6. Future Arctic ozone recovery: the importance of chemistry and dynamics

    NASA Astrophysics Data System (ADS)

    Bednarz, Ewa M.; Maycock, Amanda C.; Abraham, N. Luke; Braesicke, Peter; Dessens, Olivier; Pyle, John A.

    2016-09-01

    Future trends in Arctic springtime total column ozone, and its chemical and dynamical drivers, are assessed using a seven-member ensemble from the Met Office Unified Model with United Kingdom Chemistry and Aerosols (UM-UKCA) simulating the period 1960-2100. The Arctic mean March total column ozone increases throughout the 21st century at a rate of ˜ 11.5 DU decade-1, and is projected to return to the 1980 level in the late 2030s. However, the integrations show that even past 2060 springtime Arctic ozone can episodically drop by ˜ 50-100 DU below the corresponding long-term ensemble mean for that period, reaching values characteristic of the near-present-day average level. Consistent with the global decline in inorganic chlorine (Cly) over the century, the estimated mean halogen-induced chemical ozone loss in the Arctic lower atmosphere in spring decreases by around a factor of 2 between the periods 2001-2020 and 2061-2080. However, in the presence of a cold and strong polar vortex, elevated halogen-induced ozone losses well above the corresponding long-term mean continue to occur in the simulations into the second part of the century. The ensemble shows a significant cooling trend in the Arctic winter mid- and upper stratosphere, but there is less confidence in the projected temperature trends in the lower stratosphere (100-50 hPa). This is partly due to an increase in downwelling over the Arctic polar cap in winter, which increases transport of ozone into the polar region as well as drives adiabatic warming that partly offsets the radiatively driven stratospheric cooling. However, individual winters characterised by significantly suppressed downwelling, reduced transport and anomalously low temperatures continue to occur in the future. We conclude that, despite the projected long-term recovery of Arctic ozone, the large interannual dynamical variability is expected to continue in the future, thereby facilitating episodic reductions in springtime ozone columns

  7. Muonium chemistry and spin dynamics in sulphur, modelling interstitial hydrogen.

    PubMed

    Cox, S F J; Lord, J S; McKenzie, I; Adjizian, J-J; Heggie, M I; Jayasooriya, U A; Grinter, R; Reid, I D

    2011-08-10

    The nature of the elusive muonium centre in sulphur is re-examined in the light of new data on its level-crossing resonance and spin-lattice relaxation. The aim is to provide a model for the solid-state chemistry of interstitial hydrogen in this element, which is as yet unknown, as well as to solve one of the longest standing puzzles in μSR spectroscopy, namely the surprisingly strong depolarization of muons mimicking ion-implanted protons in this innocuous non-magnetic material. The paramagnetic muonium (and by inference hydrogen) centre is confirmed to have the character of a molecular radical, but with huge anisotropy at cryogenic temperatures and a striking shift of the resonance at ordinary temperatures, the hyperfine parameters appearing to collapse and vanish towards the melting point. New density-functional supercell calculations identify a number of possible structures for the defect centre, including a novel form of bond-centred muonium in a closed-ring S(8)Mu complex. Simulations of the spin dynamics and fits to the spectra suggest a dynamical equilibrium or chemical exchange between several configurations, with occupancy of the bond-centre site falling from unity at low cryogenic temperatures to zero near the melting point.

  8. Design of a Dynamic Undergraduate Green Chemistry Course

    ERIC Educational Resources Information Center

    Kennedy, Sarah A.

    2016-01-01

    The green chemistry course taught at Westminster College (PA) incorporates nontraditional teaching techniques and texts to educate future chemists about the importance of using green chemistry principles. The course is designed to introduce green chemistry concepts and demonstrate their inherent necessity by discussing historical missteps by the…

  9. Design of a Dynamic Undergraduate Green Chemistry Course

    ERIC Educational Resources Information Center

    Kennedy, Sarah A.

    2016-01-01

    The green chemistry course taught at Westminster College (PA) incorporates nontraditional teaching techniques and texts to educate future chemists about the importance of using green chemistry principles. The course is designed to introduce green chemistry concepts and demonstrate their inherent necessity by discussing historical missteps by the…

  10. Nonparametric Combinatorial Sequence Models

    NASA Astrophysics Data System (ADS)

    Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three sequence datasets which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.

  11. Reactive Molecular Dynamics Studies of Thermal Induced Chemistry in TATB

    NASA Astrophysics Data System (ADS)

    Germann, Timothy; Quenneville, Jason

    2007-03-01

    Equilibrium molecular dynamics (MD) simulation of high explosives can provide important information on their thermal decomposition by helping to characterize processes with timescales that are much longer than those attainable with non-equilibrium MD shock studies. A reactive force field is used with MD to probe the chemisty induced by intense heating (`cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). The force field (ReaxFF) was developed by van Duin, Goddard and coworkers [1] at CalTech and has already shown promise in predicting the chemistry in small samples of RDX under either shock compression or intense heat. Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. We will show results of 800-particle simulations at several temperatures, and detail current capabilities for large-scale (10^4 -- 10^5 atoms) systems carried out with the massively parallel GRASP MD software developed at Sandia National Lab. Finally, we will compare the reaction timescales with those of RDX and HMX. [1] A. C. T. Van Duin, et al, J. Phys. Chem. A, 1005, 9396 (2001).

  12. Molecular Dynamics Simulations of Thermal Induced Chemistry in TATB

    NASA Astrophysics Data System (ADS)

    Quenneville, Jason; Germann, Timothy

    2006-03-01

    Equilibrium molecular dynamics (MD) simulation of high explosives can provide important information on their thermal decomposition by helping to characterize processes with timescales that are much longer than those attainable with non-equilibrium MD shock studies. A reactive force field is used with MD to probe the chemisty induced by intense heating (`cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). The force field (ReaxFF) was developed by van Duin, Goddard and coworkers^ at CalTech and has already shown promise in predicting the chemistry in small samples of RDX under either shock compression or intense heat. Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. We will show results of 100,000-particle simulations at several temperatures, carried out with the massively parallel GRASP MD software developed at Sandia National Lab. Finally, we will compare the reactions and reaction timescales with those of RDX and HMX. ^ A. C. T. Van Duin, et al, J. Phys. Chem. A, 1005, 9396 (2001).

  13. Crossing the Boundaries within Computational Chemistry: From Molecular Dynamics to Cheminformatics and back.

    PubMed

    Riniker, Sereina

    2014-09-01

    The research in the group for computational chemistry at the ETH Zurich focuses on the development of methods and software for classical molecular dynamics simulations and cheminformatics, and their application to biological and chemical questions. Here, important advances and challenges in these subfields of computational chemistry are reviewed and potential opportunities for cross-fertilization are outlined.

  14. Combinatorial synthesis of anti-HIV agents--a review.

    PubMed

    Sriram, Dharmarajan; Yogeeswari, Perumal; Nagappa, Ananantha Naik

    2005-08-01

    Combinatorial chemistry has been well recognized as an important tool of drug discovery. An ongoing hand is to integrate the combinatorial approach with fundamentals of medicinal chemistry and rational drug design. The last five years has seen an explosion in the exploration and adoption of combinatorial techniques. Indeed, it is difficult to identify any other topic in chemistry that has ever caught the imagination of chemists with such fervor and with the continuous development of high throughput screening methods. There is a growing need for the synthesis of a large number of molecules. Compound libraries designed to produce specific inhibitors of therapeutic target proteins have generated significant interest in drug discovery research. Combinatorial chemistry provides the opportunity to generate large libraries of compounds for biological testing. A literature search revealed that many lead compounds have indeed been discovered from libraries and this review presents a survey of combinatorial synthesis of HIV-1 reverse transcriptase inhibitors, protease inhibitors, HIV-1 function inhibitors such as adsorption inhibitors, CCR5 antagonists and HIV-1 Tat-tar inhibitors that can be developed as potential anti-HIV drugs.

  15. Fast combinatorial optimization with parallel digital computers.

    PubMed

    Kakeya, H; Okabe, Y

    2000-01-01

    This paper presents an algorithm which realizes fast search for the solutions of combinatorial optimization problems with parallel digital computers.With the standard weight matrices designed for combinatorial optimization, many iterations are required before convergence to a quasioptimal solution even when many digital processors can be used in parallel. By removing the components of the eingenvectors with eminent negative eigenvalues of the weight matrix, the proposed algorithm avoids oscillation and realizes energy reduction under synchronous discrete dynamics, which enables parallel digital computers to obtain quasi-optimal solutions with much less time than the conventional algorithm.

  16. Combinatorial auction design

    PubMed Central

    Porter, David; Rassenti, Stephen; Roopnarine, Anil; Smith, Vernon

    2003-01-01

    Combinatorial auctions allow for more expressive bidding in which participants can submit package bids with logical constraints that limit allowable outcomes. This type of auction can be useful when participants' values are complementary or when participants have production and financial constraints. However, combinatorial auctions are currently rare in practice. The main problems confronted in implementing these auctions are that they have computational uncertainty (i.e., there is no guarantee that the winning bids for such an auction can be found in a “reasonable” amount of time when the number of bidders and items becomes larger) and that the auction is cognitively complex and can lead participants to pursue perverse bidding strategies. This article describes a type of combinatorial auction that, during laboratory testing, eliminated these problems and produced extremely efficient outcomes. PMID:12893875

  17. Street Canyon Atmospheric Composition: Coupling Dynamics and Chemistry

    NASA Astrophysics Data System (ADS)

    Bright, V.; Bloss, W. J.; Cai, X.

    2010-12-01

    Atmospheric composition within the urban environment, particularly within street canyons (formed by a road running between two rows of buildings), has a direct effect on the air quality of an environment in which a large majority of people live and work. The composition of air within a street canyon is determined by the composition of background air mixed in from above, advection of air into and out of the canyon, vehicle exhaust and other emissions from within the street, together with the mixing and chemical processing of pollutants within the canyon. This occurs on a timescale of a few seconds to minutes and as a result, within-canyon atmospheric processes can have a significant effect on atmospheric composition on such timescales. This paper outlines a modelling study of street canyon atmospheric composition, integrating the combined effects of emissions, dynamics and chemistry. This work builds upon an existing dynamical model of canyon atmospheric motion (Large Eddy Simulation (LES) model) by adding a detailed chemical reaction scheme. Previous studies have considered basic NOx-O3 cycles with only a small number of chemical reactions included. Initially, a zero-dimensional box model was used to develop and assess the accuracy of a suitable reduced chemical scheme to be included within the LES. The reduced chemical scheme, based upon a subset of the Master Chemical Mechanism (MCM), includes 51 chemical species and 136 reactions. Vehicle emissions taken from the UK National Atmospheric Emissions Inventory (NAEI) were subsequently added to the box model. These elements were then combined with the canyon dynamics simulated by the Large Eddy Simulation (LES) model. Results demonstrate that the enhanced model is a suitable tool to be used to further investigate the combined effects of mixing and chemical processing upon air quality within the street canyon. Subsequently, a number of key questions relating to urban atmospheric composition are addressed using the

  18. Coastal carbonate chemistry dynamics associated with macrophyte systems

    NASA Astrophysics Data System (ADS)

    Tanner, C. A.; Martz, T. R.; Levin, L. A.

    2010-12-01

    In the coastal zone extreme variability in carbonate chemistry dynamics is driven by fluctuations in temperature, salinity, air-sea gas exchange, mixing processes, and biology. This variability could be particularly magnified in critical coastal ecosystems such as kelp beds where photosynthesis and respiration consume and release significant amounts of dissolved inorganic carbon. This variability poses a challenge for scientists assessing the impacts of climate change for nearshore ecosystems, and complicates assessment of long-term pH reduction in the presence of variability. We carried out deployments of physical & biogeochemical sensors in order to observe these processes in situ. The “SeapHOx” instruments used in this study consist of a modified Honeywell Durafet® ISFET pH sensor, an Aanderra Optode Oxygen sensor, and a SBE-37 conductivity, temperature, pressure sensor, integrated into a single package with internal power and a central microcontroller. The instruments were deployed on subsurface moorings located inside the southern portion of the La Jolla Kelp Forest and 1 km seaward at a depth of 5m. Combining pH sensor data with a conservative relationship between total alkalinity, salinity and temperature, other parameters of the carbonate system were calculated. Our analysis goals were to (a) characterize high-frequency time scales of carbonate chemistry variability (b) evaluate the amplitude and duration of variation, and (c) predict the occurrence of extreme (physiologically-significant) low pH events. Another analysis goal was to identify the corresponding drivers of the observed changes. Results thus far reveal a mean daily pH range of 0.27 units with a maximum range of 0.4 pH units of which temperature accounts for less than 30% of the variation and the rest must be attributed to changes in the chemical component. The greatest frequency of pH variability occurs twice per day corresponding to the semi-diurnal tidal cycle. Opposite to our

  19. Manipulating Combinatorial Structures.

    ERIC Educational Resources Information Center

    Labelle, Gilbert

    This set of transparencies shows how the manipulation of combinatorial structures in the context of modern combinatorics can easily lead to interesting teaching and learning activities at every level of education from elementary school to university. The transparencies describe: (1) the importance and relations of combinatorics to science and…

  20. Increasing the dynamic control space of mammalian transcription devices by combinatorial assembly of homologous regulatory elements from different bacterial species.

    PubMed

    Bacchus, William; Weber, Wilfried; Fussenegger, Martin

    2013-01-01

    Prokaryotic transcriptional regulatory elements are widely utilized building blocks for constructing regulatory genetic circuits adapted for mammalian cells and have found their way into a broad range of biotechnological applications. Prokaryotic transcriptional repressors, fused to eukaryotic transactivation or repression domains, compose the transcription factor, which binds and adjusts transcription from chimeric promoters containing the repressor-specific operator sequence. Escherichia coli and Chlamydia trachomatis share common features in the regulatory mechanism of the biosynthesis of l-tryptophan. The repressor protein TrpR of C. trachomatis regulates the trpRBA operon and the TrpR of E. coli regulates the trpEDCBA operon, both requiring l-tryptophan as a co-repressor. Fusion of these bacterial repressors to the VP16 transactivation domain of Herpes simplex virus creates synthetic transactivators that could bind and activate chimeric promoters, assembled by placing repressor-specific operator modules adjacent to a minimal promoter, in an l-tryptophan-adjustable manner. Combinations of different transactivator and promoter variants from the same or different bacterial species resulted in a multitude of regulatory systems where l-tryptophan regulation properties, background noise, and maximal gene expression levels were significantly diverse. Different l-tryptophan analogues showed diverse regulatory capacity depending on the promoter/transactivator combination. We believe the systems approach to rationally choose promoters, transactivators and inducer molecules, to obtain desired and predefined genetic expression dynamics and control profiles, will significantly advance the design of new regulatory circuits as well as improving already existing ones. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Physical Chemistry of Reaction Dynamics in Ionic Liquid

    SciTech Connect

    Maroncelli, Mark

    2016-10-02

    Work completed over the past year mainly involves finishing studies related to solvation dynamics in ionic liquids, amplifying and extending our initial PFG-NMR work on solute diffusion, and learning how to probe rotational dynamics in ionic liquids.

  2. Dynamic sulfur chemistry as a key tool in the design of self-healing polymers

    NASA Astrophysics Data System (ADS)

    Martin, Roberto; Rekondo, Alaitz; Ruiz de Luzuriaga, Alaitz; Casuso, Pablo; Dupin, Damien; Cabañero, Germán; Grande, Hans J.; Odriozola, Ibon

    2016-08-01

    The rich variety of reversible or dynamic covalent chemistries based on sulfur offers a unique opportunity for the design of self-healing polymer networks. The reversibility of such chemical bonds can be used to create soft systems which can self-mend at ambient conditions. Here we focus on the mechanism of three different dynamic sulfur chemistries which have been used for the development of self-healing elastomers and hydrogels: thiolate/nanoparticle exchange, aromatic disulfide exchange and gold(I)-thiolate/disulfide exchange.

  3. Combinatorial library-based design with Basis Products

    NASA Astrophysics Data System (ADS)

    Zhou, Joe Zhongxiang; Shi, Shenghua; Na, Jim; Peng, Zhengwei; Thacher, Tom

    2009-10-01

    Uncovering useful lead compounds from a vast virtual library of synthesizable compounds continues to be of tremendous interest to pharmaceutical researchers. Here we present the concept of Basis Products (BPs), a new and broadly applicable method for achieving efficient selections from a combinatorial library. By definition, Basis Products are a strategically selected subset of compounds from a potentially very large combinatorial library, and any compound in a combinatorial library can represented by its BPs. In this article we will show how to use BP docking scores to find the top compounds of a combinatorial library. Compared with the brute-force docking of an entire virtual library, docking with BPs are much more efficient because of the substantial size reduction, saving both time and resources. We will also demonstrate how BPs can be used for property-based combinatorial library designs. Furthermore, BPs can also be considered as fragments carrying chemistry knowledge, hence they can potentially be used in combination with any fragment-based design method. Therefore, BPs can be used to integrate combinatorial design with structure-based design and/or fragment-based design. Other potential applications of BPs include lead hopping and consensus core building, which we will describe briefly as well in this report.

  4. Chemistry in interstellar space. [environment characteristics influencing reaction dynamics

    NASA Technical Reports Server (NTRS)

    Donn, B.

    1973-01-01

    The particular characteristics of chemistry in interstellar space are determined by the unique environmental conditions involved. Interstellar matter is present at extremely low densities. Large deviations from thermodynamic equilibrium are, therefore, to be expected. A relatively intense ultraviolet radiation is present in many regions. The temperatures are in the range from 5 to 200 K. Data concerning the inhibiting effect of small activation energies in interstellar clouds are presented in a table. A summary of measured activation energies or barrier heights for exothermic exchange reactions is also provided. Problems of molecule formation are discussed, taking into account gas phase reactions and surface catalyzed processes.

  5. Chemistry in interstellar space. [environment characteristics influencing reaction dynamics

    NASA Technical Reports Server (NTRS)

    Donn, B.

    1973-01-01

    The particular characteristics of chemistry in interstellar space are determined by the unique environmental conditions involved. Interstellar matter is present at extremely low densities. Large deviations from thermodynamic equilibrium are, therefore, to be expected. A relatively intense ultraviolet radiation is present in many regions. The temperatures are in the range from 5 to 200 K. Data concerning the inhibiting effect of small activation energies in interstellar clouds are presented in a table. A summary of measured activation energies or barrier heights for exothermic exchange reactions is also provided. Problems of molecule formation are discussed, taking into account gas phase reactions and surface catalyzed processes.

  6. Beyond Problem-Based Learning: Using Dynamic PBL in Chemistry

    ERIC Educational Resources Information Center

    Overton, Tina L.; Randles, Christopher A.

    2015-01-01

    This paper describes the development and implementation of a novel pedagogy, dynamic problem-based learning. The pedagogy utilises real-world problems that evolve throughout the problem-based learning activity and provide students with choice and different data sets. This new dynamic problem-based learning approach was utilised to teach…

  7. Beyond Problem-Based Learning: Using Dynamic PBL in Chemistry

    ERIC Educational Resources Information Center

    Overton, Tina L.; Randles, Christopher A.

    2015-01-01

    This paper describes the development and implementation of a novel pedagogy, dynamic problem-based learning. The pedagogy utilises real-world problems that evolve throughout the problem-based learning activity and provide students with choice and different data sets. This new dynamic problem-based learning approach was utilised to teach…

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Dynamics of the Chemistry of Electronically Excited Atoms in Defined Quantum States.

    DTIC Science & Technology

    1978-05-01

    laser development . In essence, this research concerns itself with the elucidation of the role of electronic energy in affecting the chemistry or photochemistry of excited halogen atoms and molecules. While much is known about the dynamics of chemical and physical processes which are carried out on the lowest potential energy hypersurface correlating with reactants and products in their electronic ground state, relatively little is known about the dynamics of such phenomena as energy transfer and chemical reactivity on higher-lying potential

  10. Combinatorial Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    van Hecke, Martin

    The structure of most mechanical metamaterials is periodic so that their design space is that of the unit cell. Here we introduce a combinatorial strategy to create a vast number of distinct mechanical metamaterials, each with a unique spatial texture and response. These are aperiodic stackings of anisotropic building blocks, and their functionality rests on both the block design and their stacking configuration which is governed by a tiling problem. We realize such metamaterials by 3D printing, and show that they act as soft machines, capable of pattern recognition and pattern analysis.

  11. Interplay between chemistry and dynamics in embedded protostellar disks

    NASA Astrophysics Data System (ADS)

    Brinch, C.; Jørgensen, J. K.

    2013-11-01

    Context. A fundamental part of the study of star formation is to place young stellar objects in an evolutionary sequence. Establishing a robust evolutionary classification scheme allows us not only to understand how the Sun was born but also to predict what kind of main sequence star a given protostar will become. Traditionally, low-mass young stellar objects are classified according to the shape of their spectral energy distributions. Such methods are, however, prone to misclassification due to degeneracy and do not constrain the temporal evolution. More recently, young stellar objects have been classified based on envelope, disk, and stellar masses determined from resolved images of their continuum and line emission at submillimeter wavelengths. Aims: Through detailed modeling of two Class I sources, we aim at determining accurate velocity profiles and explore the role of freeze-out chemistry in such objects. Methods: We present new Submillimeter Array observations of the continuum and HCO+ line emission at 1.1 mm toward two protostars, IRS 63 and IRS 43 in the Ophiuchus star forming region. The sources were modeled in detail using dust radiation transfer to fit the SED and continuum images and line radiation transfer to produce synthetic position-velocity diagrams. We used a χ2 search algorithm to find the best model fit to the data and to estimate the errors in the model variables. Results: Our best fit models present disk, envelope, and stellar masses, as well as the HCO+ abundance and inclination of both sources. We also identify a ring structure with a radius of about 200 AU in IRS 63. Conclusions: We find that freeze-out chemistry is important in IRS 63 but not for IRS 43. We show that the velocity field in IRS 43 is consistent with Keplerian rotation. Owing to molecular depletion, it is not possible to draw a similar conclusion for IRS 63. We identify a ring-shaped structure in IRS 63 on the same spatial scale as the disk outer radius. No such structure

  12. Cryptographic Combinatorial Securities Exchanges

    NASA Astrophysics Data System (ADS)

    Thorpe, Christopher; Parkes, David C.

    We present a useful new mechanism that facilitates the atomic exchange of many large baskets of securities in a combinatorial exchange. Cryptography prevents information about the securities in the baskets from being exploited, enhancing trust. Our exchange offers institutions who wish to trade large positions a new alternative to existing methods of block trading: they can reduce transaction costs by taking advantage of other institutions’ available liquidity, while third party liquidity providers guarantee execution—preserving their desired portfolio composition at all times. In our exchange, institutions submit encrypted orders which are crossed, leaving a “remainder”. The exchange proves facts about the portfolio risk of this remainder to third party liquidity providers without revealing the securities in the remainder, the knowledge of which could also be exploited. The third parties learn either (depending on the setting) the portfolio risk parameters of the remainder itself, or how their own portfolio risk would change if they were to incorporate the remainder into a portfolio they submit. In one setting, these third parties submit bids on the commission, and the winner supplies necessary liquidity for the entire exchange to clear. This guaranteed clearing, coupled with external price discovery from the primary markets for the securities, sidesteps difficult combinatorial optimization problems. This latter method of proving how taking on the remainder would change risk parameters of one’s own portfolio, without revealing the remainder’s contents or its own risk parameters, is a useful protocol of independent interest.

  13. Molecular dynamics study on mechanism of preformed particle gel transporting through nanopores: Surface chemistry and heterogeneity

    NASA Astrophysics Data System (ADS)

    Cui, Peng; Zhang, Heng; Ma, Ying; Hao, Qingquan; Liu, Gang; Sun, Jichao; Yuan, Shiling

    2017-10-01

    The translocation behavior of preformed particle gel (PPG) in porous media is crucial for its application in enhanced oil recovery. By means of non-equilibrium molecular dynamics simulation, the translocation mechanism of PPG confined in different silica nanopores were investigated. The influence of surface chemistry and chemical heterogeneity of silica nanopore on the translocation process was revealed. As the degree of surface hydroxylation increases and the heterogeneity decreases, the pulling force needed to drive PPG decreases. We infer that the nanopore's surface (i.e. surface chemistry and heterogeneity) affects the translocation of PPG indirectly by forming different hydration layers.

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

    PubMed

    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.

  15. Dynamical mean-field theory for quantum chemistry.

    PubMed

    Lin, Nan; Marianetti, C A; Millis, Andrew J; Reichman, David R

    2011-03-04

    The dynamical mean-field concept of approximating an unsolvable many-body problem in terms of the solution of an auxiliary quantum impurity problem, introduced to study bulk materials with a continuous energy spectrum, is here extended to molecules, i.e., finite systems with a discrete energy spectrum. The application to small clusters of hydrogen atoms yields ground state energies which are competitive with leading quantum chemical approaches at intermediate and large interatomic distances as well as good approximations to the excitation spectrum.

  16. JACOB: a dynamic database for computational chemistry benchmarking.

    PubMed

    Yang, Jack; Waller, Mark P

    2012-12-21

    JACOB (just a collection of benchmarks) is a database that contains four diverse benchmark studies, which in-turn included 72 data sets, with a total of 122,356 individual results. The database is constructed upon a dynamic web framework that allows users to retrieve data from the database via predefined categories. Additional flexibility is made available via user-defined text-based queries. Requested sets of results are then automatically presented as bar graphs, with parameters of the graphs being controllable via the URL. JACOB is currently available at www.wallerlab.org/jacob.

  17. Combinatorial optimization games

    SciTech Connect

    Deng, X.; Ibaraki, Toshihide; Nagamochi, Hiroshi

    1997-06-01

    We introduce a general integer programming formulation for a class of combinatorial optimization games, which immediately allows us to improve the algorithmic result for finding amputations in the core (an important solution concept in cooperative game theory) of the network flow game on simple networks by Kalai and Zemel. An interesting result is a general theorem that the core for this class of games is nonempty if and only if a related linear program has an integer optimal solution. We study the properties for this mathematical condition to hold for several interesting problems, and apply them to resolve algorithmic and complexity issues for their cores along the line as put forward in: decide whether the core is empty; if the core is empty, find an imputation in the core; given an imputation x, test whether x is in the core. We also explore the properties of totally balanced games in this succinct formulation of cooperative games.

  18. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Thirteen ideas are presented that may be of use to chemistry teachers. Topics covered include vitamin C, industrial chemistry, electrical conductivity, electrolysis, alkali metals, vibration modes infra-red, dynamic equilibrium, and some new demonstrations in gaseous combinations. (PS)

  19. Biophysical chemistry.

    PubMed

    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.

  20. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Thirteen ideas are presented that may be of use to chemistry teachers. Topics covered include vitamin C, industrial chemistry, electrical conductivity, electrolysis, alkali metals, vibration modes infra-red, dynamic equilibrium, and some new demonstrations in gaseous combinations. (PS)

  1. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  2. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  3. The Dynamics and Chemistry of Massive Starless Cores

    NASA Astrophysics Data System (ADS)

    Tan, J. C.; Kong, S.; Butler, M. J.; Caselli, P.; Fontani, F.

    2013-10-01

    How do massive stars form? They may be born from massive pre-stellar gas cores that are much more massive than the Jeans mass. The Turbulent Core Accretion model invokes such cores as being in approximate virial and pressure equilibrium with their surrounding clump medium. Their internal pressure is provided by a combination of turbulence and magnetic fields. On the other hand, the Competitive Accretion model requires strongly sub-virial initial conditions that then lead to extensive fragmentation to the thermal Jeans scale, with high-mass stars later forming by competitive Bondi-Hoyle accretion. To test these models, we have identified four prime examples of massive (˜ 100 M⊙) clumps from mid-infrared (MIR) extinction mapping of Infrared Dark Clouds (IRDCs). At ˜16″ resolution, we found high deuteration fractions of N2H+ in these objects, consistent with them being starless. We then observed these 4 clumps with ALMA in Cycle 0 to probe the N2D+(3-2) line at ˜2″ resolution, finding 6 N2D+ cores. Their observed velocity dispersions and sizes are broadly consistent with the predictions of the Turbulent Core model of virialized, magnetized (with Alfvén Mach number mA ˜ 1), self-gravitating cores that are bounded by the high pressures of their surrounding clumps. However, the most massive core with ˜ 60 M⊙, appears to require moderately enhanced magnetic fields to be in virial equilibrium, implying mA ≃ 0.3. If confirmed, this suggests magnetic fields play a greater role than turbulence in setting the initial conditions of massive star formation. In this case the timescale for the core to be assembled may be significantly longer than a local dynamical or free-fall time. This is consistent with astrochemical modeling of the deuteration ages of the cores, which indicates a core age similar to the ambipolar diffusion time.

  4. Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

    SciTech Connect

    Cawkwell, M. J. Niklasson, Anders M. N.; Dattelbaum, Dana M.

    2015-02-14

    The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

  5. Spatial and temporal dynamics of stream chemistry in a forested watershed impacted by atmospheric deposition

    NASA Astrophysics Data System (ADS)

    Piatek, K. B.; Christopher, S. F.; Mitchell, M. J.

    2008-09-01

    We analyzed spatial and temporal dynamics of solute chemistry in a forest watershed impacted by atmospheric deposition in the Adirondack Mountains of New York State, USA. Spatial dynamics of solute chemistry and natural abundance isotopes of nitrate (15N and 18O) were examined in 6 locations and the watershed outlet in 2001 and 2002. Temporal dynamics were examined during 5 discharge periods: winter, snowmelt, spring, summer, and fall, which were based on discharge levels at the outlet. Solute concentrations were statistically significantly different (p≤0.05) among stream sampling locations and discharge periods, with no interaction effects. Groundwater sources located in upper watershed controlled stream chemistry at higher elevations with highest pH, Ca2+, sum of base cations, Si, NO3-, total N, and SO42- and lowest Al concentrations. Two low elevation wetlands had a substantial influence over stream chemistry at those locations contributing lowest NO3-, total N, and highest DOC and DON. Snowmelt exhibited among the lowest pH, sum of base cations, and SO42-, and highest NO3-, total N, DON, and total Al; snowmelt appeared to dilute groundwater, and flush stored soil-derived solutes. Summer discharge, composed mainly of groundwater, exhibited the lowest flow, among the highest Mg2+, Ca2+, and lowest DON, DOC, and total Al concentrations. Isotopic analysis together with patterns of NH4+ versus NO3- dynamics indicated that NO3- was microbial, generated in fall and accumulated in winter in upper watershed soils, and flushed to stream during high discharge events. Highest discharge in snowmelt 2001, a summer drought in 2002, and fall storms following the drought were further evaluated for their specific effects on stream chemistry. Snowmelt 2001 had the lowest pH and highest NO3-, base flow during summer drought had the lowest total Al, and storms in fall 2002 had highest SO42- of all periods, but all other solute concentrations were comparable to other discharge

  6. Quantum combinatorial model of gene expression

    PubMed Central

    Grover, Monendra; Grover, Ritu; Singh, Rakesh; Kumar, Rajesh; Kumar, Sundeep

    2013-01-01

    We propose that the DNA within the chromatin behaves as a dynamic combinatorial library capable of forming novel structures by reversible processes. We also hypothesize that states within the library may be linked via quantum tunneling. RNA polymerase then could scan these states and the system decoheres to the “appropriate” state. Two ways of sustaining quantum coherence at relevant time scales could be possible, first, screening: the quantum system can be kept isolated from its decohering environment, second, the existence of decoherence free subspaces .We discuss the role of superconductivity in context of avoiding decoherence in context of our hypothesis. PMID:23422839

  7. Study of the diurnal variability of atmospheric chemistry with respect to boundary layer dynamics during DOMINO

    NASA Astrophysics Data System (ADS)

    van Stratum, B. J. H.; Vilà-Guerau de Arellano, J.; Ouwersloot, H. G.; van den Dries, K.; van Laar, T. W.; Martinez, M.; Lelieveld, J.; Diesch, J.-M.; Drewnick, F.; Fischer, H.; Hosaynali Beygi, Z.; Harder, H.; Regelin, E.; Sinha, V.; Adame, J. A.; Sörgel, M.; Sander, R.; Bozem, H.; Song, W.; Williams, J.; Yassaa, N.

    2012-03-01

    We study the interactions between atmospheric boundary layer (ABL) dynamics and atmospheric chemistry using a mixed-layer model (MXLCH) coupled to chemical reaction schemes. Guided by both atmospheric and chemical measurements obtained during the DOMINO campaign (2008), numerical experiments are performed to study the role of ABL dynamics and the accuracy of chemical schemes with different complexity: MOZART-4 and a reduced mechanism of this chemical system. Both schemes produce satisfactory results, indicating that the reduced scheme is capable of reproducing the O3-NOx-VOC-HOx diurnal cycle during conditions characterised by a low NOx regime and small O3 tendencies (less than 1 ppb per hour). By focussing on the budget equations of chemical species in the mixed-layer model, we show that for species like O3, NO and NO2, the influence of entrainment and boundary layer growth is of the same order as chemical production/loss. This indicates that an accurate representation of ABL processes is crucial in understanding the daily cycle of chemical species. By comparing the time scales of chemical reactive species with the mixing time scale of turbulence, we propose a classification based on the Damköhler number to further determine the importance of dynamics on chemistry during field campaigns. Our findings advocate an integrated approach, simultaneously solving the ABL dynamics and chemical reactions, in order to obtain a better understanding of chemical pathways and processes and the interpretation of the results obtained during measurement campaigns.

  8. Amplification without instability: applying fluid dynamical insights in chemistry and biology

    NASA Astrophysics Data System (ADS)

    McCoy, Jonathan H.

    2013-11-01

    While amplification of small perturbations often arises from instability, transient amplification is possible locally even in asymptotically stable systems. That is, knowledge of a system's stability properties can mislead one's intuition for its transient behaviors. This insight, which has an interesting history in fluid dynamics, has more recently been rediscovered in ecology. Surprisingly, many nonlinear fluid dynamical and ecological systems share linear features associated with transient amplification of noise. This paper aims to establish that these features are widespread in many other disciplines concerned with noisy systems, especially chemistry, cell biology and molecular biology. Here, using classic nonlinear systems and the graphical language of network science, we explore how the noise amplification problem can be reframed in terms of activatory and inhibitory interactions between dynamical variables. The interaction patterns considered here are found in a great variety of systems, ranging from autocatalytic reactions and activator-inhibitor systems to influential models of nerve conduction, glycolysis, cell signaling and circadian rhythms.

  9. Experimental Design for Combinatorial and High Throughput Materials Development

    NASA Astrophysics Data System (ADS)

    Cawse, James N.

    2002-12-01

    In the past decade, combinatorial and high throughput experimental methods have revolutionized the pharmaceutical industry, allowing researchers to conduct more experiments in a week than was previously possible in a year. Now high throughput experimentation is rapidly spreading from its origins in the pharmaceutical world to larger industrial research establishments such as GE and DuPont, and even to smaller companies and universities. Consequently, researchers need to know the kinds of problems, desired outcomes, and appropriate patterns for these new strategies. Editor James Cawse's far-reaching study identifies and applies, with specific examples, these important new principles and techniques. Experimental Design for Combinatorial and High Throughput Materials Development progresses from methods that are now standard, such as gradient arrays, to mathematical developments that are breaking new ground. The former will be particularly useful to researchers entering the field, while the latter should inspire and challenge advanced practitioners. The book's contents are contributed by leading researchers in their respective fields. Chapters include: -High Throughput Synthetic Approaches for the Investigation of Inorganic Phase Space -Combinatorial Mapping of Polymer Blends Phase Behavior -Split-Plot Designs -Artificial Neural Networks in Catalyst Development -The Monte Carlo Approach to Library Design and Redesign This book also contains over 200 useful charts and drawings. Industrial chemists, chemical engineers, materials scientists, and physicists working in combinatorial and high throughput chemistry will find James Cawse's study to be an invaluable resource.

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

    NASA Astrophysics Data System (ADS)

    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. Invention as a combinatorial process: evidence from US patents.

    PubMed

    Youn, Hyejin; Strumsky, Deborah; Bettencourt, Luis M A; Lobo, José

    2015-05-06

    Invention has been commonly conceptualized as a search over a space of combinatorial possibilities. Despite the existence of a rich literature, spanning a variety of disciplines, elaborating on the recombinant nature of invention, we lack a formal and quantitative characterization of the combinatorial process underpinning inventive activity. Here, we use US patent records dating from 1790 to 2010 to formally characterize invention as a combinatorial process. To do this, we treat patented inventions as carriers of technologies and avail ourselves of the elaborate system of technology codes used by the United States Patent and Trademark Office to classify the technologies responsible for an invention's novelty. We find that the combinatorial inventive process exhibits an invariant rate of 'exploitation' (refinements of existing combinations of technologies) and 'exploration' (the development of new technological combinations). This combinatorial dynamic contrasts sharply with the creation of new technological capabilities-the building blocks to be combined-that has significantly slowed down. We also find that, notwithstanding the very reduced rate at which new technologies are introduced, the generation of novel technological combinations engenders a practically infinite space of technological configurations.

  12. Invention as a combinatorial process: evidence from US patents

    PubMed Central

    Youn, Hyejin; Strumsky, Deborah; Bettencourt, Luis M. A.; Lobo, José

    2015-01-01

    Invention has been commonly conceptualized as a search over a space of combinatorial possibilities. Despite the existence of a rich literature, spanning a variety of disciplines, elaborating on the recombinant nature of invention, we lack a formal and quantitative characterization of the combinatorial process underpinning inventive activity. Here, we use US patent records dating from 1790 to 2010 to formally characterize invention as a combinatorial process. To do this, we treat patented inventions as carriers of technologies and avail ourselves of the elaborate system of technology codes used by the United States Patent and Trademark Office to classify the technologies responsible for an invention's novelty. We find that the combinatorial inventive process exhibits an invariant rate of ‘exploitation’ (refinements of existing combinations of technologies) and ‘exploration’ (the development of new technological combinations). This combinatorial dynamic contrasts sharply with the creation of new technological capabilities—the building blocks to be combined—that has significantly slowed down. We also find that, notwithstanding the very reduced rate at which new technologies are introduced, the generation of novel technological combinations engenders a practically infinite space of technological configurations. PMID:25904530

  13. Measuring and Specifying Combinatorial Coverage of Test Input Configurations.

    PubMed

    Kuhn, D Richard; Kacker, Raghu N; Lei, Yu

    2016-12-01

    A key issue in testing is how many tests are needed for a required level of coverage or fault detection. Estimates are often based on error rates in initial testing, or on code coverage. For example, tests may be run until a desired level of statement or branch coverage is achieved. Combinatorial methods present an opportunity for a different approach to estimating required test set size, using characteristics of the test set. This paper describes methods for estimating the coverage of, and ability to detect, t-way interaction faults of a test set based on a covering array. We also develop a connection between (static) combinatorial coverage and (dynamic) code coverage, such that if a specific condition is satisfied, 100% branch coverage is assured. Using these results, we propose practical recommendations for using combinatorial coverage in specifying test requirements.

  14. Interactions between snow chemistry, mercury inputs and microbial population dynamics in an Arctic snowpack.

    PubMed

    Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M

    2013-01-01

    We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79 °N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes.

  15. Triazolinediones enable ultrafast and reversible click chemistry for the design of dynamic polymer systems

    NASA Astrophysics Data System (ADS)

    Billiet, Stijn; de Bruycker, Kevin; Driessen, Frank; Goossens, Hannelore; van Speybroeck, Veronique; Winne, Johan M.; Du Prez, Filip E.

    2014-09-01

    With its focus on synthetic reactions that are highly specific and reliable, ‘click’ chemistry has become a valuable tool for many scientific research areas and applications. Combining the modular, covalently bonded nature of click-chemistry linkages with an ability to reverse these linkages and reuse the constituent reactants in another click reaction, however, is a feature that is not found in most click reactions. Here we show that triazolinedione compounds can be used in click-chemistry applications. We present examples of simple and ultrafast macromolecular functionalization, polymer-polymer linking and polymer crosslinking under ambient conditions without the need for a catalyst. Moreover, when triazolinediones are combined with indole reaction partners, the reverse reaction can also be induced at elevated temperatures, and the triazolinedione reacted with a different reaction partner, reversibly or irreversibly dependent on its exact nature. We have used this ‘transclick’ reaction to introduce thermoreversible links into polyurethane and polymethacrylate materials, which allows dynamic polymer-network healing, reshaping and recycling.

  16. Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

    NASA Astrophysics Data System (ADS)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-10-01

    A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

  17. Effects of Aircraft Wake Dynamics on Measured and Simulated NO(x) and HO(x) Wake Chemistry. Appendix B

    NASA Technical Reports Server (NTRS)

    Lewellen, D. C.; Lewellen, W. S.

    2001-01-01

    High-resolution numerical large-eddy simulations of the near wake of a B757 including simplified NOx and HOx chemistry were performed to explore the effects of dynamics on chemistry in wakes of ages from a few seconds to several minutes. Dilution plays an important basic role in the NOx-O3 chemistry in the wake, while a more interesting interaction between the chemistry and dynamics occurs for the HOx species. These simulation results are compared with published measurements of OH and HO2 within a B757 wake under cruise conditions in the upper troposphere taken during the Subsonic Aircraft Contrail and Cloud Effects Special Study (SUCCESS) mission in May 1996. The simulation provides a much finer grained representation of the chemistry and dynamics of the early wake than is possible from the 1 s data samples taken in situ. The comparison suggests that the previously reported discrepancy of up to a factor of 20 - 50 between the SUCCESS measurements of the [HO2]/[OH] ratio and that predicted by simplified theoretical computations is due to the combined effects of large mixing rates around the wake plume edges and averaging over volumes containing large species fluctuations. The results demonstrate the feasibility of using three-dimensional unsteady large-eddy simulations with coupled chemistry to study such phenomena.

  18. Combinatorial synthesis of ceramic materials

    DOEpatents

    Lauf, Robert J [Oak Ridge, TN; Walls, Claudia A [Oak Ridge, TN; Boatner, Lynn A [Oak Ridge, TN

    2010-02-23

    A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.

  19. Combinatorial synthesis of ceramic materials

    DOEpatents

    Lauf, Robert J.; Walls, Claudia A.; Boatner, Lynn A.

    2006-11-14

    A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.

  20. Microfluidic platform for combinatorial synthesis in picolitre droplets.

    PubMed

    Theberge, Ashleigh B; Mayot, Estelle; El Harrak, Abdeslam; Kleinschmidt, Felix; Huck, Wilhelm T S; Griffiths, Andrew D

    2012-04-07

    This paper presents a droplet-based microfluidic platform for miniaturized combinatorial synthesis. As a proof of concept, a library of small molecules for early stage drug screening was produced. We present an efficient strategy for producing a 7 × 3 library of potential thrombin inhibitors that can be utilized for other combinatorial synthesis applications. Picolitre droplets containing the first type of reagent (reagents A(1), A(2), …, A(m)) were formed individually in identical microfluidic chips and then stored off chip with the aid of stabilizing surfactants. These droplets were then mixed to form a library of droplets containing reagents A(1-m), each individually compartmentalized, which was reinjected into a second microfluidic chip and combinatorially fused with picolitre droplets containing the second reagent (reagents B(1), B(2), …, B(n)) that were formed on chip. The concept was demonstrated with a three-component Ugi-type reaction involving an amine (reagents A(1-3)), an aldehyde (reagents B(1-7)), and an isocyanide (held constant), to synthesize a library of small molecules with potential thrombin inhibitory activity. Our technique produced 10(6) droplets of each reaction at a rate of 2.3 kHz. Each droplet had a reaction volume of 3.1 pL, at least six orders of magnitude lower than conventional techniques. The droplets can then be divided into aliquots for different downstream screening applications. In addition to medicinal chemistry applications, this combinatorial droplet-based approach holds great potential for other applications that involve sampling large areas of chemical parameter space with minimal reagent consumption; such an approach could be beneficial when optimizing reaction conditions or performing combinatorial reactions aimed at producing novel materials.

  1. Combinatorial biosynthesis of RiPPs: Docking with marine life

    PubMed Central

    Sardar, Debosmita; Schmidt, Eric W.

    2016-01-01

    Ribosomally synthesized natural products are found in all forms of life. Their biosynthesis uses simple ribosomally synthesized peptides as starting materials that are transformed into complex structures via posttranslational modifications, enriched with elaborate chemical scaffolds that make them desirable as pharmacological tools. In addition, these natural products often exhibit combinatorial biosynthesis, making them attractive targets for engineering. An increasing knowledge of their biosynthetic machinery has provided key insights into their fascinating chemistry. Marine organisms have been a rich source of this class of natural products and here we review the lessons learned from marine life that enables exploitation of their potential for combinatorial engineering, opening up new routes for peptide-based drug discovery. PMID:26709871

  2. Gas adsorption properties of the ternary ZnO/CuO/CuCl(2) impregnated activated carbon system for multigas respirator applications assessed through combinatorial methods and dynamic adsorption studies.

    PubMed

    Romero, Jennifer V; Smith, Jock W H; Sullivan, Braden M; Mallay, Matthew G; Croll, Lisa M; Reynolds, Judy A; Andress, Carrie; Simon, Monika; Dahn, Jeff R

    2011-11-14

    A ternary library of 64 ZnO/CuO/CuCl(2) impregnated activated carbon samples was synthesized and screened automatically using a combinatorial (combi) method. The ability of the samples to adsorb toxic gases was screened gravimetrically. The stoichiometric ratio of reaction (SRR) between the moles of toxicant and the total moles of impregnant was obtained from the calculated mass increase of the samples after chemisorption, with a high SRR indicating high efficiency of toxicant removal. The combi samples that exhibited good dry SO(2) and NH(3) adsorption were prepared in bulk using the incipient wetness method and were evaluated for multigas respirator function by dynamic adsorption studies of SO(2), NH(3), HCN, and C(6)H(12) gases in either dry or humid conditions at ambient temperature. The bulk samples showed equivalent gas adsorption capacities when exposed to the different challenge gases indicating the value of the combi method for initial screening. Cu(2)Cl(OH)(3) was identified to be a potential multigas adsorbent.

  3. Why is combinatorial communication rare in the natural world, and why is language an exception to this trend?

    PubMed

    Scott-Phillips, Thomas C; Blythe, Richard A

    2013-11-06

    In a combinatorial communication system, some signals consist of the combinations of other signals. Such systems are more efficient than equivalent, non-combinatorial systems, yet despite this they are rare in nature. Why? Previous explanations have focused on the adaptive limits of combinatorial communication, or on its purported cognitive difficulties, but neither of these explains the full distribution of combinatorial communication in the natural world. Here, we present a nonlinear dynamical model of the emergence of combinatorial communication that, unlike previous models, considers how initially non-communicative behaviour evolves to take on a communicative function. We derive three basic principles about the emergence of combinatorial communication. We hence show that the interdependence of signals and responses places significant constraints on the historical pathways by which combinatorial signals might emerge, to the extent that anything other than the most simple form of combinatorial communication is extremely unlikely. We also argue that these constraints can be bypassed if individuals have the socio-cognitive capacity to engage in ostensive communication. Humans, but probably no other species, have this ability. This may explain why language, which is massively combinatorial, is such an extreme exception to nature's general trend for non-combinatorial communication.

  4. Why is combinatorial communication rare in the natural world, and why is language an exception to this trend?

    PubMed Central

    Scott-Phillips, Thomas C.; Blythe, Richard A.

    2013-01-01

    In a combinatorial communication system, some signals consist of the combinations of other signals. Such systems are more efficient than equivalent, non-combinatorial systems, yet despite this they are rare in nature. Why? Previous explanations have focused on the adaptive limits of combinatorial communication, or on its purported cognitive difficulties, but neither of these explains the full distribution of combinatorial communication in the natural world. Here, we present a nonlinear dynamical model of the emergence of combinatorial communication that, unlike previous models, considers how initially non-communicative behaviour evolves to take on a communicative function. We derive three basic principles about the emergence of combinatorial communication. We hence show that the interdependence of signals and responses places significant constraints on the historical pathways by which combinatorial signals might emerge, to the extent that anything other than the most simple form of combinatorial communication is extremely unlikely. We also argue that these constraints can be bypassed if individuals have the socio-cognitive capacity to engage in ostensive communication. Humans, but probably no other species, have this ability. This may explain why language, which is massively combinatorial, is such an extreme exception to nature's general trend for non-combinatorial communication. PMID:24047871

  5. Label-free in situ imaging of oil body dynamics and chemistry in germination

    PubMed Central

    Waschatko, Gustav; Billecke, Nils; Schwendy, Sascha; Jaurich, Henriette; Bonn, Mischa; Vilgis, Thomas A.

    2016-01-01

    Plant oleosomes are uniquely emulsified lipid reservoirs that serve as the primary energy source during seed germination. These oil bodies undergo significant changes regarding their size, composition and structure during normal seedling development; however, a detailed characterization of these oil body dynamics, which critically affect oil body extractability and nutritional value, has remained challenging because of a limited ability to monitor oil body location and composition during germination in situ. Here, we demonstrate via in situ, label-free imaging that oil bodies are highly dynamic intracellular organelles that are morphologically and biochemically remodelled extensively during germination. Label-free, coherent Raman microscopy (CRM) combined with bulk biochemical measurements revealed the temporal and spatial regulation of oil bodies in native soya bean cotyledons during the first eight days of germination. Oil bodies undergo a cycle of growth and shrinkage that is paralleled by lipid and protein compositional changes. Specifically, the total protein concentration associated with oil bodies increases in the first phase of germination and subsequently decreases. Lipids contained within the oil bodies change in saturation and chain length during germination. Our results show that CRM is a well-suited platform to monitor in situ lipid dynamics and local chemistry and that oil bodies are actively remodelled during germination. This underscores the dynamic role of lipid reservoirs in plant development. PMID:27798279

  6. Combinatorial microfluidic droplet engineering for biomimetic material synthesis

    PubMed Central

    Bawazer, Lukmaan A.; McNally, Ciara S.; Empson, Christopher J.; Marchant, William J.; Comyn, Tim P.; Niu, Xize; Cho, Soongwon; McPherson, Michael J.; Binks, Bernard P.; deMello, Andrew; Meldrum, Fiona C.

    2016-01-01

    Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated. The potential of this method is demonstrated by creating droplets with enhanced stability, where this is achieved by selecting carrier fluid chemistries that promote titanium dioxide formation at the droplet interfaces. The interface is a mixture of amorphous and crystalline phases, and the resulting composite droplets are biocompatible, supporting in vitro protein expression in their interiors. This general strategy will find widespread application in advancing emulsion properties for use in chemistry, biology, materials, and medicine. PMID:27730209

  7. Spatial and temporal dynamics of stream chemistry in a forested watershed

    NASA Astrophysics Data System (ADS)

    Piatek, K. B.; Christopher, S. F.; Mitchell, M. J.

    2009-03-01

    Spatial dynamics of solute chemistry and natural abundance isotopes of nitrate (15N and 18O) were examined in seven locations and at the watershed outlet in 2001 and 2002 in a forest watershed in the Adirondack Mountains of New York State, USA. Temporal dynamics were examined during five discharge periods: winter, snowmelt, spring, summer, and fall, based on discharge levels at the watershed outlet. Solute concentrations were variable across space and time with significant (p≤0.05) interaction effects. Year*period was significant for pH, NH4+, NO3-, total N, DOC, and total Al suggesting that inter-annual variability in discharge levels was more important for these solutes than intra-annual variability. Period*sampling point was significant for pH, Mg2+, Ca2+, sum of base cations, Si, and total Al suggesting that the differences in concentration of these solutes among sampling points were moderated by discharge levels. In general, groundwater sources located in upper watershed controlled stream chemistry at higher elevations with highest pH, Ca2+, sum of base cations, Si, and SO42- concentrations, with higher values in summer, and dilution effects during snowmelt. Two low elevation wetlands had a substantial influence over stream chemistry at those locations contributing lowest NO3- and highest DOC. Snowmelt exhibited among the lowest pH, sum of base cations, and SO42-, and highest NO3-, total N, and total Al; snowmelt appeared to dilute groundwater, and flush stored soil-derived solutes. Summer discharge, composed mainly of groundwater, exhibited the lowest flow, among the highest Mg2+, Ca2+, and lowest DON, DOC, and total Al concentrations. Isotopic analysis indicated that NO3- was microbial with primary source in upper watershed soil, from where it was flushed to stream under high discharge-conditions, or drained to groundwater which became its secondary source when discharge was low. Watershed outlet did not exhibit specific solute levels found at source

  8. Spatial and temporal dynamics of stream chemistry in a northern forest watershed.

    NASA Astrophysics Data System (ADS)

    Piatek, K. B.; Christopher, S. F.; Mitchell, M. J.

    2009-05-01

    Spatial dynamics of solute chemistry and natural abundance isotopes of nitrate (15N and 18O) were examined in six locations and at the watershed outlet in 2001 and 2002 in a forest watershed in the Adirondack Mountains of New York State, U.S.A. Temporal dynamics were examined during five discharge periods: winter, snowmelt, spring, summer, and fall, based on discharge levels at the watershed outlet. Solute concentrations were variable across space and time with significant (pÜ0.05) interaction effects. Year*period was significant for pH, NO3-, total N, DOC, and total Al suggesting that inter-annual variability in discharge levels was more important for these solutes than intra-annual variability. Period*sampling point was significant for pH, Mg2+, Ca2+, sum of base cations, Si, and total Al suggesting that the differences in concentration of these solutes among sampling points were moderated by discharge levels. In general, groundwater sources located in upper watershed controlled stream chemistry at higher elevations with highest pH, Ca2+, sum of base cations, Si, SO42- concentrations, with higher values in summer, and dilution effects during snowmelt. Two low elevation wetlands had a substantial influence over stream chemistry at those locations contributing lowest NO3- and highest DOC. Snowmelt exhibited among the lowest pH, sum of base cations, and SO42-, and highest NO3-, total N, and total Al; snowmelt appeared to dilute groundwater, and flush stored soil-derived solutes. Summer discharge, composed mainly of groundwater, exhibited the lowest flow, among the highest Mg2+, Ca2+, and lowest DON, DOC, and total Al concentrations. Isotopic analysis indicated that NO3- was microbial with primary source in upper watershed soil, from where it was flushed to stream under high discharge-conditions, or drained to groundwater which became its secondary source when discharge was less. Watershed outlet did not exhibit specific solute levels found at source-areas, but

  9. Combining research in physical chemistry and chemical education: Part A. The femtosecond molecular dynamics of small gas-phase anion clusters. Part B. Surveying student beliefs about chemistry and the development of physical chemistry learning tutorials

    NASA Astrophysics Data System (ADS)

    Barbera, Jack

    2007-12-01

    This dissertation combines work in the areas of experimental physical chemistry and chemical education. In the area of physical chemistry, femtosecond pump-probe spectroscopy is used to interrogate the time-dependence for energy redistribution, solvent reorientation, and dissociation dynamics in small gas-phase anion clusters. The chemical education research addressed in this manuscript include the development and validation of a survey to measure students' beliefs about chemistry and the learning of chemistry and the development and testing of learning tutorials for use in undergraduate physical chemistry courses in thermodynamics and kinetics. In the first part of this dissertation, the Cu(CD3OD) dynamics are investigated using a combination of femtosecond pump-probe experiments and ab initio calculations. Dissociation of this complex into Cu and CD3OD occurs on two distinct time scales: 3 and 30 ps, which arise, respectively, from the coupling of intermolecular solvent rotations and excited methyl rotor rotation into the Cu-O dissociation component upon electron photodetachment of the precursor anion. In the second part of this dissertation, the time-resolved recombination of photodissociated IBr-(CO2)n (n = 5 - 10) cluster anions is investigated. Upon excitation to the A' 2pi 1/2 state of the chromophore, the bare anion results in I- and Br products, upon solvation with CO2, the IBr- chromophore regains near-IR absorption after recombination and vibrational relaxation on the ground electronic state. The recombination times vary with the number of solvent molecules from 12 ps for n = 5 to 900 ps for n = 10. Extensive electronic structure and non-adiabatic molecular dynamic simulations provide a framework to understand this behavior. In the third part of this dissertation, the modification and validation of the Colorado Learning Attitudes about Science Survey (CLASS) for use in chemistry is presented in detail. The CLASS survey is designed to measure student

  10. An integrated microfluidic device for two-dimensional combinatorial dilution†

    PubMed Central

    Jang, Yun-Ho; Hancock, Matthew J.; Kim, Sang Bok; Selimović, Šeila; Sim, Woo Young; Bae, Hojae; Khademhosseini, Ali

    2012-01-01

    High-throughput preparation of multi-component solutions is an integral process in biology, chemistry and materials science for screening, diagnostics and analysis. Compact microfluidic systems enable such processing with low reagent volumes and rapid testing. Here we present a microfluidic device that incorporates two gradient generators, a tree-like generator and a new microfluidic active injection system, interfaced by intermediate solution reservoirs to generate diluted combinations of input solutions within an 8 × 8 or 10 × 10 array of isolated test chambers. Three input solutions were fed into the device, two to the tree-like gradient generator and one to pre-fill the test chamber array. The relative concentrations of these three input solutions in the test chambers completely characterized device behaviour and were controlled by the number of injection cycles and the flow rate. Device behaviour was modelled by computational fluid dynamics simulations and an approximate analytic formula. The device may be used for two-dimensional (2D) combinatorial dilution by adding two solutions in different relative concentrations to each of its three inputs. By appropriate choice of the two-component input solutions, test chamber concentrations that span any triangle in 2D concentration space may be obtained. In particular, explicit inputs are given for a coarse screening of a large region in concentration space followed by a more refined screening of a smaller region, including alternate inputs that span the same concentration region but with different distributions. The ability to probe arbitrary subspaces of concentration space and to control the distribution of discrete test points within those subspaces makes the device of potential benefit for high-throughput cell biology studies and drug screening. PMID:21837312

  11. Proton enhanced dynamic battery chemistry for aprotic lithium–oxygen batteries

    DOE PAGES

    Zhu, Yun Guang; Liu, Qi; Rong, Yangchun; ...

    2017-02-06

    Water is generally considered to be deteriorating to the performance of aprotic Li-air batteries, while it is challenged by the disparate effects observed recently. This has provoked a range of discussion on the role of water and its impact on the battery operation. In this work, a distinct battery chemistry that prevails in water-contaminated aprotic Li-O2 batteries was discovered. Both lithium ions and protons were found to be involved in the oxygen reduction (ORR) and evolution reactions (OER), and LiOOH and LiOH were identified as predominant materials in the discharge product. As a new lithium compound, the crystallographic and spectroscopicmore » characteristics of LiOOH∙H2O were scrutinized both experimentally and theoretically. The structure of LiOOH∙H2O was found to be closely related to that of LiOH∙H2O implying a fast conversion kinetics between the two phases. Intriguingly, LiOOH∙H2O exhibits superior dynamic property towards the reaction with I3-, which renders considerably lower overpotential during the charging process. We anticipate that the new battery chemistry unveiled in this mechanistic study would provide important insights to the understanding of nominally aprotic Li-O2 batteries and help to tackle the critical issues confronted.« less

  12. Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation.

    PubMed

    Shiraiwa, Manabu; Yee, Lindsay D; Schilling, Katherine A; Loza, Christine L; Craven, Jill S; Zuend, Andreas; Ziemann, Paul J; Seinfeld, John H

    2013-07-16

    Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality, and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosols (SOAs). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multigeneration gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface, and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a midexperiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. Although experiments need to be conducted with other SOA precursor hydrocarbons, current results demonstrate coupling between particle-phase chemistry and size distribution dynamics in the formation of SOAs, thereby opening up an avenue for analysis of the SOA formation process.

  13. Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation

    PubMed Central

    Shiraiwa, Manabu; Yee, Lindsay D.; Schilling, Katherine A.; Loza, Christine L.; Craven, Jill S.; Zuend, Andreas; Ziemann, Paul J.; Seinfeld, John H.

    2013-01-01

    Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality, and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosols (SOAs). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multigeneration gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface, and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a midexperiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. Although experiments need to be conducted with other SOA precursor hydrocarbons, current results demonstrate coupling between particle-phase chemistry and size distribution dynamics in the formation of SOAs, thereby opening up an avenue for analysis of the SOA formation process. PMID:23818634

  14. Kinetic Selectivity and Thermodynamic Features of Competitive Imine Formation in Dynamic Covalent Chemistry.

    PubMed

    Kulchat, Sirinan; Chaur, Manuel N; Lehn, Jean-Marie

    2017-08-16

    The kinetic and thermodynamic selectivities of imine formation have been investigated for several dynamic covalent libraries of aldehydes and amines. Two systems were examined, involving the reaction of different types of primary amino groups (aliphatic amines, alkoxy-amines, hydrazides and hydrazines) with two types of aldehydes, sulfobenzaldehyde and pyridoxal phosphate in aqueous solution at different pD (5.0, 8.5, 11.4) on one hand, 2-pyridinecarboxaldehyde and salicylaldehyde in organic solvents on the other hand. The reactions were performed separately for given amine/aldehyde pairs as well as in competitive conditions between an aldehyde and a mixture of amines. In the latter case, the time evolution of the dynamic covalent libraries generated was followed, taking into consideration the operation of both kinetic and thermodynamic selectivities. The results showed that, in aqueous solution, the imine of the aliphatic amine was not stable, but oxime and hydrazone formed well in a pH dependent way. On the other hand, in organic solvents, the kinetic product was the imine derived from an aliphatic amine and the thermodynamic products were oxime and hydrazone. The insights gained from these experiments provide a basis for the implementation of imine formation in selective derivatization of mono-amines in mixtures as well as of polyfunctional compounds presenting different types of amino groups. They may in principle be extended to other dynamic covalent chemistry systems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Upper atmosphere research satellite program. [to study the chemistry energetics, and dynamics

    NASA Technical Reports Server (NTRS)

    Huntress, W. T., Jr.

    1978-01-01

    A satellite program to conduct research on the chemistry, energetics, and dynamics of the upper atmosphere was developed. The scientific goals of the Upper Atmospheric Research Program, the program requirements, and the approach toward meeting those requirements are outlined. An initial series of two overlapping spacecraft missions is described. Both spacecraft are launched and recovered by the STS, one in the winter of 1983 at a 56 deg inclination, and the other a year later at a 70 deg inclination. The duration of each mission is 18 months, and each carries instruments to make global measurements of the temperature, winds, composition, irradation, and radiance in the stratosphere, mesosphere, and lower thermosphere between the tropopause and 120 km altitude. The program requires a dedicated ground-based data system and a science team organization that leads to a strong interaction between the experiments and theory. The program includes supportive observations from other platforms such as rockets, balloons, and the Spacelab.

  16. PINCA: A scalable parallel program for compressible gas dynamics with nonequilibrium chemistry

    NASA Astrophysics Data System (ADS)

    Wong, C. C.; Blottner, F. G.; Payne, J. L.; Soetrisno, M.; Imlay, S. T.

    1995-04-01

    This report documents an exploratory research work, funded by the Laboratory Directed Research and Development (LDRD) office at Sandia National Laboratories, to develop an advanced, general purpose, robust compressible flow solver for handling large, complex, chemically reacting gas dynamics problems. The deliverable of this project, a computer program called PINCA (Parallel INtegrated Computer Analysis) will run on massively parallel computers such as the Intel/Gamma and Intel/Paragon. With the development of this parallel compressible flow solver, engineers will be better able to address large three-dimensional scientific arid engineering problems involving multi-component gas mixtures with finite rate chemistry. These problems occur in high temperature industrial processes, combustion, and hypersonic: reentry of space-crafts.

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

    NASA Technical Reports Server (NTRS)

    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.

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

    NASA Technical Reports Server (NTRS)

    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.

  19. Stem cells and combinatorial science.

    PubMed

    Fang, Yue Qin; Wong, Wan Qing; Yap, Yan Wen; Orner, Brendan P

    2007-09-01

    Stem cell-based technologies have the potential to help cure a number of cell degenerative diseases. Combinatorial and high throughput screening techniques could provide tools to control and manipulate the self-renewal and differentiation of stem cells. This review chronicles historic and recent progress in the stem cell field involving both pluripotent and multipotent cells, and it highlights relevant cellular signal transduction pathways. This review further describes screens using libraries of soluble, small-molecule ligands, and arrays of molecules immobilized onto surfaces while proposing future trends in similar studies. It is hoped that by reviewing both the stem cell and the relevant high throughput screening literature, this paper can act as a resource to the combinatorial science community.

  20. a Three-Dimensional Model of Cloud Dynamics, Microphysics and Chemistry

    NASA Astrophysics Data System (ADS)

    Wang, Chien

    1992-01-01

    A three-dimensional, comprehensive cloud modeling system with detailed descriptions of dynamics, microphysics, and chemistry has been developed. This system can be used to study not only the evolution of dynamical and microphysical processes, but also those of chemical processes and the interactions or relationships among them. The primary objective of this model is the simulation of deep convective events and severe storms. The physical component of this model starts with a pseudo-elastic form of the continuity equation. The overall model is a self-consistent, time -dependent system which is easier to solve. Seven different water categories in three phases are considered in this model. Both the mass mixing ratio and concentration of each liquid or solid phase category are predicted so that a semi-spectra microphysical parameterization scheme can be formulated. More than 40 microphysical processes have been parameterized based on the spectrum-integration and the behavior of the individual particles in the microphysical interactions. Concentrations of seven chemical groups in air and in 6 liquid- or solid-phase water carriers are predicted by our chemical model. Their evolution in this model came from not only the dynamical and subgrid-scale transports, but also the chemical reactions and microphysics -related conversions. A strong convective storm, the 1 August 1981 case of CCOPE project, has been modeled by using our three-dimensional modeling system. The modeled precipitation feature and three-dimensional radar reflectivity factors are close to the observed data. The modeled main chemical parameters are also reasonable. The evolution of dynamical and thermodynamical structure of the storm, the formation and the evolution of precipitation, the redistribution of chemical species, the evolution of cloud and precipitation chemical features, and the relationships among dynamical, microphysical, and chemical processes have been studied through the case study. Some

  1. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2015-03-01

    We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.

  2. YCRD: Yeast Combinatorial Regulation Database

    PubMed Central

    Wu, Wei-Sheng; Hsieh, Yen-Chen; Lai, Fu-Jou

    2016-01-01

    In eukaryotes, the precise transcriptional control of gene expression is typically achieved through combinatorial regulation using cooperative transcription factors (TFs). Therefore, a database which provides regulatory associations between cooperative TFs and their target genes is helpful for biologists to study the molecular mechanisms of transcriptional regulation of gene expression. Because there is no such kind of databases in the public domain, this prompts us to construct a database, called Yeast Combinatorial Regulation Database (YCRD), which deposits 434,197 regulatory associations between 2535 cooperative TF pairs and 6243 genes. The comprehensive collection of more than 2500 cooperative TF pairs was retrieved from 17 existing algorithms in the literature. The target genes of a cooperative TF pair (e.g. TF1-TF2) are defined as the common target genes of TF1 and TF2, where a TF’s experimentally validated target genes were downloaded from YEASTRACT database. In YCRD, users can (i) search the target genes of a cooperative TF pair of interest, (ii) search the cooperative TF pairs which regulate a gene of interest and (iii) identify important cooperative TF pairs which regulate a given set of genes. We believe that YCRD will be a valuable resource for yeast biologists to study combinatorial regulation of gene expression. YCRD is available at http://cosbi.ee.ncku.edu.tw/YCRD/ or http://cosbi2.ee.ncku.edu.tw/YCRD/. PMID:27392072

  3. Combinatorial parallel and scientific computing.

    SciTech Connect

    Pinar, Ali; Hendrickson, Bruce Alan

    2005-04-01

    Combinatorial algorithms have long played a pivotal enabling role in many applications of parallel computing. Graph algorithms in particular arise in load balancing, scheduling, mapping and many other aspects of the parallelization of irregular applications. These are still active research areas, mostly due to evolving computational techniques and rapidly changing computational platforms. But the relationship between parallel computing and discrete algorithms is much richer than the mere use of graph algorithms to support the parallelization of traditional scientific computations. Important, emerging areas of science are fundamentally discrete, and they are increasingly reliant on the power of parallel computing. Examples include computational biology, scientific data mining, and network analysis. These applications are changing the relationship between discrete algorithms and parallel computing. In addition to their traditional role as enablers of high performance, combinatorial algorithms are now customers for parallel computing. New parallelization techniques for combinatorial algorithms need to be developed to support these nontraditional scientific approaches. This chapter will describe some of the many areas of intersection between discrete algorithms and parallel scientific computing. Due to space limitations, this chapter is not a comprehensive survey, but rather an introduction to a diverse set of techniques and applications with a particular emphasis on work presented at the Eleventh SIAM Conference on Parallel Processing for Scientific Computing. Some topics highly relevant to this chapter (e.g. load balancing) are addressed elsewhere in this book, and so we will not discuss them here.

  4. Dynamic Covalent Chemistry of Aldehyde Enamines: Bi(III) - and Sc(III) -Catalysis of Amine-Enamine Exchange.

    PubMed

    Zhang, Yang; Xie, Sheng; Yan, Mingdi; Ramström, Olof

    2017-09-04

    The dynamic exchange of enamines from secondary amines and enolizable aldehydes has been demonstrated in organic solvents. The enamine exchange with amines was efficiently catalyzed by Bi(OTf)3 and Sc(OTf)3 (2 mol %) and the equilibria (60 mm) could be attained within hours at room temperature. The formed dynamic covalent systems displayed high stabilities in basic environment with <2 % by-product formation within one week after complete equilibration. This study expands the scope of dynamic C-N bonds from imine chemistry to enamines, enabling further dynamic methodologies in exploration of this important class of structures in systems chemistry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Urban street canyons: Coupling dynamics, chemistry and within-canyon chemical processing of emissions

    NASA Astrophysics Data System (ADS)

    Bright, Vivien Bianca; Bloss, William James; Cai, Xiaoming

    2013-04-01

    Street canyons, formed by rows of buildings in urban environments, are associated with high levels of atmospheric pollutants emitted primarily from vehicles, and substantial human exposure. The street canyon forms a semi-enclosed environment, within which emissions may be entrained in a re-circulatory system; chemical processing of emitted compounds alters the composition of the air vented to the overlying boundary layer, compared with the primary emissions. As the prevailing atmospheric chemistry is highly non-linear, and the canyon mixing and predominant chemical reaction timescales are comparable, the combined impacts of dynamics and chemistry must be considered to quantify these effects. Here we report a model study of the coupled impacts of dynamical and chemical processing upon the atmospheric composition in a street canyon environment, to assess the impacts upon air pollutant levels within the canyon, and to quantify the extent to which within-canyon chemical processing alters the composition of canyon outflow, in comparison to the primary emissions within the canyon. A new model for the simulation of street canyon atmospheric chemical processing has been developed, by integrating an existing Large-Eddy Simulation (LES) dynamical model of canyon atmospheric motion with a detailed chemical reaction mechanism, a Reduced Chemical Scheme (RCS) comprising 51 chemical species and 136 reactions, based upon a subset of the Master Chemical Mechanism (MCM). The combined LES-RCS model is used to investigate the combined effects of mixing and chemical processing upon air quality within an idealised street canyon. The effect of the combination of dynamical (segregation) and chemical effects is determined by comparing the outputs of the full LES-RCS canyon model with those obtained when representing the canyon as a zero-dimensional box model (i.e. assuming mixing is complete and instantaneous). The LES-RCS approach predicts lower (canyon-averaged) levels of NOx, OH and HO

  6. Implementation of a Research-Based Lab Module in a High School Chemistry Curriculum: A Study of Classroom Dynamics

    ERIC Educational Resources Information Center

    Pilarz, Matthew

    2013-01-01

    For this study, a research-based lab module was implemented in two high school chemistry classes for the purpose of examining classroom dynamics throughout the process of students completing the module. A research-based lab module developed for use in undergraduate laboratories by the Center for Authentic Science Practice in Education (CASPiE) was…

  7. Implementation of a Research-Based Lab Module in a High School Chemistry Curriculum: A Study of Classroom Dynamics

    ERIC Educational Resources Information Center

    Pilarz, Matthew

    2013-01-01

    For this study, a research-based lab module was implemented in two high school chemistry classes for the purpose of examining classroom dynamics throughout the process of students completing the module. A research-based lab module developed for use in undergraduate laboratories by the Center for Authentic Science Practice in Education (CASPiE) was…

  8. Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

    PubMed

    Kwac, Kijeong; Lee, Chewook; Jung, Yousung; Han, Jaebeom; Kwak, Kyungwon; Zheng, Junrong; Fayer, M D; Cho, Minhaeng

    2006-12-28

    Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

  9. Comparative molecular surface analysis (CoMSA) for virtual combinatorial library screening of styrylquinoline HIV-1 blocking agents.

    PubMed

    Niedbala, Halina; Polanski, Jaroslaw; Gieleciak, Rafal; Musiol, Robert; Tabak, Dominik; Podeszwa, Barbara; Bak, Andrzej; Palka, Anna; Mouscadet, Jean-Francois; Gasteiger, Johann; Le Bret, Marc

    2006-12-01

    We used comparative molecular surface analysis to design molecules for the synthesis as part of the search for new HIV-1 integrase inhibitors. We analyzed the virtual combinatorial library (VCL) constituted from various moieties of styrylquinoline and styrylquinazoline inhibitors. Since imines can be applied in a strategy of dynamic combinatorial chemistry (DCC), we also tested similar compounds in which the -C=N- or -N=C- linker connected the heteroaromatic and aromatic moieties. We then used principal component analysis (PCA) or self-organizing maps (SOM), namely, the Kohonen neural networks to obtain a clustering plot analyzing the diversity of the VCL formed. Previously synthesized compounds of known activity, used as molecular probes, were projected onto this plot, which provided a set of promising virtual drugs. Moreover, we further modified the above mentioned VCL to include the single bond linker -C-N- or -N-C-. This allowed increasing compound stability but expanded also the diversity between the available molecular probes and virtual targets. The application of the CoMSA with SOM indicated important differences between such compounds and active molecular probes. We synthesized such compounds to verify the computational predictions.

  10. Combinatorial electrochemistry on Al Fe alloys

    NASA Astrophysics Data System (ADS)

    Ionut Mardare, Andrei; Prasad Yadav, Amar; Wieck, Andreas Dirk; Stratmann, Martin; Hassel, Achim Walter

    2008-07-01

    Combinatorial material development was combined with high throughput microelectrochemistry to allow an efficient but comprehensive investigation of the interface chemistry of Al rich Al Fe alloys as a function of their chemical composition. Composition spread thin films with a linear composition gradient were produced by thermal codeposition. A scanning droplet cell was used to determine the open circuit potential and to perform successive anodic oxide formation with intermittent impedance spectroscopy. The film formation factor, the relative permittivity of the oxides and the onset potential of oxide formation were determined quantitatively as function of the composition with a resolution of 0.5 at.%. An unexpected synergistic effect is found in a very narrow composition range between 9 and 12 at.% Fe. This effect, which shifts the onset potential by nearly 1 V, is discussed in terms of a local accumulation of Fe resulting in a redox stabilisation of space charge layer formation during high-field oxide growth. The results are supported by composition and depth dependent XPS measurements. Corrections were made to figures 5 and 6 of this article on 19 September 2008.

  11. Dynamic regulation of a cell adhesion protein complex including CADM1 by combinatorial analysis of FRAP with exponential curve-fitting.

    PubMed

    Sakurai-Yageta, Mika; Maruyama, Tomoko; Suzuki, Takashi; Ichikawa, Kazuhisa; Murakami, Yoshinori

    2015-01-01

    Protein components of cell adhesion machinery show continuous renewal even in the static state of epithelial cells and participate in the formation and maintenance of normal epithelial architecture and tumor suppression. CADM1 is a tumor suppressor belonging to the immunoglobulin superfamily of cell adhesion molecule and forms a cell adhesion complex with an actin-binding protein, 4.1B, and a scaffold protein, MPP3, in the cytoplasm. Here, we investigate dynamic regulation of the CADM1-4.1B-MPP3 complex in mature cell adhesion by fluorescence recovery after photobleaching (FRAP) analysis. Traditional FRAP analysis were performed for relatively short period of around 10 min. Here, thanks to recent advances in the sensitive laser detector systems, we examine FRAP of CADM1 complex for longer period of 60 min and analyze the recovery with exponential curve-fitting to distinguish the fractions with different diffusion constants. This approach reveals that the fluorescence recovery of CADM1 is fitted to a single exponential function with a time constant (τ) of approximately 16 min, whereas 4.1B and MPP3 are fitted to a double exponential function with two τs of approximately 40-60 sec and 16 min. The longer τ is similar to that of CADM1, suggesting that 4.1B and MPP3 have two distinct fractions, one forming a complex with CADM1 and the other present as a free pool. Fluorescence loss in photobleaching analysis supports the presence of a free pool of these proteins near the plasma membrane. Furthermore, double exponential fitting makes it possible to estimate the ratio of 4.1B and MPP3 present as a free pool and as a complex with CADM1 as approximately 3:2 and 3:1, respectively. Our analyses reveal a central role of CADM1 in stabilizing the complex with 4.1B and MPP3 and provide insight in the dynamics of adhesion complex formation.

  12. Aircraft-based investigation of Dynamics-Aerosol-Chemistry-Cloud Interactions in Southern West Africa

    NASA Astrophysics Data System (ADS)

    Flamant, Cyrille

    2017-04-01

    The EU-funded project DACCIWA (Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa, http://www.dacciwa.eu) is investigating the relationship between weather, climate and air pollution in southern West Africa. The air over the coastal region of West Africa is a unique mixture of natural and anthropogenic gases, liquids and particles, emitted in an environment, in which multi-layer cloud decks frequently form. These exert a large influence on the local weather and climate, mainly due to their impact on radiation, the surface energy balance and thus the diurnal cycle of the atmospheric boundary layer. The main objective for the aircraft detachment was to build robust statistics of cloud properties in southern West Africa in different chemical landscapes to investigate the physical processes involved in their life cycle in such a complex chemical environment. As part of the DACCIWA field campaigns, three European aircraft (the German DLR Falcon 20, the French SAFIRE ATR 42 and the British BAS Twin Otter) conducted a total of 50 research flights across Ivory Coast, Ghana, Togo, and Benin from 27 June to 16 July 2016 for a total of 155 flight hours, including hours sponsored through 3 EUFAR projects. The aircraft were used in different ways based on their strengths, but all three had comparable instrumentation with the the capability to do gas-phase chemistry, aerosol and clouds, thereby generating a rich dataset of atmospheric conditions across the region. Eight types of flight objectives were conducted to achieve the goals of the DACCIWA: (i) Stratus clouds, (ii) Land-sea breeze clouds, (iii) Mid-level clouds, (iv) Biogenic emission, (v) City emissions, (vi) Flaring and ship emissions, (vii) Dust and biomass burning aerosols, and (viii) air-sea interactions. An overview of the DACCIWA aircraft campaign as well as first highlights from the airborne observations will be presented.

  13. Spatial and Temporal Dynamics of Carbonate Chemistry in the Northwestern Hawaiian Islands

    NASA Astrophysics Data System (ADS)

    Coughlin, C.; Winn, C. D.; Kahng, S.

    2014-12-01

    The rapid increase in atmospheric and surface ocean CO2 concentrations has the potential to drastically alter the metabolic processes particularly in nearshore ecosystems. However, much of what is known about carbonate chemistry is based on observations and analysis of surface waters of the open ocean where spatial and temporal variability is far less dynamic than in nearshore coral reef ecosystems. Carbon system dynamics data from four consecutive years has been examined in the coastal and nearshore waters of the Papahānaumokuākea Marine National Monument in the Northwest Hawaiian Islands. This data has been collected for the purpose of improving our understanding of the carbon system dynamics in this unique and pristine environment. The data collected includes continuous CTD data and discrete bottle samples, as well as continuous underway measurements. In addition to standard hydrographic profile data, water column alkalinity and pH have been measured on discrete water samples, and continuous underway measurements of pCO2 and pH have been obtained. This data is used to investigate the impact of NWHI coral reef ecosystems on the carbon system in and surrounding the archipelago. The data demonstrates that a significant "island mass effect" with respect to the oceanographic carbon system exists around the islands within the archipelago. In addition, spatial and temporal variability of several oceanographic features that exhibit a radial, latitudinal, or longitudinal gradient in the nearshore waters of the NWHI islands, islets, and atolls will be described. Finally, a shallow pH maximum coincident with the shallow oxygen maximum is observed, which suggests an open ocean feature substantially influenced by turbulence surrounding the islands within the monument. The data analysis and coral reef ecosystem monitoring will aid in developing a long-term plan to assist in the sustainability of Papahānaumokuākea Marine National Monument.

  14. Strain-Induced Reactivity in the Dynamic Covalent Chemistry of Macrocyclic Imines.

    PubMed

    Ratjen, Lars; Vantomme, Ghislaine; Lehn, Jean-Marie

    2015-07-06

    The displacement of molecular structures from their thermodynamically most stable state by imposition of various types of electronic and conformational constraints generates highly strained entities that tend to release the accumulated strain energy by undergoing either structural changes or chemical reactions. The latter case amounts to strain-induced reactivity (SIR) that may enforce specific chemical transformations. A particular case concerns dynamic covalent chemistry which may present SIR, whereby reversible reactions are activated by coupling to a high-energy state. We herewith describe such a dynamic covalent chemical (DCC) system involving the reversible imine formation reaction. It is based on the formation of strained macrocyclic bis-imine metal complexes in which the macrocyclic ligand is in a high energy form enforced by the coordination of the metal cation. Subsequent demetallation generates a highly strained free macrocycle that releases its accumulated strain energy by hydrolysis and reassembly into a resting state. Specifically, the metal-templated condensation of a dialdehyde with a linear diamine leads to a bis-imine [1+1]-macrocyclic complex in which the macrocyclic ligand is in a coordination-enforced strained conformation. Removal of the metal cation by a competing ligand yields a highly reactive [1+1]-macrocycle, which then undergoes hydrolysis to transient non-cyclic aminoaldehyde species, which then recondense to a strain-free [2+2]-macrocyclic resting state. The process can be monitored by (1) H NMR spectroscopy. Energy differences between different conformational states have been evaluated by Hartree-Fock (HF) computations. One may note that the stabilisation of high-energy molecular forms by metal ion coordination followed by removal of the latter, offers a general procedure for producing out-of-equilibrium molecular states, the fate of which may then be examined, in particular when coupled to dynamic covalent chemical processes.

  15. Statistical Mechanics of Combinatorial Auctions

    NASA Astrophysics Data System (ADS)

    Galla, Tobias; Leone, Michele; Marsili, Matteo; Sellitto, Mauro; Weigt, Martin; Zecchina, Riccardo

    2006-09-01

    Combinatorial auctions are formulated as frustrated lattice gases on sparse random graphs, allowing the determination of the optimal revenue by methods of statistical physics. Transitions between computationally easy and hard regimes are found and interpreted in terms of the geometric structure of the space of solutions. We introduce an iterative algorithm to solve intermediate and large instances, and discuss competing states of optimal revenue and maximal number of satisfied bidders. The algorithm can be generalized to the hard phase and to more sophisticated auction protocols.

  16. Effect of water chemistry upsets on the dynamics of corrective reagent dosing systems at thermal power stations

    NASA Astrophysics Data System (ADS)

    Voronov, V. N.; Yegoshina, O. V.; Bolshakova, N. A.; Yarovoi, V. O.; Latt, Aie Min

    2016-12-01

    Typical disturbances in the dynamics of a corrective reagent dosing system under unsteady-state conditions during the unsatisfactory operation of a chemical control system with some water chemistry upsets at thermal and nuclear power stations are considered. An experimental setup representing a physical model for the water chemistry control system is described. The two disturbances, which are most frequently encountered in water chemistry control practice, such as a breakdown or shutdown of temperature compensation during pH measurement and an increase in the heat-transfer fluid flow rate, have been modeled in the process of study. The study of the effect produced by the response characteristics of chemical control analyzers on the operation of a reagent dosing system under unsteady-state conditions is important for the operative control of a water chemistry regime state. The effect of temperature compensation during pH measurement on the dynamics of an ammonia-dosing system in the manual and automatic cycle chemistry control modes has been studied. It has been demonstrated that the reading settling time of a pH meter in the manual ammonia- dosing mode grows with a breakdown in temperature compensation and a simultaneous increase in the temperature of a heat-transfer fluid sample. To improve the efficiency of water chemistry control, some systems for the quality control of a heat-transfer fluid by a chemical parameter with the obligatory compensation of a disturbance in its flow rate have been proposed for use. Experimental results will possibly differ from industrial data due to a great length of sampling lines. For this reason, corrective reagent dosing systems must be adapted to the conditions of a certain power-generating unit in the process of their implementation.

  17. NON-EQUILIBRIUM CHEMISTRY OF DYNAMICALLY EVOLVING PRESTELLAR CORES. II. IONIZATION AND MAGNETIC FIELD

    SciTech Connect

    Tassis, Konstantinos; Willacy, Karen; Yorke, Harold W.; Turner, Neal J.

    2012-07-20

    We study the effect that non-equilibrium chemistry in dynamical models of collapsing molecular cloud cores has on measurements of the magnetic field in these cores, the degree of ionization, and the mean molecular weight of ions. We find that OH and CN, usually used in Zeeman observations of the line-of-sight magnetic field, have an abundance that decreases toward the center of the core much faster than the density increases. As a result, Zeeman observations tend to sample the outer layers of the core and consistently underestimate the core magnetic field. The degree of ionization follows a complicated dependence on the number density at central densities up to 10{sup 5} cm{sup -3} for magnetic models and 10{sup 6} cm{sup -3} in non-magnetic models. At higher central densities, the scaling approaches a power law with a slope of -0.6 and a normalization which depends on the cosmic-ray ionization rate {zeta} and the temperature T as ({zeta}T){sup 1/2}. The mean molecular weight of ions is systematically lower than the usually assumed value of 20-30, and, at high densities, approaches a value of 3 due to the asymptotic dominance of the H{sup +}{sub 3} ion. This significantly lower value implies that ambipolar diffusion operates faster.

  18. Making the Earth: Combining dynamics and chemistry in the Solar System

    NASA Astrophysics Data System (ADS)

    Bond, Jade C.; Lauretta, Dante S.; O'Brien, David P.

    2010-02-01

    No terrestrial planet formation simulation completed to date has considered the detailed chemical composition of the planets produced. While many have considered possible water contents and late veneer compositions, none have examined the bulk elemental abundances of the planets produced as an important check of formation models. Here we report on the first study of this type. Bulk elemental abundances based on disk equilibrium studies have been determined for the simulated terrestrial planets of O'Brien et al. [O'Brien, D.P., Morbidelli, A., Levison, H.F., 2006. Icarus 184, 39-58]. These abundances are in excellent agreement with observed planetary values, indicating that the models of O'Brien et al. [O'Brien, D.P., Morbidelli, A., Levison, H.F., 2006. Icarus 184, 39-58] are successfully producing planets comparable to those of the Solar System in terms of both their dynamical and chemical properties. Significant amounts of water are accreted in the present simulations, implying that the terrestrial planets form "wet" and do not need significant water delivery from other sources. Under the assumption of equilibrium controlled chemistry, the biogenic species N and C still need to be delivered to the Earth as they are not accreted in significant proportions during the formation process. Negligible solar photospheric pollution is produced by the planetary formation process. Assuming similar levels of pollution in other planetary systems, this in turn implies that the high metallicity trend observed in extrasolar planetary systems is in fact primordial.

  19. Active Upper-atmosphere Chemistry and Dynamics from Polar Circulation Reversal on Titan

    NASA Technical Reports Server (NTRS)

    Teanby, Nicholas A.; Irwin, Patrick Gerard Joseph; Nixon, Conor A.; DeKok, Remco; Vinatier, Sandrine; Coustenis, Athena; Sefton-Nash, Elliot; Calcutt, Simon B.; Flasar, Michael F.

    2012-01-01

    Saturn's moon Titan has a nitrogen atmosphere comparable to Earth's, with a surface pressure of 1.4 bar. Numerical models reproduce the tropospheric conditions very well but have trouble explaining the observed middle-atmosphere temperatures, composition and winds. The top of the middle-atmosphere circulation has been thought to lie at an altitude of 450 to 500 kilometres, where there is a layer of haze that appears to be separated from the main haze deck. This 'detached' haze was previously explained as being due to the colocation of peak haze production and the limit of dynamical transport by the circulation's upper branch. Herewe report a build-up of trace gases over the south pole approximately two years after observing the 2009 post-equinox circulation reversal, from which we conclude that middle-atmosphere circulation must extend to an altitude of at least 600 kilometres. The primary drivers of this circulation are summer-hemisphere heating of haze by absorption of solar radiation and winter-hemisphere cooling due to infrared emission by haze and trace gases; our results therefore imply that these effects are important well into the thermosphere (altitudes higher than 500 kilometres). This requires both active upper-atmosphere chemistry, consistent with the detection of high-complexity molecules and ions at altitudes greater than 950 kilometres, and an alternative explanation for the detached haze, such as a transition in haze particle growth from monomers to fractal structures.

  20. Ozone budgets from the Dynamics and Chemistry of Marine Stratocumulus experiment

    NASA Technical Reports Server (NTRS)

    Kawa, S. R.; Pearson, R., Jr.

    1989-01-01

    Measurements from the Dynamics and Chemistry of marine Stratocumulus experiment have been used to study components of the regional ozone budget. The surface destruction rate is determined by eddy correlation of ozone and vertical velocity measured by a low-flying aircraft. Significant variability is found in the measured surface resistance; it is partially correlated with friction velocity but appears to have other controlling influences as well. The mean resistance is 4190 s/m which is higher (slower destruction) than most previous estimates for seawater. Flux and mean measurements throughout the marine boundary layer are used to estimate the net rate of in situ photochemical production/destruction of ozone. Averaged over the flights, ozone concentration is found to be near steady state, and a net of photochemical destruction of 0.02-0.07 ng/cu m per sec is diagnosed. This is an important confirmation of photochemical model results for the remote marine boundary layer. Ozone vertical distributions above the boundary layer show a strongly layered structure with very sharp gradients. These distributions are possibly related to the stratospheric ozone source.

  1. Light Weight UAVs for Unravelling the Nexus Between Chemistry, Physics and Dynamics

    NASA Astrophysics Data System (ADS)

    Ramanathan, V.

    2015-12-01

    New discoveries in atmospheric sciences involve unravelling the interactions and feedback processes between chemitsry, physics and dynamics. One of the most complex of such problems is the role of aerosol-clouds-climate interactions in climate change. During the last 7 years we have designed field experiments with light weight UAVs that are flown in stacked as well as formation flying patterns to map out the three dimensional structure of the atmosphere. Such formation and stacked formation flights have enabled us to measure simulatneously aerosol chemistry, cloud micro physics, cloud albedo, divergence of radiative heating of the atmosphere and more recently the vertical structure of turbulent fluxes of water avpor and momentum. These first-such measurments have provided new insights into the role of aerosols in cloud albedo; vertical distribution of black and brown carbon heating; role of absorbing aerosols in the melting of Himalayan glaciers; role of mixing state of aerosols in aerosol forcing and recently the link between absorbing aerosols and turbulent fluxes. All of the instruments had to be miniaturized to fit into the UAVs with maximum of 6 kg of payload. The most impprtant aspects of our studies are that the instruments and their intergration with the UAvs were all developed by post doctoral candidates and students. Thus the light weight UAVs are ideal platforms for making pioneerign studies by students and young scientists.

  2. Smart macrocyclic molecules: induced fit and ultrafast self-sorting inclusion behavior through dynamic covalent chemistry.

    PubMed

    Han, Ji-Min; Pan, Jin-Long; Lei, Ting; Liu, Chenjiang; Pei, Jian

    2010-12-10

    A family of macrocycles with oligo(ethylene glycol) chains, 4O, 5O, and 6O, was developed to construct a series of new incorporated macrocycles through dynamic covalent chemistry. These flexible macrocycles exhibited excellent "self-sorting" abilities with diamine compounds, which depended on the "induced-fit" rule. For instance, the host macrocycles underwent conformational modulation to accommodate the diamine guests, affording [1+1] intramolecular addition compounds regardless of the flexibility of the diamine. These macrocycles folded themselves to fit various diamines with different chain length through modulation of the flexible polyether chain, and afforded intramolecular condensation products. However, if the chain of the diamine was too long and rigid, oligomers or polymers were obtained from the mixture of the macromolecule and the diamine. All results demonstrated that inclusion compounds involving conformationally suitable aromatic diamines were thermodynamically favorable candidates in the mixture due to the restriction of the macrocycle size. Furthermore, kinetic and thermodynamic studies of self-sorting behaviors of both mixed 4O-5O and 4O-6O systems were investigated in detail. Finally, theoretical calculations were also employed to further understand such self-sorting behavior, and indicated that the large enthalpy change of H(2)NArArNH(2)@4O is the driving force for the sorting behavior. Our system may provide a model to further understand the principle of biomolecules with high specificity due only to their conformational self-adjusting ability.

  3. Active upper-atmosphere chemistry and dynamics from polar circulation reversal on Titan.

    PubMed

    Teanby, Nicholas A; Irwin, Patrick G J; Nixon, Conor A; de Kok, Remco; Vinatier, Sandrine; Coustenis, Athena; Sefton-Nash, Elliot; Calcutt, Simon B; Flasar, F Michael

    2012-11-29

    Saturn's moon Titan has a nitrogen atmosphere comparable to Earth's, with a surface pressure of 1.4 bar. Numerical models reproduce the tropospheric conditions very well but have trouble explaining the observed middle-atmosphere temperatures, composition and winds. The top of the middle-atmosphere circulation has been thought to lie at an altitude of 450 to 500 kilometres, where there is a layer of haze that appears to be separated from the main haze deck. This 'detached' haze was previously explained as being due to the co-location of peak haze production and the limit of dynamical transport by the circulation's upper branch. Here we report a build-up of trace gases over the south pole approximately two years after observing the 2009 post-equinox circulation reversal, from which we conclude that middle-atmosphere circulation must extend to an altitude of at least 600 kilometres. The primary drivers of this circulation are summer-hemisphere heating of haze by absorption of solar radiation and winter-hemisphere cooling due to infrared emission by haze and trace gases; our results therefore imply that these effects are important well into the thermosphere (altitudes higher than 500 kilometres). This requires both active upper-atmosphere chemistry, consistent with the detection of high-complexity molecules and ions at altitudes greater than 950 kilometres, and an alternative explanation for the detached haze, such as a transition in haze particle growth from monomers to fractal structures.

  4. Dynamic adaptive chemistry with operator splitting schemes for reactive flow simulations

    NASA Astrophysics Data System (ADS)

    Ren, Zhuyin; Xu, Chao; Lu, Tianfeng; Singer, Michael A.

    2014-04-01

    A numerical technique that uses dynamic adaptive chemistry (DAC) with operator splitting schemes to solve the equations governing reactive flows is developed and demonstrated. Strang-based splitting schemes are used to separate the governing equations into transport fractional substeps and chemical reaction fractional substeps. The DAC method expedites the numerical integration of reaction fractional substeps by using locally valid skeletal mechanisms that are obtained using the directed relation graph (DRG) reduction method to eliminate unimportant species and reactions from the full mechanism. Second-order temporal accuracy of the Strang-based splitting schemes with DAC is demonstrated on one-dimensional, unsteady, freely-propagating, premixed methane/air laminar flames with detailed chemical kinetics and realistic transport. The use of DAC dramatically reduces the CPU time required to perform the simulation, and there is minimal impact on solution accuracy. It is shown that with DAC the starting species and resulting skeletal mechanisms strongly depend on the local composition in the flames. In addition, the number of retained species may be significant only near the flame front region where chemical reactions are significant. For the one-dimensional methane/air flame considered, speed-up factors of three and five are achieved over the entire simulation for GRI-Mech 3.0 and USC-Mech II, respectively. Greater speed-up factors are expected for larger chemical kinetics mechanisms.

  5. The Department of Energy's Hydrogen Storage Activities: Challenges and Needs in Chemistry and Chemical Dynamics

    NASA Astrophysics Data System (ADS)

    Satyapal, Sunita; Ordaz, Grace; Petrovic, John; Read, Carole; Thomas, George

    2006-03-01

    Hydrogen storage is a key area of research funded by the Department of Energy. Hydrogen, the simplest diatomic molecule known, has the highest energy content of all known fuels by mass, but the practical storage of sufficient hydrogen on-board a vehicle is a significant technological challenge. Hydrogen can be stored via various mechanisms within materials such as metal hydrides (e.g. LiBH4, AlH3) chemical hydrides (e.g. organic liquids), and nanostructured sorbents (e.g. carbon nanotubes, clathrates). Examples of mechanisms include physisorption, chemisorption, dissociative adsorption or combinations of the above. In addition to weight and volume, the kinetics of hydrogen charging and discharging as well as durability must be addressed. A fundamental understanding of hydrogen storage to help optimize materials is critical. The technical requirements for hydrogen storage, as well as some of the promises and challenges will be presented, with a focus on what chemical dynamics and chemistry can offer in solving the challenge of hydrogen storage for transportation applications.

  6. Crystallization of macromolecular complexes: combinatorial complex crystallization

    NASA Astrophysics Data System (ADS)

    Stura, Enrico A.; Graille, Marc; Charbonnier, Jean-Baptiste

    2001-11-01

    antigens. We find that such binding involves only the well conserved framework region of the variable domain of the antibody heavy chain (VH) and does not affect the conformation of the hypervariable loops that define the antigen recognition site. Thus this domain could be used to complex to Fab or Fv fragments derived from a wide variety of antibodies. While protein A complexes with the VH domain, protein L recognizes the VL region of immunoglobulins. Our recent study of the interaction between an Fab and a domain of protein L shows that the situation is very similar. Indeed this domain binds to the VL framework region outside the antigen binding site. Since individual domains from each of these three multi-domain proteins bind to well separated and independent locations on immunoglobulins, they can be combined to search for a suitable crystalline lattice. This allows us to propose a combinatorial method as a rational way to exploit antibody complexation for the crystallographic structure determination of proteins that are otherwise difficult to crystallize. The overall method has strong parallels with other combinatorial methods used elsewhere in biology and chemistry, and we propose that together with stoichiometry variation screening (SVS), it may further enhance the probability of crystallization.

  7. Inorganic thin-film combinatorial studies for rapidly optimising functional properties.

    PubMed

    Kafizas, Andreas; Parkin, Ivan P

    2012-01-21

    Combinatorial chemistry is now commonplace in the pharmaceutical industry and applied rigorously in the discovery of drugs. Within materials science, combinatorial methods have been widely applied in investigating thin-films and since its re-introduction in the mid 90's more than 20 new families of materials have been discovered. Yet, given the high diversity of states that can be produced in a single deposition, such methods are now being used more prominently to optimise functional properties of existing materials; having been applied in a variety of fields. In this review we will cover the key developments in bandgap, ferro/di-electric, fuel cell anode/ cathode, H(2) storage, hardness, Li battery electrodes, luminescence, transparent ferro-magnetic, photocatalytic, photovoltaic, shape-memory, transparent conducting oxide and thermo-electric materials optimisation. The critical review focuses on how functional-property relationships have been derived from combinatorial studies (217 references).

  8. Hierarchical functional gradients of pH-responsive self-assembled monolayers using dynamic covalent chemistry on surfaces.

    PubMed

    Tauk, Lara; Schröder, André P; Decher, Gero; Giuseppone, Nicolas

    2009-11-01

    Surface chemistry is an important field of research, especially for the study and design of (bio)nanostructures in which nearly every atom lies at an interface. Here we show that dynamic covalent chemistry is an efficient tool for functionalizing surfaces in such a way that their interfacial properties can be varied controllably in space and time. Modulation of pH is used to tune the fast, selective and reversible attachment of functional amines (with different pK(a) values) to an aldehyde-coated surface. To illustrate the potential of this technique, we developed dynamic self-assembled monolayers ('DynaSAMs'), which enable the hierarchical construction of mixed gradients comprising either small functional molecules or proteins. Control of the (bio)chemical composition at any point on the surface potentially provides a simple bottom-up method to access numerous surface patterns with a broad range of functionalities.

  9. Use of a two-tiered dynamic chamber to investigate indoor air chemistry

    NASA Astrophysics Data System (ADS)

    Wainman, Thomas

    A two tiered dynamic chamber was assembled for the purpose of investigating indoor air chemistry. This design consists of a smaller chamber nested inside of a larger one and allows for conditions of temperature, relative humidity, and surfaces types to be carefully controlled. Three series of experiments were conducted investigating different aspects of indoor air chemistry. The first series of experiments investigated the effects of relative humidity and surface type on nitrous acid (HONO) formation from the reaction of nitrogen dioxide (NO2) with water vapor (H2O). The experimental results show that both surface type and relative humidity play a large role in the production and lifetime of HONO in indoor environments. Synthetic carpet increased the NO2 deposition velocity by nearly an order of magnitude and doubled the peak HONO/NO2 ratio. Vinyl wallpaper was found to act as a sink/source for HONO and the HONO emission rate from the wallpaper was found to be directly proportional to the HONO/NO 2 ratio. A second series of experiments investigated the production of nitric acid (HNO3) through the reaction of NO2 and ozone (O 3). HNO3 formation was determined by measuring particles formed by its reaction with ammonia (NH3) and was found to be dependent relative humidity. Indoor HNO3 is often considered to be the result of infiltration of ambient air. The results of this work show clearly that indoor sources of HNO3 exist. A third series of experiments investigated secondary particle formation through the reaction of O3 and limonene. Significant mass concentrations as a result of the limonene-O3 reaction were produced in all of the experiments. The occurrence of this and other indoor sources of fine particles make it seem unlikely that the new NAAQS for PM2.5 will be attained in indoor environments where people obtain a significant fraction of their total particle exposure. In view of the significance of indoor particle sources to overall exposure, long term studies

  10. Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation

    NASA Astrophysics Data System (ADS)

    Shiraiwa, M.; Yee, L. D.; Schilling, K.; Loza, C. L.; Craven, J. S.; Zuend, A.; Ziemann, P. J.; Seinfeld, J.

    2013-12-01

    Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosol (SOA). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multi-generation gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a mid-experiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. The results of the current work have a number of implications for SOA models. While the dynamics of an aerosol size distribution reflects the mechanism of growth, we demonstrate here that it provides a key constraint in interpreting laboratory and ambient SOA formation. This work, although carried out specifically for the long chain alkane, dodecane, is expected to be widely applicable to other major classes of SOA precursors. SOA consists of a myriad of organic compounds containing various functional groups, which can generally undergo heterogeneous/multiphase reactions forming low-volatility products such as oligomers and other high molecular mass compounds. If particle-phase chemistry is indeed

  11. Probing the chemistry, structure, and dynamics of the water-silica interface

    NASA Astrophysics Data System (ADS)

    Lockwood, Glenn K.

    Despite its natural abundance and wide-ranging technological relevance, much remains unknown or unclear about water-silica interfaces. Computer simulation stands to bridge the gaps of knowledge left by experiment, and a recently developed Dissociative Water Potential has enabled the simulation of large amorphous silica surfaces in contact with water without having to impose a model of surface chemistry a priori. Earlier work with this model has revealed the existence of several protonated surface sites such as SiOH2 + and Si-(OH+)-Si that have yet to be extensively characterized. However, both experiment and quantum mechanical simulation have provided an increasing body of evidence that suggests these sites exist, and these sites may play key roles in some of the unexplained phenomena observed in water-silica systems. To this end, this Dissociative Water Potential has been applied to develop a comprehensive picture of the chemistry, structure, and dynamics of the water-silica interface that is unbiased by any expectation of what sites should form. The bridging OH site, Si-(OH+)-Si, does form and is characterized as a highly acidic site that occurs predominantly on strained Si-O-Si bridges near the interface. Similarly, the transient formation of SiOH2 + is observed, and this site is found to be more acidic than Si-(OH +)-Si. In addition to H3O+ that forms near the interface, all of these sites readily deprotonate and are expected to play a role in the enhanced proton conductivity experimentally observed in hydrated mesoporous silica. The reactions between water and silica are particularly relevant to the engineering of nuclear waste forms, and the role of water-silica interactions are also explored within the context of the degradation of silica-based waste forms exposed to radiation. Despite the significant simulation effort employed in glassy waste form research, no molecular models of radiation damage in silica include the effects of moisture. This deficiency is

  12. Reversible control of pore size and surface chemistry of mesoporous silica through dynamic covalent chemistry: philicity mediated catalysis.

    PubMed

    Singh, Dheeraj Kumar; Pavan Kumar, B V V S; Eswaramoorthy, M

    2015-08-28

    Here, we report the synthesis of adaptive hybrid mesoporous silica having the ability to reconfigure its pore properties such as pore size and philicity in response to the external environment. Decyl chains were reversibly appended to the pore walls of silica through imine motifs as dynamic covalent modules to switch the pore size and philicity in response to pH. This switching of pore properties was used to gate the access of reactants to the gold nanoparticles immobilized inside the nanopores, thus enabling us to turn-on/turn-off the catalytic reaction. The use of such dynamic covalent modules to govern pore properties would enable the realization of intelligent hybrids capable of controlling many such chemical processes in response to stimuli.

  13. Reversible control of pore size and surface chemistry of mesoporous silica through dynamic covalent chemistry: philicity mediated catalysis

    NASA Astrophysics Data System (ADS)

    Singh, Dheeraj Kumar; Pavan Kumar, B. V. V. S.; Eswaramoorthy, M.

    2015-08-01

    Here, we report the synthesis of adaptive hybrid mesoporous silica having the ability to reconfigure its pore properties such as pore size and philicity in response to the external environment. Decyl chains were reversibly appended to the pore walls of silica through imine motifs as dynamic covalent modules to switch the pore size and philicity in response to pH. This switching of pore properties was used to gate the access of reactants to the gold nanoparticles immobilized inside the nanopores, thus enabling us to turn-on/turn-off the catalytic reaction. The use of such dynamic covalent modules to govern pore properties would enable the realization of intelligent hybrids capable of controlling many such chemical processes in response to stimuli.Here, we report the synthesis of adaptive hybrid mesoporous silica having the ability to reconfigure its pore properties such as pore size and philicity in response to the external environment. Decyl chains were reversibly appended to the pore walls of silica through imine motifs as dynamic covalent modules to switch the pore size and philicity in response to pH. This switching of pore properties was used to gate the access of reactants to the gold nanoparticles immobilized inside the nanopores, thus enabling us to turn-on/turn-off the catalytic reaction. The use of such dynamic covalent modules to govern pore properties would enable the realization of intelligent hybrids capable of controlling many such chemical processes in response to stimuli. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr02959g

  14. Reconstructing pedigrees: a combinatorial perspective.

    PubMed

    Steel, Mike; Hein, Jotun

    2006-06-07

    A pedigree is a directed graph that displays the relationship between individuals according to their parentage. We derive a combinatorial result that shows how any pedigree-up to individuals who have no extant (present-day) ancestors-can be reconstructed from (sex-labelled) pedigrees that describe the ancestry of single extant individuals and pairs of extant individuals. Furthermore, this reconstruction can be done in polynomial time. We also provide an example to show that the corresponding reconstruction result does not hold for pedigrees that are not sex-labelled. We then show how any pedigree can also be reconstructed from two functions that just describe certain circuits in the pedigree. Finally, we obtain an enumeration result for pedigrees that is relevant to the question of how many segregating sites are needed to reconstruct pedigrees.

  15. Combinatorial methods: aptamers and aptazymes

    NASA Astrophysics Data System (ADS)

    Ellington, Andrew D.; Hesselberth, Jay; Jhaveri, Sulay; Robertson, Michael P.

    1999-12-01

    Combinatorial methods have been used to generate nucleic acid molecules with specific characteristics. Aptamers are nucleic acid binding species, and can be modified to directly transduce molecular recognition to optical signals. Aptazymes are allosteric or effector-activated ribyzymes. We have designed or selected aptazymes that are responsive to a variety of ligands. In particular, we have selected a ribozyme ligase that is activated 10,000-fold in the presence of an oligonucleotide effector, and have designed ligases that are up to 1,600-fold dependent on small molecule effectors. Even in those instances where designed constructs were initially unresponsive, we have been able to use selection to optimize their response characteristics.

  16. Mapping the Materials Genome through Combinatorial Informatics

    NASA Astrophysics Data System (ADS)

    Rajan, Krishna

    2012-02-01

    The recently announced White House Materials Genome Initiative provides an exciting challenge to the materials science community. To meet that challenge one needs to address a critical question, namely what is the materials genome? Some guide on how to the answer this question can be gained by recognizing that a ``gene'' is a carrier of information. In the biological sciences, discovering how to manipulate these genes has generated exciting discoveries in fundamental molecular biology as well as significant advances in biotechnology. Scaling that up to molecular, cellular length scales and beyond, has spawned from genomics, fields such as proteomics, metabolomics and essentially systems biology. The ``omics'' approach requires that one needs to discover and track these ``carriers of information'' and then correlate that information to predict behavior. A similar challenge lies in materials science, where there is a diverse array of modalities of materials ``discovery'' ranging from new materials chemistries and molecular arrangements with novel properties, to the development and design of new micro- and mesoscale structures. Hence to meaningfully adapt the spirit of ``genomics'' style research in materials science, we need to first identify and map the ``genes'' across different materials science applications On the experimental side, combinatorial experiments have opened a new approach to generate data in a high throughput manner, but without a clear way to link that to models, the full value of that data is not realized. Hence along with experimental and computational materials science, we need to add a ``third leg'' to our toolkit to make the ``Materials Genome'' a reality, the science of Materials Informatics. In this presentation we provide an overview of how information science coupled to materials science can in fact achieve the goal of mapping the ``Materials Genome''.

  17. The use of dynamic surface chemistries to control msc isolation and function.

    PubMed

    Curran, J M; Pu, F; Chen, R; Hunt, J A

    2011-07-01

    Material modifications can be used to induce cell responses, in particular-CH(3) and -NH(2) have shown potential in enhancing the ability of a material to support mesenchymal stem cell (MSC) adhesion and differentiation. Currently this process is variable, due to the lack of definition of controlled contextual presentation of the chemical group of interest across the surface. This paper defines the potential of -CH(3) modified surfaces, with optimised dynamic surface chemistry, to manipulate initial MSC adhesive events, integrin binding, and subsequent cell function. An array of -CH(3) silane modified glass substrates was produced using different -CH(3) chain lengths and mechanisms of bonding to the base substrate. We show that changing the chain length affects the ability of the surfaces to support viable adult MSC adhesion, directly related to induced FGF release, and expression of STRO-1, CD29, 73, 90 and 105. Chlorodimethyloctylsilane (ODMCS) modified surfaces resulted in significant increases of associated adult MSC markers compared to all other -CH(3) modified and control substrates. In contrast Dichlorodimethylsilane (DMDCS) modified surfaces did not support adult MSC adhesion due to high levels of early FGF release, which had an inhibitory effect on adult MSC culture, but enhanced the efficiency and cell selective properties of the substrate in isolation of multi-potent progenitor/MSC from adult human whole blood. Incorporation of optimised -CH(3) groups is a cost effective route for producing substrates that significantly enhance MSC isolation and expansion, highlighting the potential of the optimised substrates to replace RGD and fibronectin modifications in selected applications. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. ALMA spectral survey of Supernova 1987A - molecular inventory, chemistry, dynamics and explosive nucleosynthesis

    NASA Astrophysics Data System (ADS)

    Matsuura, M.; Indebetouw, R.; Woosley, S.; Bujarrabal, V.; Abellán, F. J.; McCray, R.; Kamenetzky, J.; Fransson, C.; Barlow, M. J.; Gomez, H. L.; Cigan, P.; De Looze, I.; Spyromilio, J.; Staveley-Smith, L.; Zanardo, G.; Roche, P.; Larsson, J.; Viti, S.; van Loon, J. Th.; Wheeler, J. C.; Baes, M.; Chevalier, R.; Lundqvist, P.; Marcaide, J. M.; Dwek, E.; Meixner, M.; Ng, C.-Y.; Sonneborn, G.; Yates, J.

    2017-08-01

    We report the first molecular line survey of Supernova 1987A in the millimetre wavelength range. In the Atacama Large Millimeter/submillimeter Array (ALMA) 210-300 and 340-360 GHz spectra, we detected cold (20-170 K) CO, 28SiO, HCO+ and SO, with weaker lines of 29SiO from ejecta. This is the first identification of HCO+ and SO in a young supernova remnant. We find a dip in the J = 6-5 and 5-4 SiO line profiles, suggesting that the ejecta morphology is likely elongated. The difference of the CO and SiO line profiles is consistent with hydrodynamic simulations, which show that Rayleigh-Taylor instabilities cause mixing of gas, with heavier elements much more disturbed, making more elongated structure. We obtained isotopologue ratios of 28SiO/29SiO > 13, 28SiO/30SiO > 14 and 12CO/13CO > 21, with the most likely limits of 28SiO/29SiO >128, 28SiO/30SiO >189. Low 29Si and 30Si abundances in SN 1987A are consistent with nucleosynthesis models that show inefficient formation of neutron-rich isotopes in a low-metallicity environment, such as the Large Magellanic Cloud. The deduced large mass of HCO+ (∼5 × 10-6 M⊙) and small SiS mass (<6 × 10-5 M⊙) might be explained by some mixing of elements immediately after the explosion. The mixing might have caused some hydrogen from the envelope to sink into carbon- and oxygen-rich zones after the explosion, enabling the formation of a substantial mass of HCO+. Oxygen atoms may have penetrated into silicon and sulphur zones, suppressing formation of SiS. Our ALMA observations open up a new window to investigate chemistry, dynamics and explosive nucleosynthesis in supernovae.

  19. Seasonal dynamics of water and air chemistry in an indoor chlorinated swimming pool.

    PubMed

    Zare Afifi, Mehrnaz; Blatchley, Ernest R

    2015-01-01

    Although swimming is known to be beneficial in terms of cardiovascular health, as well as for some forms of rehabilitation, swimming is also known to present risks to human health, largely in the form of exposure to microbial pathogens and disinfection byproducts (DBPs). Relatively little information is available in the literature to characterize the seasonal dynamics of air and water chemistry in indoor chlorinated swimming pools. To address this issue, water samples were collected five days per week from an indoor chlorinated swimming pool facility at a high school during the academic year and once per week during summer over a fourteen-month period. The samples were analyzed for free and combined chlorine, urea, volatile DBPs, pH, temperature and total alkalinity. Membrane Introduction Mass Spectrometry (MIMS) was used to identify and measure the concentrations of eleven aqueous-phase volatile DBPs. Variability in the concentrations of these DBPs was observed. Factors that influenced variability included bather loading and mixing by swimmers. These compounds have the ability to adversely affect water and air quality and human health. A large fraction of the existing literature regarding swimming pool air quality has focused on trichloramine (NCl₃). For this work, gas-phase NCl₃ was analyzed by an air sparging-DPD/KI method. The results showed that gas-phase NCl₃ concentration is influenced by bather loading and liquid-phase NCl₃ concentration. Urea is the dominant organic-N compound in human urine and sweat, and is known to be an important precursor for producing NCl₃ in swimming pools. Results of daily measurements of urea indicated a link between bather load and urea concentration in the pool.

  20. Reconstructing monsoon dynamics on the Tibetan Plateau using ostracod shell chemistry

    NASA Astrophysics Data System (ADS)

    Boerner, N.; De Baere, B.; Yang, Q.; Francois, R. H. G. M.; Jochum, K. P.; Frenzel, P.; Schwalb, A.

    2014-12-01

    Ostracod shells have widely been used as source material for geochemical analysis of stable isotope and trace element composition in paleolimnological reconstruction of lake hydrochemistry and climate as they provide insight into past water balance and solute evolution of lakes. During five fieldtrips to the Tibetan Plateau, taking place between 2008 and 2012, we collected live and sub-recent ostracods from 333 sites. Hydrochemical parameters, such as temperature, electrical conductivity, pH as well as major and minor ion concentrations were measured at each site and show high variability between sites. Adult intact individuals from the most common ostracod taxa were selected and their shell chemistry analyzed. The trace elemental data for the living ostracods compared to the hydrological data provides a calibration dataset for further hydrological and thus climatological reconstruction. Mg/Ca, Sr/Ca and Ba/Ca ratios in ostracod shells provide information about past water temperature and salinity resulting from changes in precipitation vs. evaporation ratios and monsoon activity. Furthermore, Mn/Ca, Fe/Ca and U/Ca ratios are being explored as redox indicators to reconstruct oxygenation cycles. To reconstruct the monsoon dynamics on the Tibetan Plateau, sediment cores from different lakes on an east-west transect were taken: two long sediment cores from lakes Nam Co and Tangra Yumco, covering the past 20,000 years, and a short core from Lake Taro Co. The lakes feature an alkaline environment but show significant differences in their electrical conductivity ranging from 0.99 mS/cm (Taro Co) and 1.8 mS/cm (Nam Co) to 12 mS/cm (Tangra Yumco). The chemical composition of valves of the most common ostracod species in these lakes, Leucocytherella sinensis, was analyzed using laser ablation ICP-MS. The reconstruction provides a more extensive insight in past precipitation - evaporation balance and lake level change and provides clues about the interaction between the

  1. Chemistry and dynamics: a post-processing tool towards a real coupling

    NASA Astrophysics Data System (ADS)

    Valdivia, V.; Godard, B.; Hennebelle, P.; Gerin, M.; Lesaffre, P.

    2016-12-01

    Chemistry plays a key role in the comparison between observations and theoretical predictions, but its treatment in numerical simulations is a real challenge. In particular the full treatment of the chemistry requires to solve simultaneously hundreds to thousands of reactions, constraining the time-steps to be as small as the smallest one. Fortunately, several species reach the chemical equilibrium much faster than others, and careful choices allow to describe the chemical state in a simpler manner. Here we present a hybrid approach to treat the chemistry of the interstellar medium.

  2. Combinatorial properties of graphs and groups of physico-chemical interest.

    PubMed

    El-Basil, Sherif

    2008-11-01

    Combinatorial properties of graphs and groups of physico-chemical interest are described. A type of mathematical modeling is applied which involves "translating" algebraic expressions into graphs. The idea is applied to both graph theory and group theory. The former topic includes objects of importance in physics and chemistry such as trees, polyomino graphs, king boards, etc. Our study along these lines emphasizes nonadjacency relations, graph-generation, quasicrystals, continued fractions, fractals, and general ordering schemes of graphs. The second part of the paper considers certain colored graphs as models of several group-theoretical concepts including coset representations of groups, subduction of groups, character tables, and mark tables which are essential to the understanding of recent developments of combinatorial enumeration in chemistry.

  3. Combinatorial Synthesis and Discovery of an Antibiotic Compound. An Experiment Suitable for High School and Undergraduate Laboratories

    NASA Astrophysics Data System (ADS)

    Wolkenberg, Scott E.; Su, Andrew I.

    2001-06-01

    An exercise demonstrating solution-phase combinatorial chemistry and its application to drug discovery is described. The experiment involves the synthesis of six libraries of three hydrazones, screening the libraries for antibiotic activity, and deconvolution to determine the active individual compound. The laboratory was designed for a high school classroom, though it can easily be expanded to suit a college introductory organic laboratory course.

  4. Towards a Comprehensive Dynamic-chemistry Assimilation for Eos-Chem: Plans and Status in NASA's Data Assimilation Office

    NASA Technical Reports Server (NTRS)

    Pawson, Steven; Lin, Shian-Jiann; Rood, Richard B.; Stajner, Ivanka; Nebuda, Sharon; Nielsen, J. Eric; Douglass, Anne R.

    2000-01-01

    In order to support the EOS-Chem project, a comprehensive assimilation package for the coupled chemical-dynamical system is being developed by the Data Assimilation Office at NASA GSFC. This involves development of a coupled chemistry/meteorology model and of data assimilation techniques for trace species and meteorology. The model is being developed using the flux-form semi-Lagrangian dynamical core of Lin and Rood, the physical parameterizations from the NCAR Community Climate Model, and atmospheric chemistry modules from the Atmospheric Chemistry and Dynamics branch at NASA GSFC. To date the following results have been obtained: (i) multi-annual simulations with the dynamics-radiation model show the credibility of the package for atmospheric simulations; (ii) initial simulations including a limited number of middle atmospheric trace gases reveal the realistic nature of transport mechanisms, although there is still a need for some improvements. Samples of these results will be shown. A meteorological assimilation system is currently being constructed using the model; this will form the basis for the proposed meteorological/chemical assimilation package. The latter part of the presentation will focus on areas targeted for development in the near and far terms, with the objective of Providing a comprehensive assimilation package for the EOS-Chem science experiment. The first stage will target ozone assimilation. The plans also encompass a reanalysis (ReSTS) for the 1991-1995 period, which includes the Mt. Pinatubo eruption and the time when a large number of UARS observations were available. One of the most challenging aspects of future developments will be to couple theoretical advances in tracer assimilation with the practical considerations of a real environment and eventually a near-real-time assimilation system.

  5. Parallel and Distributed Computing Combinatorial Algorithms

    DTIC Science & Technology

    1993-10-01

    FUPNDKC %2,•, PARALLEL AND DISTRIBUTED COMPUTING COMBINATORIAL ALGORITHMS 6. AUTHOR(S) 2304/DS F49620-92-J-0125 DR. LEIGHTON 7 PERFORMING ORGANIZATION NAME...on several problems involving parallel and distributed computing and combinatorial optimization. This research is reported in the numerous papers that...network decom- position. In Proceedings of the Eleventh Annual ACM Symposium on Principles of Distributed Computing , August 1992. [15] B. Awerbuch, B

  6. Integrated microfluidic devices for combinatorial cell-based assays.

    PubMed

    Yu, Zeta Tak For; Kamei, Ken-ichiro; Takahashi, Hiroko; Shu, Chengyi Jenny; Wang, Xiaopu; He, George Wenfu; Silverman, Robert; Radu, Caius G; Witte, Owen N; Lee, Ki-Bum; Tseng, Hsian-Rong

    2009-06-01

    The development of miniaturized cell culture platforms for performing parallel cultures and combinatorial assays is important in cell biology from the single-cell level to the system level. In this paper we developed an integrated microfluidic cell-culture platform, Cell-microChip (Cell-microChip), for parallel analyses of the effects of microenvironmental cues (i.e., culture scaffolds) on different mammalian cells and their cellular responses to external stimuli. As a model study, we demonstrated the ability of culturing and assaying several mammalian cells, such as NIH 3T3 fibroblast, B16 melanoma and HeLa cell lines, in a parallel way. For functional assays, first we tested drug-induced apoptotic responses from different cell lines. As a second functional assay, we performed "on-chip" transfection of a reporter gene encoding an enhanced green fluorescent protein (EGFP) followed by live-cell imaging of transcriptional activation of cyclooxygenase 2 (Cox-2) expression. Collectively, our Cell-microChip approach demonstrated the capability to carry out parallel operations and the potential to further integrate advanced functions and applications in the broader space of combinatorial chemistry and biology.

  7. The DACCIWA Project: Dynamics-Aerosol-Chemistry-Cloud interactions in West Africa

    NASA Astrophysics Data System (ADS)

    Knippertz, Peter

    2014-05-01

    Massive economic and population growth and urbanisation are expected to lead to a tripling of anthropogenic emissions from southern West Africa (SWA) between 2000 and 2030, the impacts of which on human health, ecosystems, food security and the regional climate are largely unknown. An assessment of these impacts is complicated by (a) a superposition with effects of global climate change, (b) the strong dependence of SWA on the sensitive West African monsoon, (c) incomplete scientific understanding of interactions between emissions, clouds, radiation, precipitation and regional circulations and (d) by a lack of observations to advance our understanding and improve predictions. The purpose of this contribution is to introduce the research consortium DACCIWA (Dynamics-Aerosol-Chemistry-Cloud interactions in West Africa), which comprises 16 partners in six European and West African countries. The interdisciplinary DACCIWA team will build on the scientific and logistical foundations established by the African Monsoon Multidisciplinary Analysis (AMMA) project and collaborate closely with operational centres. DACCIWA will receive funding of about M8.75€ from the European Commission as part of Framework Programme 7 from 2015 until 2018. The DACCIWA project will conduct extensive fieldwork in SWA to collect high-quality observations, spanning the entire process chain from surface-based natural and anthropogenic emissions to impacts on health, ecosystems and climate. This will include a major field campaign in summer 2015 with three research aircrafts and two ground-based supersites. Combining the resulting benchmark dataset with a wide range of modelling activities will allow us: (a) to assess all relevant physical and chemical processes, (b) to improve the monitoring of climate and compositional parameters from space, (c) to determine health impacts from air pollution, and (d) to develop the next generation of weather and climate models capable of representing coupled

  8. First highlights of the Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa (DACCIWA) field campaigns

    NASA Astrophysics Data System (ADS)

    Liousse, C.; Knippertz, P.; Flamant, C.; Adon, J.; Akpo, A.; Annesi-Maesano, I.; Assamoi, E.; Baeza, A.; Julien, B.; Bedou, M.; Brooks, B. J.; Chiu, J. Y. C.; Chiron, C.; Coe, H.; Danuor, S.; Djossou, J.; Evans, M. J.; Fayomi, B.; Fink, A. H.; Galy-Lacaux, C.; Gardrat, E.; Jegede, O.; Kalthoff, N.; Kedote, M.; Keita, S.; Kouame, K.; Konare, A.; Leon, J. F.; Mari, C. H.; Lohou, F.; Roblou, L.; Schlager, H.; Schwarzenboeck, A.; Toure, E. N.; Veronique, Y.

    2016-12-01

    The EU-funded project DACCIWA (Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa) is investigating the relationship between weather, climate, air pollution and health in southern West Africa. The air over the coastal region of West Africa is a unique mixture of natural and anthropogenic gases, liquids and particles, emitted in an environment, in which multi-layer cloud decks frequently form. These exert a large influence on the local weather and climate, which has never been studied in detail over West Africa: this information is currently not included in the majority of weather and climate models. For the first time, the entire chain of impacts of natural and manmade emissions on the West African atmosphere was investigated in a coordinated field campaign. As part of this campaign, three research aircraft (Falcon 20, Twin Otter and ATR) based in Lomé (Togo) flew targeted 50 missions over West Africa from 27 June to 16 July 2016. In that campaign also, three highly instrumented measuring sites inland were set up with weather balloons launched several times a day across the region. The main objective was to build robust statistics of cloud properties in southern West Africa in different chemical landscapes (background state, ship/flaring emissions, polluted megacities, agricultural and forest areas, dust from the Sahel/Sahara). In addition, DACCIWA scientists working on measurements of urban emissions, air pollution, and health have set up four urban sites in Abidjan (Cote d'Ivoire) and Cotonou (Benin) focusing on main specific regional combustion sources (domestic fires, traffic and waste burning). Long-term measurements of gases and particles and census of hospital admissions for respiratory diseases were started in January 2015 and will continue until March 2017 to determine the links between human health and air pollution. Intensive measurement periods took place in July 2015, January 2016, and July 2016 (a final one is planned for January 2017) in

  9. The DACCIWA project: Dynamics-aerosol-chemistry-cloud interactions in West Africa

    NASA Astrophysics Data System (ADS)

    Knippertz, Peter

    2017-04-01

    This contribution provides an overview of the EU-funded DACCIWA (Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa) project. DACCIWA consists of 16 European and African research organisations and has strong links to universities, weather services and government organisations across West Africa. The project runs from 2010 to 2018 and is built around a major international field campaign in 2016. A key motivation for DACCIWA is the expected tripling of anthropogenic emissions in southern West Africa (SWA) between 2000 and 2030, whose impacts on human health, ecosystems, food security and the regional climate are largely unknown. An integrated assessment of this problem, which is mostly due to massive economic and population growth and urbanization, is challenging due to (a) a superposition of regional effects with global climate change, (b) a strong dependence on the variable West African monsoon, (c) incomplete scientific understanding of interactions between emissions, clouds, radiation, precipitation and regional circulations, and (d) a lack of observations. DACCIWA combines measurements in the field in SWA with extensive modelling activities and work on satellite data. In particular during the main DACCIWA field campaign in June-July 2016 high-quality observations of emissions, atmospheric composition and meteorological parameters were sampled. The campaign involved three research aircraft, three ground-based supersites, enhanced radiosonde launches, and intensive measurements at urban sites in Abidjan and Cotonou. These data have already been quality-controlled and will be freely available to the research community through a database at http://baobab.sedoo.fr/DACCIWA/ after the end of the project. The resulting benchmark dataset is currently combined with a wide range of modelling and satellite-based research activities that will ultimately allow (a) an assessment of the roles of relevant physical, chemical and biological processes, (b) an improvement

  10. Combinatorial explosion in model gene networks

    NASA Astrophysics Data System (ADS)

    Edwards, R.; Glass, L.

    2000-09-01

    The explosive growth in knowledge of the genome of humans and other organisms leaves open the question of how the functioning of genes in interacting networks is coordinated for orderly activity. One approach to this problem is to study mathematical properties of abstract network models that capture the logical structures of gene networks. The principal issue is to understand how particular patterns of activity can result from particular network structures, and what types of behavior are possible. We study idealized models in which the logical structure of the network is explicitly represented by Boolean functions that can be represented by directed graphs on n-cubes, but which are continuous in time and described by differential equations, rather than being updated synchronously via a discrete clock. The equations are piecewise linear, which allows significant analysis and facilitates rapid integration along trajectories. We first give a combinatorial solution to the question of how many distinct logical structures exist for n-dimensional networks, showing that the number increases very rapidly with n. We then outline analytic methods that can be used to establish the existence, stability and periods of periodic orbits corresponding to particular cycles on the n-cube. We use these methods to confirm the existence of limit cycles discovered in a sample of a million randomly generated structures of networks of 4 genes. Even with only 4 genes, at least several hundred different patterns of stable periodic behavior are possible, many of them surprisingly complex. We discuss ways of further classifying these periodic behaviors, showing that small mutations (reversal of one or a few edges on the n-cube) need not destroy the stability of a limit cycle. Although these networks are very simple as models of gene networks, their mathematical transparency reveals relationships between structure and behavior, they suggest that the possibilities for orderly dynamics in such

  11. Supramolecular assembly/reassembly processes: molecular motors and dynamers operating at surfaces.

    PubMed

    Ciesielski, Artur; Samorì, Paolo

    2011-04-01

    Among the many significant advances within the field of supramolecular chemistry over the past decades, the development of the so-called "dynamers" features a direct relevance to materials science. Defined as "combinatorial dynamic polymers", dynamers are constitutional dynamic systems and materials resulting from the application of the principles of supramolecular chemistry to polymer science. Like supramolecular materials in general, dynamers are reversible dynamic multifunctional architectures, capable of modifying their constitution by exchanging, recombining, incorporating components. They may exhibit a variety of novel properties and behave as adaptive materials. In this review we focus on the design of responsive switchable monolayers, i.e. monolayers capable to undergo significant changes in their physical or chemical properties as a result of external stimuli. Scanning tunneling microscopy studies provide direct evidence with a sub-nanometre resolution, on the formation and dynamic response of these self-assembled systems featuring controlled geometries and properties.

  12. Inducible and combinatorial gene manipulation in mouse brain

    PubMed Central

    Dogbevia, Godwin K.; Marticorena-Alvarez, Ricardo; Bausen, Melanie; Sprengel, Rolf; Hasan, Mazahir T.

    2015-01-01

    We have deployed recombinant adeno-associated viruses equipped with tetracycline-controlled genetic switches to manipulate gene expression in mouse brain. Here, we show a combinatorial genetic approach for inducible, cell type-specific gene expression and Cre/loxP mediated gene recombination in different brain regions. Our chemical-genetic approach will help to investigate ‘when’, ‘where’, and ‘how’ gene(s) control neuronal circuit dynamics, and organize, for example, sensory signal processing, learning and memory, and behavior. PMID:25954155

  13. Peptide affinity chromatography based on combinatorial strategies for protein purification.

    PubMed

    Camperi, Silvia Andrea; Martínez-Ceron, María Camila; Giudicessi, Silvana Laura; Marani, Mariela Mirta; Albericio, Fernando; Cascone, Osvaldo

    2014-01-01

    We describe a method to develop affinity chromatography matrices with short peptide ligands for protein purification. The method entitles the following: (a) synthesis of a combinatorial library on the hydromethylbenzoyl (HMBA)-ChemMatrix resin by the divide-couple-recombine (DCR) method using the Fmoc chemistry, (b) library screening with the protein of interest labeled with a fluorescent dye or biotin, (c) identification of peptides contained on positive beads by tandem matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS/MS), (d) solid-phase peptide ligand synthesis and immobilization in chromatographic supports, and (e) evaluation of protein adsorption on peptide affinity matrices from the equilibrium isotherms and breakthrough curves.

  14. Combinatorial Methodology for Screening Selectivity in Polymeric Pervaporation Membranes.

    PubMed

    Godbole, Rutvik V; Ma, Lan; Doerfert, Michael D; Williams, Porsche; Hedden, Ronald C

    2015-11-09

    Combinatorial methodology is described for rapid screening of selectivity in polymeric pervaporation membrane materials for alcohol-water separations. The screening technique is demonstrated for ethanol-water separation using a model polyacrylate system. The materials studied are cross-linked random copolymers of a hydrophobic comonomer (n-butyl acrylate, B) and a hydrophilic comonomer (2-hydroxyethyl acrylate, H). A matrix of materials is prepared that has orthogonal variations in two key variables, H:B ratio and cross-linker concentration. For mixtures of ethanol and water, equilibrium selectivities and distribution coefficients are obtained by combining swelling measurements with high-throughput HPLC analysis. Based on the screening results, two copolymers are selected for further study as pervaporation membranes to quantify permeability selectivity and the flux of ethanol. The screening methodology described has good potential to accelerate the search for new membrane materials, as it is adaptable to a broad range of polymer chemistries.

  15. Defining the radiation chemistry during liquid cell electron microscopy to enable visualization of nanomaterial growth and degradation dynamics.

    PubMed

    Woehl, T J; Abellan, P

    2017-02-01

    We present a critical review of methods for defining the chemical environment during liquid cell electron microscopy investigation of electron beam induced nanomaterial growth and degradation. We draw from the radiation chemistry and liquid cell electron microscopy literature to present solution chemistry and electron beam-based methods for selecting the radiolysis products formed and their relative amount during electron irradiation of liquid media in a transmission electron microscope. We outline various methods for establishing net oxidizing or net reducing reaction environments and propose solvents with minimal overall production of radicals under the electron beam. Exemplary liquid cell electron microscopy experiments in the fields of nanoparticle nucleation, growth, and degradation along with recommendations for best practices and experimental parameters are reported. We expect this review will provide researchers with a useful toolkit for designing general chemistry and materials science liquid cell electron microscopy experiments by 'directing' the effect of the electron beam to understand fundamental mechanisms of dynamic nanoscale processes as well as minimizing radiation damage to samples.

  16. Applications of dynamic nuclear polarization to the study of reactions and reagents in organic and biomolecular chemistry.

    PubMed

    Hilty, Christian; Bowen, Sean

    2010-08-07

    Nuclear Magnetic Resonance (NMR) is an important spectroscopic tool for the identification and structural characterization of molecules in chemistry and biochemistry. The most significant limitation of NMR compared to other spectroscopies is its relatively low sensitivity, which thus often requires long measurement times or large amounts of sample. A way of increasing sensitivity of single scan NMR spectra by several orders of magnitude is through hyperpolarization of nuclear spins. Dynamic nuclear polarization allows hyperpolarization of most spins in small molecules encountered in chemistry and biochemistry. NMR spectra of small amounts of samples from natural source, or from chemical synthesis can readily be acquired. Perhaps more interestingly, the availability of the entire hyperpolarized NMR signal in one single scan allows the measurement of transient processes in real time, if applied together with a stopped-flow technique. Through observation of chemical shift, different reactant and product species can be distinguished, and kinetics and mechanisms, for example in enzyme catalyzed reactions, can be elucidated. Real-time hyperpolarization-enhanced NMR is uniquely amenable to correlating atomic positions not only through space, but also over time between reactant and product species. Such correlations carry mechanistic information about a reaction, and can prove reaction pathways. Applications of this technique are emerging in different areas of chemistry concerned with rapid reactions, including not only enzymatic processes, but also chemical catalysis and protein folding.

  17. Virtual Laboratory in the Role of Dynamic Visualisation for Better Understanding of Chemistry in Primary School

    ERIC Educational Resources Information Center

    Herga, Nataša Rizman; Cagran, Branka; Dinevski, Dejan

    2016-01-01

    Understanding chemistry includes the ability to think on three levels: the macroscopic level, the symbolic level, and the level of particles--sub-microscopic level. Pupils have the most difficulty when trying to understand the sub-microscopic level because it is outside their range of experience. A virtual laboratory enables a simultaneous…

  18. Probing Student Teachers' Subject Content Knowledge in Chemistry: Case Studies Using Dynamic Computer Models

    ERIC Educational Resources Information Center

    Toplis, Rob

    2008-01-01

    This paper reports case study research into the knowledge and understanding of chemistry for six secondary science student teachers. It combines innovative student-generated computer animations, using "ChemSense" software, with interviews to probe understanding of four common chemical processes used in the secondary school curriculum. Findings…

  19. Do High School Chemistry Examinations Inhibit Deeper Level Understanding of Dynamic Reversible Chemical Reactions?

    ERIC Educational Resources Information Center

    Wheeldon, R.; Atkinson, R.; Dawes, A.; Levinson, R.

    2012-01-01

    Background and purpose: Chemistry examinations can favour the deployment of algorithmic procedures like Le Chatelier's Principle (LCP) rather than reasoning using chemical principles. This study investigated the explanatory resources which high school students use to answer equilibrium problems and whether the marks given for examination answers…

  20. Dynamic Vertical Profiles of Peat Porewater Chemistry in a Northern Peatland

    SciTech Connect

    Griffiths, Natalie A.; Sebestyen, Stephen D.

    2016-10-14

    We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large gradients with depth. pH increased by two units and calcium concentrations increased over 20 fold with depth, and may reflect peatland development from minerotrophic to ombrotrophic conditions. Ammonium concentrations increased almost 20 fold and TOC concentrations decreased by half with depth, and these patterns likely reflect mineralization of peat or decomposition of TOC. There was also considerable temporal variation in the porewater chemistry depth profiles. Ammonium, soluble reactive phosphorus, and potassium showed greater temporal variation in near-surface porewater, while pH, calcium, and TOC varied more at depth. This variation demonstrates that deep peat porewater chemistry is not static. Lastly, temporal variation in solute chemistry depth profiles was greater than spatial variation in several instances, especially in shallow porewaters. In conclusion, characterizing both temporal and spatial variability is necessary to ensure representative sampling in peatlands, especially when calculating solute pools and fluxes and parameterizing process-based models.

  1. Dynamic Vertical Profiles of Peat Porewater Chemistry in a Northern Peatland

    DOE PAGES

    Griffiths, Natalie A.; Sebestyen, Stephen D.

    2016-10-14

    We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large gradients with depth. pH increased by two units and calcium concentrations increased over 20 fold with depth, and may reflect peatland development from minerotrophic to ombrotrophic conditions. Ammonium concentrations increased almost 20 fold and TOC concentrations decreased by half with depth, and thesemore » patterns likely reflect mineralization of peat or decomposition of TOC. There was also considerable temporal variation in the porewater chemistry depth profiles. Ammonium, soluble reactive phosphorus, and potassium showed greater temporal variation in near-surface porewater, while pH, calcium, and TOC varied more at depth. This variation demonstrates that deep peat porewater chemistry is not static. Lastly, temporal variation in solute chemistry depth profiles was greater than spatial variation in several instances, especially in shallow porewaters. In conclusion, characterizing both temporal and spatial variability is necessary to ensure representative sampling in peatlands, especially when calculating solute pools and fluxes and parameterizing process-based models.« less

  2. Virtual Laboratory in the Role of Dynamic Visualisation for Better Understanding of Chemistry in Primary School

    ERIC Educational Resources Information Center

    Herga, Nataša Rizman; Cagran, Branka; Dinevski, Dejan

    2016-01-01

    Understanding chemistry includes the ability to think on three levels: the macroscopic level, the symbolic level, and the level of particles--sub-microscopic level. Pupils have the most difficulty when trying to understand the sub-microscopic level because it is outside their range of experience. A virtual laboratory enables a simultaneous…

  3. Probing Student Teachers' Subject Content Knowledge in Chemistry: Case Studies Using Dynamic Computer Models

    ERIC Educational Resources Information Center

    Toplis, Rob

    2008-01-01

    This paper reports case study research into the knowledge and understanding of chemistry for six secondary science student teachers. It combines innovative student-generated computer animations, using "ChemSense" software, with interviews to probe understanding of four common chemical processes used in the secondary school curriculum. Findings…

  4. Exploring Interactive and Dynamic Simulations Using a Computer Algebra System in an Advanced Placement Chemistry Course

    ERIC Educational Resources Information Center

    Matsumoto, Paul S.

    2014-01-01

    The article describes the use of Mathematica, a computer algebra system (CAS), in a high school chemistry course. Mathematica was used to generate a graph, where a slider controls the value of parameter(s) in the equation; thus, students can visualize the effect of the parameter(s) on the behavior of the system. Also, Mathematica can show the…

  5. Exploring Interactive and Dynamic Simulations Using a Computer Algebra System in an Advanced Placement Chemistry Course

    ERIC Educational Resources Information Center

    Matsumoto, Paul S.

    2014-01-01

    The article describes the use of Mathematica, a computer algebra system (CAS), in a high school chemistry course. Mathematica was used to generate a graph, where a slider controls the value of parameter(s) in the equation; thus, students can visualize the effect of the parameter(s) on the behavior of the system. Also, Mathematica can show the…

  6. Fabrication of combinatorial polymer scaffold libraries.

    PubMed

    Simon, Carl G; Stephens, Jean S; Dorsey, Shauna M; Becker, Matthew L

    2007-07-01

    We have designed a novel combinatorial research platform to help accelerate tissue engineering research. Combinatorial methods combine many samples into a single specimen to enable accelerated experimentation and discovery. The platform for fabricating combinatorial polymer scaffold libraries can be used to rapidly identify scaffold formulations that maximize tissue formation. Many approaches for screening cell-biomaterial interactions utilize a two-dimensional format such as a film or surface to present test substrates to cells. However, cells in vivo exist in a three-dimensional milieu of extracellular matrix and cells in vitro behave more naturally when cultured in a three-dimensional environment than when cultured on a two-dimensional surface. Thus, we have designed a method for fabricating combinatorial biomaterial libraries where the materials are presented to cells in the form of three-dimensional, porous, salt-leached, polymer scaffolds. Many scaffold variations and compositions can be screened in a single experiment so that optimal scaffold formulations for tissue formation can be rapidly identified. In summary, we have developed a platform technology for fabricating combinatorial polymer scaffold libraries that can be used to screen cell response to materials in a three-dimensional, scaffold format.

  7. Fabrication of combinatorial polymer scaffold libraries

    NASA Astrophysics Data System (ADS)

    Simon, Carl G.; Stephens, Jean S.; Dorsey, Shauna M.; Becker, Matthew L.

    2007-07-01

    We have designed a novel combinatorial research platform to help accelerate tissue engineering research. Combinatorial methods combine many samples into a single specimen to enable accelerated experimentation and discovery. The platform for fabricating combinatorial polymer scaffold libraries can be used to rapidly identify scaffold formulations that maximize tissue formation. Many approaches for screening cell-biomaterial interactions utilize a two-dimensional format such as a film or surface to present test substrates to cells. However, cells in vivo exist in a three-dimensional milieu of extracellular matrix and cells in vitro behave more naturally when cultured in a three-dimensional environment than when cultured on a two-dimensional surface. Thus, we have designed a method for fabricating combinatorial biomaterial libraries where the materials are presented to cells in the form of three-dimensional, porous, salt-leached, polymer scaffolds. Many scaffold variations and compositions can be screened in a single experiment so that optimal scaffold formulations for tissue formation can be rapidly identified. In summary, we have developed a platform technology for fabricating combinatorial polymer scaffold libraries that can be used to screen cell response to materials in a three-dimensional, scaffold format.

  8. Dynamic Iminoboronate-Based Boroxine Chemistry for the Design of Ambient Humidity-Sensitive Self-Healing Polymers.

    PubMed

    Delpierre, Sébastien; Willocq, Bertrand; De Winter, Julien; Dubois, Philippe; Gerbaux, Pascal; Raquez, Jean-Marie

    2017-05-17

    Developing intrinsic self-healing polymeric materials is of great interest nowadays to extend material lifetime and/or prevent the replacement of damaged pieces. Spontaneously humidity-sensitive healable polymer network built around dynamic covalent B-O bonds was templated by using iminoboronate-based boroxine derivatives. Taking advantage of the dynamic boroxine/boronic acid equilibrium and iminoboronate chemistry, it is possible to construct polymeric materials able to self-heal without requiring any energy-demanding external activation. Interestingly, this novel family of iminoboronate adduct-based materials can be readily produced by a relatively simple and straightforward synthesis between boronic acid and diamine-based compounds, paving the way to coatings that are self-healable at ambient humidity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine.

    PubMed

    Grimme, Stefan; Bauer, Christopher Alexander

    2015-01-01

    The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

  10. Identification of Trypanosomatids by detecting Single Nucleotide Fingerprints using DNA analysis by dynamic chemistry with MALDI-ToF.

    PubMed

    Angélica Luque-González, María; Tabraue-Chávez, Mavys; López-Longarela, Bárbara; María Sánchez-Martín, Rosario; Ortiz-González, Matilde; Soriano-Rodríguez, Miguel; Antonio García-Salcedo, José; Pernagallo, Salvatore; José Díaz-Mochón, Juan

    2018-01-01

    Protozoan parasites of the Trypanosomatidae family can cause devastating diseases in humans and animals, such as Human African Trypanosomiasis or Sleeping Sickness, Chagas disease and Leishmaniasis. Currently, there are molecular assays for detecting parasitic infections and their post-treatment monitoring based on nucleic acid amplification, but there are still certain limitations which limit the development of assays that can detect and discriminate between parasite infections with a single test. Here, we present the development of a novel molecular assay for the rapid identification of Trypanosomatids, integrating DNA analysis by dynamic chemistry in conjunction with Matrix-Assisted Laser Desorption Ionization - Time-of-Flight Mass Spectrometry (MALDI-ToF). Differentiation of Trypanosoma cruzi, Trypanosoma brucei and Leishmania spp. is now possible using a single reaction tube, and enables rapid identification of Trypanosomatids. The test is based on a singleplex PCR, using a specific primer pair that amplifies a 155 base pair segment of the 28S ribosomal RNA gene, within a conserved homology region of Trypanosomatidae species. Amplified fragments are analysed by dynamic chemistry using two abasic PNA probes and the four reactive nucleobases - containing an aldehyde functional group - with MALDI-ToF to identify unique molecular patterns created by each specie due to their single base differences (Single Nucleotide Fingerprint 'SNF') in this highly homologous region. This novel assay offers the possibility to expand routine diagnostic testing for Trypanosomatids, and monitoring of therapeutic responses to these infectious diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Combinatorial gene regulation by modulation of relative pulse timing

    PubMed Central

    Lin, Yihan; Sohn, Chang Ho; Dalal, Chiraj K.; Cai, Long; Elowitz, Michael B.

    2015-01-01

    Studies of individual living cells have revealed that many transcription factors activate in dynamic, and often stochastic, pulses within the same cell. However, it has remained unclear whether cells might modulate the relative timing of these pulses to control gene expression. Here, using quantitative single-cell time-lapse imaging of Saccharomyces cerevisiae, we show that the pulsatile transcription factors Msn2 and Mig1 combinatorially regulate their target genes through modulation of their relative pulse timing. The activator Msn2 and repressor Mig1 pulsed in either a temporally overlapping or non-overlapping manner during their transient response to different inputs, with only the non-overlapping dynamics efficiently activating target gene expression. Similarly, under constant environmental conditions, where Msn2 and Mig1 exhibit sporadic pulsing, glucose concentration modulated the temporal overlap between pulses of the two factors. Together, these results reveal a time-based mode of combinatorial gene regulation. Regulation through relative signal timing is common in engineering and neurobiology, and these results suggest that it could also function broadly within the signaling and regulatory systems of the cell. PMID:26466562

  12. Proton enhanced dynamic battery chemistry for aprotic lithium-oxygen batteries

    NASA Astrophysics Data System (ADS)

    Zhu, Yun Guang; Liu, Qi; Rong, Yangchun; Chen, Haomin; Yang, Jing; Jia, Chuankun; Yu, Li-Juan; Karton, Amir; Ren, Yang; Xu, Xiaoxiong; Adams, Stefan; Wang, Qing

    2017-02-01

    Water contamination is generally considered to be detrimental to the performance of aprotic lithium-air batteries, whereas this view is challenged by recent contrasting observations. This has provoked a range of discussions on the role of water and its impact on batteries. In this work, a distinct battery chemistry that prevails in water-contaminated aprotic lithium-oxygen batteries is revealed. Both lithium ions and protons are found to be involved in the oxygen reduction and evolution reactions, and lithium hydroperoxide and lithium hydroxide are identified as predominant discharge products. The crystallographic and spectroscopic characteristics of lithium hydroperoxide monohydrate are scrutinized both experimentally and theoretically. Intriguingly, the reaction of lithium hydroperoxide with triiodide exhibits a faster kinetics, which enables a considerably lower overpotential during the charging process. The battery chemistry unveiled in this mechanistic study could provide important insights into the understanding of nominally aprotic lithium-oxygen batteries and help to tackle the critical issues confronted.

  13. Proton enhanced dynamic battery chemistry for aprotic lithium-oxygen batteries.

    PubMed

    Zhu, Yun Guang; Liu, Qi; Rong, Yangchun; Chen, Haomin; Yang, Jing; Jia, Chuankun; Yu, Li-Juan; Karton, Amir; Ren, Yang; Xu, Xiaoxiong; Adams, Stefan; Wang, Qing

    2017-02-06

    Water contamination is generally considered to be detrimental to the performance of aprotic lithium-air batteries, whereas this view is challenged by recent contrasting observations. This has provoked a range of discussions on the role of water and its impact on batteries. In this work, a distinct battery chemistry that prevails in water-contaminated aprotic lithium-oxygen batteries is revealed. Both lithium ions and protons are found to be involved in the oxygen reduction and evolution reactions, and lithium hydroperoxide and lithium hydroxide are identified as predominant discharge products. The crystallographic and spectroscopic characteristics of lithium hydroperoxide monohydrate are scrutinized both experimentally and theoretically. Intriguingly, the reaction of lithium hydroperoxide with triiodide exhibits a faster kinetics, which enables a considerably lower overpotential during the charging process. The battery chemistry unveiled in this mechanistic study could provide important insights into the understanding of nominally aprotic lithium-oxygen batteries and help to tackle the critical issues confronted.

  14. Proton enhanced dynamic battery chemistry for aprotic lithium–oxygen batteries

    PubMed Central

    Zhu, Yun Guang; Liu, Qi; Rong, Yangchun; Chen, Haomin; Yang, Jing; Jia, Chuankun; Yu, Li-Juan; Karton, Amir; Ren, Yang; Xu, Xiaoxiong; Adams, Stefan; Wang, Qing

    2017-01-01

    Water contamination is generally considered to be detrimental to the performance of aprotic lithium–air batteries, whereas this view is challenged by recent contrasting observations. This has provoked a range of discussions on the role of water and its impact on batteries. In this work, a distinct battery chemistry that prevails in water-contaminated aprotic lithium–oxygen batteries is revealed. Both lithium ions and protons are found to be involved in the oxygen reduction and evolution reactions, and lithium hydroperoxide and lithium hydroxide are identified as predominant discharge products. The crystallographic and spectroscopic characteristics of lithium hydroperoxide monohydrate are scrutinized both experimentally and theoretically. Intriguingly, the reaction of lithium hydroperoxide with triiodide exhibits a faster kinetics, which enables a considerably lower overpotential during the charging process. The battery chemistry unveiled in this mechanistic study could provide important insights into the understanding of nominally aprotic lithium–oxygen batteries and help to tackle the critical issues confronted. PMID:28165008

  15. Dynamic vertical profiles of peat porewater chemistry in a northern peatland

    Treesearch

    Natalie A. Griffiths; Stephen D. Sebestyen

    2016-01-01

    We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large...

  16. Quantum control implemented as combinatorial optimization.

    PubMed

    Strohecker, Traci; Rabitz, Herschel

    2010-01-15

    Optimal control theory provides a general means for designing controls to manipulate quantum phenomena. Traditional implementation requires solving coupled nonlinear equations to obtain the optimal control solution, whereas this work introduces a combinatorial quantum control (CQC) algorithm to avoid this complexity. The CQC technique uses a predetermined toolkit of small time step propagators in conjunction with combinatorial optimization to identify a proper sequence for the toolkit members. Results indicate that the CQC technique exhibits invariance of search effort to the number of system states and very favorable scaling upon comparison to a standard gradient algorithm, taking into consideration that CQC is easily parallelizable.

  17. [Combinatorial optimization of synthetic biological systems].

    PubMed

    Gu, Qun; Li, Yifan; Chen, Tao

    2013-08-01

    A major challenge in synthetic biology is to engineer complex biological systems with novel functions. Due to the inherent complexity of biological systems, it is often difficult to rationally design every component in a synthetic gene network to achive an optimal performance. Combinatorial engineering is an important solution to this problem and can greatly facilitate the construction of novel biological functions. Here, we review methods and techniques developed in recent years for combinatorial optimization of synthetic biological systems, including methods for fine-tuning pathway components, strategies for systematically optimization of metabolic pathways, and techniques for introducing multiplex genome wide perturbations.

  18. A Synthesis of Fluid Dynamics and Quantum Chemistry for the Design of Nanoelectronics

    NASA Technical Reports Server (NTRS)

    MacDougall, Preston J.

    1998-01-01

    In 1959, during a famous lecture entitled "There's Plenty of Room at the Bottom", Richard Feynman focused on the startling technical possibilities that would exist at the limit of miniaturization, that being atomically precise devices with dimensions in the nanometer range. A nanometer is both a convenient unit of length for medium to large sized molecules, and the root of the name of the new interdisciplinary field of "nanotechnology". Essentially, "nanoelectronics" denotes the goal of shrinking electronic devices, such as diodes and transistors, as well as integrated circuits of such devices that can perform logical operations, down to dimensions in the range of 100 nanometers. The thirty-year hiatus in the development of nanotechnology can figuratively be seen as a period of waiting for the bottom-up and atomically precise construction skills of synthetic chemistry to meet the top-down reductionist aspirations of device physics. The sub-nanometer domain of nineteenth-century classical chemistry has steadily grown, and state-of-the-art supramolecular chemistry can achieve atomic precision in non-repeating molecular assemblies of the size desired for nanotechnology. For nanoelectronics in particular, a basic understanding of the electron transport properties of molecules must also be developed. Quantum chemistry provides powerful computational methods that can accurately predict the properties of small to medium sized molecules on a desktop workstation, and those of large molecules if one has access to a supercomputer. Of the many properties of a molecule that quantum chemistry routinely predicts, the ability to carry a current is one that had not even been considered until recently. "Currently", there is a controversy over just how to define this key property. Reminiscent of the situation in high-Tc superconductivity, much of the difficulty arises from the different models that are used to simplify the complex electronic structure of real materials. A model

  19. A Synthesis of Fluid Dynamics and Quantum Chemistry for the Design of Nanoelectronics

    NASA Technical Reports Server (NTRS)

    MacDougall, Preston J.

    1998-01-01

    In 1959, during a famous lecture entitled "There's Plenty of Room at the Bottom", Richard Feynman focused on the startling technical possibilities that would exist at the limit of miniaturization, that being atomically precise devices with dimensions in the nanometer range. A nanometer is both a convenient unit of length for medium to large sized molecules, and the root of the name of the new interdisciplinary field of "nanotechnology". Essentially, "nanoelectronics" denotes the goal of shrinking electronic devices, such as diodes and transistors, as well as integrated circuits of such devices that can perform logical operations, down to dimensions in the range of 100 nanometers. The thirty-year hiatus in the development of nanotechnology can figuratively be seen as a period of waiting for the bottom-up and atomically precise construction skills of synthetic chemistry to meet the top-down reductionist aspirations of device physics. The sub-nanometer domain of nineteenth-century classical chemistry has steadily grown, and state-of-the-art supramolecular chemistry can achieve atomic precision in non-repeating molecular assemblies of the size desired for nanotechnology. For nanoelectronics in particular, a basic understanding of the electron transport properties of molecules must also be developed. Quantum chemistry provides powerful computational methods that can accurately predict the properties of small to medium sized molecules on a desktop workstation, and those of large molecules if one has access to a supercomputer. Of the many properties of a molecule that quantum chemistry routinely predicts, the ability to carry a current is one that had not even been considered until recently. "Currently", there is a controversy over just how to define this key property. Reminiscent of the situation in high-Tc superconductivity, much of the difficulty arises from the different models that are used to simplify the complex electronic structure of real materials. A model

  20. Using Dynamic Covalent Chemistry To Drive Morphological Transitions: Controlled Release of Encapsulated Nanoparticles from Block Copolymer Vesicles.

    PubMed

    Deng, Renhua; Derry, Matthew J; Mable, Charlotte J; Ning, Yin; Armes, Steven P

    2017-06-07

    Dynamic covalent chemistry is exploited to drive morphological order-order transitions to achieve the controlled release of a model payload (e.g., silica nanoparticles) encapsulated within block copolymer vesicles. More specifically, poly(glycerol monomethacrylate)-poly(2-hydroxypropyl methacrylate) (PGMA-PHPMA) diblock copolymer vesicles were prepared via aqueous polymerization-induced self-assembly in either the presence or absence of silica nanoparticles. Addition of 3-aminophenylboronic acid (APBA) to such vesicles results in specific binding of this reagent to some of the pendent cis-diol groups on the hydrophilic PGMA chains to form phenylboronate ester bonds in mildly alkaline aqueous solution (pH ∼ 10). This leads to a subtle increase in the effective volume fraction of this stabilizer block, which in turn causes a reduction in the packing parameter and hence induces a vesicle-to-worm (or vesicle-to-sphere) morphological transition. The evolution in copolymer morphology (and the associated sol-gel transitions) was monitored using dynamic light scattering, transmission electron microscopy, oscillatory rheology, and small-angle X-ray scattering. In contrast to the literature, in situ release of encapsulated silica nanoparticles is achieved via vesicle dissociation at room temperature; moreover, the rate of release can be fine-tuned by varying the solution pH and/or the APBA concentration. Furthermore, this strategy also works (i) for relatively thick-walled vesicles that do not normally exhibit stimulus-responsive behavior and (ii) in the presence of added salt. This novel molecular recognition strategy to trigger morphological transitions via dynamic covalent chemistry offers considerable scope for the design of new stimulus-responsive copolymer vesicles (and hydrogels) for targeted delivery and controlled release of cargoes. In particular, the conditions used in this new approach are relevant to liquid laundry formulations, whereby enzymes require

  1. Estimating meme fitness in adaptive memetic algorithms for combinatorial problems.

    PubMed

    Smith, J E

    2012-01-01

    Among the most promising and active research areas in heuristic optimisation is the field of adaptive memetic algorithms (AMAs). These gain much of their reported robustness by adapting the probability with which each of a set of local improvement operators is applied, according to an estimate of their current value to the search process. This paper addresses the issue of how the current value should be estimated. Assuming the estimate occurs over several applications of a meme, we consider whether the extreme or mean improvements should be used, and whether this aggregation should be global, or local to some part of the solution space. To investigate these issues, we use the well-established COMA framework that coevolves the specification of a population of memes (representing different local search algorithms) alongside a population of candidate solutions to the problem at hand. Two very different memetic algorithms are considered: the first using adaptive operator pursuit to adjust the probabilities of applying a fixed set of memes, and a second which applies genetic operators to dynamically adapt and create memes and their functional definitions. For the latter, especially on combinatorial problems, credit assignment mechanisms based on historical records, or on notions of landscape locality, will have limited application, and it is necessary to estimate the value of a meme via some form of sampling. The results on a set of binary encoded combinatorial problems show that both methods are very effective, and that for some problems it is necessary to use thousands of variables in order to tease apart the differences between different reward schemes. However, for both memetic algorithms, a significant pattern emerges that reward based on mean improvement is better than that based on extreme improvement. This contradicts recent findings from adapting the parameters of operators involved in global evolutionary search. The results also show that local reward schemes

  2. A New Approach for Proving or Generating Combinatorial Identities

    ERIC Educational Resources Information Center

    Gonzalez, Luis

    2010-01-01

    A new method for proving, in an immediate way, many combinatorial identities is presented. The method is based on a simple recursive combinatorial formula involving n + 1 arbitrary real parameters. Moreover, this formula enables one not only to prove, but also generate many different combinatorial identities (not being required to know them "a…

  3. Hypergraph-Based Combinatorial Optimization of Matrix-Vector Multiplication

    ERIC Educational Resources Information Center

    Wolf, Michael Maclean

    2009-01-01

    Combinatorial scientific computing plays an important enabling role in computational science, particularly in high performance scientific computing. In this thesis, we will describe our work on optimizing matrix-vector multiplication using combinatorial techniques. Our research has focused on two different problems in combinatorial scientific…

  4. Hypergraph-Based Combinatorial Optimization of Matrix-Vector Multiplication

    ERIC Educational Resources Information Center

    Wolf, Michael Maclean

    2009-01-01

    Combinatorial scientific computing plays an important enabling role in computational science, particularly in high performance scientific computing. In this thesis, we will describe our work on optimizing matrix-vector multiplication using combinatorial techniques. Our research has focused on two different problems in combinatorial scientific…

  5. A combinatorial code for pattern formation in Drosophila oogenesis

    PubMed Central

    Yakoby, N.; Bristow, C.A.; Gong, D.; Schafer, X.; Lembong, J.; Zartman, J.J.; Halfon, M.S.; Schüpbach, T.; Shvartsman, S.Y.

    2010-01-01

    Summary Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggested that they follow a simple combinatorial code, based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of the inductive signals, provided by the highly conserved EGFR and DPP pathways. We demonstrated the validity of the code by testing it against a set of newly identified expression patterns, obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguished 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterized their joint dynamics over four stages of oogenesis. This work provides the first systematic analysis of the diversity and dynamics of two-dimensional gene expression patterns in a developing tissue. PMID:19000837

  6. Scanning SQUID microscopy of local superconductivity in inhomogeneous combinatorial ceramics.

    PubMed

    Iranmanesh, Mitra; Stir, Manuela; Kirtley, John R; Hulliger, Jürg

    2014-11-24

    Although combinatorial solid-state chemistry promises to be an efficient way to search for new superconducting compounds, the problem of determining which compositions are strongly diamagnetic in a mixed-phase sample is challenging. By means of reactions in a system of randomly mixed starting components (Ca, Sr, Ba, La, Y, Pb, Bi, Tl, and Cu oxides), samples were produced that showed an onset of diamagnetic response above 115 K in bulk measurements. Imaging of this diamagnetic response in ceramic samples by scanning SQUID microscopy (SSM) revealed local superconducting areas with sizes down to as small as the spatial resolution of a few micrometers. In addition, locally formed superconducting matter was extracted from mixed-phase samples by magnetic separation. The analysis of single grains (d<80 μm) by X-ray diffraction, elemental analysis, and bulk SQUID measurements allowed Tl2Ca3Ba2Cu4O12, TlCaBaSrCu2O(7-δ), BaPb(0.5)Bi(0.25)Tl(0.25)O(3-δ), TlBa2Ca2Cu3O9, Tl2Ba2CaCu2O8, and YBa2Cu3O7 phases to be identified. SSM, in combination with other diagnostic techniques, is therefore shown to be a useful instrument to analyze inhomogeneous reaction products in the solid-state chemistry of materials showing magnetic properties.

  7. Quantum Resonance Approach to Combinatorial Optimization

    NASA Technical Reports Server (NTRS)

    Zak, Michail

    1997-01-01

    It is shown that quantum resonance can be used for combinatorial optimization. The advantage of the approach is in independence of the computing time upon the dimensionality of the problem. As an example, the solution to a constraint satisfaction problem of exponential complexity is demonstrated.

  8. More Combinatorial Proofs via Flagpole Arrangements

    ERIC Educational Resources Information Center

    DeTemple, Duane; Reynolds, H. David, II

    2006-01-01

    Combinatorial identities are proved by counting the number of arrangements of a flagpole and guy wires on a row of blocks that satisfy a set of conditions. An identity is proved by first deriving and then equating two expressions that each count the number of permissible arrangements. Identities for binomial coefficients and recursion relations…

  9. A Model of Students' Combinatorial Thinking

    ERIC Educational Resources Information Center

    Lockwood, Elise

    2013-01-01

    Combinatorial topics have become increasingly prevalent in K-12 and undergraduate curricula, yet research on combinatorics education indicates that students face difficulties when solving counting problems. The research community has not yet addressed students' ways of thinking at a level that facilitates deeper understanding of how students…

  10. More Combinatorial Proofs via Flagpole Arrangements

    ERIC Educational Resources Information Center

    DeTemple, Duane; Reynolds, H. David, II

    2006-01-01

    Combinatorial identities are proved by counting the number of arrangements of a flagpole and guy wires on a row of blocks that satisfy a set of conditions. An identity is proved by first deriving and then equating two expressions that each count the number of permissible arrangements. Identities for binomial coefficients and recursion relations…

  11. Combinatorial protein reagents to manipulate protein function.

    PubMed

    Colas, P

    2000-02-01

    The design and use of combinatorial protein libraries has become a fast moving field in molecular biology. Different experimental systems supporting various selection schemes are now available. The latest breakthroughs include evolutionary experiments to improve existing binding surfaces, selections of homodimerizing peptides, the use of peptide aptamers to disrupt protein interactions inside living cells, and functional selections of aptamers to probe regulatory networks.

  12. Extended Lagrangian quantum molecular dynamics simulations of shock-induced chemistry in hydrocarbons

    SciTech Connect

    Sanville, Edward J; Bock, Nicolas; Challacombe, William M; Cawkwell, Marc J; Niklasson, Anders M N; Dattelbaum, Dana M; Sheffield, Stephen; Sewell, Thomas D

    2010-01-01

    A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.

  13. Dynamic Covalent Polymer Networks: from Old Chemistry to Modern Day Innovations.

    PubMed

    Zou, Weike; Dong, Jiante; Luo, Yingwu; Zhao, Qian; Xie, Tao

    2017-04-01

    Dynamic covalent polymer networks have long been recognized. With the initial focus on the unintended impact of dynamic covalent linkages on the viscoelasticity of commercial rubbers, efforts in modern times have transitioned into designing dynamic covalent polymer networks with unique adaptive properties. Whereas self-healing and thermoset reprocessing have been the primary motivations for studying dynamic covalent polymer networks, the recent discovery of the vitrimeric rheological behavior and solid-state plasticity for this type of material have opened up new opportunities in material innovations. This, coupled with the revelation of the dynamic characteristics of commercially relevant polymer building blocks such as esters and urethanes, suggests a promising future for this class of materials.

  14. The Chemistry and Dynamics of the Molecular Outflow in BHR71

    NASA Astrophysics Data System (ADS)

    Bovill, M. S.; Bourke, T. L.; Bergin, E. A.

    2002-12-01

    We present observations of BHR71, in rotational transitions of 12CO, 13CO and C18O and selected additional molecules. BHR71 is an isolated Bok Globule 200 pc from the Sun with an embedded protostellar system, that also contains a highly collimated outflow with unusually active chemistry. Our observations are used to probe the physical and chemical structure of this outflow. We derive the excitation temperature and opacity for several positions in the outflow using the multi-transitional CO data. With this information we estimate the mass to be 1.7 Msun and the excitation temperature to be 15 K in the outflow, slightly elevated above the temperature in the ambient gas (10 K). There is evidence for even higher temperatures towards a position in the blue lobe that is coincident with knots of H2 emission. CO column densities calculated with these temperatures are used to analyze the chemical abundances in the outflow relative to the ambient gas. SiO, CS, HCN, and H2CO all show increased abundances relative to the ambient and molecular ions (HCO+, DCO+, and N+H+) show depletion. These abundances agree qualitatively with those estimated for L1157, the only other outflow that has been extensively studied with regards to the chemistry. However, we find significant disagreements in the magnitude of the abundance changes. BHR71 abundances show agreement with chemical theory. This work was supported in part by NSF grant AST-9731923 to the SAO Summer Intern program.

  15. Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.

    PubMed

    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 simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals.

  16. Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

  17. A catalytic chiral gel microfluidic reactor assembled via dynamic covalent chemistry.

    PubMed

    Liu, Haoliang; Feng, Juan; Zhang, Jianyong; Miller, Philip W; Chen, Liuping; Su, Cheng-Yong

    2015-04-16

    A novel dynamic covalent gel strategy is reported to immobilize an asymmetric catalyst within the channels of a microfluidic flow reactor. A layer of a catalytically active Mn-salen dynamic covalent imine gel matrix was coated onto a functionalized capillary. Mn-salen active moiety was incorporated into dynamic covalent imine gel matrix via the reaction of a chiral Mn-salen dialdehyde unit with a tetraamine linker. The catalytic activity of the capillary reactor has been demonstrated in enantioselective kinetic resolution of secondary alcohols.

  18. The Interaction Between Dynamics and Chemistry of Ozone in the Set-up Phase of the Northern Hemisphere Polar Vortex

    NASA Technical Reports Server (NTRS)

    Kawa, S. R.; Bevilacqua, R.; Margitan, J. J.; Douglass, A. R.; Schoeberl, M. R.; Hoppel, K.; Sen, B.; Bhartia, P. K. (Technical Monitor)

    2001-01-01

    The morphology and evolution of the stratospheric ozone (O3) distribution at high latitudes in the Northern Hemisphere (NH) are examined for the late summer and fall seasons of 1999. This time period sets the O3 initial condition for the SOLVE/THESEO field mission performed during winter 1999-2000. In situ and satellite data are used along with a three-dimensional model of chemistry and transport (CTM) to determine the key processes that control the distribution of O3 in the lower-to-middle stratosphere. O3 in the vortex at the beginning of the winter season is found to be nearly constant from 500 to above 800 K with a value at 3 ppmv +/- approx. 10%. Values outside the vortex are up to a factor of 2 higher and increase significantly with potential temperature. The seasonal time series of data from POAM shows that relatively low O3 mixing ratios, which characterize the vortex in late fall, are already present at high latitudes at the end of summer before the vortex circulation sets up. Analysis of the CTM output shows that the minimum O3 and increase in variance in late summer are the result of: 1) stirring of polar concentric O3 gradients by nascent wave-driven transport, and 2) an acceleration of net photochemical loss with decreasing solar illumination. The segregation of low O3 mixing ratios into the vortex as the circulation strengthens through the fall suggests a possible feedback role between O3 chemistry and the vortex formation dynamics. Trajectory calculations from O3 sample points early in the fall, however, show only a weak correlation between initial O3 mixing ratio and potential vorticity later in the season consistent with order-of-magnitude calculations for the relative importance of O3 in the fall radiative balance at high latitudes. The possible connection between O3 chemistry and the dynamics of vortex formation does suggest that these feedbacks and sensitivities need to be better understood in order to make confident predictions of the recovery

  19. Some aspects of metallic ion chemistry and dynamics in the mesosphere and thermosphere

    NASA Technical Reports Server (NTRS)

    Mathews, J. D.

    1987-01-01

    The relationship between the formation of sporadic layers of metallic ion and the dumping of these ions into the upper mesosphere is discussed in terms of the tidal wind, classical (i.e., windshear) and other more complex, perhaps highly nonlinear layer formation mechanisms, and a possible circulation mechanism for these ions. Optical, incoherent scatter radar, rocket, and satellite derived evidence for various layer formation mechanisms and for the metallic ion circulation system is reviewed. The results of simple one dimensional numerical model calculations of sporadic E and intermediate layer formation are presented along with suggestions for more advanced models of intense or blanketing sporadic E. The flux of metallic ions dumped by the tidal wind system into the mesosphere is estimated and compared with estimates of total particle flux of meteoric origin. Possible effects of the metallic ion flux and of meteoric dust on D region ion chemistry are discussed.

  20. Coral reef metabolism and carbon chemistry dynamics of a coral reef flat

    NASA Astrophysics Data System (ADS)

    Albright, Rebecca; Benthuysen, Jessica; Cantin, Neal; Caldeira, Ken; Anthony, Ken

    2015-05-01

    Global carbon emissions continue to acidify the oceans, motivating growing concern for the ability of coral reefs to maintain net positive calcification rates. Efforts to develop robust relationships between coral reef calcification and carbonate parameters such as aragonite saturation state (Ωarag) aim to facilitate meaningful predictions of how reef calcification will change in the face of ocean acidification. Here we investigate natural trends in carbonate chemistry of a coral reef flat over diel cycles and relate these trends to benthic carbon fluxes by quantifying net community calcification and net community production. We find that, despite an apparent dependence of calcification on Ωarag seen in a simple pairwise relationship, if the dependence of net calcification on net photosynthesis is accounted for, knowing Ωarag does not add substantial explanatory value. This suggests that, over short time scales, the control of Ωarag on net calcification is weak relative to factors governing net photosynthesis.

  1. Do high school chemistry examinations inhibit deeper level understanding of dynamic reversible chemical reactions?

    NASA Astrophysics Data System (ADS)

    Wheeldon, R.; Atkinson, R.; Dawes, A.; Levinson, R.

    2012-07-01

    Background and purpose : Chemistry examinations can favour the deployment of algorithmic procedures like Le Chatelier's Principle (LCP) rather than reasoning using chemical principles. This study investigated the explanatory resources which high school students use to answer equilibrium problems and whether the marks given for examination answers require students to use approaches beyond direct application of LCP. Sample : The questionnaire was administered to 162 students studying their first year of advanced chemistry (age 16/17) in three high achieving London high schools. Design and methods : The students' explanations of reversible chemical systems were inductively coded to identify the explanatory approaches used and interviews with 13 students were used to check for consistency. AS level examination questions on reversible reactions were analysed to identify the types of explanations sought and the students' performance in these examinations was compared to questionnaire answers. Results : 19% of students used a holistic explanatory approach: when the rates of forward and reverse reactions are correctly described, recognising their simultaneous and mutually dependent nature. 36% used a mirrored reactions approach when the connected nature of the forward and reverse reactions is identified, but not their mutual dependency. 42% failed to recognize the interdependence of forward and reverse reactions (reactions not connected approach). Only 4% of marks for AS examination questions on reversible chemical systems asked for responses which went beyond either direct application of LCP or recall of equilibrium knowledge. 37% of students attained an A grade in their AS national examinations. Conclusions : Examinations favour the application of LCP making it possible to obtain the highest grade with little understanding of reversible chemical systems beyond a direct application of this algorithm. Therefore students' understanding may be attenuated so that they are

  2. Using water chemistry time series to model dissolved inorganic carbon dynamics in the western Amazon basin

    NASA Astrophysics Data System (ADS)

    Vihermaa, Leena; Waldron, Susan; Newton, Jason

    2013-04-01

    Two small streams (New Colpita and Main Trail) and two rivers (Tambopata and La Torre), in the Tambopata National Reserve, Madre de Dios, Peru, were sampled for water chemistry (conductivity, pH and dissolved oxygen) and hydrology (stage height and flow velocity). In the small streams water chemistry and hydrology variables were logged at 15 minute intervals from Feb 2011 to November 2012. Water samples were collected from all four channels during field campaigns spanning different seasons and targeting the hydrological extremes. All the samples were analysed for dissolved inorganic carbon (DIC) concentration and δ13C (sample size ranging from 77 to 172 depending on the drainage system) and a smaller subset for dissolved organic carbon (DOC) and particulate organic carbon (POC) concentrations. Strong positive relationships were found between conductivity and both DIC concentration and δ13C in the New Colpita stream and the La Torre river. In Tambopata river the trends were less clear and in the Main Trail stream there was very little change in DIC and isotopic composition. The conductivity data was used to model continuous DIC time series for the New Colpita stream. The modelled DIC data agreed well with the measurements; the concordance correlation coefficients between predicted and measured data were 0.91 and 0.87 for mM-DIC and δ13C-DIC, respectively. The predictions of δ13C-DIC were improved when calendar month was included in the model, which indicates seasonal differences in the δ13C-DIC conductivity relationship. At present, continuous DIC sampling still requires expensive instrumentation. Therefore, modelling DIC from a proxy variable which can be monitored continuously with ease and at relatively low cost, such as conductivity, provides a powerful alternative method of DIC determination.

  3. Influence of boundary layer dynamics and isoprene chemistry on the organic aerosol budget in a tropical forest

    NASA Astrophysics Data System (ADS)

    Janssen, R. H. H.; Vilà-Guerau de Arellano, J.; Jimenez, J. L.; Ganzeveld, L. N.; Robinson, N. H.; Allan, J. D.; Coe, H.; Pugh, T. A. M.

    2013-08-01

    We study the organic aerosol (OA) budget in a tropical forest by analyzing a case that is representative for the OP3 campaign at Borneo. A model is designed that combines the essential dynamical and chemical processes that drive the diurnal evolution of reactants in the atmospheric boundary layer (BL). In this way, the model simultaneously represents the effects and interactions of various dynamical and chemical factors on the OA budget. The model is able to reproduce the observed diurnal dynamics of the BL, including the evolution of most chemical species involved in secondary organic aerosol (SOA) formation. A budget analysis of the contributions of the dynamic and chemical processes reveals the significance of the entrainment process in the diurnal evolution of SOA. Further, we perform a series of sensitivity analyses to determine the effect of meteorological forcings and isoprene chemical pathways on the OA budget. Subsidence and advection of cool air have opposing effects on the OA concentration, although both suppress BL growth. Recycling of the OH radical in the oxidation of isoprene may affect the amount of SOA that is formed, but must be understood better before its impact can be definitely determined. SOA formation from isoprene is calculated for both the low- and high-NOx pathway, with the latter dominating the isoprene peroxy radical chemistry. Finally, we study the significance of SOA formation through the reactive uptake of isoprene epoxydiols on acidic sulfate aerosol. Despite the incorporation of these new pathways, the OA concentration is systematically underestimated by about a factor of 2.

  4. FOREWORD: Focus on Combinatorial Materials Science Focus on Combinatorial Materials Science

    NASA Astrophysics Data System (ADS)

    Chikyo, Toyohiro

    2011-10-01

    About 15 years have passed since the introduction of modern combinatorial synthesis and high-throughput techniques for the development of novel inorganic materials; however, similar methods existed before. The most famous was reported in 1970 by Hanak who prepared composition-spread films of metal alloys by sputtering mixed-material targets. Although this method was innovative, it was rarely used because of the large amount of data to be processed. This problem is solved in the modern combinatorial material research, which is strongly related to computer data analysis and robotics. This field is still at the developing stage and may be enriched by new methods. Nevertheless, given the progress in measurement equipment and procedures, we believe the combinatorial approach will become a major and standard tool of materials screening and development. The first article of this journal, published in 2000, was titled 'Combinatorial solid state materials science and technology', and this focus issue aims to reintroduce this topic to the Science and Technology of Advanced Materials audience. It covers recent progress in combinatorial materials research describing new results in catalysis, phosphors, polymers and metal alloys for shape memory materials. Sophisticated high-throughput characterization schemes and innovative synthesis tools are also presented, such as spray deposition using nanoparticles or ion plating. On a technical note, data handling systems are introduced to familiarize researchers with the combinatorial methodology. We hope that through this focus issue a wide audience of materials scientists can learn about recent and future trends in combinatorial materials science and high-throughput experimentation.

  5. Genetic algorithm-assisted combinatorial search for a new green phosphor for use in tricolor white LEDs.

    PubMed

    Sohn, Kee-Sun; Park, Duk Hyun; Cho, Sang Ho; Kim, Byung Il; Woo, Seong Ihl

    2006-01-01

    An evolutionary optimization process involving a genetic algorithm and combinatorial chemistry was employed for the development of green phosphors which are suitable for tricolor white-light-emitting diodes. To accomplish a high luminescent efficiency at 400 nm excitation, we screened a seven-cation oxide system including Tb, Gd, Ce, Mg, Si, Al, and B. The combination of a genetic algorithm and combinatorial chemistry enhanced the searching efficiency when applied for phosphor screening. As a result, the optimized composition was Tb(0.01)Gd(0.02)Ce(0.04)B(0.1)Si(0.83)O(delta), The luminance of this borosilicate glass was 67% that of ZnS:Cu,Al at 400-nm excitation.

  6. Collinear Collision Chemistry: 1. A Simple Model for Inelastic and Reactive Collision Dynamics

    ERIC Educational Resources Information Center

    Mahan, Bruce H.

    1974-01-01

    Discusses a model for the collinear collision of an atom with a diatomic molecule on a simple potential surface. Indicates that the model can provide a framework for thinking about molecular collisions and reveal many factors which affect the dynamics of reactive and inelastic collisions. (CC)

  7. Combinatorial biosynthesis--potential and problems.

    PubMed

    Floss, Heinz G

    2006-06-25

    Because of their ecological functions, natural products have been optimized in evolution for interaction with biological systems and receptors. However, they have not necessarily been optimized for other desirable drug properties and thus can often be improved by structural modification. Using examples from the literature, this paper reviews the opportunities for increasing structural diversity among natural products by combinatorial biosynthesis, i.e., the genetic manipulation of biosynthetic pathways. It distinguishes between combinatorial biosynthesis in a narrower sense to generate libraries of modified structures, and metabolic engineering for the targeted formation of specific structural analogs. Some of the problems and limitations encountered with these approaches are also discussed. Work from the author's laboratory on ansamycin antibiotics is presented which illustrates some of the opportunities and limitations.

  8. Combinatorial Biosynthesis – Potential and Problems

    PubMed Central

    Floss, Heinz G.

    2007-01-01

    Because of their ecological functions, natural products have been optimized in evolution for interaction with biological systems and receptors. However, they have not necessarily been optimized for other desirable drug properties and thus can often be improved by structural modification. Using examples from the literature, this paper reviews the opportunities for increasing structural diversity among natural products by combinatorial biosynthesis, i.e., the genetic manipulation of biosynthetic pathways. It distinguishes between combinatorial biosynthesis in a narrower sense to generate libraries of modified structures, and metabolic engineering for the targeted formation of specific structural analogs. Some of the problems and limitations encountered with these approaches are also discussed. Work from the author’s laboratory on ansamycin antibiotics is presented which illustrates some of the opportunities and limitations. PMID:16414140

  9. Exploiting Quantum Resonance to Solve Combinatorial Problems

    NASA Technical Reports Server (NTRS)

    Zak, Michail; Fijany, Amir

    2006-01-01

    Quantum resonance would be exploited in a proposed quantum-computing approach to the solution of combinatorial optimization problems. In quantum computing in general, one takes advantage of the fact that an algorithm cannot be decoupled from the physical effects available to implement it. Prior approaches to quantum computing have involved exploitation of only a subset of known quantum physical effects, notably including parallelism and entanglement, but not including resonance. In the proposed approach, one would utilize the combinatorial properties of tensor-product decomposability of unitary evolution of many-particle quantum systems for physically simulating solutions to NP-complete problems (a class of problems that are intractable with respect to classical methods of computation). In this approach, reinforcement and selection of a desired solution would be executed by means of quantum resonance. Classes of NP-complete problems that are important in practice and could be solved by the proposed approach include planning, scheduling, search, and optimal design.

  10. Dynamic Cyclic Thiodepsipeptide Libraries from Thiol-Thioester Exchange

    DTIC Science & Technology

    2010-04-01

    use in a variety of dynamic combinatorial chemistry assays. The kinetic determinants of macrocycle formation and the role of amino acid structure on...were then made in AA1, AA3, and AA4 (Table 1); by design, AA2-AA3-AA4 forms the macrocycle, and AA1 remains exocyclic. Charged amino acids (Lys, Arg...was initially included in AA3 as a turn residue that favors macrocycles. 9 Various amino acids were incorporated into AA4 to study their effect on

  11. Switched Systems and Motion Coordination: Combinatorial Challenges

    NASA Technical Reports Server (NTRS)

    Sadovsky, Alexander V.

    2016-01-01

    Problems of routing commercial air traffic in a terminal airspace encounter different constraints: separation assurance, aircraft performance limitations, regulations. The general setting of these problems is that of a switched control system. Such a system combines the differentiable motion of the aircraft with the combinatorial choices of choosing precedence when traffic routes merge and choosing branches when the routes diverge. This presentation gives an overview of the problem, the ATM context, related literature, and directions for future research.

  12. Combinatorial Cis-regulation in Saccharomyces Species.

    PubMed

    Spivak, Aaron T; Stormo, Gary D

    2016-01-15

    Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs) controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1) chromatin immunoprecipitation data for colocalization of transcription factors, (2) gene expression data for coexpression of predicted regulatory targets, and (3) gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF) occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1) combinatorial cis-regulation can be inferred by multi-genome analysis and (2) combinatorial cis-regulation can explain differences in gene expression between species. Copyright © 2016 Spivak and Stormo.

  13. Combinatorial Cis-regulation in Saccharomyces Species

    PubMed Central

    Spivak, Aaron T.; Stormo, Gary D.

    2016-01-01

    Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs) controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1) chromatin immunoprecipitation data for colocalization of transcription factors, (2) gene expression data for coexpression of predicted regulatory targets, and (3) gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF) occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1) combinatorial cis-regulation can be inferred by multi-genome analysis and (2) combinatorial cis-regulation can explain differences in gene expression between species. PMID:26772747

  14. Adaptive random testing with combinatorial input domain.

    PubMed

    Huang, Rubing; Chen, Jinfu; Lu, Yansheng

    2014-01-01

    Random testing (RT) is a fundamental testing technique to assess software reliability, by simply selecting test cases in a random manner from the whole input domain. As an enhancement of RT, adaptive random testing (ART) has better failure-detection capability and has been widely applied in different scenarios, such as numerical programs, some object-oriented programs, and mobile applications. However, not much work has been done on the effectiveness of ART for the programs with combinatorial input domain (i.e., the set of categorical data). To extend the ideas to the testing for combinatorial input domain, we have adopted different similarity measures that are widely used for categorical data in data mining and have proposed two similarity measures based on interaction coverage. Then, we propose a new version named ART-CID as an extension of ART in combinatorial input domain, which selects an element from categorical data as the next test case such that it has the lowest similarity against already generated test cases. Experimental results show that ART-CID generally performs better than RT, with respect to different evaluation metrics.

  15. Methods for combinatorial and parallel library design.

    PubMed

    Schnur, Dora M; Beno, Brett R; Tebben, Andrew J; Cavallaro, Cullen

    2011-01-01

    Diversity has historically played a critical role in design of combinatorial libraries, screening sets and corporate collections for lead discovery. Large library design dominated the field in the 1990s with methods ranging anywhere from purely arbitrary through property based reagent selection to product based approaches. In recent years, however, there has been a downward trend in library size. This was due to increased information about the desirable targets gleaned from the genomics revolution and to the ever growing availability of target protein structures from crystallography and homology modeling. Creation of libraries directed toward families of receptors such as GPCRs, kinases, nuclear hormone receptors, proteases, etc., replaced the generation of libraries based primarily on diversity while single target focused library design has remained an important objective. Concurrently, computing grids and cpu clusters have facilitated the development of structure based tools that screen hundreds of thousands of molecules. Smaller "smarter" combinatorial and focused parallel libraries replaced those early un-focused large libraries in the twenty-first century drug design paradigm. While diversity still plays a role in lead discovery, the focus of current library design methods has shifted to receptor based methods, scaffold hopping/bio-isostere searching, and a much needed emphasis on synthetic feasibility. Methods such as "privileged substructures based design" and pharmacophore based design still are important methods for parallel and small combinatorial library design. This chapter discusses some of the possible design methods and presents examples where they are available.

  16. On schemes of combinatorial transcription logic.

    PubMed

    Buchler, Nicolas E; Gerland, Ulrich; Hwa, Terence

    2003-04-29

    Cells receive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate specific genetic responses. Here we explore theoretically the potentials and limitations of combinatorial signal integration at the level of cis-regulatory transcription control. Our analysis suggests that many complex transcription-control functions of the type encountered in higher eukaryotes are already implementable within the much simpler bacterial transcription system. Using a quantitative model of bacterial transcription and invoking only specific protein-DNA interaction and weak glue-like interaction between regulatory proteins, we show explicit schemes to implement regulatory logic functions of increasing complexity by appropriately selecting the strengths and arranging the relative positions of the relevant protein-binding DNA sequences in the cis-regulatory region. The architectures that emerge are naturally modular and evolvable. Our results suggest that the transcription regulatory apparatus is a "programmable" computing machine, belonging formally to the class of Boltzmann machines. Crucial to our results is the ability to regulate gene expression at a distance. In bacteria, this can be achieved for isolated genes via DNA looping controlled by the dimerization of DNA-bound proteins. However, if adopted extensively in the genome, long-distance interaction can cause unintentional intergenic cross talk, a detrimental side effect difficult to overcome by the known bacterial transcription-regulation systems. This may be a key factor limiting the genome-wide adoption of complex transcription control in bacteria. Implications of our findings for combinatorial transcription control in eukaryotes are discussed.

  17. Combinatorially Developed Peptide Receptors for Biosensors

    NASA Astrophysics Data System (ADS)

    Nakamura, Chikashi; Miyake, Jun

    Various combinatorial libraries were screened for short peptides of 4-10 mer, which were used as sensor molecules for capturing target chemicals or biomolecules. Immuno-antibodies can be synthesized in the living bodies of higher animals even for low-molecular-weight nonnatural chemical compounds, such as dioxins or PCBs. Recently, some peptide ligands that can even bind to inorganic crystals have been reported. This indicates that the 20 natural amino acids have the potential to recognize almost all types of molecules and substances. The question arises whether one should design a “rational” mini library of peptides consisting of a limited number of amino acids according to the motifs in epitopes or paratopes or the binding pocket sequences in receptors, or a completely “random” combinatorial library containing all sequences. If one wants to obtain a peptide binder to target a small chemical compound, the answer is a “random” library, since the molecular interaction between the target compound and an amino acid cannot be precisely predicted beforehand. In this section, we discuss the possibility of using short combinatorial peptides as binders for biosensors to detect chemical compounds.

  18. ULTRAFAST CHEMISTRY: Using Time-Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics

    NASA Astrophysics Data System (ADS)

    Nibbering, Erik T. J.; Fidder, Henk; Pines, Ehud

    2005-05-01

    Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.

  19. Dynamic Covalent Chemistry-based Sensing: Pyrenyl Derivatives of Phenylboronic Acid for Saccharide and Formaldehyde

    NASA Astrophysics Data System (ADS)

    Chang, Xingmao; Fan, Jiayun; Wang, Min; Wang, Zhaolong; Peng, Haonan; He, Gang; Fang, Yu

    2016-08-01

    We synthesized two specially designed pyrenyl (Py) derivatives of phenylboronic acid, PSNB1 and PSNB2, of which PSNB2 self-assemble to form dynamic aggregate in methanol-water mixture (1:99, v/v) via intermolecular H-bonding and pi-pi stacking. Interestingly, the dynamic aggregate shows smart response to presence of fructose (F) as evidenced by fluorescence color change from green to blue. More interestingly, the fluorescence emission of the resulted PSNB2-F changes from blue to green with the addition of formaldehyde (FA). The reason behind is formation of a PSNB2-F dimer via FA cross-linking. Based upon the reactions as found, sensitive and fast sensing of F and FA in water was realized, of which the experimental DLs could be significantly lower than 10 μM for both analytes, and the response times are less than 1 min. It is believed that not only the materials as created may have the potential to find real-life applications but also the strategy as developed can be adopted to develop other dynamic materials.

  20. Shock induced chemistry in liquids studied with ultrafast dynamic ellipsometry and visible transient absorption spectroscopy.

    PubMed

    Dang, N C; Bolme, C A; Moore, D S; McGrane, S D

    2012-10-25

    The response to ultrafast laser shock loading of nine liquids was monitored in an effort to reveal evidence of chemical changes occurring during the first 350 ps following the shock front. In an effort to compare molecular structures possessing a variety of common bonding patterns, data were acquired for the liquids: cyclohexane, cyclohexene, 1,3-cyclohexadiene, benzene, water, acetonitrile, acrylonitrile, tert-butylacetylene, and phenylacetylene. Transient absorption spectra were measured in the spectral region from 440 to 780 nm over shock stress states from 7 to 20 GPa. Ultrafast dynamic ellipsometry was used to measure the shock and particle velocity as well as the shocked refractive index. Significant transient absorption attributed to chemical reaction was observed for shocked phenylacetylene and acrylonitrile. Evidence of volume decreasing chemical reactions was also observed in the ultrafast dynamic ellipsometry data for phenylacetylene and acrylonitrile. The liquid 1,3-cyclohexadiene exhibited volume decreasing reaction in the ultrafast dynamic ellipsometry data but did not exhibit an increase in the transient absorption spectra. There was no evidence of chemical reaction in cyclohexane, cyclohexene, benzene, water, acetonitrile, or tert-butylacetylene in the first 350 ps, despite the application of shock stress that was in many cases well above the reaction threshold observed at microsecond time scales.

  1. Dynamic Covalent Chemistry-based Sensing: Pyrenyl Derivatives of Phenylboronic Acid for Saccharide and Formaldehyde

    PubMed Central

    Chang, Xingmao; Fan, Jiayun; Wang, Min; Wang, Zhaolong; Peng, Haonan; He, Gang; Fang, Yu

    2016-01-01

    We synthesized two specially designed pyrenyl (Py) derivatives of phenylboronic acid, PSNB1 and PSNB2, of which PSNB2 self-assemble to form dynamic aggregate in methanol-water mixture (1:99, v/v) via intermolecular H-bonding and pi-pi stacking. Interestingly, the dynamic aggregate shows smart response to presence of fructose (F) as evidenced by fluorescence color change from green to blue. More interestingly, the fluorescence emission of the resulted PSNB2-F changes from blue to green with the addition of formaldehyde (FA). The reason behind is formation of a PSNB2-F dimer via FA cross-linking. Based upon the reactions as found, sensitive and fast sensing of F and FA in water was realized, of which the experimental DLs could be significantly lower than 10 μM for both analytes, and the response times are less than 1 min. It is believed that not only the materials as created may have the potential to find real-life applications but also the strategy as developed can be adopted to develop other dynamic materials. PMID:27498703

  2. Combinatorial diffusion assay used to identify topically active melanocyte-stimulating hormone receptor antagonists.

    PubMed Central

    Quillan, J M; Jayawickreme, C K; Lerner, M R

    1995-01-01

    alpha-Melanocyte-stimulating hormone (alpha-MSH) is implicated in pigmentation, central nervous system and immune system functions, growth, mitogenesis, and melanoma. Evaluation of these roles has been hindered by the lack of alpha-MSH antagonists. A combinatorial chemistry-based diffusion assay is used to find random tripeptides that antagonize normal frog and human melanoma MSH receptors and to identify pharmacological groups responsible for receptor interaction. The alpha-MSH antagonist D-Trp-Arg-Leu-NH2 is used to demonstrate directly the contribution of MSH to normal skin tone in frogs following injection or topical application. Images Fig. 1 Fig. 3 Fig. 4 Fig. 6 PMID:7708744

  3. Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

    DOE PAGES

    Yang, Qian; Sing-Long, Carlos A.; Reed, Evan J.

    2017-06-19

    Here, we propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. Conversely, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our methodmore » on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. Furthermore, we describe a framework in this work that paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.« less

  4. Chemistry and biochemistry of 13C hyperpolarized magnetic resonance using dynamic nuclear polarization.

    PubMed

    Keshari, Kayvan R; Wilson, David M

    2014-03-07

    The study of transient chemical phenomena by conventional NMR has proved elusive, particularly for non-(1)H nuclei. For (13)C, hyperpolarization using the dynamic nuclear polarization (DNP) technique has emerged as a powerful means to improve SNR. The recent development of rapid dissolution DNP methods has facilitated previously impossible in vitro and in vivo study of small molecules. This review presents the basics of the DNP technique, identification of appropriate DNP substrates, and approaches to increase hyperpolarized signal lifetimes. Also addressed are the biochemical events to which DNP-NMR has been applied, with descriptions of several probes that have met with in vivo success.

  5. Chemistry and biochemistry of 13C hyperpolarized magnetic resonance using dynamic nuclear polarization

    PubMed Central

    Keshari, Kayvan R.; Wilson, David M.

    2014-01-01

    The study of transient chemical phenomena by conventional NMR has proved elusive, particularly for non-1H nuclei. For 13C, hyperpolarization using the dynamic nuclear polarization (DNP) technique has emerged as a powerful means to improve SNR. The recent development of rapid dissolution DNP methods has facilitated previously impossible in vitro and in vivo study of small molecules. This review presents the basics of the DNP technique, identification of appropriate DNP substrates, and approaches to increase hyperpolarized signal lifetimes. Also addressed are the biochemical events to which DNP-NMR has been applied, with descriptions of several probes that have met with in vivo success. PMID:24363044

  6. Controlling surfaces in plasma processing: role of ions via molecular dynamics simulations of surface chemistry

    NASA Astrophysics Data System (ADS)

    Humbird, David; Graves, David B.

    2002-08-01

    A study of the interactions of energetic ions with various surfaces using molecular dynamics simulations is reported. Silicon atoms in the amorphous region are readily mixed by argon ions. Limited mixing in the crystalline layer is observed. Fluorine adsorbed on the silicon surface does not mix into the layer with argon ion impact. When an energetic F+ impacts a silicon surface, the uptake and apparent sub-surface mixing of F is much greater than Ar+-induced mixing. However, a closer examination shows that the F impacts have primarily increased the Si surface area by creating crevices and cracks, and that the F remains mainly on the surface of this layer.

  7. High pressure chemistry of thioaldehydes: A first-principles molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Zhang, Yaoting; Mosey, Nicholas J.

    2016-11-01

    First-principles molecular dynamics simulations are used to investigate the chemical behavior of bulk thioacetaldehyde (MeC(H)S) in response to changes in pressure, P. The simulations show that these molecules oligomerize in response to applied P. Oligomerization is initiated through C—S bond formation, with constrained dynamics simulations showing that the barrier to this reaction step is lowered significantly by applied P. Subsequent reactions involving the formation of additional C—S bonds or radical processes that lead to S—S and C—C bonds lengthen the oligomers. Oligomerization is terminated through proton transfer or the formation of rings. The mechanistic details of all reactions are examined. The results indicate that the P-induced reactivity of the MeC(H)S-based system differs significantly from that of analogous MeC(H)O-based systems, which have been reported previously. Comparison with the MeC(H)O study shows that replacing oxygen with sulfur significantly lowers the P required to initiate oligomerization (from 26 GPa to 5 GPa), increases the types of reactions in which systems of this type can take part, and increases the variety of products formed through these reactions. These differences can be explained in terms of the electronic structures of these systems, which may be useful for certain high P applications.

  8. Combinatorial discovery of tumor targeting peptides using phage display.

    PubMed

    Landon, Linda A; Deutscher, Susan L

    2003-10-15

    Peptides possess appropriate pharmacokinetic properties to serve as cancer imaging or therapeutic targeting agents. Currently, only a small number of rationally-derived, labeled peptide analogues that target only a limited subset of antigens are available. Thus, finding new cancer targeting peptides is a central goal in the field of molecular targeting. Novel tumor-avid peptides can be efficiently identified via affinity selections using complex random peptide libraries containing millions of peptides that are displayed on bacteriophage. In vitro and in situ affinity selections may be used to identify peptides with high affinity for the target antigen in vitro. Unfortunately, it has been found that peptides selected in vitro or in situ may not effectively target tumors in vivo due to poor peptide stability and other problems. To improve in vivo targeting, methodological combinatorial chemistry innovations allow selections to be conducted in the environment of the whole animal. Thus, new targeting peptides with optimal in vivo properties can be selected in vivo in tumor-bearing animals. In vivo selections have been proven successful in identifying peptides that target the vasculature of specific organs. In addition, in vivo selections have identified peptides that bind specifically to the surface of or are internalized into tumor cells. In the future, direct selection of peptides for cancer imaging may be expedited using genetically engineered bacteriophage libraries that encode peptides with intrinsic radiometal-chelation or fluorescent sequences.

  9. The chemistry of acetone at extreme conditions by density functional molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ferrante, Francesco; Celso, Fabrizio Lo; Triolo, Roberto; Taleyarkhan, Rusi P.

    2011-02-01

    Density functional molecular dynamics simulations have been performed in the NVT ensemble (moles (N), volume (V) and temperature (T)) on a system formed by ten acetone molecules at a temperature of 2000 K and density ρ = 1.322 g cm-3. These conditions resemble closely those realized at the interface of an acetone vapor bubble in the early stages of supercompression experiments and result in an average pressure of 5 GPa. Two relevant reactive events occur during the simulation: the condensation of two acetone molecules to give hexane-2,5-dione and dihydrogen and the isomerization to the enolic propen-2-ol form. The mechanisms of these events are discussed in detail.

  10. The chemistry of acetone at extreme conditions by density functional molecular dynamics simulations.

    PubMed

    Ferrante, Francesco; Lo Celso, Fabrizio; Triolo, Roberto; Taleyarkhan, Rusi P

    2011-02-14

    Density functional molecular dynamics simulations have been performed in the NVT ensemble (moles (N), volume (V) and temperature (T)) on a system formed by ten acetone molecules at a temperature of 2000 K and density ρ = 1.322 g cm(-3). These conditions resemble closely those realized at the interface of an acetone vapor bubble in the early stages of supercompression experiments and result in an average pressure of 5 GPa. Two relevant reactive events occur during the simulation: the condensation of two acetone molecules to give hexane-2,5-dione and dihydrogen and the isomerization to the enolic propen-2-ol form. The mechanisms of these events are discussed in detail.

  11. Molecular Seesaw: Intricate Dynamics and Versatile Chemistry of Heteroaromatics on Metal Surfaces.

    PubMed

    Filimonov, Sergey N; Liu, Wei; Tkatchenko, Alexandre

    2017-03-03

    The design of novel elementary surface processes is important for applications in catalysis, single-molecule junctions, molecular sensors, switches, and surface-mounted molecular machines. Here we demonstrate by van der Waals inclusive density functional theory calculations that a small and relatively simple heteroaromatic compound s-triazine (C3H3N3) unexpectedly possesses five metastable states when adsorbed on the Pt(111) surface. This diversity of the adsorption states stems from an interplay between versatile molecule/surface chemical bonding and van der Waals interactions and from "softening" of the aromatic ring by nitrogen substitution, which makes folding of the aromatic ring energetically much less demanding as compared to benzene. The intricate seesaw-like surface dynamics and tunable electronic structure of s-triazine show promise for applications in molecular sensors and switches. The broad implications of our findings are demonstrated for triazine- and pyrimidine-based heteroaromatic compounds and other metal surfaces.

  12. Adsorption of Hydrogen Molecules on Carbon Nanotubes Using Quantum Chemistry and Molecular Dynamics.

    PubMed

    Faginas-Lago, N; Yeni, D; Huarte, F; Wang, Y; Alcamí, M; Martin, F

    2016-08-18

    Physisorption and storage of molecular hydrogen on single-walled carbon nanotube (SWCNT) of various diameters and chiralities are studied by means of classical molecular dynamics (MD) simulations and a force field validated using DFT-D2 and CCSD(T) calculations. A nonrigid carbon nanotube model is implemented with stretching (C-C) and valence angle potentials (C-C-C) formulated as Morse and Harmonic cosine potentials, respectively. Our results evidence that the standard Lennard-Jones potential fails to describe the H2-H2 binding energies. Therefore, our simulations make use of a potential that contains two-body term with parameters obtained from fitting CCSD(T)/CBS binding energies. From our MD simulations, we have analyzed the interaction energies, radial distribution functions, gravimetric densities (% wt), and the distances of the adsorbed H2 layers to the three zigzag type of nanotubes (5,0), (10,0), and (15,0) at 100 and 300 K.

  13. Spatiotemporal dynamics of spring and stream water chemistry in a high-mountain area.

    PubMed

    Zelazny, Mirosław; Astel, Aleksander; Wolanin, Anna; Małek, Stanisław

    2011-05-01

    The present study deals with the application of the self-organizing map (SOM) technique in the exploration of spatiotemporal dynamics of spring and stream water samples collected in the Chochołowski Stream Basin located in the Tatra Mountains (Poland). The SOM-based classification helped to uncover relationships between physical and chemical parameters of water samples and factors determining the quality of water in the studied high-mountain area. In the upper part of the Chochołowski Stream Basin, located on the top of the crystalline core of the Tatras, concentrations of the majority of ionic substances were the lowest due to limited leaching. Significantly higher concentration of ionic substances was detected in spring and stream samples draining sedimentary rocks. The influence of karst-type springs on the quality of stream water was also demonstrated. Copyright © 2010 Elsevier Ltd. All rights reserved.

  14. Potential changes in arctic seasonality and plant communities may impact tundra soil chemistry and carbon dynamics

    NASA Astrophysics Data System (ADS)

    Crow, S.; Cooper, E.; Beilman, D.; Filley, T.; Reimer, P.

    2009-04-01

    On the Svalbard archipelago, as in other high Arctic regions, tundra soil organic matter (SOM) is primarily plant detritus that is largely stabilized by cold, moist conditions and low nitrogen availability. However, the resistance of SOM to decomposition is also influenced by the quality of organic matter inputs to soil. Different plant communities are likely to give different qualities to SOM, especially where lignin-rich woody species encroach into otherwise graminoid and bryophyte-dominated regions. Arctic woody plant species are particularly sensitive to changes in temperature, snow cover, and growing season length. In a changing environment, litter chemistry may emerge as an important control on tundra SOM stabilization. In summer 2007, we collected plant material and soil from the highly-organic upper horizon (appx. 0-5 cm) and the mineral-dominated lower horizon (appx. 5-10cm) from four locations in the southwest facing valleys of Svalbard, Norway. The central goal of the ongoing experiment is to determine whether a greater abundance of woody plants could provide a negative feedback to warming impacts on the carbon (C) balance of Arctic soils. Towards this, we used a combination of plant biopolymer analyses (cupric oxide oxidation and quantification of lignin-derived phenols and cutin/suberin-derived aliphatics) and radiocarbon-based estimates of C longevity and mean residence time (MRT) to characterize potential links between plant type and soil C pools. We found that graminoid species regenerate above- and belowground tissue each year, whereas woody species (Cassiope tetragona and Dryas octopetala) regenerated only leaves yearly. In contrast, C within live branches and roots persisted for 15-18 yr on average. Leaves from woody species remained nearly intact in surface litter for up to 20 yr without being incorporated into the upper soil horizon. Leaves from both graminoid and woody species were concentrated in lignin-derived phenols relative to roots, but

  15. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    PubMed

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

    In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

  16. Molecular modeling of the structural and dynamical properties of secondary plant cell walls: influence of lignin chemistry.

    PubMed

    Charlier, Landry; Mazeau, Karim

    2012-04-12

    A modeling of lignified secondary plant cell walls adapted to grass has been achieved, using molecular dynamics for time up to 180 ns, applied to systems composed of cellulose, xylan, water, and lignin. The overall model, which was 70 nm thick for a volume of 74.4 nm(3), consisted of two crystalline cellulose layers, each being two molecules deep, separated by an interlayer space where the three other components were located. Whereas the cellulose and xylan chemistry was fixed, 18 lignin systems were considered that varied not only in guaiacyl, syringyl, and p-hydroxyphenyl composition, but also in chain length, linkage types, and the presence or absence of coumaryl units. The stabilized models showed a well-defined interface between xylan and cellulose, but some interpenetration of xylan into the lignin part of the models. A survey of the 18 models showed that their lignin component was amorphous and that their density profile was very variable and essentially model dependent. This variability was also reflected in the co-orientation of the lignin phenyl rings with respect to the cellulose surfaces, some systems showing some orientation whereas others did not. The pattern of void distribution accessible to water varied from one system to the next, but the overall void volume was systematically established at around 3%, accepting around 200 water molecules. The estimated mobility of the water molecules interacting with lignin was 1.5 times greater than that interacting with carbohydrates.

  17. Code interoperability and standard data formats in quantum chemistry and quantum dynamics: The Q5/D5Cost data model.

    PubMed

    Rossi, Elda; Evangelisti, Stefano; Laganà, Antonio; Monari, Antonio; Rampino, Sergio; Verdicchio, Marco; Baldridge, Kim K; Bendazzoli, Gian Luigi; Borini, Stefano; Cimiraglia, Renzo; Angeli, Celestino; Kallay, Peter; Lüthi, Hans P; Ruud, Kenneth; Sanchez-Marin, José; Scemama, Anthony; Szalay, Peter G; Tajti, Attila

    2014-03-30

    Code interoperability and the search for domain-specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and quantum dynamics (QD) computer programs is discussed with reference to the research performed in the course of two Collaboration in Science and Technology Actions. The specific data models adopted, Q5Cost and D5Cost, are shown to work for a number of interoperating codes, regardless of the type and amount of information (small or large datasets) to be exchanged. The codes are either interfaced directly, or transfer data by means of wrappers; both types of data exchange are supported by the Q5/D5Cost library. Further, the exchange of data between QC and QD codes is addressed. As a proof of concept, the H + H2 reaction is discussed. The proposed scheme is shown to provide an excellent basis for cooperative code development, even across domain boundaries. Moreover, the scheme presented is found to be useful also as a production tool in the grid distributed computing environment. Copyright © 2013 Wiley Periodicals, Inc.

  18. The formation of Uranus and Neptune in solid-rich feeding zones: Connecting chemistry and dynamics

    NASA Astrophysics Data System (ADS)

    Dodson-Robinson, Sarah E.; Bodenheimer, Peter

    2010-05-01

    The core accretion theory of planet formation has at least two fundamental problems explaining the origins of Uranus and Neptune: (1) dynamical times in the trans-saturnian solar nebula are so long that core growth can take >15 Myr and (2) the onset of runaway gas accretion that begins when cores reach ˜10 M⊕ necessitates a sudden gas accretion cutoff just as Uranus and Neptune's cores reach critical mass. Both problems may be resolved by allowing the ice giants to migrate outward after their formation in solid-rich feeding zones with planetesimal surface densities well above the minimum-mass solar nebula. We present new simulations of the formation of Uranus and Neptune in the solid-rich disk of Dodson-Robinson et al. (Dodson-Robinson, S.E., Willacy, K., Bodenheimer, P., Turner, N.J., Beichman, C.A. [2009]. Icarus 200, 672-693) using the initial semimajor axis distribution of the Nice model (Gomes, R., Levison, H.F., Tsiganis, K., Morbidelli, A. [2005]. Nature 435, 466-469; Morbidelli, A., Levison, H.F., Tsiganis, K., Gomes, R. [2005]. Nature 435, 462-465; Tsiganis, K., Gomes, R., Morbidelli, A., Levison, H.F. [2005]. Nature 435, 459-461), with one ice giant forming at 12 AU and the other at 15 AU. The innermost ice giant reaches its present mass after 3.8-4.0 Myr and the outermost after 5.3-6 Myr, a considerable time decrease from previous one-dimensional simulations (e.g. Pollack, J.B., Hubickyj, O., Bodenheimer, P., Lissauer, J.J., Podolak, M., Greenzweig, Y. [1996]. Icarus 124, 62-85). The core masses stay subcritical, eliminating the need for a sudden gas accretion cutoff. Our calculated carbon mass fractions of 22% are in excellent agreement with the ice giant interior models of Podolak et al. (Podolak, M., Weizman, A., Marley, M. [1995]. Planet. Space Sci. 43, 1517-1522) and Marley et al. (Marley, M.S., Gómez, P., Podolak, M. [1995]. J. Geophys. Res. 100, 23349-23354). Based on the requirement that the ice giant-forming planetesimals contain >10% mass

  19. Flow path functioning identified from fundamental dynamics in sub-hourly, non-conservative stream chemistry

    NASA Astrophysics Data System (ADS)

    Chappell, N. A.; Jones, T.

    2013-12-01

    Within upland streams, concentration & load of many solutes (e.g. H+, DOC) varies very rapidly through storm periods. The shape & features of concentration or load chemographs are an expression of the fundamental dynamics in hydrologic & biogeochemical delivery mechanisms integrated at basin scales. If storm-period chemographs are grossly under-sampled so that time-series does not represent the true chemograph shape, then numerical descriptors of this shape or of the dynamic relationship between controlling variables (e.g. rainfall) & the chemograph will be distorted from true values (Littlewood 1992 IH Rpt 117; Littlewood & Croke 2013 Hydrol Res). Distortions of these dynamic response characteristics or DRCs (model parameters) can then lead to misinterpretation of hydrologic & biogeochemical processes via errors in relative contributions of identified flow paths, rates of propagation along these paths etc. A transfer function (TF) approach can be used to illustrate minimum sampling intensities needed to avoid these errors. Given 15-min observations, CAPTAIN-RIV identification routines for continuous-time TFs give Time Constants (TCs) of only 2 hrs for fast components of responses of rainfall to H+ load in Llyn Brianne streams (Chappell et al 2013 BHS). Given that Time Series Analysis dictates a sampling intensity five times finer than the TC, sampling at 24 min intervals or shorter was needed & achieved in this example. Considerable work is now focused on modeling of chemically-conservative river constituents (namely chloride & water isotopes) to help determine differences in residence times, storage & other DRCs of rainfall-streamflow & associated solute paths (Hrachowitz et al 2013 Hydrol Earth Syst Sci). Comparatively little modeling has focused on high frequency (i.e. sub-hourly), non-conservative river solutes (e.g. H+, DOC). Modeling of these basin-integrated variables should be considered complementary to that for conservative solutes, given: (1) their

  20. Dynamic High Pressure Study of Chemistry and Physics of Molecular Materials

    NASA Astrophysics Data System (ADS)

    Jezowski, Sebastian Ryszard

    Both temperature and pressure control and influence the packing of molecules in crystalline phases. Our molecular simulations indicate that at ambient pressure, the cubic polymorph of tetracyanoethylene, TCNE, is the energetically stable form up to ˜ 160 K. The observed transition from the cubic to the monoclinic polymorph occurs however only at temperatures above ˜ 318 K due to the large transition barrier. The temperature-induced phase transition in TCNE studied with high-resolution IR spectroscopy is explained in terms of the increased vibrational entropy in the crystals of the monoclinic polymorph. Based upon the inverted design of the Merril-Bassett Diamond Anvil Cell, an improved, second generation dynamic Diamond Anvil Cell was developed. Based on the fluorescence of ruby crystals, we were able to demonstrate that the pressure variation range can be further increased at least up to 7 kbar and that the dynamic pressure compression of up to 1400 GPa/s can be achieved. A new class of mechanophoric system, bis-anthracene, BA, and its photoisomer, PI, is shown to respond reversibly to a mild, static pressure induced by a Diamond Anvil Cell as well as to shear deformation based on absorption spectroscopic measurements. The forward reaction occurs upon illumination with light while the back-reaction may be accelerated upon heating or mechanical stress, coupled to a rehybridization on four equivalent carbon atoms. It is an intriguing result as high pressure stabilizes the photodimerized species in related systems. Our molecular volume simulations ruled out significant differences in the volumes between bis-anthracene and its photoisomer. Kinetic absorption measurements at several different pressures reveal a negative volume of activation in the exothermic back-reaction at room temperature. Through a series of temperature-dependent kinetic measurements it is shown that the barrier of activation for the back-reaction is reduced by more than an order of magnitude at

  1. Modelling non-equilibrium secondary organic aerosol formation and evaporation with the aerosol dynamics, gas- and particle-phase chemistry kinetic multilayer model ADCHAM

    SciTech Connect

    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.

  2. Quality management science in clinical chemistry: a dynamic framework for continuous improvement of quality.

    PubMed

    Westgard, J O; Burnett, R W; Bowers, G N

    1990-10-01

    Current quality assurance approaches will not be adequate to satisfy the needs for quality in the next decade. Quality management science (QMS), as evolving in industry today, provides the dynamic framework necessary to provide continuous improvement of quality. QMS emphasizes the importance of defining quality goals based on the needs and expectations (implied needs) of customers. The laboratory can develop customer-friendly goals and measures of quality by recognizing that customers' experiences are represented by a totality of results. Quality goals and measures are best communicated as "total performance" by specifying a limit and percentile of the distribution, rather than a mean and standard deviation. Application of quality goals within the laboratory will usually require partitioning the total performance goal into components and translating those components into specifications to guide the operation and management of production processes. QMS also extends beyond technical processes to people processes and provides guidance for improving the quality of worklife and caring for the laboratory's most essential resource--our people.

  3. Combinatorial brain decoding of people's whereabouts during visuospatial navigation

    PubMed Central

    Op de Beeck, Hans P.; Vermaercke, Ben; Woolley, Daniel G.; Wenderoth, Nicole

    2013-01-01

    Complex behavior typically relies upon many different processes which are related to activity in multiple brain regions. In contrast, neuroimaging analyses typically focus upon isolated processes. Here we present a new approach, combinatorial brain decoding, in which we decode complex behavior by combining the information which we can retrieve from the neural signals about the many different sub-processes. The case in point is visuospatial navigation. We explore the extent to which the route travelled by human subjects (N = 3) in a complex virtual maze can be decoded from activity patterns as measured with functional magnetic resonance imaging. Preliminary analyses suggest that it is difficult to directly decode spatial position from regions known to contain an explicit cognitive map of the environment, such as the hippocampus. Instead, we were able to indirectly derive spatial position from the pattern of activity in visual and motor cortex. The non-spatial representations in these regions reflect processes which are inherent to navigation, such as which stimuli are perceived at which point in time and which motor movement is executed when (e.g., turning left at a crossroad). Highly successful decoding of routes followed through the maze was possible by combining information about multiple aspects of navigation events across time and across multiple cortical regions. This “proof of principle” study highlights how visuospatial navigation is related to the combined activity of multiple brain regions, and establishes combinatorial brain decoding as a means to study complex mental events that involve a dynamic interplay of many cognitive processes. PMID:23730269

  4. Effects of Suboptimal Bidding in Combinatorial Auctions

    NASA Astrophysics Data System (ADS)

    Schneider, Stefan; Shabalin, Pasha; Bichler, Martin

    Though the VCG auction assumes a central place in the mechanism design literature, there are a number of reasons for favoring iterative combinatorial auction designs. Several promising ascending auction formats have been developed throughout the past few years based on primal-dual and subgradient algorithms and linear programming theory. Prices are interpreted as a feasible dual solution and the provisional allocation is interpreted as a feasible primal solution. iBundle( 3) (Parkes and Ungar 2000), dVSV (de Vries et al. 2007) and the Ascending Proxy auction (Ausubel and Milgrom 2002) result in VCG payoffs when the coalitional value function satisfies the buyer submodularity condition and bidders bid straightforward, which is an expost Nash equilibrium in that case. iBEA and CreditDebit auctions (Mishra and Parkes 2007) do not even require the buyer submodularity condition and achieve the same properties for general valuations. In many situations, however, one cannot assume bidders to bid straightforward and it is not clear from the theory how these non-linear personalized price auctions (NLPPAs) perform in this case. Robustness of auctions with respect to different bidding behavior is therefore a critical issue for any application. We have conducted a large number of computational experiments to analyze the performance of NLPPA designs with respect to different bidding strategies and different valuation models. We compare the results of NLPPAs to those of the VCG auction and those of iterative combinatorial auctions with approximate linear prices, such as ALPS (Bichler et al. 2009) and the Combinatorial Clock auction (Porter et al. 2003).

  5. The Chemistry and Flow Dynamics of Molecular Biological Tools Used to Confirm In Situ Bioremediation of Benzene, TBA, and MTBE

    NASA Astrophysics Data System (ADS)

    North, K. P.; Mackay, D. M.; Scow, K. M.

    2010-12-01

    In situ bioremediation has typically been confirmed by collecting sediment and groundwater samples to directly demonstrate a degradation process in a laboratory microcosm. However, recent advances in molecular biological tools present options for demonstrating degradation processes with field-based tools that are less time-consuming. We have been investigating the capability of some of these molecular biological tools to evaluate in situ biodegradation of tert-butyl alcohol (TBA), methyl tert-butyl ether (MTBE), and benzene at two field sites in California. At both sites, we have deployed Bio-Traps® (“traps”), made of Bio-Sep® beads in slotted PVC pipe, which provide ideal environments for microbial colonization. Stable Isotope Probing can be accomplished by sorbing the13C-labeled organic contaminant of concern onto Bio-Sep® beads (“baiting”); incorporation of 13C into the biomass collected by the trap would indicate that the microbial community was capable of degrading the labeled compound. In addition, we examined the chemistry and flow dynamics of these traps and present those results here. We performed a field experiment and a lab experiment to, in part, define the rate that different baits leached off various traps. At a TBA- and MTBE-contaminated site at Vandenberg AFB, Lompoc, CA, the TBA-dominant plume was effectively treated by recirculation/oxygenation of groundwater, decreasing TBA and MTBE concentrations to detection limits along predicted flowpaths created by two pairs of recirculation wells. We used the generated aerobic treatment zone to deploy traps baited with 13C-labeled MTBE or TBA in a novel, ex situ experimental setup. The groundwater flow extracted from the aerobic treatment zone was split through several chambers, each containing a trap and monitoring of influent and effluent. The chamber effluent was measured throughout a six-week deployment and analyzed for both TBA and MTBE; the majority of mass leached from the baited traps did

  6. Developing New Antibiotics with Combinatorial Biosynthesis

    NASA Astrophysics Data System (ADS)

    Pohl, Nicola L.

    2000-11-01

    Polyketide synthases (PKSs), a class of enzymes found in soil bacteria that produce antibiotics such as erythromycin, string together acetate units using basic organic reactions. The manipulation of the sequence of these reactions at the genetic level has resulted in an alteration of the corresponding chemical structure of the antibiotic produced by the bacteria. This process, called combinatorial biosynthesis, allows the generation of many presently unknown complex structures that can be tested for antibacterial activity, thereby contributing to the race against antibiotic-resistant infectious bacteria.

  7. Some useful combinatorial formulas for bosonic operators

    SciTech Connect

    Blasiak, P.; Penson, K.A.; Solomon, A.I.; Horzela, A.; Duchamp, G.H.E.

    2005-05-01

    We give a general expression for the normally ordered form of a function F[w(a,a{sup {dagger}})] where w is a function of boson creation and annihilation operators satisfying [a,a{sup {dagger}}]=1. The expectation value of this expression in a coherent state becomes an exact generating function of Feynman-type graphs associated with the zero-dimensional quantum field theory defined by F(w). This enables one to enumerate explicitly the graphs of given order in the realm of combinatorially defined sequences. We give several examples of the use of this technique, including the applications to Kerr-type and superfluidity-type Hamiltonians.

  8. Polynomial Local Improvement Algorithms in Combinatorial Optimization.

    DTIC Science & Technology

    1981-11-01

    NUMBER SOL 81- 21 IIS -J O 15 14. TITLE (am#Su&Utl & YEO RPR ERO OEE Polynomial Local Improvement Algorithms in TcnclRpr Combinatorial Optimization 6...Stanford, CA 94305 II . CONTROLLING OFFICE NAME AND ADDRESS It. REPORT DATE Office of Naval Research - Dept. of the Navy November 1981 800 N. Qu~incy Street...corresponds to a node of the tree. ii ) The father of a vertex is its optimal adjacent vertex; if a vertex is a local optimum, it has no father. The tree is

  9. Apparatus for combinatorial screening of electrochemical materials

    DOEpatents

    A high throughput combinatorial screening method and apparatus for the evaluation of electrochemical materials using a single voltage source is disclosed wherein temperature changes arising from the application of an electrical load to a cell array are used to evaluate the relative electrochemical efficiency of the materials comprising the array. The apparatus may include an array of electrochemical cells that are connected to each other in parallel or in series, an electronic load for applying a voltage or current to the electrochemical cells , and a device , external to the cells, for monitoring the relative temperature of each cell when the load is applied.

    2009-12-15

    A high throughput combinatorial screening method and apparatus for the evaluation of electrochemical materials using a single voltage source (2) is disclosed wherein temperature changes arising from the application of an electrical load to a cell array (1) are used to evaluate the relative electrochemical efficiency of the materials comprising the array. The apparatus may include an array of electrochemical cells (1) that are connected to each other in parallel or in series, an electronic load (2) for applying a voltage or current to the electrochemical cells (1), and a device (3), external to the cells, for monitoring the relative temperature of each cell when the load is applied.

  10. Aerospace applications of integer and combinatorial optimization

    NASA Technical Reports Server (NTRS)

    Padula, S. L.; Kincaid, R. K.

    1995-01-01

    Research supported by NASA Langley Research Center includes many applications of aerospace design optimization and is conducted by teams of applied mathematicians and aerospace engineers. This paper investigates the benefits from this combined expertise in solving combinatorial optimization problems. Applications range from the design of large space antennas to interior noise control. A typical problem, for example, seeks the optimal locations for vibration-damping devices on a large space structure and is expressed as a mixed/integer linear programming problem with more than 1500 design variables.

  11. Aerospace Applications of Integer and Combinatorial Optimization

    NASA Technical Reports Server (NTRS)

    Padula, S. L.; Kincaid, R. K.

    1995-01-01

    Research supported by NASA Langley Research Center includes many applications of aerospace design optimization and is conducted by teams of applied mathematicians and aerospace engineers. This paper investigates the benefits from this combined expertise in formulating and solving integer and combinatorial optimization problems. Applications range from the design of large space antennas to interior noise control. A typical problem, for example, seeks the optimal locations for vibration-damping devices on an orbiting platform and is expressed as a mixed/integer linear programming problem with more than 1500 design variables.

  12. Aerospace applications on integer and combinatorial optimization

    NASA Technical Reports Server (NTRS)

    Padula, S. L.; Kincaid, R. K.

    1995-01-01

    Research supported by NASA Langley Research Center includes many applications of aerospace design optimization and is conducted by teams of applied mathematicians and aerospace engineers. This paper investigates the benefits from this combined expertise in formulating and solving integer and combinatorial optimization problems. Applications range from the design of large space antennas to interior noise control. A typical problem. for example, seeks the optimal locations for vibration-damping devices on an orbiting platform and is expressed as a mixed/integer linear programming problem with more than 1500 design variables.

  13. Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ

    PubMed Central

    2016-01-01

    Recently, a novel pathway for heme b biosynthesis in Gram-positive bacteria has been proposed. The final poorly understood step is catalyzed by an enzyme called HemQ and includes two decarboxylation reactions leading from coproheme to heme b. Coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. In the study presented here, we focus on HemQs from Listeria monocytogenes (LmHemQ) and Staphylococcus aureus (SaHemQ) recombinantly produced as apoproteins in Escherichia coli. We demonstrate the rapid and two-phase uptake of coproheme by both apo forms and the significant differences in thermal stability of the apo forms, coproheme-HemQ and heme b-HemQ. Reduction of ferric high-spin coproheme-HemQ to the ferrous form is shown to be enthalpically favored but entropically disfavored with standard reduction potentials of −205 ± 3 mV for LmHemQ and −207 ± 3 mV for SaHemQ versus the standard hydrogen electrode at pH 7.0. Redox thermodynamics suggests the presence of a pronounced H-bonding network and restricted solvent mobility in the heme cavity. Binding of cyanide to the sixth coproheme position is monophasic but relatively slow (∼1 × 104 M–1 s–1). On the basis of the available structures of apo-HemQ and modeling of both loaded forms, molecular dynamics simulation allowed analysis of the interaction of coproheme and heme b with the protein as well as the role of the flexibility at the proximal heme cavity and the substrate access channel for coproheme binding and heme b release. Obtained data are discussed with respect to the proposed function of HemQ in monoderm bacteria. PMID:27599156

  14. Venus O2 visible and IR nightglow: Implications for lower thermosphere dynamics and chemistry

    NASA Technical Reports Server (NTRS)

    Bougher, S. W.; Borucki, W. J.

    1994-01-01

    The National Center for Atmospheric Research thermospheric general circulation model for the Venus thermosphere is modified to examine two observed night airglow features, both of which serve as sensitive tracers of the thermospheric circulation. New O2 nightglow data from the Pioneer Venus Orbiter (PVO) star tracker (O2 Herzberg II at 400-800 nm) and ground-based telescopes (O2 IR at 1.27 microns) yield additional model constraints for estimating Venus winds over 100-130 km. Atomic oxygen, produced by dayside CO2 photolysis peaking near 110 km, and transported to the nightside by the global wind system, is partially destroyed through three-body recombination, yielding the O2 Herzberg II visible nightglow. This emission is very sensitive to horizontal winds at altitudes between 100 and 130 km. Other trace species catalytic reactions also contribute to the production of the very strong nightside infrared (1.27 microns) emission. This paper examines the dynamical and chemical implications of these new data using the Venus thermospheric general circulation model (VTGCM) as an analysis tool. Three-dimensional calculations are presented for both solar maximum and solar medium conditions, corresponding to early PVO (1979-1981) and PVO entry (mid-1992) time periods. Very distinct periods are identified in which zonal winds are alternately weak and strong in the Venus lower thermosphere. VTGCM sensitivity studies are conducted to assess the impacts of potential changes in thermospheric zonal and day-to-night winds, and eddy diffusion on the corresponding nightglow intensities. It appears that cyclostrophic balance extends above 80 km periodically, owing to a reversal of the upper mesosphere latitudinal temperature gradient, and thereby producing strong zonal winds and correspondingly modified O2 nightglow distributions that are observed.

  15. Particulate matter chemistry and dynamics in the twilight zone at VERTIGO ALOHA and K2 sites

    NASA Astrophysics Data System (ADS)

    Bishop, James K. B.; Wood, T. J.

    2008-12-01

    Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERtical Transport In the Global Ocean (VERTIGO) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by ˜100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting 3 weeks, contrasted oligotrophic station ALOHA (22.75°N 158°W), sampled in June-July 2004, with a biologically productive location (47 °N 161°E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C org, N, P, Ca, Si, Sr, Ba, Mn) in <1, 1-51, and >51 μm size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C org and C-Star particle beam attenuation coefficient ( C P) were consistently related at both sites with a 27 μM m -1 conversion factor. At K2, C P profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed ˜40% and 10%, night and day, respectively to >51 μm C org of MULVFS samples in the mixed layer, but few copepods were collected in deeper waters; however, non-swimming radiolarians were quantitatively sampled. A recent hypothesis regarding POC differences between pumps and bottles is examined in light of these results. Particulate >51 μm C org, N, and P at both ALOHA and K2 showed strong attenuation with depth at both sites. Notable at ALOHA were unusually high levels of >51 μm Sr (up to 4 nM) in the mixed layer, a reflection of high abundances of SrSO 4 precipitating Acantharia. Notable at K2 were major changes in water column inventories of many particulate components to 700 m

  16. Particulate matter chemistry and dynamics in the Twilight Zone at VERTIGO ALOHA and K2 Sites

    SciTech Connect

    Bishop, James K.B.; Wood, T.J.

    2008-03-25

    Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERTIGO (VERtical Transformations In the Global Ocean) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by {approx}100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting three weeks, contrasted oligotrophic station ALOHA (22.75{sup o}N 158{sup o}W), sampled in June-July 2004, with a biologically productive location (47{sup o}N 161{sup o}E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C{sub org}, N, P, Ca, Si, Sr, Ba, Mn) in <1, 1-51, and >51 {micro}m size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C{sub org} and C-Star particle beam attenuation coefficient (C{sub P}) were consistently related at both sites with a 27 {micro}M m{sup -1} conversion factor. 26 At K2, C{sub P} profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed {approx}40% and 10%, night and day, respectively to >51 {micro}m C{sub org} of MULVFS samples in the mixed layer, but few copepods were collected in deeper waters; however, non-swimming radiolarians were quantitatively sampled. A recent hypothesis regarding POC differences between pumps and bottles is examined in light of these results. Particulate >51 {micro}m C{sub org}, N, and P at both ALOHA and K2 showed strong attenuation with depth at both sites. Notable at ALOHA were unusually high levels of >51 {micro}m Sr (up to 4 nM) in the mixed layer, a reflection of high abundances of SrSO{sub 4} precipitating

  17. Combinatorial Libraries of Bis-Heterocyclic Compounds with Skeletal Diversity

    PubMed Central

    Soural, Miroslav; Bouillon, Isabelle; Krchňák, Viktor

    2009-01-01

    Combinatorial solid-phase synthesis of bis-heterocyclic compounds, characterized by the presence of two heterocyclic cores connected by a spacer of variable length/structure, provided structurally heterogeneous libraries with skeletal diversity. Both heterocyclic rings were assembled on resin in a combinatorial fashion. PMID:18811208

  18. Smooth Constrained Heuristic Optimization of a Combinatorial Chemical Space

    DTIC Science & Technology

    2015-05-01

    ARL-TR-7294•MAY 2015 US Army Research Laboratory Smooth ConstrainedHeuristic Optimization of a Combinatorial Chemical Space by Berend Christopher...7294•MAY 2015 US Army Research Laboratory Smooth ConstrainedHeuristic Optimization of a Combinatorial Chemical Space by Berend Christopher...

  19. Self-encoding resin beads of combinatorial library screening

    NASA Astrophysics Data System (ADS)

    Lei, Du; Zhao, Yuandi; Cheng, Tongsheng; Zeng, Shaoqun; Luo, Qingming

    2003-07-01

    The latest self-encoding resin bead is a novel technology for solid phase synthesis combinatorial library screening. A new encode-positional deconvolution strategy which was based on that technology been illustrated compared with positional scanning and iterative strategies. The self-encoding resin beads technology provides an efficient method for improving the high-throughput screening of combinatorial library.

  20. Combinatorial Multiobjective Optimization Using Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Crossley, William A.; Martin. Eric T.

    2002-01-01

    The research proposed in this document investigated multiobjective optimization approaches based upon the Genetic Algorithm (GA). Several versions of the GA have been adopted for multiobjective design, but, prior to this research, there had not been significant comparisons of the most popular strategies. The research effort first generalized the two-branch tournament genetic algorithm in to an N-branch genetic algorithm, then the N-branch GA was compared with a version of the popular Multi-Objective Genetic Algorithm (MOGA). Because the genetic algorithm is well suited to combinatorial (mixed discrete / continuous) optimization problems, the GA can be used in the conceptual phase of design to combine selection (discrete variable) and sizing (continuous variable) tasks. Using a multiobjective formulation for the design of a 50-passenger aircraft to meet the competing objectives of minimizing takeoff gross weight and minimizing trip time, the GA generated a range of tradeoff designs that illustrate which aircraft features change from a low-weight, slow trip-time aircraft design to a heavy-weight, short trip-time aircraft design. Given the objective formulation and analysis methods used, the results of this study identify where turboprop-powered aircraft and turbofan-powered aircraft become more desirable for the 50 seat passenger application. This aircraft design application also begins to suggest how a combinatorial multiobjective optimization technique could be used to assist in the design of morphing aircraft.

  1. Combinatorial design of textured mechanical metamaterials.

    PubMed

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2016-07-28

    The structural complexity of metamaterials is limitless, but, in practice, most designs comprise periodic architectures that lead to materials with spatially homogeneous features. More advanced applications in soft robotics, prosthetics and wearable technology involve spatially textured mechanical functionality, which requires aperiodic architectures. However, a naive implementation of such structural complexity invariably leads to geometrical frustration (whereby local constraints cannot be satisfied everywhere), which prevents coherent operation and impedes functionality. Here we introduce a combinatorial strategy for the design of aperiodic, yet frustration-free, mechanical metamaterials that exhibit spatially textured functionalities. We implement this strategy using cubic building blocks-voxels-that deform anisotropically, a local stacking rule that allows cooperative shape changes by guaranteeing that deformed building blocks fit together as in a three-dimensional jigsaw puzzle, and three-dimensional printing. These aperiodic metamaterials exhibit long-range holographic order, whereby the two-dimensional pixelated surface texture dictates the three-dimensional interior voxel arrangement. They also act as programmable shape-shifters, morphing into spatially complex, but predictable and designable, shapes when uniaxially compressed. Finally, their mechanical response to compression by a textured surface reveals their ability to perform sensing and pattern analysis. Combinatorial design thus opens up a new avenue towards mechanical metamaterials with unusual order and machine-like functionalities.

  2. A combinatorial morphospace for angiosperm pollen

    NASA Astrophysics Data System (ADS)

    Mander, Luke

    2016-04-01

    The morphology of angiosperm (flowering plant) pollen is extraordinarily diverse. This diversity results from variations in the morphology of discrete anatomical components. These components include the overall shape of a pollen grain, the stratification of the exine, the number and form of any apertures, the type of dispersal unit, and the nature of any surface ornamentation. Different angiosperm pollen morphotypes reflect different combinations of these discrete components. In this talk, I ask the following question: given the anatomical components of angiosperm pollen that are known to exist in the plant kingdom, how many unique biologically plausible combinations of these components are there? I explore this question from the perspective of enumerative combinatorics using an algorithm I have written in the Python programming language. This algorithm (1) calculates the number of combinations of these components; (2) enumerates those combinations; and (3) graphically displays those combinations. The result is a combinatorial morphospace that reflects an underlying notion that the process of morphogenesis in angiosperm pollen can be thought of as an n choose k counting problem. I compare the morphology of extant and fossil angiosperm pollen grains to this morphospace, and suggest that from a combinatorial point of view angiosperm pollen is not as diverse as it could be, which may be a result of developmental constraints.

  3. Combinatorial design of textured mechanical metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2016-07-01

    The structural complexity of metamaterials is limitless, but, in practice, most designs comprise periodic architectures that lead to materials with spatially homogeneous features. More advanced applications in soft robotics, prosthetics and wearable technology involve spatially textured mechanical functionality, which requires aperiodic architectures. However, a naive implementation of such structural complexity invariably leads to geometrical frustration (whereby local constraints cannot be satisfied everywhere), which prevents coherent operation and impedes functionality. Here we introduce a combinatorial strategy for the design of aperiodic, yet frustration-free, mechanical metamaterials that exhibit spatially textured functionalities. We implement this strategy using cubic building blocks—voxels—that deform anisotropically, a local stacking rule that allows cooperative shape changes by guaranteeing that deformed building blocks fit together as in a three-dimensional jigsaw puzzle, and three-dimensional printing. These aperiodic metamaterials exhibit long-range holographic order, whereby the two-dimensional pixelated surface texture dictates the three-dimensional interior voxel arrangement. They also act as programmable shape-shifters, morphing into spatially complex, but predictable and designable, shapes when uniaxially compressed. Finally, their mechanical response to compression by a textured surface reveals their ability to perform sensing and pattern analysis. Combinatorial design thus opens up a new avenue towards mechanical metamaterials with unusual order and machine-like functionalities.

  4. Asymmetric Proteome Equalization of the Skeletal Muscle Proteome Using a Combinatorial Hexapeptide Library

    PubMed Central

    Rivers, Jenny; Hughes, Chris; McKenna, Thérèse; Woolerton, Yvonne; Vissers, Johannes P. C.; Langridge, James I.; Beynon, Robert J.

    2011-01-01

    Immobilized combinatorial peptide libraries have been advocated as a strategy for equalization of the dynamic range of a typical proteome. The technology has been applied predominantly to blood plasma and other biological fluids such as urine, but has not been used extensively to address the issue of dynamic range in tissue samples. Here, we have applied the combinatorial library approach to the equalization of a tissue where there is also a dramatic asymmetry in the range of abundances of proteins; namely, the soluble fraction of skeletal muscle. We have applied QconCAT and label-free methodology to the quantification of the proteins that bind to the beads as the loading is progressively increased. Although some equalization is achieved, and the most abundant proteins no longer dominate the proteome analysis, at high protein loadings a new asymmetry of protein expression is reached, consistent with the formation of complex assembles of heat shock proteins, cytoskeletal elements and other proteins on the beads. Loading at different ionic strength values leads to capture of different subpopulations of proteins, but does not completely eliminate the bias in protein accumulation. These assemblies may impair the broader utility of combinatorial library approaches to the equalization of tissue proteomes. However, the asymmetry in equalization is manifest at either low and high ionic strength values but manipulation of the solvent conditions may extend the capacity of the method. PMID:22205978

  5. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    NASA Astrophysics Data System (ADS)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  6. Microbatteries for Combinatorial Studies of Conventional Lithium-Ion Batteries

    NASA Technical Reports Server (NTRS)

    West, William; Whitacre, Jay; Bugga, Ratnakumar

    2003-01-01

    Integrated arrays of microscopic solid-state batteries have been demonstrated in a continuing effort to develop microscopic sources of power and of voltage reference circuits to be incorporated into low-power integrated circuits. Perhaps even more importantly, arrays of microscopic batteries can be fabricated and tested in combinatorial experiments directed toward optimization and discovery of battery materials. The value of the combinatorial approach to optimization and discovery has been proven in the optoelectronic, pharmaceutical, and bioengineering industries. Depending on the specific application, the combinatorial approach can involve the investigation of hundreds or even thousands of different combinations; hence, it is time-consuming and expensive to attempt to implement the combinatorial approach by building and testing full-size, discrete cells and batteries. The conception of microbattery arrays makes it practical to bring the advantages of the combinatorial approach to the development of batteries.

  7. Techniques for analysis and purification in high-throughput chemistry.

    PubMed

    Hughes, I; Hunter, D

    2001-06-01

    The success of combinatorial chemistry, and the increased emphasis on single well-characterised compounds of high purity, has had a significant impact on analytical and purification technologies. The requirement for ever-increasing throughput has led to the automation and parallelisation of these techniques. Advances have also been made in developing faster methods to augment throughput further.

  8. Combustion chemistry

    SciTech Connect

    Brown, N.J.

    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).

  9. Implementation of a research-based lab module in a high school chemistry curriculum: A study of classroom dynamics

    NASA Astrophysics Data System (ADS)

    Pilarz, Matthew

    For this study, a research-based lab module was implemented in two high school chemistry classes for the purpose of examining classroom dynamics throughout the process of students completing the module. A research-based lab module developed for use in undergraduate laboratories by the Center for Authentic Science Practice in Education (CASPiE) was modified and implemented in two high school settings. This module consisted of four phases: Skill Building, Experimental Design, Independent Research, and Results and Poster Presentation. Classroom dynamics were studied by considering the students' and teachers' perceptions of their experiences during the completion of the module and by examining the interactions between students and teachers that took place throughout the module. The results reveal that there are shifts in classroom dynamics throughout the four phases of the module. In the Skill Building phase there was a great deal of dependence on the teacher for help in completing tasks. However, there is a slight contrast to what the students and teachers reported about their experiences during this phase. The teachers describe the students as being very dependent on them and asking questions constantly during the Skill Building experiments. The students report that they tried to figure out their problems with their lab partners and students in other lab groups before asking the teacher for help. The teachers perceived that students came to them immediately for help and did not realize that students were coming to them as sort of a last resort when they could not solve problems on their own. In the Experimental Design phase the students and teachers both report that the lab groups were working together as groups to design their experiments, and rarely had interactions with anyone outside of their lab group. For the Independent Research phase both students and teachers report that lab groups worked very independently of any outside assistance and that they began to

  10. Heterogeneous chemistry and reaction dynamics of the atmospheric oxidants, O3, NO3, and OH, on organic surfaces.

    PubMed

    Chapleski, Robert C; Zhang, Yafen; Troya, Diego; Morris, John R

    2016-07-07

    Heterogeneous chemistry of the most important atmospheric oxidants, O3, NO3, and OH, plays a central role in regulating atmospheric gas concentrations, processing aerosols, and aging materials. Recent experimental and computational studies have begun to reveal the detailed reaction mechanisms and kinetics for gas-phase O3, NO3, and OH when they impinge on organic surfaces. Through new research approaches that merge the fields of traditional surface science with atmospheric chemistry, researchers are developing an understanding for how surface structure and functionality affect interfacial chemistry with this class of highly oxidizing pollutants. Together with future research initiatives, these studies will provide a more complete description of atmospheric chemistry and help others more accurately predict the properties of aerosols, the environmental impact of interfacial oxidation, and the concentrations of tropospheric gases.

  11. Dynamic nuclear polarization NMR spectroscopy allows high-throughput characterization of microporous organic polymers.

    PubMed

    Blanc, Frédéric; Chong, Samantha Y; McDonald, Tom O; Adams, Dave J; Pawsey, Shane; Caporini, Marc A; Cooper, Andrew I

    2013-10-16

    Dynamic nuclear polarization (DNP) solid-state NMR was used to obtain natural abundance (13)C and (15)N CP MAS NMR spectra of microporous organic polymers with excellent signal-to-noise ratio, allowing for unprecedented details in the molecular structure to be determined for these complex polymer networks. Sensitivity enhancements larger than 10 were obtained with bis-nitroxide radical at 14.1 T and low temperature (∼105 K). This DNP MAS NMR approach allows efficient, high-throughput characterization of libraries of porous polymers prepared by combinatorial chemistry methods.

  12. Dynamic mixtures: challenges and opportunities for the amplification and sensing of scents.

    PubMed

    Herrmann, Andreas

    2012-07-09

    Nature generates compounds as complicated mixtures, but surprisingly little is known about the synergies or inhibitory effects of compound mixtures, which is likely to become an important research area in life sciences in the near future. Some recently developed concepts in dynamic combinatorial/covalent chemistry (DCC) have been applied to amplify (increase the intensity and long-lastingness of perception) and sense (selectively detect and discriminate) individual bioactive volatile molecules in compound mixtures. This Concept article focuses on the potential of DCC to impact and modulate the biological and chemical properties of mixtures of bioactive volatile compounds to gain a more fundamental understanding of the properties of compound mixtures in molecular recognition.

  13. The Met Office HadGEM3-ES chemistry-climate model: evaluation of stratospheric dynamics and its impact on ozone

    NASA Astrophysics Data System (ADS)

    Hardiman, Steven C.; Butchart, Neal; O'Connor, Fiona M.; Rumbold, Steven T.

    2017-03-01

    Free-running and nudged versions of a Met Office chemistry-climate model are evaluated and used to investigate the impact of dynamics versus transport and chemistry within the model on the simulated evolution of stratospheric ozone. Metrics of the dynamical processes relevant for simulating stratospheric ozone are calculated, and the free-running model is found to outperform the previous model version in 10 of the 14 metrics. In particular, large biases in stratospheric transport and tropical tropopause temperature, which existed in the previous model version, are substantially reduced, making the current model more suitable for the simulation of stratospheric ozone. The spatial structure of the ozone hole, the area of polar stratospheric clouds, and the increased ozone concentrations in the Northern Hemisphere winter stratosphere following sudden stratospheric warmings, were all found to be sensitive to the accuracy of the dynamics and were better simulated in the nudged model than in the free-running model. Whilst nudging can, in general, provide a useful tool for removing the influence of dynamical biases from the evolution of chemical fields, this study shows that issues can remain in the climatology of nudged models. Significant biases in stratospheric vertical velocities, age of air, water vapour, and total column ozone still exist in the Met Office nudged model. Further, these can lead to biases in the downward flux of ozone into the troposphere.

  14. Hyperthermal oxidation and pyrolysis of carbon based materials: Chemistry and dynamics using the ReaxFF reactive force field

    NASA Astrophysics Data System (ADS)

    Srinivasan, Sriram Goverapet

    The primary focus of this work was to study the chemistry and dynamics of hyperthermal collisions of oxygen atoms with carbon based materials of the kind witnessed in the Low Earth Orbit (LEO) environment and their pyrolysis through atomistic simulations using the ReaxFF reactive force field and to develop ReaxFF potentials for such applications. In particular, ReaxFF was used to study the oxidative erosion of graphene, graphite and diamond subjected to collisions with energetic oxygen atoms at elevated surface temperatures. Prior to these simulations, the ReaxFF C/H/O potential was validated against quantum chemical (QC) data for the energetics associated with the loss of a CO2 molecule from a model graphitic system and for various other chemical reactions occurring during the collision of a hyperthermal oxygen atom with a pristine and defective graphene sheet and a diamond slab. ReaxFF based simulations suggested that the breakup of a graphene sheet and graphite structure upon hyperthermal oxygen atom impact could be divided into distinct regimes. Graphene erosion proceeded through the formation of epoxides on the surface followed by the creation and growth of vacancy defects while the breakup of graphite occurred through the formation of epoxides on the top layer, creation and growth of vacancy defects on the top layer followed by epoxide formation on the bottom layer, creation of defects and their growth on the bottom layer. As such the breakup of graphite was observed to be a layer by layer event with the rate of growth of defects much larger along the basal plane directions compared to the axial direction. With increase in temperature, the rate of mass loss from graphite was observed to increase. While the impact of the oxygen atoms occurred at hyperthermal energies, the chemical reactions leading to mass loss from graphite were thermal in nature. Furthermore, molecular dynamics simulations of carbon loss from graphite at various surface temperatures upon

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

    PubMed

    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. © 2014 Wiley Periodicals, Inc.

  16. Large eddy simulation of reactive pollutants in a deep urban street canyon: Coupling dynamics with O3-NOx-VOC chemistry.

    PubMed

    Zhong, Jian; Cai, Xiao-Ming; Bloss, William James

    2017-05-01

    A large eddy simulation (LES) model coupled with O3-NOx-VOC chemistry is implemented to simulate the coupled effects of emissions, mixing and chemical pre-processing within an idealised deep (aspect ratio = 2) urban street canyon under a weak wind condition. Reactive pollutants exhibit significant spatial variations in the presence of two vertically aligned unsteady vortices formed in the canyon. Comparison of the LES results from two chemical schemes (simple NOx-O3 chemistry and a more comprehensive Reduced Chemical Scheme (RCS) chemical mechanism) shows that the concentrations of NO2 and Ox inside the street canyon are enhanced by approximately 30-40% via OH/HO2 chemistry. NO, NOx, O3, OH and HO2 are chemically consumed, while NO2 and Ox (total oxidant) are chemically produced within the canyon environment. Within-canyon pre-processing increases oxidant fluxes from the canyon to the overlying boundary layer, and this effect is greater for deeper street canyons (as found in many traditional European urban centres) than shallower (lower aspect ratio) streets. There is clear evidence of distinct behaviours for emitted chemical species and entrained chemical species, and positive (or negative) values of intensities of segregations are found between pairs of species with similar (or opposite) behaviour. The simplified two-box model underestimated NO and O3 levels, but overestimated NO2 levels for both the lower and upper canyon compared with the more realistic LES-chemistry model. This suggests that the segregation effect due to incomplete mixing reduces the chemical conversion rate of NO to NO2. This study reveals the impacts of nonlinear O3-NOx-VOC photochemical processes in the incomplete mixing environment and provides a better understanding of the pre-processing of emissions within canyons, prior to their release to the urban boundary layer, through the coupling of street canyon dynamics and chemistry. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Characterizing the combinatorial beam angle selection problem

    NASA Astrophysics Data System (ADS)

    Bangert, Mark; Ziegenhein, Peter; Oelfke, Uwe

    2012-10-01

    The beam angle selection (BAS) problem in intensity-modulated radiation therapy is often interpreted as a combinatorial optimization problem, i.e. finding the best combination of η beams in a discrete set of candidate beams. It is well established that the combinatorial BAS problem may be solved efficiently with metaheuristics such as simulated annealing or genetic algorithms. However, the underlying parameters of the optimization process, such as the inclusion of non-coplanar candidate beams, the angular resolution in the space of candidate beams, and the number of evaluated beam ensembles as well as the relative performance of different metaheuristics have not yet been systematically investigated. We study these open questions in a meta-analysis of four strategies for combinatorial optimization in order to provide a reference for future research related to the BAS problem in intensity-modulated radiation therapy treatment planning. We introduce a high-performance inverse planning engine for BAS. It performs a full fluence optimization for ≈3600 treatment plans per hour while handling up to 50 GB of dose influence data (≈1400 candidate beams). For three head and neck patients, we compare the relative performance of a genetic, a cross-entropy, a simulated annealing and a naive iterative algorithm. The selection of ensembles with 5, 7, 9 and 11 beams considering either only coplanar or all feasible candidate beams is studied for an angular resolution of 5°, 10°, 15° and 20° in the space of candidate beams. The impact of different convergence criteria is investigated in comparison to a fixed termination after the evaluation of 10 000 beam ensembles. In total, our simulations comprise a full fluence optimization for about 3000 000 treatment plans. All four combinatorial BAS strategies yield significant improvements of the objective function value and of the corresponding dose distributions compared to standard beam configurations with equi

  18. Combinatorial strategies for combating invasive fungal infections.

    PubMed

    Spitzer, Michaela; Robbins, Nicole; Wright, Gerard D

    2017-02-17

    Invasive fungal infections are an important cause of human mortality and morbidity, particularly for immunocompromised populations. However, there remains a paucity of antifungal drug treatments available to combat these fungal pathogens. Further, antifungal compounds are plagued with problems such as host toxicity, fungistatic activity, and the emergence of drug resistance in pathogen populations. A promising therapeutic strategy to increase drug effectiveness and mitigate the emergence of drug resistance is through the use of combination drug therapy. In this review we describe the current arsenal of antifungals in medicine and elaborate on the benefits of combination therapy to expand our current antifungal drug repertoire. We examine those antifungal combinations that have shown potential against fungal pathogens and discuss strategies being employed to discover novel combination therapeutics, in particular combining antifungal agents with non-antifungal bioactive compounds. The findings summarized in this review highlight the promise of combinatorial strategies in combatting invasive mycoses.

  19. Combinatorial and computational challenges for biocatalyst design

    NASA Astrophysics Data System (ADS)

    Arnold, Frances H.

    2001-01-01

    Nature provides a fantastic array of catalysts extremely well suited to supporting life, but usually not so well suited for technology. Whether biocatalysis will have a significant technological impact depends on our finding robust routes for tailoring nature's catalysts or redesigning them anew. Laboratory evolution methods are now used widely to fine-tune the selectivity and activity of enzymes. The current rapid development of these combinatorial methods promises solutions to more complex problems, including the creation of new biosynthetic pathways. Computational methods are also developing quickly. The marriage of these approaches will allow us to generate the efficient, effective catalysts needed by the pharmaceutical, food and chemicals industries and should open up new opportunities for producing energy and chemicals from renewable resources.

  20. A scalable approach to combinatorial library design.

    PubMed

    Sharma, Puneet; Salapaka, Srinivasa; Beck, Carolyn

    2011-01-01

    In this chapter, we describe an algorithm for the design of lead-generation libraries required in combinatorial drug discovery. This algorithm addresses simultaneously the two key criteria of diversity and representativeness of compounds in the resulting library and is computationally efficient when applied to a large class of lead-generation design problems. At the same time, additional constraints on experimental resources are also incorporated in the framework presented in this chapter. A computationally efficient scalable algorithm is developed, where the ability of the deterministic annealing algorithm to identify clusters is exploited to truncate computations over the entire dataset to computations over individual clusters. An analysis of this algorithm quantifies the trade-off between the error due to truncation and computational effort. Results applied on test datasets corroborate the analysis and show improvement by factors as large as ten or more depending on the datasets.

  1. Combinatorial optimization methods for disassembly line balancing

    NASA Astrophysics Data System (ADS)

    McGovern, Seamus M.; Gupta, Surendra M.

    2004-12-01

    Disassembly takes place in remanufacturing, recycling, and disposal with a line being the best choice for automation. The disassembly line balancing problem seeks a sequence which: minimizes workstations, ensures similar idle times, and is feasible. Finding the optimal balance is computationally intensive due to factorial growth. Combinatorial optimization methods hold promise for providing solutions to the disassembly line balancing problem, which is proven to belong to the class of NP-complete problems. Ant colony optimization, genetic algorithm, and H-K metaheuristics are presented and compared along with a greedy/hill-climbing heuristic hybrid. A numerical study is performed to illustrate the implementation and compare performance. Conclusions drawn include the consistent generation of optimal or near-optimal solutions, the ability to preserve precedence, the speed of the techniques, and their practicality due to ease of implementation.

  2. Carbonate chemistry dynamics over a Caribbean shelf reef (Cayo Enrique) at the Atlantic Ocean Acidification Test-bed, La Parguera, Puerto Rico

    NASA Astrophysics Data System (ADS)

    Gledhill, D. K.; Corredor, J. E.; Langdon, C.; Manzello, D.; Sabine, C. L.; Hensley, V.; Brocco, B.; Musielewicz, S.; Lawrence-Slavas, N.; Capella, J. E.

    2010-12-01

    Changes in surface ocean chemistry in direct response to rising atmospheric carbon dioxide (CO2) concentration may pose challenges to a range of marine ecosystems in coming decades. Monitoring this ocean acidification (OA) at regional and local-scales is an important requirement towards improving our understanding of the potential long-term consequences. Coral reef ecosystems are of particular concern given the potential effects OA may have on net community calcification and ultimately reef accretion rates. While the dynamics and trends in oceanic carbonate chemistry are reasonably well constrained, how OA is manifested within the shallow coastal waters where coral reef ecosystems reside is less understood. Community-scale metabolic processes impart an important control on near-reef carbonate chemistry. Constraining the near-reef variability in carbonate chemistry across diel, seasonal, and annual scales is a critical requirement towards assigning potential biogeochemical thresholds of OA. The Atlantic OA Test-bed in the La Parguera Marine Reserve, Puerto Rico was established in 2009 to provide sustained high temporal resolution monitoring of carbonate chemistry within an Atlantic tropical coral reef ecosystem. Presented here are the results of over a year’s worth of sustained monitoring at the Cayo Enrique forereef characterizing the temporal dynamics in carbonate chemistry. The Cayo Enrique reef is a source of CO2 to the atmosphere (1.7 mmol CO2 m-2 d-1, SE = 0.1) with both calcification and respiration serving to consistently elevate pCO2,sw relative to oceanic waters. Once pCO2,sw increase by a further 100 µatm in response to rising atmospheric CO2, these waters will likely reach undersaturation with respect to 13 mol % MgCO3 phases during winter months. While high-Mg calcites are prominent mineral phases of shallow tropical carbonate marine sediments, their relative importance as cementing agents of modern coral reef frameworks demands further investigation

  3. Dynamical amplification of the stratospheric solar response simulated with the Chemistry-Climate Model LMDz-Reprobus

    NASA Astrophysics Data System (ADS)

    Marchand, M.; Keckhut, P.; Lefebvre, S.; Claud, C.; Cugnet, D.; Hauchecorne, A.; Lefèvre, F.; Lefebvre, M.-P.; Jumelet, J.; Lott, F.; Hourdin, F.; Thuillier, G.; Poulain, V.; Bossay, S.; Lemennais, P.; David, C.; Bekki, S.

    2012-02-01

    The impact of the 11-year solar cycle on the stratosphere and, in particular, on the polar regions is investigated using simulations from the Chemistry Climate Model (CCM) LMDz-Reprobus. The annual solar signal clearly shows a stratospheric response largely driven by radiative and photochemical processes, especially in the upper stratosphere. A month-by-months analysis suggests that dynamical feedbacks play an important role in driving the stratospheric response on short timescales. CCM outputs on a 10 days frequency indicate how, in the northern hemisphere, changes in solar heating in the winter polar stratosphere may influence the upward propagation of planetary waves and thus their deposition of momentum, ultimately modifying the strength of the mean stratospheric overtuning circulation at middle and high latitudes. The model results emphasize that the main temperature and wind responses in the northern hemisphere can be explained by a different timing in the occurrence of Sudden Stratospheric Warmings (SSWs) that are caused by small changes in planetary wave propagation depending on solar conditions. The differences between simulations forced by different solar conditions indicate successive positive and negative responses during the course of the winter. The solar minimum simulation generally indicates a slightly stronger polar vortex early in the winter while the solar maximum simulation experiences more early SSWs with a stronger wave-mean flow interaction and reduced zonal wind at mid-latitudes in the upper stratosphere. The opposite response is observed during mid-winter, in February, with more SSWs simulated for solar minimum conditions while solar maximum conditions are associated with a damped planetary wave activity and a reinforced vortex after the initial stratospheric warming period. In late winter, the response is again reversed, as noticed in the temperature differences, with major SSW mostly observed in the solar maximum simulation and less

  4. Summer carbonate chemistry dynamics in the Southern Yellow Sea and the East China Sea: Regional variations and controls

    NASA Astrophysics Data System (ADS)

    Qu, Baoxiao; Song, Jinming; Yuan, Huamao; Li, Xuegang; Li, Ning; Duan, Liqin; Chen, Xin; Lu, Xi

    2015-12-01

    Surface partial pressure of CO2 (pCO2) and pertinent parameters (i.e., pH, total alkalinity, dissolved oxygen, chlorophyll a) were investigated in the southern Yellow Sea (SYS) and the East China Sea (ECS) basing on two surveys conducted in June and August of 2013. The results suggested carbonate chemistry dynamics and related controlling factors were provided with significant temporal and spatial variations in different subregions of these two continental shelf seas. The western of SYS (SYSW) was CO2-undersaturated both in June and August, with the average FCO2 -1.88 mmol m-2 d-1 and -3.72 mmol m-2 d-1, respectively. The phytoplankton initiated CO2-absorption and the suspended sediment induced CO2-emission jointly controlled the air-sea CO2 exchange there. The center of SYS (SYSC) also behaved as an obvious CO2 sink (-1.57 mmol m-2 d-1and -3.99 mmol m-2 d-1 in June and August, respectively), probably due to elevated TA/DIC ratio and the subsequent effects of spring bloom. As for the Yangtze River estuary (YRE), it changed from an obvious CO2 sink (-1.28 mmol m-2 d-1) in June into a very weak CO2 source (0.04 mmol m-2 d-1) in August. This change was probably associated with the rising of seawater temperature and monthly variation of Yangtze River discharge. The inner shelf of ECS (ECSS) experienced obvious air-sea CO2 flux changes during from June (-8.88 mmol m-2 d-1) to August (-0.36 mmol m-2 d-1) as well. Biological DIC consumption in the upper layer and DIC regenerated from respiration in the subsurface jointly controlled this pCO2 variation. As a whole, the SYS and ECS acted as an obvious CO2 sink during summer and could absorb atmospheric CO2 with the average air-sea flux (FCO2) -2.68 mmol m-2 d-1. The summary of air-sea CO2 flux in the ECS and SYS during recent two decades indicated the ECS served as quite a stable CO2 sink, whereas the SYS experienced obvious change. Discharge of Yangtze River and anthropogenic nutrients loading could profoundly affect the

  5. Available pathways database (APD): an essential resource for combinatorial biology.

    PubMed

    Pirrung, M C; Silva, C M; Jaeger, J

    2000-10-01

    A relational database, the Available Pathways Database (APD), has been constructed of microbial natural products, their producing strains, and their biosynthetic pathways. The database allows the ready selection of donor strains for combinatorial biology experiments. It provides the same type of resource for combinatorial biology as the Available Chemicals Directory (ACD) does for combinatorial chemical library generation. Its cataloging ability can also provide insight into novel aspects of biosynthetic routes. In particular, no 10-unit Type I polyketides were found in the compilation of this edition of the APD (Version I).

  6. Hybrid Self-Adaptive Evolution Strategies Guided by Neighborhood Structures for Combinatorial Optimization Problems.

    PubMed

    Coelho, V N; Coelho, I M; Souza, M J F; Oliveira, T A; Cota, L P; Haddad, M N; Mladenovic, N; Silva, R C P; Guimarães, F G

    2016-01-01

    This article presents an Evolution Strategy (ES)--based algorithm, designed to self-adapt its mutation operators, guiding the search into the solution space using a Self-Adaptive Reduced Variable Neighborhood Search procedure. In view of the specific local search operators for each individual, the proposed population-based approach also fits into the context of the Memetic Algorithms. The proposed variant uses the Greedy Randomized Adaptive Search Procedure with different greedy parameters for generating its initial population, providing an interesting exploration-exploitation balance. To validate the proposal, this framework is applied to solve three different [Formula: see text]-Hard combinatorial optimization problems: an Open-Pit-Mining Operational Planning Problem with dynamic allocation of trucks, an Unrelated Parallel Machine Scheduling Problem with Setup Times, and the calibration of a hybrid fuzzy model for Short-Term Load Forecasting. Computational results point out the convergence of the proposed model and highlight its ability in combining the application of move operations from distinct neighborhood structures along the optimization. The results gathered and reported in this article represent a collective evidence of the performance of the method in challenging combinatorial optimization problems from different application domains. The proposed evolution strategy demonstrates an ability of adapting the strength of the mutation disturbance during the generations of its evolution process. The effectiveness of the proposal motivates the application of this novel evolutionary framework for solving other combinatorial optimization problems.

  7. A Combinatorial Kin Discrimination System in Bacillus subtilis

    PubMed Central

    Lyons, Nicholas A.; Kraigher, Barbara; Stefanic, Polonca; Mandic-Mulec, Ines; Kolter, Roberto

    2016-01-01

    SUMMARY Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism. Our results identified many molecules involved in cell surface modification and antimicrobial production and response. These genes varied significantly in expression level and mutation phenotype among B. subtilis strains, suggesting interstrain variation in the exact kin discrimination mechanism used. Genome analyses revealed a substantial diversity of antimicrobial genes present in unique combinations in different strains, with many likely acquired by horizontal gene transfer. The dynamic combinatorial effect derived from this plethora of kin discrimination genes creates a tight relatedness cutoff for cooperation that has likely led to rapid diversification within the species. Our data suggest that genes likely originally selected for competitive purposes also generate preferential interactions among kin, thus stabilizing multicellular lifestyles. PMID:26923784

  8. A Combinatorial Kin Discrimination System in Bacillus subtilis.

    PubMed

    Lyons, Nicholas A; Kraigher, Barbara; Stefanic, Polonca; Mandic-Mulec, Ines; Kolter, Roberto

    2016-03-21

    Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism. Our results identified many molecules involved in cell-surface modification and antimicrobial production and response. These genes varied significantly in expression level and mutation phenotype among B. subtilis strains, suggesting interstrain variation in the exact kin discrimination mechanism used. Genome analyses revealed a substantial diversity of antimicrobial genes present in unique combinations in different strains, with many likely acquired by horizontal gene transfer. The dynamic combinatorial effect derived from this plethora of kin discrimination genes creates a tight relatedness cutoff for cooperation that has likely led to rapid diversification within the species. Our data suggest that genes likely originally selected for competitive purposes also generate preferential interactions among kin, thus stabilizing multicellular lifestyles.

  9. Combinatorial semantics strengthens angular-anterior temporal coupling.

    PubMed

    Molinaro, Nicola; Paz-Alonso, Pedro M; Duñabeitia, Jon Andoni; Carreiras, Manuel

    2015-04-01

    The human semantic combinatorial system allows us to create a wide number of new meanings from a finite number of existing representations. The present study investigates the neural dynamics underlying the semantic processing of different conceptual constructions based on predictions from previous neuroanatomical models of the semantic processing network. In two experiments, participants read sentences for comprehension containing noun-adjective pairs in three different conditions: prototypical (Redundant), nonsense (Anomalous) and low-typical but composable (Contrastive). In Experiment 1 we examined the processing costs associated to reading these sentences and found a processing dissociation between Anomalous and Contrastive word pairs, compared to prototypical (Redundant) stimuli. In Experiment 2, functional connectivity results showed strong co-activation across conditions between inferior frontal gyrus (IFG) and posterior middle temporal gyrus (MTG), as well as between these two regions and middle frontal gyrus (MFG), anterior temporal cortex (ATC) and fusiform gyrus (FG), consistent with previous neuroanatomical models. Importantly, processing of low-typical (but composable) meanings relative to prototypical and anomalous constructions was associated with a stronger positive coupling between ATC and angular gyrus (AG). Our results underscore the critical role of IFG-MTG co-activation during semantic processing and how other relevant nodes within the semantic processing network come into play to handle visual-orthographic information, to maintain multiple lexical-semantic representations in working memory and to combine existing representations while creatively constructing meaning.

  10. Combinatorial cell-3D biomaterials cytocompatibility screening for tissue engineering using bioinspired superhydrophobic substrates.

    PubMed

    Salgado, Christiane L; Oliveira, Mariana B; Mano, João F

    2012-03-01

    We report on the development of a new array-based screening flat platform with the potential to be used as a high-throughput device based on biomimetic polymeric substrates for combinatorial cell/3D biomaterials screening assays in the context of tissue engineering. Polystyrene was used to produce superhydrophobic surfaces based on the so-called lotus effect. Arrays of hydrophilic regions could be patterned in such surfaces using UV/ozone radiation, generating devices onto which combinatorial hydrogel spots were deposited. The biological performance of encapsulated cells in hydrogels could be tested in an in vitro 3D environment assuming that each site was isolated from the others due to the high contrast of wettability between the patterned spots and the superhydrophobic surroundings. Three different polymers-chitosan, collagen and hyaluronic acid-were combined with alginate in different proportions in order to obtain combinatorial binary alginate-based polymeric arrays. The effect of the addition of gelatin to the binary structures was also tested. The gels were chemically analyzed by FTIR microscopic mapping. Cell culture results varied according to the hydrogel composition and encapsulated cell types (L929 fibroblast cells and MC3T3-E1 pre-osteoblast cells). Cell viability and number could be assessed by conventional methods, such as MTS reduction test and dsDNA quantification. Non-destructive image analysis was performed using cytoskeleton and nuclei staining agents and the results were consistent with the ones obtained by conventional sample-destructive techniques. Briefly, L929 cells showed higher number and viability for higher alginate-content and collagen-containing hydrogels, while MC3T3-E1 showed higher cell viability and cell number in lower alginate-content and chitosan containing hydrogels. The addition of gelatin did not influence significantly cell metabolic activity or cell number in any of the encapsulated cell types. This journal is © The Royal

  11. DNA-mediated gold nanoparticle signal transducers for combinatorial logic operations and heavy metal ions sensing.

    PubMed

    Zhang, Yuhuan; Liu, Wei; Zhang, Wentao; Yu, Shaoxuan; Yue, Xiaoyue; Zhu, Wenxin; Zhang, Daohong; Wang, Yanru; Wang, Jianlong

    2015-10-15

    Herein, the structure of two DNA strands which are complementary except fourteen T-T and C-C mismatches was programmed for the design of the combinatorial logic operation by utilizing the different protective capacities of single chain DNA, part-hybridized DNA and completed-hybridized DNA on unmodified gold nanoparticles. In the presence of either Hg(2+) or Ag(+), the T-Hg(2+)-T or C-Ag(+)-C coordination chemistry could lead to the formation of part-hybridized DNA which keeps gold nanoparticles from clumping after the addition of 40 μL 0.2M NaClO4 solution, but the protection would be screened by 120 μL 0.2M NaClO4 solution. While the coexistence of Hg(2+), Ag(+) caused the formation of completed-hybridized DNA and the protection for gold nanoparticles lost in either 40 μL or 120 μL NaClO4 solutions. Benefiting from sharing of the same inputs of Hg(2+) and Ag(+), OR and AND logic gates were easily integrated into a simple colorimetric combinatorial logic operation in one system, which make it possible to execute logic gates in parallel to mimic arithmetic calculations on a binary digit. Furthermore, two other logic gates including INHIBIT1 and INHIBIT2 were realized to integrated with OR logic gate both for simultaneous qualitative discrimination and quantitative determination of Hg(2+) and Ag(+). Results indicate that the developed logic system based on the different protective capacities of DNA structure on gold nanoparticles provides a new pathway for the design of the combinatorial logic operation in one system and presents a useful strategy for development of advanced sensors, which may have potential applications in multiplex chemical analysis and molecular-scale computer design. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Combinatorial and high-throughput screening approaches for strain engineering.

    PubMed

    Liu, Wenshan; Jiang, Rongrong

    2015-03-01

    Microbes have long been used in the industry to produce valuable biochemicals. Combinatorial engineering approaches, new strain engineering tools derived from inverse metabolic engineering, have started to attract attention in recent years, including genome shuffling, error-prone DNA polymerase, global transcription machinery engineering (gTME), random knockout/overexpression libraries, ribosome engineering, multiplex automated genome engineering (MAGE), customized optimization of metabolic pathways by combinatorial transcriptional engineering (COMPACTER), and library construction of "tunable intergenic regions" (TIGR). Since combinatorial approaches and high-throughput screening methods are fundamentally interconnected, color/fluorescence-based, growth-based, and biosensor-based high-throughput screening methods have been reviewed. We believe that with the help of metabolic engineering tools and new combinatorial approaches, plus effective high-throughput screening methods, researchers will be able to achieve better results on improving microorganism performance under stress or enhancing biochemical yield.

  13. Combinatorial Dyson-Schwinger equations and inductive data types

    NASA Astrophysics Data System (ADS)

    Kock, Joachim

    2016-06-01

    The goal of this contribution is to explain the analogy between combinatorial Dyson-Schwinger equations and inductive data types to a readership of mathematical physicists. The connection relies on an interpretation of combinatorial Dyson-Schwinger equations as fixpoint equations for polynomial functors (established elsewhere by the author, and summarised here), combined with the now-classical fact that polynomial functors provide semantics for inductive types. The paper is expository, and comprises also a brief introduction to type theory.

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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…

  16. Signal dimensionality and the emergence of combinatorial structure.

    PubMed

    Little, Hannah; Eryılmaz, Kerem; de Boer, Bart

    2017-11-01

    In language, a small number of meaningless building blocks can be combined into an unlimited set of meaningful utterances. This is known as combinatorial structure. One hypothesis for the initial emergence of combinatorial structure in language is that recombining elements of signals solves the problem of overcrowding in a signal space. Another hypothesis is that iconicity may impede the emergence of combinatorial structure. However, how these two hypotheses relate to each other is not often discussed. In this paper, we explore how signal space dimensionality relates to both overcrowding in the signal space and iconicity. We use an artificial signalling experiment to test whether a signal space and a meaning space having similar topologies will generate an iconic system and whether, when the topologies differ, the emergence of combinatorially structured signals is facilitated. In our experiments, signals are created from participants' hand movements, which are measured using an infrared sensor. We found that participants take advantage of iconic signal-meaning mappings where possible. Further, we use trajectory predictability, measures of variance, and Hidden Markov Models to measure the use of structure within the signals produced and found that when topologies do not match, then there is more evidence of combinatorial structure. The results from these experiments are interpreted in the context of the differences between the emergence of combinatorial structure in different linguistic modalities (speech and sign). Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Combinatorial effects of odorants on mouse behavior

    PubMed Central

    Saraiva, Luis R.; Kondoh, Kunio; Ye, Xiaolan; Yoon, Kyoung-hye; Hernandez, Marcus; Buck, Linda B.

    2016-01-01

    The mechanisms by which odors induce instinctive behaviors are largely unknown. Odor detection in the mouse nose is mediated by >1, 000 different odorant receptors (ORs) and trace amine-associated receptors (TAARs). Odor perceptions are encoded combinatorially by ORs and can be altered by slight changes in the combination of activated receptors. However, the stereotyped nature of instinctive odor responses suggests the involvement of specific receptors and genetically programmed neural circuits relatively immune to extraneous odor stimuli and receptor inputs. Here, we report that, contrary to expectation, innate odor-induced behaviors can be context-dependent. First, different ligands for a given TAAR can vary in behavioral effect. Second, when combined, some attractive and aversive odorants neutralize one another’s behavioral effects. Both a TAAR ligand and a common odorant block aversion to a predator odor, indicating that this ability is not unique to TAARs and can extend to an aversive response of potential importance to survival. In vitro testing of single receptors with binary odorant mixtures indicates that behavioral blocking can occur without receptor antagonism in the nose. Moreover, genetic ablation of a single receptor prevents its cognate ligand from blocking predator odor aversion, indicating that the blocking requires sensory input from the receptor. Together, these findings indicate that innate odor-induced behaviors can depend on context, that signals from a single receptor can block innate odor aversion, and that instinctive behavioral responses to odors can be modulated by interactions in the brain among signals derived from different receptors. PMID:27208093

  18. Linear combinatorial approach to thin film research

    SciTech Connect

    Matias, Vladimir; Gibbons, Brady J.

    2007-07-15

    We describe high-throughput experimentation of film synthesis by use of a linear tape transport system (similar to a web-coating system). Metal tape is fed continuously in a reel-to-reel transport system inside the vacuum deposition chamber. Ion-beam assisted deposition (IBAD) texturing is used to enable the growth of epitaxial films on flexible, polycrystalline metal tapes which further enhances the capability of this research. The tape that is continuously fed can be used as a sample itself, via the use of IBAD-textured templates on the tape, or can be a carrier of other smaller substrates (even nonflexible ones). Characterization of samples is done by means of in situ monitoring as well as ex situ sequential analysis. We utilize in situ reflection high-energy electron diffraction for high-throughput analysis of samples. Epitaxial films are deposited on heated samples by evaporation and by pulsed laser deposition. Here, we explain the techniques and the methodologies developed for this type of combinatorial experimentation and show some examples of the material research completed.

  19. Scalable Combinatorial Tools for Health Disparities Research

    PubMed Central

    Langston, Michael A.; Levine, Robert S.; Kilbourne, Barbara J.; Rogers, Gary L.; Kershenbaum, Anne D.; Baktash, Suzanne H.; Coughlin, Steven S.; Saxton, Arnold M.; Agboto, Vincent K.; Hood, Darryl B.; Litchveld, Maureen Y.; Oyana, Tonny J.; Matthews-Juarez, Patricia; Juarez, Paul D.

    2014-01-01

    Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size and heterogeneity of available data needed to illuminate latent gene x environment interactions. This has prompted the adaptation and application of scalable combinatorial methods, many from genome science research, to the study of population health. Most of these powerful tools are algorithmically sophisticated, highly automated and mathematically abstract. Their utility motivates the main theme of this paper, which is to describe real applications of innovative transdisciplinary models and analyses in an effort to help move the research community closer toward identifying the causal mechanisms and associated environmental contexts underlying health disparities. The public health exposome is used as a contemporary focus for addressing the complex nature of this subject. PMID:25310540

  20. Scalable combinatorial tools for health disparities research.

    PubMed

    Langston, Michael A; Levine, Robert S; Kilbourne, Barbara J; Rogers, Gary L; Kershenbaum, Anne D; Baktash, Suzanne H; Coughlin, Steven S; Saxton, Arnold M; Agboto, Vincent K; Hood, Darryl B; Litchveld, Maureen Y; Oyana, Tonny J; Matthews-Juarez, Patricia; Juarez, Paul D

    2014-10-10

    Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual's genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size and heterogeneity of available data needed to illuminate latent gene x environment interactions. This has prompted the adaptation and application of scalable combinatorial methods, many from genome science research, to the study of population health. Most of these powerful tools are algorithmically sophisticated, highly automated and mathematically abstract. Their utility motivates the main theme of this paper, which is to describe real applications of innovative transdisciplinary models and analyses in an effort to help move the research community closer toward identifying the causal mechanisms and associated environmental contexts underlying health disparities. The public health exposome is used as a contemporary focus for addressing the complex nature of this subject.

  1. Fast combinatorial RNS processors for DSP applications

    SciTech Connect

    Di Claudio, E.D.; Piazza, F.; Orlandi, G.

    1995-05-01

    It is known that RNS VLSI processors can parallelize fixed-point addition and multiplication operations by the use of the Chinese Remainder Theorem (CRT). The required modular operations, however, must use specialized hardware whose design and implementation can create several problems. In this paper a modified residue arithmetic, called pseudo-RNS is introduced in order to alleviate some of the RNS problems when Digital Signal Processing (DSP) structures are implemented. Pseudo-RNS requires only the use of modified binary processors and exhibits a speed performance comparable with other RNS traditional approaches. Some applications of the pseudo-RNS to common DSP architectures, such as multipliers and filters, are also presented in this paper. They are compared in terms of the Area-Time Square product versus other RNS and weighted binary structures. It is proven that existing combinatorial or look-up table approaches for RNS are tailored to small designs or special applications, while the pseudo-RNS approach remains competitive also for complex systems. 32 refs.

  2. Combinatorial approaches for inverse metabolic engineering applications

    PubMed Central

    Skretas, Georgios; Kolisis, Fragiskos N.

    2013-01-01

    Traditional metabolic engineering analyzes biosynthetic and physiological pathways, identifies bottlenecks, and makes targeted genetic modifications with the ultimate goal of increasing the production of high-value products in living cells. Such efforts have led to the development of a variety of organisms with industrially relevant properties. However, there are a number of cellular phenotypes important for research and the industry for which the rational selection of cellular targets for modification is not easy or possible. In these cases, strain engineering can be alternatively carried out using “inverse metabolic engineering”, an approach that first generates genetic diversity by subjecting a population of cells to a particular mutagenic process, and then utilizes genetic screens or selections to identify the clones exhibiting the desired phenotype. Given the availability of an appropriate screen for a particular property, the success of inverse metabolic engineering efforts usually depends on the level and quality of genetic diversity which can be generated. Here, we review classic and recently developed combinatorial approaches for creating such genetic diversity and discuss the use of these methodologies in inverse metabolic engineering applications. PMID:24688681

  3. Combinatorial molecular optimization of cement hydrates

    PubMed Central

    Abdolhosseini Qomi, M.J.; Krakowiak, K.J.; Bauchy, M.; Stewart, K.L.; Shahsavari, R.; Jagannathan, D.; Brommer, D.B.; Baronnet, A.; Buehler, M.J.; Yip, S.; Ulm, F.-J; Van Vliet, K.J.; Pellenq, R.J-.M.

    2014-01-01

    Despite its ubiquitous presence in the built environment, concrete’s molecular-level properties are only recently being explored using experimental and simulation studies. Increasing societal concerns about concrete’s environmental footprint have provided strong motivation to develop new concrete with greater specific stiffness or strength (for structures with less material). Herein, a combinatorial approach is described to optimize properties of cement hydrates. The method entails screening a computationally generated database of atomic structures of calcium-silicate-hydrate, the binding phase of concrete, against a set of three defect attributes: calcium-to-silicon ratio as compositional index and two correlation distances describing medium-range silicon-oxygen and calcium-oxygen environments. Although structural and mechanical properties correlate well with calcium-to-silicon ratio, the cross-correlation between all three defect attributes reveals an indentation modulus-to-hardness ratio extremum, analogous to identifying optimum network connectivity in glass rheology. We also comment on implications of the present findings for a novel route to optimize the nanoscale mechanical properties of cement hydrate. PMID:25248305

  4. Improved Crystallographic Structures using Extensive Combinatorial Refinement

    PubMed Central

    Nwachukwu, Jerome C.; Southern, Mark R.; Kiefer, James R.; Afonine, Pavel V.; Adams, Paul D.; Terwilliger, Thomas C.; Nettles, Kendall W.

    2013-01-01

    Summary Identifying errors and alternate conformers, and modeling multiple main-chain conformers in poorly ordered regions are overarching problems in crystallographic structure determination that have limited automation efforts and structure quality. Here, we show that implementation of a full factorial designed set of standard refinement approaches, which we call ExCoR (Extensive Combinatorial Refinement), significantly improves structural models compared to the traditional linear tree approach, in which individual algorithms are tested linearly, and only incorporated if the model improves. ExCoR markedly improved maps and models, and reveals building errors and alternate conformations that were masked by traditional refinement approaches. Surprisingly, an individual algorithm that renders a model worse in isolation could still be necessary to produce the best overall model, suggesting that model distortion allows escape from local minima of optimization target function, here shown to be a hallmark limitation of the traditional approach. ExCoR thus provides a simple approach to improving structure determination. PMID:24076406

  5. Discovery of novel anti-HIV agents via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry-based approach.

    PubMed

    Gao, Ping; Sun, Lin; Zhou, Junsu; Li, Xiao; Zhan, Peng; Liu, Xinyong

    2016-09-01

    In recent years, a variety of new synthetic methodologies and concepts have been proposed in the search for new pharmaceutical lead structures and optimization. Notably, the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry approach has drawn great attention and has become a powerful tool for the generation of privileged medicinal skeletons in the discovery of anti-HIV agents. This is due to the high degree of reliability, complete specificity (chemoselectivity and regioselectivity), mild conditions, and the biocompatibility of the reactants. Herein, the authors describe the progress thus far on the discovery of novel anti-HIV agents via the CuAAC click chemistry-based approach. CuAAC click chemistry is a proven protocol for synthesizing triazole products which could serve as basic pharmacophores, act as replacements of traditional scaffold or substituent modification, be a linker of dual-target or dual-site inhibitors and more for the discovery of novel anti-HIV agents. What's more, it also provides convenience and feasibility for dynamic combinatorial chemistry and in situ screening. It is envisioned that click chemistry will draw more attention and make more contributions in anti-HIV drug discovery in the future.

  6. Design of combinatorial libraries for the exploration of virtual hits from fragment space searches with LoFT.

    PubMed

    Lessel, Uta; Wellenzohn, Bernd; Fischer, J Robert; Rarey, Matthias

    2012-02-27

    A case study is presented illustrating the design of a focused CDK2 library. The scaffold of the library was detected by a feature trees search in a fragment space based on reactions from combinatorial chemistry. For the design the software LoFT (Library optimizer using Feature Trees) was used. The special feature called FTMatch was applied to restrict the parts of the queries where the reagents are permitted to match. This way a 3D scoring function could be simulated. Results were compared with alternative designs by GOLD docking and ROCS 3D alignments.

  7. Room-temperature combinatorial screening of cyclometallated iridium(III) complexes for a step towards molecular control of colour purity.

    PubMed

    Baranoff, Etienne; Jung, Il; Scopelliti, Rosario; Solari, Euro; Grätzel, Michael; Nazeeruddin, Md Khaja

    2011-07-14

    A library of emission spectra of 90 bis-cyclometallated iridium complexes has been obtained using a simple combinatorial approach performed at room temperature. Trends in emission maxima are rationalized using Hammett parameters and invoking inter ligand energy transfer (ILET) processes. The screening approach allowed us to observe trends in the broadness of emission spectra opening the way for a rational approach to the engineering of the emission colour purity at a molecular level. Finally limitations to the screening strategy are discussed using a case study that involves two different monodentate ligands. This journal is © The Royal Society of Chemistry 2011

  8. Strategies and applications of combinatorial methods and high throughput screening to the discovery of non-noble metal catalyst

    NASA Astrophysics Data System (ADS)

    Bricker, Maureen L.; Sachtler, J. W. Adriaan; Gillespie, Ralph D.; McGonegal, Charles P.; Vega, Honorio; Bem, Dave S.; Holmgren, Jennifer S.

    2004-02-01

    The integrated End-to-End™ combinatorial process for catalyst preparation and screening, with emphasis on its capability to vary both process and compositional parameters will be demonstrated. Additionally, each step of the combinatorial screening process has been validated against results from traditional screening methods. The greatest challenge of all has been the adherence to the core concepts of the combinatorial approach. Catalyst libraries have been made and tested for naphthalene dehydrogenation chemistry. The preparation of these libraries has included the application of high throughput techniques for: metal impregnation; catalyst finishing; catalyst screening. The catalyst screening system has been used to find a non-noble metal catalyst system that can replace Pt in dehydrogenation applications in the petroleum industry. A proprietary catalytic composition was developed for the dehydrogenation of methylcyclohexane (MCH) to toluene starting with four non-noble metals of different proportions and four different supports (alumina, titania, zirconia and silica) prepared in different ways and applying a statistical design of experiments. These data demonstrate that all steps of catalyst preparation and screening are performed in a rapid, useful, high throughput manner. Data will be presented from the catalyst screening efforts will demonstrate that optimized metal composition is dependent on the support type.

  9. Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents: a chemometric and molecular modeling assessment.

    PubMed

    Minovski, Nikola; Perdih, Andrej; Solmajer, Tom

    2012-05-01

    The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of three well known 6-FQ inhibitors. The druggability properties of the generated combinatorial 6-FQs were assessed using an in-house developed drug-likeness filter integrating the Lipinski/Veber rule-sets. The compounds recognized as drug-like were used as an external set for prediction of the biological activity values using a neural-networks (NN) model based on an experimentally-determined set of active 6-FQs. Furthermore, a subset of compounds was extracted from the pool of drug-like 6-FQs, with predicted biological activity, and subsequently used in virtual screening (VS) campaign combining pharmacophore modeling and molecular docking studies. This complex scheme, a powerful combination of chemometric and molecular modeling approaches provided novel QSAR guidelines that could aid in the further lead development of 6-FQs agents.

  10. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology.

    PubMed

    Weissman, Kira J

    2016-02-01

    Multienzyme polyketide synthases (PKSs) are molecular-scale assembly lines which construct complex natural products in bacteria. The underlying modular architecture of these gigantic catalysts inspired, from the moment of their discovery, attempts to modify them by genetic engineering to produce analogues of predictable structure. These efforts have resulted in hundreds of metabolites new to nature, as detailed in this review. However, in the face of many failures, the heady days of imagining the possibilities for a truly 'combinatorial biosynthesis' of polyketides have faded. It is now more appropriate to talk about 'PKS synthetic biology' with its more modest goals of delivering specific derivatives of known structure in combination with and as a complement to synthetic chemistry approaches. The reasons for these failures will be discussed in terms of our growing understanding of the three-dimensional architectures and mechanisms of these systems. Finally, some thoughts on the future of the field will be presented.

  11. A General Method for Insertion of Functional Proteins within Proteins via Combinatorial Selection of Permissive Junctions.

    PubMed

    Peng, Yingjie; Zeng, Wenwen; Ye, Hui; Han, Kyung Ho; Dharmarajan, Venkatasubramanian; Novick, Scott; Wilson, Ian A; Griffin, Patrick R; Friedman, Jeffrey M; Lerner, Richard A

    2015-08-20

    A major goal of modern protein chemistry is to create new proteins with different functions. One approach is to amalgamate secondary and tertiary structures from different proteins. This is difficult for several reasons, not the least of which is the fact that the junctions between secondary and tertiary structures are not degenerate and usually affect the function and folding of the entire complex. Here, we offer a solution to this problem by coupling a large combinatorial library of about 10(7) different N- and C-terminal junctions to a powerful system that selects for function. Using this approach, the entire Leptin and follicle-stimulating hormone (FSH) were inserted into an antibody. Complexes with full retention of function in vivo and in vitro, although rare, were found easily by using an autocrine selection system to search for hormonal activity. Such large diversity systems, when coupled to robust selection systems, should enable construction of novel therapeutic proteins.

  12. Chemistry Dashboard

    EPA Pesticide Factsheets

    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.

  13. Chemistry Notes

    ERIC Educational Resources Information Center

    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)

  14. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and chemistry experiments. Topics include sublimation, electronegativity, electrolysis, experimental aspects of strontianite, halide test, evaluation of present and future computer programs in chemistry, formula building, care of glass/saturated calomel…

  15. Chemistry Notes

    ERIC Educational Resources Information Center

    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)

  16. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and chemistry experiments. Topics include sublimation, electronegativity, electrolysis, experimental aspects of strontianite, halide test, evaluation of present and future computer programs in chemistry, formula building, care of glass/saturated calomel…

  17. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1978

    1978-01-01

    Describes experiments, demonstrations, activities and ideas relating to various fields of chemistry to be used in chemistry courses of secondary schools. Three experiments concerning differential thermal analysis are among these notes presented. (HM)

  18. Dynamics of seawater carbonate chemistry, production, and calcification of a coral reef flat, central Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Albright, R.; Langdon, C.; Anthony, K. R. N.

    2013-10-01

    Ocean acidification is projected to shift coral reefs from a state of net accretion to one of net dissolution this century. Presently, our ability to predict global-scale changes to coral reef calcification is limited by insufficient data relating seawater carbonate chemistry parameters to in situ rates of reef calcification. Here, we investigate diel and seasonal trends in carbonate chemistry of the Davies Reef flat in the central Great Barrier Reef and relate these trends to benthic carbon fluxes by quantifying net ecosystem calcification (nec) and net community production (ncp). Results show that seawater carbonate chemistry of the Davies Reef flat is highly variable over both diel and seasonal cycles. pH (total scale) ranged from 7.92 to 8.17, pCO2 ranged from 272 to 542 μatm, and aragonite saturation state (Ωarag) ranged from 2.9 to 4.1. Diel cycles in carbonate chemistry were primarily driven by ncp, and warming explained 35% and 47% of the seasonal shifts in pCO2 and pH, respectively. Daytime ncp averaged 37 ± 19 mmol C m-2 h-1 in summer and 33 ± 13 mmol C m-2 h-1 in winter; nighttime ncp averaged -30 ± 25 and -7 ± 6 mmol C m-2 h-1 in summer and winter, respectively. Daytime nec averaged 11 ± 4 mmol CaCO3 m-2 h-1 in summer and 8 ± 3 mmol CaCO3 m-2 h-1 in winter, whereas nighttime nec averaged 2 ± 4 mmol and -1 ± 3 mmol CaCO3 m-2 h-1 in summer and winter, respectively. Net ecosystem calcification was highly sensitive to changes in Ωarag for both seasons, indicating that relatively small shifts in Ωarag may drive measurable shifts in calcification rates, and hence carbon budgets, of coral reefs throughout the year.

  19. The Interaction Between Dynamics and Chemistry of Ozone in the Set-Up Phase of the Northern Hemisphere Polar Vortex

    NASA Technical Reports Server (NTRS)

    Kawa, S.R.; Douglass, A. R.; Bevilacqua, R.; Margitan, J. J.; Sen, B.; Einaudi, Franco (Technical Monitor)

    2000-01-01

    Understanding stratospheric ozone loss to the point of accurately predicting ozone in the future requires correctly distinguishing chemical from transport-induced changes in ozone. For example, evaluating the impact of chlorine reduction in controlling stratospheric ozone loss requires estimating the amount of ozone lost in chemical reactions in the polar winter and spring. The Northern Hemisphere winter polar region is a particularly crucial and interesting area because it appears that the Northern vortex may currently be poised near the threshold of extreme ozone destruction such as that which now occurs annually in the Antarctic ozone "hole." In this presentation we explore the interaction of ozone transport and chemistry through the Northern late summer and fall seasons as the vortex circulation becomes established. This phase of the seasonal cycle determines the starting point for heterogeneous processes and chlorine-driven loss that take control in the winter vortex. Using a combination of profile data from POAM, HALOE, and in situ measurements, we show that relatively low ozone at high latitudes in the middle stratosphere is associated with vortex airmasses and that these ozone abundances evolve photochemically from characteristically higher values at the end of the summer. The zonal variance of ozone mixing ratio also increases greatly at this time consistent with increasing wave-driven transport. Comparison with a three-dimensional chemistry-transport model is used to generalize the findings from the limited set of observations and quantify the relative roles of transport and chemistry in determining the ozone mixing ratio distributions.

  20. Neural blackboard architectures of combinatorial structures in cognition.

    PubMed

    van der Velde, Frank; de Kamps, Marc

    2006-02-01

    Human cognition is unique in the way in which it relies on combinatorial (or compositional) structures. Language provides ample evidence for the existence of combinatorial structures, but they can also be found in visual cognition. To understand the neural basis of human cognition, it is therefore essential to understand how combinatorial structures can be instantiated in neural terms. In his recent book on the foundations of language, Jackendoff described four fundamental problems for a neural instantiation of combinatorial structures: the massiveness of the binding problem, the problem of 2, the problem of variables, and the transformation of combinatorial structures from working memory to long-term memory. This paper aims to show that these problems can be solved by means of neural "blackboard" architectures. For this purpose, a neural blackboard architecture for sentence structure is presented. In this architecture, neural structures that encode for words are temporarily bound in a manner that preserves the structure of the sentence. It is shown that the architecture solves the four problems presented by Jackendoff. The ability of the architecture to instantiate sentence structures is illustrated with examples of sentence complexity observed in human language performance. Similarities exist between the architecture for sentence structure and blackboard architectures for combinatorial structures in visual cognition, derived from the structure of the visual cortex. These architectures are briefly discussed, together with an example of a combinatorial structure in which the blackboard architectures for language and vision are combined. In this way, the architecture for language is grounded in perception. Perspectives and potential developments of the architectures are discussed.

  1. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and experiments for chemistry. Topics include superheavy elements, polarizing power and chemistry of alkali metals, particulate carbon from combustion, tips for the chemistry laboratory, interesting/colorful experiments, behavior of bismuth (III) iodine, and…

  2. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and experiments for chemistry. Topics include superheavy elements, polarizing power and chemistry of alkali metals, particulate carbon from combustion, tips for the chemistry laboratory, interesting/colorful experiments, behavior of bismuth (III) iodine, and…

  3. Combinatorial Optimization by Amoeba-Based Neurocomputer with Chaotic Dynamics

    NASA Astrophysics Data System (ADS)

    Aono, Masashi; Hirata, Yoshito; Hara, Masahiko; Aihara, Kazuyuki

    We demonstrate a computing system based on an amoeba of a true slime mold Physarum capable of producing rich spatiotemporal oscillatory behavior. Our system operates as a neurocomputer because an optical feedback control in accordance with a recurrent neural network algorithm leads the amoeba's photosensitive branches to search for a stable configuration concurrently. We show our system's capability of solving the traveling salesman problem. Furthermore, we apply various types of nonlinear time series analysis to the amoeba's oscillatory behavior in the problem-solving process. The results suggest that an individual amoeba might be characterized as a set of coupled chaotic oscillators.

  4. Prominent Chemists Team Up to Review Frontiers in Chemistry.

    ERIC Educational Resources Information Center

    Baum, Rudy M.

    1989-01-01

    Discusses a symposium which focused on the influence of inorganic chemistry on organic synthesis, the impact of organic chemistry on biochemistry and vice versa, chemical reaction dynamics, and advances in inorganic chemistry. Explains the purpose of the symposium was to illustrate the intellectual dynamism of modern chemistry. (MVL)

  5. Prominent Chemists Team Up to Review Frontiers in Chemistry.

    ERIC Educational Resources Information Center

    Baum, Rudy M.

    1989-01-01

    Discusses a symposium which focused on the influence of inorganic chemistry on organic synthesis, the impact of organic chemistry on biochemistry and vice versa, chemical reaction dynamics, and advances in inorganic chemistry. Explains the purpose of the symposium was to illustrate the intellectual dynamism of modern chemistry. (MVL)

  6. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  7. Forensic chemistry.

    PubMed

    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.

  8. Combinatorial effects on clumped isotopes and their significance in biogeochemistry

    NASA Astrophysics Data System (ADS)

    Yeung, Laurence Y.

    2016-01-01

    The arrangement of isotopes within a collection of molecules records their physical and chemical histories. Clumped-isotope analysis interrogates these arrangements, i.e., how often rare isotopes are bound together, which in many cases can be explained by equilibrium and/or kinetic isotope fractionation. However, purely combinatorial effects, rooted in the statistics of pairing atoms in a closed system, are also relevant, and not well understood. Here, I show that combinatorial isotope effects are most important when two identical atoms are neighbors on the same molecule (e.g., O2, N2, and D-D clumping in CH4). When the two halves of an atom pair are either assembled with different isotopic preferences or drawn from different reservoirs, combinatorial effects cause depletions in clumped-isotope abundance that are most likely between zero and -1‰, although they could potentially be -10‰ or larger for D-D pairs. These depletions are of similar magnitude, but of opposite sign, to low-temperature equilibrium clumped-isotope effects for many small molecules. Enzymatic isotope-pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect, although it is not limited to biological reactions. Chemical-kinetic isotope effects, which are related to a bond-forming transition state, arise independently and express second-order combinatorial effects related to the abundance of the rare isotope. Heteronuclear moeties (e.g., Csbnd O and Csbnd H), are insensitive to direct combinatorial influences, but secondary combinatorial influences are evident. In general, both combinatorial and chemical-kinetic factors are important for calculating and interpreting clumped-isotope signatures of kinetically controlled reactions. I apply this analytical framework to isotope-pairing reactions relevant to geochemical oxygen, carbon, and nitrogen cycling that may be influenced by combinatorial

  9. The priming of basic combinatory responses in MEG.

    PubMed

    Blanco-Elorrieta, Esti; Ferreira, Victor S; Del Prato, Paul; Pylkkänen, Liina

    2017-09-21

    Priming has been a powerful tool for the study of human memory and especially the memory representations relevant for language. However, although it is well established that lexical access can be primed, we do not know exactly what types of computations can be primed above the word level. This work took a neurobiological approach and assessed the ways in which the complex representation of a minimal combinatory phrase, such as red boat, can be primed, as evidenced by the spatiotemporal profiles of magnetoencephalography (MEG) signals. Specifically, we built upon recent progress on the neural signatures of phrasal composition and tested whether the brain activities implicated for the basic combination of two words could be primed. In two experiments, MEG was recorded during a picture naming task where the prime trials were designed to replicate previously reported combinatory effects and the target trials to test whether those combinatory effects could be primed. The manipulation of the primes was successful in eliciting larger activity for adjective-noun combinations than single nouns in left anterior temporal and ventromedial prefrontal cortices, replicating prior MEG studies on parallel contrasts. Priming of similarly timed activity was observed during target trials in anterior temporal cortex, but only when the prime and target shared an adjective. No priming in temporal cortex was observed for single word repetition and two control tasks showed that the priming effect was not elicited if the prime pictures were simply viewed but not named. In sum, this work provides evidence that very basic combinatory operations can be primed, with the necessity for some lexical overlap between prime and target suggesting combinatory conceptual, as opposed to syntactic processing. Both our combinatory and priming effects were early, onsetting between 100 and 150ms after picture onset and thus are likely to reflect the very earliest planning stages of a combinatory message

  10. Recent advances in combinatorial biosynthesis for drug discovery

    PubMed Central

    Sun, Huihua; Liu, Zihe; Zhao, Huimin; Ang, Ee Lui

    2015-01-01

    Because of extraordinary structural diversity and broad biological activities, natural products have played a significant role in drug discovery. These therapeutically important secondary metabolites are assembled and modified by dedicated biosynthetic pathways in their host living organisms. Traditionally, chemists have attempted to synthesize natural product analogs that are important sources of new drugs. However, the extraordinary structural complexity of natural products sometimes makes it challenging for traditional chemical synthesis, which usually involves multiple steps, harsh conditions, toxic organic solvents, and byproduct wastes. In contrast, combinatorial biosynthesis exploits substrate promiscuity and employs engineered enzymes and pathways to produce novel “unnatural” natural products, substantially expanding the structural diversity of natural products with potential pharmaceutical value. Thus, combinatorial biosynthesis provides an environmentally friendly way to produce natural product analogs. Efficient expression of the combinatorial biosynthetic pathway in genetically tractable heterologous hosts can increase the titer of the compound, eventually resulting in less expensive drugs. In this review, we will discuss three major strategies for combinatorial biosynthesis: 1) precursor-directed biosynthesis; 2) enzyme-level modification, which includes swapping of the entire domains, modules and subunits, site-specific mutagenesis, and directed evolution; 3) pathway-level recombination. Recent examples of combinatorial biosynthesis employing these strategies will also be highlighted in this review. PMID:25709407

  11. Dynamics of seawater carbonate chemistry, production, and calcification of a coral reef flat, Central Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Albright, R.; Langdon, C.; Anthony, K. R. N.

    2013-05-01

    Ocean acidification is projected to shift coral reefs from a state of net accretion to one of net dissolution this century. Presently, our ability to predict global-scale changes to coral reef calcification is limited by insufficient data relating seawater carbonate chemistry parameters to in situ rates of reef calcification. Here, we investigate natural trends in carbonate chemistry of the Davies Reef flat in the central Great Barrier Reef on diel and seasonal timescales and relate these trends to benthic carbon fluxes by quantifying net ecosystem calcification (nec) and net community production (ncp). Results show that seawater carbonate chemistry of the Davies Reef flat is highly variable over both diel and seasonal timescales. pH (total scale) ranged from 7.92 to 8.17, pCO2 ranged from 272 to 542 μatm, and aragonite saturation state (Ωarag) ranged from 2.9 to 4.1. Diel cycles in carbonate chemistry were primarily driven by ncp, and warming explained 35% and 47% of the seasonal shifts in pCO2 and pH, respectively. Daytime ncp averaged 36 ± 19 mmol C m-2 h-1 in summer and 33 ± 13 mmol C m-2 h-1 in winter; nighttime ncp averaged -22 ± 20 and -7 ± 6 mmol C m-2 h-1 in summer and winter, respectively. Daytime nec averaged 11 ± 4 mmol CaCO3 m-2 h-1 in summer and 8 ± 3 mmol CaCO3 m-2 h-1 in winter, whereas nighttime nec averaged 2 ± 4 mmol and -1 ± 3 mmol CaCO3 m-2 h-1 in summer and winter, respectively. Net ecosystem calcification was positively correlated with Ωarag for both seasons. Linear correlations of nec and Ωarag indicate that the Davies Reef flat may transition from a state of net calcification to net dissolution at Ωarag values of 3.4 in summer and 3.2 in winter. Diel trends in Ωarag indicate that the reef flat is currently below this calcification threshold 29.6% of the time in summer and 14.1% of the time in winter.

  12. Development of a system to evaluate compound identity, purity, and concentration in a single experiment and its application in quality assessment of combinatorial libraries and screening hits.

    PubMed

    Yurek, David A; Branch, Derek L; Kuo, Ming-Shang

    2002-01-01

    The development and use of a new assay system for the simultaneous determination of identity, purity, and concentration of sample components from combinatorial libraries produced by parallel synthesis are described. The system makes use of high-performance liquid chromatography with UV/vis photodiode array (PDA), evaporative light scattering (ELSD), chemiluminescent nitrogen (CLND), and time-of-flight mass spectrometer (TOFMS) detectors (HPLC-PDA-ELSD-CLND-TOFMS). Although these detectors have previously been utilized separately for the analysis of combinatorial chemistry libraries, the use of TOFMS along with CLND provides a synergistic combination enabling target and side-product structures to be identified and their concentrations and purities determined in a single experiment from a solution containing microgram levels of material. The CLND was found to give a linear response based on the number of moles of nitrogen present. Therefore, if the number of nitrogens per molecule is known, the concentration of each nitrogen-containing sample component may be determined utilizing an unrelated co-injected standard. A molecular formula for an impurity may often be calculated from the exact mass determined by the TOFMS and knowledge of the chemistry involved. Thus, if the sample components contain nitrogen, the concentration of every identified HPLC peak may be determined even in the absence of primary standards. This combination of detectors enabled the characterization of both target compounds and byproducts in combinatorial libraries, allowing the optimization of library synthetic procedures. This system was also used to survey the quality of libraries, enabling the selection of the best libraries for screening. This method also facilitated the characterization of samples from combinatorial libraries found as hits in high-throughput screening to establish the potency of the leads based on their actual concentration. In addition, concentrations and potencies of

  13. Chemistry and dynamics of the lower troposphere over North America and the North Atlantic Ocean in fall 1997 observed using an airborne UV DIAL system

    NASA Technical Reports Server (NTRS)

    Grant, William B.; Butler, Carolyn F.; Fenn, Marta A.; Kooi, Susan A.; Browell, Edward V.; Fuelberg, Henry

    1998-01-01

    The NASA Langley Research Center's airborne UV Differential Absorption Lidar (DIAL) system participated in the Subsonic Assessment, Ozone and Nitrogen Oxide Experiment (SONEX) mission from October 13 to November 12, 1997. The purpose of the mission was to study the upper troposphere/lower stratosphere in and near the North Atlantic flight corridor to better understand this region of the atmosphere and how civilian air travel in the corridor might be affecting the atmospheric chemistry. Bases of operations included NASA Ames, California (37.4 deg N, 122.1 deg W); Bangor, Maine (44.8 deg N, 68.8 deg W); Shannon, Ireland (52.7 deg N, 8.9 deg W); and Lajes, Terceira Island, Azores (38.8 deg N, 27.1 deg W). Since the UV DIAL system observes in the nadir as well as the zenith, aerosol and ozone data were obtained from near the Earth's surface to the lower stratosphere. A number of interesting features were noted relating to both chemistry and dynamics of the troposphere, which are reported here.

  14. View Discovery in OLAP Databases through Statistical Combinatorial Optimization

    SciTech Connect

    Joslyn, Cliff A.; Burke, Edward J.; Critchlow, Terence J.

    2009-05-01

    The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of ``views'' of an OLAP database as a combinatorial object of all projections and subsets, and ``view discovery'' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline ``hop-chaining'' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a ``spiraling'' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.

  15. Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.

    PubMed

    McIsaac, R Scott; Petti, Allegra A; Bussemaker, Harmen J; Botstein, David

    2012-08-01

    In yeast, the pathways of sulfur assimilation are combinatorially controlled by five transcriptional regulators (three DNA-binding proteins [Met31p, Met32p, and Cbf1p], an activator [Met4p], and a cofactor [Met28p]) and a ubiquitin ligase subunit (Met30p). This regulatory system exerts combinatorial control not only over sulfur assimilation and methionine biosynthesis, but also on many other physiological functions in the cell. Recently we characterized a gene induction system that, upon the addition of an inducer, results in near-immediate transcription of a gene of interest under physiological conditions. We used this to perturb levels of single transcription factors during steady-state growth in chemostats, which facilitated distinction of direct from indirect effects of individual factors dynamically through quantification of the subsequent changes in genome-wide patterns of gene expression. We were able to show directly that Cbf1p acts sometimes as a repressor and sometimes as an activator. We also found circumstances in which Met31p/Met32p function as repressors, as well as those in which they function as activators. We elucidated and numerically modeled feedback relationships among the regulators, notably feedforward regulation of Met32p (but not Met31p) by Met4p that generates dynamic differences in abundance that can account for the differences in function of these two proteins despite their identical binding sites.

  16. From linking of metal-oxide building blocks in a dynamic library to giant clusters with unique properties and towards adaptive chemistry.

    PubMed

    Müller, Achim; Gouzerh, Pierre

    2012-11-21

    Following Nature's lessons, today chemists can cross the boundary of the small molecule world to construct multifunctional and highly complex molecular nano-objects up to protein size and even cell-like nanosystems showing responsive sensing. Impressive examples emerge from studies of the solutions of some oxoanions of the early transition metals especially under reducing conditions which enable the controlled linking of metal-oxide building blocks. The latter are available from constitutional dynamic libraries, thus providing the option to generate multifunctional unique nanoscale molecular systems with exquisite architectures, which even opens the way towards adaptive and evolutive (Darwinian) chemistry. The present review presents the first comprehensive report of current knowledge (including synthesis aspects not discussed before) regarding the related giant metal-oxide clusters mainly of the type {Mo(57)M'(6)} (M' = Fe(III), V(IV)) (torus structure), {M(72)M'(30)} (M = Mo, M' = V(IV), Cr(III), Fe(III), Mo(V)), {M(72)Mo(60)} (M = Mo, W) (Keplerates), {Mo(154)}, {Mo(176)}, {Mo(248)} ("big wheels"), and {Mo(368)} ("blue lemon") - all having the important transferable pentagonal {(M)M(5)} groups in common. These discoveries expanded the frontiers of inorganic chemistry to the mesoscopic world, while there is probably no collection of discrete inorganic compounds which offers such a versatile chemistry and the option to study new phenomena of interdisciplinary interest. The variety of different properties of the sphere- and wheel-type metal-oxide-based clusters can directly be related to their unique architectures: The spherical Keplerate-type capsules having 20 crown-ether-type pores and tunable internal functionalities allow the investigation of confined matter as well as that of sphere-surface-supramolecular and encapsulation chemistry - including related new aspects of the biologically important hydrophobic effects - but also of nanoscale ion transport and

  17. Surface layer ozone and nitric oxides in the Arctic: The inuence of boundary layer dynamics, snowpack chemistry, surface exchanges, and seasonality

    NASA Astrophysics Data System (ADS)

    Van Dam, Brie A.

    The snowpack is a region of active chemistry. Aqueous chemistry in a quasi-liquid layer on snow grains and gas-phase chemical reactions in snow interstitial air can lead to the production or destruction of important trace gases. Physical transport parameters such as wind pumping and diffusion affect the vertical distribution of gases within the snowpack. The resulting emission or uptake of trace gases at the atmosphere-snowpack interface can have significant in uence on the chemistry of the lower atmosphere. In this work the dynamic interactions between the snowpack and atmosphere are examined from multiple perspectives. The primary focus is on ozone (O3) and nitrogen oxides (NOx) in the Arctic, a region undergoing widespread environmental change. To investigate an ice-sheet location with year round snow cover, data from a two-year campaign at Summit, Greenland are implemented. At Summit this study examines (1) the processes contributing to vigorous chemistry in snow interstitial air, and (2) the role of the boundary layer over snow in determining surface layer NOx. Physical and chemical processes are shown to contribute to distinct seasonal and diurnal cycles of O3, NO, and NO2 in the snowpack. Boundary layer depths estimated from sonic anemometer turbulence quantities are used alongside sodar-derived values to show that the depth of the stable to weakly stable boundary layer at Summit was not a primary factor in determining NO x in early summer. Motivated by observations of an increase in the length of the snow-free season in the Arctic in recent decades, data from a one-year experiment at the seasonally-snow covered location of Toolik Lake, AK are also incorporated. This study shows the first observations of springtime ozone depletion events at a location over 200 km from the coast in the Arctic. FLEXPART analysis is used to illustrate that these inland events are linked to transport conditions. Lastly at this location, eddy-covariance O3 uxes were calculated to

  18. Molecular dynamics simulation of organometallic reaction dynamics, and, Enhancing achievement in chemistry for African American students through innovations in pedagogy aligned with supporting assessment and curriculum and integrated under an alternative research paradigm

    NASA Astrophysics Data System (ADS)

    Mebane, Sheryl Dee

    Part I. Molecular dynamics simulation of organometallic reaction dynamics. To study the interplay of solute and solvent dynamics, large-scale molecular dynamics simulations were employed. Lennard-Jones and electrostatic models of potential energies from solvent-only studies were combined with solute potentials generated from ab-initio calculations. Radial distribution functions and other measures revealed the polar solvent's response to solute dynamics following CO dissociation. In future studies, the time-scale for solvent coordination will be confirmed with ultrafast spectroscopy data. Part II. Enhancing achievement in chemistry for African American students through innovations in pedagogy aligned with supporting assessment and curriculum and integrated under an alternative research paradigm. Much progress has been made in the area of research in education that focuses on teaching and learning in science. Much effort has also centered on documenting and exploring the disparity in academic achievement between underrepresented minority students and students comprising a majority in academic circles. However, few research projects have probed educational inequities in the context of mainstream science education. In order to enrich this research area and to better reach underserved learning communities, the educational experience of African American students in an ethnically and academically diverse high school science class has been examined throughout one, largely successful, academic year. The bulk of data gathered during the study was obtained through several qualitative research methods and was interpreted using research literature that offered fresh theoretical perspectives on equity that may better support effective action.

  19. Were arachnids the first to use combinatorial peptide libraries?

    PubMed

    Sollod, Brianna L; Wilson, David; Zhaxybayeva, Olga; Gogarten, J Peter; Drinkwater, Roger; King, Glenn F

    2005-01-01

    Spiders, scorpions, and cone snails are remarkable for the extent and diversity of gene-encoded peptide neurotoxins that are expressed in their venom glands. These toxins are produced in the form of structurally constrained combinatorial peptide libraries in which there is hypermutation of essentially all residues in the mature-toxin sequence with the exception of a handful of strictly conserved cysteines that direct the three-dimensional fold of the toxin. This gene-based combinatorial peptide library strategy appears to have been first implemented by arachnids almost 400 million years ago, long before cone snails evolved a similar mechanism for generating peptide diversity.

  20. Vertical dynamics of the aquifer microbial community associated with groundwater chemistry in the artificial recharge site in Korea

    NASA Astrophysics Data System (ADS)

    Moon, Hee Sun; Hyun, Sung Pil; Kim, Boa; Shin, Doyun; Ha, Kyoochul

    2014-05-01

    Artificial groundwater recharge offers an opportunity to better manage groundwater resources by storing water in aquifers and increasing the amount of groundwater available for abstraction during high demand periods. It is important to understand the linkage of microbial ecology to groundwater chemistry to assess changes in groundwater quality caused by artificial groundwater recharge. In this study, we investigated how the structure and diversity of this subsurface microbial community correlates with and impacts upon groundwater chemistry. Groundwater samples at two different depths (10 and 33 m) were collected from three monitoring wells (MLW 1, MLW 2 and MLW 3) in the artificial groundwater recharge demonstration site in Changwon, Korea. The groundwater samples were filtered with 0.45 um membrane filters and then used for the anion and cation analysis. A 4L of each groundwater sample was immediately filtered with 0.2 um membrane filters and the filters were used for DNA extraction using Fast DNA Spin Kit for soil (MP Bio, USA). Further molecular work processes including pyrosequencing were carried out at Chunlab, Inc. (Seoul, Korea). Pyrosequencing results showed all major phyla were OD 1, OD3, and OD 11 in shallow groundwater samples while Proteobacteria (β-proteobacteria and δ-proteobacteria) and Bacterioidetes were dominant phyla in deep groundwater. The Shannon diversity index indicated that the microbial community was much more diverse in shallow groundwater than in deep groundwater. Heat map and hierarchical cluster analysis based on the relative abundance of OTUs at genus level showed a clear distinction between shallow and deep groundwater. Differences in the vertical community structure were driven by the major species such as Sufuicurvum sp., Pseudomonas sp., Acidiferrobacter sp., Gallionella sp., and Ferribacterium sp. The results show that several distinct factors such as iron and sulfate concentration control the vertical composition of microbial

  1. The Lens of Chemistry

    ERIC Educational Resources Information Center

    Thalos, Mariam

    2013-01-01

    Chemistry possesses a distinctive theoretical lens--a distinctive set of theoretical concerns regarding the dynamics and transformations of a perplexing variety of organic and nonorganic substances--to which it must be faithful. Even if it is true that chemical facts bear a special (reductive) relationship to physical facts, nonetheless it will…

  2. The Lens of Chemistry

    ERIC Educational Resources Information Center

    Thalos, Mariam

    2013-01-01

    Chemistry possesses a distinctive theoretical lens--a distinctive set of theoretical concerns regarding the dynamics and transformations of a perplexing variety of organic and nonorganic substances--to which it must be faithful. Even if it is true that chemical facts bear a special (reductive) relationship to physical facts, nonetheless it will…

  3. Fast Combinatorial Algorithm for the Solution of Linearly Constrained Least Squares Problems

    DOEpatents

    Van Benthem, Mark H.; Keenan, Michael R.

    2008-11-11

    A fast combinatorial algorithm can significantly reduce the computational burden when solving general equality and inequality constrained least squares problems with large numbers of observation vectors. The combinatorial algorithm provides a mathematically rigorous solution and operates at great speed by reorganizing the calculations to take advantage of the combinatorial nature of the problems to be solved. The combinatorial algorithm exploits the structure that exists in large-scale problems in order to minimize the number of arithmetic operations required to obtain a solution.

  4. An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.

    PubMed

    Pickard, Frank C; König, Gerhard; Simmonett, Andrew C; Shao, Yihan; Brooks, Bernard R

    2016-10-15

    The non-Boltzmann Bennett (NBB) free energy estimator method is applied to 21 molecules from the blind subset of the SAMPL4 challenge. When NBB is applied with the SMD implicit solvent model, and the OLYP/DZP level of quantum chemistry, highly accurate hydration free energy calculations are obtained with respect to experiment (RMSD=0.89kcal·mol(-1)). Other quantum chemical methods are also tested, and the effects of solvent model, density functional, basis set are explored in this benchmarking study, providing a framework for improvements in calculating hydration free energies. We provide a practical guide for using the best QM-NBB protocols that are consistently more accurate than either pure QM or pure MM alone. In situations where high accuracy hydration free energy predictions are needed, the QM-NBB method with SMD implicit solvent should be the first choice of quantum chemists. Published by Elsevier Ltd.

  5. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Twelve new chemistry expermiments are described. Broad areas covered include atomic structure, solubility, gaseous diffusion, endothermic reactions, alcohols, equilibrium, atomic volumes, and some improvised apparatus. (PS)

  6. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Twelve new chemistry expermiments are described. Broad areas covered include atomic structure, solubility, gaseous diffusion, endothermic reactions, alcohols, equilibrium, atomic volumes, and some improvised apparatus. (PS)

  7. Technetium chemistry

    SciTech Connect

    Burns, C.; Bryan, J.; Cotton, F.; Ott, K.; Kubas, G.; Haefner, S.; Barrera, J.; Hall, K.; Burrell, A.

    1996-04-01

    Technetium chemistry is a young and developing field. Despite the limited knowledge of its chemistry, technetium is the workhorse for nuclear medicine. Technetium is also a significant environmental concern because it is formed as a byproduct of nuclear weapons production and fission-power generators. Development of new technetium radio-pharmaceuticals and effective environmental control depends strongly upon knowledge of basic technetium chemistry. The authors performed research into the basic coordination and organometallic chemistry of technetium and used this knowledge to address nuclear medicine and environmental applications. This is the final report of a three-year Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL).

  8. Click chemistry: 1,2,3-triazoles as pharmacophores.

    PubMed

    Agalave, Sandip G; Maujan, Suleman R; Pore, Vandana S

    2011-10-04

    The copper(I)-catalyzed 1,2,3-triazole-forming reaction between azides and terminal alkynes has become the gold standard of 'click chemistry' due to its reliability, specificity, and biocompatibility. Applications of click chemistry are increasingly found in all aspects of drug discovery; they range from lead finding through combinatorial chemistry and target-templated in vitro chemistry, to proteomics and DNA research by using bioconjugation reactions. The triazole products are more than just passive linkers; they readily associate with biological targets, through hydrogen-bonding and dipole interactions. The present review will focus mainly on the recent literature for applications of this reaction in the field of medicinal chemistry, in particular on use of the 1,2,3-triazole moiety as pharmacophore.

  9. Dynamic Chemistry-Based Sensing: A Molecular System for Detection of Saccharide, Formaldehyde, and the Silver Ion.

    PubMed

    Chang, Xingmao; Wang, Zhaolong; Qi, Yanyu; Kang, Rui; Cui, Xinwen; Shang, Congdi; Liu, Kaiqiang; Fang, Yu

    2017-09-05

    Development of artificial complex molecular systems is of great importance in understanding complexity in natural processes and for achieving new functionalities. One of the strategies is to create them via optimized utilization of noncovalent interactions and dynamic covalent bonds. We report here on a new complex molecular system, which was constructed by integrating the multiple interactions containing a dynamic covalent interaction between 1,2-diol and boronic acid, a coordination interaction between the silver ion and pyridyl, and an easy accessible reaction between secondary amine and formaldehyde. By employing the three dynamic interactions, a pyrene (Py) labeled fluorophore, PPB, was designed and synthesized. The compound reacts with fructose (F), a monosaccharide, in aqueous phase and produces a fluorescent adduct, PPB-F, which can be further used as a sensing platform for formaldehyde (FA) and the silver ion. The respective dynamic interactions are accompanied with color changes due to the reversible switching between Py-monomer emission and excimer emission. The respective experimental detection limits (DLs) for the three analytes are much lower than 0.2 mM, 0.1 mM, and 2.5 μM, respectively. The presence of relevant compounds or ions shows little effect upon the sensing. No doubt, the results as presented show that the integration of supramolecular interactions including dynamic covalent bonds can be employed as a general strategy to develop new functional molecular systems or materials.

  10. Combinatorial nanodiamond in pharmaceutical and biomedical applications.

    PubMed

    Lim, Dae Gon; Prim, Racelly Ena; Kim, Ki Hyun; Kang, Eunah; Park, Kinam; Jeong, Seong Hoon

    2016-11-30

    One of the newly emerging carbon materials, nanodiamond (ND), has been exploited for use in traditional electric materials and this has extended into biomedical and pharmaceutical applications. Recently, NDs have attained significant interests as a multifunctional and combinational drug delivery system. ND studies have provided insights into granting new potentials with their wide ranging surface chemistry, complex formation with biopolymers, and combination with biomolecules. The studies that have proved ND inertness, biocompatibility, and low toxicity have made NDs much more feasible for use in real in vivo applications. This review gives an understanding of NDs in biomedical engineering and pharmaceuticals, focusing on the classified introduction of ND/drug complexes. In addition, the diverse potential applications that can be obtained with chemical modification are presented. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. International Society of Heterocyclic Chemistry--17th international congress. 1-6 August 1999, Vienna, Austria.

    PubMed

    Daneshtalab, M

    1999-10-01

    Approximately 1200 scientists attended this congress of heterocyclic chemistry, which focused on: New synthetic methods in heterocyclic chemistry; synthesis of bioactive heterocycles including natural products; heterocycles and asymmetric synthesis; heterocycles in bioorganic chemistry; new heterocyclic materials; structure and properties of heterocyclic compounds; solid-phase synthesis, combinatorial chemistry and heterocyclic scaffolds. These topics were covered in 600 posters and 100 plenary, invited and oral presentations. This report summarizes the highlights of the presentations related to the category of the synthesis of bioactive heterocycles including natural products.

  12. 5-(hydroxymethyl)oxazoles: versatile scaffolds for combinatorial solid-phase synthesis of 5-substituted oxazoles.

    PubMed

    Grabowska, U; Rizzo, A; Farnell, K; Quibell, M

    2000-01-01

    A scheme combining the preparation of building blocks in solution followed by solid-phase combinatorial chemistry has been developed to side-chain diversify 5-(hydroxymethyl)oxazole scaffold (1) into aryl ethers, thioethers, sulfones, sulfonamides, and carboxamides. Protected heterocyclic scaffolds 2 were linked to the solid phase and N-terminal derivatized using active ester chemistry, providing chemset 4¿1-4,1-4¿. The free side-chain hydroxyl of 4 was smoothly converted to aryl ethers 6 under Mitsunobu conditions, with a broad range of substituted phenols. Alternatively, quantitative conversion of hydroxyl to bromide followed by displacement with alkyl and aryl thiols gave thioethers 8. Thioethers were optionally oxidized to sulfones 9. Bromide displacement by azide, followed by reduction to amine and acylation with a range of carboxylic acids and sulfonyl chlorides gave carboxamides 11 and sulfonamides 13, respectively. Crude purity at typically >90% was observed for each of the five modifications detailed. A series of 20 compounds, exemplifying each modification, was reprepared, purified, and fully characterized.

  13. Identities for Generalized Fibonacci Numbers: A Combinatorial Approach

    ERIC Educational Resources Information Center

    Plaza, A.; Falcon, S.

    2008-01-01

    This note shows a combinatorial approach to some identities for generalized Fibonacci numbers. While it is a straightforward task to prove these identities with induction, and also by arithmetical manipulations such as rearrangements, the approach used here is quite simple to follow and eventually reduces the proof to a counting problem. (Contains…

  14. Identities for Generalized Fibonacci Numbers: A Combinatorial Approach

    ERIC Educational Resources Information Center

    Plaza, A.; Falcon, S.

    2008-01-01

    This note shows a combinatorial approach to some identities for generalized Fibonacci numbers. While it is a straightforward task to prove these identities with induction, and also by arithmetical manipulations such as rearrangements, the approach used here is quite simple to follow and eventually reduces the proof to a counting problem. (Contains…

  15. Combinatorial structure of k-semiprimitive matrix families

    NASA Astrophysics Data System (ADS)

    Al'pin, Yu A.; Al'pina, V. S.

    2016-05-01

    Protasov's Theorem on the combinatorial structure of k-primitive families of non-negative matrices is generalized to k-semiprimitive matrix families. The main tool is the binary relation of colour compatibility on the vertices of the coloured graph of the matrix family. Bibliography: 14 titles.

  16. Influence of Dynamics and Chemistry on the Diurnal Variation of VOCs in the Planetary Boundary Layer above a Mixed Forest Canopy in the Southeastern United States

    NASA Astrophysics Data System (ADS)

    Guenther, A. B.; Su, L.; Patton, E. G.; Vila-Guerau Arellano, J.; Mak, J. E.

    2014-12-01

    The planetary boundary layer (PBL) is a region of inherent interest because reactive VOCs emitted from the forest canopy are mixed with the residual and free tropospheric air masses, oxidized, and/or otherwise removed in this region. The characterization of diurnal variation of VOCs in the PBL is limited due to the lack of appropriate sampling platforms that are able to probe all the regions of interest: from the surface to the entrainment zone. Here we present the application of the Whole Air Sample Profiler (WASP) system during the 2013 Southeast Atmosphere Study (SAS) campaign. A total of 41 research flights (RFs) were carried out during the 2013 SAS campaign between June 1 and June 14 over the Alabama Aquatic Biodiversity Center (AABC) site and the SEARCH site. During each RF, ambient air sampling started from 50-100 m above the canopy top and stopped at ~1200 m above the mean sea level (a.m.s.l). The air samples were subsequently analyzed by using a proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOF-MS). Here we analyze the vertical profiles and averaged diurnal variation of the mixing ratios of several reactive VOC species, including isoprene, the sum of monoterpenes, and first generation oxidation products of isoprene: methyl vinyl ketone and methacrolein (MVK+MACR). A MiXed Layer Chemistry (MXLCH) model, guided by the meteorological and chemical observations during the SAS campaign, is used to study the influence of boundary layer dynamics and new isoprene oxidation mechanism on the diurnal variation of major biogenic VOCs emitted from the forest canopy. The new scheme includes OH recycling through two pathways under low-NOx regime: (1) hydroxyl peroxy radicals (HOC5H8OO•; ISOPO2) unimolecular isomerization, and (2) ISOPO2+HO2. The model is able to reproduce the evolution of the boundary layer dynamics (including potential temperature, and boundary layer height) during the selected simulation dates. Based on the model results, budget

  17. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Outlines laboratory procedures, demonstrations, teaching suggestions, and content information related to chemistry. Topics include polarizing power; calorimetry and momentum; microcomputers in school chemistry; a constant-volume dispenser for liquids, floating magnets, and crystal lattices; preparation of chromium; and solvent polarity and…

  18. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Outlines laboratory procedures, demonstrations, teaching suggestions, and content information related to chemistry. Topics include polarizing power; calorimetry and momentum; microcomputers in school chemistry; a constant-volume dispenser for liquids, floating magnets, and crystal lattices; preparation of chromium; and solvent polarity and…

  19. The effect of breaking gravity waves on the dynamics and chemistry of the mesosphere and lower thermosphere (invited review)

    NASA Technical Reports Server (NTRS)

    Garcia, R. R.

    1986-01-01

    The influence of breaking gravity waves on the dynamics and chemical composition of the 60 to 110 km region is investigated with a two dimensional model that includes a parameterization of gravity wave momentum deposition and diffusion. The dynamical model is described by Garcia and Solomon (1983) and Solomon and Garcia (1983) and includes a complete chemical scheme for the mesosphere and lower thermosphere. The parameterization of Lindzen (1981) is used to calculate the momentum deposited and the turbulent diffusion produced by the gravity waves. It is found that wave momentum deposition drives a very vigorous mean meridional circulation, produces a very cold summer mesopause and reverse the zonal wind jets above about 85 km. The seasonal variation of the turbulent diffusion coefficient is consistent with the behavior of mesospheric turbulences inferred from MST radar echoes. The large degree of consistency between model results and various types of dynamical and chemical data supports very strongly the hypothesis that breaking gravity waves play a major role in determining the zonally-averaged dynamical and chemical structure of the 60 to 110 km region of the atmosphere.

  20. Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

    ERIC Educational Resources Information Center

    Fuson, Michael M.

    2017-01-01

    Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

  1. Polynomial functors and combinatorial Dyson-Schwinger equations

    NASA Astrophysics Data System (ADS)

    Kock, Joachim

    2017-04-01

    We present a general abstract framework for combinatorial Dyson-Schwinger equations, in which combinatorial identities are lifted to explicit bijections of sets, and more generally equivalences of groupoids. Key features of combinatorial Dyson-Schwinger equations are revealed to follow from general categorical constructions and universal properties. Rather than beginning with an equation inside a given Hopf algebra and referring to given Hochschild 1-cocycles, our starting point is an abstract fixpoint equation in groupoids, shown canonically to generate all the algebraic structures. Precisely, for any finitary polynomial endofunctor P defined over groupoids, the system of combinatorial Dyson-Schwinger equations X = 1 + P(X) has a universal solution, namely the groupoid of P-trees. The isoclasses of P-trees generate naturally a Connes-Kreimer-like bialgebra, in which the abstract Dyson-Schwinger equation can be internalised in terms of canonical B+-operators. The solution to this equation is a series (the Green function), which always enjoys a Faà di Bruno formula, and hence generates a sub-bialgebra isomorphic to the Faà di Bruno bialgebra. Varying P yields different bialgebras, and cartesian natural transformations between various P yield bialgebra homomorphisms and sub-bialgebras, corresponding for example to truncation of Dyson-Schwinger equations. Finally, all constructions can be pushed inside the classical Connes-Kreimer Hopf algebra of trees by the operation of taking core of P-trees. A byproduct of the theory is an interpretation of combinatorial Green functions as inductive data types in the sense of Martin-Löf type theory (expounded elsewhere).

  2. Structure-based design of combinatorial mutagenesis libraries

    PubMed Central

    Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris

    2015-01-01

    The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called “Structure-based Optimization of Combinatorial Mutagenesis” (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states. PMID:25611189

  3. Paths and partitions: Combinatorial descriptions of the parafermionic states

    NASA Astrophysics Data System (ADS)

    Mathieu, Pierre

    2009-09-01

    The Zk parafermionic conformal field theories, despite the relative complexity of their modes algebra, offer the simplest context for the study of the bases of states and their different combinatorial representations. Three bases are known. The classic one is given by strings of the fundamental parafermionic operators whose sequences of modes are in correspondence with restricted partitions with parts at distance k -1 differing at least by 2. Another basis is expressed in terms of the ordered modes of the k -1 different parafermionic fields, which are in correspondence with the so-called multiple partitions. Both types of partitions have a natural (Bressoud) path representation. Finally, a third basis, formulated in terms of different paths, is inherited from the solution of the restricted solid-on-solid model of Andrews-Baxter-Forrester. The aim of this work is to review, in a unified and pedagogical exposition, these four different combinatorial representations of the states of the Zk parafermionic models. The first part of this article presents the different paths and partitions and their bijective relations; it is purely combinatorial, self-contained, and elementary; it can be read independently of the conformal-field-theory applications. The second part links this combinatorial analysis with the bases of states of the Zk parafermionic theories. With the prototypical example of the parafermionic models worked out in detail, this analysis contributes to fix some foundations for the combinatorial study of more complicated theories. Indeed, as we briefly indicate in ending, generalized versions of both the Bressoud and the Andrews-Baxter-Forrester paths emerge naturally in the description of the minimal models.

  4. Structure-based design of combinatorial mutagenesis libraries.

    PubMed

    Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris

    2015-05-01

    The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called "Structure-based Optimization of Combinatorial Mutagenesis" (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states.

  5. Ligand-Based Peptide Design and Combinatorial Peptide Libraries to Target G Protein-Coupled Receptors

    PubMed Central

    Gruber, Christian W.; Muttenthaler, Markus; Freissmuth, Michael

    2016-01-01

    G protein-coupled receptors (GPCRs) are considered to represent the most promising drug targets; it has been repeatedly said that a large fraction of the currently marketed drugs elicit their actions by binding to GPCRs (with cited numbers varying from 30–50%). Closer scrutiny, however, shows that only a modest fraction of (~60) GPCRs are, in fact, exploited as drug targets, only ~20 of which are peptide-binding receptors. The vast majority of receptors in the humane genome have not yet been explored as sites of action for drugs. Given the drugability of this receptor class, it appears that opportunities for drug discovery abound. In addition, GPCRs provide for binding sites other than the ligand binding sites (referred to as the “orthosteric site”). These additional sites include (i) binding sites for ligands (referred to as “allosteric ligands”) that modulate the affinity and efficacy of orthosteric ligands, (ii) the interaction surface that recruits G proteins and arrestins, (iii) the interaction sites of additional proteins (GIPs, GPCR interacting proteins that regulate G protein signaling or give rise to G protein-independent signals). These sites can also be targeted by peptides. Combinatorial and natural peptide libraries are therefore likely to play a major role in identifying new GPCR ligands at each of these sites. In particular the diverse natural peptide libraries such as the venom peptides from marine cone-snails and plant cyclotides have been established as a rich source of drug leads. High-throughput screening and combinatorial chemistry approaches allow for progressing from these starting points to potential drug candidates. This will be illustrated by focusing on the ligand-based drug design of oxytocin (OT) and vasopressin (AVP) receptor ligands using natural peptide leads as starting points. PMID:20687879

  6. FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections

    PubMed Central

    Alam, Khalid K; Chang, Jonathan L; Burke, Donald H

    2015-01-01

    High-throughput sequence (HTS) analysis of combinatorial selection populations accelerates lead discovery and optimization and offers dynamic insight into selection processes. An underlying principle is that selection enriches high-fitness sequences as a fraction of the population, whereas low-fitness sequences are depleted. HTS analysis readily provides the requisite numerical information by tracking the evolutionary trajectory of individual sequences in response to selection pressures. Unlike genomic data, for which a number of software solutions exist, user-friendly tools are not readily available for the combinatorial selections field, leading many users to create custom software. FASTAptamer was designed to address the sequence-level analysis needs of the field. The open source FASTAptamer toolkit counts, normalizes and ranks read counts in a FASTQ file, compares populations for sequence distribution, generates clusters of sequence families, calculates fold-enrichment of sequences throughout the course of a selection and searches for degenerate sequence motifs. While originally designed for aptamer selections, FASTAptamer can be applied to any selection strategy that can utilize next-generation DNA sequencing, such as ribozyme or deoxyribozyme selections, in vivo mutagenesis and various surface display technologies (peptide, antibody fragment, mRNA, etc.). FASTAptamer software, sample data and a user's guide are available for download at http://burkelab.missouri.edu/fastaptamer.html. PMID:25734917

  7. Motor imagery classification via combinatory decomposition of ERP and ERSP using sparse nonnegative matrix factorization.

    PubMed

    Lu, Na; Yin, Tao

    2015-07-15

    Brain activities could be measured by devices like EEG, MEG, MRI etc. in terms of electric or magnetic signal, which could provide information from three domains, i.e., time, frequency and space. Combinatory analysis of these features could definitely help to improve the classification performance on brain activities. NMF (nonnegative matrix factorization) has been widely applied in pattern extraction tasks (e.g., face recognition, gene data analysis) which could provide physically meaningful explanation of the data. However, brain signals also take negative values, so only spectral feature has been employed in existing NMF studies for brain computer interface. In addition, sparsity is an intrinsic characteristic of electric signals. To incorporate sparsity constraint and enable analysis of time domain feature using NMF, a new solution for motor imagery classification is developed, which combinatorially analyzes the ERP (event related potential, time domain) and ERSP (event related spectral perturbation, frequency domain) features via a modified mixed alternating least square based NMF method (MALS-NMF for short). Extensive experiments have verified the effectivity the proposed method. The results also showed that imposing sparsity constraint on the coefficient matrix in ERP factorization and basis matrix in ERSP factorization could better improve the algorithm performance. Comparisons with other eight representative methods have further verified the superiority of the proposed method. The MALS-NMF method is an effective solution for motor imagery classification and has shed some new light into the field of brain dynamics pattern analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Combinatorial Investigations of High Temperature CuNb Oxide Phases for Photoelectrochemical Water Splitting.

    PubMed

    Skorupska, Katarzyna; Maggard, Paul A; Eichberger, Rainer; Schwarzburg, Klaus; Shahbazi, Paria; Zoellner, Brandon; Parkinson, Bruce A

    2015-12-14

    High-throughput combinatorial methods have been useful in identifying new oxide semiconductors with the potential to be applied to solar water splitting. Most of these techniques have been limited to producing and screening oxide phases formed at temperatures below approximately 550 °C. We report the development of a combinatorial approach to discover and optimize high temperature phases for photoelectrochemical water splitting. As a demonstration material, we chose to produce thin films of high temperature CuNb oxide phases by inkjet printing on two different substrates: fluorine-doped tin oxide and crystalline Si, which required different sample pyrolysis procedures. The selection of pyrolysis parameters, such as temperature/time programs, and the use of oxidizing, nonreactive or reducing atmospheres determines the composition of the thin film materials and their photoelectrochemical performance. XPS, XRD, and SEM analyses were used to determine the composition and oxidation states within the copper niobium oxide phases and to then guide the production of target Cu(1+)Nb(5+)-oxide phases. The charge carrier dynamics of the thin films produced by the inkjet printing are compared with pure CuNbO3 microcrystalline material obtained from inorganic bulk synthesis.

  9. Parallel Combinatorial Synthesis of Azo Dyes: A Combinatorial Experiment Suitable for Undergraduate Laboratories

    ERIC Educational Resources Information Center

    Gung, Benjamin W.; Taylor, Richard T.

    2004-01-01

    An experiment in the parallel synthesis of azo dyes that demonstrates the concepts of structure-activity relationships and chemical diversity with vivid colors is described. It is seen that this experiment is suitable for the second-semester organic chemistry laboratory and also for the one-semester organic laboratory.

  10. Parallel Combinatorial Synthesis of Azo Dyes: A Combinatorial Experiment Suitable for Undergraduate Laboratories

    ERIC Educational Resources Information Center

    Gung, Benjamin W.; Taylor, Richard T.

    2004-01-01

    An experiment in the parallel synthesis of azo dyes that demonstrates the concepts of structure-activity relationships and chemical diversity with vivid colors is described. It is seen that this experiment is suitable for the second-semester organic chemistry laboratory and also for the one-semester organic laboratory.

  11. Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics.

    PubMed

    Ufimtsev, Ivan S; Martinez, Todd J

    2009-10-13

    We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.

  12. NON-EQUILIBRIUM CHEMISTRY OF DYNAMICALLY EVOLVING PRESTELLAR CORES. I. BASIC MAGNETIC AND NON-MAGNETIC MODELS AND PARAMETER STUDIES

    SciTech Connect

    Tassis, Konstantinos; Willacy, Karen; Yorke, Harold W.; Turner, Neal J.

    2012-07-01

    We combine dynamical and non-equilibrium chemical modeling of evolving prestellar molecular cloud cores and investigate the evolution of molecular abundances in the contracting core. We model both magnetic cores, with varying degrees of initial magnetic support, and non-magnetic cores, with varying collapse delay times. We explore, through a parameter study, the competing effects of various model parameters in the evolving molecular abundances, including the elemental C/O ratio, the temperature, and the cosmic-ray ionization rate. We find that different models show their largest quantitative differences at the center of the core, whereas the outer layers, which evolve slower, have abundances which are severely degenerate among different dynamical models. There is a large range of possible abundance values for different models at a fixed evolutionary stage (central density), which demonstrates the large potential of chemical differentiation in prestellar cores. However, degeneracies among different models, compounded with uncertainties induced by other model parameters, make it difficult to discriminate among dynamical models. To address these difficulties, we identify abundance ratios between particular molecules, the measurement of which would have maximal potential for discrimination among the different models examined here. In particular, we find that the ratios between NH{sub 3} and CO, NH{sub 2} and CO, and NH{sub 3} and HCO{sup +} are sensitive to the evolutionary timescale, and that the ratio between HCN and OH is sensitive to the C/O ratio. Finally, we demonstrate that measurements of the central deviation (central depletion or enhancement) of abundances of certain molecules are good indicators of the dynamics of the core.

  13. Influence of boundary layer dynamics and isoprene chemistry on the organic aerosol budget: a case study for a tropical forest and implications for the SE US

    NASA Astrophysics Data System (ADS)

    Janssen, R.; Vila-Guerau Arellano, J.; Jimenez, J. L.; Ganzeveld, L.; Robinson, N.; Allan, J. D.; Coe, H.; Pugh, T.

    2013-12-01

    We studied the organic aerosol (OA) budget in a tropical forest by analyzing a case that is representative for the OP3 campaign at Borneo. When interpreting observations of chemical species made in the atmospheric boundary layer (ABL), it is important to realize that the evolution of those species is a function of chemical conversion, emission/deposition, advection, and the vertical exchange of compounds between the free troposphere (FT) and the ABL driven by entrainment, and gas/particle-partitioning in case of secondary organic aerosol (SOA). Therefore, we designed a model that combines the essential dynamical and chemical processes that drive the diurnal evolution of reactants in the ABL. In this way, the model simultaneously represents the effects and interactions of various dynamical and chemical factors on the OA budget. Our model is able to reproduce the observed diurnal dynamics of the ABL, including the evolution of most chemical species involved in SOA formation. A budget analysis of the contributions of the dynamical and chemical processes reveals the significance of the entrainment process in the diurnal evolution of OA, which shows that the ABL dynamics cannot be neglected when interpreting OA observations during field campaigns. Further, we perform a series of sensitivity analyses to determine the effect of isoprene chemical pathways on the OA budget. First, we study the significance of SOA formation through the reactive uptake of isoprene epoxydiols (IEPOX) on acidic sulfate aerosol. Although the low-NOx pathways that leads to the formation of IEPOX is only of minor significance for the reactivity of the isoprene peroxy radicals, the amount of SOA formed through this pathway represents about half of the observed OA. This suggests that a minor pathway in the gas-phase chemistry of isoprene can still lead to substantial SOA formation. Finally, we find that recycling of the OH radical in the oxidation of isoprene may affect the amount of SOA that is

  14. Circumstellar chemistry

    NASA Technical Reports Server (NTRS)

    Glassgold, Alfred E.; Huggins, Patrick J.

    1987-01-01

    The study of the outer envelopes of cool evolved stars has become an active area of research. The physical properties of CS envelopes are presented. Observations of many wavelengths bands are relevant. A summary of observations and a discussion of theoretical considerations concerning the chemistry are summarized. Recent theoretical considerations show that the thermal equilibrium model is of limited use for understanding the chemistry of the outer CS envelopes. The theoretical modeling of the chemistry of CS envelopes provides a quantitive test of chemical concepts which have a broader interest than the envelopes themselves.

  15. EDITORIAL: Combinatorial and High-Throughput Materials Research

    NASA Astrophysics Data System (ADS)

    Potyrailo, Radislav A.; Takeuchi, Ichiro

    2005-01-01

    The success of combinatorial and high-throughput methodologies relies greatly on the availability of various characterization tools with new and improved capabilities [1]. Indeed, how useful can a combinatorial library of 250, 400, 25 000 or 2 000 000 compounds be [2-5] if one is unable to characterize its properties of interest fairly quickly? How useful can a set of thousands of spectra or chromatograms be if one is unable to analyse them in a timely manner? For these reasons, the development of new approaches for materials characterization is one of the most active areas in combinatorial materials science. The importance of this aspect of research in the field has been discussed in numerous conferences including the Pittsburgh Conferences, the American Chemical Society Meetings, the American Physical Society Meetings, the Materials Research Society Symposia and various Gordon Research Conferences. Naturally, the development of new measurement instrumentation attracts the attention not only of practitioners of combinatorial materials science but also of those who design new software for data manipulation and mining. Experimental designs of combinatorial libraries are pursued with available and realistic synthetic and characterization capabilities in mind. It is becoming increasingly critical to link the design of new equipment for high-throughput parallel materials synthesis with integrated measurement tools in order to enhance the efficacy of the overall experimental strategy. We have received an overwhelming response to our proposal and call for papers for this Special Issue on Combinatorial Materials Science. The papers in this issue of Measurement Science and Technology are a very timely collection that captures the state of modern combinatorial materials science. They demonstrate the significant advances that are taking place in the field. In some cases, characterization tools are now being operated in the factory mode. At the same time, major challenges

  16. Extending students' practice of metacognitive regulation strategies in the undergraduate chemistry laboratory and investigation of Pb2+ binding to calmodulin with circular dichroism and molecular dynamics modeling

    NASA Astrophysics Data System (ADS)

    Valencia Navarro, Laura N.

    The following dissertation was composed of two projects in chemistry education and benchwork/computational biochemistry. The chemistry education research explored students' practice of metacognitive strategies while solving open-ended laboratory problems when engaged in an instructional environment, the Science Writing Heuristic (SWH), that was characterized as supporting metacognitive regulation strategy use. Through in-depth interviews with students, results demonstrated that students in the SWH environment, compared to non-SWH students, used metacognitive strategies to a greater degree and to a greater depth when solving open-ended laboratory problems. As students engaged in higher levels of metacognitive regulation, their elective use of peers became a prominent path for supporting the practice of metacognitive strategies. Students claimed that the structure of the SWH weekly laboratory experiments improved their ability to solve open-ended lab problems. This research not only provided a lens into students' descriptions of their regulation strategy practices in the laboratory, but it also supported that the way that a laboratory environment is arranged can affect these regulation strategy practices and their transfer to new situations. In the biochemical study on the binding of Pb2+ to calmodulin (CaM), data was acquired via circular dichroism (CD) and molecular dynamics modeling. CD signal data indicated a unique signal from Pb-CaM and a significantly smaller ratio theta208/theta222 for Pb-CaM than Ca-CaM. An analysis of secondary structure content indicated that alpha-helical structure decreased and random coil structure increased when CaM was saturated with Pb2+ compared to Ca2+ saturated CaM. A molecular dynamics simulation of Pb2+ binding to CaM showed that Pb2+ ions bound to sites outside of the known canonical binding sites including the linker region, and indicated change in secondary structure. These results support the theory of opportunistic binding

  17. Modelling non-equilibrium secondary organic aerosol formation and evaporation with the aerosol dynamics, gas- and particle-phase chemistry kinetic multi-layer model ADCHAM

    NASA Astrophysics Data System (ADS)

    Roldin, P.; Eriksson, A. C.; Nordin, E. Z.; Hermansson, E.; Mogensen, D.; Rusanen, A.; Boy, M.; Swietlicki, E.; Svenningsson, B.; Zelenyuk, A.; Pagels, J.

    2014-01-01

    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. ADCHAM is able to capture the observed α-pinene SOA mass increase in the presence of NH3(g). Organic salts of ammonium and carboxylic acids predominantly form during the early stage of SOA formation. These salts contribute substantially to the initial growth of the homogeneously nucleated particles. The model simulations of evaporating α-pinene SOA particles support the recent experimental findings that these particles have a semi-solid tar like amorphous phase state. ADCHAM is able to reproduce the main features of the observed slow evaporation rates if low-volatility and viscous oligomerized SOA material accumulates in the particle surface layer upon evaporation. The evaporation rate is mainly governed by the reversible decomposition of oligomers back to monomers. Finally, we demonstrate that the mass transfer limited uptake of condensable organic compounds onto wall deposited particles or directly onto the Teflon chamber walls of smog chambers can have profound influence on the

  18. Basic Studies in Combinatorial and Nondifferentiable Optimization.

    DTIC Science & Technology

    1978-03-01

    control problems with linear dynamics, convex cost, and convex inequality state and control constraints is analyzed...points. S.K. MITTER, Lagrange Duality Theory for Convex Control Problems , (with W.W. Hager), Journal of Control and Optimization , 14, August 1976, pp...Lagrange Duality Theory for Convex Control Problems ,” Journal of Control and Optimization , 14, August 1976, pp. 843—856. T.

  19. Quantum adiabatic optimization and combinatorial landscapes

    NASA Astrophysics Data System (ADS)

    Smelyanskiy, V. N.; Knysh, S.; Morris, R. D.

    2004-09-01

    In this paper we analyze the performance of the Quantum Adiabatic Evolution algorithm on a variant of the satisfiability problem for an ensemble of random graphs parametrized by the ratio of clauses to variables, γ=M/N . We introduce a set of macroscopic parameters (landscapes) and put forward an ansatz of universality for random bit flips. We then formulate the problem of finding the smallest eigenvalue and the excitation gap as a statistical mechanics problem. We use the so-called annealing approximation with a refinement that a finite set of macroscopic variables (instead of only energy) is used, and are able to show the existence of a dynamic threshold γ=γd starting with some value of K —the number of variables in each clause. Beyond the dynamic threshold, the algorithm should take an exponentially long time to find a solution. We compare the results for extended and simplified sets of landscapes and provide numerical evidence in support of our universality ansatz. We have been able to map the ensemble of random graphs onto another ensemble with fluctuations significantly reduced. This enabled us to obtain tight upper bounds on the satisfiability transition and to recompute the dynamical transition using the extended set of landscapes.

  20. Chemistry and isotopic composition of precipitation and surface waters in Khumbu valley (Nepal Himalaya): N dynamics of high elevation basins.

    PubMed

    Balestrini, Raffaella; Polesello, Stefano; Sacchi, Elisa

    2014-07-01

    We monitored the chemical and isotopic compositions of wet depositions, at the Pyramid International Laboratory (5050 ma.s.l.), and surrounding surface waters, in the Khumbu basin, to understand precipitation chemistry and to obtain insights regarding ecosystem responses to atmospheric inputs. The major cations in the precipitation were NH4(+) and Ca(2+), whereas the main anion was HCO3(-), which constituted approximately 69% of the anions, followed by NO3(-), SO4(2-) and Cl(-). Data analysis suggested that Na(+), Cl(-) and K(+) were derived from the long-range transport of marine aerosols. Ca(2+), Mg(2+) and HCO3(-) were related to rock and soil dust contributions and the NO3(-) and SO4(2-) concentrations were derived from anthropogenic sources. Furthermore, NH4(+) was derived from gaseous NH3 scavenging. The isotopic composition of weekly precipitation ranged from -1.9 to -23.2‰ in δ(18)O, and from -0.8 to -174‰ in δ(2)H, with depleted values characterizing the central part of the monsoon period. The chemical composition of the stream water was dominated by calcite and/or gypsum dissolution. However, the isotopic composition of the stream water did not fully reflect the composition of the monsoon precipitation, which suggested that other water sources contributed to the stream flow. Precipitation contents for all ions were the lowest ones among those measured in high elevation sites around the world. During the monsoon periods the depositions were not substantially influenced by anthropogenic inputs, while in pre- and post-monsoon seasons the Himalayas could not represent an effective barrier for airborne pollution. In the late monsoon phase, the increase of ionic contents in precipitation could also be due to a change in the moisture source. The calculated atmospheric N load (0.30 kg ha(-1) y(-1)) was considerably lower than the levels that were measured in other high-altitude environments. Nevertheless, the NO3(-) concentrations in the surface waters

  1. Trace Chemistry

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan; Whitefield, Philip

    1999-01-01

    , in addition, of the pressure, temperature, and velocity. A near term goal of the experimental program should be to confirm the nonlinear effects of sulfur speciation, and if present, to provide an explanation for them. It is also desirable to examine if the particulate matter retains any sulfur. The recommendation is to examine the effects on SOx production of variations in fuel-bound sulfur and aromatic content (which may affect the amount of particulates formed). These experiments should help us to understand if there is a coupling between particulate formation and SO, concentration. Similarly, any coupling with NOx can be examined either by introducing NOx into the combustion air or by using fuel-bound nitrogen. Also of immediate urgency is the need to establish and validate a detailed mechanism for sulfur oxidation/aerosol formation, whose chemistry is concluded to be homogeneous, because there is not enough surface area for heterogeneous effects. It is envisaged that this work will involve both experimental and theoretical programs. The experimental work will require, in addition to the measurements described above, fundamental studies in devices such as flow reactors and shock tubes. Complementing this effort should be modeling and theoretical activities. One impediment to the successful modeling of sulfur oxidation is the lack of reliable data for thermodynamic and transport properties for several species, such as aqueous nitric acid, sulfur oxides, and sulfuric acid. Quantum mechanical calculations are recommended as a convenient means of deriving values for these properties. Such calculations would also help establish rate constants for several important reactions for which experimental measurements are inherently fraught with uncertainty. Efforts to implement sufficiently detailed chemistry into computational fluid dynamic codes should be continued. Zero- and one-dimensional flow models are also useful vehicles for elucidating the minimal set of species and

  2. Trace Chemistry

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan; Whitefield, Philip

    1999-01-01

    , in addition, of the pressure, temperature, and velocity. A near term goal of the experimental program should be to confirm the nonlinear effects of sulfur speciation, and if present, to provide an explanation for them. It is also desirable to examine if the particulate matter retains any sulfur. The recommendation is to examine the effects on SOx production of variations in fuel-bound sulfur and aromatic content (which may affect the amount of particulates formed). These experiments should help us to understand if there is a coupling between particulate formation and SO, concentration. Similarly, any coupling with NOx can be examined either by introducing NOx into the combustion air or by using fuel-bound nitrogen. Also of immediate urgency is the need to establish and validate a detailed mechanism for sulfur oxidation/aerosol formation, whose chemistry is concluded to be homogeneous, because there is not enough surface area for heterogeneous effects. It is envisaged that this work will involve both experimental and theoretical programs. The experimental work will require, in addition to the measurements described above, fundamental studies in devices such as flow reactors and shock tubes. Complementing this effort should be modeling and theoretical activities. One impediment to the successful modeling of sulfur oxidation is the lack of reliable data for thermodynamic and transport properties for several species, such as aqueous nitric acid, sulfur oxides, and sulfuric acid. Quantum mechanical calculations are recommended as a convenient means of deriving values for these properties. Such calculations would also help establish rate constants for several important reactions for which experimental measurements are inherently fraught with uncertainty. Efforts to implement sufficiently detailed chemistry into computational fluid dynamic codes should be continued. Zero- and one-dimensional flow models are also useful vehicles for elucidating the minimal set of species and

  3. The molecular dissociation of formaldehyde at medium photoexcitation energies: A quantum chemistry and direct quantum dynamics study

    SciTech Connect

    Araujo, Marta; Magalhaes, Alexandre L.; Lasorne, Benjamin; Worth, Graham A.; Bearpark, Michael J.; Robb, Michael A.

    2009-10-14

    The mechanisms of radiationless decay involved in the photodissociation of formaldehyde into H{sub 2} and CO have been investigated using complete active space self-consistent field (CASSCF) calculations and direct dynamics variational multiconfiguration Gaussian (DD-vMCG) quantum dynamics in the S{sub 1}, T{sub 1}, and S{sub 0} states. A commonly accepted scheme involves Fermi Golden Rule internal conversion from S{sub 1} followed by dissociation of vibrationally hot H{sub 2}CO in S{sub 0}. We recently proposed a novel mechanism [M. Araujo et al., J. Phys. Chem. A 112, 7489 (2008)] whereby internal conversion and dissociation take place in concert through a seam of conical intersection between S{sub 1} and S{sub 0} after the system has passed through an S{sub 1} transition barrier. The relevance of this mechanism depends on the efficiency of tunneling in S{sub 1}. At lower energy, an alternative scheme to internal conversion involves intersystem crossing via T{sub 1} to regenerate the reactant before the S{sub 0} barrier to dissociation. We propose here a previously unidentified mechanism leading directly to H{sub 2} and CO products via T{sub 1}. This channel opens at medium energies, near or above the T{sub 1} barrier to dissociation and still lower than the S{sub 1} barrier, thus making T{sub 1} a possible shortcut to molecular dissociation.

  4. Catalytic Chemistry.

    ERIC Educational Resources Information Center

    Borer, Londa; And Others

    1996-01-01

    Describes an approach for making chemistry relevant to everyday life. Involves the study of kinetics using the decomposition of hydrogen peroxide by vegetable juices. Allows students to design and carry out experiments and then draw conclusions from their results. (JRH)

  5. Nuclear Chemistry.

    ERIC Educational Resources Information Center

    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)

  6. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Describes 13 activities, experiments and demonstrations, including the preparation of iron (III) chloride, simple alpha-helix model, investigating camping gas, redox reactions of some organic compounds, a liquid crystal thermometer, and the oxidation number concept in organic chemistry. (JN)

  7. Precolumbian Chemistry.

    ERIC Educational Resources Information Center

    Robinson, Janet Bond

    1995-01-01

    Describes the content and development of a curriculum that provides an approach to descriptive chemistry and the history of technology through consideration of the pottery, metallurgy, pigments, dyes, agriculture, and medicine of pre-Columbian people. (DDR)

  8. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1980

    1980-01-01

    Describes equipment, activities, and experiments useful in chemistry instruction, including among others, a rapid method to determine available chlorine in bleach, simple flame testing apparatus, and a simple apparatus demonstrating the technique of flash photolysis. (SK)

  9. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1973

    1973-01-01

    Several ideas are proposed for chemistry teachers to try in their classrooms. Subjects included are polymerization of acrylate, polymerization of styrene, conductivity, pollution, preparation of chlorine, redox equations, chemiluminescence, and molecular sieves. (PS)

  10. Catalytic Chemistry.

    ERIC Educational Resources Information Center

    Borer, Londa; And Others

    1996-01-01

    Describes an approach for making chemistry relevant to everyday life. Involves the study of kinetics using the decomposition of hydrogen peroxide by vegetable juices. Allows students to design and carry out experiments and then draw conclusions from their results. (JRH)

  11. Nuclear Chemistry.

    ERIC Educational Resources Information Center

    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)

  12. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1973

    1973-01-01

    Several ideas are proposed for chemistry teachers to try in their classrooms. Subjects included are polymerization of acrylate, polymerization of styrene, conductivity, pollution, preparation of chlorine, redox equations, chemiluminescence, and molecular sieves. (PS)

  13. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1980

    1980-01-01

    Describes equipment, activities, and experiments useful in chemistry instruction, including among others, a rapid method to determine available chlorine in bleach, simple flame testing apparatus, and a simple apparatus demonstrating the technique of flash photolysis. (SK)

  14. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Describes 13 activities, experiments and demonstrations, including the preparation of iron (III) chloride, simple alpha-helix model, investigating camping gas, redox reactions of some organic compounds, a liquid crystal thermometer, and the oxidation number concept in organic chemistry. (JN)

  15. Precolumbian Chemistry.

    ERIC Educational Resources Information Center

    Robinson, Janet Bond

    1995-01-01

    Describes the content and development of a curriculum that provides an approach to descriptive chemistry and the history of technology through consideration of the pottery, metallurgy, pigments, dyes, agriculture, and medicine of pre-Columbian people. (DDR)

  16. Stratospheric chemistry

    NASA Astrophysics Data System (ADS)

    Brune, William H.

    Advances in stratospheric chemistry made by investigators in the United States from 1987 to 1990 are reviewed. Subject areas under consideration include photochemistry of the polar stratosphere, photochemistry of the global stratosphere, and assessments of inadvertent modification of the stratosphere by anthropogenic activity. Particular attention is given to early observations and theories, gas phase chemistry, Antarctic observations, Arctic observations, odd-oxygen, odd-hydrogen, odd-nitrogen, halogens, aerosols, modeling of stratospheric ozone, and reactive nitrogen effects.

  17. Stratospheric chemistry

    SciTech Connect

    Brune, W.H. )

    1991-01-01

    Advances in stratospheric chemistry made by investigators in the United States from 1987 to 1990 are reviewed. Subject areas under consideration include photochemistry of the polar stratosphere, photochemistry of the global stratosphere, and assessments of inadvertent modification of the stratosphere by anthropogenic activity. Particular attention is given to early observations and theories, gas phase chemistry, Antarctic observations, Arctic observations, odd-oxygen, odd-hydrogen, odd-nitrogen, halogens, aerosols, modeling of stratospheric ozone, and reactive nitrogen effects.

  18. Ab initio multiple spawning dynamics study of dimethylnitramine and dimethylnitramine-Fe complex to model their ultrafast nonadiabatic chemistry

    NASA Astrophysics Data System (ADS)

    Bera, Anupam; Ghosh, Jayanta; Bhattacharya, Atanu

    2017-07-01

    Conical intersections are now firmly established to be the key features in the excited electronic state processes of polyatomic energetic molecules. In the present work, we have explored conical intersection-mediated nonadiabatic chemical dynamics of a simple analogue nitramine molecule, dimethylnitramine (DMNA, containing one N-NO2 energetic group), and its complex with an iron atom (DMNA-Fe). For this task, we have used the ab initio multiple spawning (AIMS) dynamics simulation at the state averaged-complete active space self-consistent field(8,5)/6-31G(d) level of theory. We have found that DMNA relaxes back to the ground (S0) state following electronic excitation to the S1 excited state [which is an (n,π*) excited state] with a time constant of approximately 40 fs. This AIMS result is in very good agreement with the previous surface hopping-result and femtosecond laser spectroscopy result. DMNA does not dissociate during this fast internal conversion from the S1 to the S0 state. DMNA-Fe also undergoes extremely fast relaxation from the upper S1 state to the S0 state; however, this relaxation pathway is dissociative in nature. DMNA-Fe undergoes initial Fe-O, N-O, and N-N bond dissociations during relaxation from the upper S1 state to the ground S0 state through the respective conical intersection. The AIMS simulation reveals the branching ratio of these three channels as N-N:Fe-O:N-O = 6:3:1 (based on 100 independent simulations). Furthermore, the AIMS simulation reveals that the Fe-O bond dissociation channel exhibits the fastest (time constant 24 fs) relaxation, while the N-N bond dissociation pathway features the slowest (time constant 128 fs) relaxation. An intermediate time constant (30 fs) is found for the N-O bond dissociation channel. This is the first nonadiabatic chemical dynamics study of metal-contained energetic molecules through conical intersections.

  19. Time-resolved radiation chemistry: Dynamics of electron attachment to uracil following UV excitation of iodide-uracil complexes

    SciTech Connect

    King, Sarah B.; Yandell, Margaret A.; Stephansen, Anne B.; Neumark, Daniel M.

    2014-12-14

    Electron attachment to uracil was investigated by applying time-resolved photoelectron imaging to iodide-uracil (I{sup –}U) complexes. In these studies, an ultraviolet pump pulse initiated charge transfer from the iodide to the uracil, and the resulting dynamics of the uracil temporary negative ion were probed. Five different excitation energies were used, 4.00 eV, 4.07 eV, 4.14 eV, 4.21 eV, and 4.66 eV. At the four lowest excitation energies, which lie near the vertical detachment energy of the I{sup –}U complex (4.11 eV), signatures of both the dipole bound (DB) as well as the valence bound (VB) anion of uracil were observed. In contrast, only the VB anion was observed at 4.66 eV, in agreement with previous experiments in this higher energy range. The early-time dynamics of both states were highly excitation energy dependent. The rise time of the DB anion signal was ∼250 fs at 4.00 eV and 4.07 eV, ∼120 fs at 4.14 eV and cross-correlation limited at 4.21 eV. The VB anion rise time also changed with excitation energy, ranging from 200 to 300 fs for excitation energies 4.00–4.21 eV, to a cross-correlation limited time at 4.66 eV. The results suggest that the DB state acts as a “doorway” state to the VB anion at 4.00–4.21 eV, while direct attachment to the VB anion occurs at 4.66 eV.

  20. Towards Teaching Chemistry as a Language

    NASA Astrophysics Data System (ADS)

    Laszlo, Pierre

    2013-07-01

    This paper presents views on the teaching of chemistry and directions for its further development. A detailed critical analysis is offered for the inadequacy of much of the current teaching, weighed that it is by a conventional, traditional and, as it turns out, rather outdated sense of the material to be covered. The ambient meta-discourse on the nature of chemistry is unduly dominated by the physicalist assumption, believing chemistry to be reducible to physics, which I hold to be unrefutable and thus parascientific. This all-too-tenuous link is countered with a parallel, bolstered by a slew of examples and analogies, between chemistry and linguistics: it is both more legitimate, in terms of the supporting evidence, considerably more effective than a physicalist approach. Chemical teaching needs to hybridize the bottom-up and the top-down communication vectors between the students and their teacher. It can only benefit from infusion of a strong dose of history. Chemistry ought to be taught in like manner to a language, on the dual evidence of the existence of an iconic chemical language, of formulas and equations; and of chemical science being language-like and a combinatorial art.