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Sample records for dynamic combinatorial chemistry

  1. 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…

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

    PubMed

    Huang, Renjie; Leung, Ivanhoe K H

    2016-01-01

    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. PMID:27438816

  3. 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

  4. Algorithmic Strategies in Combinatorial Chemistry

    SciTech Connect

    GOLDMAN,DEBORAH; ISTRAIL,SORIN; LANCIA,GIUSEPPE; PICCOLBONI,ANTONIO; WALENZ,BRIAN

    2000-08-01

    Combinatorial Chemistry is a powerful new technology in drug design and molecular recognition. It is a wet-laboratory methodology aimed at ``massively parallel'' screening of chemical compounds for the discovery of compounds that have a certain biological activity. The power of the method comes from the interaction between experimental design and computational modeling. Principles of ``rational'' drug design are used in the construction of combinatorial libraries to speed up the discovery of lead compounds with the desired biological activity. This paper presents algorithms, software development and computational complexity analysis for problems arising in the design of combinatorial libraries for drug discovery. The authors provide exact polynomial time algorithms and intractability results for several Inverse Problems-formulated as (chemical) graph reconstruction problems-related to the design of combinatorial libraries. These are the first rigorous algorithmic results in the literature. The authors also present results provided by the combinatorial chemistry software package OCOTILLO for combinatorial peptide design using real data libraries. The package provides exact solutions for general inverse problems based on shortest-path topological indices. The results are superior both in accuracy and computing time to the best software reports published in the literature. For 5-peptoid design, the computation is rigorously reduced to an exhaustive search of about 2% of the search space; the exact solutions are found in a few minutes.

  5. 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. PMID:24296754

  6. 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.

  7. 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. PMID:26014116

  8. Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment-Based Drug Design Facilitated by Dynamic Combinatorial Chemistry.

    PubMed

    Mondal, Milon; Radeva, Nedyalka; Fanlo-Virgós, Hugo; Otto, Sijbren; Klebe, Gerhard; Hirsch, Anna K H

    2016-08-01

    Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X-ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization. PMID:27400756

  9. Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries

    PubMed Central

    Diemer, Sanna L.; Kristensen, Morten; Rasmussen, Brian; Beeren, Sophie R.; Pittelkow, Michael

    2015-01-01

    Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs) ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system. PMID:26378519

  10. 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.

  11. Method and apparatus for combinatorial chemistry

    DOEpatents

    Foote, Robert S.

    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.

  12. 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.

  13. Mesofluidic Devices for DNA-Programmed Combinatorial Chemistry

    PubMed Central

    Weisinger, Rebecca M.; Marinelli, Robert J.; Wrenn, S. Jarrett; Harbury, Pehr B.

    2012-01-01

    Hybrid combinatorial chemistry strategies that use DNA as an information-carrying medium are proving to be powerful tools for molecular discovery. In order to extend these efforts, we present a highly parallel format for DNA-programmed chemical library synthesis. The new format uses a standard microwell plate footprint and is compatible with commercially available automation technology. It can accommodate a wide variety of combinatorial synthetic schemes with up to 384 different building blocks per chemical step. We demonstrate that fluidic routing of DNA populations in the highly parallel format occurs with excellent specificity, and that chemistry on DNA arrayed into 384 well plates proceeds robustly, two requirements for the high-fidelity translation and efficient in vitro evolution of small molecules. PMID:22479318

  14. 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.

  15. 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…

  16. 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

  17. Strategies for the discovery of new catalysts with combinatorial chemistry

    NASA Astrophysics Data System (ADS)

    Kirsten, Guido; Maier, Wilhelm F.

    2004-02-01

    The combination of random selection and evolutionary strategies with the high-throughput approaches of combinatorial chemistry is demonstrated for the discovery of new heterogeneous catalysts. An approach entirely based on software control was used and a high degree of automation could be achieved. As model reaction we chose CO-oxidation and used heats of reactions monitored by emissivity corrected IR-thermography as figure of merit. New catalysts compositions have been discovered. The catalytic activity of selected compositions was confirmed by conventional catalyst preparation and testing with a conventional fixed bed reactor. Multi-element materials appear to dominate the catalyst evolution.

  18. Kinetically controlled phenomena in dynamic combinatorial libraries.

    PubMed

    Ji, Qing; Lirag, Rio Carlo; Miljanić, Ognjen Š

    2014-03-21

    Dynamic combinatorial libraries (DCLs) are collections of structurally related compounds that can interconvert through reversible chemical reaction(s). Such reversibility endows DCLs with adaptability to external stimuli, as rapid interconversion allows quick expression of those DCL components which best respond to the disturbing stimulus. This Tutorial Review focuses on the kinetically controlled phenomena that occur within DCLs. Specifically, it will describe dynamic chiral resolution of DCLs, their self-sorting under the influence of irreversible chemical and physical stimuli, and the autocatalytic behaviours within DCLs which can result in self-replicating systems. A brief discussion of precipitation-induced phenomena will follow and the review will conclude with the presentation of covalent organic frameworks (COFs)-porous materials whose synthesis critically depends on the fine tuning of the crystal growth and error correction rates within large DCLs. PMID:24445841

  19. 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.

  20. 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.

  1. Parallel Combinatorial Esterification: A Simple Experiment for Use in the Second-Semester Organic Chemistry Laboratory

    NASA Astrophysics Data System (ADS)

    Birney, David M.; Starnes, Stephen D.

    1999-11-01

    Combinatorial chemistry has revolutionized the way potential new drugs are discovered. This simple experiment utilizes the Fischer esterification, a common reaction in second-semester organic laboratories, to demonstrate the fundamentals of combinatorial methods. These include simultaneous synthesis of numerous compounds, a selective assay for a desired activity, and an algorithm for identifying the active structure. Using a parallel synthesis combinatorial method, each student in a lab section prepares a different ester. The targeted activity (the characteristic odor of wintergreen) is easily detected by smell. The student's enjoyment of the lab is enhanced by the preparation of several other characteristic odors as well.

  2. 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.

  3. Solid-Phase Organic Synthesis and Combinatorial Chemistry: A Laboratory Preparation of Oligopeptides

    NASA Astrophysics Data System (ADS)

    Truran, George A.; Aiken, Karelle S.; Fleming, Thomas R.; Webb, Peter J.; Hodge Markgraf, J.

    2002-01-01

    The principles and practice of solid-phase organic synthesis and combinatorial chemistry are utilized in a laboratory preparation of oligopeptides. A parallel synthesis scheme is used to generate a series of tripeptides. A divergent synthesis scheme is used to prepare two pentapeptides, one of which is leucine enkephalin, a neurotransmitter known to be an analgesic agent.

  4. Late stage modification of receptors identified from dynamic combinatorial libraries.

    PubMed

    Pinkin, Nicholas K; N Power, Amanie; Waters, Marcey L

    2015-11-28

    Small molecule receptors are attractive potential sensors of post-translational modifications, including methylated lysine and methylated arginine. Using dynamic combinatorial chemistry (DCC), our lab previously identified a suite of receptors that bind to Kme3 with a range of affinities ranging from low micromolar to high nanomolar, each with a unique selectivity for Kme3 over the lower methylation states. To enable these receptors to have broad application as Kme3 sensors, we have developed a method for their late-stage modification, which we used to synthesize biotinylated derivatives of A2B, A2D, and A2G in a single step. For our most attractive receptor for applications, A2N, we needed to develop an alternative method for its selective functionalization, which we achieved by "activating" the carboxylic acids on the constituent monomer A or N by pre-functionalizing them with glycine (Gly). Using the resulting Gly-A and Gly-N monomers, we synthesized the novel A2N variants A2Gly-N, Gly-A2N, and Gly-A2Gly-N, which enabled the late stage biotinylation of A2N wherever Gly was incorporated. Finally, we performed ITC and NMR binding experiments to study the effect that carboxylate spacing has on the affinity and selectivity of A2Gly-N and Gly-A2N for KmeX guests compared to A2N. These studies revealed the proximity of the carboxylates to play a complex role in the molecular recognition event, despite their positioning on the outside of the receptor. PMID:26384269

  5. Dynamic combinatorial enrichment of polyconformational D-/L-peptide dimers.

    PubMed

    Jadhav, Kirtikumar B; Lichtenecker, Roman J; Bullach, Anke; Mandal, Bhubaneswar; Arndt, Hans-Dieter

    2015-04-01

    D-/L-peptides such as gramicidin A (gA) adopt unique dimeric β-helical structures of different topologies. To overcome their conformational promiscuity and enrich individual components, a dynamic combinatorial approach assisted by thiol tags was developed. This method led to identification of the preferential formation of antiparallel dimers under a broad range of conditions, which was independent of peptide side-chain polarity. Exclusive formation of an antiparallel cyclic dimer was achieved in the presence of cesium ions. PMID:25711604

  6. Dynamic foldamer chemistry.

    PubMed

    Le Bailly, Bryden A F; Clayden, Jonathan

    2016-04-01

    Foldamers can be made more than pieces of static, conformationally uniform molecular architecture by designing into their structure the conformational dynamism characteristic of functional molecular machines. We show that these dynamic foldamers display biomimetic properties reminiscent of allosteric proteins and receptor molecules. They can translate chemical signals into conformational changes, and hence into chemical outputs such as control of reactivity and selectivity. Future developments could see dynamic foldamers operating in the membrane phase providing artificial mechanisms for communication and control that integrate synthetic chemistry into synthetic biology. PMID:26955864

  7. 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.

  8. Development of combinatorial chemistry methods for coatings: high-throughput weathering evaluation and scale-up of combinatorial leads.

    PubMed

    Potyrailo, Radislav A; Ezbiansky, Karin; Chisholm, Bret J; Morris, William G; Cawse, James N; Hassib, Lamyaa; Medford, George; Reitz, Hariklia

    2005-01-01

    Combinatorial screening of materials formulations followed by the scale-up of combinatorial leads has been applied for the development of high-performance coating materials for automotive applications. We replaced labor-intensive coating formulation, testing, and measurement with a "combinatorial factory" that includes robotic formulation of coatings, their deposition as 48 coatings on a 9x12-cm plastic substrate, accelerated performance testing, and automated spectroscopic and image analysis of resulting performance. This high-throughput (HT) performance testing and measurement of the resulting properties provided a powerful set of tools for the 10-fold accelerated discovery of these coating materials. Performance of coatings is evaluated with respect to their weathering, because this parameter is one of the primary considerations in end-use automotive applications. Our HT screening strategy provides previously unavailable capabilities of (1) high speed and reproducibility of testing by using robotic automation and (2) improved quantification by using optical spectroscopic analysis of discoloration of coating-substrate structure and automatic imaging of the integrity loss of coatings. Upon testing, the coatings undergo changes that are impossible to quantitatively predict using existing knowledge. Using our HT methodology, we have developed several cost-competitive coatings leads that match the performance of more costly coatings. These HT screening results for the best coating compositions have been validated on the traditional scales of coating formulation and weathering testing. These validation results have confirmed the improved weathering performance of combinatorially developed coatings over conventional coatings on the traditional scale. PMID:15762746

  9. 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. PMID:22133077

  10. Combinatorial computational chemistry approach as a promising method for design of Fischer Tropsch catalysts based on Fe and Co

    NASA Astrophysics Data System (ADS)

    Belosludov, Rodion V.; Sakahara, Satoshi; Yajima, Kenji; Takami, Seiichi; Kubo, Momoji; Miyamoto, Akira

    2002-04-01

    The combinatorial computational chemistry approach was applied to design new types of catalysts, which can be used in the Fisher-Tropsh (FT) synthesis for the production of ecologically high-quality transportation fuels. For this purpose, the density functional theory (DFT) was used to investigate the CO adsorption on Fe- and Co-based multi-component catalysts. The energetic, electronic and structural properties of CO on the catalyst surfaces were calculated. It was found that Mn, Mo, and Zr could be used as additional elements in the Fe- and Co-based catalysts, since one cannot observe a degradation of the adsorption properties of the active sites as well as showing a high sulfur tolerance. For the Co-based catalyst, the same tendency is also found in the case of the Si promoter. The obtained results are in agreement with available experimental data that confirmed the validity of combinatorial computational chemistry approach.

  11. 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. PMID:25019572

  12. 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. PMID:25321326

  13. 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…

  14. Combinatorial insulin secretion dynamics of recombinant hepatic and enteroendocrine cells.

    PubMed

    Durvasula, Kiranmai; Thulé, Peter M; Sambanis, Athanassios

    2012-04-01

    One of the most promising cell-based therapies for combating insulin-dependent diabetes entails the use of genetically engineered non-β cells that secrete insulin in response to physiologic stimuli. A normal pancreatic β cell secretes insulin in a biphasic manner in response to glucose. The first phase is characterized by a transient stimulation of insulin to rapidly lower the blood glucose levels, which is followed by a second phase of insulin secretion to sustain the lowered blood glucose levels over a longer period of time. Previous studies have demonstrated hepatic and enteroendocrine cells to be appropriate hosts for recombinant insulin expression. Due to different insulin secretion kinetics from these cells, we hypothesized that a combination of the two cell types would mimic the biphasic insulin secretion of normal β cells with higher fidelity than either cell type alone. In this study, insulin secretion experiments were conducted with two hepatic cell lines (HepG2 and H4IIE) transduced with 1 of 3 adenoviruses expressing the insulin transgene and with a stably transfected recombinant intestinal cell line (GLUTag-INS). Insulin secretion was stimulated by exposing the cells to glucose only (hepatic cells), meat hydrolysate only (GLUTag-INS), or to a cocktail of the two secretagogues. It was found experimentally that the recombinant hepatic cells secreted insulin in a more sustained manner, whereas the recombinant intestinal cell line exhibited rapid insulin secretion kinetics upon stimulation. The insulin secretion profiles were computationally combined at different cell ratios to arrive at the combinatorial kinetics. Results indicate that combinations of these two cell types allow for tuning the first and second phase of insulin secretion better than either cell type alone. This work provides the basic framework in understanding the secretion kinetics of the combined system and advances it towards preclinical studies. PMID:22094821

  15. Combinatorial Insulin Secretion Dynamics of Recombinant Hepatic and Enteroendocrine Cells

    PubMed Central

    Durvasula, Kiranmai; Thulé, Peter M.; Sambanis, Athanassios

    2012-01-01

    One of the more promising cell-based therapies for combating insulin-dependent diabetes entails the use of genetically engineered non-β cells that secrete insulin in response to physiologic stimuli. A normal pancreatic β cell secretes insulin in a biphasic manner in response to glucose. The first phase is characterized by a transient stimulation of insulin to rapidly lower the blood glucose levels, which is followed by a second phase of insulin secretion to sustain the lowered blood glucose levels over a longer period of time. Previous studies have demonstrated hepatic and enteroendocrine cells to be appropriate hosts for recombinant insulin expression. Due to different insulin secretion kinetics from these cells, we hypothesized that a combination of the two cell types would mimic the biphasic insulin secretion of normal β cells with higher fidelity than either cell type alone. In this study, insulin secretion experiments were conducted with two hepatic cell lines (HepG2 and H4IIE) transduced with one of three adenoviruses expressing the insulin transgene and with a stably transfected recombinant intestinal cell line (GLUTag-INS). Insulin secretion was stimulated by exposing the cells to glucose only (hepatic cells), meat hydrolysate only (GLUTag-INS), or to a cocktail of the two secretagogues. It was found experimentally that the recombinant hepatic cells secreted insulin in a more sustained manner, whereas the recombinant intestinal cell line exhibited rapid insulin secretion kinetics upon stimulation. The insulin secretion profiles were computationally combined at different cell ratios to arrive at the combinatorial kinetics. Results indicate that combinations of these two cell types allow for tuning the first and second phase of insulin secretion better than either cell type alone. This work provides the basic framework in understanding the secretion kinetics of the combined system and advances it towards pre-clinical studies. PMID:22094821

  16. LIGNIFICATION: ARE LIGNINS BIOSYNTHESIZED VIA SIMPLE COMBINATORIAL CHEMISTRY OR VIA PROTEINACEOUS CONTROL AND TEMPLATE REPLICATION?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current debate on the mechanism of lignification needs to be scrutinized. In examining arguments raised against the existing Freudenberg theory of chemically-controlled combinatorial synthesis, or for the new contender advocating absolute proteinaceous control, we conclude that the challenger fails ...

  17. Dynamic combinatorial synthesis of a catenane based on donor–acceptor interactions in water

    PubMed Central

    Au-Yeung, Ho Yu; Pantoş, G. Dan; Sanders, Jeremy K. M.

    2009-01-01

    A new type of neutral donor–acceptor [2]-catenane, containing both complementary units in the same ring was synthesized from a dynamic combinatorial library in water. The yield of the water soluble [2]-catenane is enhanced by increasing either building-block concentrations or ionic strength, or by the addition of an electron-rich template. NMR spectroscopy demonstrates that the template is intercalated between the 2 electron-deficient naphthalenediimide units of the catenane. PMID:19171892

  18. Selection dynamic of Escherichia coli host in M13 combinatorial peptide phage display libraries.

    PubMed

    Zanconato, Stefano; Minervini, Giovanni; Poli, Irene; De Lucrezia, Davide

    2011-01-01

    Phage display relies on an iterative cycle of selection and amplification of random combinatorial libraries to enrich the initial population of those peptides that satisfy a priori chosen criteria. The effectiveness of any phage display protocol depends directly on library amino acid sequence diversity and the strength of the selection procedure. In this study we monitored the dynamics of the selective pressure exerted by the host organism on a random peptide library in the absence of any additional selection pressure. The results indicate that sequence censorship exerted by Escherichia coli dramatically reduces library diversity and can significantly impair phage display effectiveness. PMID:21512219

  19. 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.

  20. High-throughput flow cytometric screening of combinatorial chemistry bead libraries for proteomics and drug discovery

    NASA Astrophysics Data System (ADS)

    Leary, James F.; Reece, Lisa M.; Yang, Xian-Bin; Gorenstein, David

    2005-04-01

    For proteomics drug discovery applications, combinatorial microbead thioaptamer libraries (one thioaptamer sequence per bead) are being created by split synthesis method, creating a "proteomics library" of protein capture beads which can be analyzed by high-throughput screening methods in this case, flow cytometry and cell sorting. Thioaptamers, oligonucleotides with thiophosphate backbone substitutions, function like antibodies in terms of recognizing specific protein sequences but have a number of advantages over antibody libraries. These proteomics beads can then be analyzed by high-speed flow cytometry and sorted to single-bead level depending on relative fluorescence brightness of fluorescently-labeled proteins, or for a specific protein from all of the molecules of cell subpopulations being analyzed. The thioaptamer sequences on a given bead showing high affinity for that protein can then be sequenced. Alternatively, the protein-capturing beads can be analyzed by MALDI-TOF mass spectrometry for analysis of the bound proteins. The beads can be thought of as equivalent to single-element positions of a proteomics chip arrays but with the advantage of being able to much more rapidly analyze hundreds of millions of possible amino acid sequences/epitopes on the basis of thioaptamer sequence affinities to select single sequences of interest. Additionally, those beads can be manipulated and isolated at the single bead level by high-throughput flow cytometry/cell sorting for subsequent sequencing of the thioaptamer sequences.

  1. 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.

  2. 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

  3. Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite.

    PubMed

    Saraf, Anita; Cervantes, Serena; Bunnik, Evelien M; Ponts, Nadia; Sardiu, Mihaela E; Chung, Duk-Won D; Prudhomme, Jacques; Varberg, Joseph M; Wen, Zhihui; Washburn, Michael P; Florens, Laurence; Le Roch, Karine G

    2016-08-01

    A major obstacle in understanding the complex biology of the malaria parasite remains to discover how gene transcription is controlled during its life cycle. Accumulating evidence indicates that the parasite's epigenetic state plays a fundamental role in gene expression and virulence. Using a comprehensive and quantitative mass spectrometry approach, we determined the global and dynamic abundance of histones and their covalent post-transcriptional modifications throughout the intraerythrocytic developmental cycle of Plasmodium falciparum. We detected a total of 232 distinct modifications, of which 160 had never been detected in Plasmodium and 88 had never been identified in any other species. We further validated over 10% of the detected modifications and their expression patterns by multiple reaction monitoring assays. In addition, we uncovered an unusual chromatin organization with parasite-specific histone modifications and combinatorial dynamics that may be directly related to transcriptional activity, DNA replication, and cell cycle progression. Overall, our data suggest that the malaria parasite has a unique histone modification signature that correlates with parasite virulence. PMID:27291344

  4. 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.

  5. 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. PMID:24951713

  6. 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.

  7. Development of combinatorial chemistry methods for coatings: high-throughput screening of abrasion resistance of coatings libraries.

    PubMed

    Potyrailo, Radislav A; Chisholm, Bret J; Olson, Daniel R; Brennan, Michael J; Molaison, Chris A

    2002-10-01

    Design, validation, and implementation of an optical spectroscopic system for high-throughput analysis of combinatorially developed protective organic coatings are reported. Our approach replaces labor-intensive coating evaluation steps with an automated system that rapidly analyzes 8 x 6 arrays of coating elements that are discretely deposited on a single plastic substrate. Each coating element of the library is 10 mm in diameter and 2-5 microm thick. Performance of coatings is evaluated with respect to their resistance to wear abrasion because this parameter is one of the primary considerations in end-use applications. Upon testing, the coating materials undergo changes that are impossible to quantitatively predict using existing knowledge. Coatings are abraded using industry-accepted abrasion test methods at a single or multiple abrasion conditions followed by the high-throughput analysis of abrasion-induced light scatter. The developed automated system is optimized for the analysis of diffusively scattered light that corresponds to 0-30% haze. System precision of 0.1-2.5% relative standard deviation provides capability for the reliable ranking of coatings performance. Although the system was implemented for high-throughput screening of combinatorially developed organic protective coatings for automotive applications, it can be applied for a variety of other applications for which materials ranking can be achieved using optical spectroscopic tools. PMID:12380837

  8. From dynamic combinatorial ‘hit’ to lead: in vitro and in vivo activity of compounds targeting the pathogenic RNAs that cause myotonic dystrophy

    PubMed Central

    Ofori, Leslie O.; Hoskins, Jason; Nakamori, Masayuki; Thornton, Charles A.; Miller, Benjamin L.

    2012-01-01

    The myotonic dystrophies (DM) are human diseases in which the accumulation of toxic RNA (CUG or CCUG) repeats in the cell causes sequestration of splicing factors, including MBNL1, leading to clinical symptoms such as muscle wasting and myotonia. We previously used Dynamic Combinatorial Chemistry to identify the first compounds known to inhibit (CUG)-MBNL1 binding in vitro. We now report transformation of those compounds into structures with activity in vivo. Introduction of a benzo[g]quinoline substructure previously unknown in the context of RNA recognition, as well as other modifications, provided several molecules with enhanced binding properties, including compounds with strong selectivity for CUG repeats over CAG repeats or CAG–CUG duplex RNA. Compounds readily penetrate cells, and improve luciferase activity in a mouse myoblast assay in which enzyme function is coupled to a release of nuclear CUG–RNA retention. Most importantly, two compounds are able to partially restore splicing in a mouse model of DM1. PMID:22492623

  9. 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.

  10. 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

  11. 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…

  12. Probing the geometric constraints of RNA binding via dynamic covalent chemistry.

    PubMed

    McAnany, John D; Reichert, John P; Miller, Benjamin L

    2016-09-01

    Dynamic Combinatorial Chemistry (DCC) has proven to be a reliable method for identifying hit compounds for target nucleic acid (DNA and RNA) sequences. Typically, these hit compounds are subjected to a lengthy process of optimization via traditional medicinal chemistry. Here, we examine the potential of DCC to also generate and test variations on a hit compound as a method for probing the binding site of an RNA-targeted compound. Specifically, we demonstrate that addition of linker dithiols to a disulfide library containing a known binder to the HIV-1 frameshift-stimulatory RNA (a critical regulator of the HIV life cycle) can yield a mixture of new bridged structures incorporating the dithiol, depending on dithiol structure. Equilibration of this library with the HIV FSS RNA resulted in selection of the original disulfide in preference to bridged structures, suggesting incorporation of the bridge is not compatible with this particular binding site. Application of this strategy to other RNA targets should allow for rapidly profiling the affinity of modified compounds. PMID:26935941

  13. 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.

  14. 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.

  15. 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

  16. Optimization of Combinatorial Mutagenesis

    NASA Astrophysics Data System (ADS)

    Parker, Andrew S.; Griswold, Karl E.; Bailey-Kellogg, Chris

    Protein engineering by combinatorial site-directed mutagenesis evaluates a portion of the sequence space near a target protein, seeking variants with improved properties (stability, activity, immunogenicity, etc.). In order to improve the hit-rate of beneficial variants in such mutagenesis libraries, we develop methods to select optimal positions and corresponding sets of the mutations that will be used, in all combinations, in constructing a library for experimental evaluation. Our approach, OCoM (Optimization of Combinatorial Mutagenesis), encompasses both degenerate oligonucleotides and specified point mutations, and can be directed accordingly by requirements of experimental cost and library size. It evaluates the quality of the resulting library by one- and two-body sequence potentials, averaged over the variants. To ensure that it is not simply recapitulating extant sequences, it balances the quality of a library with an explicit evaluation of the novelty of its members. We show that, despite dealing with a combinatorial set of variants, in our approach the resulting library optimization problem is actually isomorphic to single-variant optimization. By the same token, this means that the two-body sequence potential results in an NP-hard optimization problem. We present an efficient dynamic programming algorithm for the one-body case and a practically-efficient integer programming approach for the general two-body case. We demonstrate the effectiveness of our approach in designing libraries for three different case study proteins targeted by previous combinatorial libraries - a green fluorescent protein, a cytochrome P450, and a beta lactamase. We found that OCoM worked quite efficiently in practice, requiring only 1 hour even for the massive design problem of selecting 18 mutations to generate 107 variants of a 443-residue P450. We demonstrate the general ability of OCoM in enabling the protein engineer to explore and evaluate trade-offs between quality and

  17. Controlling Chemistry in Dynamic Nanoscale Systems

    NASA Astrophysics Data System (ADS)

    Jesorka, Aldo; Lizana, Ludvig; Konkoli, Zoran; Czolkos, Ilja; Orwar, Owe

    The biological cell, the fundamental building block of the living world, is a complex maze of compartmentalized biochemical reactors that embed tens of thousands of chemical reactions running in parallel. Several, if not all, reactors are systematically interconnected by a web of nanofluidic transporters, such as nanotubes, vesicles, and membrane pores with ever-changing shapes and structures [1]. To initiate, terminate, or control chemical reactions, small-scale poly-/pleiomorphic systems undergo rapid and violent shape changes with energy barriers close to kBT , where, due to the small dimensions, diffusional mixing of reactants is rapid. The geometry, i.e. volume, and shape changes can be utilized to control both kinetic and thermodynamic properties of the system. This is in sharp contrast to the man-made macroscopic bioreactors, in which mixing of reactants is aided by mechanical means, such as stirring or sonication, under the assumption that reactions take place in volumes that do not change over time. Such reaction volumes are compact, like a sphere, a cube, or a cylinder, and do not provide for variation of shape. Ordinarily, reaction rates, mechanisms, and thermodynamic properties of chemical reactions in condensed media are based on these assumptions. A number of important questions and challenges arise from these facts. For example, how will we achieve fundamental understanding of how reactor shape affects chemistry on the nanoscale, how do we develop appropriate and powerful experimental model systems, and last but not least what impact will this knowledge have on the design and function of nanotechnological devices with new operation modes derived from natural principles.

  18. 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

  19. 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

  20. Optimization of combinatorial mutagenesis.

    PubMed

    Parker, Andrew S; Griswold, Karl E; Bailey-Kellogg, Chris

    2011-11-01

    Protein engineering by combinatorial site-directed mutagenesis evaluates a portion of the sequence space near a target protein, seeking variants with improved properties (e.g., stability, activity, immunogenicity). In order to improve the hit-rate of beneficial variants in such mutagenesis libraries, we develop methods to select optimal positions and corresponding sets of the mutations that will be used, in all combinations, in constructing a library for experimental evaluation. Our approach, OCoM (Optimization of Combinatorial Mutagenesis), encompasses both degenerate oligonucleotides and specified point mutations, and can be directed accordingly by requirements of experimental cost and library size. It evaluates the quality of the resulting library by one- and two-body sequence potentials, averaged over the variants. To ensure that it is not simply recapitulating extant sequences, it balances the quality of a library with an explicit evaluation of the novelty of its members. We show that, despite dealing with a combinatorial set of variants, in our approach the resulting library optimization problem is actually isomorphic to single-variant optimization. By the same token, this means that the two-body sequence potential results in an NP-hard optimization problem. We present an efficient dynamic programming algorithm for the one-body case and a practically-efficient integer programming approach for the general two-body case. We demonstrate the effectiveness of our approach in designing libraries for three different case study proteins targeted by previous combinatorial libraries--a green fluorescent protein, a cytochrome P450, and a beta lactamase. We found that OCoM worked quite efficiently in practice, requiring only 1 hour even for the massive design problem of selecting 18 mutations to generate 10⁷ variants of a 443-residue P450. We demonstrate the general ability of OCoM in enabling the protein engineer to explore and evaluate trade-offs between quality and

  1. 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

  2. A combinatorial chemistry approach to new materials for non-linear optics. II. 4-(Dimethylamino)cinnamaldehyde and a molecular complex of 4-methoxycinnamaldehyde with 2,4-dinitroaniline

    PubMed

    Nesterov; Timofeeva; Antipin; Clark

    2000-08-01

    The combinatorial chemistry approach has been used to synthesize an array of Schiff bases. The structures of five of these Schiff bases have been confirmed by X-ray analysis [Nesterov, Timofeeva, Borbulevych, Antipin & Clark (2000). Acta Cryst. C56, 971-975]. In two cases, the reaction conditions were not sufficient to obtain the products in question. In one case, a molecular complex, C(10)H(10)O(2).C(6)H(5)N(3)O(4), of the starting products 4-methoxycinnamaldehyde and 2,4-dinitroaniline was found. X-ray analysis revealed hydrogen-bond formation between the molecules of these reagents in the crystal. In the other case, X-ray analysis demonstrated that no chemical reaction occurred under the reaction conditions, and only one starting reagent, 4-(dimethylamino)cinnamaldehyde, C(11)H(13)NO, was found in the precipitate. PMID:10944294

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. Molecular Dynamics Studies of Thermal Induced Chemistry in Tatb

    NASA Astrophysics Data System (ADS)

    Quenneville, J.; Germann, T. C.; Thompson, A. P.; Kober, E. M.

    2007-12-01

    A reactive force field (ReaxFF) is used with molecular dynamics to probe the chemistry induced by intense heating (`accelerated cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 32-molecule simulations, we calculate the reaction rate as a function of temperature and compare the Arrhenius-predicted activation energy with experiment. Decomposition product evolution (mainly N2, H2O, CO2 and graphitic carbon clusters) is followed using a 576-molecule larger simulation, which also illustrates the effect of system size on both carbon clustering and reaction rate.

  9. 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

  10. 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

  11. Quantitative Reactivity Scales for Dynamic Covalent and Systems Chemistry.

    PubMed

    Zhou, Yuntao; Li, Lijie; Ye, Hebo; Zhang, Ling; You, Lei

    2016-01-13

    Dynamic covalent chemistry (DCC) has become a powerful tool for the creation of molecular assemblies and complex systems in chemistry and materials science. Herein we developed for the first time quantitative reactivity scales capable of correlation and prediction of the equilibrium of dynamic covalent reactions (DCRs). The reference reactions are based upon universal DCRs between imines, one of the most utilized structural motifs in DCC, and a series of O-, N-, and S- mononucleophiles. Aromatic imines derived from pyridine-2-carboxyaldehyde exhibit capability for controlling the equilibrium through distinct substituent effects. Electron-donating groups (EDGs) stabilize the imine through quinoidal resonance, while electron-withdrawing groups (EWGs) stabilize the adduct by enhancing intramolecular hydrogen bonding, resulting in curvature in Hammett analysis. Notably, unique nonlinearity induced by both EDGs and EWGs emerged in Hammett plot when cyclic secondary amines were used. This is the first time such a behavior is observed in a thermodynamically controlled system, to the best of our knowledge. Unified quantitative reactivity scales were proposed for DCC and defined by the correlation log K = S(N) (R(N) + R(E)). Nucleophilicity parameters (R(N) and S(N)) and electrophilicity parameters (R(E)) were then developed from DCRs discovered. Furthermore, the predictive power of those parameters was verified by successful correlation of other DCRs, validating our reactivity scales as a general and useful tool for the evaluation and modeling of DCRs. The reactivity parameters proposed here should be complementary to well-established kinetics based parameters and find applications in many aspects, such as DCR discovery, bioconjugation, and catalysis. PMID:26652793

  12. 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.

  13. 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…

  14. Evolutionary combinatorial chemistry, a novel tool for SAR studies on peptide transport across the blood-brain barrier. Part 2. Design, synthesis and evaluation of a first generation of peptides.

    PubMed

    Teixidó, Meritxell; Belda, Ignasi; Zurita, Esther; Llorà, Xavier; Fabre, Myriam; Vilaró, Senén; Albericio, Fernando; Giralt, Ernest

    2005-12-01

    The use of high-throughput methods in drug discovery allows the generation and testing of a large number of compounds, but at the price of providing redundant information. Evolutionary combinatorial chemistry combines the selection and synthesis of biologically active compounds with artificial intelligence optimization methods, such as genetic algorithms (GA). Drug candidates for the treatment of central nervous system (CNS) disorders must overcome the blood-brain barrier (BBB). This paper reports a new genetic algorithm that searches for the optimal physicochemical properties for peptide transport across the blood-brain barrier. A first generation of peptides has been generated and synthesized. Due to the high content of N-methyl amino acids present in most of these peptides, their syntheses were especially challenging due to over-incorporations, deletions and DKP formations. Distinct fragmentation patterns during peptide cleavage have been identified. The first generation of peptides has been studied by evaluation techniques such as immobilized artificial membrane chromatography (IAMC), a cell-based assay, log Poctanol/water calculations, etc. Finally, a second generation has been proposed. PMID:15942930

  15. Combinatorial Geometry Printer Plotting.

    Energy Science and Technology Software Center (ESTSC)

    1987-01-05

    Picture generates plots of two-dimensional slices through the three-dimensional geometry described by the combinatorial geometry (CG) package used in such codes as MORSE and QAD-CG. These plots are printed on a standard line printer.

  16. Combinatorial Interdependence in Lottery

    ERIC Educational Resources Information Center

    Helman, Danny

    2005-01-01

    This paper examines a real life question of gamble facing lottery players. Combinatorial dependence plays a central role in shaping the game probabilistic structure, but might not carry the merited weight in punters' considerations.

  17. 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).

  18. 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).

  19. Parallel combinatorial chemical synthesis using single-layer poly(dimethylsiloxane) microfluidic devices

    PubMed Central

    Dexter, Joseph P.; Parker, William

    2009-01-01

    Improving methods for high-throughput combinatorial chemistry has emerged as a major area of research because of the importance of rapidly synthesizing large numbers of chemical compounds for drug discovery and other applications. In this investigation, a novel microfluidic chip for performing parallel combinatorial chemical synthesis was developed. Unlike past microfluidic systems designed for parallel combinatorial chemistry, the chip is a single-layer device made of poly(dimethylsiloxane) that is extremely easy and inexpensive to fabricate. Using the chip, a 2×2 combinatorial series of amide-formation reactions was performed. The results of this combinatorial synthesis indicate that the new device is an effective platform for running parallel organic syntheses at significantly higher throughput than with past methodologies. Additionally, a design algorithm for scaling up the 2×2 combinatorial synthesis chip to address more complex cases was developed. PMID:20216962

  20. Combinatorial stresses kill pathogenic Candida species.

    PubMed

    Kaloriti, Despoina; Tillmann, Anna; Cook, Emily; Jacobsen, Mette; You, Tao; Lenardon, Megan; Ames, Lauren; Barahona, Mauricio; Chandrasekaran, Komelapriya; Coghill, George; Goodman, Daniel; Gow, Neil A R; Grebogi, Celso; Ho, Hsueh-Lui; Ingram, Piers; McDonagh, Andrew; de Moura, Alessandro P S; Pang, Wei; Puttnam, Melanie; Radmaneshfar, Elahe; Romano, Maria Carmen; Silk, Daniel; Stark, Jaroslav; Stumpf, Michael; Thiel, Marco; Thorne, Thomas; Usher, Jane; Yin, Zhikang; Haynes, Ken; Brown, Alistair J P

    2012-10-01

    Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to the characterization of the adaptive responses to each of these stresses. In the wild, cells are frequently exposed simultaneously to combinations of these stresses and yet the effects of such combinatorial stresses have not been explored. We have developed a common experimental platform to facilitate the comparison of combinatorial stress responses in C. glabrata and C. albicans. This platform is based on the growth of cells in buffered rich medium at 30°C, and was used to define relatively low, medium and high doses of osmotic (NaCl), oxidative (H(2)O(2)) and nitrosative stresses (e.g., dipropylenetriamine (DPTA)-NONOate). The effects of combinatorial stresses were compared with the corresponding individual stresses under these growth conditions. We show for the first time that certain combinations of combinatorial stress are especially potent in terms of their ability to kill C. albicans and C. glabrata and/or inhibit their growth. This was the case for combinations of osmotic plus oxidative stress and for oxidative plus nitrosative stress. We predict that combinatorial stresses may be highly significant in host defences against these pathogenic yeasts. PMID:22463109

  1. 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…

  2. Dynamical Evolution and Chemistry of the Mantle (Invited)

    NASA Astrophysics Data System (ADS)

    Davies, G. F.

    2009-12-01

    Numerical models of mantle dynamics and evolution have yielded some important insights bearing on the depletion of the earliest mantle, the thickness of oceanic crust through time and the viability of plate tectonics, possible episodic layering of the early mantle alternating with dramatic breakthroughs, the formation of a D” layer, and the refractory trace element chemistry of MORBs and OIBs, including the ~2 Ga apparent age recorded by lead isotopes. Recent work also bears on the mass balances of incompatible elements and the enigmatic place of noble gases without resort to a hidden layer. It is becoming possible to contemplate a single dynamical model that can embrace and integrate the geophysical, geochemical and geological constraints on mantle structure and evolution. Because the early mantle was hotter and therefore less viscous, subducted oceanic crust, which is denser than average mantle, would more readily have settled out of the upper mantle, leaving it depleted of fertile component and incompatible trace elements. This can explain the strong source depletion recorded in the oldest surviving rocks. It also results in reduced melting and therefore thinner (<5 km) oceanic crust, notwithstanding higher mantle temperatures. This would have greatly facilitated subduction, compared with the >30-km early crust expected from fertile mantle, and would therefore facilitate plate tectonics through most of Earth history. Subducted oceanic crust is denser than average mantle through most of the mantle depth, except for the depth interval 660-750 km, where it is less dense. This results in the early formation of a ‘basalt barrier’ in this interval that blocks flow and separates mantle convection into two layers. Layering breaks down episodically, resulting in major tectono-magmatic episodes that could resurface much of the Earth. In evolving models the episodic layering ceases after 1.5-2 Gyr as the mantle cools. A series of models in two and three dimensions

  3. 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. PMID:23178502

  4. Research on Universal Combinatorial Coding

    PubMed Central

    Lu, Jun; Zhang, Zhuo; Mo, Juan

    2014-01-01

    The conception of universal combinatorial coding is proposed. Relations exist more or less in many coding methods. It means that a kind of universal coding method is objectively existent. It can be a bridge connecting many coding methods. Universal combinatorial coding is lossless and it is based on the combinatorics theory. The combinational and exhaustive property make it closely related with the existing code methods. Universal combinatorial coding does not depend on the probability statistic characteristic of information source, and it has the characteristics across three coding branches. It has analyzed the relationship between the universal combinatorial coding and the variety of coding method and has researched many applications technologies of this coding method. In addition, the efficiency of universal combinatorial coding is analyzed theoretically. The multicharacteristic and multiapplication of universal combinatorial coding are unique in the existing coding methods. Universal combinatorial coding has theoretical research and practical application value. PMID:24772019

  5. Research on universal combinatorial coding.

    PubMed

    Lu, Jun; Zhang, Zhuo; Mo, Juan

    2014-01-01

    The conception of universal combinatorial coding is proposed. Relations exist more or less in many coding methods. It means that a kind of universal coding method is objectively existent. It can be a bridge connecting many coding methods. Universal combinatorial coding is lossless and it is based on the combinatorics theory. The combinational and exhaustive property make it closely related with the existing code methods. Universal combinatorial coding does not depend on the probability statistic characteristic of information source, and it has the characteristics across three coding branches. It has analyzed the relationship between the universal combinatorial coding and the variety of coding method and has researched many applications technologies of this coding method. In addition, the efficiency of universal combinatorial coding is analyzed theoretically. The multicharacteristic and multiapplication of universal combinatorial coding are unique in the existing coding methods. Universal combinatorial coding has theoretical research and practical application value. PMID:24772019

  6. Spontaneous formation of organic helical architectures through dynamic covalent chemistry.

    PubMed

    Li, Wenfang; Dong, Zeyuan; Zhu, Junyan; Luo, Quan; Liu, Junqiu

    2014-12-01

    The spontaneous formation of organic helical structures, accompanied with an amplification of chirality, by dynamic covalent bonds between achiral and chiral building blocks is reported. PMID:25325888

  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 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.

  9. 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.

  10. 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.

  11. Chemistry and dynamics of the Antarctic Ozone Hole

    NASA Astrophysics Data System (ADS)

    Newman, Paul A.

    The Antarctic ozone hole is caused by human-produced chlorine and bromine compounds. The unique cold conditions of the Antarctic lower stratosphere in winter and spring allow for the development of polar stratospheric clouds. Chemical reactions on these stratospheric cloud particle surfaces (heterogeneous chemistry) release chlorine from reservoir species into highly reactive species that are easily photolyzed. Chlorine and bromine catalytic cycles result in massive ozone depletion during August and September. By early October, ozone is completely destroyed in the lower stratosphere over Antarctica. The amount of total ozone began a downward trend in the 1970s and stopped in the early 1990s. Current models indicate an ozone hole return date around 2067.

  12. 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.

  13. 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.

  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. PMID:25578410

  15. Metascalable molecular dynamics simulation of nano-mechano-chemistry

    NASA Astrophysics Data System (ADS)

    Shimojo, F.; Kalia, R. K.; Nakano, A.; Nomura, K.; Vashishta, P.

    2008-07-01

    We have developed a metascalable (or 'design once, scale on new architectures') parallel application-development framework for first-principles based simulations of nano-mechano-chemical processes on emerging petaflops architectures based on spatiotemporal data locality principles. The framework consists of (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms, (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these scalable algorithms onto hardware. The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics (MD) and 17.7-million-atom (1.56 trillion electronic degrees of freedom) quantum mechanical (QM) MD in the framework of the density functional theory (DFT) on adaptive multigrids, in addition to 201-billion-atom nonreactive MD, on 196 608 IBM BlueGene/L processors. We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on demand and tasks were migrated according to unexpected faults. The paper presents the application of the framework to the study of nanoenergetic materials: (1) combustion of an Al/Fe2O3 thermite and (2) shock initiation and reactive nanojets at a void in an energetic crystal.

  16. Dynamic coupling of bulk chemistry, trace elements and mantle flow

    NASA Astrophysics Data System (ADS)

    Davies, J. H.; Heck, H. V.; Nowacki, A.; Wookey, J. M.; Elliott, T.; Porcelli, D.

    2015-12-01

    Fully dynamical models that not only track the evolution of chemical heterogeneities through the mantle, but also incorporate the effect of chemical heterogeneities on the dynamics of mantle convection are now emerging. Since in general analytical solutions to these complex problems are lacking, careful testing and investigations of the effect and usefulness of these models is needed. We extend our existing numerical mantle convection code that can track fluid flow in 3D spherical geometry and tracks both bulk chemical components (basal fraction) and different trace elements. The chemical components fractionate upon melting when and where the solidus is crossed. Now, the chemical information will effect the flow of the fluid in the following ways: The bulk composition will link to density and the (radioactive) trace element abundance to heat production. Results will be reported of the effect of different density structures; either starting with a primordial dense layer at the base of the mantle, having all density variation originate from melting (basalt production), or a combination between these two end-member scenarios. In particular we will focus on the connection between large scale bulk chemical structures in the (deep) mantle and the evolution of the distribution of noble gasses (He and Ar). The distribution of noble gasses depend upon 1) assumptions on the initial distributions in the mantle, 2) the mantle flow, 3) radioactive production and, 4) outgassing to the atmosphere upon melting close to the surface.

  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. High-performance combinatorial algorithms

    SciTech Connect

    Pinar, Ali

    2003-10-31

    Combinatorial algorithms have long played an important role in many applications of scientific computing such as sparse matrix computations and parallel computing. The growing importance of combinatorial algorithms in emerging applications like computational biology and scientific data mining calls for development of a high performance library for combinatorial algorithms. Building such a library requires a new structure for combinatorial algorithms research that enables fast implementation of new algorithms. We propose a structure for combinatorial algorithms research that mimics the research structure of numerical algorithms. Numerical algorithms research is nicely complemented with high performance libraries, and this can be attributed to the fact that there are only a small number of fundamental problems that underlie numerical solvers. Furthermore there are only a handful of kernels that enable implementation of algorithms for these fundamental problems. Building a similar structure for combinatorial algorithms will enable efficient implementations for existing algorithms and fast implementation of new algorithms. Our results will promote utilization of combinatorial techniques and will impact research in many scientific computing applications, some of which are listed.

  19. Multiplexed tracking of combinatorial genomic mutations in engineered cell populations.

    PubMed

    Zeitoun, Ramsey I; Garst, Andrew D; Degen, George D; Pines, Gur; Mansell, Thomas J; Glebes, Tirzah Y; Boyle, Nanette R; Gill, Ryan T

    2015-06-01

    Multiplexed genome engineering approaches can be used to generate targeted genetic diversity in cell populations on laboratory timescales, but methods to track mutations and link them to phenotypes have been lacking. We present an approach for tracking combinatorial engineered libraries (TRACE) through the simultaneous mapping of millions of combinatorially engineered genomes at single-cell resolution. Distal genomic sites are assembled into individual DNA constructs that are compatible with next-generation sequencing strategies. We used TRACE to map growth selection dynamics for Escherichia coli combinatorial libraries created by recursive multiplex recombineering at a depth 10(4)-fold greater than before. TRACE was used to identify genotype-to-phenotype correlations and to map the evolutionary trajectory of two individual combinatorial mutants in E. coli. Combinatorial mutations in the human ES2 ovarian carcinoma cell line were also assessed with TRACE. TRACE completes the combinatorial engineering cycle and enables more sophisticated approaches to genome engineering in both bacteria and eukaryotic cells than are currently possible. PMID:25798935

  20. Carbon dynamics in peat bogs: Insights from substrate macromolecular chemistry

    NASA Astrophysics Data System (ADS)

    Kuder, Tomasz; Kruge, Michael A.

    2001-09-01

    The macromolecular compositions of subfossil plants from boreal Sphagnum bogs and restiad bogs (New Zealand) have been studied by pyrolysis-gas chromatography/mass spectrometry to evaluate the extent of degradation in the anoxic zone (catotelm) of a peat bog. Degradation of vascular plant polysaccharides was apparent only into the upper catotelm. Sphagnum was degraded more slowly than vascular plants, but no cessation of degradation was observed. The inferred rate of degradation varied depending on type of plant, extent of aerobic, precatotelmic degradation, and mode of litter deposition (rooting versus at the surface). Environmental forcing on anaerobic carbon dynamics would potentially be largest if the hydrology was disturbed at a wet and vascular plant-rich site. Peat deposited under a dry regime would be relatively inert in anaerobic conditions. Although catotelmic degradation is usually not extensive, in some cases, if labile organic matter is retained in the aerobic phase (e.g., restiad bogs) a major fraction of peat is degraded in catotelm, potentially resulting in a delayed major export of 14C-old methane.

  1. Coupling dynamics and chemistry in the air pollution modelling of street canyons: A review.

    PubMed

    Zhong, Jian; Cai, Xiao-Ming; Bloss, William James

    2016-07-01

    Air pollutants emitted from vehicles in street canyons may be reactive, undergoing mixing and chemical processing before escaping into the overlying atmosphere. The deterioration of air quality in street canyons occurs due to combined effects of proximate emission sources, dynamical processes (reduced dispersion) and chemical processes (evolution of reactive primary and formation of secondary pollutants). The coupling between dynamics and chemistry plays a major role in determining street canyon air quality, and numerical model approaches to represent this coupling are reviewed in this article. Dynamical processes can be represented by Computational Fluid Dynamics (CFD) techniques. The choice of CFD approach (mainly the Reynolds-Averaged Navier-Stokes (RANS) and Large-Eddy Simulation (LES) models) depends on the computational cost, the accuracy required and hence the application. Simplified parameterisations of the overall integrated effect of dynamics in street canyons provide capability to handle relatively complex chemistry in practical applications. Chemical processes are represented by a chemical mechanism, which describes mathematically the chemical removal and formation of primary and secondary species. Coupling between these aspects needs to accommodate transport, dispersion and chemical reactions for reactive pollutants, especially fast chemical reactions with time scales comparable to or shorter than those of typical turbulent eddies inside the street canyon. Different approaches to dynamical and chemical coupling have varying strengths, costs and levels of accuracy, which must be considered in their use for provision of reference information concerning urban canopy air pollution to stakeholders considering traffic and urban planning policies. PMID:27149146

  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. On the relationship between total ozone and atmospheric dynamics and chemistry at mid-latitudes - Part 1: Statistical models and spatial fingerprints of atmospheric dynamics and chemistry

    NASA Astrophysics Data System (ADS)

    Frossard, L.; Rieder, H. E.; Ribatet, M.; Staehelin, J.; Maeder, J. A.; Di Rocco, S.; Davison, A. C.; Peter, T.

    2012-05-01

    We use models for mean and extreme values of total column ozone on spatial scales to analyze "fingerprints" of atmospheric dynamics and chemistry on long-term ozone changes at northern and southern mid-latitudes. The r-largest order statistics method is used for pointwise analysis of extreme events in low and high total ozone (termed ELOs and EHOs, respectively). For the corresponding mean value analysis a pointwise autoregressive moving average model (ARMA) is used. The statistical models include important atmospheric covariates to describe the dynamical and chemical state of the atmosphere: the solar cycle, the Quasi-Biennial Oscillation (QBO), ozone depleting substances (ODS) in terms of equivalent effective stratospheric chlorine (EESC), the North Atlantic Oscillation (NAO), the Antarctic Oscillation (AAO), the El~Niño/Southern Oscillation (ENSO), and aerosol load after the volcanic eruptions of El Chichón and Mt. Pinatubo. The influence of the individual covariates on mean and extreme levels in total column ozone is derived on a grid cell basis. The results show that "fingerprints", i.e., significant influence, of dynamical and chemical features are captured in both the "bulk" and the tails of the ozone distribution, respectively described by means and EHOs/ELOs. While results for the solar cycle, QBO and EESC are in good agreement with findings of earlier studies, unprecedented spatial fingerprints are retrieved for the dynamical covariates.

  4. 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)

  5. An Indexed Combinatorial Library: The Synthesis and Testing of Insect Repellents

    NASA Astrophysics Data System (ADS)

    Miles, William H.; Gelato, Kathy A.; Pompizzi, Kristen M.; Scarbinsky, Aislinn M.; Albrecht, Brian K.; Reynolds, Elaine R.

    2001-04-01

    An indexed combinatorial library of amides was prepared by the reaction of amines and acid chlorides. A simple test for insect repellency using fruit flies (Drosophila melanogaster) allowed the determination of the most repellent sublibraries. The student-generated data were collected and analyzed to determine the most active amide(s) in the library. This experiment illustrates the fundamentals of combinatorial chemistry, a field that has undergone explosive growth in the last decade.

  6. Accelerated electronic structure-based molecular dynamics simulations of shock-induced chemistry

    NASA Astrophysics Data System (ADS)

    Cawkwell, Marc

    2015-06-01

    The initiation and progression of shock-induced chemistry in organic materials at moderate temperatures and pressures are slow on the time scales available to regular molecular dynamics simulations. Accessing the requisite time scales is particularly challenging if the interatomic bonding is modeled using accurate yet expensive methods based explicitly on electronic structure. We have combined fast, energy conserving extended Lagrangian Born-Oppenheimer molecular dynamics with the parallel replica accelerated molecular dynamics formalism to study the relatively sluggish shock-induced chemistry of benzene around 13-20 GPa. We model interatomic bonding in hydrocarbons using self-consistent tight binding theory with an accurate and transferable parameterization. Shock compression and its associated transient, non-equilibrium effects are captured explicitly by combining the universal liquid Hugoniot with a simple shrinking-cell boundary condition. A number of novel methods for improving the performance of reactive electronic structure-based molecular dynamics by adapting the self-consistent field procedure on-the-fly will also be discussed. The use of accelerated molecular dynamics has enabled us to follow the initial stages of the nucleation and growth of carbon clusters in benzene under thermodynamic conditions pertinent to experiments.

  7. 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.

  8. SMMH - A Parallel Heuristic for Combinatorial Optimization Problems

    SciTech Connect

    Domingues, Guilherme; Morie, Yoshiyuki; Gu, Feng Long; Nanri, Takeshi; Murakami, Kazuaki

    2007-12-26

    The process of finding one or more optimal solutions for answering combinatorial optimization problems bases itself on the use of algorithms instances. Those instances usually have to explore a very large search spaces. Heuristics search focusing on the use of High-Order Hopfield neural networks is a largely deployed technique for very large search space. It can be established a very powerful analogy towards the dynamics evolution of a physics spin-glass system while minimizing its own energy and the energy function of the network. This paper presents a new approach for solving combinatorial optimization problems through parallel simulations, based on a High-Order Hopfield neural network using MPI specification.

  9. SMMH--A Parallel Heuristic for Combinatorial Optimization Problems

    SciTech Connect

    Domingues, Guilherme; Morie, Yoshiyuki; Gu, Feng Long; Nanri, Takeshi; Murakami, Kazuaki

    2007-12-26

    The process of finding one or more optimal solutions for answering combinatorial optimization problems bases itself on the use of algorithms instances. Those instances usually have to explore a very large search spaces. Heuristics search focusing on the use of High-Order Hopfield neural networks is a largely deployed technique for very large search space. It can be established a very powerful analogy towards the dynamics evolution of a physics spin-glass system while minimizing its own energy and the energy function of the network. This paper presents a new approach for solving combinatorial optimization problems through parallel simulations, based on a High-Order Hopfield neural network using MPI specification.

  10. 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.

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

    PubMed

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

    2015-05-01

    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

  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. Impact Of Geo-engineered Aerosols On Stratospheric Chemistry And Dynamics

    NASA Astrophysics Data System (ADS)

    Tilmes, S.; Garcia, R. R.; Kinnison, D. E.; Gettelman, A.; Rasch, P. J.

    2008-12-01

    Geo-engineering schemes have been proposed to alleviate the consequences of global warming; one proposed scheme is to inject sulfur into the stratosphere so as to mimic the effects of large volcanic eruptions. Past volcanic eruptions have shown that strongly enhanced sulfate aerosols in the stratosphere result in a higher planetary albedo, leading to surface cooling. However, the increase of sulfate aerosol surface area enhances heterogeneous reactions in the stratosphere that lead to ozone loss. The potential for high Arctic ozone depletion in the context of geo-engineering is known. On the other hand, halogen compounds are now decreasing in the atmosphere as a result of the enforcement of the Montreal Protocol and its amendments, and this is expected to bring about the recovery of the ozone layer and to lessen the potential impact of aerosols. In this study we present results of calculations made with NCAR's Whole Atmosphere Community Climate Model (WACCM), focusing on the impact of Geo-engineering on stratospheric chemistry and dynamics. Aside from changes in heterogeneous reactions, changes in stratospheric dynamics have a significant impact on ozone. On average, changes of both chemistry and dynamics result in a slowdown of the recovery of ozone for mid- and high latitudes. An increase of ozone depletion as a result of geo-engineering was found in both polar regions for the period between 2040-2050.

  14. Combined effects of surface conditions, boundary layer dynamics and chemistry on diurnal SOA evolution

    NASA Astrophysics Data System (ADS)

    Janssen, R. H. H.; Vilà-Guerau de Arellano, J.; Ganzeveld, L. N.; Kabat, P.; Jimenez, J. L.; Farmer, D. K.; van Heerwaarden, C. C.; Mammarella, I.

    2012-08-01

    We study the combined effects of land surface conditions, atmospheric boundary layer dynamics and chemistry on the diurnal evolution of biogenic secondary organic aerosol in the atmospheric boundary layer, using a model that contains the essentials of all these components. First, we evaluate the model for a case study in Hyytiälä, Finland, and find that it is able to satisfactorily reproduce the observed dynamics and gas-phase chemistry. We show that the exchange of organic aerosol between the free troposphere and the boundary layer (entrainment) must be taken into account in order to explain the observed diurnal cycle in organic aerosol (OA) concentration. An examination of the budgets of organic aerosol and terpene concentrations show that the former is dominated by entrainment, while the latter is mainly driven by emission and chemical transformation. We systematically investigate the role of the land surface, which governs both the surface energy balance partitioning and terpene emissions, and the large-scale atmospheric process of vertical subsidence. Entrainment is especially important for the dilution of organic aerosol concentrations under conditions of dry soils and low terpene emissions. Subsidence suppresses boundary layer growth while enhancing entrainment. Therefore, it influences the relationship between organic aerosol and terpene concentrations. Our findings indicate that the diurnal evolution of secondary organic aerosols (SOA) in the boundary layer is the result of coupled effects of the land surface, dynamics of the atmospheric boundary layer, chemistry, and free troposphere conditions. This has potentially some consequences for the design of both field campaigns and large-scale modeling studies.

  15. On the relationship between total ozone and atmospheric dynamics and chemistry at mid-latitudes - Part 1: Statistical models and spatial fingerprints of atmospheric dynamics and chemistry

    NASA Astrophysics Data System (ADS)

    Frossard, L.; Rieder, H. E.; Ribatet, M.; Staehelin, J.; Maeder, J. A.; Di Rocco, S.; Davison, A. C.; Peter, T.

    2013-01-01

    We use statistical models for mean and extreme values of total column ozone to analyze "fingerprints" of atmospheric dynamics and chemistry on long-term ozone changes at northern and southern mid-latitudes on grid cell basis. At each grid cell, the r-largest order statistics method is used for the analysis of extreme events in low and high total ozone (termed ELOs and EHOs, respectively), and an autoregressive moving average (ARMA) model is used for the corresponding mean value analysis. In order to describe the dynamical and chemical state of the atmosphere, the statistical models include important atmospheric covariates: the solar cycle, the Quasi-Biennial Oscillation (QBO), ozone depleting substances (ODS) in terms of equivalent effective stratospheric chlorine (EESC), the North Atlantic Oscillation (NAO), the Antarctic Oscillation (AAO), the El Niño/Southern Oscillation (ENSO), and aerosol load after the volcanic eruptions of El Chichón and Mt. Pinatubo. The influence of the individual covariates on mean and extreme levels in total column ozone is derived on a grid cell basis. The results show that "fingerprints", i.e., significant influence, of dynamical and chemical features are captured in both the "bulk" and the tails of the statistical distribution of ozone, respectively described by mean values and EHOs/ELOs. While results for the solar cycle, QBO, and EESC are in good agreement with findings of earlier studies, unprecedented spatial fingerprints are retrieved for the dynamical covariates. Column ozone is enhanced over Labrador/Greenland, the North Atlantic sector and over the Norwegian Sea, but is reduced over Europe, Russia and the Eastern United States during the positive NAO phase, and vice-versa during the negative phase. The NAO's southern counterpart, the AAO, strongly influences column ozone at lower southern mid-latitudes, including the southern parts of South America and the Antarctic Peninsula, and the central southern mid-latitudes. Results

  16. Does filler surface chemistry impact filler dispersion, polymer dynamics and conductivity in nanofilled solid polymer electrolytes?

    NASA Astrophysics Data System (ADS)

    Ganapatibhotla, Lalitha; Maranas, Janna

    2012-02-01

    We study the impact of nanofiller surface chemistry on filler dispersion, polymer dynamics and ionic conductivity in acidic α-Al2O3 filled PEO+LiClO4 solid polymer electrolytes (SPEs).SPEs are the key to light-weight and high energy density rechargeable Li ion batteries but suffer from low room temperature ionic conductivity. Addition of ceramic nanofillers improves conductivity of SPEs and their surface chemistry influences extent of conductivity enhancement. The ionic conductivity of acidic α-Al2O3 filled SPE is enhanced for salt concentrations at and below eutectic, while neutral γ-Al2O3 filler enhances conductivity only at eutectic composition. Li ion motion is coupled to segmental mobility of polymer and we study how this is affected by addition of α-Al2O3 using quasi-elastic neutron scattering. Aggregation extent of nanoparticles in SPE matrix, a less explored factor in filled SPEs, can affect segmental mobility of polymer. This can vary with surface chemistry of particles and we quantify this using small angle neutron scattering. All measurements are performed as a function of Li concentration, nanoparticle loading and temperature.

  17. 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.

  18. Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

    PubMed Central

    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. PMID:24282515

  19. Mechanisms of Auger-induced chemistry derived from wave packet dynamics.

    PubMed

    Su, Julius T; Goddard, William A

    2009-01-27

    To understand how core ionization and subsequent Auger decay lead to bond breaking in large systems, we simulate the wave packet dynamics of electrons in the hydrogenated diamond nanoparticle C(197)H(112). We find that surface core ionizations cause emission of carbon fragments and protons through a direct Auger mechanism, whereas deeper core ionizations cause hydrides to be emitted from the surface via remote heating, consistent with results from photon-stimulated desorption experiments [Hoffman A, Laikhtman A, (2006) J Phys Condens Mater 18:S1517-S1546]. This demonstrates that it is feasible to study the chemistry of highly excited large-scale systems using simulation and analysis tools comparable in simplicity to those used for classical molecular dynamics. PMID:19164568

  20. Mechanisms of Auger-induced chemistry derived from wave packet dynamics

    PubMed Central

    Su, Julius T.; Goddard, William A.

    2009-01-01

    To understand how core ionization and subsequent Auger decay lead to bond breaking in large systems, we simulate the wave packet dynamics of electrons in the hydrogenated diamond nanoparticle C197H112. We find that surface core ionizations cause emission of carbon fragments and protons through a direct Auger mechanism, whereas deeper core ionizations cause hydrides to be emitted from the surface via remote heating, consistent with results from photon-stimulated desorption experiments [Hoffman A, Laikhtman A, (2006) J Phys Condens Mater 18:S1517–S1546]. This demonstrates that it is feasible to study the chemistry of highly excited large-scale systems using simulation and analysis tools comparable in simplicity to those used for classical molecular dynamics. PMID:19164568

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

    PubMed

    Martinson, Liisa; Alveteg, Mattias; Warfvinge, Per

    2003-01-01

    Sulfate adsorption was implemented in the dynamic, multi-layer soil chemistry model SAFE. The process is modeled by an isotherm in which sulfate adsorption is considered to be fully reversible and dependent on sulfate concentration as well as pH in soil solution. The isotherm was parameterized by a site-specific series of simple batch experiments at different pH (3.8-5.0) and sulfate concentration (10-260 micromol 1(-1)) levels. Application of the model to the Lake Gardsj6n roof covered site shows that including sulfate adsorption improves the dynamic behavior of the model and sulfate adsorption and desorption delay acidification and recovery of the soil. The modeled adsorbed pool of sulfate at the site reached a maximum level of 700 mmol/m(2) in the late 1980s, well in line with experimental data. PMID:12683988

  2. Logical Structures Underlying Combinatorial Reasoning.

    ERIC Educational Resources Information Center

    Glick, Rochelle; Martorano, Suzanne

    This study was designed to examine the processes underlying developmental changes in children's (1) use of combinatorial strategy, and (2) comprehension of conjunctive and disjunctive propositional relationships. A total of 108 children from third, sixth and eighth grades participated in this study. Each child was administered three tasks…

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. Statistical analysis of cellular detonation dynamics from numerical simulations: one-step chemistry

    NASA Astrophysics Data System (ADS)

    Sharpe, G. J.; Radulescu, M. I.

    2011-10-01

    In this paper, two methods are developed for statistically analysing the nonlinear cellular dynamics from numerical simulations of gaseous detonations, one use of which is the systematic determination of detonation cell sizes from such simulations. Both these methods rely on signed vorticity records in which the individual families of transverse waves are captured independently. The first method involves an automated extraction of the main triple-point tracks from the vorticity records, allowing statistical analysis of the spacings between neighbouring tracks. The second method uses the autocorrelation function to spectrally analyse the vorticity records. These methods are then employed for a preliminary analysis of the cellular dynamics of the standard, idealized one-step chemistry model. Evidence is found for 'cell size doubling' bifurcations in the one-step model as the cellular dynamics become more irregular (e.g. as the activation is increased). It is also shown that the statistical models converge slowly due to systematic 'shot-to-shot' variation in the cellular dynamics for fixed parameters with different initial perturbations. Instead, it appears that a range of equally probable cell sizes can be obtained for given parameters.

  8. 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. PMID:23818634

  9. Chaotic itinerancy, temporal segmentation and spatio-temporal combinatorial codes

    NASA Astrophysics Data System (ADS)

    Dias, Juliana R.; Oliveira, Rodrigo F.; Kinouchi, Osame

    2008-01-01

    We study a deterministic dynamics with two time scales in a continuous state attractor network. To the usual (fast) relaxation dynamics towards point attractors (“patterns”) we add a slow coupling dynamics that makes the visited patterns lose stability, leading to an itinerant behavior in the form of punctuated equilibria. One finds that the transition frequency matrix for transitions between patterns shows non-trivial statistical properties in the chaotic itinerant regime. We show that mixture input patterns can be temporally segmented by the itinerant dynamics. The viability of a combinatorial spatio-temporal neural code is also demonstrated.

  10. 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.

  11. 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.

  12. 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.

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

    SciTech Connect

    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.

  14. Dynamic Chemistry of Disulfide Terminated Oligonucleotides in Duplexes and Double-Crossover Tiles.

    PubMed

    De Stefano, Mattia; Vesterager Gothelf, Kurt

    2016-06-16

    Designed nanostructures formed by self-assembly of multiple DNA strands suffer from low stability at elevated temperature and under other denaturing conditions. Here, we propose a method for covalent coupling of DNA strands in such structures by the formation of disulfide bonds; this allows disassembly of the structure under reducing conditions. The dynamic chemistry of disulfides and thiols was applied to crosslink DNA strands with terminal disulfide modifications. The formation of disulfide-linked DNA duplexes consisting of three strands is demonstrated, as well as a more-complex DNA double-crossover tile. All the strands in the fully disulfide-linked structures are covalently and geometrically interlocked, and it is demonstrated that the structures are stable under heating and in the presence of denaturants. Such a reversible system can be exploited in applications where higher DNA stability is needed only temporarily, such as delivery of cargoes to cells by DNA nanostructures. PMID:26994867

  15. 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

  16. The Role of Disk Volatile Chemistry and Dynamics in Shaping the Compositions of Nascent Planets

    NASA Astrophysics Data System (ADS)

    Piso, Ana-Maria; Oberg, Karin I.; Birnstiel, Tilman; Murray-Clay, Ruth

    2016-01-01

    The elemental composition of planets define their chemistry, and could potentially be used as beacons for their formation location if the elemental gas and grain ratios of planet birth environments, i.e. protoplanetary disks, are well understood. In disks, the ratios of volatile elements (e.g., C/O) is regulated by the presence of snowlines of major volatiles at different distances from the central star. We explore the effects of dynamical processes, such as radial drift of solids and viscous gas accretion onto the central star, molecular compositions, and the ice morphology of dust grains in disks on the snowline locations of the main C, O and N carriers in a protoplanetary disk, and their consequences for the C/O/N ratio in gas and dust throughout the disk. We find that radial drift and accretion alone can reduce the snow line radii by 40-60% of the main C and O carriers, i.e. H2O, CO2 and CO, compared to static disks, substantially changing the disk regions where C/O is enhanced over the stellar value. A similar effect is seen for the major nitrogen carriers. We note that N/O enhancements in disk gas can be even more extreme than C/O in the outer disk due to the low volatility of N2 compared to all major C and O carriers. I will discuss these results together with the effects of additional dynamical processes, and outline a path toward a coupled drift-desorption-chemistry model that will provide robust quantitative results for volatile snowline locations and C/N/O abundance ratios as the disk evolves in time.

  17. 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

  18. 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…

  19. Self-healing gels based on constitutional dynamic chemistry and their potential applications.

    PubMed

    Wei, Zhao; Yang, Jian Hai; Zhou, Jinxiong; Xu, Feng; Zrínyi, Miklós; Dussault, Patrick H; Osada, Yoshihito; Chen, Yong Mei

    2014-12-01

    As representative soft materials with widespread applications, gels with various functions have been developed. However, traditional gels are vulnerable to stress-induced formation of cracks. The propagation of these cracks may affect the integrity of network structures of gels, resulting in the loss of functionality and limiting the service life of the gels. To address this challenge, self-healing gels that can restore their functionalities and structures after damage have been developed as "smart" soft materials. In this paper, we present an overview of the current strategies for synthesizing self-healing gels based on the concept of constitutional dynamic chemistry, which involves molecular structures capable of establishing dynamic networks based upon physical interactions or chemical reactions. The characterization methods of self-healing gels and the key factors that affect self-healing properties are analyzed. We also illustrate the emerging applications of self-healing gels, with emphasis on their usage in industry (coatings, sealants) and biomedicine (tissue adhesives, agents for drug or cell delivery). We conclude with a perspective on challenges facing the field, along with prospects for future development. PMID:25144925

  20. Dynamic Regulation of a Cell Adhesion Protein Complex Including CADM1 by Combinatorial Analysis of FRAP with Exponential Curve-Fitting

    PubMed Central

    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 10min. 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. PMID:25780926

  1. 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. PMID:17168681

  2. 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.

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

    PubMed

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

    2015-07-01

    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. PMID

  4. Analysis of Combinatorial Epigenomic States.

    PubMed

    Soloway, Paul D

    2016-03-18

    Hundreds of distinct chemical modifications to DNA and histone amino acids have been described. Regulation exerted by these so-called epigenetic marks is vital to normal development, stability of cell identity through mitosis, and nongenetic transmission of traits between generations through meiosis. Loss of this regulation contributes to many diseases. Evidence indicates epigenetic marks function in combinations, whereby a given modification has distinct effects on local genome control, depending on which additional modifications are locally present. This review summarizes emerging methods for assessing combinatorial epigenomic states, as well as challenges and opportunities for their refinement. PMID:26555135

  5. Multispecies TASEP and combinatorial R

    NASA Astrophysics Data System (ADS)

    Kuniba, Atsuo; Maruyama, Shouya; Okado, Masato

    2015-08-01

    We identify the algorithm for constructing steady states of the n-species totally asymmetric simple exclusion process (TASEP) on an L site periodic chain by Ferrari and Martin with a composition of combinatorial R for the quantum affine algebra {U}q({\\widehat{{sl}}}L) in crystal base theory. Based on this connection and the factorized form of the R matrix derived recently from the tetrahedron equation, we establish a new matrix product formula for the steady state of the TASEP, which is expressed in terms of corner transfer matrices of the q-oscillator valued five-vertex model at q = 0. Dedicated to the memory of Professor Ryogo Hirota.

  6. Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study

    NASA Astrophysics Data System (ADS)

    Damjanović, Ana; Kosztin, Ioan; Kleinekathöfer, Ulrich; Schulten, Klaus

    2002-03-01

    The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with an approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of light-harvesting (LH) complexes was performed on an 87 055 atom system comprised of a LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. For each of the 16 B850 bacteriochlorophylls (BChls), we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function, are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 BChl ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption and circular dichroism spectra of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained results are found to be in good agreement with the experimentally measured absorption and circular dichroism spectra.

  7. 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.

  8. 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.

  9. 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.

  10. Bifurcation characteristics and flame dynamics of a ducted non-premixed flame with finite rate chemistry

    NASA Astrophysics Data System (ADS)

    Rana, Subhas Chandra; Sujith, Raman

    2015-09-01

    The influence of system parameters such as the flame location, Peclet number and Damköhler number on the bifurcation characteristics and flame dynamics of a ducted non-premixed flame with finite rate chemistry is presented in this paper. In the bifurcation plot with flame location as the bifurcation parameter, subcritical Hopf bifurcation is found for lower values of flame location and supercritical Hopf bifurcation for higher values of flame location, for all the Damköhler numbers used in this study. The flame shapes are captured at eight different phases of a cycle of time series data of acoustic velocity at both the fold and Hopf points for bifurcation with flame location as the parameter. We find that the range of flame height variations at the Hopf point is more than the range of flame height variations obtained at the fold point. We also find that the flame oscillates in the same phase as pressure fluctuation but in a phase different from both velocity and heat release rate fluctuations in the region of hysteresis for bifurcation with flame location. The non-dimensional hysteresis width is plotted as a function of Damköhler number for variation of flame location in the subcritical region. An inverse power law relation is found between the non-dimensional hysteresis width and the Damköhler number. The bifurcation plot with Peclet number as parameter shows a subcritical Hopf bifurcation.

  11. 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.

  12. 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

  13. Constitutional Dynamic Chemistry-based New Concept of Molecular Beacons for High Efficient Development of Fluorescent Probes.

    PubMed

    Chang, Xingmao; Yu, Chunmeng; Wang, Gang; Fan, Jiayun; Zhang, Jianyun; Qi, Yanyu; Liu, Kaiqiang; Fang, Yu

    2015-06-01

    Inspired by the concept of constitutional dynamic chemistry, we propose a new and well-adaptable strategy for developing molecular beacon (MB)-like fluorescent probes. To demonstrate the strategy, we synthesized and used an amino group containing pyrenyl derivative of cholesterol (CP) for the construction of new fluorescent probes with EDTA and sulfuric acid. The probes as created were successfully used for n-hexane purity checking and Ba(2+)and Pb(2+)sensing, respectively. PMID:25985384

  14. New Electrocatalysts by Combinatorial Methods

    NASA Astrophysics Data System (ADS)

    Smotkin, Eugene S.; Diaz-Morales, Robert R.

    2003-08-01

    Combinatorial methods provide a means for accelerating the discovery of fuel cell catalysts. The first example of parallel fuel cell catalysts screening was an indirect method that used fluorescent chemosensors to detect changes in pH in proximity to electrocatalyst spots. Serial direct electrochemical methods have been developed that use voltammetry, chronoamperometry, and scanning electrochemical microscopy. An array fuel cell screens catalysts simultaneously, using high-performance fuel cell components. Heuristic models based on mechanistic and spectroscopic studies provide guidance for library development, and detailed studies of discovered catalysts can help to refine these models. The remaining challenges are the development of high throughput synthetic methods that can enable the use of discovery level and focus level screening. Until these synthetic methods are developed, a greater emphasis should be placed on smaller libraries with design of experiment strategies leveraged with informatics and data mining.

  15. Accelerated luminophore discovery through combinatorial synthesis.

    PubMed

    Lowry, Michael S; Hudson, William R; Pascal, Robert A; Bernhard, Stefan

    2004-11-01

    A method for accelerating the discovery of ionic luminophores using combinatorial techniques is reported. The photophysical properties of the resulting transition-metal-based chromophores were compared against a series of analogous, traditionally prepared species. The strong overlap between these two sets confirms the identity of the parallel synthesis products and supports the truthfulness of the combinatorial results. Further support for the combinatorial method comes from the adherence of these complexes to the energy gap law. The relationship between the structure of a complex and its photophysical properties was also considered, and static DFT calculations were used to assess whether it is feasible to predict the luminescent behavior of novel materials. PMID:15506778

  16. 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. PMID:25462781

  17. 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''.

  18. 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

  19. The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry

    NASA Astrophysics Data System (ADS)

    Adams, C.; Strong, K.; Zhao, X.; Bourassa, A. E.; Daffer, W. H.; Degenstein, D.; Drummond, J. R.; Farahani, E. E.; Fraser, A.; Lloyd, N. D.; Manney, G. L.; McLinden, C. A.; Rex, M.; Roth, C.; Strahan, S. E.; Walker, K. A.; Wohltmann, I.

    2012-08-01

    In spring 2011, the Arctic polar vortex was stronger than in any other year on record. As the polar vortex started to break up in April, ozone and NO2 columns were measured with UV-visible spectrometers above the Polar Environment Atmospheric Research Laboratory (PEARL) in Eureka, Canada (80.05° N, 86.42° W) using the differential optical absorption spectroscopy (DOAS) technique. These ground-based column measurements were complemented by Ozone Monitoring Instrument (OMI) and Optical Spectrograph and Infra-Red Imager System (OSIRIS) satellite measurements, Global Modeling Initiative (GMI) simulations, and dynamical parameters. On 8 April 2011, NO2 columns above PEARL from the DOAS, OMI, and GMI datasets were approximately twice as large as in previous years. On this day, temperatures and ozone volume mixing ratios above Eureka were high, suggesting enhanced chemical production of NO2 from NO. Additionally, GMI NOx and N2O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO2. The anticyclone that transported lower-latitude NOx above PEARL became frozen-in and persisted in dynamical and GMI N2O fields until the end of the measurement period on 31 May 2011. Ozone isolated within this frozen-in anticyclone (FrIAC) in the middle stratosphere was depleted due to reactions with the enhanced NOx. Ozone loss was calculated using the passive tracer technique, with passive ozone profiles from the Lagrangian Chemistry and Transport Model, ATLAS. At 600 K, ozone losses between 1 December 2010 and 20 May 2011 reached 4.2 parts per million by volume (ppmv) (58%) and 4.4 ppmv (61%), when calculated using GMI and OSIRIS ozone profiles, respectively. This middle-stratosphere gas-phase ozone loss led to a more rapid decrease in ozone column amounts in April/May 2011 compared with previous years. Ground-based, OMI, and GMI ozone total columns within the FrIAC all decreased by more than 100 DU

  20. 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.

  1. The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry

    NASA Astrophysics Data System (ADS)

    Adams, C.; Strong, K.; Zhao, X.; Bourassa, A. E.; Daffer, W. H.; Degenstein, D.; Drummond, J. R.; Farahani, E. E.; Fraser, A.; Lloyd, N. D.; Manney, G. L.; McLinden, C. A.; Rex, M.; Roth, C.; Strahan, S. E.; Walker, K. A.; Wohltmann, I.

    2013-01-01

    In spring 2011, the Arctic polar vortex was stronger than in any other year on record. As the polar vortex started to break up in April, ozone and NO2 columns were measured with UV-visible spectrometers above the Polar Environment Atmospheric Research Laboratory (PEARL) in Eureka, Canada (80.05° N, 86.42° W) using the differential optical absorption spectroscopy (DOAS) technique. These ground-based column measurements were complemented by Ozone Monitoring Instrument (OMI) and Optical Spectrograph and Infra-Red Imager System (OSIRIS) satellite measurements, Global Modeling Initiative (GMI) simulations, and meteorological quantities. On 8 April 2011, NO2 columns above PEARL from the DOAS, OMI, and GMI datasets were approximately twice as large as in previous years. On this day, temperatures and ozone volume mixing ratios above Eureka were high, suggesting enhanced chemical production of NO2 from NO. Additionally, GMI NOx (NO + NO2) and N2O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO2. The anticyclone that transported lower-latitude NOx above PEARL became frozen-in and persisted in dynamical and GMI N2O fields until the end of the measurement period on 31 May 2011. Ozone isolated within this frozen-in anticyclone (FrIAC) in the middle stratosphere was lost due to reactions with the enhanced NOx. Below the FrIAC (from the tropopause to 700 K), NOx driven ozone loss above Eureka was larger than in previous years, according to GMI monthly average ozone loss rates. Using the passive tracer technique, with passive ozone profiles from the Lagrangian Chemistry and Transport Model, ATLAS, ozone losses since 1 December 2010 were calculated at 600 K. In the air mass that was above Eureka on 20 May 2011, ozone losses reached 4.2 parts per million by volume (ppmv) (58%) and 4.4 ppmv (61%), when calculated using GMI and OSIRIS ozone profiles, respectively. This gas-phase ozone loss

  2. 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

  3. Groundwater phosphate dynamics in a river riparian zone: effects of hydrologic flowpaths, lithology and redox chemistry

    NASA Astrophysics Data System (ADS)

    Carlyle, G. C.; Hill, A. R.

    2001-07-01

    This study examines the influence of riparian zone hydrology, lithology and redox chemistry on groundwater phosphate dynamics. Patterns of soluble reactive phosphorus (SRP), dissolved oxygen (DO) and ferrous iron (Fe 2+) in combination with hydrologic data and sediment characteristics were studied in a forested floodplain connected to a large upland sand aquifer in an agricultural region of southern Ontario, Canada. Groundwater discharge from the upland aquifer flowed laterally beneath peat in a 2-4 m thick zone of permeable sands across the floodplain to the river. Within the sands, low SRP concentrations (<25 μg L -1) occurred in a plume of groundwater with DO concentrations >3 mg L -1 and Fe 2+ concentrations <0.2 mg L -1 which extended for a horizontal distance of 100-140 m across the riparian zone. High SRP concentrations (50-950 μg L -1) were associated with low DO and high Fe 2+ concentrations which exceeded 1 mg L -1 in buried channel sediments near the river bank. Sediment P fractionation indicated that the buried channel sediments contained a much higher pool of total P and Fe+Al-P than the sands. Groundwater SRP concentrations at the river bank were 25-80 μg L -1 compared to <10 μg L -1 in river water indicating that the floodplain was a source of SRP to the river. Areas of elevated SRP and Fe 2+ within the floodplain expanded in August when DO concentrations in groundwater were lower than in late spring or autumn. These data suggest that the microbial reduction of Fe 3+ to soluble Fe 2+ in anaerobic conditions influences groundwater SRP concentrations in the riparian zone. This study shows that well-organized patterns of groundwater SRP concentrations occur in riparian zones which reflect the interaction of hydrologic flowpaths and environments of different redox state. Internal sources of P associated with buried channel sediments can also influence subsurface SRP transport and release to streams.

  4. 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.

  5. Liquid-phase combinatorial synthesis.

    PubMed Central

    Han, H; Wolfe, M M; Brenner, S; Janda, K D

    1995-01-01

    A concept termed liquid-phase combinatorial synthesis (LPCS) is described. The central feature of this methodology is that it combines the advantages that classic organic synthesis in solution offers with those that solid-phase synthesis can provide, through the application of a linear homogeneous polymer. To validate this concept two libraries were prepared, one of peptide and the second of nonpeptide origin. The peptide-based library was synthesized by a recursive deconvolution strategy [Erb, E., Janda, K. D. & Brenner, S. (1994) Proc. Natl. Acad. Sci. USA 91, 11422-11426] and several ligands were found within this library to bind a monoclonal antibody elicited against beta-endorphin. The non-peptide molecules synthesized were arylsulfonamides, a class of compounds of known clinical bactericidal efficacy. The results indicate that the reaction scope of LPCS should be general, and its value to multiple, high-throughput screening assays could be of particular merit, since multimilligram quantities of each library member can readily be attained. PMID:7541541

  6. Combinatorial Engineering of Dextransucrase Specificity

    PubMed Central

    Irague, Romain; Tarquis, Laurence; André, Isabelle; Moulis, Claire; Morel, Sandrine; Monsan, Pierre; Potocki-Véronèse, Gabrielle; Remaud-Siméon, Magali

    2013-01-01

    We used combinatorial engineering to investigate the relationships between structure and linkage specificity of the dextransucrase DSR-S from Leuconostoc mesenteroides NRRL B-512F, and to generate variants with altered specificity. Sequence and structural analysis of glycoside-hydrolase family 70 enzymes led to eight amino acids (D306, F353, N404, W440, D460, H463, T464 and S512) being targeted, randomized by saturation mutagenesis and simultaneously recombined. Screening of two libraries totaling 3.6.104 clones allowed the isolation of a toolbox comprising 81 variants which synthesize high molecular weight α-glucans with different proportions of α(1→3) linkages ranging from 3 to 20 %. Mutant sequence analysis, biochemical characterization and molecular modelling studies revealed the previously unknown role of peptide 460DYVHT464 in DSR-S linkage specificity. This peptide sequence together with residue S512 contribute to defining +2 subsite topology, which may be critical for the enzyme regiospecificity. PMID:24204991

  7. 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

  8. INVESTIGATION OF SHIP-PLUME CHEMISTRY USING A NEWLY-DEVELOPED PHOTOCHEMICAL/DYNAMIC SHIP-PLUME MODEL

    NASA Astrophysics Data System (ADS)

    Song, C. H.; Kim, H.

    2009-12-01

    A photochemical/dynamic ship-plume model, which can consider the ship-plume dynamics and ship-plume chemistry, simultaneously, was developed to gain a better understanding of atmospheric impact of ship emissions. The model performance was then evaluated by a comparison with the observation data measured on a NOAA WP-3D flight during the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2K2) airborne field campaign. The simulation conditions and parameters, such as meteorological conditions, emission rates, and background gas and particulate species concentrations, were obtained directly and/or inferred indirectly from the ITCT 2K2 observation data. The model-predicted concentrations showed good agreement with the observed concentrations of five ambient species (NOx, NOy, ozone, HNO3, and H2SO4) at the eight plume transects by the WP-3D flight with strong correlations around the 1:1 line (0.64≤R≤0.85). In addition, a set of tests were carried out to approximate the magnitude of the reaction probability of HNO3 onto sea-salt particles in the model-observation comparison framework. These results suggest that the reaction probability of HNO3 onto sea-salt particles may be in the order of 0.05-0.1. The equivalent NOx lifetime throughout the “entire plume” was also estimated from photochemical/dynamic ship-plume modeling. The NOx lifetimes estimated throughout the entire ship plume ranged from 2.64 hrs to 3.76 hrs under stable to neutral stability conditions. The short NOx lifetime over the entire ship plume clearly shows that the ship-plume chemistry shortens the NOx lifetime considerably. Therefore, the ship-plume chemistry model should be used to model the changes in ship-plume chemical compositions and better evaluate the atmospheric impact of ocean-going ship emissions.

  9. Investigation of ship-plume chemistry using a newly-developed photochemical/dynamic ship-plume model

    NASA Astrophysics Data System (ADS)

    Kim, H. S.; Song, C. H.; Park, R. S.; Huey, G.; Ryu, J. Y.

    2009-10-01

    A photochemical/dynamic ship-plume model, which can consider the ship-plume dynamics and ship-plume chemistry, simultaneously, was developed to gain a better understanding of atmospheric impact of ship emissions. The model performance was then evaluated by a comparison with the observation data measured on a NOAA WP-3D flight during the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2K2) airborne field campaign. The simulation conditions and parameters, such as meteorological conditions, emission rates, and background gas and particulate species concentrations, were obtained directly and/or inferred indirectly from the ITCT 2K2 observation data. The model-predicted concentrations showed good agreement with the observed concentrations of five ambient species (NOx, NOy, ozone, HNO3, and H2SO4) at the eight plume transects by the WP-3D flight with strong correlations around the 1:1 line (0.64≤R≤0.85). In addition, a set of tests were carried out to approximate the magnitude of the reaction probability of HNO3 onto sea-salt particles in the model-observation comparison framework. These results suggest that the reaction probability of HNO3 onto sea-salt particles may be in the order of 0.05-0.1. The equivalent NOx lifetime throughout the "entire plume" was also estimated from photochemical/dynamic ship-plume modeling. The NOx lifetimes estimated throughout the entire ship plume ranged from 2.64 h to 3.76 h under stable to neutral stability conditions. The short NOx lifetime over the entire ship plume clearly shows that the ship-plume chemistry shortens the NOx lifetime considerably. Therefore, the ship-plume chemistry model should be used to model the changes in ship-plume chemical compositions and better evaluate the atmospheric impact of ocean-going ship emissions.

  10. 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…

  11. 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…

  12. 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…

  13. 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…

  14. A 3-D microfluidic combinatorial cell array.

    PubMed

    Liu, Mike C; Tai, Yu-Chong

    2011-02-01

    We present the development of a three-dimensional (3-D) combinatorial cell culture array device featured with integrated three-input, eight-output combinatorial mixer and cell culture chambers. The device is designed for cell-based screening of multiple compounds simultaneously on a microfluidic platform. The final assembled device is composed of a porous membrane integrated in between a Parylene 3-D microfluidic chip and a PDMS microfluidic chip. The membrane turned the cell culture chambers into two-level configuration to facilitate cell loading and to maintain cells in a diffusion dominated space during device operation. Experimentally, we first characterized the combined compound concentration profile at each chamber using a fluorescence method. We then successfully demonstrated the functionality of the quantitative cell-based assay by culturing B35 rat neuronal cells on this device and screening the ability of three compounds (1,5-dihydroxyisoquinoline, deferoxamine, and 3-aminobenzoic acid) to attenuate cell death caused by cytotoxic hydrogen peroxide. In another experiment, we assayed for the combinatorial effects of three chemotherapeutic compound exposures (vinorelbine, paclitaxel, and γ-linolenic acid) on human breast cancer cells, MDA-MB-231. The same technology will enable the construction of inexpensive lab-on-a-chip devices with high-input combinatorial mixer for performing high-throughput cell-based assay and highly parallel and combinatorial chemical or biochemical reactions. PMID:21063783

  15. 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

  16. 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

  17. 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

  18. 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…

  19. 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…

  20. 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.

  1. Running Clubs--A Combinatorial Investigation.

    ERIC Educational Resources Information Center

    Nissen, Phillip; Taylor, John

    1991-01-01

    Presented is a combinatorial problem based on the Hash House Harriers rule which states that the route of the run should not have previously been traversed by the club. Discovered is how many weeks the club can meet before the rule has to be broken. (KR)

  2. 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.

  3. 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…

  4. Students' Verification Strategies for Combinatorial Problems

    ERIC Educational Resources Information Center

    Mashiach Eizenberg, Michal; Zaslavsky, Orit

    2004-01-01

    We focus on a major difficulty in solving combinatorial problems, namely, on the verification of a solution. Our study aimed at identifying undergraduate students' tendencies to verify their solutions, and the verification strategies that they employ when solving these problems. In addition, an attempt was made to evaluate the level of efficiency…

  5. Dynamic chemistry in the perched groundwater flowing through weathered bedrock underling a steep forested hillslope, north California

    NASA Astrophysics Data System (ADS)

    Kim, H.; Rempe, D. M.; Bishop, J. K.; Dietrich, W.; Fung, I.; Wood, T. J.

    2012-12-01

    average the water table remained elevated as subsequent rainstorms repeatedly recharged the system. Well10 solute concentration slowly increased at the end of the rainy season when the water table fell. In contrast, at the foot of the hill slope, even though the water table was responsive to each rainfall event, its water chemistry developed a strong dilution signatures only during the intense rainstorms (total rainfall > 70mm); the solute concentration decreased (e.g. [Mg] = 0.1mM) during the rising limb of the well hydrograph and recovered back to its pre-event value (e.g. [Mg] = 0.3mM) during the falling limb of the well hydrograph. During small storms, the solute concentration of Well 1 either did not change or slightly increased. Mid-slope showed similar behavior to Well 1. The Well 3 solute concentration was diluted about 3 fold (e.g. [Mg] 0.3mM to 0.1mM) as the water table rose and increased as the water table receded. However unlike Well 1, the water chemistry of Well 3 did not recover to its pre-event composition at any point during the rainy season and the recovery rate was slower than that of Well 1. These water chemistry observations provide insight into the dynamics of water movement within the fractured, weathered bedrock zone, and point to both vertical and lateral mixing processes that influence the chemical evolution of waters.

  6. Dynamical climatology of the NASA Langley Research Center Interactive Modeling Project for Atmospheric Chemistry and Transport (IMPACT) model

    NASA Astrophysics Data System (ADS)

    Pierce, R. Bradley; Al-Saadi, Jassim A.; Eckman, Richard S.; Fairlie, T. Duncan; Grose, William L.; Kleb, Mary M.; Natarajan, Murali; Olson, Jennifer R.

    2000-12-01

    A comparison of the NASA Langley Research Center (LaRC) Interactive Modeling Project for Atmospheric Chemistry and Transport (IMPACT) model's dynamical characteristics with assimilated data sets and observations is presented to demonstrate the ability of the model to represent the dynamical characteristics of Earth's troposphere and stratosphere. The LaRC IMPACT model is a coupled chemical/dynamical general circulation model (GCM) of the Earth's atmosphere extending from the surface to the lower mesosphere. It has been developed as a tool for assessing the effects of chemical, dynamical, and radiative coupling in the stratosphere on the Earth's climate. The LaRC IMPACT model winds and temperatures are found to be in fairly good agreement with Upper Atmospheric Research Satellite (UARS) United Kingdom Meteorological Office (UKMO) assimilated winds and temperatures in the lower stratosphere. The model upper stratospheric zonal mean temperatures are also in good agreement with the UARS-UKMO climatology except for a cold winter pole which results from the upward extension of the cold vortex temperatures and an elevated winter stratopause in the model. The cold pole bias is consistent with the overprediction of the winter stratospheric jet strength, and is characteristic of stratospheric GCMs in general. The model northern and southern hemisphere stratospheric eddy heat and momentum fluxes are within the expected interannual variability of the UARS-UKMO climatology. The combined effects of water vapor transport, radiative, convective, and planetary boundary layer parameterizations are shown to produce tropospheric winds and circulation statistics that are in good agreement with the UARS-UKMO climatology, although the model tropopause and upper tropospheric temperatures are generally cold relative to the UARS-UKMO temperatures. Comparisons between the model and UARS-UKMO climatology indicate that the model does a reasonable job in reproducing the frequency of observed

  7. Multi-Point Combinatorial Optimization Method with Distance Based Interaction

    NASA Astrophysics Data System (ADS)

    Yasuda, Keiichiro; Jinnai, Hiroyuki; Ishigame, Atsushi

    This paper proposes a multi-point combinatorial optimization method based on Proximate Optimality Principle (POP), which method has several advantages for solving large-scale combinatorial optimization problems. The proposed algorithm uses not only the distance between search points but also the interaction among search points in order to utilize POP in several types of combinatorial optimization problems. The proposed algorithm is applied to several typical combinatorial optimization problems, a knapsack problem, a traveling salesman problem, and a flow shop scheduling problem, in order to verify the performance of the proposed algorithm. The simulation results indicate that the proposed method has higher optimality than the conventional combinatorial optimization methods.

  8. Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics

    NASA Astrophysics Data System (ADS)

    Mansbach, Rachael A.; Ferguson, Andrew L.

    2015-03-01

    The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

  9. 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. PMID:26801683

  10. Molecular dynamics based chemistry models of hypervelocity collisions of O(3P) + SO2(X, 1A1) in DSMC.

    PubMed

    Parsons, Neal; Levin, Deborah A; van Duin, Adri C T

    2013-01-28

    A significant process in the formation of the unique atmosphere of Io, a Jovian moon, is collision-induced dissociation of sulfur dioxide. The direct simulation Monte Carlo method (DSMC) is used to model the rarefied gas dynamics of the Ionian atmosphere. However, there is a lack of reliable reaction and collision cross sections needed for hypervelocity conditions. In this work, collisions between SO(2) and O were studied using molecular dynamics/quasi-classical trajectories methods with the potential of Murrell and a force field for reactive systems (ReaxFF). Dissociation to SO was found to be the significant reacting process, but at higher collision energies, complete atomization of SO(2) was found to frequently occur. In contrast, dissociation to O(2) was found to be mostly negligible and formation of SO(3) occurred only at low impact velocities. The chemistry and collision models developed from the Murrell and ReaxFF methods were implemented in DSMC simulations and compared to the baseline DSMC collision and reaction models. It was found that the selection of both the dissociation reaction cross section and the non-reactive collision model has a significant effect on the counterflow, shock gas dynamic structure. PMID:23387593

  11. Synthesis of a Two-Dimensional Covalent Organic Monolayer through Dynamic Imine Chemistry at the Air/Water Interface.

    PubMed

    Dai, Wenyang; Shao, Feng; Szczerbiński, Jacek; McCaffrey, Ryan; Zenobi, Renato; Jin, Yinghua; Schlüter, A Dieter; Zhang, Wei

    2016-01-01

    A two-dimensional covalent organic monolayer was synthesized from simple aromatic triamine and dialdehyde building blocks by dynamic imine chemistry at the air/water interface (Langmuir-Blodgett method). The obtained monolayer was characterized by optical microscopy, scanning electron microscopy, and atomic force microscopy, which unambiguously confirmed the formation of a large (millimeter range), unimolecularly thin aromatic polyimine sheet. The imine-linked chemical structure of the obtained monolayer was characterized by tip-enhanced Raman spectroscopy, and the peak assignment was supported by spectra simulated by density functional theory. Given the modular nature and broad substrate scope of imine formation, the work reported herein opens up many new possibilities for the synthesis of customizable 2D polymers and systematic studies of their structure-property relationships. PMID:26768822

  12. 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.

  13. 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.

  14. 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.

  15. Aquatic chemistry of actinides: Is a thermodynamic approach appropriate to describe natural dynamic systems?

    NASA Astrophysics Data System (ADS)

    Kim, J. I.

    2000-07-01

    The worldwide civilian use of nuclear energy generates yearly about 11,000 tons of spent-fuel from 433 nuclear power plants (NPP) in operation for the moment with an installed capacity of approximately 350 GWe (36 NPP are being under construction). This contributes to the world electricity production about 17%. The hitherto discharged spent-fuel is estimated to be around 220,000 tons, which contain about 1,400 tons of plutonium and a considerable amount of minor actinides and fission products. The total quantity of long-lived radioactive elements mostly actinides, increases steadily. The foreseeable solution for their isolation from the biosphere is a geological disposal with safe confinement. The long-term safety assessment of such containment entails well-founded knowledge on the aquatic chemistry of actinides, most of all, their thermodynamic properties in the geochemical environment.

  16. 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.

  17. 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

  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. Combinatorial approaches to gene recognition.

    PubMed

    Roytberg, M A; Astakhova, T V; Gelfand, M S

    1997-01-01

    Recognition of genes via exon assembly approaches leads naturally to the use of dynamic programming. We consider the general graph-theoretical formulation of the exon assembly problem and analyze in detail some specific variants: multicriterial optimization in the case of non-linear gene-scoring functions; context-dependent schemes for scoring exons and related procedures for exon filtering; and highly specific recognition of arbitrary gene segments, oligonucleotide probes and polymerase chain reaction (PCR) primers. PMID:9440930

  20. 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.

  1. 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)

  2. Carbonate Chemistry Dynamics in an Area of Active Gas Seepage: the Hudson Canyon, US Atlantic Margin

    NASA Astrophysics Data System (ADS)

    Garcia-Tigreros Kodovska, F.; Kessler, J. D.; Leonte, M.; Chepigin, A.; Kellermann, M. Y.; Arrington, E. C.; Valentine, D. L.

    2015-12-01

    The fate of oceanic methane and its impact on the global climate has been of particular interest to the global community. The potential for vast amounts of methane to be emitted from the seafloor into the atmosphere due to gas hydrate decomposition has been under scientific evaluation. However, despite the great extent of these geological reservoirs, much of the methane released from the seafloor in deep ocean environments does not reach the atmosphere. Once dissolved in ocean water, the emitted methane can be microbially converted to either carbon dioxide or assimilated to biomass. Here, we will present results from a research cruise to the Hudson Canyon, northern US Atlantic Margin, where we investigated changes in ocean water carbonate chemistry induced by the oxidation of methane released from gas seeps. We will be presenting high precision pH data as well as methane and DIC concentrations, natural stable isotopes, and methane oxidation rates collected inside and adjacent to the Hudson Canyon in the summer of 2014.

  3. Variation in rubber chemistry and dynamic mechanical properties of the milking liner barrel with age.

    PubMed

    Boast, D; Hale, M; Turner, D; Hillerton, J E

    2008-06-01

    The milking liner is the interface between the milking machine and the cow. Liner properties important to milking performance were investigated for liners of different ages using discriminating tests rather than the normal, rubber-industry quality control-based tests. Large variations in the liner mechanical properties occurred depending on where the sample was taken; stiffness increased 4-fold 40 to 50 mm below the top of the liner. This was related to changes in the chemistry of the rubber created by absorption of milk-derived products (MDP) into the rubber and losses of formulation components, particularly 50% of the plasticizer and all of the antidegradent 40 to 50 mm below the top of the liner, with age and use. The presence of MDP leads to calcium and phosphate deposits on the inner surface of the liner barrel where the MDP was absorbed. The detailed liner properties can be used to explain the forces on the cow's teat and its reactions and effects on milk flow behavior, and to guide future liner development. PMID:18487647

  4. 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.

  5. Combinatorial reliability analysis of multiprocessor computers

    SciTech Connect

    Hwang, K.; Tian-Pong Chang

    1982-12-01

    The authors propose a combinatorial method to evaluate the reliability of multiprocessor computers. Multiprocessor structures are classified as crossbar switch, time-shared buses, and multiport memories. Closed-form reliability expressions are derived via combinatorial path enumeration on the probabilistic-graph representation of a multiprocessor system. The method can analyze the reliability performance of real systems like C.mmp, Tandem 16, and Univac 1100/80. User-oriented performance levels are defined for measuring the performability of degradable multiprocessor systems. For a regularly structured multiprocessor system, it is fast and easy to use this technique for evaluating system reliability with statistically independent component reliabilities. System availability can be also evaluated by this reliability study. 6 references.

  6. Neurotransmitters drive combinatorial multistate postsynaptic density networks.

    PubMed

    Coba, Marcelo P; Pocklington, Andrew J; Collins, Mark O; Kopanitsa, Maksym V; Uren, Rachel T; Swamy, Sajani; Croning, Mike D R; Choudhary, Jyoti S; Grant, Seth G N

    2009-01-01

    The mammalian postsynaptic density (PSD) comprises a complex collection of approximately 1100 proteins. Despite extensive knowledge of individual proteins, the overall organization of the PSD is poorly understood. Here, we define maps of molecular circuitry within the PSD based on phosphorylation of postsynaptic proteins. Activation of a single neurotransmitter receptor, the N-methyl-D-aspartate receptor (NMDAR), changed the phosphorylation status of 127 proteins. Stimulation of ionotropic and metabotropic glutamate receptors and dopamine receptors activated overlapping networks with distinct combinatorial phosphorylation signatures. Using peptide array technology, we identified specific phosphorylation motifs and switching mechanisms responsible for the integration of neurotransmitter receptor pathways and their coordination of multiple substrates in these networks. These combinatorial networks confer high information-processing capacity and functional diversity on synapses, and their elucidation may provide new insights into disease mechanisms and new opportunities for drug discovery. PMID:19401593

  7. 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.

  8. Carbon atom, dimer and trimer chemistry on diamond surfaces from molecular dynamics simulations

    SciTech Connect

    Valone, S.M.

    1995-07-01

    Spectroscopic studies of various atmospheres appearing in diamond film synthesis suggest evidence for carbon atoms, dimers, or trimers. Molecular dynamics simulations with the Brenner hydrocarbon potential are being used to investigate the elementary reactions of these species on a hydrogen-terminated diamond (111) surface. In principle these types of simulations can be extended to simulations of growth morphologies, in the 1-2 monolayer regime presently.

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

    PubMed

    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

  10. 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.

  11. 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

  12. Combinatorial protein design strategies using computational methods.

    PubMed

    Kono, Hidetoshi; Wang, Wei; Saven, Jeffery G

    2007-01-01

    Computational methods continue to facilitate efforts in protein design. Most of this work has focused on searching sequence space to identify one or a few sequences compatible with a given structure and functionality. Probabilistic computational methods provide information regarding the range of amino acid variability permitted by desired functional and structural constraints. Such methods may be used to guide the construction of both individual sequences and combinatorial libraries of proteins. PMID:17041256

  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. Combinatorial Cis-regulation in Saccharomyces Species.

    PubMed

    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

  15. The Combinatorial Trace Method in Action

    ERIC Educational Resources Information Center

    Krebs, Mike; Martinez, Natalie C.

    2013-01-01

    On any finite graph, the number of closed walks of length k is equal to the sum of the kth powers of the eigenvalues of any adjacency matrix. This simple observation is the basis for the combinatorial trace method, wherein we attempt to count (or bound) the number of closed walks of a given length so as to obtain information about the graph's…

  16. Combinatorial and algorithm aspects of hyperbolic polynomials

    SciTech Connect

    Gurvits, Leonid I.

    2004-01-01

    Univariate polynomials with real roots appear quite often in modern combinatorics, especially in the context of integer polytopes. We discovered in this paper rather unexpected and very likely far-reaching connections between hyperbolic polynomials and many classical combinatorial and algorithmic problems. There are still several open problems. The most interesting is a hyperbolic generalization of the van der Waerden conjecture for permanents of doubly stochastic matrices.

  17. Ultrafast spectroscopy of prototypes of electronically nonadiabatic dynamics in solution chemistry

    NASA Astrophysics Data System (ADS)

    Silva, Carlos

    Femtosecond pump-probe spectroscopy of the equilibrated hydrated electron has been recorded with 35-femtosecond time resolution, revealing unprecedented transient features on the 30-80 fs time scales, which exhibit a solvent deuterium isotope effect (τ(D2O)/τ(H2O)~1.4). These previously unresolved dynamics have been assigned to inertial solvation dynamics of the photoexcited excess electron. The results support the importance of librational water motion in the relaxation dynamics of the hydrated electron. High excitation-pulse-intensity measurements reveal evidence of a two-photon channel involving ejection of the hydrated electron from its initial site to a different site in the solvent. Further pump-probe spectroscopy of the equilibrated solvated electron in alcohols has been studied with ~300 fs time resolution. At low pump power the observed dynamics are assigned to s→p excitation and subsequent relaxation of a localized solvated electron. In contrast, at high pump power, two-photon absorption apparently produces mobile 'conduction band' electrons, which are subsequently trapped and relax at a remote site from the initial equilibrated electron as observed for the hydrated electron. The two-photon excitation channel is also observed to induce an ultrafast proton-transfer reaction from the solvent to the excess electron. The metal-metal, charge-transfer (MMCT) absorption bands of the mixed-valence compounds (NH3)5RuIIINCRuII(CN)5/sp- (RuRu) and (NH3)5RuIIINCFeII(CN)5/sp- (RuFe) are studied with sufficient time resolution to measure the back-electron transfer (b-ET) time. In RuRu, the b-ET occurs in 85 ± 10 fs in H2O and increases to 122 ± 20 fs in D2O. Similar b-ET rates in these solvents are also observed for RuFe. The deuterium isotope effect is shown to originate from the solvent demonstrating that hydrogenic solvent motions are directly coupled to the electron transfer event. The pump-probe spectroscopy on the MMCT band also provides information on the

  18. Adaptive Random Testing with Combinatorial Input Domain

    PubMed Central

    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. PMID:24772036

  19. Gravitational instabilities in a protosolar-like disc - I. Dynamics and chemistry

    NASA Astrophysics Data System (ADS)

    Evans, M. G.; Ilee, J. D.; Boley, A. C.; Caselli, P.; Durisen, R. H.; Hartquist, T. W.; Rawlings, J. M. C.

    2015-10-01

    To date, most simulations of the chemistry in protoplanetary discs have used 1 + 1D or 2D axisymmetric α-disc models to determine chemical compositions within young systems. This assumption is inappropriate for non-axisymmetric, gravitationally unstable discs, which may be a significant stage in early protoplanetary disc evolution. Using 3D radiative hydrodynamics, we have modelled the physical and chemical evolution of a 0.17 M⊙ self-gravitating disc over a period of 2000 yr. The 0.8 M⊙ central protostar is likely to evolve into a solar-like star, and hence this Class 0 or early Class I young stellar object may be analogous to our early Solar system. Shocks driven by gravitational instabilities enhance the desorption rates, which dominate the changes in gas-phase fractional abundances for most species. We find that at the end of the simulation, a number of species distinctly trace the spiral structure of our relatively low-mass disc, particularly CN. We compare our simulation to that of a more massive disc, and conclude that mass differences between gravitationally unstable discs may not have a strong impact on the chemical composition. We find that over the duration of our simulation, successive shock heating has a permanent effect on the abundances of HNO, CN and NH3, which may have significant implications for both simulations and observations. We also find that HCO+ may be a useful tracer of disc mass. We conclude that gravitational instabilities induced in lower mass discs can significantly, and permanently, affect the chemical evolution, and that observations with high-resolution instruments such as Atacama Large Millimeter/submillimeter Array (ALMA) offer a promising means of characterizing gravitational instabilities in protosolar discs.

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

    PubMed

    Keshari, Kayvan R; Wilson, David M

    2014-03-01

    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. PMID:24363044

  1. 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

  2. Combinatorial investigation of ferromagnetic shape memory materials

    NASA Astrophysics Data System (ADS)

    Famodu, Olugbenga O.

    2005-07-01

    Combinatorial synthesis is research methodology which allows one to systemically study a large number of compositionally varying samples simultaneously. We apply this technique to the investigation of multifunctional materials. Different designs of combinatorial libraries and various characterization tools are implemented in order to rapidly map composition-structure-property relationships in a variety of materials systems. In this thesis, I will discuss combinatorial investigation of various shape memory alloys. We have utilized the combinatorial magnetron co-sputtering deposition technique for fabricating composition spreads of ternary alloy systems containing ferromagnetic shape memory alloys (FSMAs) and thermoelastic shape memory alloys (SMAs). Magnetic properties of the composition spreads were rapidly characterized using a room temperature scanning semiconducting quantum interference device (SQUID) microscope which provides mapping of the magnetic field emanating from different parts of the composition spreads. By applying the inversion technique to the mapping of the magnetic field distribution, we have mapped the magnetic phase diagram of the Ni-Mn-Ga and Ni-Mn-Al systems whose Heusler compositions Ni2MnGa and Ni2MnAl are well known ferromagnetic shape memory alloys (FSMAs). In addition, a rapid visual inspection technique was developed for detection of reversible martensites using arrays of micromachined cantilevers. A large, previously unexplored compositional region of FSMAs outside the Heusler composition was found. In search of novel FSMAs, we have also investigated a number of other ternary alloys systems. These systems included Ni-Mn-In, Gd-Ge-Si, Co-Mn-Ga, Ni-Fe-Al, and Co-Ni-Ga. A summary of the results from the investigation of these systems is presented. We have used the combinatorial technique to search for "ideal" SMAs with minimal hysteresis. For pursuing this, we had first set out to verify the geometric non-linear theory of martensites which

  3. Plume and wake dynamics, mixing, and chemistry behind an HSCT aircraft

    NASA Technical Reports Server (NTRS)

    Miake-Lye, R. C.; Martinez-Sanchez, M.; Brown, R. C.; Kolb, C. E.

    1991-01-01

    The chemical evolution and mixing and vortical motion of a High Speed Civil Transport's engine exhausts must be analyzed in order to track the gas and its speciation as emissions are mixed to atmospheric scales. Attention is presently given to an analytic model of the wake dynamical processes which accounts for the roll-up of the trailing vorticity, its breakup due to the Crow instability, and the subsequent evolution and motion of the reconnected vorticity. The concentrated vorticity is noted to wrap up the buoyant exhaust and suppress its continued mixing and dilution. The species tracked encompass those which could be heterogeneously reactive on the surfaces of the condensed ice particles, and those capable of reacting with exhaust soot particle surfaces to form active contrail and/or cloud condensation nuclei.

  4. 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. PMID:21168942

  5. 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. PMID:21322700

  6. Direct screening of solution phase combinatorial libraries encoded with externally sensitized photolabile tags

    PubMed Central

    Kottani, Rudresha; Valiulin, Roman A.; Kutateladze, Andrei G.

    2006-01-01

    Solution phase combinatorial chemistry holds an enormous promise for modern drug discovery. Much needed are direct methods to assay such libraries for binding of biological targets. An approach to encoding and screening of solution phase libraries has been developed based on the conditional photorelease of externally sensitized photolabile tags. The encoding tags are released into solution only when a sought-for binding event occurs between the ligand and the receptor, outfitted with an electron-transfer sensitizer. The released tags are analyzed in solution revealing the identity of the lead ligand or narrowing the range of potential leads. PMID:16956977

  7. 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. PMID:2208645

  8. 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. PMID:27467122

  9. Structure of 1-butylpyridinium tetrafluoroborate ionic liquid: quantum chemistry and molecular dynamic simulation studies.

    PubMed

    Sun, Hui; Qiao, Baofu; Zhang, Dongju; Liu, Chengbu

    2010-03-25

    Density functional theory (DFT) calculations combined with molecular dynamic (MD) simulations have been performed to show in detail the structure characteristic of 1-butylpyridinium tetrafluoroborate ([BPy(+)][BF(4)(-)]), a representative of pyridinium-based ionic liquids (ILs). It is found that the relative stability for ion pair configurations is synergically determined by the electrostatic attractions and the H-bond interactions between the ions of opposite charge. [BPy(+)][BF(4)(-)] IL possesses strong long-range ordered structure with cations and anions alternately arranging. The spatial distributions of anions and cations around the given cations are clearly shown, and T-shaped orientation is indicated to play a key role in the interaction between two pyridine rings. DFT calculations and MD simulations uniformly suggest that the H-bonds of the fluorine atoms with the hydrogen atoms on the pyridine rings are stronger than those of the fluorine atoms with the butyl chain hydrogens. The present results can offer useful information for understanding the physicochemical properties of [BPy(+)][BF(4)(-)] IL and further designing new pyridinium-based ILs. PMID:20078103

  10. The chemical mechanism of the limonene ozonolysis reaction in the SOA formation: A quantum chemistry and direct dynamic study

    NASA Astrophysics Data System (ADS)

    Sun, Tingli; Wang, Yudong; Zhang, Chenxi; Sun, Xiaomin; Wang, Wenxing

    2011-03-01

    The ozonolysis of limonene is one of the most important processes for secondary organic aerosol formation and a detailed understanding of the atmospheric chemistry of d-limonene is highly urgent. In this paper, the reaction of d-limonene with O 3 has been studied using high level molecular orbital theory. A detailed description of the possible ozonolysis mechanism in the presence of H 2O or NO is provided. The main products obtained are keto-limonene, limononic acid and 7OH-lim, which are low vapor pressure compounds. On the basis of the quantum chemical information, the direct dynamic calculation is performed and the rate constants are calculated over a temperature range of 200˜800 K using the transition state theory and canonical varitional transition state theory with small-curvature tunneling effect. The four-parameter formula of rate constants with the temperature is fitted and the lifetimes of the reaction species in the troposphere are estimated according to the rate constants, which can provide helpful information to the model simulation study.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1994-02-01

    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.

  13. Recursive deconvolution of combinatorial chemical libraries.

    PubMed

    Erb, E; Janda, K D; Brenner, S

    1994-11-22

    A recursive strategy that solves for the active members of a chemical library is presented. A pentapeptide library with an alphabet of Gly, Leu, Phe, and Tyr (1024 members) was constructed on a solid support by the method of split synthesis. One member of this library (NH2-Tyr-Gly-Gly-Phe-Leu) is a native binder to a beta-endorphin antibody. A variation of the split synthesis approach is used to build the combinatorial library. In four vials, a member of the library's alphabet is coupled to a solid support. After each coupling, a portion of the resin from each of the four reaction vials was set aside and catalogued. The solid support from each vial is then combined, mixed, and redivided. The steps of (i) coupling, (ii) saving and cataloging, and (iii) randomizing were repeated until a pentapeptide library was obtained. The four pentapeptide libraries where the N-terminal amino acid is defined were screened against the beta-endorphin antibody and quantitated via an ELISA. The amino acid of the four pools that demonstrated the most binding was then coupled to the four tetrapeptide partial libraries that had been set aside and catalogued during the split synthesis. This recursive deconvolution was repeated until the best binders were deduced. Besides the anticipated native binder, two other members of the library displayed significant binding. This recursive method of deconvolution does not use a molecular tag, requires only one split synthesis, and can be applied to the deconvolution of nonlinear small-molecule combinatorial libraries and linear oligomeric combinatorial libraries, since it is based only on the procedure of the synthesis. PMID:7972077

  14. On schemes of combinatorial transcription logic

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

    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. Abbreviations: TF, transcription factor RNAP, RNA polymerase DNF, disjunctive normal form CNF, conjunctive normal form

  15. Asymmetric coordination chemistry by chiral-auxiliary-mediated dynamic resolution under thermodynamic control.

    PubMed

    Lin, Zhijie; Gong, Lei; Celik, Mehmet Ali; Harms, Klaus; Frenking, Gernot; Meggers, Eric

    2011-02-01

    A method is presented for the asymmetric synthesis of chiral ruthenium polypyridyl complexes that starts from racemic cis-[Ru(pp)(2)Cl(2)] (pp=2,2'-bipyridine or 1,10-phenanthroline ligands). The chiral bidentate ligands (R)-2-(isopropylsulfinyl)phenol, (R)-SO, and preferably the more electron-rich derivative (R)-2-(isopropylsulfinyl)-4-methoxyphenol, (R)-SO', serve as convenient chiral auxiliaries for the conversion of racemic starting complexes (1a: pp=2,2'-bipyridine; 1b: pp=5,5'-dimethyl-2,2'-bipyridine; c: pp=1,10-phenanthroline) into single diastereomers Λ-[Ru(pp)(2){(R)-SO}]PF(6) (Λ-(S)-2a-c) or Λ-[Ru(pp)(2){(R)-SO'}]PF(6) (Λ-(S)-2a') under a thermodynamically controlled dynamic transformation. The complexes Λ-(S)-2a-c and Λ-(S)-2a' themselves are direct precursors for the generation of optically active ruthenium-polypyridyl complexes by trifluoroacetic-acid-induced replacement of the sulfinylphenolate auxiliaries with bidentate pp ligands under retention of configuration, thereby affording Λ-[Ru(pp)(3)](PF(6))(2) (3a-c) complexes with high enantiomeric ratios of ≥98:2. In particular, by employing the methoxy-modified chiral auxiliary (R)-SO', enantiomeric ratios of >99:1 were reached. In the strategy introduced here, the high steric crowding of an octahedral coordination sphere was exploited by placing a sulfur-based stereocenter in direct proximity to the ruthenium stereocenter, thereby leading to a large difference in the stabilities of the intermediate Λ-S and Δ-S diastereomers and thus providing the opportunity to find suitable reaction conditions for conversion of the destabilized diastereomer into the thermodynamically more-stable one. This method should be of high practical value for the asymmetric synthesis of ruthenium-polypyridyl complexes because it allows one to use readily available racemic ruthenium complexes as starting materials. PMID:21254425

  16. Coordination Chemistry and Structural Dynamics of a Long and Flexible Piperazine-Derived Ligand.

    PubMed

    Hawes, Chris S; Hamilton, Sophie E; Hicks, Jamie; Knowles, Gregory P; Chaffee, Alan L; Turner, David R; Batten, Stuart R

    2016-07-01

    A long and highly flexible internally functionalized dipyridyl ligand α,α'-p-xylylenebis(1-(4-pyridylmethylene)-piper-4-azine), L, has been employed in the synthesis of a series of coordination polymer materials with Co(II), Cd(II), and Ag(I) ions. In poly-[Cd(L)(TPA)] 1 and poly-[Co(L)(IPA)], 2, (TPA = terephthalate, IPA = isophthalate) the ligand adopts a similar linear conformation to that seen in the structure of the unbound molecule and provides a long (2.6 nm) metal-metal bridging distance. Due to the mismatch of edge lengths with that provided by the carboxylate coligands, geometric distortions from the regular dia and (4,4) network geometries for 1 and 2, respectively, are observed. In poly-[Ag2(CF3SO3)2(L)], 3, the ligand coordinates through both pyridine groups and two of the four piperazine nitrogen donors, forming a high-connectivity 2-dimensional network. The compound poly-[Ag2(L)](BF4)2·2MeCN, 4, a porous 3-dimensional cds network, undergoes a fascinating and rapid single-crystal-to-single-crystal rearrangement on exchange of the acetonitrile guests for water in ambient air, forming a nonporous hydrated network poly-[Ag2(L)](BF4)2·2H2O, 5, in which the well-ordered guest water molecules mediate the rearrangement of the tetrafluoroborate anions and the framework itself through hydrogen bonding. The dynamics of the system are examined in greater detail through the preparation of a kinetic product, the dioxane-solvated species poly-[Ag2(L)](BF4)2·2C4H8O2, 6, which undergoes a slow conversion to 5 over the course of approximately 16 h, a transition which can be monitored in real time. The reverse transformation can also be observed on immersing the hydrate 5 in dioxane. The structural features and physical properties of each of the materials can be rationalized based on the flexible and multifunctional nature of the ligand molecule, as well as the coordination behavior of the chosen metal ions. PMID:27328206

  17. 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.

  18. 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.

  19. Solving combinatorial problems: the 15-puzzle.

    PubMed

    Pizlo, Zygmunt; Li, Zheng

    2005-09-01

    We present a series of experiments in which human subjects were tested with a well-known combinatorial problem called the 15-puzzle and in different-sized variants of this puzzle. Subjects can solve these puzzles reliably by systematically building a solution path, without performing much search and without using distances among the states of the problem. The computational complexity of the underlying mental mechanisms is very low. We formulated a computational model of the underlying cognitive processes on the basis of our results. This model applied a pyramid algorithm to individual stages of each problem. The model's performance proved to be quite similar to the subjects' performance. PMID:16496727

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. Cryptographic Combinatorial Clock-Proxy Auctions

    NASA Astrophysics Data System (ADS)

    Parkes, David C.; Rabin, Michael O.; Thorpe, Christopher

    We present a cryptographic protocol for conducting efficient, provably correct and secrecy-preserving combinatorial clock-proxy auctions. The “clock phase” functions as a trusted auction despite price discovery: bidders submit encrypted bids, and prove for themselves that they meet activity rules, and can compute total demand and thus verify price increases without revealing any information about individual demands. In the sealed-bid “proxy phase”, all bids are revealed the auctioneer via time-lapse cryptography and a branch-and-bound algorithm is used to solve the winner-determination problem. Homomorphic encryption is used to prove the correctness of the solution, and establishes the correctness of the solution to any interested party. Still an NP-hard optimization problem, the use of homomorphic encryption imposes additional computational time on winner-determination that is linear in the size of the branch-and-bound search tree, and thus roughly linear in the original (search-based) computational time. The result is a solution that avoids, in the usual case, the exponential complexity of previous cryptographically-secure combinatorial auctions.

  8. 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. PMID:27466125

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. Systematic control of experimental inconsistency in combinatorial materials science.

    PubMed

    Sharma, Asish Kumar; Kulshreshtha, Chandramouli; Sohn, Keemin; Sohn, Kee-Sun

    2009-01-01

    We developed a method to systematically control experimental inconsistency, which is one of the most troublesome and difficult problems in high-throughput combinatorial experiments. The topic of experimental inconsistency is never addressed, even though all scientists in the field of combinatorial materials science face this very serious problem. Experimental inconsistency and material property were selected as dual objective functions that were simultaneously optimized. Specifically, in an attempt to search for promising phosphors with high reproducibility, photoluminescence (PL) intensity was maximized, and experimental inconsistency was minimized by employing a multiobjective evolutionary optimization-assisted combinatorial materials search (MOEO combinatorial material search) strategy. A tetravalent manganese-doped alkali earth germanium/titanium oxide system was used as a model system to be screened using MOEO combinatorial materials search. As a result of MOEO reiteration, we identified a halide-detached deep red phosphor with improved PL intensity and reliable reproducibility. PMID:19061418

  15. 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

  16. Streamwater chemistry and flow dynamics along vegetation-soil gradient in a subalpine Abies fabri forest watershed, China.

    PubMed

    Shan, Bao-Qing; Wang, Wei-Dong; Yin, Cheng-Qing

    2004-01-01

    Streamwater chemistry and spatial flow dynamics from a subalpine Abies fabri forest in an experimental watershed located in the east slope of Gongga Mountain were analyzed to gain insights into the gradient effect of primary community succession on the stream biogeochemical process. Results showed that high sand content (exceeding 80%) and porosity in the soil(exceeding 20% in A horizon and 35% in B horizon), as well as a thick humus layer on the soil surface, made the water exchange quickly in the Huangbengliu (HBL) watershed. Consequently, no surface runoff was observed, and the stream discharge changed rapidly with the daily precipitation. The flow trends of base ions in the stream water were influenced by the Abies fabri succession gradient. Ca2+ , HCO- and SO4(2-) were the dominant anions in the streamwater in this region. A significant difference of Ca2+, HCO3(-) and SO4(2-) concentration exported between the succession stages in the watershed can be found. But they had the similar temporal change in the stream flow. Ca2+, HCO3(-) and SO4(2-) showed significantly negative correlations with the daily precipitation and the stream discharge. Concentrations of Cl-, Na+, K+, and Mg2+ were low in all streamwaters monitored and we observed no differences along the Abies fabri succession gradient. Low ratios of Na: (Na + Ca) (range from 0.1 to 0.2) implied cations were from bedrock weathering (internal source process in the soil system) in this region. But, a variance analysis showed there were almost no differences between rainwater and streamwaters for Mg2+ , Na+, K+, and Cl- concentrations. This indicated that they might be come from rainfall inputs(external source). The highly mobile capacity, rapid water exchange between precipitation and discharge, and long-term export lead to this observed pattern were suggested. PMID:15559799

  17. 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

  18. 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).

  19. 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

    2016-07-01

    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. PMID:26555710

  20. 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.

  1. Combinatorial Approach to Modeling Quantum Systems

    NASA Astrophysics Data System (ADS)

    Kornyak, Vladimir V.

    2016-02-01

    Using the fact that any linear representation of a group can be embedded into permutations, we propose a constructive description of quantum behavior that provides, in particular, a natural explanation of the appearance of complex numbers and unitarity in the formalism of the quantum mechanics. In our approach, the quantum behavior can be explained by the fundamental impossibility to trace the identity of the indistinguishable objects in their evolution. Any observation only provides information about the invariant relations between such objects. The trajectory of a quantum system is a sequence of unitary evolutions interspersed with observations—non-unitary projections. We suggest a scheme to construct combinatorial models of quantum evolution. The principle of selection of the most likely trajectories in such models via the large numbers approximation leads in the continuum limit to the principle of least action with the appropriate Lagrangians and deterministic evolution equations

  2. Fast combinatorial optimization using generalized deterministic annealing

    NASA Astrophysics Data System (ADS)

    Acton, Scott T.; Ghosh, Joydeep; Bovik, Alan C.

    1993-08-01

    Generalized Deterministic Annealing (GDA) is a useful new tool for computing fast multi-state combinatorial optimization of difficult non-convex problems. By estimating the stationary distribution of simulated annealing (SA), GDA yields equivalent solutions to practical SA algorithms while providing a significant speed improvement. Using the standard GDA, the computational time of SA may be reduced by an order of magnitude, and, with a new implementation improvement, Windowed GDA, the time improvements reach two orders of magnitude with a trivial compromise in solution quality. The fast optimization of GDA has enabled expeditious computation of complex nonlinear image enhancement paradigms, such as the Piecewise Constant (PICO) regression examples used in this paper. To validate our analytical results, we apply GDA to the PICO regression problem and compare the results to other optimization methods. Several full image examples are provided that show successful PICO image enhancement using GDA in the presence of both Laplacian and Gaussian additive noise.

  3. 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.

  4. Combinatorial Investigation of Crazes in Polymer Nanocomposites

    NASA Astrophysics Data System (ADS)

    Lee, Jong-Young; Crosby, Alfred

    2005-03-01

    Self-assembled block copolymer nanocomposite thin films aligned by external fields or surface energetics have potential applications as photonic crystals as well as magnetic storage media. However, the presence of surface terraces and embedded nanoparticles can initiate defects such as crazes which can alter the materials' intended functions. We combine the copper grid technique and combinatorial approaches to quantify craze growth in these systems. We present results on the effects of film thickness, surface terraces, and nanoparticles on crazing phenomena in polystyrene and model poly(styrene-b-2-vinyl pyridine) copolymers. These results guide the future design of advanced nanocomposite films while providing fundamental insight into the molecular interactions of polymers and inorganic nanoparticles under mechanical strain.

  5. Solid-state combinatorial screening of (Sr,Ca,Ba, Mg)₂Si₅N₈:Eu(2+) phosphors.

    PubMed

    Lee, Bonghyun; Lee, Sangjun; Jeong, Hyung Gon; Sohn, Kee-Sun

    2011-03-14

    We employed a solid-state combinatorial chemistry technique to screen 4 ternary phosphor systems: (Sr,Ca,Ba)(2)Si(5)N(8):Eu(2+), (Sr,Ca,Mg)(2)Si(5)N(8):Eu(2+), (Sr,Mg,Ba)(2)Si(5)N(8):Eu(2+), and (Ca,Ba,Mg)(2)Si(5)N(8):Eu(2+). The current pure nitride-based system did not allow for the use of conventional liquid solution-based high-throughput experimentation, so that a specially designed solid-state high-throughput powder-dispensing synthesis technique was employed. As a result, four well-defined ternary combinatorial libraries were developed in terms of photoluminescent (PL) intensity and color chromaticity with no skipped compositions, which provided a quantitative relationship between PL properties and the composition of AE(2)Si(5)N(8):Eu(2+) (AE = alkaline earth elements) phosphors. PMID:21275428

  6. 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). PMID:11076562

  7. 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

  8. Geometric differential evolution for combinatorial and programs spaces.

    PubMed

    Moraglio, A; Togelius, J; Silva, S

    2013-01-01

    Geometric differential evolution (GDE) is a recently introduced formal generalization of traditional differential evolution (DE) that can be used to derive specific differential evolution algorithms for both continuous and combinatorial spaces retaining the same geometric interpretation of the dynamics of the DE search across representations. In this article, we first review the theory behind the GDE algorithm, then, we use this framework to formally derive specific GDE for search spaces associated with binary strings, permutations, vectors of permutations and genetic programs. The resulting algorithms are representation-specific differential evolution algorithms searching the target spaces by acting directly on their underlying representations. We present experimental results for each of the new algorithms on a number of well-known problems comprising NK-landscapes, TSP, and Sudoku, for binary strings, permutations, and vectors of permutations. We also present results for the regression, artificial ant, parity, and multiplexer problems within the genetic programming domain. Experiments show that overall the new DE algorithms are competitive with well-tuned standard search algorithms. PMID:23270388

  9. 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. PMID:26923784

  10. 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. PMID:25682046

  11. Droplet pairing and coalescence control for generation of combinatorial signals

    NASA Astrophysics Data System (ADS)

    Um, Eujin; Rogers, Matthew; Stone, Howard

    2013-03-01

    A co-flowing aqueous phase with an immiscible oil phase in a microchannel generates uniformly spaced, monodisperse droplets, which retain their shape by not touching each other or by being stabilized with surfactants at the oil-water interface. However, droplet coalescence is required in many advanced applications, which can be achieved by a complex channel geometry or size differences in the droplets, and as well as by procedures to reduce the effect of a surfactant. These approaches, again, hinder the stability of droplets further downstream. We designed a microchannel which consistently inserts gas-bubble between droplets so that pairing and coalescence of droplets occurs even in the presence of surfactant, and yet prevents unwanted merging with other droplets. Aqueous droplets placed between the bubbles alter their relative speeds and spacing, and consequently we study the change in the number of droplet pairings in relation to the characteristics of the bubbles and the volume of aqueous droplets. By integrating this approach with droplets of different materials, we can program the output sequence of droplet compositions, and such complex combinatorial signals generated are aimed for concentration gradient generation and dynamic stimulation of biological cells with chemicals.

  12. On the existence of binary simplex codes. [using combinatorial construction

    NASA Technical Reports Server (NTRS)

    Taylor, H.

    1977-01-01

    Using a simple combinatorial construction, the existence of a binary simplex code with m codewords for all m is greater than or equal to 1 is proved. The problem of the shortest possible length is left open.

  13. Polysiloxane-Based Autonomic Self-Healing Elastomers Obtained through Dynamic Boronic Ester Bonds Prepared by Thiol-Ene "Click" Chemistry.

    PubMed

    Zuo, Yujing; Gou, Zhiming; Zhang, Changqiao; Feng, Shengyu

    2016-07-01

    Cross-linked silicone elastomers constructed with dynamic-covalent boronic esters are first synthesized by photoinitiated radical thiol-ene "click" chemistry. The resultant samples can be cut with a sharp knife into two pieces and then healed via the reversibility of the boronic ester cross-linkages to restore the original silicone sample within 30 min. Regulation of luminescent properties is achieved by incorporating organic dye into the elastomers through a "one-pot" thiol-ene reaction. The proposed synthesis procedure demonstrates a new strategy to produce boronic acid silicone materials capable of self-healing without external forces. PMID:27159536

  14. 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.

  15. 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. PMID:25985196

  16. 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…

  17. Combinatorial effects of odorants on mouse behavior.

    PubMed

    Saraiva, Luis R; Kondoh, Kunio; Ye, Xiaolan; Yoon, Kyoung-Hye; Hernandez, Marcus; Buck, Linda B

    2016-06-01

    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. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. The impacts of volcanic aerosol on stratospheric ozone and the Northern Hemisphere polar vortex: separating radiative-dynamical changes from direct effects due to enhanced aerosol heterogeneous chemistry

    NASA Astrophysics Data System (ADS)

    Muthers, S.; Arfeuille, F.; Raible, C. C.; Rozanov, E.

    2015-10-01

    After major volcanic eruptions the enhanced aerosol causes ozone changes due to greater heterogeneous chemistry on the particle surfaces (HET-AER) and from dynamical effects related to the radiative heating of the lower stratosphere (RAD-DYN). We carry out a series of experiments with an atmosphere-ocean-chemistry-climate model to assess how these two processes change stratospheric ozone and Northern Hemispheric (NH) polar vortex dynamics. Ensemble simulations are performed under present day and preindustrial conditions, and with aerosol forcings representative of different eruption strength, to investigate changes in the response behaviour. We show that the halogen component of the HET-AER effect dominates under present-day conditions with a global reduction of ozone (-21 DU for the strongest eruption) particularly at high latitudes, whereas the HET-AER effect increases stratospheric ozone due to N2O5 hydrolysis in a preindustrial atmosphere (maximum anomalies +4 DU). The halogen-induced ozone changes in the present-day atmosphere offset part of the strengthening of the NH polar vortex during mid-winter (reduction of up to -16 m s-1 in January) and slightly amplify the dynamical changes in the polar stratosphere in late winter (+11 m s-1 in March). The RAD-DYN mechanism leads to positive column ozone anomalies which are reduced in a present-day atmosphere by amplified polar ozone depletion (maximum anomalies +12 and +18 DU for present day and preindustrial, respectively). For preindustrial conditions, the ozone response is consequently dominated by RAD-DYN processes, while under present-day conditions, HET-AER effects dominate. The dynamical response of the stratosphere is dominated by the RAD-DYN mechanism showing an intensification of the NH polar vortex in winter (up to +10 m s-1 in January). Ozone changes due to the RAD-DYN mechanism slightly reduce the response of the polar vortex after the eruption under present-day conditions.

  5. nifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N2 -fixing community dynamics.

    PubMed

    Collavino, Mónica M; Tripp, H James; Frank, Ildiko E; Vidoz, María L; Calderoli, Priscila A; Donato, Mariano; Zehr, Jonathan P; Aguilar, O Mario

    2014-10-01

    A dataset of 87 020 nifH reads and 16 782 unique nifH protein sequences obtained over 2 years from four locations across a gradient of agricultural soil types in Argentina were analysed to provide a detailed and comprehensive picture of the diversity, abundance and responses of the N2 -fixing community in relation to differences in soil chemistry and agricultural practices. Phylogenetic analysis revealed an expected high proportion of Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria, mainly relatives to Bradyrhizobium and Methylosinus/Methylocystis, but a surprising paucity of Gammaproteobacteria. Analysis of variance and stepwise regression modelling suggested location and treatment-specific influences of soil type on diazotrophic community composition and organic carbon concentrations on nifH diversity. nifH gene abundance, determined by quantitative real-time polymerase chain reaction, was higher in agricultural soils than in non-agricultural soils, and was influenced by soil chemistry under intensive crop rotation but not under monoculture. At some locations, sustainable increased crop yields might be possible through the management of soil chemistry to improve the abundance and diversity of N2 -fixing bacteria. PMID:25314671

  6. 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.

  7. 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.

  8. 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)

  9. 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…

  10. ENVIRONMENTAL CHEMISTRY

    EPA Science Inventory

    Environmental chemistry is applied to estimating the exposure of ecosystems and humans to various chemical environmental stressors. Among the stressors of concern are mercury, pesticides, and arsenic. Advanced analytical chemistry techniques are used to measure these stressors ...

  11. HTS by NMR of Combinatorial Libraries: A Fragment-Based Approach to Ligand Discovery

    PubMed Central

    Wu, Bainan; Zhang, Ziming; Noberini, Roberta; Barile, Elisa; Giulianotti, Marc; Pinilla, Clemencia; Houghten, Richard A.; Pasquale, Elena B.; Pellecchia, Maurizio

    2014-01-01

    SUMMARY Fragment-based ligand design (FBLD) approaches have become more widely used in drug discovery projects from both academia and industry, and are even often preferred to traditional high-throughput screening (HTS) of large collection of compounds (>105). A key advantage of FBLD approaches is that these often rely on robust biophysical methods such as NMR spectroscopy for detection of ligand binding, hence are less prone to artifacts that too often plague the results from HTS campaigns. In this article, we introduce a screening strategy that takes advantage of both the robustness of protein NMR spectroscopy as the detection method, and the basic principles of combinatorial chemistry to enable the screening of large libraries of fragments (>105 compounds) preassembled on a common backbone. We used the method to identify compounds that target protein-protein interactions. PMID:23352136

  12. 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…

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. Forensic Chemistry

    NASA Astrophysics Data System (ADS)

    Bell, Suzanne

    2009-07-01

    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.

  18. Cellular phosphatases facilitate combinatorial processing of receptor-activated signals

    PubMed Central

    Kumar, Dhiraj; Dua, Raina; Srikanth, Ravichandran; Jayaswal, Shilpi; Siddiqui, Zaved; Rao, Kanury VS

    2008-01-01

    Background Although reciprocal regulation of protein phosphorylation represents a key aspect of signal transduction, a larger perspective on how these various interactions integrate to contribute towards signal processing is presently unclear. For example, a key unanswered question is that of how phosphatase-mediated regulation of phosphorylation at the individual nodes of the signaling network translates into modulation of the net signal output and, thereby, the cellular phenotypic response. Results To address the above question we, in the present study, examined the dynamics of signaling from the B cell antigen receptor (BCR) under conditions where individual cellular phosphatases were selectively depleted by siRNA. Results from such experiments revealed a highly enmeshed structure for the signaling network where each signaling node was linked to multiple phosphatases on the one hand, and each phosphatase to several nodes on the other. This resulted in a configuration where individual signaling intermediates could be influenced by a spectrum of regulatory phosphatases, but with the composition of the spectrum differing from one intermediate to another. Consequently, each node differentially experienced perturbations in phosphatase activity, yielding a unique fingerprint of nodal signals characteristic to that perturbation. This heterogeneity in nodal experiences, to a given perturbation, led to combinatorial manipulation of the corresponding signaling axes for the downstream transcription factors. Conclusion Our cumulative results reveal that it is the tight integration of phosphatases into the signaling network that provides the plasticity by which perturbation-specific information can be transmitted in the form of a multivariate output to the downstream transcription factor network. This output in turn specifies a context-defined response, when translated into the resulting gene expression profile. PMID:18798986

  19. 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.

  20. Development of a combinatorial atmospheric pressure cold plasma processor

    NASA Astrophysics Data System (ADS)

    Terajima, Takeshi; Koinuma, Hideomi

    2004-02-01

    Low-temperature plasma can be generated under atmospheric pressure by applying an RF (13.56 MHz) voltage between parallel electrodes, the surfaces of which are preferably covered with an insulator. Applications of this atmospheric pressure cold plasma include thin film deposition, chemical synthesis, etching, resist-ashing, surface treatment, and sterilization. For seeking further improvement of the system and more applications, we have developed a combinatorial atmospheric pressure cold plasma generator to fabricate composition spread thin films by synchronizing the variation of feeding gas ratio with the substrate stage motion. This system can be extended to fabricating a variety of combinatorial libraries by controlling other parameters in the operation such as the gas flow rate, the RF power, substrate temperature, and the treatment time. The utility of this combinatorial plasma process has been demonstrated with the plasma copolymerization of CO 2 with ethylene to fix CO 2 into the plasma polymerized film in the form of ester linkage.

  1. Massively parallel high-order combinatorial genetics in human cells

    PubMed Central

    Wong, Alan S L; Choi, Gigi C G; Cheng, Allen A; Purcell, Oliver; Lu, Timothy K

    2016-01-01

    The systematic functional analysis of combinatorial genetics has been limited by the throughput that can be achieved and the order of complexity that can be studied. To enable massively parallel characterization of genetic combinations in human cells, we developed a technology for rapid, scalable assembly of high-order barcoded combinatorial genetic libraries that can be quantified with high-throughput sequencing. We applied this technology, combinatorial genetics en masse (CombiGEM), to create high-coverage libraries of 1,521 two-wise and 51,770 three-wise barcoded combinations of 39 human microRNA (miRNA) precursors. We identified miRNA combinations that synergistically sensitize drug-resistant cancer cells to chemotherapy and/or inhibit cancer cell proliferation, providing insights into complex miRNA networks. More broadly, our method will enable high-throughput profiling of multifactorial genetic combinations that regulate phenotypes of relevance to biomedicine, biotechnology and basic science. PMID:26280411

  2. 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.

  3. A combinatorial approach to the discovery of advanced materials

    NASA Astrophysics Data System (ADS)

    Sun, Xiao-Dong

    This thesis discusses the application of combinatorial methods to the search of advanced materials. The goal of this research is to develop a "parallel" or "fast sequential" methodology for both the synthesis and characterization of materials with novel electronic, magnetic and optical properties. Our hope is to dramatically accelerate the rate at which materials are generated and studied. We have developed two major combinatorial methodologies to this end. One involves generating thin film materials libraries using a combination of various thin film deposition and masking strategies with multi-layer thin film precursors. The second approach is to generate powder materials libraries with solution precursors delivered with a multi-nozzle inkjet system. The first step in this multistep combinatorial process involves the design and synthesis of high density libraries of diverse materials aimed at exploring a large segment of the compositional space of interest based on our understanding of the physical and structural properties of a particular class of materials. Rapid, sensitive measurements of one or more relevant physical properties of each library member result in the identification of a family of "lead" compositions with a desired property. These compositions are then optimized by continuously varying the stoichiometries of a more focused set of precursors. Materials with the optimal composition are then synthesized in quantities sufficient for detailed characterization of their structural and physical properties. Finally, the information obtained from this process should enhance our predictive ability in subsequent experiments. Combinatorial methods have been successfully used in the synthesis and discovery of materials with novel properties. For example, a class of cobaltite based giant magnetoresistance (GMR) ceramics was discovered; Application of this method to luminescence materials has resulted in the discovery of a few highly efficient tricolor

  4. Combinatorial measurements of Hall effect and resistivity in oxide films.

    PubMed

    Clayhold, J A; Kerns, B M; Schroer, M D; Rench, D W; Logvenov, G; Bollinger, A T; Bozovic, I

    2008-03-01

    A system for the simultaneous measurement of the Hall effect in 31 different locations as well as the measurement of the resistivity in 30 different locations on a single oxide thin film grown with a composition gradient is described. Considerations for designing and operating a high-throughput system for characterizing highly conductive oxides with Hall coefficients as small as 10(-10) m3/C are discussed. Results from measurements on films grown using combinatorial molecular beam epitaxy show the usefulness of characterizing combinatorial libraries via both the resistivity and the Hall effect. PMID:18377026

  5. Mitigation of Control Channel Jamming via Combinatorial Key Distribution

    NASA Astrophysics Data System (ADS)

    Falahati, Abolfazl; Azarafrooz, Mahdi

    The problem of countering control channel jamming against internal adversaries in wireless ad hoc networks is addressed. Using combinatorial key distribution, a new method to secure the control channel access is introduced. This method, utilizes the established keys in the key establishment phase to hide the location of control channels without the need for a secure BS. This is in obtained by combination of a collision free one-way function and a combinatorial key establishment method. The proposed scheme can be considered as a special case of the ALOHA random access schemes which uses the common established keys as its seeds to generate the pattern of transmission.

  6. Some functional metrics in algebraic and combinatorial coding

    NASA Astrophysics Data System (ADS)

    Choen, G.

    1980-06-01

    Three approaches to coding problems can be systematically distinguished: probabilistic (essentially existential), algebraic, and combinatorial. This last approach searches for optimal configurations and relegates to the second order, the problems of complexity related to decoding. Enumeration, graphs, designs, and the extreme theory of groups are used. The optimization of a functional metric was used with the combinatorial approach in order to define the space considered and the distance. The codes then become particular groups of the metric space, which is defined by parameters such as length, number of words, and capacity for correction. Some of these parameters are imposed.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. Theory of site-specific interactions of the combinatorial transcription factors with DNA

    NASA Astrophysics Data System (ADS)

    Murugan, R.

    2010-05-01

    We derive a functional relationship between the mean first passage time associated with the concurrent binding of multiple transcription factors (TFs) at their respective combinatorial cis-regulatory module sites (CRMs) and the number n of TFs involved in the regulation of the initiation of transcription of a gene of interest. Our results suggest that the overall search time τs that is required by the n TFs to locate their CRMs which are all located on the same DNA chain scales with n as τs~nα where α ~ (2/5). When the jump size k that is associated with the dynamics of all the n TFs along DNA is higher than that of the critical jump size kc that scales with the size of DNA N as kc ~ N2/3, we observe a similar power law scaling relationship and also the exponent α. When k < kc, α shows a strong dependence on both n and k. Apparently there is a critical number of combinatorial TFs nc ~ 20 that is required to efficiently regulate the initiation of transcription of a given gene below which (2/5) < α < 1 and beyond which α > 1. These results seem to be independent of the initial distances between the TFs and their corresponding CRMs and also suggest that the maximum number of TFs involved in a given combinatorial regulation of the initiation of transcription of a gene of interest seems to be restricted by the degree of condensation of the genomic DNA. The optimum number mopt of roadblock protein molecules per genome at which the search time associated with these n TFs to locate their binding sites is a minimum seems to scale as mopt~Lnα/2 where L is the sliding length of TFs whose maximum value seems to be such that L <= 104 bps for the E. coli bacterial genome.

  13. 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)

  14. 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)

  15. 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).

  16. 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…

  17. 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.

  18. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

    PubMed Central

    2014-01-01

    Background Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is the most widely used method for characterizing the epigenetic states of chromatin on a genomic scale. With the recent availability of large genome-wide data sets, often comprising several epigenetic marks, novel approaches are required to explore functionally relevant interactions between histone modifications. Computational discovery of "chromatin states" defined by such combinatorial interactions enabled descriptive annotations of genomes, but more quantitative approaches are needed to progress towards predictive models. Results We propose non-negative matrix factorization (NMF) as a new unsupervised method to discover combinatorial patterns of epigenetic marks that frequently co-occur in subsets of genomic regions. We show that this small set of combinatorial "codes" can be effectively displayed and interpreted. NMF codes enable dimensionality reduction and have desirable statistical properties for regression and classification tasks. We demonstrate the utility of codes in the quantitative prediction of Pol2-binding and the discrimination between Pol2-bound promoters and enhancers. Finally, we show that specific codes can be linked to molecular pathways and targets of pluripotency genes during differentiation. Conclusions We have introduced and evaluated a new computational approach to represent combinatorial patterns of epigenetic marks as quantitative variables suitable for predictive modeling and supervised machine learning. To foster widespread adoption of this method we make it available as an open-source software-package – epicode at https://github.com/mcieslik-mctp/epicode. PMID:24472558

  19. 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…

  20. Combinatorial thin film composition mapping using three dimensional deposition profiles.

    PubMed

    Suram, Santosh K; Zhou, Lan; Becerra-Stasiewicz, Natalie; Kan, Kevin; Jones, Ryan J R; Kendrick, Brian M; Gregoire, John M

    2015-03-01

    Many next-generation technologies are limited by material performance, leading to increased interest in the discovery of advanced materials using combinatorial synthesis, characterization, and screening. Several combinatorial synthesis techniques, such as solution based methods, advanced manufacturing, and physical vapor deposition, are currently being employed for various applications. In particular, combinatorial magnetron sputtering is a versatile technique that provides synthesis of high-quality thin film composition libraries. Spatially addressing the composition of these thin films generally requires elemental quantification measurements using techniques such as energy-dispersive X-ray spectroscopy or X-ray fluorescence spectroscopy. Since these measurements are performed ex-situ and post-deposition, they are unable to provide real-time design of experiments, a capability that is required for rapid synthesis of a specific composition library. By using three quartz crystal monitors attached to a stage with translational and rotational degrees of freedom, we measure three-dimensional deposition profiles of deposition sources whose tilt with respect to the substrate is robotically controlled. We exhibit the utility of deposition profiles and tilt control to optimize the deposition geometry for specific combinatorial synthesis experiments. PMID:25832242

  1. Combinatorial thin film composition mapping using three dimensional deposition profiles

    NASA Astrophysics Data System (ADS)

    Suram, Santosh K.; Zhou, Lan; Becerra-Stasiewicz, Natalie; Kan, Kevin; Jones, Ryan J. R.; Kendrick, Brian M.; Gregoire, John M.

    2015-03-01

    Many next-generation technologies are limited by material performance, leading to increased interest in the discovery of advanced materials using combinatorial synthesis, characterization, and screening. Several combinatorial synthesis techniques, such as solution based methods, advanced manufacturing, and physical vapor deposition, are currently being employed for various applications. In particular, combinatorial magnetron sputtering is a versatile technique that provides synthesis of high-quality thin film composition libraries. Spatially addressing the composition of these thin films generally requires elemental quantification measurements using techniques such as energy-dispersive X-ray spectroscopy or X-ray fluorescence spectroscopy. Since these measurements are performed ex-situ and post-deposition, they are unable to provide real-time design of experiments, a capability that is required for rapid synthesis of a specific composition library. By using three quartz crystal monitors attached to a stage with translational and rotational degrees of freedom, we measure three-dimensional deposition profiles of deposition sources whose tilt with respect to the substrate is robotically controlled. We exhibit the utility of deposition profiles and tilt control to optimize the deposition geometry for specific combinatorial synthesis experiments.

  2. 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…

  3. Semiconducting single-walled carbon nanotubes sorting with a removable solubilizer based on dynamic supramolecular coordination chemistry

    NASA Astrophysics Data System (ADS)

    Toshimitsu, Fumiyuki; Nakashima, Naotoshi

    2014-10-01

    Highly pure semiconducting single-walled carbon nanotubes (SWNTs) are essential for the next generation of electronic devices, such as field-effect transistors and photovoltaic applications; however, contamination by metallic SWNTs reduces the efficiency of their associated devices. Here we report a simple and efficient method for the separation of semiconducting- and metallic SWNTs based on supramolecular complex chemistry. We here describe the synthesis of metal-coordination polymers (CP-Ms) composed of a fluorene-bridged bis-phenanthroline ligand and metal ions. On the basis of a difference in the ‘solubility product’ of CP-M-solubilized semiconducting SWNTs and metallic SWNTs, we readily separated semiconducting SWNTs. Furthermore, the CP-M polymers on the SWNTs were simply removed by adding a protic acid and inducing depolymerization to the monomer components. We also describe molecular mechanics calculations to reveal the difference of binding and wrapping mode between CP-M/semiconducting SWNTs and CP-M/metallic SWNTs. This study opens a new stage for the use of such highly pure semiconducting SWNTs in many possible applications.

  4. Chemistry and dynamics of the secondary ozone layer during the sudden stratospheric warming in the southern hemisphere in 2002, using WACCM-SD

    NASA Astrophysics Data System (ADS)

    Smith-Johnsen, Christine; Limpasuvan, Varavut; Yvan, Orsolini; Frode, Stordal

    2015-04-01

    A sudden stratospheric warming (SSW) will affect the chemistry and dynamics of the middle atmosphere, and up to the thermosphere. The major warmings occur roughly every other year in the northern hemispheric winter, but has only been observed once in the southern hemisphere, during the antarctic winter of 2002. In this paper we will investigate the effects of the 2002 southern hemispheric warming on the upper atmosphere, by using the National Centre for Atmospheric Research's Whole Atmosphere Community Climate Model with specified dynamics (WACCM-SD). The secondary ozone layer at around 90km altitude will be the focus, and chemical compounds such as hydrogen, oxygen, carbon monoxide and nitric oxide will be studied as well as the temperature and zonal, meridional and vertical winds, all outputs from WACCM-SD. Three reductions of the zonal mean zonal wind occurs before the final reversal from westerlies to easterlies winds defines the onset of the SSW. At about the same time, at 90 km altitude, an increase of O3 can be seen, and a decrease of NOX, O, CO, H and temperature.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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. PMID:26505910

  10. 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

  11. Extreme events in total ozone over Arosa - Part 2: Fingerprints of atmospheric dynamics and chemistry and effects on mean values and long-term changes

    NASA Astrophysics Data System (ADS)

    Rieder, H. E.; Staehelin, J.; Maeder, J. A.; Peter, T.; Ribatet, M.; Davison, A. C.; Stübi, R.; Weihs, P.; Holawe, F.

    2010-10-01

    In this study the frequency of days with extreme low (termed ELOs) and extreme high (termed EHOs) total ozone values and their influence on mean values and trends are analyzed for the world's longest total ozone record (Arosa, Switzerland). The results show (i) an increase in ELOs and (ii) a decrease in EHOs during the last decades and (iii) that the overall trend during the 1970s and 1980s in total ozone is strongly dominated by changes in these extreme events. After removing the extremes, the time series shows a strongly reduced trend (reduction by a factor of 2.5 for trend in annual mean). Excursions in the frequency of extreme events reveal "fingerprints" of dynamical factors such as ENSO or NAO, and chemical factors, such as cold Arctic vortex ozone losses, as well as major volcanic eruptions of the 20th century (Gunung Agung, El Chichón, Mt. Pinatubo). Furthermore, atmospheric loading of ozone depleting substances leads to a continuous modification of column ozone in the Northern Hemisphere also with respect to extreme values (partly again in connection with polar vortex contributions). Application of extreme value theory allows the identification of many more such "fingerprints" than conventional time series analysis of annual and seasonal mean values. The analysis shows in particular the strong influence of dynamics, revealing that even moderate ENSO and NAO events have a discernible effect on total ozone. Overall the approach to extremal modelling provides new information on time series properties, variability, trends and the influence of dynamics and chemistry, complementing earlier analyses focusing only on monthly (or annual) mean values.

  12. Extreme events in total ozone over Arosa - Part 2: Fingerprints of atmospheric dynamics and chemistry and effects on mean values and long-term changes

    NASA Astrophysics Data System (ADS)

    Rieder, H. E.; Staehelin, J.; Maeder, J. A.; Peter, T.; Ribatet, M.; Davison, A. C.; Stübi, R.; Weihs, P.; Holawe, F.

    2010-05-01

    In this study the frequency of days with extreme low (termed ELOs) and extreme high (termed EHOs) total ozone values and their influence on mean values and trends are analyzed for the world's longest total ozone record (Arosa, Switzerland). The results show (a) an increase in ELOs and (b) a decrease in EHOs during the last decades and (c) that the overall trend during the 1970s and 1980s in total ozone is strongly dominated by changes in these extreme events. After removing the extremes, the time series shows a strongly reduced trend (reduction by a factor of 2.5 for trend in annual mean). Excursions in the frequency of extreme events reveal "fingerprints" of dynamical factors such as ENSO or NAO, and chemical factors, such as cold Arctic vortex ozone losses, as well as major volcanic eruptions of the 20th century (Gunung Agung, El Chichón, Mt. Pinatubo). Furthermore, atmospheric loading of ozone depleting substances leads to a continuous modification of column ozone in the Northern Hemisphere also with respect to extreme values (partly again in connection with polar vortex contributions). Application of extreme value theory allows the identification of many more such "fingerprints" than conventional time series analysis of annual and seasonal mean values. The analysis shows in particular the strong influence of dynamics, revealing that even moderate ENSO and NAO events have a discernible effect on total ozone. Overall the approach to extremal modelling provides new information on time series properties, variability, trends and the influence of dynamics and chemistry, complementing earlier analyses focusing only on monthly (or annual) mean values.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. Pb-free electronics: from nanotechnology to combinatorial materials science

    NASA Astrophysics Data System (ADS)

    Diaz Gonzalez, Alfredo J.

    The elimination of lead (Pb) from the electronics industry due to a government directive caused problems on the manufacturing and use of electronic components. The current alloys used to attach components have a significant higher processing temperature (~30-40°C) that those containing Pb. The higher processing temperatures cause damage to the electronic components; printed circuit boards (PCB) and represents an increase in energetic costs for the manufacurer. Tin whiskers are out-of-plane structures that grow from tin (Sn) plated surfaces and cause short circuits and metal vapor arc. The electrical connection of components to the PCB relies on leads that are close to each other and are manufactured from tin-plated copper. Materials have shown a tendency to modify their bulk properties depending on powder particle size. Nanoparticle's coalescence temperature tends to decrease as particle size decreases. Exploiting this behavior, a nanoparticle based solder paste has been developed for attaching electronic components at a lower processing temperature to avoid thermally induced damage and reduce energy consumption. Tin nanoparticles were successfully synthesized via a wet chemistry route using tin (II) chloride dihydrated (metal precursor), 1,10-Phenanthroline (surfactant), and sodium borohydride (reducing agent). A flux system was developed based on Ethylene Glycol. Results showed acceptable coalescence of the non-capped nanoparticles at temperatures as low as 200°C with a processing time of 20 minutes. Synthesized nanoparticles with capping agent required higher flux content thus resulting in a poor metallic load paste. A reduction in processing temperature of approximately 40°C have been found when comparing the developed solder paste with typical SAC lead-free solders (~240°C). The electrical behavior was found to be an order of magnitude below that of bulk tin. Compositional libraries have been developed in an attempt to screen, via a high through-put method

  18. 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

  19. 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

  20. 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)

  1. 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)

  2. 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)

  3. 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)

  4. 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)

  5. 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)

  6. 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.

  7. 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.

  8. Single-molecule decoding of combinatorially modified nucleosomes.

    PubMed

    Shema, Efrat; Jones, Daniel; Shoresh, Noam; Donohue, Laura; Ram, Oren; Bernstein, Bradley E

    2016-05-01

    Different combinations of histone modifications have been proposed to signal distinct gene regulatory functions, but this area is poorly addressed by existing technologies. We applied high-throughput single-molecule imaging to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. We identified definitively bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. We showed that genetic and chemical perturbations of chromatin enzymes preferentially affect nucleosomes harboring specific modification states. Last, we combined this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes. This single-molecule technology has the potential to address fundamental questions in chromatin biology and epigenetic regulation. PMID:27151869

  9. Characterization of Combinatorial Polymer Blend Composition Gradients by FTIR Microspectroscopy

    PubMed Central

    Eidelman, Naomi; Simon, Carl G.

    2004-01-01

    A new FTIR technique was developed for characterizing thin polymer films used in combinatorial materials science. Fourier transform infrared microspectroscopy mapping technique was used to determine the composition of polymer blend gradients. Composition gradients were made from poly(L-lactic acid) (PLLA) and poly(D,L-lactic acid) (PDLLA) in the form of thin films (6 cm × 2 cm) deposited on IR reflective substrates. Three composition gradient films were prepared and characterized. The results demonstrate the reproducibility and feasibility of a new, high-throughput approach for preparing and characterizing polymer composition gradients. The combination of composition gradient film technology and automated nondestructive FTIR microspectroscopy makes it possible to rapidly and quantitatively characterize polymer composition gradients for use in combinatorial materials science. PMID:27366606

  10. Combinatorial geometry domain decomposition strategies for Monte Carlo simulations

    SciTech Connect

    Li, G.; Zhang, B.; Deng, L.; Mo, Z.; Liu, Z.; Shangguan, D.; Ma, Y.; Li, S.; Hu, Z.

    2013-07-01

    Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)

  11. Elements of informatics for combinatorial solid-state materials science

    NASA Astrophysics Data System (ADS)

    Meguro, S.; Ohnishi, T.; Lippmaa, M.; Koinuma, H.

    2005-01-01

    The main purpose of using combinatorial techniques for materials science studies is to achieve higher experimental throughput than what is possible when samples are synthesized and characterized one at a time. The instrumentation needed for performing high-throughput synthesis and characterization has seen rapid development in recent years. The software tools needed to connect all parts of the materials development process are still largely lacking. In this paper we discuss the requirements of a combinatorial informatics system for materials science experiments. Specifically, we focus on solid-state thin film synthesis. We also describe an implementation of such a system that is based on widely-available open-source software. The system offers features such as remote access via a Web browser, an electronic notebook-style Web interface, automatic upload of new measurement or processing results and rapid preview of experimental data.

  12. An atlas of combinatorial transcriptional regulation in mouse and man

    PubMed Central

    2010-01-01

    SUMMARY Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution. PMID:20211142

  13. Visualizing the chemistry and structure dynamics in lithium-ion batteries by in-situ neutron diffraction

    PubMed Central

    Wang, Xun-Li; An, Ke; Cai, Lu; Feng, Zhili; Nagler, Stephen E.; Daniel, Claus; Rhodes, Kevin J.; Stoica, Alexandru D.; Skorpenske, Harley D.; Liang, Chengdu; Zhang, Wei; Kim, Joon; Qi, Yue; Harris, Stephen J.

    2012-01-01

    We report an in-situ neutron diffraction study of a large format pouch battery cell. The succession of Li-Graphite intercalation phases was fully captured under an 1C charge-discharge condition (i.e., charge to full capacity in 1 hour). However, the lithiation and dilithiation pathways are distinctively different and, unlike in slowing charging experiments with which the Li-Graphite phase diagram was established, no LiC24 phase was found during charge at 1C rate. Approximately 75 mol. % of the graphite converts to LiC6 at full charge, and a lattice dilation as large as 4% was observed during a charge-discharge cycle. Our work demonstrates the potential of in-situ, time and spatially resolved neutron diffraction study of the dynamic chemical and structural changes in “real-world” batteries under realistic cycling conditions, which should provide microscopic insights on degradation and the important role of diffusion kinetics in energy storage materials. PMID:23087812

  14. Size and surface chemistry of nanoparticles lead to a variant behavior in the unfolding dynamics of human carbonic anhydrase.

    PubMed

    Nasir, Irem; Lundqvist, Martin; Cabaleiro-Lago, Celia

    2015-11-01

    The adsorption induced conformational changes of human carbonic anhydrase I (HCAi) and pseudo wild type human carbonic anhydrase II truncated at the 17th residue at the N-terminus (trHCAii) were studied in presence of nanoparticles of different sizes and polarities. Isothermal titration calorimetry (ITC) studies showed that the binding to apolar surfaces is affected by the nanoparticle size in combination with the inherent protein stability. 8-Anilino-1-naphthalenesulfonic acid (ANS) fluorescence revealed that HCAs adsorb to both hydrophilic and hydrophobic surfaces, however the dynamics of the unfolding at the nanoparticle surfaces drastically vary with the polarity. The size of the nanoparticles has opposite effects depending on the polarity of the nanoparticle surface. The apolar nanoparticles induce seconds timescale structural rearrangements whereas polar nanoparticles induce hours timescale structural rearrangements on the same charged HCA variant. Here, a simple model is proposed where the difference in the timescales of adsorption is correlated with the energy barriers for initial docking and structural rearrangements which are firmly regulated by the surface polarity. Near-UV circular dichorism (CD) further supports that both protein variants undergo structural rearrangements at the nanoparticle surfaces regardless of being "hard" or "soft". However, the conformational changes induced by the apolar surfaces differ for each HCA isoform and diverge from the previously reported effect of silica nanoparticles. PMID:26445221

  15. Visualizing the chemistry and structure dynamics in lithium-ion batteries by in-situ neutron diffraction

    SciTech Connect

    Wang, Xun-Li; An, Ke; Cai, Lu; Feng, Zhili; Nagler, Stephen E.; Daniel, Claus; Rhodes, Kevin J.; Stoica, Alexandru D.; Skorpenske, Harley D.; Liang, Chengdu; Zhang, Wei; Kim, Joon; Qi, Yue; Harris, Stephen J.

    2012-10-19

    We report an in-situ neutron diffraction study of a large format pouch battery cell. The succession of Li-Graphite intercalation phases was fully captured under an 1C charge-discharge condition (i.e., charge to full capacity in 1 hour). However, the lithiation and dilithiation pathways are distinctively different and, unlike in slowing charging experiments with which the Li-Graphite phase diagram was established, no LiC24 phase was found during charge at 1C rate. Approximately 75 mol. % of the graphite converts to LiC6 at full charge, and a lattice dilation as large as 4% was observed during a charge-discharge cycle. Our work demonstrates the potential of in-situ, time and spatially resolved neutron diffraction study of the dynamic chemical and structural changes in “real-world” batteries under realistic cycling conditions, which should provide microscopic insights on degradation and the important role of diffusion kinetics in energy storage materials.

  16. Simulation of changes in global ozone and atmospheric dynamics in the 21st century with the chemistry-climate model SOCOL

    NASA Astrophysics Data System (ADS)

    Zubov, V. A.; Rozanov, E. V.; Rozanova, I. V.; Egorova, T. A.; Kiselev, A. A.; Karol', I. L.; Schmutz, V.

    2011-06-01

    The solar climate ozone links (SOCOL) three-dimensional chemistry-climate model is used to estimate changes in the ozone and atmospheric dynamics over the 21st century. With this model, four numerical time-slice experiments were conducted for 1980, 2000, 2050, and 2100 conditions. Boundary conditions for sea-surface temperatures, sea-ice parameters, and concentrations of greenhouse and ozone-depleting gases were set following the IPCC A1B scenario and the WMO A1 scenario. From the model results, a statistically significant cooling of the model stratosphere was obtained to be 4-5 K for 2000-2050 and 3-5 K for 2050-2100. The temperature of the lower atmosphere increases by 2-3 K over the 21st century. Tropospheric heating significantly enhances the activity of planetary-scale waves at the tropopause. As a result, the Eliassen-Palm flux divergence considerable increases in the middle and upper stratosphere. The intensity of zonal circulation decreases and the meridional residual circulation increases, especially in the winter-spring period of each hemisphere. These dynamic changes, along with a decrease in the concentrations of ozone-depleting gases, result in a faster growth of O3 outside the tropics. For example, by 2050, the total ozone in the middle and high latitudes approaches its model level of 1980 and the ozone hole in Antarctica fills up. The superrecovery of the model ozone layer in the middle and high latitudes of both hemispheres occurs in 2100. The tropical ozone layer recovers far less slowly, reaching a 1980 level only by 2100.

  17. Combinatorial synthesis of deuterium-enriched (S)-oxybutynin.

    PubMed

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

    2016-08-01

    The concept of deuterium enrichment has gained more attention due to its advantages in the studies of clinical pharmacokinetics and metabolic profiles. In addition, it is cost and time efficient to develop deuterium-enriched drugs. Herein we built a combinatorial library of deuterated (S)-oxybutynins which all 8 D-compounds were characterized by MS, [Formula: see text] NMR and [Formula: see text]C NMR. PMID:26852022

  18. Authorizing multiple chemical passwords by a combinatorial molecular keypad lock.

    PubMed

    Rout, Bhimsen; Milko, Petr; Iron, Mark A; Motiei, Leila; Margulies, David

    2013-10-16

    A combinatorial fluorescent molecular sensor operates as a highly efficient molecular security system. The ability of a pattern-generating molecule to process diverse sets of chemical inputs, discriminate among their concentrations, and form multivalent and kinetically stable complexes is demonstrated as a powerful tool for processing a wide range of chemical "passwords" of different lengths. This system thus indicates the potential for obtaining unbreakable combination locks at the molecular scale. PMID:24088016

  19. Thermal analysis of combinatorial solid geometry models using SINDA

    NASA Technical Reports Server (NTRS)

    Gerencser, Diane; Radke, George; Introne, Rob; Klosterman, John; Miklosovic, Dave

    1993-01-01

    Algorithms have been developed using Monte Carlo techniques to determine the thermal network parameters necessary to perform a finite difference analysis on Combinatorial Solid Geometry (CSG) models. Orbital and laser fluxes as well as internal heat generation are modeled to facilitate satellite modeling. The results of the thermal calculations are used to model the infrared (IR) images of targets and assess target vulnerability. Sample analyses and validation are presented which demonstrate code products.

  20. Combinatorial aspects of representations of U(n)

    SciTech Connect

    Louck, J.D.

    1996-12-31

    The boson operator theory of the representations of the unitary group, its Wigner-Clebsch-Gordan, and Racah coefficients is reformulated in terms of the ring of polynomials in any number of indeterminates with the goal of bringing the theory, as nearly as possible, under the purview of combinatorial oriented concepts. Four of the basic relations in unitary group theory are interpreted from this viewpoint.

  1. ORGBUG -- A windows-based combinatorial geometry debugger

    SciTech Connect

    Burns, T.J.

    1993-06-01

    ORGBUG is the second half of a two part graphical display and debugging system for combinatorial geometry. The first part of the system consists of a ``view`` generator, CGVIEW. ORGBUG itself is a Microsoft Windows-based application designed to run on a 386 personal computer and to display the ``view`` produced by CGVIEW as an aid to debugging. ORGBUG also includes specific tools to facilitate the identification of geometric features which are inconsistent or in error.

  2. ORGBUG -- A windows-based combinatorial geometry debugger

    SciTech Connect

    Burns, T.J.

    1993-06-01

    ORGBUG is the second half of a two part graphical display and debugging system for combinatorial geometry. The first part of the system consists of a view'' generator, CGVIEW. ORGBUG itself is a Microsoft Windows-based application designed to run on a 386 personal computer and to display the view'' produced by CGVIEW as an aid to debugging. ORGBUG also includes specific tools to facilitate the identification of geometric features which are inconsistent or in error.

  3. Dynamic covalent hydrazine chemistry as a selective extraction and cleanup technique for the quantification of the Fusarium mycotoxin zearalenone in edible oils.

    PubMed

    Siegel, David; Andrae, Karsten; Proske, Matthias; Kochan, Cindy; Koch, Matthias; Weber, Marcus; Nehls, Irene

    2010-04-01

    A novel, cost-efficient method for the analytical extraction of the Fusarium mycotoxin zearalenone (ZON) from edible oils by dynamic covalent hydrazine chemistry (DCHC) was developed and validated for its application with high performance liquid chromatography-fluorescence detection (HPLC-FLD). ZON is extracted from the edible oil by hydrazone formation on a polymer resin functionalised with hydrazine groups and subsequently released by hydrolysis. Specifity and precision of this approach are superior to liquid partitioning or gel permeation chromatography (GPC). DCHC also extracts zearalanone (ZAN) but not alpha-/beta-zearalenol or -zearalanol. The hydrodynamic properties of ZON, which were estimated using molecular simulation data, indicate that the compound is unaffected by nanofiltration through the resin pores and thus selectively extracted. The method's levels of detection and quantification are 10 and 30 microg/kg, using 0.2g of sample. Linearity is given in the range of 10-20,000 microg/kg, the average recovery being 89%. Bias and relative standard deviations do not exceed 7%. In a sample survey of 44 commercial edible oils based on various agricultural commodities (maize, olives, nuts, seeds, etc.) ZON was detected in four maize oil samples, the average content in the positive samples being 99 microg/kg. The HPLC-FLD results were confirmed by HPLC-tandem mass spectrometry and compared to those obtained by a liquid partitioning based sample preparation procedure. PMID:20207360

  4. Manipulation of gold colloidal nanoparticles with atomic force microscopy in dynamic mode: influence of particle–substrate chemistry and morphology, and of operating conditions

    PubMed Central

    Darwich, Samer; Rao, Akshata; Gnecco, Enrico; Jayaraman, Shrisudersan; Haidara, Hamidou

    2011-01-01

    Summary One key component in the assembly of nanoparticles is their precise positioning to enable the creation of new complex nano-objects. Controlling the nanoscale interactions is crucial for the prediction and understanding of the behaviour of nanoparticles (NPs) during their assembly. In the present work, we have manipulated bare and functionalized gold nanoparticles on flat and patterned silicon and silicon coated substrates with dynamic atomic force microscopy (AFM). Under ambient conditions, the particles adhere to silicon until a critical drive amplitude is reached by oscillations of the probing tip. Beyond that threshold, the particles start to follow different directions, depending on their geometry, size and adhesion to the substrate. Higher and respectively, lower mobility was observed when the gold particles were coated with methyl (–CH3) and hydroxyl (–OH) terminated thiol groups. This major result suggests that the adhesion of the particles to the substrate is strongly reduced by the presence of hydrophobic interfaces. The influence of critical parameters on the manipulation was investigated and discussed viz. the shape, size and grafting of the NPs, as well as the surface chemistry and the patterning of the substrate, and finally the operating conditions (temperature, humidity and scan velocity). Whereas the operating conditions and substrate structure are shown to have a strong effect on the mobility of the particles, we did not find any differences when manipulating ordered vs random distributed particles. PMID:21977418

  5. Manipulation of gold colloidal nanoparticles with atomic force microscopy in dynamic mode: influence of particle-substrate chemistry and morphology, and of operating conditions.

    PubMed

    Darwich, Samer; Mougin, Karine; Rao, Akshata; Gnecco, Enrico; Jayaraman, Shrisudersan; Haidara, Hamidou

    2011-01-01

    One key component in the assembly of nanoparticles is their precise positioning to enable the creation of new complex nano-objects. Controlling the nanoscale interactions is crucial for the prediction and understanding of the behaviour of nanoparticles (NPs) during their assembly. In the present work, we have manipulated bare and functionalized gold nanoparticles on flat and patterned silicon and silicon coated substrates with dynamic atomic force microscopy (AFM). Under ambient conditions, the particles adhere to silicon until a critical drive amplitude is reached by oscillations of the probing tip. Beyond that threshold, the particles start to follow different directions, depending on their geometry, size and adhesion to the substrate. Higher and respectively, lower mobility was observed when the gold particles were coated with methyl (-CH(3)) and hydroxyl (-OH) terminated thiol groups. This major result suggests that the adhesion of the particles to the substrate is strongly reduced by the presence of hydrophobic interfaces. The influence of critical parameters on the manipulation was investigated and discussed viz. the shape, size and grafting of the NPs, as well as the surface chemistry and the patterning of the substrate, and finally the operating conditions (temperature, humidity and scan velocity). Whereas the operating conditions and substrate structure are shown to have a strong effect on the mobility of the particles, we did not find any differences when manipulating ordered vs random distributed particles. PMID:21977418

  6. A combinatorial perspective of the protein inference problem.

    PubMed

    Yang, Chao; He, Zengyou; Yu, Weichuan

    2013-01-01

    In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to facilitate the identification of proteins from peptide identification results. However, the relationship between protein identification and peptide identification has not been thoroughly explained before. In this paper, we devote ourselves to a combinatorial perspective of the protein inference problem. We employ combinatorial mathematics to calculate the conditional protein probabilities (protein probability means the probability that a protein is correctly identified) under three assumptions, which lead to a lower bound, an upper bound, and an empirical estimation of protein probabilities, respectively. The combinatorial perspective enables us to obtain an analytical expression for protein inference. Our method achieves comparable results with ProteinProphet in a more efficient manner in experiments on two data sets of standard protein mixtures and two data sets of real samples. Based on our model, we study the impact of unique peptides and degenerate peptides (degenerate peptides are peptides shared by at least two proteins) on protein probabilities. Meanwhile, we also study the relationship between our model and ProteinProphet. We name our program ProteinInfer. Its Java source code, our supplementary document and experimental results are available at: >http://bioinformatics.ust.hk/proteininfer. PMID:24407311

  7. View discovery in OLAP databases through statistical combinatorial optimization

    SciTech Connect

    Hengartner, Nick W; Burke, John; Critchlow, Terence; Joslyn, Cliff; Hogan, Emilie

    2009-01-01

    OnLine Analytical Processing (OLAP) is a relational database technology providing users with rapid access to summary, aggregated views of a single large database, and is widely recognized for knowledge representation and discovery in high-dimensional relational databases. OLAP technologies provide intuitive and graphical access to the massively complex set of possible summary views available in large relational (SQL) structured data repositories. 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.

  8. Controlling Combinatorial Complexity in Software and Malware Behavior Computation

    SciTech Connect

    Pleszkoch, Mark G; Linger, Richard C

    2015-01-01

    Virtually all software is out of intellectual control in that no one knows its full behavior. Software Behavior Computation (SBC) is a new technology for understanding everything software does. SBC applies the mathematics of denotational semantics implemented by function composition in Functional Trace Tables (FTTs) to compute the behavior of programs, expressed as disjoint cases of conditional concurrent assignments. In some circumstances, combinatorial explosions in the number of cases can occur when calculating the behavior of sequences of multiple branching structures. This paper describes computational methods that avoid combinatorial explosions. The predicates that control branching structures such as ifthenelses can be organized into three categories: 1) Independent, resulting in no behavior case explosion, 2) Coordinated, resulting in two behavior cases, or 3) Goaloriented, with potential exponential growth in the number of cases. Traditional FTT-based behavior computation can be augmented by two additional computational methods, namely, Single-Value Function Abstractions (SVFAs) and, introduced in this paper, Relational Trace Tables (RTTs). These methods can be applied to the three predicate categories to avoid combinatorial growth in behavior cases while maintaining mathematical correctness.

  9. Combinatorial search for oxygen reduction reaction electrocatalysts: A review

    NASA Astrophysics Data System (ADS)

    Jeon, Min Ku; Lee, Chang Hwa; Park, Geun Il; Kang, Kweon Ho

    2012-10-01

    Oxygen reduction reaction (ORR) is one of the most interesting research issues in the academia and industries due to its importance in polymer electrolyte membrane fuel cells. Development of new ORR catalysts with low cost and high activity is under intensive research, but it is a time-consuming process because of wide range of alloys to be explored. Combinatorial synthesis and high-throughput screening techniques were suggested as new experimental approaches to accelerate the ORR electrocatalyst research. The combinatorial method is focused on the synthesis of concentrated arrays and quick evaluation of the arrays via various screening techniques. In this report, the combinatorial approaches for the ORR catalyst research were reviewed based on the screening methods. Four screening techniques of optical screening, scanning electrochemical microscopy, multielectrode half cell, and multielectrode full cell were introduced as the representative ones. Other approaches were also briefly introduced. Merits and limitations of each method were discussed and representative research results of each method were shown in detail.

  10. Size and surface chemistry of nanoparticles lead to a variant behavior in the unfolding dynamics of human carbonic anhydrase

    NASA Astrophysics Data System (ADS)

    Nasir, Irem; Lundqvist, Martin; Cabaleiro-Lago, Celia

    2015-10-01

    The adsorption induced conformational changes of human carbonic anhydrase I (HCAi) and pseudo wild type human carbonic anhydrase II truncated at the 17th residue at the N-terminus (trHCAii) were studied in presence of nanoparticles of different sizes and polarities. Isothermal titration calorimetry (ITC) studies showed that the binding to apolar surfaces is affected by the nanoparticle size in combination with the inherent protein stability. 8-Anilino-1-naphthalenesulfonic acid (ANS) fluorescence revealed that HCAs adsorb to both hydrophilic and hydrophobic surfaces, however the dynamics of the unfolding at the nanoparticle surfaces drastically vary with the polarity. The size of the nanoparticles has opposite effects depending on the polarity of the nanoparticle surface. The apolar nanoparticles induce seconds timescale structural rearrangements whereas polar nanoparticles induce hours timescale structural rearrangements on the same charged HCA variant. Here, a simple model is proposed where the difference in the timescales of adsorption is correlated with the energy barriers for initial docking and structural rearrangements which are firmly regulated by the surface polarity. Near-UV circular dichorism (CD) further supports that both protein variants undergo structural rearrangements at the nanoparticle surfaces regardless of being ``hard'' or ``soft''. However, the conformational changes induced by the apolar surfaces differ for each HCA isoform and diverge from the previously reported effect of silica nanoparticles.The adsorption induced conformational changes of human carbonic anhydrase I (HCAi) and pseudo wild type human carbonic anhydrase II truncated at the 17th residue at the N-terminus (trHCAii) were studied in presence of nanoparticles of different sizes and polarities. Isothermal titration calorimetry (ITC) studies showed that the binding to apolar surfaces is affected by the nanoparticle size in combination with the inherent protein stability. 8-Anilino

  11. ISOGENIE: Linking geochemistry, isotopic chemistry and microbial dynamics & community composition in a thawing permafrost peatland, Stordalen Mire, Abisco, Sweden.

    NASA Astrophysics Data System (ADS)

    Chanton, J.; Crill, P. M.; Rich, V.; McCalley, C. K.; Hodgkins, S. B.; Tyson, G.; Logan, T.; Wehr, R.; Mondav, R.; Li, C.; Frolking, S.; Saleska, S. R.

    2011-12-01

    As permafrost thaws, increasing CH4 emissions from northern wetlands are likely to cause positive feedback to atmospheric warming. One of the over-arching goals of this project is to connect geochemical processes, particularly focusing on methane production, to underlying microbial population dynamics and genomics. Recent transformative technical advances in both high throughput investigations of microbial communities and high temporal resolution biogeochemical isotope measurements now permit a uniquely comprehensive approach to opening the microbial "black boxes" that impact carbon cycling on global scales. This project links detailed microbial sampling with detailed geochemical and isotopic sampling on seasonal and diel timescales and has an extensive modeling component. Gas exchange is monitored across the wetland gradients in a series of automated chambers and isotopes of emitted and belowground methane and carbon dioxide are measured with a QC laser system. The mire is in a state of partial thaw. With this thaw is an apparent ecological session in wetland community structure and associated changes in organic matter lability, rates of methane production and microbial community. Our group's study sites range from palsa with underlying permanently frozen peat, to recently collapsed and flooded palsa, to flooded palsa colonized by Sphagnum, to flooded eriophorum sites, to sites populated by Carex, to open water lakes. Across this environmental gradient pH ranges from 4 to 6.5. This change is driven by changes in hydrology as the surface of the thawing permafrost subsides and an adjacent lake drains into the mire. Along this environmental gradient, from palsa to Carex, the lability of the peat increases significantly as determined in incubations of peat material and monitoring of methane and carbon dioxide production rates. Coincident with this environmental gradient is a decrease in the apparent fractionation factor between methane and carbon dioxide and methane

  12. Quantum Adiabatic Optimization and Combinatorial Landscapes

    NASA Technical Reports Server (NTRS)

    Smelyanskiy, V. N.; Knysh, S.; Morris, R. D.

    2003-01-01

    In this paper we analyze the performance of the Quantum Adiabatic Evolution (QAE) algorithm on a variant of Satisfiability problem for an ensemble of random graphs parametrized by the ratio of clauses to variables, gamma = 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 (verses only energy) is used, and are able to show the existence of a dynamic threshold gamma = gammad, beyond which QAE 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.

  13. Combinatorial Regulation in Yeast Transcription Networks

    NASA Astrophysics Data System (ADS)

    Li, Hao

    2006-03-01

    Yeast has evolved a complex network to regulate its transcriptional program in response to changes in environment. It is quite common that in response to an external stimulus, several transcription factors will be activated and they work in combinations to control different subsets of genes in the genome. We are interested in how the promoters of genes are designed to integrate signals from multiple transcription factors and what are the functional and evolutionary constraints. To answer how, we have developed a number of computational algorithms to systematically map the binding sites and target genes of transcription factors using sequence and gene expression data. To analyze the functional constraints, we have employed mechanistic models to study the dynamic behavior of genes regulated by multiple factors. We have also developed methods to trace the evolution of transcriptional networks via comparative analysis of multiple species.

  14. 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.

  15. Radiation Chemistry

    NASA Astrophysics Data System (ADS)

    Wojnárovits, L.

    Ionizing radiation causes chemical changes in the molecules of the interacting medium. The initial molecules change to new molecules, resulting in changes of the physical, chemical, and eventually biological properties of the material. For instance, water decomposes to its elements H2 and O2. In polymers, degradation and crosslinking take place. In biopolymers, e.g., DNS strand breaks and other alterations occur. Such changes are to be avoided in some cases (radiation protection), however, in other cases they are used for technological purposes (radiation processing). This chapter introduces radiation chemistry by discussing the sources of ionizing radiation (radionuclide sources, machine sources), absorption of radiation energy, techniques used in radiation chemistry research, and methods of absorbed energy (absorbed dose) measurements. Radiation chemistry of different classes of inorganic (water and aqueous solutions, inorganic solids, ionic liquids (ILs)) and organic substances (hydrocarbons, halogenated compounds, polymers, and biomolecules) is discussed in concise form together with theoretical and experimental backgrounds. An essential part of the chapter is the introduction of radiation processing technologies in the fields of polymer chemistry, food processing, and sterilization. The application of radiation chemistry to nuclear technology and to protection of environment (flue gas treatment, wastewater treatment) is also discussed.

  16. Carbonate chemistry dynamics and biological processes along a river-sea gradient (Gulf of Trieste, northern Adriatic Sea)

    NASA Astrophysics Data System (ADS)

    Ingrosso, Gianmarco; Giani, Michele; Cibic, Tamara; Karuza, Ana; Kralj, Martina; Del Negro, Paola

    2016-03-01

    In this paper we investigated, for two years and with a bi-monthly frequency, how physical, chemical, and biological processes affect the marine carbonate system in a coastal area characterized by high alkalinity riverine discharge (Gulf of Trieste, northern Adriatic Sea, Mediterranean Sea). By combining synoptic measurements of the carbonate system with in situ determinations of the primary production (14C incorporation technique) and secondary prokaryotic carbon production (3H-leucine incorporation) along a river-sea gradient, we showed that the conservative mixing between river endmember and off-shore waters was the main driver of the dissolved inorganic carbon (DIC) distribution and seasonal variation. However, during spring and summer seasons also the influence of biological uptake and release of DIC was significant. In the surface water of June 2012, the spreading and persistence of nutrient-rich freshwater stimulated the primary production (3.21 μg C L- 1 h- 1) and net biological DIC decrease (- 100 μmol kg- 1), reducing the dissolved CO2 concentration and increasing the pHT. Below the pycnocline of August 2012, instead, an elevated bacterial carbon production rate (0.92 μg C L- 1 h- 1) was related with net DIC increase (92 μmol kg- 1), low dissolved oxygen concentration, and strong pHT reduction, suggesting the predominance of bacterial heterotrophic respiration over primary production. The flux of carbon dioxide estimated at the air-sea interface exerted a low influence on the seasonal variation of the carbonate system. A complex temporal and spatial dynamic of the air-sea CO2 exchange was also detected, due to the combined effects of seawater temperature, river discharge, and water circulation. On annual scale the system was a sink of atmospheric CO2. However, in summer and during elevated riverine discharges, the area close to the river's mouth acted as a source of carbon dioxide. Also the wind speed was crucial in controlling the air-sea CO2

  17. Dynamic Processes in Biology, Chemistry, and Materials Science: Opportunities for UltraFast Transmission Electron Microscopy - Workshop Summary Report

    SciTech Connect

    Kabius, Bernd C.; Browning, Nigel D.; Thevuthasan, Suntharampillai; Diehl, Barbara L.; Stach, Eric A.

    2012-07-25

    This report summarizes a 2011 workshop that addressed the potential role of rapid, time-resolved electron microscopy measurements in accelerating the solution of important scientific and technical problems. A series of U.S. Department of Energy (DOE) and National Academy of Science workshops have highlighted the critical role advanced research tools play in addressing scientific challenges relevant to biology, sustainable energy, and technologies that will fuel economic development without degrading our environment. Among the specific capability needs for advancing science and technology are tools that extract more detailed information in realistic environments (in situ or operando) at extreme conditions (pressure and temperature) and as a function of time (dynamic and time-dependent). One of the DOE workshops, Future Science Needs and Opportunities for Electron Scattering: Next Generation Instrumentation and Beyond, specifically addressed the importance of electron-based characterization methods for a wide range of energy-relevant Grand Scientific Challenges. Boosted by the electron optical advancement in the last decade, a diversity of in situ capabilities already is available in many laboratories. The obvious remaining major capability gap in electron microscopy is in the ability to make these direct in situ observations over a broad spectrum of fast (µs) to ultrafast (picosecond [ps] and faster) temporal regimes. In an effort to address current capability gaps, EMSL, the Environmental Molecular Sciences Laboratory, organized an Ultrafast Electron Microscopy Workshop, held June 14-15, 2011, with the primary goal to identify the scientific needs that could be met by creating a facility capable of a strongly improved time resolution with integrated in situ capabilities. The workshop brought together more than 40 leading scientists involved in applying and/or advancing electron microscopy to address important scientific problems of relevance to DOE’s research

  18. A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules

    PubMed Central

    Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried

    2015-01-01

    A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis. PMID:26355961

  19. High-flexibility combinatorial peptide synthesis with laser-based transfer of monomers in solid matrix material

    PubMed Central

    Loeffler, Felix F.; Foertsch, Tobias C.; Popov, Roman; Mattes, Daniela S.; Schlageter, Martin; Sedlmayr, Martyna; Ridder, Barbara; Dang, Florian-Xuan; von Bojničić-Kninski, Clemens; Weber, Laura K.; Fischer, Andrea; Greifenstein, Juliane; Bykovskaya, Valentina; Buliev, Ivan; Bischoff, F. Ralf; Hahn, Lothar; Meier, Michael A. R.; Bräse, Stefan; Powell, Annie K.; Balaban, Teodor Silviu; Breitling, Frank; Nesterov-Mueller, Alexander

    2016-01-01

    Laser writing is used to structure surfaces in many different ways in materials and life sciences. However, combinatorial patterning applications are still limited. Here we present a method for cost-efficient combinatorial synthesis of very-high-density peptide arrays with natural and synthetic monomers. A laser automatically transfers nanometre-thin solid material spots from different donor slides to an acceptor. Each donor bears a thin polymer film, embedding one type of monomer. Coupling occurs in a separate heating step, where the matrix becomes viscous and building blocks diffuse and couple to the acceptor surface. Furthermore, we can consecutively deposit two material layers of activation reagents and amino acids. Subsequent heat-induced mixing facilitates an in situ activation and coupling of the monomers. This allows us to incorporate building blocks with click chemistry compatibility or a large variety of commercially available non-activated, for example, posttranslationally modified building blocks into the array's peptides with >17,000 spots per cm2. PMID:27296868

  20. High-flexibility combinatorial peptide synthesis with laser-based transfer of monomers in solid matrix material

    NASA Astrophysics Data System (ADS)

    Loeffler, Felix F.; Foertsch, Tobias C.; Popov, Roman; Mattes, Daniela S.; Schlageter, Martin; Sedlmayr, Martyna; Ridder, Barbara; Dang, Florian-Xuan; von Bojničić-Kninski, Clemens; Weber, Laura K.; Fischer, Andrea; Greifenstein, Juliane; Bykovskaya, Valentina; Buliev, Ivan; Bischoff, F. Ralf; Hahn, Lothar; Meier, Michael A. R.; Bräse, Stefan; Powell, Annie K.; Balaban, Teodor Silviu; Breitling, Frank; Nesterov-Mueller, Alexander

    2016-06-01

    Laser writing is used to structure surfaces in many different ways in materials and life sciences. However, combinatorial patterning applications are still limited. Here we present a method for cost-efficient combinatorial synthesis of very-high-density peptide arrays with natural and synthetic monomers. A laser automatically transfers nanometre-thin solid material spots from different donor slides to an acceptor. Each donor bears a thin polymer film, embedding one type of monomer. Coupling occurs in a separate heating step, where the matrix becomes viscous and building blocks diffuse and couple to the acceptor surface. Furthermore, we can consecutively deposit two material layers of activation reagents and amino acids. Subsequent heat-induced mixing facilitates an in situ activation and coupling of the monomers. This allows us to incorporate building blocks with click chemistry compatibility or a large variety of commercially available non-activated, for example, posttranslationally modified building blocks into the array's peptides with >17,000 spots per cm2.

  1. High-flexibility combinatorial peptide synthesis with laser-based transfer of monomers in solid matrix material.

    PubMed

    Loeffler, Felix F; Foertsch, Tobias C; Popov, Roman; Mattes, Daniela S; Schlageter, Martin; Sedlmayr, Martyna; Ridder, Barbara; Dang, Florian-Xuan; von Bojničić-Kninski, Clemens; Weber, Laura K; Fischer, Andrea; Greifenstein, Juliane; Bykovskaya, Valentina; Buliev, Ivan; Bischoff, F Ralf; Hahn, Lothar; Meier, Michael A R; Bräse, Stefan; Powell, Annie K; Balaban, Teodor Silviu; Breitling, Frank; Nesterov-Mueller, Alexander

    2016-01-01

    Laser writing is used to structure surfaces in many different ways in materials and life sciences. However, combinatorial patterning applications are still limited. Here we present a method for cost-efficient combinatorial synthesis of very-high-density peptide arrays with natural and synthetic monomers. A laser automatically transfers nanometre-thin solid material spots from different donor slides to an acceptor. Each donor bears a thin polymer film, embedding one type of monomer. Coupling occurs in a separate heating step, where the matrix becomes viscous and building blocks diffuse and couple to the acceptor surface. Furthermore, we can consecutively deposit two material layers of activation reagents and amino acids. Subsequent heat-induced mixing facilitates an in situ activation and coupling of the monomers. This allows us to incorporate building blocks with click chemistry compatibility or a large variety of commercially available non-activated, for example, posttranslationally modified building blocks into the array's peptides with >17,000 spots per cm(2). PMID:27296868

  2. Long-term changes and trends in total ozone over the northern mid-latitudes: Influence of atmospheric dynamics and chemistry and contribution from extreme events

    NASA Astrophysics Data System (ADS)

    Rieder, H. E.; Staehelin, J.; Maeder, J. A.; Ribatet, M.; di Rocco, S.; Frossard, L.; Jancso, L. M.; Peter, T.; Davison, A. C.

    2010-12-01

    Downward trends in global stratospheric ozone during recent decades have been shown to be directly linked to increasing surface UV-radiation. In the past, long-term ozone trends were determined from homogenized data series by fitting with multiple linear regression models, in which suitable independent variables (so-called explanatory variables) were used to represent atmospheric variability, such as the Quasi-Biennial Oscillation (QBO), the 11-year solar cycle, and a linear trend attributed to anthropogenic ozone depletion. Previous studies have identified a number of other processes influencing total ozone at mid-latitudes, such as synoptic-scale meteorological variability, decadal or long-term climate variability, described e.g. by the Northern Atlantic Oscillation (NAO), the Arctic Oscillation (AO), atmospheric circulation indices ENSO, temperature at the 470-K isentrope level, and volcanic eruptions. Due to the successful implementation of the Montreal Protocol the discussion about a recovery or possible “super recovery” started within the scientific community. Here we address long-term changes and trends in a different framework. As statistical analysis showed that previously used concepts assuming a Gaussian distribution of total ozone data do not address the internal data structure concerning extremes adequately methods from extreme value theory are applied on local (various long-term ground based total ozone records) and regional (high resolution homogenized satellite data) scale. Within the extreme value theory framework days with extreme low (ELOs) and high (EHOs) total ozone are analyzed and their frequency is linked to changes in atmospheric chemistry and dynamics. The results show: (i) an increase in ELOs and (ii) a decrease in EHOs during the last decades and (iii) that the overall trend during the 1970s and 1980s in total ozone is strongly dominated by changes in these extreme events. After removing the extremes, the different time series show a

  3. Atmospheric Chemistry Data Products

    NASA Technical Reports Server (NTRS)

    2003-01-01

    This presentation poster covers data products from the Distributed Active Archive Center (DAAC) of the Goddard Earth Sciences (GES) Data and Information Services Center (DISC). Total Ozone Mapping Spectrometer products (TOMS) introduced in the presentation include TOMS Version 8 as well as Aura, which provides 25 years of TOMS and Upper Atmosphere Research Satellite (UARS) data. The presentation lists a number of atmospheric chemistry and dynamics data sets at DAAC.

  4. Evolution on folding landscapes in combinatorial structures

    SciTech Connect

    Fraser, S.M.; Reidys, C.M.

    1997-11-01

    In this paper the authors investigate the evolution of molecular structures by random point mutations. They will consider two types of molecular structures: (a) (RNA) secondary structures, and (b) random structures. In both cases structure consists of: (1) a contact graph, and (2) a family of relations imposed on its adjacent vertices. The vertex set of the contact graph is simply the set of all indices of a sequence, and its edges are the bonds. The corresponding relations associated with the edges are viewed as secondary base pairing rules and tertiary interaction rules respectively. Mapping of sequences into secondary and random structures are modeled and analyzed. Here, the set of all sequences that map into a particular structure is modeled as a random graph in the sequence space, the so called neutral network and they study how neutral networks are embedded in sequence space. A basic replication of deletion experiment reveals how effective secondary and random structures can be searched by random point mutations and to what extent the structure effects the dynamics of this optimization process. In particular the authors can report a nonlinear relation between the fraction of tertiary interactions in random structures, and the times taken for a population of sequences to find a high fitness target random structure.

  5. SYNTHESIS OF NEW WATER-SOLUBLE METAL-BINDING POLYMERS: COMBINATORIAL CHEMISTRY APPROACH

    EPA Science Inventory

    A variety of metals that require removal and concentration exist in DOE waste, ground, or process waters. These can include, for example, RCRA metals such as mercury in mixed waste, valuable metals such as copper in acid mine drainage, actinides in plutonium processing facilities...

  6. LIGNIFICATION: ARE LIGNINS BIOSYNTHESIZED VIA SIMPLE COMBINATORIAL CHEMISTRY OR VIA PROTEINACEOUS CONTROL AND TEMPLATE REPLICATION?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lignification is the plant cell wall process by which lignin polymers are produced from phenolic monomers. These monomers are primarily the three hydroxycinnamyl (p-coumaryl, coniferyl and sinapyl) alcohols. Structural analysis of cell wall lignins and mechanistic studies of possible biosynthetic pa...

  7. Synthesis of New Water-Soluble Metal-Binding Polymers combinatorial Chemistry Approach

    SciTech Connect

    R. Bryan Miller

    2004-05-07

    (1) Synthesis of Fused Tetraheterocyclic Azepines: (2) Synthesis of Linear Bidentate Diisoxazole and Bidentate Isoxazole-Furyl/Thienyl/Pyridyl Motifs: (3) Synthesis of Pyrazolo[3,4-g] [2,1] dihydrobenzoisoxazol(in)es: (4) Synthesis of Spiro-Fused (C5)-Isozazoline-(C4)-Pyrazolones:

  8. Chemistry Experiments

    NASA Technical Reports Server (NTRS)

    Brasseur, Guy; Remsberg, Ellis; Purcell, Patrick; Bhatt, Praful; Sage, Karen H.; Brown, Donald E.; Scott, Courtney J.; Ko, Malcolm K. W.; Tie, Xue-Xi; Huang, Theresa

    1999-01-01

    The purpose of the chemistry component of the model comparison is to assess to what extent differences in the formulation of chemical processes explain the variance between model results. Observed concentrations of chemical compounds are used to estimate to what degree the various models represent realistic situations. For readability, the materials for the chemistry experiment are reported in three separate sections. This section discussed the data used to evaluate the models in their simulation of the source gases and the Nitrogen compounds (NO(y)) and Chlorine compounds (Cl(y)) species.

  9. Tropospheric chemistry

    NASA Technical Reports Server (NTRS)

    Mohnen, V. A.; Chameides, W.; Demerjian, K. L.; Lenschow, D. H.; Logan, J. A.; Mcneal, R. J.; Penkett, S. A.; Platt, U.; Schurath, U.; Dias, P. D.

    1985-01-01

    The chemistry of the background troposphere, the source region, and the transition regions are discussed. The troposphere is governed by heterogeneous chemistry far more so than the stratosphere. Heterogeneous processes of interest involve scavenging of trace gases by aerosols, cloud and precipitation elements leading to aqueous phase chemical reactions and to temporary and permanent removal of material from the gas phase. Dry deposition is a major removal process for ozone, as well as for other gases of importance in tropospheric photochemistry. These processes are also discussed.

  10. Polymer Chemistry

    NASA Technical Reports Server (NTRS)

    Williams, Martha; Roberson, Luke; Caraccio, Anne

    2010-01-01

    This viewgraph presentation describes new technologies in polymer and material chemistry that benefits NASA programs and missions. The topics include: 1) What are Polymers?; 2) History of Polymer Chemistry; 3) Composites/Materials Development at KSC; 4) Why Wiring; 5) Next Generation Wiring Materials; 6) Wire System Materials and Integration; 7) Self-Healing Wire Repair; 8) Smart Wiring Summary; 9) Fire and Polymers; 10) Aerogel Technology; 11) Aerogel Composites; 12) Aerogels for Oil Remediation; 13) KSC's Solution; 14) Chemochromic Hydrogen Sensors; 15) STS-130 and 131 Operations; 16) HyperPigment; 17) Antimicrobial Materials; 18) Conductive Inks Formulations for Multiple Applications; and 19) Testing and Processing Equipment.

  11. CCLab--a multi-objective genetic algorithm based combinatorial library design software and an application for histone deacetylase inhibitor design.

    PubMed

    Fang, Guanghua; Xue, Mengzhu; Su, Mingbo; Hu, Dingyu; Li, Yanlian; Xiong, Bing; Ma, Lanping; Meng, Tao; Chen, Yuelei; Li, Jingya; Li, Jia; Shen, Jingkang

    2012-07-15

    The introduction of the multi-objective optimization has dramatically changed the virtual combinatorial library design, which can consider many objectives simultaneously, such as synthesis cost and drug-likeness, thus may increase positive rates of biological active compounds. Here we described a software called CCLab (Combinatorial Chemistry Laboratory) for combinatorial library design based on the multi-objective genetic algorithm. Tests of the convergence ability and the ratio to re-take the building blocks in the reference library were conducted to assess the software in silico, and then it was applied to a real case of designing a 5×6 HDAC inhibitor library. Sixteen compounds in the resulted library were synthesized, and the histone deactetylase (HDAC) enzymatic assays proved that 14 compounds showed inhibitory ratios more than 50% against tested 3 HDAC enzymes at concentration of 20 μg/mL, with IC(50) values of 3 compounds comparable to SAHA. These results demonstrated that the CCLab software could enhance the hit rates of the designed library and would be beneficial for medicinal chemists to design focused library in drug development (the software can be downloaded at: http://202.127.30.184:8080/drugdesign.html). PMID:22738629

  12. Coupled phases and combinatorial selection in fluctuating hydrothermal pools: a scenario to guide experimental approaches to the origin of cellular life.

    PubMed

    Damer, Bruce; Deamer, David

    2015-01-01

    Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an "experiment" in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life. PMID:25780958

  13. Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life

    PubMed Central

    Damer, Bruce; Deamer, David

    2015-01-01

    Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an “experiment” in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life. PMID:25780958

  14. Analytical reduction of combinatorial complexity arising from multiple protein modification sites.

    PubMed

    Birtwistle, Marc R

    2015-02-01

    Combinatorial complexity is a major obstacle to ordinary differential equation (ODE) modelling of biochemical networks. For example, a protein with 10 sites that can each be unphosphorylated, phosphorylated or bound to adaptor protein requires 3(10) ODEs. This problem is often dealt with by making ad hoc assumptions which have unclear validity and disallow modelling of site-specific dynamics. Such site-specific dynamics, however, are important in many biological systems. We show here that for a common biological situation where adaptors bind modified sites, binding is slow relative to modification/demodification, and binding to one modified site hinders binding to other sites, for a protein with n modification sites and m adaptor proteins the number of ODEs needed to simulate the site-specific dynamics of biologically relevant, lumped bound adaptor states is independent of the number of modification sites and equal to m + 1, giving a significant reduction in system size. These considerations can be relaxed considerably while retaining reasonably accurate descriptions of the true system dynamics. We apply the theory to model, using only 11 ODEs, the dynamics of ligand-induced phosphorylation of nine tyrosines on epidermal growth factor receptor (EGFR) and primary recruitment of six signalling proteins (Grb2, PI3K, PLCγ1, SHP2, RasA1 and Shc1). The model quantitatively accounts for experimentally determined site-specific phosphorylation and dephosphorylation rates, differential affinities of binding proteins for the phosphorylated sites and binding protein expression levels. Analysis suggests that local concentration of site-specific phosphatases such as SHP2 in membrane subdomains by a factor of approximately 10(7) is critical for effective site-specific regulation. We further show how our framework can be extended with minimal effort to consider binding cooperativity between Grb2 and c-Cbl, which is important for receptor trafficking. Our theory has potentially

  15. Time-dependent combinatory effects of active mechanical loading and passive topographical cues on cell orientation.

    PubMed

    Wang, Qian; Huang, Hanyang; Wei, Kang; Zhao, Yi

    2016-10-01

    Mechanical stretching and topographical cues are both effective mechanical stimulations for regulating cell morphology, orientation, and behaviors. The competition of these two mechanical stimulations remains largely underexplored. Previous studies have suggested that a small cyclic mechanical strain is not able to reorient cells that have been pre-aligned by relatively large linear microstructures, but can reorient those pre-aligned by small linear micro/nanostructures if the characteristic dimension of these structures is below a certain threshold. Likewise, for micro/nanostructures with a given characteristic dimension, the strain must exceed a certain magnitude to overrule the topographic cues. There are however no in-depth investigations of such "thresholds" due to the lack of close examination of dynamic cell orientation during and shortly after the mechanical loading. In this study, the time-dependent combinatory effects of active and passive mechanical stimulations on cell orientation are investigated by developing a micromechanical stimulator. The results show that the cells pre-aligned by linear micro/nanostructures can be altered by cyclic in-plane strain, regardless of the structure size. During the loading, the micro/nanostructures can resist the reorientation effects by cyclic in-plane strain while the resistive capability (measured by the mean orientation angle change and the reorientation speed) increases with the increasing characteristic dimension. The micro/nanostructures also can recover the cell orientation after the cessation of cyclic in-plane strain, while the recovering capability increases with the characteristic dimension. The previously observed thresholds are largely dependent on the observation time points. In order to accurately evaluate the combinatory effects of the two mechanical stimulations, observations during the active loading with a short time interval or endpoint observations shortly after the loading are preferred. This

  16. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Short articles on the kinetics of the hydrogen peroxide-iodide ion reaction, simulation of fluidization catalysis, the use of Newman projection diagrams to represent steric relationships in organic chemistry, the use of synthetic substrates for proteolytic enzyme reactions, and two simple clock reactions"--hydrolysis of halogenoalkanes and…

  17. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents chemistry experiments, laboratory procedures, demonstrations, teaching suggestions, and classroom materials/activities. These include: game for teaching ionic formulas; method for balancing equations; description of useful redox series; computer programs (with listings) for water electrolysis simulation and for determining chemical…

  18. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1978

    1978-01-01

    Describes some laboratory apparatus, chemistry experiments and demonstrations, such as a Kofler block melting point apparatus, chromatographic investigation of the phosphoric acid, x-ray diffraction, the fountain experiment, endothermic sherbet, the measurement of viscosity, ionization energies and electronic configurations. (GA)

  19. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents procedures, experiments, demonstrations, teaching suggestions, and information on a variety of chemistry topics including, for example, inert gases, light-induced reactions, calculators, identification of substituted acetophenones, the elements, analysis of copper minerals, extraction of metallic strontium, equilibrium, halogens, and…

  20. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1980

    1980-01-01

    Presents 12 chemistry notes for British secondary school teachers. Some of these notes are: (1) a simple device for testing pH-meters; (2) portable fume cupboard safety screen; and (3) Mass spectroscopy-analysis of a mass peak. (HM)

  1. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1976

    1976-01-01

    Describes several chemistry projects, including solubility, formula for magnesium oxide, dissociation of dinitrogen tetroxide, use of 1-chloro-2, 4-dinitrobenzene, migration of ions, heats of neutralizations, use of pocket calculators, sonic cleaning, oxidation states of manganese, and cell potentials. Includes an extract from Chemical Age on…

  2. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents chemistry experiments, laboratory procedures, demonstrations, and classroom materials/activities. These include: experiments on colloids, processing of uranium ore, action of heat on carbonates; color test for phenols and aromatic amines; solvent properties of non-electrolytes; stereoscopic applications/methods; a valency balance;…

  3. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Short articles on the alkylation of aniline, the preparation and properties of perbromate, using scrap copper in chemistry instruction, a safe method of burning hydrogen, and the use of an ion-charge model as an alternative to the mole concept in secondary school instruction. (AL)

  4. Combinatorial Development of Biomaterials for Clonal Growth of Human Pluripotent Stem Cells

    PubMed Central

    Mei, Ying; Saha, Krishanu; Bogatyrev, Said R.; Yang, Jing; Hook, Andrew L.; Kalcioglu, Z. Ilke; Cho, Seung-Woo; Mitalipova, Maisam; Pyzocha, Neena; Rojas, Fredrick; Van Vliet, Krystyn J.; Davies, Martyn C.; Alexander, Morgan R.; Langer, Robert; Jaenisch, Rudolf; Anderson, Daniel G.

    2010-01-01

    Both human embryonic stem (hES) cells and induced pluripotent stem (hiPS) cells can self-renew indefinitely in culture, however current methods to clonally grow them are inefficient and poorly-defined for genetic manipulation and therapeutic purposes. Here we develop the first chemically-defined, xeno-free, feeder-free synthetic substrates to support robust self-renewal of fully-dissociated hES and hiPS cells. Materials properties including wettability, surface topography, surface chemistry and indentation elastic modulus of all polymeric substrates were quantified using high-throughput methods to develop structure/function relationships between materials properties and biological performance. These analyses show that optimal hES cell substrates are generated from monomers with high acrylate content, have a moderate wettability, and employ integrin αvβ3 and αvβ5 engagement with adsorbed vitronectin to promote colony formation. The structure/function methodology employed herein provides a general framework for the combinatorial development of synthetic substrates for stem cell culture. PMID:20729850

  5. Combinatorial development of biomaterials for clonal growth of human pluripotent stem cells

    NASA Astrophysics Data System (ADS)

    Mei, Ying; Saha, Krishanu; Bogatyrev, Said R.; Yang, Jing; Hook, Andrew L.; Kalcioglu, Z. Ilke; Cho, Seung-Woo; Mitalipova, Maisam; Pyzocha, Neena; Rojas, Fredrick; van Vliet, Krystyn J.; Davies, Martyn C.; Alexander, Morgan R.; Langer, Robert; Jaenisch, Rudolf; Anderson, Daniel G.

    2010-09-01

    Both human embryonic stem cells and induced pluripotent stem cells can self-renew indefinitely in culture; however, present methods to clonally grow them are inefficient and poorly defined for genetic manipulation and therapeutic purposes. Here we develop the first chemically defined, xeno-free, feeder-free synthetic substrates to support robust self-renewal of fully dissociated human embryonic stem and induced pluripotent stem cells. Material properties including wettability, surface topography, surface chemistry and indentation elastic modulus of all polymeric substrates were quantified using high-throughput methods to develop structure-function relationships between material properties and biological performance. These analyses show that optimal human embryonic stem cell substrates are generated from monomers with high acrylate content, have a moderate wettability and employ integrin αvβ3 and αvβ5 engagement with adsorbed vitronectin to promote colony formation. The structure-function methodology employed herein provides a general framework for the combinatorial development of synthetic substrates for stem cell culture.

  6. Sugar amino acid based scaffolds--novel peptidomimetics and their potential in combinatorial synthesis.

    PubMed

    Chakraborty, Tushar K; Jayaprakash, Sarva; Ghosh, Subhash

    2002-08-01

    To meet the growing demands for the development of new molecular entities for discovering new drugs and materials, organic chemists have started looking for new concepts to supplement traditional approaches. In one such approach, the expertise gained over the years in the area of organic synthesis and the rational drug-design concepts are combined together to create "nature-like" and yet unnatural organic molecules that are expected to provide leads in discovering new molecules. Emulating the basic principles followed by nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl groups provide an excellent opportunity for organic chemists to create structural diversities akin to nature's molecular arsenal. Recent advances in the area of combinatorial chemistry give unprecedented technological support for rapid compilations of sugar amino acid-based libraries exploiting the diversities of carbohydrate molecules and well-developed solid-phase peptide synthesis methods. This review chronicles the development of sugar amino acids as a novel class of peptidomimetic building blocks and their applications in generating desired secondary structures in peptides as well as in creating mimics of natural biopolymers. PMID:12180903

  7. Decoding Split and Pool Combinatorial Libraries with Electron-Transfer Dissociation Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Sarkar, Mohosin; Pascal, Bruce D.; Steckler, Caitlin; Aquino, Claudio; Micalizio, Glenn C.; Kodadek, Thomas; Chalmers, Michael J.

    2013-07-01

    Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening "hit" are essential. Here we describe an electron-transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described "chiral oligomers of pentenoic amides (COPAs)" yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated 79Br/81Br isotope "tags" to differentiate N- and C-terminal product ions. In addition, we have created "Hit-Find," a software program that allows users to generate libraries in silico . The user can then search all possible members of the chemical library for those that fall within a user-defined mass error.

  8. Decoding Split and Pool Combinatorial Libraries with Electron Transfer Dissociation Tandem Mass Spectrometry

    PubMed Central

    Sarkar, Mohosin; Pascal, Bruce D.; Steckler, Caitlin; Aquino, Claudio; Micalizio, Glenn C.; Kodadek, Thomas; Chalmers, Michael J.

    2015-01-01

    Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening “hit” are essential. Here we describe an electron transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described “chiral oligomers of pentenoic amides (COPAs)” yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated 79Br/81Br isotope “tags” to differentiate N- and C-terminal product ions. In addition, we have created “Hit-Find,” a software program that allows users to generate libraries in silico. The user can then search all possible members of the chemical library for those that fall within a user-defined mass error. PMID:23636859

  9. Development of Combinatorial Methods for Alloy Design and Optimization

    SciTech Connect

    Pharr, George M.; George, Easo P.; Santella, Michael L

    2005-07-01

    The primary goal of this research was to develop a comprehensive methodology for designing and optimizing metallic alloys by combinatorial principles. Because conventional techniques for alloy preparation are unavoidably restrictive in the range of alloy composition that can be examined, combinatorial methods promise to significantly reduce the time, energy, and expense needed for alloy design. Combinatorial methods can be developed not only to optimize existing alloys, but to explore and develop new ones as well. The scientific approach involved fabricating an alloy specimen with a continuous distribution of binary and ternary alloy compositions across its surface--an ''alloy library''--and then using spatially resolved probing techniques to characterize its structure, composition, and relevant properties. The three specific objectives of the project were: (1) to devise means by which simple test specimens with a library of alloy compositions spanning the range interest can be produced; (2) to assess how well the properties of the combinatorial specimen reproduce those of the conventionally processed alloys; and (3) to devise screening tools which can be used to rapidly assess the important properties of the alloys. As proof of principle, the methodology was applied to the Fe-Ni-Cr ternary alloy system that constitutes many commercially important materials such as stainless steels and the H-series and C-series heat and corrosion resistant casting alloys. Three different techniques were developed for making alloy libraries: (1) vapor deposition of discrete thin films on an appropriate substrate and then alloying them together by solid-state diffusion; (2) co-deposition of the alloying elements from three separate magnetron sputtering sources onto an inert substrate; and (3) localized melting of thin films with a focused electron-beam welding system. Each of the techniques was found to have its own advantages and disadvantages. A new and very powerful technique for

  10. Identifying combinatorial regulation of transcription factors and binding motifs

    PubMed Central

    Kato, Mamoru; Hata, Naoya; Banerjee, Nilanjana; Futcher, Bruce; Zhang, Michael Q

    2004-01-01

    Background Combinatorial interaction of transcription factors (TFs) is important for gene regulation. Although various genomic datasets are relevant to this issue, each dataset provides relatively weak evidence on its own. Developing methods that can integrate different sequence, expression and localization data have become important. Results Here we use a novel method that integrates chromatin immunoprecipitation (ChIP) data with microarray expression data and with combinatorial TF-motif analysis. We systematically identify combinations of transcription factors and of motifs. The various combinations of TFs involved multiple binding mechanisms. We reconstruct a new combinatorial regulatory map of the yeast cell cycle in which cell-cycle regulation can be drawn as a chain of extended TF modules. We find that the pairwise combination of a TF for an early cell-cycle phase and a TF for a later phase is often used to control gene expression at intermediate times. Thus the number of distinct times of gene expression is greater than the number of transcription factors. We also see that some TF modules control branch points (cell-cycle entry and exit), and in the presence of appropriate signals they can allow progress along alternative pathways. Conclusions Combining different data sources can increase statistical power as demonstrated by detecting TF interactions and composite TF-binding motifs. The original picture of a chain of simple cell-cycle regulators can be extended to a chain of composite regulatory modules: different modules may share a common TF component in the same pathway or a TF component cross-talking to other pathways. PMID:15287978

  11. Star clusters evolution simulation on basement of linguo- combinatorial approach

    NASA Astrophysics Data System (ADS)

    Ignatyev, Mikhail B.

    2015-08-01

    Each of the clusters of star systems can be described using linguo- combinatorial approach through a formula that determines the number of arbitrary factors in the structure of equivalent equations as the number of combinations of n by m + 1, where n - number of stars in the cluster, m - number of constraints imposed on the stars cluster(M.Ignatyev “The linguo- combinatorial simulation in modern physics”\\\\ J. of Modern Physics,USA, 2012, Vol.1, No 1, p.7-11). Such clusters can be multiple, they can be combined into larger clusters or clusters can decay based on the effect of the collective. For example, if we have two clusters are characterized by the number of arbitrary coefficients S1 and S2, wherem1 + 1 m2 + 1S1 = C S2 = Cn1 n2then by imposing general restrictions mcol we will havem1 + m2 + mcol +1Scol = Cn1 + n2At the same time, depending on the specific parameters can be Scol > S1 + S2, when the union in collective increases the adaptive capabilities, and can be Scol < S1 + S2, where adaptive capacity of less than the sum of the collective adaptation a possibly initial clusters. In the first case, we can observe the effect of the formation of new large clusters, in the second case - the collapse of large clusters into smaller ones. The report deals with the simulation of the evolution of star clusters on the basement of linguo- combinatorial approach.

  12. Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila

    PubMed Central

    Warnefors, Maria; Hartmann, Britta; Thomsen, Stefan; Alonso, Claudio R.

    2016-01-01

    Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control. We also note that the gene regulatory roles of intronic and intergenic UCEs (iUCEs) are distinct from those found in exonic UCEs (eUCEs). In iUCEs, transcription factor (TF) and epigenetic factor binding data strongly support iUCE roles in transcriptional and epigenetic regulation. In contrast, analyses of eUCEs indicate that they are two orders of magnitude more likely than the expected to simultaneously include protein-coding sequence, TF-binding sites, splice sites, and RNA editing sites but have reduced roles in transcriptional or epigenetic regulation. Furthermore, we use a Drosophila cell culture system and transgenic Drosophila embryos to validate the notion of UCE combinatorial regulatory roles using an eUCE within the Hox gene Ultrabithorax and show that its protein-coding region also contains alternative splicing regulatory information. Taken together our experiments indicate that UCEs emerge as a result of combinatorial gene regulatory roles and highlight common features in mammalian and insect UCEs implying that similar processes might underlie ultraconservation in diverse animal taxa. PMID:27247329

  13. Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila.

    PubMed

    Warnefors, Maria; Hartmann, Britta; Thomsen, Stefan; Alonso, Claudio R

    2016-09-01

    Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control. We also note that the gene regulatory roles of intronic and intergenic UCEs (iUCEs) are distinct from those found in exonic UCEs (eUCEs). In iUCEs, transcription factor (TF) and epigenetic factor binding data strongly support iUCE roles in transcriptional and epigenetic regulation. In contrast, analyses of eUCEs indicate that they are two orders of magnitude more likely than the expected to simultaneously include protein-coding sequence, TF-binding sites, splice sites, and RNA editing sites but have reduced roles in transcriptional or epigenetic regulation. Furthermore, we use a Drosophila cell culture system and transgenic Drosophila embryos to validate the notion of UCE combinatorial regulatory roles using an eUCE within the Hox gene Ultrabithorax and show that its protein-coding region also contains alternative splicing regulatory information. Taken together our experiments indicate that UCEs emerge as a result of combinatorial gene regulatory roles and highlight common features in mammalian and insect UCEs implying that similar processes might underlie ultraconservation in diverse animal taxa. PMID:27247329

  14. Combinatorial synthesis and screening of fuel cell catalysts

    NASA Astrophysics Data System (ADS)

    Jayaraman, Shrisudersan

    Polymer electrolyte membrane fuel cells (PEMFCs) are compact power sources that can operate with high efficiencies and low emission of environmentally harmful gases. One of the major barriers impeding the development of PEMFCs as a competitive energy source is the inability of existing anode catalysts to oxidize fuels other than hydrogen at sufficient levels due to catalyst deactivation by carbon monoxide (CO) and other partial oxidation products. The focus of this research is the development and application of combinatorial strategies to construct and interrogate electrooxidation (anode) catalysts pertaining to PEMFCs to discover catalysts with enhanced performance in catalyst deactivating environments. A novel method (known as the "gel-transfer" method) for synthesizing catalyst composition gradient libraries for combinatorial catalyst discovery was developed. This method involved transferring a spatial concentration gradient of precursor metal salts created within a polymer gel on to a solid conducting substrate by electrochemical reduction. Chemically sensitive surface-imaging techniques, namely, scanning electrochemical microscopy (SECM) and optical screening with a pH-dependent fluorescence probe were used to characterize the combinatorial catalyst samples. The utility of SECM as a screening tool to measure the activity of multicomponent catalyst libraries towards fuel cell electrooxidation reactions was established with simple catalyst libraries including a platinum coverage gradient and platinum-ruthenium and platinum-ruthenium-molybdenum arrays. A platinum-ruthenium surface composition gradient was constructed through the gel-transfer method and its reactivity towards hydrogen oxidation in the presence of a catalyst poison (CO) was mapped using the SECM. Ruthenium composition between 20 and 30% exhibited superior performance than the rest of the binary. The gel-transfer method was extended to construct a ternary platinum-ruthenium-rhodium catalyst library

  15. Discovery of methanol electro-oxidation catalysts by combinatorial analysis

    SciTech Connect

    Mallouk, T.E.; Reddington, E.; Pu, C.

    1996-12-31

    Hydrogen fuel cells are likely to become a major energy source in the next century, but they are not ideal for all applications. A safe alternative fuel with a high energy density will be necessary for transportation and mobile applications. Direct methanol-air fuel cells (DMFCs) are an attractive alternative to hydrogen fuel cells because of the high energy density and low cost of methanol as a fuel. However, in order for DMFCs to become commercially viable, better electrocatalysts for the anode reaction need to be developed. This paper describes a combinatorial technique for generating an array of electrodes with varying metal compositions.

  16. A macromolecular prodrug strategy for combinatorial drug delivery.

    PubMed

    Li, Nan-Nan; Lin, Jiantao; Gao, Di; Zhang, Li-Ming

    2014-03-01

    A novel macromolecular prodrug strategy was developed for the combinatorial delivery of two poorly water-soluble drugs, dexamethasone and doxorubicin. In this work, dexamethasone was firstly conjugated onto a water-soluble modified polysaccharide by an acid-labile hydrazone linkage. The resultant macromolecular prodrug had an amphiphilic character and could self-assemble into spherical polymeric micelles in aqueous system. With these micelles, doxorubicin was then encapsulated into their hydrophobic cores. For the conjugated dexamethasone and encapsulated doxorubicin, they could exhibit independent and acid-sensitive release characteristics. For the doxorubicin-loaded prodrug micelles, they were easily be internalized by living cells and showed obvious antitumor activity. PMID:24407691

  17. A matrix product state method for solving combinatorial optimization problems

    NASA Astrophysics Data System (ADS)

    Pelton, S. S.; Chamon, C.; Mucciolo, E. R.

    2015-03-01

    We present a method based on a matrix product state representation to solve combinatorial optimization problems. All constraints are met by mapping Boolean gates into projection operators and applying operators sequentially. The method provides exact solutions with high success probability, even in the case of frustrated systems. The computational cost of the method is controlled by the maximum relative entropy of the system. Results of numerical simulations for several types of problems will be shown and discussed. NSF Grants CCF-1116590 and CCF-1117241.

  18. Plasma sputtering system for deposition of thin film combinatorial libraries

    NASA Astrophysics Data System (ADS)

    Cooper, James S.; Zhang, Guanghai; McGinn, Paul J.

    2005-06-01

    The design of a plasma sputtering system for the deposition of combinatorial libraries is described. A rotating carousel is used to position shadow masks between the targets and the substrate. Multilayer films are built up by depositing sequentially through various masks. Postdeposition annealing is used to promote interdiffusion of the layered structures. Either discrete or compositional gradient libraries can be deposited in this system. Samples appropriate for characterization with a scanning electrochemical microscope or a multichannel microelectrode array system can be produced. The properties of some deposited Pt-Ru films for fuel cell applications are described.

  19. Computational chemistry

    NASA Technical Reports Server (NTRS)

    Arnold, J. O.

    1987-01-01

    With the advent of supercomputers, modern computational chemistry algorithms and codes, a powerful tool was created to help fill NASA's continuing need for information on the properties of matter in hostile or unusual environments. Computational resources provided under the National Aerodynamics Simulator (NAS) program were a cornerstone for recent advancements in this field. Properties of gases, materials, and their interactions can be determined from solutions of the governing equations. In the case of gases, for example, radiative transition probabilites per particle, bond-dissociation energies, and rates of simple chemical reactions can be determined computationally as reliably as from experiment. The data are proving to be quite valuable in providing inputs to real-gas flow simulation codes used to compute aerothermodynamic loads on NASA's aeroassist orbital transfer vehicles and a host of problems related to the National Aerospace Plane Program. Although more approximate, similar solutions can be obtained for ensembles of atoms simulating small particles of materials with and without the presence of gases. Computational chemistry has application in studying catalysis, properties of polymers, all of interest to various NASA missions, including those previously mentioned. In addition to discussing these applications of computational chemistry within NASA, the governing equations and the need for supercomputers for their solution is outlined.

  20. To Think without Thinking: The Implications of Combinatory Play and the Creative Process for Neuroaesthetics

    ERIC Educational Resources Information Center

    Stevens, Victoria

    2014-01-01

    The author considers combinatory play as an intersection between creativity, play, and neuroaesthetics. She discusses combinatory play as vital to the creative process in art and science, particularly with regard to the incubation of new ideas. She reviews findings from current neurobiological research and outlines the way that the brain activates…

  1. A barcode-free combinatorial screening platform for matrix metalloproteinase screening.

    PubMed

    Rane, Tushar D; Zec, Helena C; Wang, Tza-Huei

    2015-02-01

    Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application. PMID:25543856

  2. A Barcode-Free Combinatorial Screening Platform for Matrix Metalloproteinase Screening

    PubMed Central

    2015-01-01

    Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application. PMID:25543856

  3. Muons in chemistry

    NASA Astrophysics Data System (ADS)

    Clayden, N. J.

    2013-12-01

    Positive muons have long been used as extrinsic probes in chemistry, offering unique properties for the investigation of local magnetism, dynamics, transport and radical kinetics. Exciting new developments in muon beam lines offer the opportunity of extending these studies selectively to surfaces permitting, for example, the detection of increased mobility of polymer chains at the surface of a polymer film. So called pump and probe methods, involving external perturbations by laser irradiation to manipulate vibrational and electronic states, can be followed by muon pulses allowing the probing of the properties of these states. Muoniated radical probes are finding greater use in soft matter. Selectivity is achieved in these complex systems through an appropriate target molecule giving the chance to measure partitioning and interfacial transfer in surfactant systems. Improvements in sample environments allow the observation of muons in increasingly extreme combinations of temperature and pressure, such as supercritical water, allowing the characterization of the chemistry in these systems.

  4. Combinatorial influence of environmental parameters on transcription factor activity

    PubMed Central

    Knijnenburg, T.A.; Wessels, L.F.A.; Reinders, M.J.T.

    2008-01-01

    Motivation: Cells receive a wide variety of environmental signals, which are often processed combinatorially to generate specific genetic responses. Changes in transcript levels, as observed across different environmental conditions, can, to a large extent, be attributed to changes in the activity of transcription factors (TFs). However, in unraveling these transcription regulation networks, the actual environmental signals are often not incorporated into the model, simply because they have not been measured. The unquantified heterogeneity of the environmental parameters across microarray experiments frustrates regulatory network inference. Results: We propose an inference algorithm that models the influence of environmental parameters on gene expression. The approach is based on a yeast microarray compendium of chemostat steady-state experiments. Chemostat cultivation enables the accurate control and measurement of many of the key cultivation parameters, such as nutrient concentrations, growth rate and temperature. The observed transcript levels are explained by inferring the activity of TFs in response to combinations of cultivation parameters. The interplay between activated enhancers and repressors that bind a gene promoter determine the possible up- or downregulation of the gene. The model is translated into a linear integer optimization problem. The resulting regulatory network identifies the combinatorial effects of environmental parameters on TF activity and gene expression. Availability: The Matlab code is available from the authors upon request. Contact: t.a.knijnenburg@tudelft.nl Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18586711

  5. Combinatorial function of ETS transcription factors in the developing vasculature

    PubMed Central

    Pham, Van N.; Lawson, Nathan D.; Mugford, Joshua W.; Dye, Louis; Castranova, Daniel; Lo, Brigid; Weinstein, Brant M.

    2007-01-01

    Members of the ETS family of transcription factors are among the first genes expressed in the developing vasculature, but loss-of-function experiments for individual ETS factors in mice have not uncovered important early functional roles for these genes. However, multiple ETS factors are expressed in spatially and temporally overlapping patterns in the developing vasculature, suggesting possible functional overlap. We have taken a comprehensive approach to exploring the function of these factors during vascular development by employing the genetic and experimental tools available in the zebrafish to analyze four ETS family members expressed together in the zebrafish vasculature; fli1, fli1b, ets1, and etsrp. We isolated and characterized an ENU-induced mutant with defects in trunk angiogenesis and positionally cloned the defective gene from this mutant, etsrp. Using the etsrp morpholinos targeting each of the four genes, we show that the four ETS factors function combinatorially during vascular and hematopoietic development. Reduction of etsrp or any of the other genes alone results in either partial or no defects in endothelial differentiation, while combined reduction in the function of all four genes causes dramatic loss of endothelial cells. Our results demonstrate that combinatorial ETS factor function is essential for early endothelial specification and differentiation. PMID:17125762

  6. Combinatorial Strategies for the Development of Bulk Metallic Glasses

    NASA Astrophysics Data System (ADS)

    Ding, Shiyan

    The systematic identification of multi-component alloys out of the vast composition space is still a daunting task, especially in the development of bulk metallic glasses that are typically based on three or more elements. In order to address this challenge, combinatorial approaches have been proposed. However, previous attempts have not successfully coupled the synthesis of combinatorial libraries with high-throughput characterization methods. The goal of my dissertation is to develop efficient high-throughput characterization methods, optimized to identify glass formers systematically. Here, two innovative approaches have been invented. One is to measure the nucleation temperature in parallel for up-to 800 compositions. The composition with the lowest nucleation temperature has a reasonable agreement with the best-known glass forming composition. In addition, the thermoplastic formability of a metallic glass forming system is determined through blow molding a compositional library. Our results reveal that the composition with the largest thermoplastic deformation correlates well with the best-known formability composition. I have demonstrated both methods as powerful tools to develop new bulk metallic glasses.

  7. Combinatorial approach to cancer immunotherapy: strength in numbers.

    PubMed

    Vilgelm, Anna E; Johnson, Douglas B; Richmond, Ann

    2016-08-01

    Immune-checkpoint blockade therapy with antibodies targeting CTLA-4 and PD-1 has revolutionized melanoma treatment by eliciting responses that can be remarkably durable and is now advancing to other malignancies. However, not all patients respond to immune-checkpoint inhibitors. Extensive preclinical evidence suggests that combining immune-checkpoint inhibitors with other anti-cancer treatments can greatly improve the therapeutic benefit. The first clinical success of the combinatorial approach to cancer immunotherapy was demonstrated using a dual-checkpoint blockade with CTLA-4 and PD-1 inhibitors, which resulted in accelerated FDA approval of this therapeutic regimen. In this review, we discuss the combinations of current and emerging immunotherapeutic agents in clinical and preclinical development and summarize the insights into potential mechanisms of synergistic anti-tumor activity gained from animal studies. These promising combinatorial partners for the immune-checkpoint blockade include therapeutics targeting additional inhibitory receptors of T cells, such as TIM-3, LAG-3, TIGIT, and BTLA, and agonists of T cell costimulatory receptors 4-1BB, OX40, and GITR, as well as agents that promote cancer cell recognition by the immune system, such as tumor vaccines, IDO inhibitors, and agonists of the CD40 receptor of APCs. We also review the therapeutic potential of regimens combining the immune-checkpoint blockade with therapeutic interventions that have been shown to enhance immunogenicity of cancer cells, including oncolytic viruses, RT, epigenetic therapy, and senescence-inducing therapy. PMID:27256570

  8. Device for preparing combinatorial libraries in powder metallurgy.

    PubMed

    Yang, Shoufeng; Evans, Julian R G

    2004-01-01

    This paper describes a powder-metering, -mixing, and -dispensing mechanism that can be used as a method for producing large numbers of samples for metallurgical evaluation or electrical or mechanical testing from multicomponent metal and cermet powder systems. It is designed to make use of the same commercial powders that are used in powder metallurgy and, therefore, to produce samples that are faithful to the microstructure of finished products. The particle assemblies produced by the device could be consolidated by die pressing, isostatic pressing, laser sintering, or direct melting. The powder metering valve provides both on/off and flow rate control of dry powders in open capillaries using acoustic vibration. The valve is simple and involves no relative movement, avoiding seizure with fine powders. An orchestra of such valves can be arranged on a building platform to prepare multicomponent combinatorial libraries. As with many combinatorial devices, identification and evaluation of sources of mixing error as a function of sample size is mandatory. Such an analysis is presented. PMID:15244416

  9. High Divergence of the Precursor Peptides in Combinatorial Lanthipeptide Biosynthesis

    PubMed Central

    2015-01-01

    Lanthionine-containing peptides (lanthipeptides) are a rapidly growing family of polycyclic peptide natural products belonging to the large class of ribosomally synthesized and post-translationally modified peptides (RiPPs). These compounds are widely distributed in taxonomically distant species, and their biosynthetic systems and biological activities are diverse. A unique example of lanthipeptide biosynthesis is the prochlorosin synthetase ProcM from the marine cyanobacterium Prochlorococcus MIT9313, which transforms up to 29 different precursor peptides (ProcAs) into a library of lanthipeptides called prochlorosins (Pcns) with highly diverse sequences and ring topologies. Here, we show that many ProcM-like enzymes from a variety of bacteria have the capacity to carry out post-translational modifications on highly diverse precursor peptides, providing new examples of natural combinatorial biosynthesis. We also demonstrate that the leader peptides come from different evolutionary origins, suggesting that the combinatorial biosynthesis is tied to the enzyme and not a specific type of leader peptide. For some precursor peptides encoded in the genomes, the leader peptides apparently have been truncated at the N-termini, and we show that these N-terminally truncated peptides are still substrates of the enzymes. Consistent with this hypothesis, we demonstrate that about two-thirds of the ProcA N-terminal sequence is not essential for ProcM activity. Our results also highlight the potential of exploring this class of natural products by genome mining and bioengineering. PMID:25244001

  10. A combinatorial approach to diffeomorphism invariant quantum gauge theories

    SciTech Connect

    Zapata, J.A.

    1997-11-01

    Quantum gauge theory in the connection representation uses functions of holonomies as configuration observables. Physical observables (gauge and diffeomorphism invariant) are represented in the Hilbert space of physical states; physical states are gauge and diffeomorphism invariant distributions on the space of functions of the holonomies of the edges of a certain family of graphs. Then a family of graphs embedded in the space manifold (satisfying certain properties) induces a representation of the algebra of physical observables. We construct a quantum model from the set of piecewise linear graphs on a piecewise linear manifold, and another manifestly combinatorial model from graphs defined on a sequence of increasingly refined simplicial complexes. Even though the two models are different at the kinematical level, they provide unitarily equivalent representations of the algebra of physical observables in {ital separable} Hilbert spaces of physical states (their s-knot basis is countable). Hence, the combinatorial framework is compatible with the usual interpretation of quantum field theory. {copyright} {ital 1997 American Institute of Physics.}

  11. Novel Heterotypic Rox Sites for Combinatorial Dre Recombination Strategies

    PubMed Central

    Chuang, Katherine; Nguyen, Eileen; Sergeev, Yuri; Badea, Tudor C.

    2015-01-01

    Site-specific recombinases (SSRs) such as Cre are widely used in gene targeting and genetic approaches for cell labeling and manipulation. They mediate DNA strand exchange between two DNA molecules at dedicated recognition sites. Precise understanding of the Cre recombination mechanism, including the role of individual base pairs in its loxP target site, guided the generation of mutant lox sites that specifically recombine with themselves but not with the wild type loxP. This has led to the development of a variety of combinatorial Cre-dependent genetic strategies, such as multicolor reporters, irreversible inversions, or recombination-mediated cassette exchange. Dre, a Cre-related phage integrase that recognizes roxP sites, does not cross-react with the Cre-loxP system, but has similar recombination efficiency. We have previously described intersectional genetic strategies combining Dre and Cre. We now report a mutagenesis screen aimed at identifying roxP base pairs critical for self-recognition. We describe several rox variant sites that are incompatible with roxP, but are able to efficiently recombine with themselves in either purified systems or bacterial and eukaryotic tissue culture systems. These newly identified rox sites are not recognized by Cre, thus enabling potential combinatorial strategies involving Cre, Dre, and target loci including multiple loxP and roxP variants. PMID:26715092

  12. A combinatorial approach to the design of vaccines.

    PubMed

    Martínez, Luis; Milanič, Martin; Legarreta, Leire; Medvedev, Paul; Malaina, Iker; de la Fuente, Ildefonso M

    2015-05-01

    We present two new problems of combinatorial optimization and discuss their applications to the computational design of vaccines. In the shortest λ-superstring problem, given a family S1,...,S(k) of strings over a finite alphabet, a set Τ of "target" strings over that alphabet, and an integer λ, the task is to find a string of minimum length containing, for each i, at least λ target strings as substrings of S(i). In the shortest λ-cover superstring problem, given a collection X1,...,X(n) of finite sets of strings over a finite alphabet and an integer λ, the task is to find a string of minimum length containing, for each i, at least λ elements of X(i) as substrings. The two problems are polynomially equivalent, and the shortest λ-cover superstring problem is a common generalization of two well known combinatorial optimization problems, the shortest common superstring problem and the set cover problem. We present two approaches to obtain exact or approximate solutions to the shortest λ-superstring and λ-cover superstring problems: one based on integer programming, and a hill-climbing algorithm. An application is given to the computational design of vaccines and the algorithms are applied to experimental data taken from patients infected by H5N1 and HIV-1. PMID:24859149

  13. Combinatorial metabolic engineering of Saccharomyces cerevisiae for terminal alkene production.

    PubMed

    Chen, Binbin; Lee, Dong-Yup; Chang, Matthew Wook

    2015-09-01

    Biological production of terminal alkenes has garnered a significant interest due to their industrial applications such as lubricants, detergents and fuels. Here, we engineered the yeast Saccharomyces cerevisiae to produce terminal alkenes via a one-step fatty acid decarboxylation pathway and improved the alkene production using combinatorial engineering strategies. In brief, we first characterized eight fatty acid decarboxylases to enable and enhance alkene production. We then increased the production titer 7-fold by improving the availability of the precursor fatty acids. We additionally increased the titer about 5-fold through genetic cofactor engineering and gene expression tuning in rich medium. Lastly, we further improved the titer 1.8-fold to 3.7 mg/L by optimizing the culturing conditions in bioreactors. This study represents the first report of terminal alkene biosynthesis in S. cerevisiae, and the abovementioned combinatorial engineering approaches collectively increased the titer 67.4-fold. We envision that these approaches could provide insights into devising engineering strategies to improve the production of fatty acid-derived biochemicals in S. cerevisiae. PMID:26164646

  14. Single-Parameter Combinatorial Auctions with Partially Public Valuations

    NASA Astrophysics Data System (ADS)

    Goel, Gagan; Karande, Chinmay; Wang, Lei

    We consider the problem of designing truthful auctions, when the bidders' valuations have a public and a private component. In particular, we consider combinatorial auctions where the valuation of an agent i for a set S of items can be expressed as v i f(S), where v i is a private single parameter of the agent, and the function f is publicly known. Our motivation behind studying this problem is two-fold: (a) Such valuation functions arise naturally in the case of ad-slots in broadcast media such as Television and Radio. For an ad shown in a set S of ad-slots, f(S) is, say, the number of unique viewers reached by the ad, and v i is the valuation per-unique-viewer. (b) From a theoretical point of view, this factorization of the valuation function simplifies the bidding language, and renders the combinatorial auction more amenable to better approximation factors. We present a general technique, based on maximal-in-range mechanisms, that converts any α-approximation non-truthful algorithm (α ≤ 1) for this problem into Ω(α/log{n}) and Ω(α)-approximate truthful mechanisms which run in polynomial time and quasi-polynomial time, respectively.

  15. Combinatorial evolution of regression nodes in feedforward neural networks.

    PubMed

    Schmitz, Gregor P.J.; Aldrich, Chris

    1999-01-01

    A number of techniques exist with which neural network architectures such as multilayer perceptrons and radial basis function networks can be trained. These include backpropagation, k-means clustering and evolutionary algorithms. The latter method is particularly useful as it is able to avoid local optima in the search space and can optimise parameters for which no gradient information exists. Unfortunately, only moderately sized networks can be trained by this method, owing to the fact that evolutionary optimisation is very computationally intensive. In this paper a novel algorithm (CERN) is therefore proposed which uses a special form of combinatorial search to optimise groups of neural nodes. Oriented, ellipsoidal basis nodes optimised with CERN achieved significantly better accuracy with fewer nodes than spherical basis nodes optimised by k-means clustering. Multilayer perceptrons optimised by CERN were found to be as accurate as those trained by advanced gradient descent techniques. CERN was also found to be significantly more efficient than a conventional evolutionary algorithm that does not use a combinatorial search. PMID:12662726

  16. LOGICAL REASONING ABILITY AND STUDENT PERFORMANCE IN GENERAL CHEMISTRY

    PubMed Central

    Bird, Lillian

    2010-01-01

    Logical reasoning skills of students enrolled in General Chemistry at the University of Puerto Rico in Río Piedras were measured using the Group Assessment of Logical Thinking (GALT) test. The results were used to determine the students’ cognitive level (concrete, transitional, formal) as well as their level of performance by logical reasoning mode (mass/volume conservation, proportional reasoning, correlational reasoning, experimental variable control, probabilistic reasoning and combinatorial reasoning). This information was used to identify particular deficiencies and gender effects, and to determine which logical reasoning modes were the best predictors of student performance in the general chemistry course. Statistical tests to analyze the relation between (a) operational level and final grade in both semesters of the course; (b) GALT test results and performance in the ACS General Chemistry Examination; and (c) operational level and student approach (algorithmic or conceptual) towards a test question that may be answered correctly using either strategy, were also performed. PMID:21373364

  17. Historical Account And Branching To Rarefied Gas Dynamics Of Atomic and Molecular Beams : A Continuing And Fascinating Odyssey Commemorated By Nobel Prizes Awarded To 23 Laureates In Physics And Chemistry

    NASA Astrophysics Data System (ADS)

    Campargue, Roger

    2005-05-01

    This Historical Account derived in part from D. R. Herschbach was presented as an opening lecture of the Molecular Beam Session organized at the 24th International Symposium on Rarefied Gas Dynamics held in Bari, Italy, in July 2004. The emphasis is on the impressive results due to the molecular beam techniques in the last century. The first section summarizes the historical beam experiments performed by 14 Nobel Prize laureates having used the thermally effusive sources to establish the basic principles of Modern Physics. The second section is on the branching of Molecular Beams to Rarefied Gas Dynamics having permitted to investigate the physics of supersonic free jets and transform the molecular beam techniques. Finally, the last section relates the spectacular molecular beam experiments in helium free jet ultracooling, molecular spectroscopy, chemical reaction dynamics, clustering and modification of low density matter, and biomolecule mass spectrometry, rewarded by nine Nobel Prizes in Chemistry from 1986 to 2002.

  18. Evaluating the CALIOPE air quality modelling system: dynamics and chemistry over Europe and Iberian Peninsula for 2004 at high horizontal resolution

    NASA Astrophysics Data System (ADS)

    Piot, M.; Pay, M. T.; Jorba, O.; Baldasano, J. M.; Jiménez-Guerrero, P.; López, E.; Pérez, C.; Gassó, S.

    2009-04-01

    Often in Europe, population exposure to air pollution exceeds standards set by the EU and the World Health Organization (WHO). Urban/suburban areas are predominantly impacted upon, although exceedances of particulate matter (PM10 and PM2.5) and Ozone (O3) also take place in rural areas. In the frame of the CALIOPE project (Baldasano et al., 2008a), a high-resolution air quality forecasting system, WRF-ARW/HERMES/CMAQ/DREAM, has been developed and applied to the European domain (12km x 12km, 1hr) as well as to the Iberian Peninsula domain (4km x 4km, 1hr) to provide air quality forecasts for Spain (http://www.bsc.es/caliope/). The simulation of such high-resolution model system has been made possible by its implementation on the MareNostrum supercomputer. To reassure potential users and reduce uncertainties, the model system must be evaluated to assess its performances in terms of air quality levels and dynamics reproducibility. The present contribution describes a thorough quantitative evaluation study performed for a reference year (2004). The CALIOPE modelling system is configured with 38 vertical layers reaching up to 50 hPa for the meteorological core. Atmospheric initial and boundary conditions are obtained from the NCEP final analysis data. The vertical resolution of the CMAQ chemistry-transport model for gas-phase and aerosols has been increased from 8 to 15 layers in order to simulate vertical exchanges more accurately. Gas phase boundary conditions are provided by the LMDz-INCA2 global climate-chemistry model (see Hauglustaine et al., 2004). The DREAM model simulates long-range transport of mineral dust over the domains under study. For the European simulation, emissions are disaggregated from the EMEP expert emission inventory for 2004 to the utilized resolution using the criteria implemented in the HERMES emission model (Baldasano et al., 2008b). The HERMES model system, using a bottom-up approach, was adopted to estimate emissions for the Iberian

  19. (Pesticide chemistry)

    SciTech Connect

    Barnthouse, L.W.

    1990-09-04

    This report summarizes a trip by L. W. Barnthouse of the Environmental Sciences Division (ESD), Oak Ridge National Laboratory (ORNL), to Hamburg, Federal Republic of Germany (FRG), where he participated in the 7th International Congress of Pesticide Chemistry. He chaired a workshop on experimental systems for determining effects of pesticides on nontarget organisms and gave an oral presentation at a symposium on pesticide risk assessment. Before returning to the United States, Dr. Barnthouse visited the Netherlands Institute for Sea Research in Texel, the Netherlands.

  20. Dynamic mixtures: challenges and opportunities for the amplification and sensing of scents.

    PubMed

    Herrmann, Andreas

    2012-07-01

    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. PMID:22588709

  1. Combinatorial Strategies for the Induction of Immunogenic Cell Death

    PubMed Central

    Bezu, Lucillia; Gomes-da-Silva, Ligia C.; Dewitte, Heleen; Breckpot, Karine; Fucikova, Jitka; Spisek, Radek; Galluzzi, Lorenzo; Kepp, Oliver; Kroemer, Guido

    2015-01-01

    The term “immunogenic cell death” (ICD) is commonly employed to indicate a peculiar instance of regulated cell death (RCD) that engages the adaptive arm of the immune system. The inoculation of cancer cells undergoing ICD into immunocompetent animals elicits a specific immune response associated with the establishment of immunological memory. Only a few agents are intrinsically endowed with the ability to trigger ICD. These include a few chemotherapeutics that are routinely employed in the clinic, like doxorubicin, mitoxantrone, oxaliplatin, and cyclophosphamide, as well as some agents that have not yet been approved for use in humans. Accumulating clinical data indicate that the activation of adaptive immune responses against dying cancer cells is associated with improved disease outcome in patients affected by various neoplasms. Thus, novel therapeutic regimens that trigger ICD are urgently awaited. Here, we discuss current combinatorial approaches to convert otherwise non-immunogenic instances of RCD into bona fide ICD. PMID:25964783

  2. Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.

    PubMed

    Jeschek, Markus; Gerngross, Daniel; Panke, Sven

    2016-01-01

    Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways. PMID:27029461

  3. Combinatorial evolution of site- and enantioselective catalysts for polyene epoxidation

    NASA Astrophysics Data System (ADS)

    Lichtor, Phillip A.; Miller, Scott J.

    2012-12-01

    Selectivity in the catalytic functionalization of complex molecules is a major challenge in chemical synthesis. The problem is magnified when there are several possible stereochemical outcomes and when similar functional groups occur repeatedly within the same molecule. Selective polyene oxidation provides an archetypical example of this challenge. Historically, enzymatic catalysis has provided the only precedents. Although non-enzymatic catalysts that meet some of these challenges became known, a comprehensive solution has remained elusive. Here, we describe low molecular weight peptide-based catalysts, discovered through a combinatorial synthesis and screening protocol, that exhibit site- and enantioselective oxidation of certain positions of various isoprenols. This diversity-based approach, which exhibits features reminiscent of the directed evolution of enzymes, delivers catalysts that compare favourably to the state-of-the-art for the asymmetric oxidation of these compounds. Moreover, the approach culminated in catalysts that exhibit alternative-site selectivity in comparison to oxidation catalysts previously described.

  4. Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort

    PubMed Central

    Jeschek, Markus; Gerngross, Daniel; Panke, Sven

    2016-01-01

    Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways. PMID:27029461

  5. Selecting agonists from single cells infected with combinatorial antibody libraries.

    PubMed

    Zhang, Hongkai; Yea, Kyungmoo; Xie, Jia; Ruiz, Diana; Wilson, Ian A; Lerner, Richard A

    2013-05-23

    We describe a system for direct selection of antibodies that are receptor agonists. Combinatorial antibody libraries in lentiviruses are used to infect eukaryotic cells that contain a fluorescent reporter system coupled to the receptor for which receptor agonist antibodies are sought. In this embodiment of the method, very large numbers of candidate antibodies expressing lentivirus and eukaryotic reporter cells are packaged together in a format where each is capable of replication, thereby forging a direct link between genotype and phenotype. Following infection, cells that fluoresce are sorted and the integrated genes encoding the agonist antibodies recovered. We validated the system by illustrating its ability to generate rapidly potent antibody agonists that are complete thrombopoietin phenocopies. The system should be generalizable to any pathway where its activation can be linked to production of a selectable phenotype. PMID:23706638

  6. Combinatorial discovery of alloy electrocatalysts for amperometric glucose sensors.

    PubMed

    Sun, Y; Buck, H; Mallouk, T E

    2001-04-01

    Combinatorial methods were used to search for active alloy electrocatalysts for use in enzyme-free amperometric glucose sensors. Electrode arrays (715-member) containing combinations of Pt, Pb, Au, Pd, and Rh were prepared and screened by converting anodic current to visible fluorescence. The most active compositions contained both Pt and Pb. Bulk quantities of catalysts with compositions corresponding to those identified in the screening experiments were prepared and characterized. The best alloy electrocatalysts catalyzed glucose oxidation at substantially more negative potentials than pure platinum in enzyme-free voltammetric measurements. They were also insensitive to potential interfering agents (ascorbic and uric acids, and 4-acetamidophenol), which are oxidized at slightly more positive potentials. Rotating disk electrode (RDE) experiments were carried out to study the catalytic mechanism. The improvement in catalytic performance was attributed to the inhibition of adsorption of oxidation products, which poison Pt electrodes. PMID:11321315

  7. Combinatorial Exploration of Novel Transparent Conducting Oxide Materials

    SciTech Connect

    Ginley, D. S.; van Hest, M. F. A. M.; Young, D.; Teplin, C. W.; Alleman, J. L.; Dabney, M. S.; Gedvilas, L. M.; Keyes, B. M.; To, B.; Perkins, J. D.; Taylor, M. P.; Readey, D.

    2005-11-01

    High-throughput combinatorial approaches have been used for the discovery and optimization of transparent conducting oxide (TCO) materials for PV applications. We report on current investigations in In-Zn-O, In-Ti-O and In-Mo-O systems. The InZnO system is shown to be amorphous in the best conducting range with a conductivity of ~ 3000 Ω-cm-1 for 50%-70% In/Zn. The amorphous InZnO films are very smooth (2..ANG.. rms). In-Ti-O is found to be an excellent high-mobility TCO with mobilities of greater than 80 cm2/v-sec and conductivities of more than 6000 Ω-cm-1 for sputtered thin film materials.

  8. High-pressure combinatorial process integrating hot isostatic pressing.

    PubMed

    Fujimoto, Kenjiro; Morita, Hiroki; Goshima, Yuji; Ito, Shigeru

    2013-12-01

    A high-pressure combinatorial process integrating hot isostatic pressing (HIP) was developed by providing a reaction vessel with a high-pressure tightness based on a commercial flange. The reaction vessel can be used up to 200 MPa and 500 °C under HIP processing condition. Preparation of spinel-type MgAl2O4 from Mg(OH)2, Al(OH)3 and AlOOH was performed using the reaction vessel under 200 MPa and 500 °C as demonstration. The entire powder library was characterized using powder X-ray diffraction patterns, and the single phase of spinel-type MgAl2O4 was obtained from Mg(OH)2+Al(OH)3. These assessments corresponded with previously published data. PMID:24168067

  9. Behavioural correlates of combinatorial versus temporal features of odour codes.

    PubMed

    Saha, Debajit; Li, Chao; Peterson, Steven; Padovano, William; Katta, Nalin; Raman, Baranidharan

    2015-01-01

    Most sensory stimuli evoke spiking responses that are distributed across neurons and are temporally structured. Whether the temporal structure of ensemble activity is modulated to facilitate different neural computations is not known. Here, we investigated this issue in the insect olfactory system. We found that an odourant can generate synchronous or asynchronous spiking activity across a neural ensemble in the antennal lobe circuit depending on its relative novelty with respect to a preceding stimulus. Regardless of variations in temporal spiking patterns, the activated combinations of neurons robustly represented stimulus identity. Consistent with this interpretation, locusts reliably recognized both solitary and sequential introductions of trained odourants in a quantitative behavioural assay. However, predictable behavioural responses across locusts were observed only to novel stimuli that evoked synchronized spiking patterns across neural ensembles. Hence, our results indicate that the combinatorial ensemble response encodes for stimulus identity, whereas the temporal structure of the ensemble response selectively emphasizes novel stimuli. PMID:25912016

  10. Combinatorial optimization of cyanobacterial 2,3-butanediol production.

    PubMed

    Oliver, John W K; Machado, Iara M P; Yoneda, Hisanari; Atsumi, Shota

    2014-03-01

    A vital goal of renewable technology is the capture and re-energizing of exhausted CO₂ into usable carbon products. Cyanobacteria fix CO₂ more efficiently than plants, and can be engineered to produce carbon feedstocks useful for making plastics, solvents, and medicines. However, fitness of this technology in the economy is threatened by low yields in engineered strains. Robust engineering of photosynthetic microorganisms is lagging behind model microorganisms that rely on energetic carbon, such as Escherichia coli, due in part to slower growth rates and increased metabolic complexity. In this work we show that protein expression from characterized parts is unpredictable in Synechococcus elongatus sp. strain PCC 7942, and may contribute to slow development. To overcome this, we apply a combinatorial approach and show that modulation of the 5'-untranslated region (UTR) can produce a range of protein expression sufficient to optimize chemical feedstock production from CO₂. PMID:24412567

  11. What Diagrams Argue in Late Imperial Chinese Combinatorial Texts.

    PubMed

    Bréard, Andrea

    2015-01-01

    Attitudes towards diagrammatic reasoning and visualization in mathematics were seldom spelled out in texts from pre-modern China, although illustrations figure prominently in mathematical literature since the eleventh century. Taking the sums of finite series and their combinatorial interpretation as a case study, this article investigates the epistemological function of illustrations from the eleventh to the nineteenth century that encode either the mathematical objects themselves or represent their related algorithms. It particularly focuses on the two illustrations given in Wang Lai's (1768-1813) Mathematical Principles of Sequential Combinations, arguing that they reflect a specific mode of nineteenth-century mathematical argumentative practice and served as a heuristic model for later authors. PMID:26411068

  12. Statistical physics of hard combinatorial optimization: Vertex cover problem

    NASA Astrophysics Data System (ADS)

    Zhao, Jin-Hua; Zhou, Hai-Jun

    2014-07-01

    Typical-case computation complexity is a research topic at the boundary of computer science, applied mathematics, and statistical physics. In the last twenty years, the replica-symmetry-breaking mean field theory of spin glasses and the associated message-passing algorithms have greatly deepened our understanding of typical-case computation complexity. In this paper, we use the vertex cover problem, a basic nondeterministic-polynomial (NP)-complete combinatorial optimization problem of wide application, as an example to introduce the statistical physical methods and algorithms. We do not go into the technical details but emphasize mainly the intuitive physical meanings of the message-passing equations. A nonfamiliar reader shall be able to understand to a large extent the physics behind the mean field approaches and to adjust the mean field methods in solving other optimization problems.

  13. Direct selection for a catalytic mechanism from combinatorial antibody libraries.

    PubMed Central

    Janda, K D; Lo, C H; Li, T; Barbas, C F; Wirsching, P; Lerner, R A

    1994-01-01

    Semisynthetic combinatorial antibody library methodology in the phage-display format was used to select for a cysteine residue in complementarity-determining regions. Libraries were panned with an alpha-phenethyl pyridyl disulfide that undergoes disulfide interchange. Out of 10 randomly picked clones, two contained an unpaired cysteine, one of which was studied. The antibody catalyzed the hydrolysis of the corresponding thioester where the electrophilic carbonyl occupies the three-dimensional space that was defined by the reactive sulfur atom during selection. The reaction operates by covalent catalysis. Although the steady-state rate enhancement relative to the activated thiol ester substrate is modest, hydrolysis of the acylated cysteine intermediate is remarkably efficient with a catalytic advantage of about four orders of magnitude. The results suggest that iterative mechanism-based selection procedures can recapitulate the enzymatic mechanisms refined through evolution. Images PMID:8146149

  14. Combinatorial approach to Mathieu and Lamé equations

    SciTech Connect

    He, Wei

    2015-07-15

    Based on some recent progress on a relation between four dimensional super Yang-Mills gauge theory and quantum integrable system, we study the asymptotic spectrum of the quantum mechanical problems described by the Mathieu equation and the Lamé equation. The large momentum asymptotic expansion of the eigenvalue is related to the instanton partition function of supersymmetric gauge theories which can be evaluated by a combinatorial method. The electro-magnetic duality of gauge theory indicates that in the parameter space, there are three asymptotic expansions for the eigenvalue, and we confirm this fact by performing the Wentzel–Kramers–Brillouin (WKB) analysis in each asymptotic expansion region. The results presented here give some new perspective on the Floquet theory about periodic differential equation.

  15. Multiplex cell and lineage tracking with combinatorial labels.

    PubMed

    Loulier, Karine; Barry, Raphaëlle; Mahou, Pierre; Le Franc, Yann; Supatto, Willy; Matho, Katherine S; Ieng, Siohoi; Fouquet, Stéphane; Dupin, Elisabeth; Benosman, Ryad; Chédotal, Alain; Beaurepaire, Emmanuel; Morin, Xavier; Livet, Jean

    2014-02-01

    We present a method to label and trace the lineage of multiple neural progenitors simultaneously in vertebrate animals via multiaddressable genome-integrative color (MAGIC) markers. We achieve permanent expression of combinatorial labels from new Brainbow transgenes introduced in embryonic neural progenitors with electroporation of transposon vectors. In the mouse forebrain and chicken spinal cord, this approach allows us to track neural progenitor's descent during pre- and postnatal neurogenesis or perinatal gliogenesis in long-term experiments. Color labels delineate cytoarchitecture, resolve spatially intermixed clones, and specify the lineage of astroglial subtypes and adult neural stem cells. Combining colors and subcellular locations provides an expanded marker palette to individualize clones. We show that this approach is also applicable to modulate specific signaling pathways in a mosaic manner while color-coding the status of individual cells regarding induced molecular perturbations. This method opens new avenues for clonal and functional analysis in varied experimental models and contexts. PMID:24507188

  16. Behavioural correlates of combinatorial versus temporal features of odour codes

    PubMed Central

    Saha, Debajit; Li, Chao; Peterson, Steven; Padovano, William; Katta, Nalin; Raman, Baranidharan

    2015-01-01

    Most sensory stimuli evoke spiking responses that are distributed across neurons and are temporally structured. Whether the temporal structure of ensemble activity is modulated to facilitate different neural computations is not known. Here, we investigated this issue in the insect olfactory system. We found that an odourant can generate synchronous or asynchronous spiking activity across a neural ensemble in the antennal lobe circuit depending on its relative novelty with respect to a preceding stimulus. Regardless of variations in temporal spiking patterns, the activated combinations of neurons robustly represented stimulus identity. Consistent with this interpretation, locusts reliably recognized both solitary and sequential introductions of trained odourants in a quantitative behavioural assay. However, predictable behavioural responses across locusts were observed only to novel stimuli that evoked synchronized spiking patterns across neural ensembles. Hence, our results indicate that the combinatorial ensemble response encodes for stimulus identity, whereas the temporal structure of the ensemble response selectively emphasizes novel stimuli. PMID:25912016

  17. Topological transition in disordered planar matching: combinatorial arcs expansion

    NASA Astrophysics Data System (ADS)

    Lokhov, Andrey Y.; Valba, Olga V.; Nechaev, Sergei K.; Tamm, Mikhail V.

    2014-12-01

    In this paper, we investigate analytically the properties of the disordered Bernoulli model of planar matching. This model is characterized by a topological phase transition, yielding complete planar matching solutions only above a critical density threshold. We develop a combinatorial procedure of arcs expansion that explicitly takes into account the contribution of short arcs and allows us to obtain an accurate analytical estimation of the critical value by reducing the global constrained problem to a set of local ones. As an application to a toy representation of the RNA secondary structures, we suggest generalized models that incorporate a one-to-one correspondence between the contact matrix and the RNA-type sequence, thus giving sense to the notion of effective non-integer alphabets.

  18. Automatic labeling of EEG electrodes using combinatorial optimization.

    PubMed

    Péchaud, Mickaël; Keriven, Renaud; Papadopoulo, Théo; Badier, Jean-Michel

    2007-01-01

    An important issue in electroencephalography (EEG) experiments is to measure accurately the three dimensional (3D) positions of electrodes. We propose a system where these positions are automatically estimated from several images using computer vision techniques. Yet, only a set of undifferentiated points are recovered this way and remains the problem of labeling them, i.e. of finding which electrode corresponds to each point. This paper proposes a fast and robust solution to this latter problem based on combinatorial optimization. We design a specific energy that we minimize with a modified version of the Loopy Belief Propagation algorithm. Experiments on real data show that, with our method, a manual labeling of two or three electrodes only is sufficient to get the complete labeling of a 64 electrodes cap in less than 10 seconds. However, it is shown to be robust to missing electrodes in the reconstructed data. PMID:18002979

  19. Combinatorial optimization for electrode labeling of EEG caps.

    PubMed

    Péchaud, Mickaël; Keriven, Renaud; Papadopoulo, Théo; Badier, Jean-Michel

    2007-01-01

    An important issue in electroencephalographiy (EEG) experiments is to measure accurately the three dimensional (3D) positions of the electrodes. We propose a system where these positions are automatically estimated from several images using computer vision techniques. Yet, only a set of undifferentiated points are recovered this way and remains the problem of labeling them, i.e. of finding which electrode corresponds to each point. This paper proposes a fast and robust solution to this latter problem based on combinatorial optimization. We design a specific energy that we minimize with a modified version of the Loopy Belief Propagation algorithm. Experiments on real data show that, with our method, a manual labeling of two or three electrodes only is sufficient to get the complete labeling of a 64 electrodes cap in less than 10 seconds. PMID:18044641

  20. Combinatorial study of zinc tin oxide thin-film transistors

    SciTech Connect

    McDowell, M. G.; Sanderson, R. J.; Hill, I. G.

    2008-01-07

    Groups of thin-film transistors using a zinc tin oxide semiconductor layer have been fabricated via a combinatorial rf sputtering technique. The ZnO:SnO{sub 2} ratio of the film varies as a function of position on the sample, from pure ZnO to SnO{sub 2}, allowing for a study of zinc tin oxide transistor performance as a function of channel stoichiometry. The devices were found to have mobilities ranging from 2 to 12 cm{sup 2}/V s, with two peaks in mobility in devices at ZnO fractions of 0.80{+-}0.03 and 0.25{+-}0.05, and on/off ratios as high as 10{sup 7}. Transistors composed predominantly of SnO{sub 2} were found to exhibit light sensitivity which affected both the on/off ratios and threshold voltages of these devices.

  1. Combinatorially selected defense peptides protect plant roots from pathogen infection

    PubMed Central

    Fang, Zhiwei David; Laskey, James G.; Huang, Shaoxing; Bilyeu, Kristin D.; Morris, Roy O.; Schmidt, Francis J.; English, James T.

    2006-01-01

    Agricultural productivity and sustainability are continually challenged by emerging and indigenous pathogens. Currently, many pathogens can be combated only with biocides or environmentally dangerous fumigants. Here, we report a rapid and pathogen-specific strategy to reduce infection by organisms that target plant roots. Combinatorially selected defense peptides, previously shown to effect premature encystment of Phytophthora capsici zoospores, were fused to maize cytokinin oxidase/dehydrogenase as a display scaffold. When expressed in tomato roots, the peptide-scaffold constructs were secreted and accumulated to sufficient concentrations in the rhizosphere to induce zoospore encystment and thereby deter taxis to the root surface. Pathogen infection was significantly inhibited in roots expressing bioactive peptides fused to the maize cytokinin oxidase/dehydrogenase scaffold. This peptide-delivery technology is broadly applicable for rapid development of plant defense attributes against plant pathogens. PMID:17030803

  2. PCB Drill Path Optimization by Combinatorial Cuckoo Search Algorithm

    PubMed Central

    Lim, Wei Chen Esmonde; Kanagaraj, G.; Ponnambalam, S. G.

    2014-01-01

    Optimization of drill path can lead to significant reduction in machining time which directly improves productivity of manufacturing systems. In a batch production of a large number of items to be drilled such as printed circuit boards (PCB), the travel time of the drilling device is a significant portion of the overall manufacturing process. To increase PCB manufacturing productivity and to reduce production costs, a good option is to minimize the drill path route using an optimization algorithm. This paper reports a combinatorial cuckoo search algorithm for solving drill path optimization problem. The performance of the proposed algorithm is tested and verified with three case studies from the literature. The computational experience conducted in this research indicates that the proposed algorithm is capable of efficiently finding the optimal path for PCB holes drilling process. PMID:24707198

  3. PCB drill path optimization by combinatorial cuckoo search algorithm.

    PubMed

    Lim, Wei Chen Esmonde; Kanagaraj, G; Ponnambalam, S G

    2014-01-01

    Optimization of drill path can lead to significant reduction in machining time which directly improves productivity of manufacturing systems. In a batch production of a large number of items to be drilled such as printed circuit boards (PCB), the travel time of the drilling device is a significant portion of the overall manufacturing process. To increase PCB manufacturing productivity and to reduce production costs, a good option is to minimize the drill path route using an optimization algorithm. This paper reports a combinatorial cuckoo search algorithm for solving drill path optimization problem. The performance of the proposed algorithm is tested and verified with three case studies from the literature. The computational experience conducted in this research indicates that the proposed algorithm is capable of efficiently finding the optimal path for PCB holes drilling process. PMID:24707198

  4. Combinatorial discovery of two-photon photoremovable protecting groups.

    PubMed

    Pirrung, Michael C; Pieper, Wolfgang H; Kaliappan, Krishna P; Dhananjeyan, Mugunthu R

    2003-10-28

    A design principle for a two-photon photochemically removable protecting group based on sequential one-photon processes has been established. The expected performance of such groups in spatially directed photoactivation/photodeprotection has been shown by a kinetic analysis. One particular molecular class fitting into this design, the nitrobenzyl ethers of o-hydroxycinnamates, has been presented. An initial demonstration of two-photon deprotection of one such group prompted further optimization with respect to photochemical deprotection rate. This was accomplished by the preparation and screening of a 135-member indexed combinatorial library. Optimum performance for lambda >350 nm deprotection in organic solvent was found with 4,5-dialkoxy and -cyano substitution in the nitrobenzyl group and 4-methoxy substitution in the cinnamate. PMID:14557545

  5. Eighteenth annual West Coast theoretical chemistry conference

    SciTech Connect

    1997-05-01

    Abstracts are presented from the eighteenth annual west coast theoretical chemistry conference. Topics include molecular simulations; quasiclassical simulations of reactions; photodissociation reactions; molecular dynamics;interface studies; electronic structure; and semiclassical methods of reactive systems.

  6. Combinatorial transcriptional control of the lactose operon of Escherichia coli.

    PubMed

    Kuhlman, Thomas; Zhang, Zhongge; Saier, Milton H; Hwa, Terence

    2007-04-01

    The goal of systems biology is to understand the behavior of the whole in terms of knowledge of the parts. This is hard to achieve in many cases due to the difficulty of characterizing the many constituents involved in a biological system and their complex web of interactions. The lac promoter of Escherichia coli offers the possibility of confronting "system-level" properties of transcriptional regulation with the known biochemistry of the molecular constituents and their mutual interactions. Such confrontations can reveal previously unknown constituents and interactions, as well as offer insight into how the components work together as a whole. Here we study the combinatorial control of the lac promoter by the regulators Lac repressor (LacR) and cAMP-receptor protein (CRP). A previous in vivo study [Setty Y, Mayo AE, Surette MG, Alon U (2003) Proc Natl Acad Sci USA 100:7702-7707] found gross disagreement between the observed promoter activities and the expected behavior based on the known molecular mechanisms. We repeated the study by identifying and removing several extraneous factors that significantly modulated the expression of the lac promoter. Through quantitative, systematic characterization of promoter activity for a number of key mutants and guided by the thermodynamic model of transcriptional regulation, we were able to account for the combinatorial control of the lac promoter quantitatively, in terms of a cooperative interaction between CRP and LacR-mediated DNA looping. Specifically, our analysis indicates that the sensitivity of the inducer response results from LacR-mediated DNA looping, which is significantly enhanced by CRP. PMID:17376875

  7. Affinity chromatography based on a combinatorial strategy for rerythropoietin purification.

    PubMed

    Martínez-Ceron, María C; Marani, Mariela M; Taulés, Marta; Etcheverrigaray, Marina; Albericio, Fernando; Cascone, Osvaldo; Camperi, Silvia A

    2011-05-01

    Small peptides containing fewer than 10 amino acids are promising ligand candidates with which to build affinity chromatographic systems for industrial protein purification. The application of combinatorial peptide synthesis strategies greatly facilitates the discovery of suitable ligands for any given protein of interest. Here we sought to identify peptide ligands with affinity for recombinant human erythropoietin (rhEPO), which is used for the treatment of anemia. A combinatorial library containing the octapeptides X-X-X-Phe-X-X-Ala-Gly, where X = Ala, Asp, Glu, Phe, His, Leu, Asn, Pro, Ser, or Thr, was synthesized on HMBA-ChemMatrix resin by the divide-couple-recombine method. For the library screening, rhEPO was coupled to either Texas Red or biotin. Fluorescent beads or beads showing a positive reaction with streptavidin-peroxidase were isolated. After cleavage, peptides were sequenced by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Fifty-seven beads showed a positive reaction. Peptides showing more consensuses were synthesized, and their affinity to rhEPO was assessed using a plasma resonance biosensor. Dissociation constant values in the range of 1-18 μM were obtained. The best two peptides were immobilized on Sepharose, and the resultant chromatographic matrixes showed affinity for rhEPO with dissociation constant values between 1.8 and 2.7 μM. Chinese hamster ovary (CHO) cell culture supernatant was spiked with rhEPO, and the artificial mixture was loaded on Peptide-Sepharose columns. The rhEPO was recovered in the elution fraction with a yield of 90% and a purity of 95% and 97% for P1-Sepharose and P2-Sepharose, respectively. PMID:21495625

  8. A versatile modular vector system for rapid combinatorial mammalian genetics.

    PubMed

    Albers, Joachim; Danzer, Claudia; Rechsteiner, Markus; Lehmann, Holger; Brandt, Laura P; Hejhal, Tomas; Catalano, Antonella; Busenhart, Philipp; Gonçalves, Ana Filipa; Brandt, Simone; Bode, Peter K; Bode-Lesniewska, Beata; Wild, Peter J; Frew, Ian J

    2015-04-01

    Here, we describe the multiple lentiviral expression (MuLE) system that allows multiple genetic alterations to be introduced simultaneously into mammalian cells. We created a toolbox of MuLE vectors that constitute a flexible, modular system for the rapid engineering of complex polycistronic lentiviruses, allowing combinatorial gene overexpression, gene knockdown, Cre-mediated gene deletion, or CRISPR/Cas9-mediated (where CRISPR indicates clustered regularly interspaced short palindromic repeats) gene mutation, together with expression of fluorescent or enzymatic reporters for cellular assays and animal imaging. Examples of tumor engineering were used to illustrate the speed and versatility of performing combinatorial genetics using the MuLE system. By transducing cultured primary mouse cells with single MuLE lentiviruses, we engineered tumors containing up to 5 different genetic alterations, identified genetic dependencies of molecularly defined tumors, conducted genetic interaction screens, and induced the simultaneous CRISPR/Cas9-mediated knockout of 3 tumor-suppressor genes. Intramuscular injection of MuLE viruses expressing oncogenic H-RasG12V together with combinations of knockdowns of the tumor suppressors cyclin-dependent kinase inhibitor 2A (Cdkn2a), transformation-related protein 53 (Trp53), and phosphatase and tensin homolog (Pten) allowed the generation of 3 murine sarcoma models, demonstrating that genetically defined autochthonous tumors can be rapidly generated and quantitatively monitored via direct injection of polycistronic MuLE lentiviruses into mouse tissues. Together, our results demonstrate that the MuLE system provides genetic power for the systematic investigation of the molecular mechanisms that underlie human diseases. PMID:25751063

  9. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

    PubMed Central

    Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J.

    2013-01-01

    For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding. PMID:23592960

  10. Tropospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Mohnen, V.

    1984-01-01

    The fundamental processes that control the chemical composition and cycles of the global troposphere and how these processes and properties affect the physical behavior of the atmosphere are examined. The long-term information needs for tropospheric chemistry are: to be able to predict tropospheric responses to perturbations, both natural and anthropogenic, of these cycles, and to provide the information required for the maintenance and effective future management of the atmospheric component of our global life support system. The processes controlling global tropospheric biogeochemical cycles include: the input of trace species into the troposphere, their long-range transport and distribution as affected by the mean wind and vertical venting, their chemical transformations, including gas to particle conversion, leading to the appearance of aerosols or aqueous phase reactions inside cloud droplets, and their removal from the troposphere via wet (precipitation) and dry deposition.

  11. Dynamics and chemistry of Venus' large and complex cloud system : a science case for an in-situ long-term chemical laboratory

    NASA Astrophysics Data System (ADS)

    Widemann, Thomas; Määttänen, Anni; Wilquet, Valérie; McGouldrick, Kevin; Jessup, Kandis Lea; Wilson, Colin; Limaye, Sanjay; EuroVenus Consortium, the

    2014-05-01

    combine through meso-scale convection. In situ sampling of these aerosols represents a key measurement for constraining their properties, and identifying their role in the sulfurohydrological cycle by means of microphysical models of steadily increasing complexity. A probe/lander making a single descent will lack the spatial, temporal and local time coverage to address the coupling of compositional variations with radiative and dynamical properties of the atmosphere at cloud level, requiring a long duration flight. Establishing a long-term chemical laboratory in the cloud layer which would measure the detailed composition of both gas and liquid phases, and their latitudinal, diurnal and vertical variability using a combination of mass spectrometry, gas chromatography, tunable laser transmission spectrometry, and polar nephelometry would significantly address all of these objectives. It would allow the determination of the size distribution, shape, and real and imaginary refractive indices of the cloud particles, and the measurement of intensity and polarization phase functions. Our target species would include those known to be associated with cloud formation (e.g. H2SO4, SO3, SO2, H2O), as well as species important in stratospheric chemistry (e.g. CO, ClCOx, Ox, HCl, HF) and surface-atmosphere buffering (e.g. CO, OCS, SOx, Ox, H2S).

  12. Physical chemistry and the environment

    SciTech Connect

    Dunning, T.H. Jr.; Garrett, B.C.; Kolb, C.E. Jr.; Shaw, R.W.; Choppin, G.R.; Wagner, A.F.

    1994-08-01

    From the ozone hole and the greenhouse effect to plastics recycling and hazardous waste disposal, society faces a number of issues, the solutions to which require an unprecedented understanding of the properties of molecules. We are coming to realize that the environment is a coupled set of chemical systems, its dynamics determining the welfare of the biosphere and of humans in particular. These chemical systems are governed by fundamental molecular interactions, and they present chemists with an unparalleled challenge. The application of current concepts of molecular behavior and of up-to-date experimental and computational techniques can provide us with insights into the environment that are needed to mitigate past damage, to anticipate the impact of current human activity, and to avoid future insults to the environment. Environmental chemistry encompasses a number of separate, yet interlocking, areas of research. In all of these areas progress is limited by an inadequate understanding of the underlying chemical processes involved. Participation of all chemical approaches -- experimental, theoretical and computational -- and of all disciplines of chemistry -- organic, inorganic, physical, analytical and biochemistry -- will be required to provide the necessary fundamental understanding. The Symposium on ``Physical Chemistry and the Environment`` was designed to bring the many exciting and challenging physical chemistry problems involved in environmental chemistry to the attention of a larger segment of the physical chemistry community.

  13. Why Teach Environmental Chemistry?

    ERIC Educational Resources Information Center

    Gardner, Marjorie H.

    1974-01-01

    Discusses the importance of teaching environmental chemistry in secondary school science classes, and outlines five examples of environmental chemistry problems that focus on major concepts of chemistry and have critical implications for human survival and well-being. (JR)

  14. Science Update: Inorganic Chemistry

    ERIC Educational Resources Information Center

    Rawls, Rebecca

    1978-01-01

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

  15. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1984

    1984-01-01

    Presents an experiment which links mass spectrometry to gas chromatography. Also presents a simulation of iron extraction using a ZX81 computer and discussions of Fehling versus Benedict's solutions, transition metal ammine complexes, electrochemical and other chemical series, and a simple model of dynamic equilibria. (JN)

  16. Evolutionary models of interstellar chemistry

    NASA Technical Reports Server (NTRS)

    Prasad, Sheo S.

    1987-01-01

    The goal of evolutionary models of interstellar chemistry is to understand how interstellar clouds came to be the way they are, how they will change with time, and to place them in an evolutionary sequence with other celestial objects such as stars. An improved Mark II version of an earlier model of chemistry in dynamically evolving clouds is presented. The Mark II model suggests that the conventional elemental C/O ratio less than one can explain the observed abundances of CI and the nondetection of O2 in dense clouds. Coupled chemical-dynamical models seem to have the potential to generate many observable discriminators of the evolutionary tracks. This is exciting, because, in general, purely dynamical models do not yield enough verifiable discriminators of the predicted tracks.

  17. Laser direct writing of combinatorial libraries of idealized cellular constructs: Biomedical applications

    NASA Astrophysics Data System (ADS)

    Schiele, Nathan R.; Koppes, Ryan A.; Corr, David T.; Ellison, Karen S.; Thompson, Deanna M.; Ligon, Lee A.; Lippert, Thomas K. M.; Chrisey, Douglas B.

    2009-03-01

    The ability to control cell placement and to produce idealized cellular constructs is essential for understanding and controlling intercellular processes and ultimately for producing engineered tissue replacements. We have utilized a novel intra-cavity variable aperture excimer laser operated at 193 nm to reproducibly direct write mammalian cells with micrometer resolution to form a combinatorial array of idealized cellular constructs. We deposited patterns of human dermal fibroblasts, mouse myoblasts, rat neural stem cells, human breast cancer cells, and bovine pulmonary artery endothelial cells to study aspects of collagen network formation, breast cancer progression, and neural stem cell proliferation, respectively. Mammalian cells were deposited by matrix assisted pulsed laser evaporation direct write from ribbons comprised of a UV transparent quartz coated with either a thin layer of extracellular matrix or triazene as a dynamic release layer using CAD/CAM control. We demonstrate that through optical imaging and incorporation of a machine vision algorithm, specific cells on the ribbon can be laser deposited in spatial coherence with respect to geometrical arrays and existing cells on the receiving substrate. Having the ability to direct write cells into idealized cellular constructs can help to answer many biomedical questions and advance tissue engineering and cancer research.

  18. Brain embodiment of syntax and grammar: discrete combinatorial mechanisms spelt out in neuronal circuits.

    PubMed

    Pulvermüller, Friedemann

    2010-03-01

    Neuroscience has greatly improved our understanding of the brain basis of abstract lexical and semantic processes. The neuronal devices underlying words and concepts are distributed neuronal assemblies reaching into sensory and motor systems of the cortex and, at the cognitive level, information binding in such widely dispersed circuits is mirrored by the sensorimotor grounding of form and meaning of symbols. Recent years have seen the emergence of evidence for similar brain embodiment of syntax. Neurophysiological studies have accumulated support for the linguistic notion of abstract combinatorial rules manifest as functionally discrete neuronal assemblies. Concepts immanent to the theory of abstract automata could be grounded in observations from modern neuroscience, so that it became possible to model abstract pushdown storage - which is critical for building linguistic tree structure representations - as ordered dynamics of memory circuits in the brain. At the same time, neurocomputational research showed how sequence detectors already known from animal brains can be neuronally linked so that they merge into larger functionally discrete units, thereby underpinning abstract rule representations that syntactically bind lexicosemantic classes of morphemes and words into larger meaningful constituents. Specific predictions of brain-based grammar models could be confirmed by neurophysiological and brain imaging experiments using MEG, EEG and fMRI. Neuroscience and neurocomputational research offering perspectives on understanding abstract linguistic mechanisms in terms of neuronal circuits and their interactions therefore point programmatic new ways to future theory-guided experimental investigation of the brain basis of grammar. PMID:20132977

  19. Science Update: Inorganic Chemistry.

    ERIC Educational Resources Information Center

    Rawls, Rebecca

    1981-01-01

    Describes areas of inorganic chemistry which have changed dramatically in the past year or two, including photochemistry, electrochemistry, organometallic complexes, inorganic reaction theory, and solid state chemistry. (DS)

  20. Chemical budgets and stream-chemistry dynamics of a headwater stream in the Catskill Mountains of New York, October 1, 1983 through September 30, 1985. Water Resources Investigation

    SciTech Connect

    Murdoch, P.S.

    1991-01-01

    The purpose of the study was to evaluate the chemical effects of atmospherically derived acidity on stream water in Biscuit Brook and to compare the effects of stormflows on the annual chemical budgets with the effects of base flow. This report summarizes the results of water-quality analyses and chemical budgets on Biscuit Brook during water years 1984 and 1985, and assesses the relation between discharge and stream chemistry during 14 storms observed from April 1983 through May 1986 at Biscuit Brook.

  1. Application of combinatorial biocatalysis for a unique ring expansion of dihydroxymethylzearalenone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Combinatorial biocatalysis was applied to generate a diverse set of dihydroxymethylzearalenone derivatives with modified ring structure. In one chemoenzymatic reaction sequence, dihydroxymethylzearalenone was first subjected to a unique enzyme-catalyzed oxidative ring opening reaction that creates ...

  2. Combinatorial investigation of nanolaminate ternary carbide thin films

    NASA Astrophysics Data System (ADS)

    Scabarozi, Theodore H., Jr.

    In this research, investigations of thin film MAX phase ternary carbides synthesized by magnetron sputtering and a combinatorial method in the temperature range of RT-1000°C are reported. The M2AC MAX phases that formed in the following systems, Ti-Nb-Al-C, V-Cr-Al-C, V-Cr-Ge-C, were examined. In all solutions, only mixing of the M elements was investigated. All textured films grew epitaxially (c-axis) on c-sapphire substrates or deposited binary carbide buffer layers. The lowest synthesis temperature resulting in textured growth was for V 2AlC at 600°C, however; formation of nanocrystalline Cr2AlC was observed at 550°C as indicated by Raman spectroscopy. High temperature X-ray diffraction of amorphous Cr-Al-C and Cr-Ge-C films showed textured growth of the MAX phase occurred around 650°C, and 725°C, respectively. All combinatorial studies were performed at 850°C with (Ti1- xNbx)2AlC films grown on TiC buffer layers while (V1-xCr x)2AlC and (V1-xCr x)2GeC grown directly on sapphire. Complete solubility across the entire range of x was observed for all systems. Additionally, new thin film phases of V3AlC2, V 4AlC3, Nb5Al3Cx, Cr 5Ge3Cx, (Ti1- xNbx)3AlC2, (Ti1-xNbx) 4AlC3, and (V1-xCr x)4AlC3 were discovered. The M-element impacts many different properties of MAX phase films. The surface of most films were rough, some containing large hexagonal crystals. Yet, this work has demonstrated that the surface roughness can be tuned using elemental substitutions on the M-sites. While friction testing found all films to have relatively low coefficients of friction (<0.12), this too was found to be influenced by the M-element. Raman spectroscopy of (Ti1- xNbx)2AlC films indicates possible stiffening around x = 0.75 explicitly demonstrating the role of the M-element in this solid solution. All films were good electrical conductors with metal-like conduction down to 2K with magnitude and temperature dependence of the resistance tunable through composition. The Hall

  3. Combinatorial investigation of rare-earth free permanent magnets

    NASA Astrophysics Data System (ADS)

    Fackler, Sean Wu

    The combinatorial high throughput method allows one to rapidly study a large number of samples with systematically changing parameters. We apply this method to study Fe-Co-V alloys as alternatives to rare-earth permanent magnets. Rare-earth permanent magnets derive their unmatched magnetic properties from the hybridization of Fe and Co with the f-orbitals of rare-earth elements, which have strong spin-orbit coupling. It is predicted that Fe and Co may also have strong hybridization with 4d and 5d refractory transition metals with strong spin-orbit coupling. Refractory transition metals like V also have the desirable property of high temperature stability, which is important for permanent magnet applications in traction motors. In this work, we focus on the role of crystal structure, composition, and secondary phases in the origin of competitive permanent magnetic properties of a particular Fe-Co-V alloy. Fe38Co52V10, compositions are known as Vicalloys. Fe-CoV composition spreads were sputtered onto three-inch silicon wafers and patterned into discrete sample pads forming a combinatorial library. We employed highthroughput screening methods using synchrotron X-rays, wavelength dispersive spectroscopy, and magneto-optical Kerr effect (MOKE) to rapidly screen crystal structure, composition, and magnetic properties, respectively. We found that in-plane magnetic coercive fields of our Vicalloy thin films agree with known bulk values (300 G), but found a remarkable eight times increase of the out-of-plane coercive fields (˜2,500 G). To explain this, we measured the switching fields between in-plane and out-of-plane thin film directions which revealed that the Kondorsky model of 180° domain wall reversal was responsible for Vicalloy's enhanced out-of-plane coercive field and possibly its permanent magnetic properties. The Kondorsky model suggests that domain-wall pinning is the origin of Vicalloy's permanent magnetic properties, in contrast to strain, shape, or

  4. Combinatorial Properties of Arnoux Rauzy Subshifts and Applications to Schrödinger Operators

    NASA Astrophysics Data System (ADS)

    Damanik, D.; Zamboni, Luca Q.

    We consider Arnoux Rauzy subshifts X and study various combinatorial questions: When is X linearly recurrent? What is the maximal power occurring in X? What is the number of palindromes of a given length occurring in X? We present applications of our combinatorial results to the spectral theory of discrete one-dimensional Schrödinger operators with potentials given by Arnoux Rauzy sequences.

  5. Evaluation of the Current Status of the Combinatorial Approach for the Study of Phase Diagrams

    PubMed Central

    Wong-Ng, W.

    2012-01-01

    This paper provides an evaluation of the effectiveness of using the high throughput combinatorial approach for preparing phase diagrams of thin film and bulk materials. Our evaluation is based primarily on examples of combinatorial phase diagrams that have been reported in the literature as well as based on our own laboratory experiments. Various factors that affect the construction of these phase diagrams are examined. Instrumentation and analytical approaches needed to improve data acquisition and data analysis are summarized. PMID:26900530

  6. Chemistry Division: Annual progress report for period ending March 31, 1987

    SciTech Connect

    Not Available

    1987-08-01

    This report is divided into the following sections: coal chemistry; aqueous chemistry at high temperatures and pressures; geochemistry of crustal processes to high temperatures and pressures; chemistry of advanced inorganic materials; structure and dynamics of advanced polymeric materials; chemistry of transuranium elements and compounds; separations chemistry; reactions and catalysis in molten salts; surface science related to heterogeneous catalysis; electron spectroscopy; chemistry related to nuclear waste disposal; computational modeling of security document printing; and special topics. (DLC)

  7. On the relationship between total ozone and atmospheric dynamics and chemistry at mid-latitudes - Part 2: The effects of the El Niño/Southern Oscillation, volcanic eruptions and contributions of atmospheric dynamics and chemistry to long-term total ozone changes

    NASA Astrophysics Data System (ADS)

    Rieder, H. E.; Frossard, L.; Ribatet, M.; Staehelin, J.; Maeder, J. A.; Di Rocco, S.; Davison, A. C.; Peter, T.; Weihs, P.; Holawe, F.

    2013-01-01

    We present the first spatial analysis of "fingerprints" of the El Niño/Southern Oscillation (ENSO) and atmospheric aerosol load after major volcanic eruptions (El Chichón and Mt. Pinatubo) in extreme low and high (termed ELOs and EHOs, respectively) and mean values of total ozone for the northern and southern mid-latitudes (defined as the region between 30° and 60° north and south, respectively). Significant influence on ozone extremes was found for the warm ENSO phase in both hemispheres during spring, especially towards low latitudes, indicating the enhanced ozone transport from the tropics to the extra-tropics. Further, the results confirm findings of recent work on the connection between the ENSO phase and the strength and extent of the southern ozone "collar". For the volcanic eruptions the analysis confirms findings of earlier studies for the northern mid-latitudes and gives new insights for the Southern Hemisphere. The results provide evidence that the negative effect of the eruption of El Chichón might be partly compensated by a strong warm ENSO phase in 1982-1983 at southern mid-latitudes. The strong west-east gradient in the coefficient estimates for the Mt. Pinatubo eruption and the analysis of the relationship between the AAO and ENSO phase, the extent and the position of the southern ozone "collar" and the polar vortex structure provide clear evidence for a dynamical "masking" of the volcanic signal at southern mid-latitudes. The paper also analyses the contribution of atmospheric dynamics and chemistry to long-term total ozone changes. Here, quite heterogeneous results have been found on spatial scales. In general the results show that EESC and the 11-yr solar cycle can be identified as major contributors to long-term ozone changes. However, a strong contribution of dynamical features (El Niño/Southern Oscillation (ENSO), North Atlantic Oscillation (NAO), Antarctic Oscillation (AAO), Quasi-Biennial Oscillation (QBO)) to ozone variability and

  8. On the relationship between total ozone and atmospheric dynamics and chemistry at mid-latitudes - Part 2: The effects of the El Niño/Southern Oscillation, volcanic eruptions and contributions of atmospheric dynamics and chemistry to long-term total ozone changes

    NASA Astrophysics Data System (ADS)

    Rieder, H. E.; Frossard, L.; Ribatet, M.; Staehelin, J.; Maeder, J. A.; Di Rocco, S.; Davison, A. C.; Peter, T.; Weihs, P.; Holawe, F.

    2012-05-01

    We present the first spatial analysis of "fingerprints" of the El Niño/Southern Oscillation (ENSO) and atmospheric aerosol load after major volcanic eruptions (El Chichón and Mt. Pinatubo) in extreme low and high (termed ELOs and EHOs, respectively) and mean values of total ozone for the northern and southern mid-latitudes (defined as the region between 30° and 60° north and south, respectively). Significant influence on ozone extremes was found for the warm ENSO phase in both hemispheres during spring, especially towards low latitudes, indicating the enhanced ozone transport from the tropics to the extra-tropics. Further, the results confirm findings of recent work on the connection between the ENSO phase and the strength and extent of the southern ozone "collar". For the volcanic eruptions the analysis confirms findings of earlier studies for the northern mid-latitudes and gives new insights for the Southern Hemisphere. The results provide evidence that the negative effect of the eruption of El Chichón might be partly compensated by a strong warm ENSO phase in 1982-83 at southern mid-latitudes. The strong west-east gradient in the coefficient estimates for the Mt. Pinatubo eruption and the analysis of the relationship between the AAO and ENSO phase, the extent and the position of the southern ozone "collar" and the polar vortex structure provide clear evidence for a dynamical "masking" of the volcanic signal at southern mid-latitudes. The paper also analyses the contribution of atmospheric dynamics and chemistry to long-term total ozone changes. Here, quite heterogeneous results have been found on spatial scales. In general the results show that EESC and the 11-yr solar cycle can be identified as major contributors to long-term ozone changes. However, a strong contribution of dynamical features (El Niño/Southern Oscillation (ENSO), North Atlantic Oscillation (NAO), Antarctic Oscillation (AAO), Quasi-Biennial Oscillation (QBO)) to ozone variability and

  9. Combinatorial MAPLE gradient thin film assemblies signalling to human osteoblasts.

    PubMed

    Axente, Emanuel; Sima, Felix; Elena Sima, Livia; Erginer, Merve; Eroglu, Mehmet S; Serban, Natalia; Ristoscu, Carmen; Petrescu, Stefana M; Toksoy Oner, Ebru; Mihailescu, Ion N

    2014-09-01

    There is increased interest in smart bioactive materials to control tissue regeneration for the engineering of cell instructive scaffolds. We introduced combinatorial matrix-assisted pulsed laser evaporation (C-MAPLE) as a new method for the fabrication of organic thin films with a compositional gradient. Synchronized C-MAPLE of levan and oxidized levan was employed to assemble a two-compound biopolymer film structure. The gradient of the film composition was validated by fluorescence microscopy. In this study, we investigated the cell response induced by the compositional gradient using imaging of early osteoblast attachment and analysis of signalling phosphoprotein expression. Cells attached along the gradient in direct proportion to oxidized levan concentration. During this process distinct areas of the binary gradient have been shown to modulate the osteoblasts' extracellular signal-regulated kinase signalling with different propensity. The proposed fabrication method results in the preparation of a new bioactive material, which could control the cell signalling response. This approach can be extended to screen new bioactive interfaces for tissue regeneration. PMID:24867882

  10. Combinatorial approach to hepadnavirus-like particle vaccine design.

    PubMed

    Billaud, Jean-Noel; Peterson, Darrell; Barr, Margaret; Chen, Antony; Sallberg, Matti; Garduno, Fermin; Goldstein, Phillip; McDowell, Wendy; Hughes, Janice; Jones, Joyce; Milich, David

    2005-11-01

    The particulate hepatitis core protein (HBcAg) represents an efficient carrier platform with many of the characteristics uniquely required for the delivery of weak immunogens to the immune system. Although the HBcAg is highly immunogenic, the existing HBcAg-based platform technology has a number of theoretical and practical limitations, most notably the "preexisting immunity" and "assembly" problems. To address the assembly problem, we have developed the core protein from the woodchuck hepadnavirus (WHcAg) as a new particulate carrier platform system. WHcAg appears to tolerate insertions of foreign epitopes at a greater number of positions than HBcAg. For example, both within the external loop region and outside the loop region a total of 17 insertion sites were identified on WHcAg. Importantly, the identification of an expanded number of insertion sites was dependent on additional modifications to the C terminus that appear to stabilize the various internal insertions. Indeed, 21 separate C-terminal modifications have been generated that can be used in combination with the 17 insertion sites to ensure efficient hybrid WHcAg particle assembly. This combinatorial technology is also dependent on the sequence of the heterologous insert. Therefore, the three variables of insert position, C terminus, and epitope sequence are relevant in the design of hybrid WHcAg particles for vaccine purposes. PMID:16227285

  11. Combinatorial optimization: Current successes and directions for the future

    NASA Astrophysics Data System (ADS)

    Hoffman, Karla L.

    2000-12-01

    Our ability to solve large, important combinatorial optimization problems has improved dramatically in the past decade. The availability of reliable software, extremely fast and inexpensive hardware and high-level languages that make the modeling of complex problems much faster have led to a much greater demand for optimization tools. This paper highlights the major breakthroughs and then describes some very exciting future opportunities. Previously, large research projects required major data collection efforts, expensive mainframes and substantial analyst manpower. Now, we can solve much larger problems on personal computers, much of the necessary data is routinely collected and tools exist to speed up both the modeling and the post-optimality analysis. With the information-technology revolution taking place currently, we now have the opportunity to have our tools embedded into supply-chain systems that determine production and distribution schedules, process-design and location-allocation decisions. These tools can be used industry-wide with only minor modifications being done by each user.

  12. Linear effects models of signaling pathways from combinatorial perturbation data

    PubMed Central

    Szczurek, Ewa; Beerenwinkel, Niko

    2016-01-01

    Motivation: Perturbations constitute the central means to study signaling pathways. Interrupting components of the pathway and analyzing observed effects of those interruptions can give insight into unknown connections within the signaling pathway itself, as well as the link from the pathway to the effects. Different pathway components may have different individual contributions to the measured perturbation effects, such as gene expression changes. Those effects will be observed in combination when the pathway components are perturbed. Extant approaches focus either on the reconstruction of pathway structure or on resolving how the pathway components control the downstream effects. Results: Here, we propose a linear effects model, which can be applied to solve both these problems from combinatorial perturbation data. We use simulated data to demonstrate the accuracy of learning the pathway structure as well as estimation of the individual contributions of pathway components to the perturbation effects. The practical utility of our approach is illustrated by an application to perturbations of the mitogen-activated protein kinase pathway in Saccharomyces cerevisiae. Availability and Implementation: lem is available as a R package at http://www.mimuw.edu.pl/∼szczurek/lem. Contact: szczurek@mimuw.edu.pl; niko.beerenwinkel@bsse.ethz.ch Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307630

  13. Synthesis and characterization of catalysts and electrocatalysts using combinatorial methods

    NASA Astrophysics Data System (ADS)

    Ramanathan, Ramnarayanan

    This thesis documents attempts at solving three problems. Bead-based parallel synthetic and screening methods based on matrix algorithms were developed. The method was applied to search for new heterogeneous catalysts for dehydrogenation of methylcyclohexane. The most powerful use of the method to date was to optimize metal adsorption and evaluate catalysts as a function of incident energy, likely to be important in the future, should availability of energy be an optimization parameter. This work also highlighted the importance of order of addition of metal salts on catalytic activity and a portion of this work resulted in a patent with UOP LLC, Desplaines, Illinois. Combinatorial methods were also investigated as a tool to search for carbon-monoxide tolerant anode electrocatalysts and methanol tolerant cathode electrocatalysts, resulting in discovery of no new electrocatalysts. A physically intuitive scaling criterion was developed to analyze all experiments on electrocatalysts, providing insight for future experiments. We attempted to solve the CO poisoning problem in polymer electrolyte fuel cells using carbon molecular sieves as a separator. This approach was unsuccessful in solving the CO poisoning problem, possibly due to the tendency of the carbon molecular sieves to concentrate CO and CO 2 in pore walls.

  14. HIV Eradication: Combinatorial Approaches to Activate Latent Viruses

    PubMed Central

    De Crignis, Elisa; Mahmoudi, Tokameh

    2014-01-01

    The concept of eradication of the Human Immune Deficiency Virus (HIV) from infected patients has gained much attention in the last few years. While combination Anti-Retroviral Therapy (c-ART) has been extremely effective in suppressing viral replication, it is not curative. This is due to the presence of a reservoir of latent HIV infected cells, which persist in the presence of c-ART. Recently, pharmaceutical approaches have focused on the development of molecules able to induce HIV-1 replication from latently infected cells in order to render them susceptible to viral cytopathic effects and host immune responses. Alternative pathways and transcription complexes function to regulate the activity of the HIV promoter and might serve as molecular targets for compounds to activate latent HIV. A combined therapy coupling various depressors and activators will likely be the most effective in promoting HIV replication while avoiding pleiotropic effects at the cellular level. Moreover, in light of differences among HIV subtypes and variability in integration sites, the combination of multiple agents targeting multiple pathways will increase likelihood of therapeutic effectiveness and prevent mutational escape. This review provides an overview of the mechanisms that can be targeted to induce HIV activation focusing on potential combinatorial approaches. PMID:25421889

  15. Combinatorial approaches to evaluate nanodiamond uptake and induced cellular fate

    PubMed Central

    Eldawud, Reem; Reitzig, Manuela; Opitz, Jörg; Rojansakul, Yon; Jiang, Wenjuan; Nangia, Shikha; Dinu, Cerasela Zoica

    2016-01-01

    Nanodiamonds (NDs) are an emerging class of engineered nanomaterials that hold great promise for the next generation of bionanotechnological products to be used for drug and gene delivery, or for bio-imaging and biosensing. Previous studies have shown that upon their cellular uptake, NDs exhibit high biocompatibility in various in vitro and in vivo set-ups. Herein we hypothesized that the increased NDs biocompatibility is a result of minimum membrane perturbations and their reduced ability to induce disruption or damage during cellular translocation. Using multi-scale combinatorial approaches that simulate ND-membrane interactions, we correlated NDs real-time cellular uptake and kinetics with the ND-induced membrane fluctuations to derive energy requirements for the uptake to occur. Our discrete and real-time analyses showed that the majority of NDs internalization occurs within 2 h of cellular exposure, however, with no effects on cellular viability, proliferation or cellular behavior. Furthermore, our simulation analyses using coarse-grained models identified key changes in the energy profile, membrane deformation and recovery time, all functions of the average ND or ND-based agglomerate size. Understanding the mechanisms responsible for ND-cell membrane interactions could possibly advance their implementation in various biomedical applications. PMID:26820775

  16. Combinatorial approaches to evaluate nanodiamond uptake and induced cellular fate

    NASA Astrophysics Data System (ADS)

    Eldawud, Reem; Reitzig, Manuela; Opitz, Jörg; Rojansakul, Yon; Jiang, Wenjuan; Nangia, Shikha; Zoica Dinu, Cerasela

    2016-02-01

    Nanodiamonds (NDs) are an emerging class of engineered nanomaterials that hold great promise for the next generation of bionanotechnological products to be used for drug and gene delivery, or for bio-imaging and biosensing. Previous studies have shown that upon their cellular uptake, NDs exhibit high biocompatibility in various in vitro and in vivo set-ups. Herein we hypothesized that the increased NDs biocompatibility is a result of minimum membrane perturbations and their reduced ability to induce disruption or damage during cellular translocation. Using multi-scale combinatorial approaches that simulate ND-membrane interactions, we correlated NDs real-time cellular uptake and kinetics with the ND-induced membrane fluctuations to derive energy requirements for the uptake to occur. Our discrete and real-time analyses showed that the majority of NDs internalization occurs within 2 h of cellular exposure, however, with no effects on cellular viability, proliferation or cellular behavior. Furthermore, our simulation analyses using coarse-grained models identified key changes in the energy profile, membrane deformation and recovery time, all functions of the average ND or ND-based agglomerate size. Understanding the mechanisms responsible for ND-cell membrane interactions could possibly advance their implementation in various biomedical applications.

  17. Rational and combinatorial tailoring of bioactive cyclic dipeptides

    PubMed Central

    Giessen, Tobias W.; Marahiel, Mohamed A.

    2015-01-01

    Modified cyclic dipeptides represent a diverse family of microbial secondary metabolites. They display a broad variety of biological and pharmacological activities and have long been recognized as privileged structures with the ability to bind to a wide range of receptors. This is due to their conformationally constrained 2, 5-diketopiperazine (DKP) scaffold and the diverse set of DKP tailoring enzymes present in nature. After initial DKP assembly through different biosynthetic systems modifying enzymes are responsible for installing functional groups crucial for the biological activities of the resulting modified DKPs. They represent a vast and largely untapped enzyme repository very useful for synthetic biology approaches aiming at introducing structural variations into DKP scaffolds. In this review we focus on these DKP modification enzymes found in various microbial secondary metabolite gene clusters. We will give a brief overview of their distribution and highlight a select number of characterized DKP tailoring enzymes before turning to their application potential in combinatorial biosynthesis with the aim of producing molecules with improved or entirely new biological and medicinally relevant properties. PMID:26284060

  18. HIV eradication: combinatorial approaches to activate latent viruses.

    PubMed

    De Crignis, Elisa; Mahmoudi, Tokameh

    2014-11-01

    The concept of eradication of the Human Immune Deficiency Virus (HIV) from infected patients has gained much attention in the last few years. While combination Anti-Retroviral Therapy (c-ART) has been extremely effective in suppressing viral replication, it is not curative. This is due to the presence of a reservoir of latent HIV infected cells, which persist in the presence of c-ART. Recently, pharmaceutical approaches have focused on the development of molecules able to induce HIV-1 replication from latently infected cells in order to render them susceptible to viral cytopathic effects and host immune responses. Alternative pathways and transcription complexes function to regulate the activity of the HIV promoter and might serve as molecular targets for compounds to activate latent HIV. A combined therapy coupling various depressors and activators will likely be the most effective in promoting HIV replication while avoiding pleiotropic effects at the cellular level. Moreover, in light of differences among HIV subtypes and variability in integration sites, the combination of multiple agents targeting multiple pathways will increase likelihood of therapeutic effectiveness and prevent mutational escape. This review provides an overview of the mechanisms that can be targeted to induce HIV activation focusing on potential combinatorial approaches. PMID:25421889

  19. Free-Riding and Free-Labor in Combinatorial Agency

    NASA Astrophysics Data System (ADS)

    Babaioff, Moshe; Feldman, Michal; Nisan, Noam

    This paper studies a setting where a principal needs to motivate teams of agents whose efforts lead to an outcome that stochastically depends on the combination of agents’ actions, which are not directly observable by the principal. In [1] we suggest and study a basic “combinatorial agency” model for this setting. In this paper we expose a somewhat surprising phenomenon found in this setting: cases where the principal can gain by asking agents to reduce their effort level, even when this increased effort comes for free. This phenomenon cannot occur in a setting where the principal can observe the agents’ actions, but we show that it can occur in the hidden-actions setting. We prove that for the family of technologies that exhibit “increasing returns to scale” this phenomenon cannot happen, and that in some sense this is a maximal family of technologies for which the phenomenon cannot occur. Finally, we relate our results to a basic question in production design in firms.

  20. Systems and methods for the combinatorial synthesis of novel materials

    DOEpatents

    Wu, Xin Di; Wang, Youqi; Goldwasser, Isy

    2000-01-01

    Methods and apparatus for the preparation of a substrate having an array of diverse materials in predefined regions thereon. A substrate having an array of diverse materials thereon is generally prepared by depositing components of target materials to predefined regions on the substrate, and, in some embodiments, simultaneously reacting the components to form at least two resulting materials. In particular, the present invention provides novel masking systems and methods for applying components of target materials onto a substrate in a combinatorial fashion, thus creating arrays of resulting materials that differ slightly in composition, stoichiometry, and/or thickness. Using the novel masking systems of the present invention, components can be delivered to each site in a uniform distribution, or in a gradient of stoichiometries, thicknesses, compositions, etc. Resulting materials which can be prepared using the methods and apparatus of the present invention include, for example, covalent network solids, ionic solids and molecular solids. Once prepared, these resulting materials can be screened sequentially, or in parallel, for useful properties including, for example, electrical, thermal, mechanical, morphological, optical, magnetic, chemical and other properties.