WorldWideScience

Sample records for chemical structure information

  1. Trends in information theory-based chemical structure codification.

    Science.gov (United States)

    Barigye, Stephen J; Marrero-Ponce, Yovani; Pérez-Giménez, Facundo; Bonchev, Danail

    2014-08-01

    This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go "back to the roots" of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed.

  2. Mining chemical structural information from the drug literature.

    Science.gov (United States)

    Banville, Debra L

    2006-01-01

    It is easier to find too many documents on a life science topic than to find the right information inside these documents. With the application of text data mining to biological documents, it is no surprise that researchers are starting to look at applications that mine out chemical information. The mining of chemical entities--names and structures--brings with it some unique challenges, which commercial and academic efforts are beginning to address. Ultimately, life science text data mining applications need to focus on the marriage of biological and chemical information.

  3. Automated extraction of chemical structure information from digital raster images

    Directory of Open Access Journals (Sweden)

    Shedden Kerby A

    2009-02-01

    Full Text Available Abstract Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links

  4. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  5. Information Theory and Voting Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures.

    Science.gov (United States)

    Saeed, Faisal; Salim, Naomie; Abdo, Ammar

    2013-07-01

    Many consensus clustering methods have been applied in different areas such as pattern recognition, machine learning, information theory and bioinformatics. However, few methods have been used for chemical compounds clustering. In this paper, an information theory and voting based algorithm (Adaptive Cumulative Voting-based Aggregation Algorithm A-CVAA) was examined for combining multiple clusterings of chemical structures. The effectiveness of clusterings was evaluated based on the ability of the clustering method to separate active from inactive molecules in each cluster, and the results were compared with Ward's method. The chemical dataset MDL Drug Data Report (MDDR) and the Maximum Unbiased Validation (MUV) dataset were used. Experiments suggest that the adaptive cumulative voting-based consensus method can improve the effectiveness of combining multiple clusterings of chemical structures.

  6. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    Science.gov (United States)

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

  7. A large scale analysis of information-theoretic network complexity measures using chemical structures.

    Directory of Open Access Journals (Sweden)

    Matthias Dehmer

    Full Text Available This paper aims to investigate information-theoretic network complexity measures which have already been intensely used in mathematical- and medicinal chemistry including drug design. Numerous such measures have been developed so far but many of them lack a meaningful interpretation, e.g., we want to examine which kind of structural information they detect. Therefore, our main contribution is to shed light on the relatedness between some selected information measures for graphs by performing a large scale analysis using chemical networks. Starting from several sets containing real and synthetic chemical structures represented by graphs, we study the relatedness between a classical (partition-based complexity measure called the topological information content of a graph and some others inferred by a different paradigm leading to partition-independent measures. Moreover, we evaluate the uniqueness of network complexity measures numerically. Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases.

  8. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    Science.gov (United States)

    Shen, Yang; Bax, Ad

    2015-01-01

    Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.

  9. Chemical information science coverage in Chemical Abstracts.

    Science.gov (United States)

    Wiggins, G

    1987-02-01

    For many years Chemical Abstracts has included in its coverage publications on chemical documentation or chemical information science. Although the bulk of those publications can be found in section 20 of Chemical Abstracts, many relevant articles were found scattered among 39 other sections of CA in 1984-1985. In addition to the scattering of references in CA, the comprehensiveness of Chemical Abstracts as a secondary source for chemical information science is called into question. Data are provided on the journals that contributed the most references on chemical information science and on the languages of publication of relevant articles.

  10. Prediction of bioactive compound pathways using chemical interaction and structural information.

    Science.gov (United States)

    Cheng, Shiwen; Zhu, Changming; Chu, Chen; Huang, Tao; Kong, Xiangyin; Zhu, Liu Cun

    2016-01-01

    The functional screening of compounds is an important topic in chemistry and biomedicine that can uncover the essential properties of compounds and provide information concerning their correct use. In this study, we investigated the bioactive compounds reported in Selleckchem, which were assigned to 22 pathways. A computational method was proposed to identify the pathways of the bioactive compounds. Unlike most existing methods that only consider compound structural information, the proposed method adopted both the structural and interaction information from the compounds. The total accuracy achieved by our method was 61.79% based on jackknife analysis of a dataset of 1,832 bioactive compounds. Its performance was quite good compared with that of other machine learning algorithms (with total accuracies less than 46%). Finally, some of the false positives obtained by the method were analyzed to investigate the likelihood of compounds being annotated to new pathways.

  11. Applications of the Information Theory to Problems of Molecular Electronic Structure and Chemical Reactivity

    Directory of Open Access Journals (Sweden)

    Roman F. Nalewajski

    2002-04-01

    Full Text Available Abstract: Recent studies on applications of the information theoretic concepts to molecular systems are reviewed. This survey covers the information theory basis of the Hirshfeld partitioning of molecular electron densities, its generalization to many electron probabilities, the local information distance analysis of molecular charge distributions, the charge transfer descriptors of the donor-acceptor reactive systems, the elements of a “thermodynamic” description of molecular charge displacements, both “vertical” (between molecular fragments for the fixed overall density and “horizontal” (involving different molecular densities, with the entropic representation description provided by the information theory. The average uncertainty measures of bond multiplicities in molecular “communication” systems are also briefly summarized. After an overview of alternative indicators of the information distance (entropy deficiency, missing information between probability distributions the properties of the “stockholder” densities, which minimize the entropy deficiency relative to the promolecule reference, are summarized. In particular, the surprisal analysis of molecular densities is advocated as an attractive information-theoretic tool in the electronic structure theory, supplementary to the familiar density difference diagrams. The subsystem information density equalization rules satisfied by the Hirshfeld molecular fragments are emphasized: the local values of alternative information distance densities of subsystems are equal to the corresponding global value, characterizing the molecule as a whole. These local measures of the information content are semi-quantitatively related to the molecular density difference function. In the density functional theory the effective external potentials of molecular fragments are defined, for which

  12. Information Extraction From Chemical Patents

    Directory of Open Access Journals (Sweden)

    Sandra Bergmann

    2012-01-01

    Full Text Available The development of new chemicals or pharmaceuticals is preceded by an indepth analysis of published patents in this field. This information retrieval is a costly and time inefficient step when done by a human reader, yet it is mandatory for potential success of an investment. The goal of the research project UIMA-HPC is to automate and hence speed-up the process of knowledge mining about patents. Multi-threaded analysis engines, developed according to UIMA (Unstructured Information Management Architecture standards, process texts and images in thousands of documents in parallel. UNICORE (UNiform Interface to COmputing Resources workflow control structures make it possible to dynamically allocate resources for every given task to gain best cpu-time/realtime ratios in an HPC environment.

  13. Extraction of structural and chemical information from high angle annular dark-field image by an improved peaks finding method.

    Science.gov (United States)

    Yin, Wenhao; Huang, Rong; Qi, Ruijuan; Duan, Chungang

    2016-09-01

    With the development of spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM), high angle annular dark filed (HAADF) imaging technique has been widely applied in the microstructure characterization of various advanced materials with atomic resolution. However, current qualitative interpretation of the HAADF image is not enough to extract all the useful information. Here a modified peaks finding method was proposed to quantify the HAADF-STEM image to extract structural and chemical information. Firstly, an automatic segmentation technique including numerical filters and watershed algorithm was used to define the sub-areas for each atomic column. Then a 2D Gaussian fitting was carried out to determine the atomic column positions precisely, which provides the geometric information at the unit-cell scale. Furthermore, a self-adaptive integration based on the column position and the covariance of statistical Gaussian distribution were performed. The integrated intensities show very high sensitivity on the mean atomic number with improved signal-to-noise (S/N) ratio. Consequently, the polarization map and strain distributions were rebuilt from a HAADF-STEM image of the rhombohedral and tetragonal BiFeO3 interface and a MnO2 monolayer in LaAlO3 /SrMnO3 /SrTiO3 heterostructure was discerned from its neighbor TiO2 layers. Microsc. Res. Tech. 79:820-826, 2016. © 2016 Wiley Periodicals, Inc.

  14. Biological and Chemical Information Technologies

    DEFF Research Database (Denmark)

    Amos, Martyn; Dittrich, Peter; McCaskill, John;

    2011-01-01

    Biological and chemical information technologies (bio/chem IT) have the potential to reshape the scientific and technological landscape. In this paper we briefly review the main challenges and opportunities in the field, before presenting several case studies based on ongoing FP7 research projects....

  15. Multimedia environmental chemical partitioning from molecular information.

    Science.gov (United States)

    Martínez, Izacar; Grifoll, Jordi; Giralt, Francesc; Rallo, Robert

    2010-12-15

    The prospect of assessing the environmental distribution of chemicals directly from their molecular information was analyzed. Multimedia chemical partitioning of 455 chemicals, expressed in dimensionless compartmental mass ratios, was predicted by SimpleBox 3, a Level III Fugacity model, together with the propagation of reported uncertainty for key physicochemical and transport properties, and degradation rates. Chemicals, some registered in priority lists, were selected according to the availability of experimental property data to minimize the influence of predicted information in model development. Chemicals were emitted in air or water in a fixed geographical scenario representing the Netherlands and characterized by five compartments (air, water, sediments, soil and vegetation). Quantitative structure-fate relationship (QSFR) models to predict mass ratios in different compartments were developed with support vector regression algorithms. A set of molecular descriptors, including the molecular weight and 38 counts of molecular constituents were adopted to characterize the chemical space. Out of the 455 chemicals, 375 were used for training and testing the QSFR models, while 80 were excluded from model development and were used as an external validation set. Training and test chemicals were selected and the domain of applicability (DOA) of the QSFRs established by means of self-organizing maps according to structural similarity. Best results were obtained with QSFR models developed for chemicals belonging to either the class [C] and [C; O], or the class with at least one heteroatom different than oxygen in the structure. These two class-specific models, with respectively 146 and 229 chemicals, showed a predictive squared coefficient of q(2) ≥ 0.90 both for air and water, which respectively dropped to q(2)≈ 0.70 and 0.40 for outlying chemicals. Prediction errors were of the same order of magnitude as the deviations associated to the uncertainty of the

  16. An Introduction to the Foundations of Chemical Information Theory. Tarski–Lesniewski Logical Structures and the Organization of Natural Sorts and Kinds

    Directory of Open Access Journals (Sweden)

    Jerry L. R. Chandler

    2017-01-01

    Full Text Available Organic mathematics is an applied mathematics of philosophical atomism. The order of the chemical elements in the table of elements is the source of order for the logical operations of addition and subtraction of atomic numbers. The inverse square laws of physics are the source of organization of subatomic structures of chemical atoms (atomic and molecular structures. These facts are foundational to the logic of the chemical sciences and are therefore the scientific basis for chemical information theory. The theories and facts of the chemical sciences are so perplex that several forms of symbolic representations are necessary to communicate the broad range of scientific concepts used to inquire into the nature of natural sorts and kinds. The logics proposed by Tarski, Lesniewski and Malatesta are applied to the construction of a numerical “spine” of perplex numbers representing atomic numbers as meta-symbols in meta-languages. The orbital angular momenta of certain collections of electrical particles (also known as “handedness” are critical components in constructing the logical propositions of the perplex number “spine”. Biological communication channels can function if and only if the natural sorts and kinds are consistent with the matching patterns of the optical isomers. The terms spinners and twisters are introduced to express the electro-mechanical torques necessary for encoding chemical information. This hypothesis can be tested by several categories of experiments, including clinical pharmaco-dynamics and clinical toxico-dynamics of dissymmetric isomers of different sorts and kinds.

  17. Chemical Information Literacy at a Liberal Arts College

    Science.gov (United States)

    Greco, George E.

    2016-01-01

    Chemistry majors at Goucher College are now required to take a 1-credit course in their sophomore year entitled Chemical Information Literacy. Students in the course learn the structure and organization of the chemical literature, and how to carry out searches of various databases for topic, author, chemical compound, or structure. They learn…

  18. Chemical Bonding and Structural Information of Black CarbonReference Materials and Individual Carbonaceous AtmosphericAerosols

    Energy Technology Data Exchange (ETDEWEB)

    Hopkins, Rebecca J.; Tivanski, Alexei V.; Marten, Bryan D.; Gilles, Mary K.

    2007-04-25

    The carbon-to-oxygen ratios and graphitic nature of a rangeof black carbon standard reference materials (BC SRMs), high molecularmass humic-like substances (HULIS) and atmospheric particles are examinedusing scanning transmission X-ray microscopy (STXM) coupled with nearedge X-ray absorption fine structure (NEXAFS) spectroscopy. UsingSTXM/NEXAFS, individual particles with diameter>100 nm are studied,thus the diversity of atmospheric particles collected during a variety offield missions is assessed. Applying a semi-quantitative peak fittingmethod to the NEXAFS spectra enables a comparison of BC SRMs and HULIS toparticles originating from anthropogenic combustion and biomass burns,thus allowing determination of the suitability of these materials forrepresenting atmospheric particles. Anthropogenic combustion and biomassburn particles can be distinguished from one another using both chemicalbonding and structural ordering information. While anthropogeniccombustion particles are characterized by a high proportion ofaromatic-C, the presence of benzoquinone and are highly structurallyordered, biomass burn particles exhibit lower structural ordering, asmaller proportion of aromatic-C and contain a much higher proportion ofoxygenated functional groups.

  19. Structuring the Information Gap.

    Science.gov (United States)

    Edge, Julian

    1984-01-01

    Describes an information gap procedure to teach a new structure which requires students to look for and exchange information in order to complete a task in an English as a second language class. Illustrates the method with a set of materials and suggests ways for teachers to produce similar materials. (SED)

  20. The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Lei Chen

    Full Text Available Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer.

  1. Identification of Chemical Toxicity Using Ontology Information of Chemicals

    Directory of Open Access Journals (Sweden)

    Zhanpeng Jiang

    2015-01-01

    Full Text Available With the advance of the combinatorial chemistry, a large number of synthetic compounds have surged. However, we have limited knowledge about them. On the other hand, the speed of designing new drugs is very slow. One of the key causes is the unacceptable toxicities of chemicals. If one can correctly identify the toxicity of chemicals, the unsuitable chemicals can be discarded in early stage, thereby accelerating the study of new drugs and reducing the R&D costs. In this study, a new prediction method was built for identification of chemical toxicities, which was based on ontology information of chemicals. By comparing to a previous method, our method is quite effective. We hope that the proposed method may give new insights to study chemical toxicity and other attributes of chemicals.

  2. Information Structure: Afterword

    Directory of Open Access Journals (Sweden)

    Craige Roberts

    2012-12-01

    Full Text Available This is the afterword to the 2012 republication of "Information structure in discourse: Towards an integrated formal theory of pragmatics". See also the annotated bibliography on related topics at http://www.ling.ohio-state.edu/~croberts/QUDbib/. http://dx.doi.org/10.3765/sp.5.7 BibTeX info

  3. Chemical Thermodynamics and Information Theory with Applications

    CERN Document Server

    Graham, Daniel J

    2011-01-01

    Thermodynamics and information touch theory every facet of chemistry. However, the physical chemistry curriculum digested by students worldwide is still heavily skewed toward heat/work principles established more than a century ago. Rectifying this situation, Chemical Thermodynamics and Information Theory with Applications explores applications drawn from the intersection of thermodynamics and information theory--two mature and far-reaching fields. In an approach that intertwines information science and chemistry, this book covers: The informational aspects of thermodynamic state equations The

  4. Structure validation in chemical crystallography.

    Science.gov (United States)

    Spek, Anthony L

    2009-02-01

    Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.

  5. The PubChem chemical structure sketcher

    Directory of Open Access Journals (Sweden)

    Ihlenfeldt Wolf D

    2009-12-01

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

  6. 77 FR 74685 - Chemical Facility Anti-Terrorism Standards (CFATS) Chemical-Terrorism Vulnerability Information...

    Science.gov (United States)

    2012-12-17

    ... SECURITY Chemical Facility Anti-Terrorism Standards (CFATS) Chemical- Terrorism Vulnerability Information... financial information, Chemical-terrorism Vulnerability Information (CVI), Sensitive Security Information... represents a national-level effort to minimize terrorism risk to such facilities. Its design...

  7. Information Structures and Undergraduate Students

    Science.gov (United States)

    Lee, Hur-Li

    2008-01-01

    This study explores how undergraduates seek information across various information structures. Taking part in an interview, fifteen students of diverse backgrounds described their information seeking. The findings pointed to several issues relating to the underlying structures of information resources. Suggestions are made for structural…

  8. Web-accessible Chemical Compound Information

    OpenAIRE

    Roth, Dana L

    2008-01-01

    Web-accessible chemical compound information resources are widely available. In addition to fee-based resources, such as SciFinder Scholar and Beilstein, there is a wide variety of freely accessible resources such as ChemSpider and PubChem. The author provides a general description of various fee-based and free chemical compound resources. The free resources generally offer an acceptable alternative to fee-based resources for quick retrieval. It is assumed that readers will be familiar with ...

  9. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C [University of Illinois, Urbana-Champaign; Nesbitt, Anna E [University of Illinois, Urbana-Champaign; Hallock, Michael J [University of Illinois, Urbana-Champaign; Rupasinghe, Sanjeewa [University of Illinois, Urbana-Champaign; Tang, Ming [University of Illinois, Urbana-Champaign; Harris, Jason B [ORNL; Baudry, Jerome Y [ORNL; Schuler, Mary A [University of Illinois, Urbana-Champaign; Rienstra, Chad M [University of Illinois, Urbana-Champaign

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  10. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C.; Nesbitt, Anna E.; Hallock, Michael J. [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Rupasinghe, Sanjeewa G. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Tang Ming [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Harris, Jason; Baudry, Jerome [University of Tennessee, Department of Biochemistry, Cellular and Molecular Biology (United States); Schuler, Mary A. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Rienstra, Chad M., E-mail: rienstra@illinois.edu [University of Illinois at Urbana-Champaign, Department of Chemistry (United States)

    2012-01-15

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., {sup 13}C-{sup 13}C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  11. Allelophaty - the chemical information system in plants adaptation

    Directory of Open Access Journals (Sweden)

    Eugenia CHIRCA

    1985-08-01

    Full Text Available The plant, as a living system, is an informational system too, with transmission and reception of different messages between the individuals of the community in which is integrated. The most common and most efficient system in the plant kingdom is of chemical nature. Through this system energy and information are transmitted among individuals, or even communities, in order to ensure the homeostasis of the system. The study of these signals in the supraindividual level is designated as ecochemistry (Florkin, 1966 or ecological biochemistry (Schlee, 1981. Plant metabolic substance - especially those designed as "secondary" organic substances works as allelopathic information signalsin plant communities and function as stabilisers in a agiven community Owing to this chemical mediators the stability of the structure and the function in an ecosystem is granted. In industrialized societies a lot of pseudosignals of chemical nature may occur (pollution, pesticides, herbicides, fertilizers which may alter considerably the normal allelopathic relations. Research in this direction is almost neglected.

  12. 78 FR 16698 - Chemical Facility Anti-Terrorism Standards (CFATS) Chemical-Terrorism Vulnerability Information...

    Science.gov (United States)

    2013-03-18

    ... SECURITY Chemical Facility Anti-Terrorism Standards (CFATS) Chemical- Terrorism Vulnerability Information... Collection Request, Chemical Facility Anti- Terrorism Standards (CFATS) Chemical-terrorism Vulnerability... minimize terrorism risk to such facilities. Its design and implementation balance maintaining...

  13. Mapping chemical performance on molecular structures using locally interpretable explanations

    CERN Document Server

    Whitmore, Leanne S; Hudson, Corey M

    2016-01-01

    In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for classifying biologically produced fuel compounds with regard to Research Octane Number. This method of "painting" locally interpretable explanations onto 2-D chemical structures replicates the chemical intuition of synthetic chemists, allowing researchers in the field to directly accept, reject, inform and evaluate decisions underlying inscrutably complex quantitative structure-activity relationship models.

  14. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Science.gov (United States)

    2010-01-01

    ... 6 Domestic Security 1 2010-01-01 2010-01-01 false Chemical-terrorism vulnerability information. 27... FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information. (a... that constitute Chemical-terrorism Vulnerability Information (CVI), as defined in § 27.400(b)....

  15. Valence-Bond Theory and Chemical Structure.

    Science.gov (United States)

    Klein, Douglas J.; Trinajstic, Nenad

    1990-01-01

    Discussed is the importance of valence bond theory on the quantum-mechanical theory of chemical structure and the nature of the chemical bond. Described briefly are early VB theory, development of VB theory, modern versions, solid-state applications, models, treatment in textbooks, and flaws in criticisms of valence bond theory. (KR)

  16. Structure information from fusion barriers

    Indian Academy of Sciences (India)

    S V S Sastry; S Santra

    2000-06-01

    It is shown that the analysis of fusion barrier distributions is not always an unambiguous test or a ‘fingerprint’ of the structure information of the colliding nuclei. Examples are presented with same fusion barrier distributions for nuclei having different structures. The fusion excitation functions for 16O+208Pb, using the coupled reaction channel (CRC) method and correct structure information, have been analysed. The barrier distributions derived from these excitation functions including many of the significant channels are featureless, although these channels have considerable effects on the fusion excitation function. However, a simultaneous analysis of the fusion, elastic and quasi-elastic channels would fix the structure and the reaction unambiguously

  17. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...... is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  18. Chemical Carcinogenesis Research Information System (CCRIS)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The CCRIS database contains chemical records with carcinogenicity, mutagenicity, tumor promotion, and tumor inhibition test results. CCRIS provides historical...

  19. Visually Guiding and Controlling the Search While Mining Chemical Structures

    OpenAIRE

    Max Pereira; Vitor Santos Costa; Rui Camacho; Fonseca, Nuno A.

    2009-01-01

    In this paper we present the work in progress on LogCHEM, an ILP based tool for discriminative interactive mining of chemical fragments. In particular, we describe the integration with a molecule visualisation software that allows the chemist to graphically control the search for interesting patterns in chemical fragments. Furthermore, we show how structured information, such as rings, functional groups like carboxyl, amine, methyl, ester, etc are integrated and exploited in LogCHEM.

  20. Diffusion phenomena in chemically stabilized multilayer structures

    NARCIS (Netherlands)

    Bruijn, Saskia

    2011-01-01

    Multilayered thin film structures are widely applied as reflective coatings for optical elements in the extreme ultraviolet wavelength regime. In this thesis we investigate the structural and chemical changes that occur in Mo/Si based multilayers as a result of radiation induced thermal loads and ot

  1. Chemical structure and dynamics. Annual report 1995

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1996-05-01

    The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

  2. Chemical structure and dynamics: Annual report 1996

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1997-03-01

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.

  3. Annual Report 2000. Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Colson, Steven D.; McDowell, Robin S.

    2001-04-15

    This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

  4. Informational laws of genome structures

    Science.gov (United States)

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-06-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  5. Structure of adsorbed monolayers. The surface chemical bond

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, G.A.; Bent, B.E.

    1984-06-01

    This paper attempts to provide a summary of what has been learned about the structure of adsorbed monolayers and about the surface chemical bond from molecular surface science. While the surface chemical bond is less well understood than bonding of molecules in the gas phase or in the solid state, our knowledge of its properties is rapidly accumulating. The information obtained also has great impact on many surface science based technologies, including heterogeneous catalysis and electronic devices. It is hoped that much of the information obtained from studies at solid-gas interfaces can be correlated with molecular behavior at solid-liquid interfaces. 31 references, 42 figures, 1 table.

  6. ASTM Data Banks and Chemical Information Sources

    Science.gov (United States)

    Batik, Albert; Hale, Eleanor

    1972-01-01

    Among the data described are infrared indexes, mass spectral data, chromatographic data, X-ray emmission data, odor and taste threshold data, and thermodynamics data. This paper provides the chemical documentarian a complete reference source to a wide variety of analytical data. (Author/NH)

  7. The hierarchical structure of chemical engineering

    Institute of Scientific and Technical Information of China (English)

    Mooson KWAUK

    2007-01-01

    Around the turn of the present century, scholars began to recognize chemical engineering as a complex system, and have been searching for a convenient point of entry for refreshing its knowledge base. From our study of the dynamic structures of dispersed particles in fluidization and the resulting multi-scale method, we have been attempting to extend our findings to structures prevailing in other multiphase systems as well as in the burgeoning industries producing functional materials. Chemical engineering itself is hierarchically structured. Besides structures based on space and time, such hierarchy could be built from ChE history scaled according to science content, or from ChE operation according to the expenditure of manpower and capital investment.

  8. Introducing Graduate Students to the Chemical Information Landscape: The Ongoing Evolution of a Graduate-Level Chemical Information Course

    Science.gov (United States)

    Currano, Judith N.

    2016-01-01

    The University of Pennsylvania's doctoral chemistry curriculum has included a required course in chemical information since 1995. Twenty years later, the course has evolved from a loosely associated series of workshops on information resources to a holistic examination of the chemical literature and its place in the general research process. The…

  9. Powerful chemical technique. [CSIR uses new x-ray diffractometer for structural chemical analysis

    Energy Technology Data Exchange (ETDEWEB)

    The CSIR's National Chemical Research Laboratory (NCRL) is now using one of the most powerful techniques available to determine the structure of molecules. It has recently acquired a Single Crystal X-ray Diffractometer. This powerful method provides the only means of determining the structure of certain compounds. NCRL scientists often carry out structure determinations to find out the relative or absolute stereochemistry of molecules. This is important when correlating physiological activity and structure, information which is necessary for synthesizing medicines with specific characteristics.

  10. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  11. Chemical Structure and Dynamics annual report 1997

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1998-03-01

    The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

  12. Department of Environmental Management Chemical Information System (DEMCIS). User documentation

    Energy Technology Data Exchange (ETDEWEB)

    Atkins, D.P.; Clark, T.T.

    1985-10-01

    This document is a reference tool to be used by those responsible for updating and maintaining the twelve files in the Chemical Information System. Detailed information is given on how to display information in the data base as well as how to add, change, and/or delete records.

  13. Annual Report 1998: Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    SD Colson; RS McDowell

    1999-05-10

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

  14. Chemical information transfer in freshwater plankton

    NARCIS (Netherlands)

    Van Donk, E.

    2007-01-01

    The structure of aquatic ecosystems is determined by complex interactions among individual organisms at different trophic levels. Although our basic understanding of how top-down and bottom-up processes interact to determine food-web dynamics has advanced, we still lack insights into how complex int

  15. Encoding information into precipitation structures

    Science.gov (United States)

    Martens, Kirsten; Bena, Ioana; Droz, Michel; Rácz, Zoltan

    2008-12-01

    Material design at submicron scales would be profoundly affected if the formation of precipitation patterns could be easily controlled. It would allow the direct building of bulk structures, in contrast to traditional techniques which consist of removing material in order to create patterns. Here, we discuss an extension of our recent proposal of using electrical currents to control precipitation bands which emerge in the wake of reaction fronts in A+ + B- → C reaction-diffusion processes. Our main result, based on simulating the reaction-diffusion-precipitation equations, is that the dynamics of the charged agents can be guided by an appropriately designed time-dependent electric current so that, in addition to the control of the band spacing, the width of the precipitation bands can also be tuned. This makes straightforward the encoding of information into precipitation patterns and, as an amusing example, we demonstrate the feasibility by showing how to encode a musical rhythm.

  16. Quantum Information with Structured Light

    Science.gov (United States)

    Mirhosseini, Mohammad

    Quantum information science promises dramatic progress in a variety of fields such as cryptography, computation, and metrology. Although the proof-of-principle attempts for implementing quantum protocols have often relied on only a few qubits, the utilization of more sophisticated quantum systems is required for practical applications. In this thesis, we investigate the emerging role of high-dimensional optical states as a resource for encoding quantum information. We begin the first chapter with a review of orbital angular momentum (OAM) as a prime candidate for realizing multilevel quantum states and follow with a brief introduction to the quantum measurement theory. The second and the third chapters are dedicated to the application of OAM modes in quantum cryptography. In the second chapter, we discuss the challenges of projective measurement of OAM at the single-photon level, a crucial task required for quantum information processing. We then present our development of an efficient and accurate mode-sorting device that is capable of projectively measuring the orbital angular momentum of single photons. In the third chapter, we discuss the role of OAM modes in increasing the information capacity of quantum cryptography. We start this chapter by establishing the merits of encoding information on the quantum index of OAM modes in a free-space link. We then generalizing the BB-84 QKD protocol to the Hilbert space spanned by a finite number of OAM modes and outline our experimental realization. The last two chapters are dedicated to the tomography of structured light fields. We start the fourth chapter by applying the recently found method of direct measurement to the characterization of OAM superpositions. We find the quantum state in the Hilbert space spanned by 27 OAM modes by performing a weak measurement of orbital angular momentum (OAM) followed by a strong measurement of azimuthal angle. We then introduce the concept of compressive direct measurement (CDM

  17. A quantum informational approach for dissecting chemical reactions

    CERN Document Server

    Duperrouzel, Corinne; Boguslawski, Katharina; Barcza, Gergerly; Legeza, Örs; Ayers, Paul W

    2014-01-01

    We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected which allows us to monitor the interplay of back-bonding and $\\pi$-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

  18. Application Specific Chemical Information Microprocessor (ASCI mu P)

    Science.gov (United States)

    2016-06-13

    Washington Headquarters Services , Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302...Application Specific Chemical Information Microprocessor (ASCI µP) David Fries U. South Florida, Marine Science Dept, 140 7TH Ave So. St. Petersburg...N000149810848 LONG-TERM GOALS The overall goal of this work involves the development of a self contained, integrated microfluidic chemical sensor

  19. The hierarchical structure of chemical engineering

    Institute of Scientific and Technical Information of China (English)

    Mooson; KWAUK

    2007-01-01

    Around the turn of the present century,scholars began to recognize chemical engineering as a com-plex system,and have been searching for a convenient point of entry for refreshing its knowledge base.From our study of the dynamic structures of dispersed particles in fluidization and the resultingmulti-scale method,we have been attempting to extend our findings to structures prevailing in othermultiphase systems as well as in the burgeoning industries producing functional materials.Chemicalengineering itself is hierarchically structured.Besides structures based on space and time,such hier-archy could be built from ChE history scaled according to science content,or from ChE operation ac-cording to the expenditure of manpower and capital investment.

  20. Protein secondary structure prediction using NMR chemical shift data.

    Science.gov (United States)

    Zhao, Yuzhong; Alipanahi, Babak; Li, Shuai Cheng; Li, Ming

    2010-10-01

    Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes.

  1. Structure activity relationships to assess new chemicals under TSCA

    Energy Technology Data Exchange (ETDEWEB)

    Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

  2. Construction of a Linux based chemical and biological information system.

    Science.gov (United States)

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  3. Computerized management information systems and organizational structures

    Science.gov (United States)

    Zannetos, Z. S.; Sertel, M. R.

    1970-01-01

    The computerized management of information systems and organizational structures is discussed. The subjects presented are: (1) critical factors favoring centralization and decentralization of organizations, (2) classification of organizations by relative structure, (3) attempts to measure change in organization structure, and (4) impact of information technology developments on organizational structure changes.

  4. Ice Cream Seminars for Graduate Students: Imparting Chemical Information Literacy

    Science.gov (United States)

    Garritano, Jeremy R.

    2007-01-01

    This article provides information on a chemical information literacy program designed primarily for new graduate students. The full implementation of this program is discussed, including defining its purpose, topics covered, content presented, methods of marketing, and evaluation. The result is a series of voluntary seminars given biweekly…

  5. SYSTEM PERFORMANCE SPECIFICATION FOR A NATIONAL CHEMICAL INFORMATION SYSTEM.

    Science.gov (United States)

    Information Management, Inc., Burlington, MA.

    THIS DOCUMENT CONTAINS A SET OF STATEMENTS ABOUT INFORMATION NEEDS, SYSTEM GOALS, SYSTEM REQUIREMENTS, AND SYSTEM SPECIFICATIONS FOR THE DEVELOPMENT OF A NATIONAL CHEMICAL INFORMATION SYSTEM. IN ITS PRESENT FORM, THE DOCUMENT CONSTITUTES A BASIS FOR FUTURE PLANNING. AS POLICY DECISIONS ARE MADE, TECHNICAL PROBLEMS SOLVED AND PLANS ARE ALTERED, THE…

  6. Textual and chemical information processing: different domains but similar algorithms

    Directory of Open Access Journals (Sweden)

    Peter Willett

    2000-01-01

    Full Text Available This paper discusses the extent to which algorithms developed for the processing of textual databases are also applicable to the processing of chemical structure databases, and vice versa. Applications discussed include: an algorithm for distribution sorting that has been applied to the design of screening systems for rapid chemical substructure searching; the use of measures of inter-molecular structural similarity for the analysis of hypertext graphs; a genetic algorithm for calculating term weights for relevance feedback searching for determining whether a molecule is likely to exhibit biological activity; and the use of data fusion to combine the results of different chemical similarity searches.

  7. The chemical bond structure and dynamics

    CERN Document Server

    Zewail, Ahmed

    1992-01-01

    This inspired book by some of the most influential scientists of our time--including six Nobel laureates--chronicles our emerging understanding of the chemical bond through the last nine decades and into the future. From Pauling's early structural work using x-ray and electron diffraction to Zewail's femtosecond lasers that probe molecular dynamics in real time; from Crick's molecular biology to Rich's molecular recognition, this book explores a rich tradition of scientific heritage and accomplishment. The perspectives given by Pauling, Perutz, Rich, Crick, Porter, Polanyi, Herschbach, Zewail,

  8. Computational analysis of RNA structures with chemical probing data.

    Science.gov (United States)

    Ge, Ping; Zhang, Shaojie

    2015-06-01

    RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed.

  9. Informational uncertainties of risk assessment about accidents of chemicals

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An analysis system of informational uncertainties for accidental risk assessment of chemicals is introduced. Statistical test methods and fuzzy sets method can do the quantitative analysis of the input parameters. The uncertainties of the model can be used by quantitative compared method for the leakage accidents of chemicals. The estimation of the leaking time is important for discussing accidental source term. The uncertain analyses of the release accident for pipeline gas (CO) liquid chlorine and liquid propane gas (LPG) have been discussed.

  10. Applications of the Cambridge Structural Database in chemical education.

    Science.gov (United States)

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

  11. [International Chemical Safety Cards: information source on hazards caused by chemical substances].

    Science.gov (United States)

    Pakulska, Daria; Czerczak, Sławomir

    2007-01-01

    International Chemical Safety Cards (ICSC) are produced by the International Programme on Chemical Safety (IPCS) in collaboration with the European Commission and various IPCS-participating institutions in different countries. ICSCs disseminate essential information on chemicals to promote their safe production, transport and use. Application of standard terminology along with relevant criteria facilitates the comparison of risk related to different chemicals, which makes the cards a successful hazard-communication tool. Translation of the cards into various languages all over the world reflects the range of their growing use. A multi-stage compilation of information contained in ICSCs, based on the most up-to-date world literature and professional databases, assures its reliability. Their concise form makes them easy in everyday use as a source of information on chemical safety. The range of information contained in ICSCs corresponds to that provided by Material Safety Data Sheets (MSDS), however, the former are more concise and simpler. Although ICSCs have no legal status they may complement a 16-point MSDSs and help in the implementation of labeling and classification of chemicals according to the Globally Harmonized System.

  12. Chemical Information in Scirus and BASE (Bielefeld Academic Search Engine)

    Science.gov (United States)

    Bendig, Regina B.

    2009-01-01

    The author sought to determine to what extent the two search engines, Scirus and BASE (Bielefeld Academic Search Engines), would be useful to first-year university students as the first point of searching for chemical information. Five topics were searched and the first ten records of each search result were evaluated with regard to the type of…

  13. 76 FR 61692 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2011-10-05

    ... marketing'' purposes, which is referred to as a test marketing exemption, or TME. For more information about... application for a test marketing exemption (TME), and to publish in the Federal Register periodic status... new chemical substance for a non-exempt commercial purpose is required by TSCA section 5 to...

  14. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

    Science.gov (United States)

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

  15. Typography, Color, and Information Structure.

    Science.gov (United States)

    Keyes, Elizabeth

    1993-01-01

    Focuses on how typography and color complement and differ from each other in signaling an underlying content structure; the synergism between typography, color, and page layout (use of white space) that aids audience understanding and use; and the characteristics of typography and of color that are most important in these contexts. (SR)

  16. A Grammar Library for Information Structure

    Science.gov (United States)

    Song, Sanghoun

    2014-01-01

    This dissertation makes substantial contributions to both the theoretical and computational treatment of information structure, with an eye toward creating natural language processing applications such as multilingual machine translation systems. The aim of the present dissertation is to create a grammar library of information structure for the…

  17. Information Structure, Grammar and Strategy in Discourse

    Science.gov (United States)

    Stevens, Jon

    2013-01-01

    This dissertation examines two information-structural phenomena, Givenness and Focus, from the perspective of both syntax and pragmatics. Evidence from English, German and other languages suggests a "split" analysis of information structure--the notions of Focus and Givenness, often thought to be closely related, exist independently at…

  18. Study of the Chemical Space of Selected Bacteriostatic Sulfonamides from an Information Theory Point of View.

    Science.gov (United States)

    López-Rosa, Sheila; Molina-Espíritu, Moyocoyani; Esquivel, Rodolfo O; Soriano-Correa, Catalina; Dehesa, Jésus S

    2016-12-05

    The relative structural location of a selected group of 27 sulfonamide-like molecules in a chemical space defined by three information theory quantities (Shannon entropy, Fisher information, and disequilibrium) is discussed. This group is composed of 15 active bacteriostatic molecules, 11 theoretically designed ones, and para-aminobenzoic acid. This endeavor allows molecules that share common chemical properties through the molecular backbone, but with significant differences in the identity of the chemical substituents, which might result in bacteriostatic activity, to be structurally classified and characterized. This is performed by quantifying the structural changes on the electron density distribution due to different functional groups and number of electrons. The macroscopic molecular features are described by means of the entropy-like notions of spatial electronic delocalization, order, and uniformity. Hence, an information theory three-dimensional space (IT-3D) emerges that allows molecules with common properties to be gathered. This space witnesses the biological activity of the sulfonamides. Some structural aspects and information theory properties can be associated, as a result of the IT-3D chemical space, with the bacteriostatic activity of these molecules. Most interesting is that the active bacteriostatic molecules are more similar to para-aminobenzoic acid than to the theoretically designed analogues.

  19. Invalidating Policies using Structural Information

    DEFF Research Database (Denmark)

    Kammuller, Florian; Probst, Christian W.

    2013-01-01

    Insider threats are a major threat to many organisations. Even worse, insider attacks are usually hard to detect, especially if an attack is based on actions that the attacker has the right to perform. In this paper we present a step towards detecting the risk for this kind of attacks by invalida...... on these examples, the organisation can identify real attack vectors that might result in an insider attack. This information can be used to refine access control system or policies.......Insider threats are a major threat to many organisations. Even worse, insider attacks are usually hard to detect, especially if an attack is based on actions that the attacker has the right to perform. In this paper we present a step towards detecting the risk for this kind of attacks...

  20. Invalidating Policies using Structural Information

    DEFF Research Database (Denmark)

    Kammuller, Florian; Probst, Christian W.

    2014-01-01

    Insider threats are a major threat to many organisations. Even worse, insider attacks are usually hard to detect, especially if an attack is based on actions that the attacker has the right to perform. In this paper we present a step towards detecting the risk for this kind of attacks...... on these examples, the organisation can identify real attack vectors that might result in an insider attack. This information can be used to refine access control systems or policies. We provide case studies showing how mechanical verification tools, i.e. modelchecking with MCMAS and interactive theorem proving...... in Isabelle/HOL, can be applied to support the invalidation and thereby the identification of the attack vectors....

  1. Teaching Chemical Information in a Liberal Arts Curriculum

    Science.gov (United States)

    Ricker, Alison Scott; Thompson, Robert Q.

    1999-11-01

    We first offered Chemical Information as a one-credit, semester-long course in 1993 and have continued to team-teach it each fall. We offer this summary of our course as a model that might be adapted in other settings, acknowledging that no single course can adequately prepare chemists for the many challenges involved in finding, evaluating, and utilizing chemical information. The focus on information retrieval, evaluation, and presentation in a separate course has worked well for us, successfully integrating concepts of information literacy in a chemical context. We cover a wide array of topics, beginning with print and electronic resources on our campus and moving quickly to databases and other sources on the Internet. Searching CA Online via STN Express and STN Easy is emphasized more than any other single source. We have described the course in some detail elsewhere and give here a synopsis of our current approach and significant changes in the course over the last two years.

  2. Structures and Stabilization Mechanisms in Chemically Stabilized Ceramics

    Science.gov (United States)

    Gai-Boyes, Pratibha L.; Saltzberg, Michael A.; Vega, Alexander

    1993-09-01

    Structural complexities and disorder in chemically stabilized cristobalites (CSC), which are room temperature silica-based ceramics, prepared by a wet chemical route, are described. CSC displays many of the structural characteristics of the high temperature cristobalite, elucidated by HREM and X-ray diffraction. In-situ electron diffraction and NMR results suggest that the disorder is structural and is static.

  3. Chemical structure of odorants and perceptual similarity in ants.

    Science.gov (United States)

    Bos, Nick; d'Ettorre, Patrizia; Guerrieri, Fernando J

    2013-09-01

    Animals are often immersed in a chemical world consisting of mixtures of many compounds rather than of single substances, and they constantly face the challenge of extracting relevant information out of the chemical landscape. To this purpose, the ability to discriminate among different stimuli with different valence is essential, but it is also important to be able to generalise, i.e. to treat different but similar stimuli as equivalent, as natural variation does not necessarily affect stimulus valence. Animals can thus extract regularities in their environment and make predictions, for instance about distribution of food resources. We studied perceptual similarity of different plant odours by conditioning individual carpenter ants to one odour, and subsequently testing their response to another, structurally different odour. We found that asymmetry in generalisation, where ants generalise from odour A to B, but not from B to A, is dependent on both chain length and functional group. By conditioning ants to a binary mixture, and testing their reaction to the individual components of the mixture, we show that overshadowing, where parts of a mixture are learned better than others, is rare. Additionally, generalisation is dependent not only on the structural similarity of odorants, but also on their functional value, which might play a crucial role. Our results provide insight into how ants make sense of the complex chemical world around them, for example in a foraging context, and provide a basis with which to investigate the neural mechanisms behind perceptual similarity.

  4. Predictive Modeling of Chemical Hazard by Integrating Numerical Descriptors of Chemical Structures and Short-term Toxicity Assay Data

    Science.gov (United States)

    Rusyn, Ivan; Sedykh, Alexander; Guyton, Kathryn Z.; Tropsha, Alexander

    2012-01-01

    Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR–like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage. PMID:22387746

  5. Approaches to Chemical and Biochemical Information and Signal Processing

    Science.gov (United States)

    Privman, Vladimir

    2012-02-01

    We outline models and approaches for error control required to prevent buildup of noise when ``gates'' and other ``network elements'' based on (bio)chemical reaction processes are utilized to realize stable, scalable networks for information and signal processing. We also survey challenges and possible future research. [4pt] [1] Control of Noise in Chemical and Biochemical Information Processing, V. Privman, Israel J. Chem. 51, 118-131 (2010).[0pt] [2] Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic, V. Privman, J. Halamek, M. A. Arugula, D. Melnikov, V. Bocharova and E. Katz, J. Phys. Chem. B 114, 14103-14109 (2010).[0pt] [3] Towards Biosensing Strategies Based on Biochemical Logic Systems, E. Katz, V. Privman and J. Wang, in: Proc. Conf. ICQNM 2010 (IEEE Comp. Soc. Conf. Publ. Serv., Los Alamitos, California, 2010), pages 1-9.

  6. Automated Physico-Chemical Cell Model Development through Information Theory

    Energy Technology Data Exchange (ETDEWEB)

    Peter J. Ortoleva

    2005-11-29

    The objective of this project was to develop predictive models of the chemical responses of microbial cells to variations in their surroundings. The application of these models is optimization of environmental remediation and energy-producing biotechnical processes.The principles on which our project is based are as follows: chemical thermodynamics and kinetics; automation of calibration through information theory; integration of multiplex data (e.g. cDNA microarrays, NMR, proteomics), cell modeling, and bifurcation theory to overcome cellular complexity; and the use of multiplex data and information theory to calibrate and run an incomplete model. In this report we review four papers summarizing key findings and a web-enabled, multiple module workflow we have implemented that consists of a set of interoperable systems biology computational modules.

  7. Progressively Fostering Students' Chemical Information Skills in a Three-Year Chemical Engineering Program in France

    Science.gov (United States)

    Gozzi, Christel; Arnoux, Marie-Jose´; Breuzard, Jere´my; Marchal, Claire; Nikitine, Clémence; Renaudat, Alice; Toulgoat, Fabien

    2016-01-01

    Literature searches are essential for scientists. Thus, courses on how to do a good literature search have been integrated in studies at CPE Lyon for many years. Recently, we modified our pedagogical approach in order to initiate students progressively in the search for chemical information. In addition, this new teaching organization is now based…

  8. Feature Selection for Chemical Sensor Arrays Using Mutual Information

    Science.gov (United States)

    Wang, X. Rosalind; Lizier, Joseph T.; Nowotny, Thomas; Berna, Amalia Z.; Prokopenko, Mikhail; Trowell, Stephen C.

    2014-01-01

    We address the problem of feature selection for classifying a diverse set of chemicals using an array of metal oxide sensors. Our aim is to evaluate a filter approach to feature selection with reference to previous work, which used a wrapper approach on the same data set, and established best features and upper bounds on classification performance. We selected feature sets that exhibit the maximal mutual information with the identity of the chemicals. The selected features closely match those found to perform well in the previous study using a wrapper approach to conduct an exhaustive search of all permitted feature combinations. By comparing the classification performance of support vector machines (using features selected by mutual information) with the performance observed in the previous study, we found that while our approach does not always give the maximum possible classification performance, it always selects features that achieve classification performance approaching the optimum obtained by exhaustive search. We performed further classification using the selected feature set with some common classifiers and found that, for the selected features, Bayesian Networks gave the best performance. Finally, we compared the observed classification performances with the performance of classifiers using randomly selected features. We found that the selected features consistently outperformed randomly selected features for all tested classifiers. The mutual information filter approach is therefore a computationally efficient method for selecting near optimal features for chemical sensor arrays. PMID:24595058

  9. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    Directory of Open Access Journals (Sweden)

    Janna Hastings

    Full Text Available Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA.

  10. Information-Theoretical Complexity Analysis of Selected Elementary Chemical Reactions

    Science.gov (United States)

    Molina-Espíritu, M.; Esquivel, R. O.; Dehesa, J. S.

    We investigate the complexity of selected elementary chemical reactions (namely, the hydrogenic-abstraction reaction and the identity SN2 exchange reaction) by means of the following single and composite information-theoretic measures: disequilibrium (D), exponential entropy(L), Fisher information (I), power entropy (J), I-D, D-L and I-J planes and Fisher-Shannon (FS) and Lopez-Mancini-Calbet (LMC) shape complexities. These quantities, which are functionals of the one-particle density, are computed in both position (r) and momentum (p) spaces. The analysis revealed that the chemically significant regions of these reactions can be identified through most of the single information-theoretic measures and the two-component planes, not only the ones which are commonly revealed by the energy, such as the reactant/product (R/P) and the transition state (TS), but also those that are not present in the energy profile such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer process (CT). The analysis of the complexities shows that the energy profile of the abstraction reaction bears the same information-theoretical features of the LMC and FS measures, however for the identity SN2 exchange reaction does not hold a simple behavior with respect to the LMC and FS measures. Most of the chemical features of interest (BCER, B-B/F and CT) are only revealed when particular information-theoretic aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.

  11. Structure Of Management Information In SNMP

    Directory of Open Access Journals (Sweden)

    Oancea DANIEL

    2003-12-01

    Full Text Available In this article we present the Structure of Management Information from SNMP, for all three versions of SNMP, as well as the main differences between them. In the first part, two version of SNMP are presented: version 1, version 2; and in the last part the third version, that uses a security model for information protection, is presented.

  12. Structural Information Retention in Visual Art Processing.

    Science.gov (United States)

    Koroscik, Judith Smith

    The accuracy of non-art college students' longterm retention of structural information presented in Leonardo da Vinci's "Mona Lisa" was tested. Seventeen female undergraduates viewed reproductions of the painting and copies that closely resembled structural attributes of the original. Only 3 of the 17 subjects reported having viewed a reproduction…

  13. Advanced Data Structure and Geographic Information Systems

    Science.gov (United States)

    Peuquet, D. (Principal Investigator)

    1984-01-01

    The current state of the art in specified areas of Geographic Information Systems GIS technology is examined. Study of the question of very large, efficient, heterogeneous spatial databases is required in order to explore the potential application of remotely sensed data for studying the long term habitability of the Earth. Research includes a review of spatial data structures and storage, development of operations required by GIS, and preparation of a testbed system to compare Vaster data structure with NASA's Topological Raster Structure.

  14. A probabilistic model for secondary structure prediction from protein chemical shifts.

    Science.gov (United States)

    Mechelke, Martin; Habeck, Michael

    2013-06-01

    Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts.

  15. Entering new publication territory in chemoinformatics and chemical information science.

    Science.gov (United States)

    Bajorath, Jürgen

    2015-01-01

    The F1000Research publishing platform offers the opportunity to launch themed article collections as a part of its dynamic publication environment. The idea of article collections is further expanded through the generation of publication channels that focus on specific scientific areas or disciplines. This editorial introduces the Chemical Information Science channel of F1000Research designed to collate high-quality publications and foster a culture of open peer review. Articles will be selected by guest editor(s) and a group of experts, the channel Editorial Board, and subjected to open peer review.

  16. COST ES0602: towards a European network on chemical weather forecasting and information systems

    Directory of Open Access Journals (Sweden)

    J. Kukkonen

    2009-04-01

    Full Text Available The COST ES0602 action provides a forum for benchmarking approaches and practices in data exchange and multi-model capabilities for chemical weather forecasting and near real-time information services in Europe. The action includes approximately 30 participants from 19 countries, and its duration is from 2007 to 2011 (http://www.chemicalweather.eu/. Major efforts have been dedicated in other actions and projects to the development of infrastructures for data flow. We have therefore aimed for collaboration with ongoing actions towards developing near real-time exchange of input data for air quality forecasting. We have collected information on the operational air quality forecasting models on a regional and continental scale in a structured form, and inter-compared and evaluated the physical and chemical structure of these models. We have also constructed a European chemical weather forecasting portal that includes links to most of the available chemical weather forecasting systems in Europe. The collaboration also includes the examination of the case studies that have been organized within COST-728, in order to inter-compare and evaluate the models against experimental data. We have also constructed an operational model forecasting ensemble. Data from a representative set of regional background stations have been selected, and the operational forecasts for this set of sites will be inter-compared and evaluated. The Action has investigated, analysed and reviewed existing chemical weather information systems and services, and will provide recommendations on best practices concerning the presentation and dissemination of chemical weather information towards the public and decision makers.

  17. Information Processing Structure of Quantum Gravity

    Science.gov (United States)

    Gyongyosi, Laszlo; Imre, Sandor

    2014-05-01

    The theory of quantum gravity is aimed to fuse general relativity with quantum theory into a more fundamental framework. Quantum gravity provides both the non-fixed causality of general relativity and the quantum uncertainty of quantum mechanics. In a quantum gravity scenario, the causal structure is indefinite and the processes are causally non-separable. We provide a model for the information processing structure of quantum gravity. We show that the quantum gravity environment is an information resource-pool from which valuable information can be extracted. We analyze the structure of the quantum gravity space and the entanglement of the space-time geometry. We study the information transfer capabilities of quantum gravity space and define the quantum gravity channel. We characterize the information transfer of the gravity space and the correlation measure functions of the gravity channel. We investigate the process of stimulated storage for quantum gravity memories, a phenomenon that exploits the information resource-pool property of quantum gravity. The results confirm that the benefits of the quantum gravity space can be exploited in quantum computations, particularly in the development of quantum computers. The results are supported by the grant COST Action MP1006.

  18. Structuring medication related activities for information management.

    Science.gov (United States)

    Luukkonen, Irmeli; Mykkänen, Juha; Kivekäs, Eija; Saranto, Kaija

    2014-01-01

    Medication treatment and the related information management are central parts of a patient's health care. As a cross-organizational and cooperative process, medication information management is a complex domain for development activities. We studied medication activities and related information management in a regional project in order to produce a shared broad picture of its processes and to understand the main issues and the needs for improvement. In this paper we provide a summary of the findings in a structured form, based on a six-dimensioned framework for design and analysis of activities and processes.

  19. Toxics Release Inventory Chemical Hazard Information Profiles (TRI-CHIP) Dataset

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Toxics Release Inventory (TRI) Chemical Hazard Information Profiles (TRI-CHIP) dataset contains hazard information about the chemicals reported in TRI. Users can...

  20. Optimal Control Strategies in Delayed Sharing Information Structures

    CERN Document Server

    Nayyar, Ashutosh; Teneketzis, Demosthenis

    2010-01-01

    The $n$-step delayed sharing information structure is investigated. This information structure comprises of $K$ controllers that share their information with a delay of $n$ time steps. This information structure is a link between the classical information structure, where information is shared perfectly between the controllers, and a non-classical information structure, where there is no "lateral" sharing of information among the controllers. Structural results for optimal control strategies for systems with such information structures are presented. A sequential methodology for finding the optimal strategies is also derived. The solution approach provides an insight for identifying structural results and sequential decomposition for general decentralized stochastic control problems.

  1. Management Information Systems and Organizational Structure.

    Science.gov (United States)

    Cox, Bruce B.

    1987-01-01

    Discusses the context within which office automation takes place by using the models of the Science of Creative Intelligence and Transcendental Meditation. Organizational structures are compared to the phenomenon of the "collective consciousness" and the development of automated information systems from manual methods of organizational…

  2. Marine chemical ecology: chemical signals and cues structure marine populations, communities, and ecosystems.

    Science.gov (United States)

    Hay, Mark E

    2009-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized.

  3. Value of Information Analysis in Structural Safety

    DEFF Research Database (Denmark)

    Konakli, Katerina; Faber, Michael Havbro

    2014-01-01

    Pre-posterior analysis can be used to assess the potential of an experiment to enhance decision making by providing information on parameters characterized by uncertainty. The present paper describes a framework for pre-posterior analysis for support of decisions related to maintenance of structu......Pre-posterior analysis can be used to assess the potential of an experiment to enhance decision making by providing information on parameters characterized by uncertainty. The present paper describes a framework for pre-posterior analysis for support of decisions related to maintenance...... of structural systems. In this context, experiments may refer to inspections or techniques of structural health monitoring. The Value of Information concept provides a powerful tool for determining whether the experimental cost is justified by the expected benefit and for identifying the optimal among different...

  4. An information criterion for marginal structural models.

    Science.gov (United States)

    Platt, Robert W; Brookhart, M Alan; Cole, Stephen R; Westreich, Daniel; Schisterman, Enrique F

    2013-04-15

    Marginal structural models were developed as a semiparametric alternative to the G-computation formula to estimate causal effects of exposures. In practice, these models are often specified using parametric regression models. As such, the usual conventions regarding regression model specification apply. This paper outlines strategies for marginal structural model specification and considerations for the functional form of the exposure metric in the final structural model. We propose a quasi-likelihood information criterion adapted from use in generalized estimating equations. We evaluate the properties of our proposed information criterion using a limited simulation study. We illustrate our approach using two empirical examples. In the first example, we use data from a randomized breastfeeding promotion trial to estimate the effect of breastfeeding duration on infant weight at 1 year. In the second example, we use data from two prospective cohorts studies to estimate the effect of highly active antiretroviral therapy on CD4 count in an observational cohort of HIV-infected men and women. The marginal structural model specified should reflect the scientific question being addressed but can also assist in exploration of other plausible and closely related questions. In marginal structural models, as in any regression setting, correct inference depends on correct model specification. Our proposed information criterion provides a formal method for comparing model fit for different specifications.

  5. A robust algorithm for optimizing protein structures with NMR chemical shifts.

    Science.gov (United States)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.

  6. Information Processing Structure of Quantum Gravity

    CERN Document Server

    Gyongyosi, Laszlo

    2014-01-01

    The theory of quantum gravity is aimed to fuse general relativity with quantum theory into a more fundamental framework. The space of quantum gravity provides both the non-fixed causality of general relativity and the quantum uncertainty of quantum mechanics. In a quantum gravity scenario, the causal structure is indefinite and the processes are causally non-separable. In this work, we provide a model for the information processing structure of quantum gravity. We show that the quantum gravity environment is an information resource-pool from which valuable information can be extracted. We analyze the structure of the quantum gravity space and the entanglement of the space-time geometry. We study the information transfer capabilities of quantum gravity space and define the quantum gravity channel. We reveal that the quantum gravity space acts as a background noise on the local environment states. We characterize the properties of the noise of the quantum gravity space and show that it allows the separate local...

  7. Nematic films at chemically structured surfaces

    Science.gov (United States)

    Silvestre, N. M.; Telo da Gama, M. M.; Tasinkevych, M.

    2017-02-01

    We investigate theoretically the morphology of a thin nematic film adsorbed at flat substrate patterned by stripes with alternating aligning properties, normal and tangential respectively. We construct a simple ‘exactly-solvable’ effective interfacial model where the liquid crystal distortions are accounted for via an effective interface potential. We find that chemically patterned substrates can strongly deform the nematic-air interface. The amplitude of this substrate-induced undulations increases with decreasing average film thickness and with increasing surface pattern pitch. We find a regime where the interfacial deformation may be described in terms of a material-independent universal scaling function. Surprisingly, the predictions of the effective interfacial model agree semi-quantitatively with the results of the numerical solution of a full model based on the Landau-de Gennes theory coupled to a square-gradient phase field free energy functional for a two phase system.

  8. Exploiting structural information in patent specifications for key compound prediction.

    Science.gov (United States)

    Tyrchan, Christian; Boström, Jonas; Giordanetto, Fabrizio; Winter, Jon; Muresan, Sorel

    2012-06-25

    Patent specifications are one of many information sources needed to progress drug discovery projects. Understanding compound prior art and novelty checking, validation of biological assays, and identification of new starting points for chemical explorations are a few areas where patent analysis is an important component. Cheminformatics methods can be used to facilitate the identification of so-called key compounds in patent specifications. Such methods, relying on structural information extracted from documents by expert curation or text mining, can complement or in some cases replace the traditional manual approach of searching for clues in the text. This paper describes and compares three different methods for the automatic prediction of key compounds in patent specifications using structural information alone. For this data set, the cluster seed analysis described by Hattori et al. (Hattori, K.; Wakabayashi, H.; Tamaki, K. Predicting key example compounds in competitors' patent applications using structural information alone. J. Chem. Inf. Model.2008, 48, 135-142) is superior in terms of prediction accuracy with 26 out of 48 drugs (54%) correctly predicted from their corresponding patents. Nevertheless, the two new methods, based on frequency of R-groups (FOG) and maximum common substructure (MCS) similarity measures, show significant advantages due to their inherent ability to visualize relevant structural features. The results of the FOG method can be enhanced by manual selection of the scaffolds used in the analysis. Finally, a successful example of applying FOG analysis for designing potent ATP-competitive AXL kinase inhibitors with improved properties is described.

  9. ChemCloud: Chemical e-Science Information Cloud

    CERN Document Server

    Todor, Alexandru; Heineke, Stephan

    2010-01-01

    Our Chemical e-Science Information Cloud (ChemCloud) - a Semantic Web based eScience infrastructure - integrates and automates a multitude of databases, tools and services in the domain of chemistry, pharmacy and bio-chemistry available at the Fachinformationszentrum Chemie (FIZ Chemie), at the Freie Universitaet Berlin (FUB), and on the public Web. Based on the approach of the W3C Linked Open Data initiative and the W3C Semantic Web technologies for ontologies and rules it semantically links and integrates knowledge from our W3C HCLS knowledge base hosted at the FUB, our multi-domain knowledge base DBpedia (Deutschland) implemented at FUB, which is extracted from Wikipedia (De) providing a public semantic resource for chemistry, and our well-established databases at FIZ Chemie such as ChemInform for organic reaction data, InfoTherm the leading source for thermophysical data, Chemisches Zentralblatt, the complete chemistry knowledge from 1830 to 1969, and ChemgaPedia the largest and most frequented e-Learning...

  10. Information transfer in community structured multiplex networks

    Directory of Open Access Journals (Sweden)

    Albert eSolé Ribalta

    2015-08-01

    Full Text Available The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.. The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer networks with community structure. The final goal is to understand and quantify, if the existence of well-defined community structure at the level of individual layers, together with the multilayer structure of the whole network, enhances or deteriorates the diffusion of packets of information.

  11. Chemical isomeric effects on propanol glassy structures

    CERN Document Server

    Cuello, G J; Bermejo, F J; Cabrillo, C

    2002-01-01

    We have studied the structure of both propanol isomers in their glassy and crystalline states by neutron diffraction. The glass-transition temperatures of 1- and 2-propanol are about 98 and 115 K, respectively and, surprisingly, even larger differences are observed for the melting temperatures of the stable crystals, which are 148 and 185 K, respectively. Their supercooled liquid phases show rather different relaxation spectra, 1-propanol manifesting strong deviations from Debye behavior, whereas 2-propanol shows a far weaker effect. We discuss the spectra obtained for the static structure factor and the static pair correlation function D(r). There is a noticeable difference in the position of the first sharp diffraction peak, which clearly indicates a density change, well correlated with the period of the intermolecular oscillations shown by D(r). (orig.)

  12. Information and hierarchical structure in financial markets

    Science.gov (United States)

    Mantegna, R. N.

    1999-09-01

    I investigate the information content present in the time series of stock prices of a portfolio of stocks traded in a financial market. By investigating the correlation coefficient between pairs of stocks I provide a working definition of a generalized distance between the stocks of the portfolio. This generalized distance is used to obtain an ultrametric distance matrix between the stocks. The ultrametric structure of the portfolio investigated has associated a taxonomy which is meaningful from an economic point of view.

  13. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    2015-01-01

    Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term...... content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain......Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...

  14. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  15. Enhancing community detection by local structural information

    CERN Document Server

    Xiang, Ju; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-01-01

    Many real-world networks such as the gene networks, protein-protein interaction networks and metabolic networks exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have positive effect on community detection in the networks. Here, various local similarity measures are used to extract the local structural information and then are applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial to the improvement for the community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and the applied community detection methods.

  16. Structural Change of Wood Molecules and Chemorheological Behaviors during Chemical Treatment

    Institute of Scientific and Technical Information of China (English)

    Xie Manhua; Zhao Guangjie

    2004-01-01

    It is very important to clarify the relationship of changes of molecular combinations in wood cell walls and the chemical rheological behavior during various chemical reagent treatments, for it would be helpful to develop new wood modification technologies and to enrich the theory of chemical rheology of wood. Based on previous investigations on the chemorheological properties of wood by chemical treatments and the applied methods in chemical rheology of wool fibers, this paper proposes the study of various additional reagents to wood saturated in water for long periods of time in order to investigate the chemical rheology of wood, which can provide information about the character of combinations between wood molecules and the structural changes of molecules and further put forward the idea of modifying wood in a decrystallized state.

  17. Structural and Chemical Diversity of Tl-Based Cuprate Superconductors

    Institute of Scientific and Technical Information of China (English)

    信赢

    2003-01-01

    The Tl-based cuprate superconductor family is the largest family in crystal structure and chemical composition among all high Tc cuprate superconductors. The Tl family can be divided into two sub-families, the Tl single layer family and the Tl double layer family, based on their crystal structural characteristics. The Tl single layer family is an ideal material for investigating the evolution of crystalline formation, charge carrier density, chemical composition, transport properties, superconductivity and their relationships. The Tl family contains almostall possible crystal structures discovered in high-Tc cuprate superconductors. Tl cuprate superconductors are of great importance not only in studying high-temperature superconductivity but also in commercial applications.

  18. Classification of fossil fuels according to structural-chemical characteristics

    Energy Technology Data Exchange (ETDEWEB)

    A.M. Gyul' maliev; G.S. Golovin; S.G. Gagarin [Institute for Fossil Fuels, Moscow (Russian Federation)

    2007-10-15

    On the basis of a set of linear equations that relate the amount of major elements n{sub E} (E = C, H, O, N, S) in the organic matter of fossil fuels to structural characteristics, such as the number of cycles R, the number of atoms n{sub E}, the number of mutual chemical bonds, the degree of unsaturation of the structure {delta}, and the extent of its reduction B, a structural-chemical classification of fossil coals that is closely related to the parameters of the industrial-genetic classification (GOST 25543-88) is proposed. Structural-chemical classification diagrams are constructed for power-generating coals of Russia; coking coals; and coals designed for nonfuel purposes including the manufacture of adsorbents, synthetic liquid fuel, ion exchangers, thermal graphite, and carbon-graphite materials.

  19. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...... Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term......, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction....

  20. Chemical Tagging Can Work: Identification of Stellar Phase-space Structures Purely by Chemical-abundance Similarity

    Science.gov (United States)

    Hogg, David W.; Casey, Andrew R.; Ness, Melissa; Rix, Hans-Walter; Foreman-Mackey, Daniel; Hasselquist, Sten; Ho, Anna Y. Q.; Holtzman, Jon A.; Majewski, Steven R.; Martell, Sarah L.; Mészáros, Szabolcs; Nidever, David L.; Shetrone, Matthew

    2016-12-01

    Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were, in fact, born together (in the same molecular cloud) long ago. This idea has not yielded much practical success, presumably because of the noise and incompleteness in chemical-abundance measurements. We have succeeded in substantially improving spectroscopic measurements with The Cannon, which has now delivered 15 individual abundances for ∼ {10}5 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are indeed clusters in phase space, and we recover some known phase-space clusters and find other interesting structures. This is the first-ever project to identify phase-space structures at the survey-scale by blind search purely in abundance space; it verifies the precision of the abundance measurements delivered by The Cannon the prospects for future data sets appear very good.

  1. English-Chinese Translating from Perspective of Information Structure

    Institute of Scientific and Technical Information of China (English)

    汪世纪

    2014-01-01

    The application of information structure theory in translation is a dynamic communicative approach. The fluency of translation relies on the rearrangement of the given information and the new information and as well as the proper reproduction of information focuses. Therefore, a translator should be aware of information structure and information focus and thus make some adjustments while translating.

  2. Structuring Broadcast Audio for Information Access

    Directory of Open Access Journals (Sweden)

    Gauvain Jean-Luc

    2003-01-01

    Full Text Available One rapidly expanding application area for state-of-the-art speech recognition technology is the automatic processing of broadcast audiovisual data for information access. Since much of the linguistic information is found in the audio channel, speech recognition is a key enabling technology which, when combined with information retrieval techniques, can be used for searching large audiovisual document collections. Audio indexing must take into account the specificities of audio data such as needing to deal with the continuous data stream and an imperfect word transcription. Other important considerations are dealing with language specificities and facilitating language portability. At Laboratoire d′Informatique pour la Mécanique et les Sciences de l′Ingénieur (LIMSI, broadcast news transcription systems have been developed for seven languages: English, French, German, Mandarin, Portuguese, Spanish, and Arabic. The transcription systems have been integrated into prototype demonstrators for several application areas such as audio data mining, structuring audiovisual archives, selective dissemination of information, and topic tracking for media monitoring. As examples, this paper addresses the spoken document retrieval and topic tracking tasks.

  3. Physico-Chemical and Structural Properties of DeNOx and SO2 Oxidation Catalysts

    DEFF Research Database (Denmark)

    Masters, Stephen Grenville; Oehlers, Cord; Nielsen, Kurt;

    1996-01-01

    Commercial catalysts for NOx removal and SO2 oxidation and their model systems have been investigated by spectroscopic, thermal, electrochemical and X-ray methods. Structural information on the vanadium complexes and compounds as well as physico-chemical properties for catalyst model systems have...... been obtained. The results are discussed in relation to proposed reaction mechanisms....

  4. An informationally structured room for robotic assistance.

    Science.gov (United States)

    Tsuji, Tokuo; Mozos, Oscar Martinez; Chae, Hyunuk; Pyo, Yoonseok; Kusaka, Kazuya; Hasegawa, Tsutomu; Morooka, Ken'ichi; Kurazume, Ryo

    2015-04-22

    The application of assistive technologies for elderly people is one of the most promising and interesting scenarios for intelligent technologies in the present and near future. Moreover, the improvement of the quality of life for the elderly is one of the first priorities in modern countries and societies. In this work, we present an informationally structured room that is aimed at supporting the daily life activities of elderly people. This room integrates different sensor modalities in a natural and non-invasive way inside the environment. The information gathered by the sensors is processed and sent to a centralized management system, which makes it available to a service robot assisting the people. One important restriction of our intelligent room is reducing as much as possible any interference with daily activities. Finally, this paper presents several experiments and situations using our intelligent environment in cooperation with our service robot.

  5. Information transfer in community structured multiplex networks

    CERN Document Server

    Solé-Ribalta, Albert; Gómez, Sergio; Arenas, Alex

    2015-01-01

    The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.). The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer ...

  6. 78 FR 20101 - Access to Confidential Business Information by Chemical Abstract Services

    Science.gov (United States)

    2013-04-03

    ... From the Federal Register Online via the Government Publishing Office ENVIRONMENTAL PROTECTION AGENCY Access to Confidential Business Information by Chemical Abstract Services AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: EPA expects to authorize its contractor, Chemical...

  7. Chemical Information Literacy: pK[subscript a] Values--Where Do Students Go Wrong?

    Science.gov (United States)

    Flynn, Alison B.; Amellal, Delphine G.

    2016-01-01

    Chemical information literacy is an essential skillset for navigating, evaluating, and using the wealth of print and online information. Accordingly, efforts are underway to improve students' acquisition and mastery of this skillset. However, less is known about students' abilities related to finding and using chemical information to solve…

  8. Shot detection combining Bayesian and structural information

    Science.gov (United States)

    Han, Seung H.; Kweon, In-So

    2000-12-01

    There are a number of shots in a video, each of which has boundary types, such as cut, fade, dissolve and wipe. Many previous approaches can find the cut boundary without difficulty. However, most of them often produce false alarms for the videos with large motions of camera and objects. We propose a shot boundary detection method combining Bayesian and structural information. In the Bayesian approach, a probability distribution function models each transition type, e.g., normal, abrupt, gradual transition, and also models shot length. But inseparability between those distributions causes unwanted results and degrades the precision. In this paper, we demonstrate that the shape of the filtered frame difference, called the structural information, provides an important cue to distinguish fade and dissolve effects form cut effects and gradual changes caused by motion of camera and objects. The proposed method has been tested for a few golf video segments and shown good performances in detecting fade and dissolve effects as well as cut.

  9. Visualization of database structures for information retrieval

    Directory of Open Access Journals (Sweden)

    Grete Lisbjerg Jensen

    1994-12-01

    Full Text Available This paper describes the Book House system, which is designed to support children's information retrieval in libraries as part of their education. It is a shareware program available on CD-ROM or floppy disks, and comprises functionality for database searching as well as for classifying and storing book information in the database. The system concept is based on an understanding of children's domain structures and their capabilities for categorization of information needs in connection with their activities in schools, in school libraries or in public libraries. These structures are visualized in the interface by using metaphors and multimedia technology. Through the use of text, images and animation, the Book House encourages children - even at a very early age - to learn by doing in an enjoyable way, which plays on their previous experiences with computer games. Both words and pictures can be used for searching; this makes the system suitable for all age groups. Even children who have not yet learned to read properly can, by selecting pictures, search for and find those books they would like to have read aloud. Thus, at the very beginning of their school life, they can learn to search for books on their own. For the library community, such a system will provide an extended service which will increase the number of children's own searches and also improve the relevance, quality and utilization of the book collections in the libraries. A market research report on the need for an annual indexing service for books in the Book House format is in preparation by the Danish Library Centre A/S.

  10. Grammar and information structure. A study with reference to Russian

    NARCIS (Netherlands)

    Slioussar, N.

    2007-01-01

    This thesis is dedicated to the study of information structure (IS) dividing information into given/new, salient/backgrounded etc. There is an information structure represented in the discourse mental model and an information structure encoded in the grammar, which indirectly reflects it (as the ten

  11. Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality

    CERN Document Server

    Labushev, Mikhail M

    2012-01-01

    The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

  12. The multifractal structure of chaotically advected chemical fields

    CERN Document Server

    Neufeld, Z; Hernández-García, E; Tél, T; Neufeld, Zoltan; Lopez, Cristobal; Hernandez-Garcia, Emilio; Tel, Tamas

    1999-01-01

    The structure of the concentration field of a decaying substance produced by chemical sources and advected by a smooth incompressible two-dimensional flow is investigated. We focus our attention on the non-uniformities of the Hölder exponent of the resulting filamental chemical field. They appear most evidently in the case of open flows where irregularities of the field exhibit strong spatial intermittency as they are restricted to a fractal manifold. Non-uniformities of the Hölder exponent of the chemical field in closed flows appears as a consequence of the non-uniform stretching of the fluid elements. We study how this affects the scaling exponents of the structure functions, displaying anomalous scaling, and relate the scaling exponents to the distribution of finite-time Lyapunov exponents of the advection dynamics. Theoretical predictions are compared with numerical experiments.

  13. Rule-Based Classification of Chemical Structures by Scaffold.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Varin, Thibault

    2011-08-01

    Databases for small organic chemical molecules usually contain millions of structures. The screening decks of pharmaceutical companies contain more than a million of structures. Nevertheless chemical substructure searching in these databases can be performed interactively in seconds. Because of this nobody has really missed structural classification of these databases for the purpose of finding data for individual chemical substructures. However, a full deck high-throughput screen produces also activity data for more than a million of substances. How can this amount of data be analyzed? Which are the active scaffolds identified by an assays? To answer such questions systematic classifications of molecules by scaffolds are needed. In this review it is described how molecules can be hierarchically classified by their scaffolds. It is explained how such classifications can be used to identify active scaffolds in an HTS data set. Once active classes are identified, they need to be visualized in the context of related scaffolds in order to understand SAR. Consequently such visualizations are another topic of this review. In addition scaffold based diversity measures are discussed and an outlook is given about the potential impact of structural classifications on a chemically aware semantic web.

  14. Structural studies of chemical constituents of Thithonia Tagetiflora Desv (Asteraceae)

    DEFF Research Database (Denmark)

    Ngoc Huynh, Vinh; Nguyen Thi Hoai, Thu; Phi Phung Nguyen, Kim

    2013-01-01

    Tithonia tagetiflora Desv. (Asteraceae) is a widespread plant in Vietnam, and the species of Tithonia are known as plants containing many biologically active compounds. However, T. tagetiflora's chemical composition remains mostly unknown. Therefore, we now report the structural elucidation of two...

  15. 77 FR 24705 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2012-04-25

    ... material (S) Copper(2+), Inc. for production tetraamine-, of copper dichloride. chemicals; raw material for.... P-12-0035 03/27/2012 03/25/2012 (G) Cobalt iron manganese oxide, carboxylic acid-modified....

  16. PACSY, a relational database management system for protein structure and chemical shift analysis.

    Science.gov (United States)

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

  17. Occupational and Qualification Structures in the Field of Environmental Protection in the Metal and Chemical Industries in the United Kingdom.

    Science.gov (United States)

    European Centre for the Development of Vocational Training, Berlin (Germany).

    A study analyzed the occupational structure and qualifications associated with the field of environmental protection in the metal and chemical industries in the United Kingdom. The analysis included nine case studies based on interviews with firms in the chemicals and metals sectors. Information was gathered within an analytical framework that…

  18. Cuticle Structure in Relation to Chemical Composition: Re-assessing the Prevailing Model

    Science.gov (United States)

    Fernández, Victoria; Guzmán-Delgado, Paula; Graça, José; Santos, Sara; Gil, Luis

    2016-01-01

    The surface of most aerial plant organs is covered with a cuticle that provides protection against multiple stress factors including dehydration. Interest on the nature of this external layer dates back to the beginning of the 19th century and since then, several studies facilitated a better understanding of cuticular chemical composition and structure. The prevailing undertanding of the cuticle as a lipidic, hydrophobic layer which is independent from the epidermal cell wall underneath stems from the concept developed by Brongniart and von Mohl during the first half of the 19th century. Such early investigations on plant cuticles attempted to link chemical composition and structure with the existing technologies, and have not been directly challenged for decades. Beginning with a historical overview about the development of cuticular studies, this review is aimed at critically assessing the information available on cuticle chemical composition and structure, considering studies performed with cuticles and isolated cuticular chemical components. The concept of the cuticle as a lipid layer independent from the cell wall is subsequently challenged, based on the existing literature, and on new findings pointing toward the cell wall nature of this layer, also providing examples of different leaf cuticle structures. Finally, the need for a re-assessment of the chemical and structural nature of the plant cuticle is highlighted, considering its cell wall nature and variability among organs, species, developmental stages, and biotic and abiotic factors during plant growth. PMID:27066059

  19. Cuticle structure in relation to chemical composition: re-assessing the prevailing model

    Directory of Open Access Journals (Sweden)

    Victoria eFernandez

    2016-03-01

    Full Text Available The surface of most aerial plant organs is covered with a cuticle that provides protection against multiple stress factors including dehydration. Interest on the nature of this external layer dates back to the beginning of the 19th century and since then, several studies facilitated a better understanding of cuticular chemical composition and structure. The prevailing undertanding of the cuticle as a lipidic, hydrophobic layer which is independent from the epidermal cell wall underneath stems from the concept developed by Brongniart and von Mohl during the first half of the 19th century. Such early investigations on plant cuticles attempted to link chemical composition and structure with the existing technologies, and have not been directly challenged for decades. Beginning with a historical overview about the development of cuticular studies, this review is aimed at critically assessing the information available on cuticle chemical composition and structure, considering studies performed with cuticles and isolated cuticular chemical components. The concept of the cuticle as a lipid layer independent from the cell wall is subsequently challenged, based on the existing literature, and on new findings pointing towards the cell wall nature of this layer, also providing examples of different leaf cuticle structures. Finally, the need for a re-assessment of the chemical and structural nature of the plant cuticle is highlighted, considering its cell wall nature and variability among organs, species, developmental stages, and biotic and abiotic factors during plant growth.

  20. Global Materials Structure Search with Chemically Motivated Coordinates.

    Science.gov (United States)

    Panosetti, Chiara; Krautgasser, Konstantin; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces.

  1. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

    Science.gov (United States)

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2011-01-01

    Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

  2. MULTILEVEL INDEX STRUCTURE FOR INFORMATION FILTERING BASED ON USER CHARACTERISTIC

    Institute of Scientific and Technical Information of China (English)

    He jun; Zhou Mingtian

    2001-01-01

    Aimed at information overload and personalized characteristic of user information requirement, this letter presents a type of multilevel index structure and algorithm which is applied to large scale information filtering system and has better performance and stronger scalability.

  3. Using Patent Classification to Discover Chemical Information in a Free Patent Database: Challenges and Opportunities

    Science.gov (United States)

    Ha¨rtinger, Stefan; Clarke, Nigel

    2016-01-01

    Developing skills for searching the patent literature is an essential element of chemical information literacy programs at the university level. The present article creates awareness of patents as a rich source of chemical information. Patent classification is introduced as a key-component in comprehensive search strategies. The free Espacenet…

  4. Optical disk toxic information online system at Sumitomo Chemical Co. through telecommunication network in Japan

    Science.gov (United States)

    Kishida, Fumio; Omodaka, Hisakata; Ishihara, Koichiro; Yamada, Yoshinori; Kato, Hiromi

    Toxicity data about several hundred chemicals, handled and commercialized by Sumitomo Chemical Co., have been collected and estimated. These data are stored in an optical disk filing system "sanfile 8500D". Because the system is mounted with a keyword input panel "Word selecter", information retrieval system is simplified but precised. Online system through telecommunication network is extended between Sumitomo Chemical's works, laboratories, and others. Image informations are mailed from installed facsimili in sanfile 8500D directly.

  5. AUTOMATED DETECTION OF STRUCTURAL ALERTS (CHEMICAL FRAGMENTS IN (ECOTOXICOLOGY

    Directory of Open Access Journals (Sweden)

    Alban Lepailleur

    2013-02-01

    Full Text Available This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (ecotoxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.

  6. 75 FR 57770 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2010-09-22

    ... marketing exemption (TME), and to publish periodic status reports on the chemicals under review and the...-cyclohexene-1- Incorporated fragrance mixtures, propanal, 4,4- that in turn are dimethyl- used in perfumes... received: II. 1 Test Marketing Exemption Notices Received From: 07/30/10 to 08/31/10 Projected Notice...

  7. 77 FR 5096 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2012-02-01

    .... producing packaging films. P-12-0089 12/06/2011 03/04/2012 Brueggemann (G) Zinc is a (S) Process Chemical U...) Isocyanate crosslinker P-11-0591 12/02/2011 11/23/2011 (G) Ipdi modified polyester resin P-11-0622...

  8. The Stepping Stone Approach to Teaching Chemical Information Skills

    Science.gov (United States)

    Yeagley, Andrew A.; Porter, Sarah E. G.; Rhoten, Melissa C.; Topham, Benjamin J.

    2016-01-01

    Information literacy is of paramount importance to any successful research program. Information techniques and skills should be infused throughout a student's undergraduate curriculum rather than being the focus of a single course. To this end, we have created several courses, beginning in the first year, where students review current scientific…

  9. Information diffusion in structured online social networks

    Science.gov (United States)

    Li, Pei; Zhang, Yini; Qiao, Fengcai; Wang, Hui

    2015-05-01

    Nowadays, due to the word-of-mouth effect, online social networks have been considered to be efficient approaches to conduct viral marketing, which makes it of great importance to understand the diffusion dynamics in online social networks. However, most research on diffusion dynamics in epidemiology and existing social networks cannot be applied directly to characterize online social networks. In this paper, we propose models to characterize the information diffusion in structured online social networks with push-based forwarding mechanism. We introduce the term user influence to characterize the average number of times that messages are browsed which is incurred by a given type user generating a message, and study the diffusion threshold, above which the user influence of generating a message will approach infinity. We conduct simulations and provide the simulation results, which are consistent with the theoretical analysis results perfectly. These results are of use in understanding the diffusion dynamics in online social networks and also critical for advertisers in viral marketing who want to estimate the user influence before posting an advertisement.

  10. Characterization of iron-phosphate-silicate chemical garden structures.

    Science.gov (United States)

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life.

  11. Chemical and structural effects of base modifications in messenger RNA

    Science.gov (United States)

    Harcourt, Emily M.; Kietrys, Anna M.; Kool, Eric T.

    2017-01-01

    A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification -- the epitranscriptome -- is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles.

  12. A Study on the Structural Analysis of Controllability in Chemical Processes

    Energy Technology Data Exchange (ETDEWEB)

    Lee, B.W.; Kim, Y.S.; Yoon, E.S. [Division of Chemical Engineering, Seoul National University, Seoul (Korea)

    1999-04-01

    Chemical processes are highly nonlinear, multivariable systems and have complex structures. However, the controllability evaluation procedures are complicated, and the required information is very often unknown at the early design stage. Therefore, it is necessary to develop a procedure to evaluate and enhance controllability while designing processes and plants. To evaluate controllability in the design stage, it is most efficient to analyze process structure. Relative order can be used as a measure of 'physical closeness' between input and output variable. Structural controllability analysis using relative order is shown to be effective in a case study of heat exchanger network synthesis. 9 refs., 3 figs.

  13. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  14. Chemical compatibility of structural materials in alkali metals

    Energy Technology Data Exchange (ETDEWEB)

    Natesan, K.; Rink, D.L.; Haglund, R. [Argonne National Lab., Chicago, IL (United States)] [and others

    1995-04-01

    The objectives of this task are to (a) evaluate the chemical compatibility of structural alloys such as V-5 wt.%Cr-5 wt.%Ti alloy and Type 316 stainless steel for application in liquid alkali metals such as lithium and sodium-78 wt.% potassium (NaK) at temperatures in the range that are of interest for International Thermonuclear Experimental Reactor (ITER); (b) evaluate the transfer of nonmetallic elements such as oxygen, nitrogen, carbon, and hydrogen between structural materials and liquid metals; and (c) evaluate the effects of such transfers on the mechanical and microstructural characteristics of the materials for long-term service in liquid-metal-environments.

  15. 77 FR 5100 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2012-02-01

    ... language for your requested changes. iv. Describe any assumptions and provide any technical information and.../2012 CBI (G) Specialty (G) Polyamine additive. derivative ] P-12-0112 12/21/2011 03/19/2012 CBI...

  16. 75 FR 32751 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2010-06-09

    ... identification, pass through a metal detector, and sign the EPA visitor log. All visitor bags are processed... visible at all times in the building and returned upon departure. FOR FURTHER INFORMATION CONTACT:...

  17. 78 FR 17656 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2013-03-22

    ... (S) Automotive metal recovery. If you are interested in information that is not included in these... show photographic identification, pass through a metal detector, and sign the EPA visitor log. All.... adhesive. Benzenedicarboxylic acid, polymer with substituted alkanediol, dodecanedioic acid,...

  18. Design of LTCC-based Ceramic Structure for Chemical Microreactor

    Directory of Open Access Journals (Sweden)

    D. Belavic

    2012-04-01

    Full Text Available The design of ceramic chemical microreactor for the production of hydrogen needed in portable polymer-electrolyte membrane (PEM fuel cells is presented. The microreactor was developed for the steam reforming of liquid fuels with water into hydrogen. The complex three-dimensional ceramic structure of the microreactor includes evaporator(s, mixer(s, reformer and combustor. Low-temperature co-fired ceramic (LTCC technology was used to fabricate the ceramic structures with buried cavities and channels, and thick-film technology was used to make electrical heaters, temperature sensors and pressure sensors. The final 3D ceramic structure consists of 45 LTCC tapes. The dimensions of the structure are 75 × 41 × 9 mm3 and the weight is about 73 g.

  19. Application of chemical structure and bonding of actinide oxide materials for forensic science

    Energy Technology Data Exchange (ETDEWEB)

    Wilkerson, Marianne Perry [Los Alamos National Laboratory

    2010-01-01

    We are interested in applying our understanding of actinide chemical structure and bonding to broaden the suite of analytical tools available for nuclear forensic analyses. Uranium- and plutonium-oxide systems form under a variety of conditions, and these chemical species exhibit some of the most complex behavior of metal oxide systems known. No less intriguing is the ability of AnO{sub 2} (An: U, Pu) to form non-stoichiometric species described as AnO{sub 2+x}. Environmental studies have shown the value of utilizing the chemical signatures of these actinide oxide materials to understand transport following release into the environment. Chemical speciation of actinide-oxide samples may also provide clues as to the age, source, or process history of the material. The scientific challenge is to identify, measure and understand those aspects of speciation of actinide analytes that carry information about material origin and history most relevant to forensics. Here, we will describe our efforts in material synthesis and analytical methods development that we will use to provide the fundamental science to characterize actinide oxide molecular structures for forensic science. Structural properties and initial results to measure structural variability of uranium oxide samples using synchrotron-based X-ray Absorption Fine Structure will be discussed.

  20. Information performances and illative sequences: Sequential organization of explanations of chemical phase equilibrium

    Science.gov (United States)

    Brown, Nathaniel James Swanton

    While there is consensus that conceptual change is surprisingly difficult, many competing theories of conceptual change co-exist in the literature. This dissertation argues that this discord is partly the result of an inadequate account of the unwritten rules of human social interaction that underlie the field's preferred methodology---semi-structured interviewing. To better understand the contributions of interaction during explanations, I analyze eight undergraduate general chemistry students as they attempt to explain to various people, for various reasons, why phenomena involving chemical phase equilibrium occur. Using the methods of interaction analysis, I characterize the unwritten, but systematic, rules that these participants follow as they explain. The result is a description of the contributions of interaction to explaining. Each step in each explanation is a jointly performed expression of a subject-predicate relation, an interactive accomplishment I call an information performance (in-form, for short). Unlike clauses, in-forms need not have a coherent grammatical structure. Unlike speaker turns, in-forms have the clear function of expressing information. Unlike both clauses and speaker turns, in-forms are a co-construction, jointly performed by both the primary speaker and the other interlocutor. The other interlocutor strongly affects the form and content of each explanation by giving or withholding feedback at the end of each in-form, moments I call feedback-relevant places. While in-forms are the bricks out of which the explanation is constructed, they are secured by a series of inferential links I call an illative sequence. Illative sequences are forward-searching, starting with a remembered fact or observation and following a chain of inferences in the hope it leads to the target phenomenon. The participants treat an explanation as a success if the illative sequence generates an in-form that describes the phenomenon. If the illative sequence does

  1. Chemical and physical structures of proteinoids and related polyamino acids

    Science.gov (United States)

    Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

    Studies of polyamino acid formation pathways in the prebiotic condition are important for the study of the origins of life. Several pathways of prebiotic polyamino acid formation have been reported. Heating of monoammonium malate [1] and heating of amino acids in molten urea [2] are important pathways of the prebiotic peptide formation. The former case, globular structure called proteinoid microsphere is formed in aqueous conditions. The later case, polyamino acids are formed from unrestricted amino acid species. Heating of aqueous aspargine is also interesting pathway for the prebiotic polyamino acid formation, because polyamino acid formation proceeds in aqueous condition [3]. In this study, we analyzed the chemical structure of the proteinoids and related polyamino acids formed in the above three pathways using with mass spectrometer. In addition, their physical structures are analyzed by the electron and optical microscopes, in order to determine the self-organization abilities. We discuss the relation between the chemical and the physical structures for the origins of life. References [1] Harada, K., J. Org. Chem., 24, 1662 (1959), Fox, S. W., Harada, K., and Kendrick, J., Science, 129, 1221 (1959). [2] Terasaki, M., Nomoto, S., Mita, H., and Shimoyama, A., Chem. Lett., 480 (2002), Mita, H., Nomoto, S., Terasaki, M., Shimoyama, A., and Yamamoto, Y., Int. J. Astrobiol., 4, 145 (2005). [3] Kovacs, K and Nagy, H., Nature, 190, 531 (1961), Munegumi, T., Tanikawa, N., Mita, H. and Harada, K., Viva Origino, 22, 109 (1994).

  2. Temporal and Statistical Information in Causal Structure Learning

    Science.gov (United States)

    McCormack, Teresa; Frosch, Caren; Patrick, Fiona; Lagnado, David

    2015-01-01

    Three experiments examined children's and adults' abilities to use statistical and temporal information to distinguish between common cause and causal chain structures. In Experiment 1, participants were provided with conditional probability information and/or temporal information and asked to infer the causal structure of a 3-variable mechanical…

  3. Chemical structure analysis of starch and cellulose derivatives.

    Science.gov (United States)

    Mischnick, Petra; Momcilovic, Dane

    2010-01-01

    Starch and cellulose are the most abundant and important representatives of renewable biomass. Since the mid-19th century their properties have been changed by chemical modification for commercial and scientific purposes, and there substituted polymers have found a wide range of applications. However, the inherent polydispersity and supramolecular organization of starch and cellulose cause the products resulting from their modification to display high complexity. Chemical composition analysis of these mixtures is therefore a challenging task. Detailed knowledge on substitution patterns is fundamental for understanding structure-property relationships in modified cellulose and starch, and thus also for the improvement of reproducibility and rational design of properties. Substitution patterns resulting from kinetically or thermodynamically controlled reactions show certain preferences for the three available hydroxyl functions in (1→4)-linked glucans. Spurlin, seventy years ago, was the first to describe this in an idealized model, and nowadays this model has been extended and related to the next hierarchical levels, namely, the substituent distribution in and over the polymer chains. This structural complexity, with its implications for data interpretation, and the analytical approaches developed for its investigation are outlined in this article. Strategies and methods for the determination of the average degree of substitution (DS), monomer composition, and substitution patterns at the polymer level are presented and discussed with respect to their limitations and interpretability. Nuclear magnetic resonance spectroscopy, chromatography, capillary electrophoresis, and modern mass spectrometry (MS), including tandem MS, are the main instrumental techniques employed, in combination with appropriate sample preparation by chemical and enzymatic methods.

  4. 76 FR 57734 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2011-09-16

    ... application for a test marketing exemption (TME), and to publish in the Federal Register periodic status... marketing'' purposes, which is referred to as a test marketing exemption, or TME. For more information about... alkyl modified polymethylsiloxane. P-10-0508 6/23/2011 5/27/2011 (G) Mixed mono and di carboxylic...

  5. 78 FR 17680 - Information Collection Request; Chemical Facility Anti-Terrorism Standards Personnel Surety Program

    Science.gov (United States)

    2013-03-22

    ... SECURITY Information Collection Request; Chemical Facility Anti-Terrorism Standards Personnel Surety...-Terrorism Standards (CFATS) Personnel Surety Program pursuant to 6 CFR 27.230(a)(12)(iv). \\1\\ A 60-day...-terrorism Vulnerability Information (CVI),\\2\\ Sensitive Security Information (SSI),\\3\\ or Protected...

  6. The chemical structure and the crystalline structures of Bombyx mori silk fibroin.

    Science.gov (United States)

    Lotz, B; Colonna Cesari, F

    1979-01-01

    Some recent data (i.e. published in the last ten years) on the chemical and crystalline structures of B. mori silk are reviewed. The main emphasis is put on the crystallizable portion of silk fibroin, including its chemical constitution and its molecular conformation (at the crystallographic unit-cell level) in the two crystalline modifications : the beta pleated sheet and the silk I structures. The structural aspects are based on a discussion of X-ray and electron diffraction data, and on conformational energy analyses of a model (Ala-Gly)n polypeptide of silk fibroin.

  7. Linear complexions: Confined chemical and structural states at dislocations.

    Science.gov (United States)

    Kuzmina, M; Herbig, M; Ponge, D; Sandlöbes, S; Raabe, D

    2015-09-04

    For 5000 years, metals have been mankind's most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states.

  8. Chemically Resolved Structure of the Sn/Ge(111) Surface

    Science.gov (United States)

    Lee, Tien-Lin; Warren, Samantha; Cowie, Bruce C. C.; Zegenhagen, Jörg

    2006-02-01

    The structure and chemical states of the Sn/Ge(111) surface are characterized by x-ray standing waves combined with photoemission. For the room temperature 3×3 phase two chemical components, approximately 0.4 eV apart, are observed for both Sn 3d and 4d core levels. Our model-independent, x-ray standing wave analysis shows unambiguously that the two components originate from Sn adatoms located at two different heights separated vertically by 0.23 Å, in favor of a model composed of a fluctuating Sn layer. Contrary to the most accepted scenario, the stronger Sn 3d and 4d components, which appear at the lower binding-energy sides and account for 2/3 of the Sn adatoms, are identified to be associated with the higher Sn position, manifesting their filled valence state character.

  9. 78 FR 35904 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2013-06-14

    ...) Polyurethane aqueous dispersion. P-12-0080......... 4/12/2013 4/8/2013 (G) Fluoroethylene- vinylether copolymer... polyether-ester for panel polyurethane lamination and prepolymer. other structural assemblies. P-13-0353.... phenylsulfonamide compound. P-13-0372......... 4/2/2013 6/30/2013 CBI (G) Polymer...... (G) Polyether...

  10. Pattern information extraction from crystal structures

    OpenAIRE

    Okuyan, Erhan

    2005-01-01

    Cataloged from PDF version of article. Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. This work provides a tool that will extract crystal parameters such as primitive vect...

  11. Musical information processing reflecting its structure

    OpenAIRE

    Hiraga, Rumi

    1999-01-01

    In pursuit of generating expressive musical rendition with rules, the computer music project Psyche has greatly concerned musical structure. Although described implicitly, musical structure exists innately and absolutely in musical scores. This thesis demonstrates the successful introduction of musical structure to computer music systems that are related to performance synthesis. Two systems, a performance visualization system and a computer-assisted musical analysis system Daphne, are descri...

  12. The double-layered chemical structure in DB white dwarfs

    CERN Document Server

    Althaus, L G

    2004-01-01

    We study the structure and evolution of white dwarf stars with helium-rich atmospheres (DB) in a self-consistent way with the predictions of time-dependent element diffusion. Our treatment of diffusion includes gravitational settling and chemical and thermal diffusion. OPAL radiative opacities for arbitrary metallicity and carbon-and oxygen-rich compositions are employed. Emphasis is placed on the evolution of the diffusion-modeled double-layered chemical structure. This structure, which is characterized by a pure helium envelope atop an intermediate remnant shell rich in helium, carbon and oxygen, is expected for pulsating DB white dwarfs, assuming that they are descendants of hydrogen-deficient PG1159 post-AGB stars. We find that, depending on the stellar mass, if DB white dwarf progenitors are formed with a helium content smaller than \\approx 10^-3 M_*, a single-layered configuration is expected to emerge during the DB pulsation instability strip. We also explore the consequences of diffusively evolving ch...

  13. Geographic Names Information System (GNIS) Structures

    Data.gov (United States)

    Department of Homeland Security — The Geographic Names Information System (GNIS) is the Federal standard for geographic nomenclature. The U.S. Geological Survey developed the GNIS for the U.S. Board...

  14. Phenomenological description of selected elementary chemical reaction mechanisms: An information-theoretic study

    Energy Technology Data Exchange (ETDEWEB)

    Esquivel, R.O., E-mail: esquivel@xanum.uam.m [Departamento de Quimica, Universidad Autonoma Metropolitana, 09340 Mexico D.F. (Mexico); Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain); Flores-Gallegos, N.; Iuga, C.; Carrera, E.M. [Departamento de Quimica, Universidad Autonoma Metropolitana, 09340 Mexico D.F. (Mexico); Angulo, J.C. [Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain); Antolin, J. [Departamento de Fisica Aplicada, EUITIZ, Universidad de Zaragoza, 50018-Zaragoza (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain)

    2010-02-01

    The information-theoretic description of the course of two elementary chemical reactions allows a phenomenological description of the chemical course of the hydrogenic abstraction and the S{sub N}2 identity reactions by use of Shannon entropic measures in position and momentum spaces. The analyses reveal their synchronous/asynchronous mechanistic behavior.

  15. Information resources for assessing health effects from chemical exposure: Office of pesticides programs

    Energy Technology Data Exchange (ETDEWEB)

    Fenner-Crisp, P. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    The US Environmental Protection Agency (EPA) Office of Pesticide Programs is trying to develop a complete picture of a chemical`s toxicity and exposure profile. It is also important to share information in the office`s files because of pesticides, particularly as a consequence of agricultural use, find their way into places not necessarily intended.

  16. Predicting RNA Structure Using Mutual Information

    DEFF Research Database (Denmark)

    Freyhult, E.; Moulton, V.; Gardner, P. P.

    2005-01-01

    Background: With the ever-increasing number of sequenced RNAs and the establishment of new RNA databases, such as the Comparative RNA Web Site and Rfam, there is a growing need for accurately and automatically predicting RNA structures from multiple alignments. Since RNA secondary structure......, to display and predict conserved RNA secondary structure (including pseudoknots) from an alignment. Results: We show that MIfold can be used to predict simple pseudoknots, and that the performance can be adjusted to make it either more sensitive or more selective. We also demonstrate that the overall...... performance of MIfold improves with the number of aligned sequences for certain types of RNA sequences. In addition, we show that, for these sequences, MIfold is more sensitive but less selective than the related RNAalifold structure prediction program and is comparable with the COVE structure prediction...

  17. The US EPA Geographic Information System for mapping environmental releases of toxic chemical release inventory (TRI) chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Stockwell, J.R.; Sorensen, J.W.; Eckert, J.W. Jr.; Carreras, E.M. (Environmental Protection Agency, Atlanta, GA (United States))

    1993-04-01

    This study characterizes the environmental releases of toxic chemicals of the Toxic Chemical Release Inventory (TRI) in the southeastern United States by using the US Environmental Protection Agency (EPA) Geographic Information System (GIS) to map them. These maps show that the largest quantities of TRI releases in the Southeast are usually near densely populated areas. This GIS mapping approach takes the first steps in defining those areas in the region which may be potential exposure zones and which could be strategic targets for future risk screening efforts in this geographic area. 8 refs., 6 figs., 1 tab.

  18. Electronic and chemical properties of graphene-based structures:

    DEFF Research Database (Denmark)

    Vanin, Marco

    hydrogen passivation. A joint experimental and theoretical study of the mechanism by which suspended graphene is etched by catalytically active silver nanoparticles have been studied. The experimental observation of zigzag channels is elucidated by the DFT calculations, which show that the armchair edges...... are easier to remove and therefore only zigzag edges are left. Finally, functionalized graphene has been investigated as catalyst for the electrochemical reduction of CO2 to chemical fuels and comparisons are made with traditional transition-metal surfaces. The investigated porphyrin-like structures...

  19. CLiDE Pro: the latest generation of CLiDE, a tool for optical chemical structure recognition.

    Science.gov (United States)

    Valko, Aniko T; Johnson, A Peter

    2009-04-01

    We present CLiDE Pro, the latest version of the output of the long-term CLiDE project for the development of tools for automatic extraction of chemical information from the literature. CLiDE Pro is concerned with the extraction of chemical structure and generic structure information from electronic images of chemical molecules available online as well as pages of scanned chemical documents. The information is extracted in three phases, first the image is segmented into text and graphical regions, then graphical regions are analyzed and where possible the connection tables are reconstructed, and finally any generic structures are interpreted by matching R-groups found in structure diagrams with the ones located in the text. The program has been tested on a large set of images of chemical structures originating from various sources. The results demonstrate good performance in the reconstruction of connection tables with few errors in the interpretation of the individual drawing features found in the structure diagrams. This full test set is presented for use in the validation of other similar systems.

  20. Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels.

    Science.gov (United States)

    Kim, Eunkyoung; Liu, Yi; Ben-Yoav, Hadar; Winkler, Thomas E; Yan, Kun; Shi, Xiaowen; Shen, Jana; Kelly, Deanna L; Ghodssi, Reza; Bentley, William E; Payne, Gregory F

    2016-10-01

    The Information Age transformed our lives but it has had surprisingly little impact on the way chemical information (e.g., from our biological world) is acquired, analyzed and communicated. Sensor systems are poised to change this situation by providing rapid access to chemical information. This access will be enabled by technological advances from various fields: biology enables the synthesis, design and discovery of molecular recognition elements as well as the generation of cell-based signal processors; physics and chemistry are providing nano-components that facilitate the transmission and transduction of signals rich with chemical information; microfabrication is yielding sensors capable of receiving these signals through various modalities; and signal processing analysis enhances the extraction of chemical information. The authors contend that integral to the development of functional sensor systems will be materials that (i) enable the integrative and hierarchical assembly of various sensing components (for chemical recognition and signal transduction) and (ii) facilitate meaningful communication across modalities. It is suggested that stimuli-responsive self-assembling biopolymers can perform such integrative functions, and redox provides modality-spanning communication capabilities. Recent progress toward the development of electrochemical sensors to manage schizophrenia is used to illustrate the opportunities and challenges for enlisting sensors for chemical information processing.

  1. EFFECT OF CHEMICAL STRUCTURE OF POLYCARBONATES ON ENTANGLEMENT SPACING

    Institute of Scientific and Technical Information of China (English)

    Wei Ning; Wen-xiang Zhu; Bao-qing Zhang; Chun-cheng Li; Chen-yang Liu; Du-jin Wang

    2012-01-01

    The master curves of a series of aliphatic polycarbonates (APCs) with different lengths of methylene segments in the repeat unit were obtained by dynamic rheological measurements.The plateau modulus and entanglement molecular weight were determined and cross-checked by different methods.Though having distinct difference in chemical structure of repeat units,both APCs and bisphenol-A polycarbonates have the similar entanglement weight and entanglement spacing.On the other side,the plateau modulus decreases with increasing the length of the side group of atiphatic polycarbonates with different side-chain lengths in the literature.The packing length model can explain the relationship between chain structure and entanglements.

  2. A reactive data structure for geographic information systems

    NARCIS (Netherlands)

    Oosterom, P.J.M. van

    1989-01-01

    We introduce a Reactive Data Structure, that is a spatial data structure with detail levels. The two properties, spatial organization and detail levels, are the basis for a Geographic Information System with a multi-scale database. A reactive data structure is a novel type of data structure catering

  3. Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network.

    Science.gov (United States)

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle.

  4. Pattern information extraction from crystal structures

    Science.gov (United States)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

    Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summaryTitle of program: BilKristal Catalogue identifier: ADYU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries Computer: Personal Computers with Windows operating system Operating system: Windows XP Professional RAM: 20-60 MB No. of lines in distributed program, including test data, etc.:899 779 No. of bytes in distributed program, including test date, etc.:9 271 521 Distribution format:tar.gz External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from

  5. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics.

    Science.gov (United States)

    Leitner, Alexander; Walzthoeni, Thomas; Kahraman, Abdullah; Herzog, Franz; Rinner, Oliver; Beck, Martin; Aebersold, Ruedi

    2010-08-01

    Chemical cross-linking of reactive groups in native proteins and protein complexes in combination with the identification of cross-linked sites by mass spectrometry has been in use for more than a decade. Recent advances in instrumentation, cross-linking protocols, and analysis software have led to a renewed interest in this technique, which promises to provide important information about native protein structure and the topology of protein complexes. In this article, we discuss the critical steps of chemical cross-linking and its implications for (structural) biology: reagent design and cross-linking protocols, separation and mass spectrometric analysis of cross-linked samples, dedicated software for data analysis, and the use of cross-linking data for computational modeling. Finally, the impact of protein cross-linking on various biological disciplines is highlighted.

  6. Phase structure rewrite systems in information retrieval

    Science.gov (United States)

    Klingbiel, P. H.

    1985-01-01

    Operational level automatic indexing requires an efficient means of normalizing natural language phrases. Subject switching requires an efficient means of translating one set of authorized terms to another. A phrase structure rewrite system called a Lexical Dictionary is explained that performs these functions. Background, operational use, other applications and ongoing research are explained.

  7. Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties

    Directory of Open Access Journals (Sweden)

    Monika Batke

    2016-09-01

    Full Text Available 1.AbstractInterest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g. the European Union´s Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine structural similarity with shared mechanisms of action. Substances with similar chemical structure and toxicological profile form candidate categories suitable for read-across. We combined two databases on repeated dose toxicity, RepDose database and ELINCS database to form a common database for the identification of categories. The resulting database contained physicochemical, structural and toxicological data, which were refined and curated for cluster analyses. We applied the Predictive Clustering Tree (PCT approach for clustering chemicals based on structural and on toxicological information to detect groups of chemicals with similar toxic profiles and pathways/mechanisms of toxicity. As many of the experimental toxicity values were not available, this data was imputed by predicting them with a multi-label classification method, prior to clustering. The clustering results were evaluated by assessing chemical and toxicological similarities with the aim of identifying clusters with a concordance between structural information and toxicity profiles/mechanisms. From these chosen clusters, seven were selected for a quantitative read-across, based on a small ratio of NOAEL of the members with the highest and the lowest NOAEL in the cluster (<5. We discuss

  8. The Interaction of Information Structure and Syntactic Representation in Chinese

    Science.gov (United States)

    Hsu, Yu-Yin

    2013-01-01

    This dissertation concerns the interaction of syntax and information structure in Mandarin Chinese and puts the theoretical assumption of parallelism between clauses and noun phrases to the test. It examines and validates the information structural status of the object phrases preposed to clause-internal positions. I argue that Rizzi's (1997)…

  9. Teaching Text Structure: Examining the Affordances of Children's Informational Texts

    Science.gov (United States)

    Jones, Cindy D.; Clark, Sarah K.; Reutzel, D. Ray

    2016-01-01

    This study investigated the affordances of informational texts to serve as model texts for teaching text structure to elementary school children. Content analysis of a random sampling of children's informational texts from top publishers was conducted on text structure organization and on the inclusion of text features as signals of text…

  10. Modelling of structural effects on chemical reactions in turbulent flows

    Energy Technology Data Exchange (ETDEWEB)

    Gammelsaeter, H.R.

    1997-12-31

    Turbulence-chemistry interactions are analysed using algebraic moment closure for the chemical reaction term. The coupling between turbulence and chemical length and time scales generate a complex interaction process. This interaction process is called structural effects in this work. The structural effects are shown to take place on all scales between the largest scale of turbulence and the scales of the molecular motions. The set of equations describing turbulent correlations involved in turbulent reacting flows are derived. Interactions are shown schematically using interaction charts. Algebraic equations for the turbulent correlations in the reaction rate are given using the interaction charts to include the most significant couplings. In the frame of fundamental combustion physics, the structural effects appearing on the small scales of turbulence are proposed modelled using a discrete spectrum of turbulent scales. The well-known problem of averaging the Arrhenius law, the specific reaction rate, is proposed solved using a presumed single variable probability density function and a sub scale model for the reaction volume. Although some uncertainties are expected, the principles are addressed. Fast chemistry modelling is shown to be consistent in the frame of algebraic moment closure when the turbulence-chemistry interaction is accounted for in the turbulent diffusion. The modelling proposed in this thesis is compared with experimental data for an laboratory methane flame and advanced probability density function modelling. The results show promising features. Finally it is shown a comparison with full scale measurements for an industrial burner. All features of the burner are captured with the model. 41 refs., 33 figs.

  11. Concept of chemical bond and aromaticity based on quantum information theory

    CERN Document Server

    Szilvási, T; Legeza, Ö

    2015-01-01

    Quantum information theory (QIT) emerged in physics as standard technique to extract relevant information from quantum systems. It has already contributed to the development of novel fields like quantum computing, quantum cryptography, and quantum complexity. This arises the question what information is stored according to QIT in molecules which are inherently quantum systems as well. Rigorous analysis of the central quantities of QIT on systematic series of molecules offered the introduction of the concept of chemical bond and aromaticity directly from physical principles and notions. We identify covalent bond, donor-acceptor dative bond, multiple bond, charge-shift bond, and aromaticity indicating unified picture of fundamental chemical models from ab initio.

  12. Semantic illusion depends on information structure: ERP evidence

    NARCIS (Netherlands)

    Wang, L.; Hagoort, P.; Yang, Y.

    2009-01-01

    Next to propositional content, speakers distribute information in their utterances in such a way that listeners can make a distinction between new (focused) and given (non-focused) information. This is referred to as information structure. We measured event-related potentials (ERPs) to explore the r

  13. Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

    Science.gov (United States)

    Astakhov, Vadim

    2009-01-01

    Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

  14. Quantitative Survey and Structural Classification of Fracking Chemicals Reported in Unconventional Gas Exploitation

    Science.gov (United States)

    Elsner, Martin; Schreglmann, Kathrin

    2015-04-01

    Few technologies are being discussed in such controversial terms as hydraulic fracturing ("fracking") in the recovery of unconventional gas. Particular concern regards the chemicals that may return to the surface as a result of hydraulic fracturing. These are either "fracking chemicals" - chemicals that are injected together with the fracking fluid to optimize the fracturing performance or geogenic substances which may turn up during gas production, in the so-called produced water originating from the target formation. Knowledge about them is warranted for several reasons. (1) Monitoring. Air emissions are reported to arise from well drilling, the gas itself or condensate tanks. In addition, potential spills and accidents bear the danger of surface and shallow groundwater contaminations. Monitoring strategies are therefore warranted to screen for "indicator" substances of potential impacts. (2) Chemical Analysis. To meet these analytical demands, target substances must be defined so that adequate sampling approaches and analytical methods can be developed. (3) Transformation in the Subsurface. Identification and classification of fracking chemicals (aromatics vs. alcohols vs. acids, esters, etc.) is further important to assess the possibility of subsurface reactions which may potentially generate new, as yet unidentified transformation products. (4) Wastewater Treatment. For the same reason chemical knowledge is important for optimized wastewater treatment strategies. (5) Human and Ecosystem Health. Knowledge of the most frequent fracking chemicals is further essential for risk assessment (environmental behavior, toxicity) (6) Public Discussions. Finally, an overview of reported fracking chemicals can provide unbiased scientific into current public debates and enable critical reviews of Green Chemistry approaches. Presently, however, such information is not readily available. We aim to close this knowledge gap by providing a quantitative overview of chemical

  15. Evolution of polymer photovoltaic performances from subtle chemical structure variations.

    Science.gov (United States)

    Yan, Han; Li, Denghua; Lu, Kun; Zhu, Xiangwei; Zhang, Yajie; Yang, Yanlian; Wei, Zhixiang

    2012-11-21

    Conjugated polymers are promising replacements for their inorganic counterparts in photovoltaics due to their low cost, ease of processing, and straightforward thin film formation. New materials have been able to improve the power conversion efficiency of photovoltaic cells up to 8%. However, rules for rational material design are still lacking, and subtle chemical structure variations usually result in large performance discrepancies. The present paper reports a detailed study on the crystalline structure, morphology, and in situ optoelectronic properties of blend films of polythiophene derivatives and [6,6]-phenyl C61-butyric acid methyl ester by changing the alkyl side chain length and position of polythiophene. The correlation among the molecular structure, mesoscopic morphology, mesoscopic optoelectronic property and macroscopic device performance (highest efficiency above 4%) was directly established. Both solubility and intermolecular interactions should be considered in rational molecular design. Knowledge obtained from this study can aid the selection of appropriate processing conditions that improve blend film morphology, charge transport property, and overall solar cell efficiency.

  16. Using Fisher Information Criteria for Chemical Sensor Selection via Convex Optimization Methods

    Science.gov (United States)

    2016-11-16

    best sensors after an optimization procedure. Due to the positive definite nature of the Fisher information matrix, convex optimization may be used to...parametrized to select the best sensors after an optimization procedure. Due to the positive definite nature of the Fisher information matrix, convex op...Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6180--16-9711 Using Fisher Information Criteria for Chemical Sensor Selection via Convex

  17. Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

    Directory of Open Access Journals (Sweden)

    H. V. Lee

    2014-01-01

    Full Text Available Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate’s application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein.

  18. The Physical and Chemical Structure of Hot Molecular Cores

    CERN Document Server

    Nomura, H

    2004-01-01

    We have made self-consistent models of the density and temperature profiles of the gas and dust surrounding embedded luminous objects using a detailed radiative transfer model together with observations of the spectral energy distribution of hot molecular cores. Using these profiles we have investigated the hot core chemistry which results when grain mantles are evaporated, taking into account the different binding energies of the mantle molecules, as well a model in which we assume that all molecules are embedded in water ice and have a common binding energy. We find that most of the resulting column densities are consistent with those observed toward the hot core G34.3+0.15 at a time around 10$^4$ years after central luminous star formation. We have also investigated the dependence of the chemical structure on the density profile which suggests an observational possibility of constraining density profiles from determination of the source sizes of line emission from desorbed molecules.

  19. Lipids: From Chemical Structures, Biosynthesis, and Analyses to Industrial Applications.

    Science.gov (United States)

    Li-Beisson, Yonghua; Nakamura, Yuki; Harwood, John

    2016-01-01

    Lipids are one of the major subcellular components, and play numerous essential functions. As well as their physiological roles, oils stored in biomass are useful commodities for a variety of biotechnological applications including food, chemical feedstocks, and fuel. Due to their agronomic as well as economic and societal importance, lipids have historically been subjected to intensive studies. Major current efforts are to increase the energy density of cell biomass, and/or create designer oils suitable for specific applications. This chapter covers some basic aspects of what one needs to know about lipids: definition, structure, function, metabolism and focus is also given on the development of modern lipid analytical tools and major current engineering approaches for biotechnological applications. This introductory chapter is intended to serve as a primer for all subsequent chapters in this book outlining current development in specific areas of lipids and their metabolism.

  20. Structural simplification of chemical reaction networks in partial steady states.

    Science.gov (United States)

    Madelaine, Guillaume; Lhoussaine, Cédric; Niehren, Joachim; Tonello, Elisa

    2016-11-01

    We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate intermediate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten's simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rules repeatedly and applied it to reaction networks from systems biology.

  1. Analysis of crack propagation in concrete structures with structural information entropy

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The propagation of cracks in concrete structures causes energy dissipation and release, and also causes energy redistribution in the structures. Entropy can characterize the energy redistribution. To investigate the relation between the propagation of cracks and the entropy in concrete structures, cracked concrete structures are treated as dissipative structures. Structural information entropy is defined for concrete structures. A compact tension test is conducted. Meanwhile, numerical simulations are also carried out. Both the test and numerical simulation results show that the structural information entropy in the structures can characterize the propagation of cracks in concrete structures.

  2. Structural and Optical Study of Chemical Bath Deposited Nano-Structured CdS Thin Films

    Science.gov (United States)

    Kumar, Suresh; Sharma, Dheeraj; Sharma, Pankaj; Sharma, Vineet; Barman, P. B.; Katyal, S. C.

    2011-12-01

    CdS is commonly used as window layer in polycrystalline solar cells. The paper presents a structural and optical study of CdS nano-structured thin films. High quality CdS thin films are grown on commercial glass by means of chemical bath deposition. It involves an alkaline solution of cadmium salt, a complexant, a chalcogen source and a non-ionic surfactant. The films have been prepared under various process parameters. The chemically deposited films are annealed to estimate its effect on the structural and optical properties of films. These films (as -deposited and annealed) have been characterized by means of XRD, SEM and UV-Visible spectrophotometer. XRD of films show the nano-crystalline nature. The energy gap of films is found to be of direct in nature.

  3. Quantitative structure-property relationships for chemical functional use and weight fractions in consumer articles

    Science.gov (United States)

    Chemical functional use -- the functional role a chemical plays in processes or products -- may be a useful heuristic for predicting human exposure potential in that it comprises information about the compound's likely physical properties and the product formulations or articles ...

  4. On the Possibility of Quantum Informational Structural Realism

    CERN Document Server

    Bynum, Terrell Ward

    2013-01-01

    In The Philosophy of Information (2011 book), Luciano Floridi presents an ontological theory of Being qua Being, which he calls "Informational Structural Realism", a theory which applies, he says, to every possible world. He identifies primordial information ("dedomena") as the foundation of any structure in any possible world. The present essay examines Floridi's defense of that theory, as well as his refutation of "Digital Ontology" (which some people might confuse with his own). Then, using Floridi's ontology as a starting point, the present essay adds quantum features to dedomena, yielding an ontological theory for our own universe, Quantum Informational Structural Realism, which provides a metaphysical interpretation of key quantum phenomena, and diminishes the "weirdness" or "spookiness" of quantum mechanics. Key Words: digital ontology, dedomena, structural realism, quantum information, primordial qubit

  5. Perspective: On the relevance of slower-than-femtosecond time scales in chemical structural-dynamics studies

    Directory of Open Access Journals (Sweden)

    Philip Coppens

    2015-03-01

    Full Text Available A number of examples illustrate structural-dynamics studies of picosecond and slower photo-induced processes. They include molecular rearrangements and excitations. The information that can be obtained from such studies is discussed. The results are complementary to the information obtained from femtosecond studies. The point is made that all pertinent time scales should be covered to obtain comprehensive insight in dynamic processes of chemical and biological importance.

  6. Structural prediction of dynamic Bayesian network with partial prior information.

    Science.gov (United States)

    Maiti, Aniruddha; Reddy, Ramakanth; Mukherjee, Anirban

    2015-01-01

    The prediction of the structure of a hidden dynamic Bayesian network (DBN) from a noisy dataset is an important and challenging task. This work presents a generalized framework to infer the DBN network structure with partial prior information. In the proposed framework, the partial information about the network structure is provided in the form of prior. The proposed method makes use of the prior information regarding the presence and as well as absence of some of the edges. Using the noisy dataset and partial prior information, this method is able to infer nearly accurate structure of the network. The proposed method is validated using simulated datasets. In addition, two real biological datasets are used to infer hidden biological interaction networks.

  7. Information Entropy Measures for Stand Structural Diversity:Joint Entropy

    Institute of Scientific and Technical Information of China (English)

    Lei Xiangdong; Lu Yuanchang

    2004-01-01

    Structural diversity is the key attribute of a stand. A set of biodiversity measures in ecology was introduced in forest management for describing stand structure, of which Shannon information entropy (Shannon index) has been the most widely used measure of species diversity. It is generally thought that tree size diversity could serve as a good proxy for height diversity. However, tree size diversity and height diversity for stand structure is not completely consistent. Stand diameter cannot reflect height information completely. Either tree size diversity or height diversity is one-dimensional information entropy measure. This paper discussed the method of multiple-dimensional information entropy measure with the concept of joint entropy. It is suggested that joint entropy is a good measure for describing overall stand structural diversity.

  8. Structured Information Management Using New Techniques for Processing Text.

    Science.gov (United States)

    Gibb, Forbes; Smart, Godfrey

    1990-01-01

    Describes the development of a software system, SIMPR (Structured Information Management: Processing and Retrieval), that will process documents by indexing them and classifying their subjects. Topics discussed include information storage and retrieval, file inversion techniques, modelling the user, natural language searching, automatic indexing,…

  9. Chemical tagging can work: Identification of stellar phase-space structures purely by chemical-abundance similarity

    CERN Document Server

    Hogg, David W; Ness, Melissa; Rix, Hans-Walter; Foreman-Mackey, Daniel

    2016-01-01

    Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were in fact born together (in the same molecular cloud), long ago. This idea has not previously yielded scientific successes, probably because of the noise and incompleteness in chemical-abundance measurements. However, we have succeeded in substantially improving spectroscopic measurements with The Cannon, which has delivered 15 individual abundances for 100,000 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are...

  10. How much information do extinction and backscattering measurements contain about the chemical composition of atmospheric aerosol?

    Science.gov (United States)

    Kahnert, Michael; Andersson, Emma

    2017-03-01

    We theoretically and numerically investigate the problem of assimilating multiwavelength lidar observations of extinction and backscattering coefficients of aerosols into a chemical transport model. More specifically, we consider the inverse problem of determining the chemical composition of aerosols from these observations. The main questions are how much information the observations contain to determine the particles' chemical composition, and how one can optimize a chemical data assimilation system to make maximum use of the available information. We first quantify the information content of the measurements by computing the singular values of the scaled observation operator. From the singular values we can compute the number of signal degrees of freedom, Ns, and the reduction in Shannon entropy, H. As expected, the information content as expressed by either Ns or H grows as one increases the number of observational parameters and/or wavelengths. However, the information content is strongly sensitive to the observation error. The larger the observation error variance, the lower the growth rate of Ns or H with increasing number of observations. The right singular vectors of the scaled observation operator can be employed to transform the model variables into a new basis in which the components of the state vector can be partitioned into signal-related and noise-related components. We incorporate these results in a chemical data assimilation algorithm by introducing weak constraints that restrict the assimilation algorithm to acting on the signal-related model variables only. This ensures that the information contained in the measurements is fully exploited, but not overused. Numerical tests show that the constrained data assimilation algorithm provides a solution to the inverse problem that is considerably less noisy than the corresponding unconstrained algorithm. This suggests that the restriction of the algorithm to the signal-related model variables suppresses

  11. Aged nano-structured platinum based catalyst: effect of chemical treatment on adsorption and catalytic activity.

    Science.gov (United States)

    Shim, Wang Geun; Nahm, Seung Won; Park, Hyuk Ryeol; Yun, Hyung Sun; Seo, Seong Gyu; Kim, Sang Chai

    2011-02-01

    To examine the effect of chemical treatment on the adsorption and catalytic activity of nanostructured platinum based catalyst, the aged commercial Pt/AC catalyst was pretreated with sulfuric acid (H2SO4) and a cleaning agent (Hexane). Several reliable methods such as nitrogen adsorption, X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and inductively coupled plasma (ICP) were employed to characterize the aged Pt/AC catalyst and its chemically pretreated Pt/AC catalysts. The catalytic and adsorption activities of nano-structured heterogeneous Pt/AC catalyst were investigated on the basis of toluene oxidation and adsorption isotherm data. In addition, the adsorption isotherms of toluene were used to calculate the adsorption energy distribution functions for the parent catalyst and its pre-treated nano-structured Pt/AC catalysts. It was found that sulfuric acid aqueous treatment can enhance the catalytic performance of aged Pt/AC catalyst toward catalytic oxidation of toluene. It was also shown that a comparative analysis of the energy distribution functions for nano-structured Pt/AC catalysts as well as the pore size distribution provides valuable information about their structural and energetic heterogeneity.

  12. Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

    Science.gov (United States)

    Otero, Toribio F

    2017-01-18

    In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (Ea), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. Ea, k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

  13. Nepheline structural and chemical dependence on melt composition

    Energy Technology Data Exchange (ETDEWEB)

    Marcial, José; Crum, Jarrod; Neill, Owen; McCloy, John

    2016-02-01

    Nepheline crystallizes upon slow-cooling in some melts concentrated in Na2O and Al2O3, which can result in a residual glass phase of low chemical durability. Nepheline can incorporate many components often found in high-level waste radioactive borosilicate glass, including glass network ions (e.g., Si, Al, Fe), alkali metals (e.g., Cs, K, Na, and possibly Li), alkaline-earth metals (e.g., Ba, Sr, Ca, Mg), and transition metals (e.g., Mn, and possibly Cr, Zn, Ni). When crystallized from melts of different compositions, nepheline chemistry varies as a function of starting glass composition. Five simulated high level nuclear waste borosilicate glasses shown to crystallize large fractions of nepheline on slow cooling, were selected for study. These melts constituted a range of Al2O3, B2O3, CaO, Na2O, K2O, Fe2O3, and SiO2 compositions. Compositional analyses of nepheline crystals in glass by electron probe micro-analysis (EPMA) indicate that boron is unlikely to be present in any significant concentration, if at all, in nepheline. Also, several models are presented for calculating the fraction of vacancies in the nepheline structure.

  14. Chemical etching of deformation sub-structures in quartz

    Science.gov (United States)

    Wegner, M. W.; Christie, J. M.

    1983-02-01

    Chemical etching of dislocations has been studied in natural and synthetic quartz single crystals, in deformed synthetic quartz and in naturally and experimentally deformed quartzites. The ability of different etchants to produce polished or preferentially etched surfaces on quartz is described. Dislocation etching was achieved on all crystal planes examined by using a saturated solution of ammonium bifluoride as the etchant. Appropriate etching times were determined for etching quartzites for grain size, subgrain boundaries, deformation lamellae, dislocations and twins. Growth and polished surfaces of synthetic single crystal quartz were similarly etched and dislocation etch pits, characteristic of various orientations were found. The use of ammonium bifluoride proved to be expecially advantageous for the basal plane, producing a polished surface with etch pits, suitable for dislocation etch pit counting. “Double” etch pits have been found on Dauphiné twin boundaries on the basal plane and the first order prism, using this etchant. Slip lines and deformation bands were suitably etched on deformed synthetic crystal surfaces for identification of the slip planes. Other acidic etchants have been explored and their application to the study of deformation structures in quartz crystals is discussed.

  15. Nuclear Structure References (NSR) file. [Mostly information for input

    Energy Technology Data Exchange (ETDEWEB)

    Ewbank, W.B.

    1978-08-01

    The use of the Nuclear Structure References file by the Nuclear Data Project at ORNL is described. Much of the report concerns format information of interest only to those preparing input to the system or otherwise needing detailed knowledge of its internal structure. 17 figures. (RWR)

  16. Information Structure and the Licensing of English Subjects

    Science.gov (United States)

    Mack, Jennifer Elaine

    2010-01-01

    Most approaches to argument realization in English are grounded in lexical semantic structure. While it is widely acknowledged that there is an intimate relationship between information structure and grammatical relations such as "subject," there have been few attempts to formalize this observation. This dissertation proposes an "interface model…

  17. 75 FR 63827 - Integrated Risk Information System (IRIS); Request for Chemical Substance Nominations for 2011...

    Science.gov (United States)

    2010-10-18

    ... AGENCY Integrated Risk Information System (IRIS); Request for Chemical Substance Nominations for 2011.... The status and planned milestone dates can be found on the IRIS track system, accessible on the IRIS... http://www.regulations.gov Web site is an ``anonymous access'' system, which means EPA will not...

  18. Information parameters for realization of adaptive charge of secondary chemical sources of a current

    Directory of Open Access Journals (Sweden)

    Zhitnik N. E.

    2008-10-01

    Full Text Available A chrono-potentiometric method of control of the state of chemical sources of current (CSC is offered. The method allows from chrono-potentiogram (CPG, representing CSC reaction on the charge current impulse, to get practically all informative parameters, necessary for practical realization of adaptive charge.

  19. On the evolving open peer review culture for chemical information science.

    Science.gov (United States)

    Walters, W Patrick; Bajorath, Jürgen

    2015-01-01

    Compared to the traditional anonymous peer review process, open post-publication peer review provides additional opportunities -and challenges- for reviewers to judge scientific studies. In this editorial, we comment on the open peer review culture and provide some guidance for reviewers of manuscripts submitted to the Chemical Information Science channel of F1000Research.

  20. The Effect of Peer Review on Information Literacy Outcomes in a Chemical Literature Course

    Science.gov (United States)

    Zwicky, David A.; Hands, Michael D.

    2016-01-01

    This article describes the use of peer review in a writing project involving upper-level chemistry students in a chemical literature course, with the goal of improving student performance in meeting information literacy outcomes. Students were asked to find articles on a topic of their choice over the course of a semester and assemble the results…

  1. Incorporating Chemical Information Instruction and Environmental Science into the First-Year Organic Chemistry Laboratory

    Science.gov (United States)

    Landolt, R. G.

    2006-01-01

    The chemical information instruction and environmental science which is incorporated into a first-year organic chemistry laboratory is presented. The students are charged with devised search strategies, conducting online searches and limiting the project scope to ocean systems. The laboratory serves to provide for search strategy development…

  2. 76 FR 7841 - Agency Information Collection Activities; Proposed Collections; Toxic Chemical Release Reporting...

    Science.gov (United States)

    2011-02-11

    ... AGENCY Agency Information Collection Activities; Proposed Collections; Toxic Chemical Release Reporting... codes other than SIC codes 20 through 39): 212111, 212112, 212113 (correspond to SIC 12, Coal Mining (except 1241)); or 212221, 212222, 212231, 212234, 212299 (correspond to SIC 10, Metal Mining (except...

  3. Chemical Industry Corrosion Management: A Comprehensive Information System (ASSET 2). Final Report

    Energy Technology Data Exchange (ETDEWEB)

    John, Randy C. [Shell Global Solutions, Houston, TX (United States); Young, Arthur L. [Humberside Solutions, Toronto, ON (Canada); Pelton, Arthur D. [CRCT, Ecole Polytechnique de Montreal, Quebec (Canada); Thompson, William T. [Royal Military College of Canada, Kingston, ON (Canada); Wright, Ian G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2008-10-10

    The research sponsored by this project has greatly expanded the ASSET corrosion prediction software system to produce a world-class technology to assess and predict engineering corrosion of metals and alloys corroding by exposure to hot gases. The effort included corrosion data compilation from numerous industrial sources and data generation at Shell Oak Ridge National Laboratory and several other companies for selected conditions. These data were organized into groupings representing various combinations of commercially available alloys and corrosion by various mechanisms after acceptance via a critical screening process to ensure the data were for alloys and conditions, which were adequately well defined, and of sufficient repeatability. ASSET is the largest and most capable, publicly-available technology in the field of corrosion assessment and prediction for alloys corroding by high temperature processes in chemical plants, hydrogen production, energy conversion processes, petroleum refining, power generation, fuels production and pulp/paper processes. The problems addressed by ASSET are: determination of the likely dominant corrosion mechanism based upon information available to the chemical engineers designing and/or operating various processes and prediction of engineering metal losses and lifetimes of commercial alloys used to build structural components. These assessments consider exposure conditions (metal temperatures, gas compositions and pressures), alloy compositions and exposure times. Results of the assessments are determination of the likely dominant corrosion mechanism and prediction of the loss of metal/alloy thickness as a function of time, temperature, gas composition and gas pressure. The uses of these corrosion mechanism assessments and metal loss predictions are that the degradation of processing equipment can be managed for the first time in a way which supports efforts to reduce energy consumption, ensure structural integrity of equipment

  4. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    Energy Technology Data Exchange (ETDEWEB)

    Sadtler, Bryce F [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2009-05-01

    Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions ofa nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size and shape to examine the spatial organization of materials within the resulting nanocrystal heterostructures. The selectivity for cation exchange to take place at different facets of the nanocrystal plays an important role in determining the resulting morphology of the binary heterostructure. The exchange of copper (I) (Cu+) cations in CdS nanorods occurs preferentially at the ends of the nanorods. Theoretical modeling of epitaxial attachments between different facets of CdS and Cu2S indicate that the selectivity for cation exchange at the ends of the nanorods is a result of the low formation energy of the interfaces produced. During silver (I) (Ag+) cation exchange in CdS nanorods, non-selective nucleation of silver sulfide (Ag2S), followed by partial phase segregation leads to significant changes in the spatial arrangement of CdS and Ag2S regions at the exchange reaction proceeds through the nanocrystal. A well-ordered striped pattern of alternating CdS and Ag2S segments is found at intermediate fractions of exchange. The forces mediating this spontaneous process are a combination of Ostwald ripening to reduce the interfacial area along with a strain-induced repulsive interaction between Ag2S segments. To elucidate why Cu+ and Ag+ cation exchange with CdS nanorods produce different morphologies, models for epitaxial attachments between various facets of CdS with Cu2S or

  5. Access and use of information resources in assessing health risks from chemical exposure: Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    1990-12-31

    Health risk assessment is based on access to comprehensive information about potentially hazardous agents in question. Relevant information is scattered throughout the literature, and often is not readily accessible. To be useful in assessment efforts, emerging scientific findings, risk assess parameters, and associated data must be compiled and evaluated systemically. The US Environmental Protection Agency (EPA) and Oak Ridge National Laboratory (ORNL) are among the federal agencies heavily involved in this effort. This symposium was a direct response by EPA and ORNL to the expressed needs of individuals involved in assessing risks from chemical exposure. In an effort to examine the state of the risk assessment process, the availability of toxicological information, and the future development and transfer of this information, the symposium provided an excellent cadre of speakers and participants from state and federal agencies, academia and research laboratories to address these topics. This stimulating and productive gathering discussed concerns associated with (1) environmental contamination by chemicals; (2) laws regulating chemicals; (3) information needs and resources; (4) applications; (5) challenges and priorities; and (6)future issues. Individual reports are processed separately for the data bases.

  6. DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile

    Science.gov (United States)

    Arjunan, V.; Thillai Govindaraja, S.; Jose, Sujin P.; Mohan, S.

    2014-07-01

    The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G**, high level 6-311++G** and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors.

  7. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    Directory of Open Access Journals (Sweden)

    Oscar Martínez-Santiago

    2016-05-01

    Full Text Available This report examines the interpretation of the Graph Derivative Indices (GDIs from three different perspectives (i.e., in structural, steric and electronic terms. It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.

  8. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    Science.gov (United States)

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  9. Effect of chemical composition and density of the pelvic structure in intracavitary brachytherapy dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Chavez-Aguilera, N. [Coordinacion de Investigacion y Estudios de Posgrado, Facultad de Medicina, Universidad Autonoma del Estado de Mexico, Paseo Tollocan s/n Esquina con Jesus Carranza, 50180 Toluca (Mexico); Departamento de Fisica Medica, Instituto Estatal de Cancerologia ' Dr. Arturo Beltran Ortega' , Acapulco, Guerrero (Mexico); Torres-Garcia, E., E-mail: etorresg@uaemex.m [Coordinacion de Investigacion y Estudios de Posgrado, Facultad de Medicina, Universidad Autonoma del Estado de Mexico, Paseo Tollocan s/n Esquina con Jesus Carranza, 50180 Toluca (Mexico); Mitsoura, E. [Coordinacion de Investigacion y Estudios de Posgrado, Facultad de Medicina, Universidad Autonoma del Estado de Mexico, Paseo Tollocan s/n Esquina con Jesus Carranza, 50180 Toluca (Mexico)

    2011-03-15

    High dose rate (HDR) and low dose rate (LDR) intracavitary brachytherapies dosimetry in clinical practice are typically performed by commercial treatment planning systems. However, these systems do not fully consider the heterogeneities present in the real structure of the patient. The aim of this work is to obtain isodose curves and surfaces around the usual array of sources used in LDR ({sup 137}Cs) and HDR ({sup 192}Ir) intracavitary brachytherapy by Monte Carlo simulation, considering the real anatomic structure, density and chemical composition of media and tissues from the female pelvic region. The structural information was obtained from computed tomography images in the DICOM format. A voxel phantom (VP) was developed to perform ionizing radiation transport, considering the gamma spectrum of {sup 137}Cs and {sup 192}Ir. The absorbed dose was computed within each voxel of 2x2x3 mm{sup 3}. Four materials were considered in the VP-air, fat, muscle tissue and bone; however, one material per voxel was defined. Results show and quantify the effect of density and chemical composition of the medium on the absorbed dose distribution. According to them, the treatment planning systems underestimate the absorbed dose by 8% approximately for both radionuclides. In a heterogeneous medium, the absorbed dose distribution of {sup 192}Ir is more irregular than that of {sup 137}Cs but spatially better defined.

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

    Science.gov (United States)

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2016-01-01

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

  11. Information resources for assessing health effects from chemical exposure: Challenges, priorities, and future issues

    Energy Technology Data Exchange (ETDEWEB)

    Seigel, S. [National Library of Medicine, Bethesda, MD (United States)

    1990-12-31

    Issues related to developing information resources for assessing the health effects from chemical exposure include the question of how to address the individual political issues relevant to identifying and determining the timeliness, scientific credibility, and completeness of such kinds of information resources. One of the important ways for agencies to share information is through connection tables. This type of software is presently being used to build information products for some DHHS agencies. One of the challenges will be to convince vendors of data of the importance of trying to make data files available to communities that need them. In the future, information processing will be conducted with neural networks, object-oriented database management systems, and fuzzy-set technologies, and meta analysis techniques.

  12. Environmental Product Development Combining the Life Cycle Perspective with Chemical Hazard Information

    DEFF Research Database (Denmark)

    Askham, Cecilia

    in the design or redesign process. This thesis concerns marrying the life cycle perspective with chemical hazard information, in order to advance the practice of environmental product development, and hence takes further steps towards sustainable development. The need to consider the full value chain...... for the life cycle of products meant that systems theory and systems engineering principles were important in this work. Life cycle assessment methodology was important for assessing environmental impacts for case products. The new European regulation for chemicals (REACH) provided the main driver...

  13. Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

    Energy Technology Data Exchange (ETDEWEB)

    Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

    2005-03-01

    Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

  14. Community detection using global and local structural information

    Indian Academy of Sciences (India)

    Hai-Long Yan; Ju Xiang; Xiao-Yu Zhang; Jun-Feng Fan; Fang Chane; Gen-Yi Fu; Er-Min Guo; Xin-Guang Hu; Ke Hu; Ru-Min Wang

    2013-01-01

    Community detection is of considerable importance for understanding both the structure and function of complex networks. In this paper, we introduced the general procedure of the community detection algorithms using global and local structural information, where the edge betweenness and the local similarity measures respectively based on local random walk dynamics and local cyclic structures were used. The algorithms were tested on artificial and real-world networks. The results clearly show that all the algorithms have excellent performance in the tests and the local similarity measure based on local random walk dynamics is superior to that based on local cyclic structures.

  15. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts.

    Science.gov (United States)

    Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

    2016-09-01

    A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.

  16. Interaction between Syntactic Structure and Information Structure in the Processing of a Head-Final Language

    Science.gov (United States)

    Koizumi, Masatoshi; Imamura, Satoshi

    2017-01-01

    The effects of syntactic and information structures on sentence processing load were investigated using two reading comprehension experiments in Japanese, a head-final SOV language. In the first experiment, we discovered the main effects of syntactic and information structures, as well as their interaction, showing that interaction of these two…

  17. Correlating structural order with structural rearrangement in dusty plasma liquids: can structural rearrangement be predicted by static structural information?

    Science.gov (United States)

    Su, Yen-Shuo; Liu, Yu-Hsuan; I, Lin

    2012-11-09

    Whether the static microstructural order information is strongly correlated with the subsequent structural rearrangement (SR) and their predicting power for SR are investigated experimentally in the quenched dusty plasma liquid with microheterogeneities. The poor local structural order is found to be a good alarm to identify the soft spot and predict the short term SR. For the site with good structural order, the persistent time for sustaining the structural memory until SR has a large mean value but a broad distribution. The deviation of the local structural order from that averaged over nearest neighbors serves as a good second alarm to further sort out the short time SR sites. It has the similar sorting power to that using the temporal fluctuation of the local structural order over a small time interval.

  18. Characterization of Electrochemical and Morphological Properties of Iron-Phosphate-Silicate Chemical Garden Structures

    Science.gov (United States)

    Doloboff, I. J.; Barge, L. M.; Russell, M. J.; Kanik, I.

    2012-03-01

    Examination of the growth of Fe^2^+, phosphate, and silicate chemical garden structures to understand properties of similar structures that may have formed at Hadean alkaline hydrothermal vents which may play an important role in the emergence of life.

  19. Risk Management of Large RC Structures within Spatial Information System

    DEFF Research Database (Denmark)

    Qin, Jianjun; Faber, Michael Havbro

    2012-01-01

    subject to corrosion and geographical information system based risk modeling concerning large‐scale risk management. The term “risk management” here refers in particular to the process of condition assessment and optimization of the inspection and repair activities. The SIS facilitates the storage......Abstract: The present article addresses the development of a spatial information system (SIS), which aims to facilitate risk management of large‐scale concrete structures. The formulation of the SIS is based on ideas developed in the context of indicator‐based risk modeling for concrete structures...... and handling of all relevant information to the risk management. The probabilistic modeling utilized in the condition assessment takes basis in a Bayesian hierarchical modeling philosophy. It facilitates the updating of risks as well as optimizing inspection plans whenever new information about the condition...

  20. Structural Identification and Monitoring based on Uncertain/Limited Information

    Directory of Open Access Journals (Sweden)

    Chatzi Eleni N.

    2015-01-01

    Full Text Available The goal of the present study is to propose a structural identification framework able to exploit both vibrational response and operational condition information in extracting structural models, able to represent the systemspecific structural behavior in its complete operational spectrum. In doing so, a scheme need be derived for the extraction of salient features, which are indicative of structural condition. Such a scheme should account for variations attributed to operational effects, such as environmental and operational load variations, and which likely lie within regular structural condition bounds, versus variations which indicate short- or long-term damage effects. The latter may be achieved via coupling of sparse, yet diverse, monitoring information with appropriate stochastic tools, able to infer the underlying dependences between the monitored input and output data. This in turn allows for extraction of quantities, or features, relating to structural condition, which may further be utilized as performance indicators. The computational tool developed herein for realizing such a framework, termed the PCE-ICA scheme, is based on the use of Polynomial Chaos Expansion (PCE tool, along with an Independent Component Analysis (ICA algorithm. The benefits of additionally fusing a data-driven system model will further be discussed for the case of complex structural response. The method is assessed via implementation on field data acquired from diverse structural systems, namely a benchmark bridge case study and a wind turbine tower structure, revealing a robust condition assessment tool.

  1. Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

    Science.gov (United States)

    Bae, Juhee; Watson, Benjamin

    2014-12-01

    In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

  2. Accessing and using chemical databases

    DEFF Research Database (Denmark)

    Nikolov, Nikolai Georgiev; Pavlov, Todor; Niemelä, Jay Russell

    2013-01-01

    , and dissemination. Structure and functionality of chemical databases are considered. The typical kinds of information found in a chemical database are considered-identification, structural, and associated data. Functionality of chemical databases is presented, with examples of search and access types. More details...... are included about the OASIS database and platform and the Danish (Q)SAR Database online. Various types of chemical database resources are discussed, together with a list of examples.......Computer-based representation of chemicals makes it possible to organize data in chemical databases-collections of chemical structures and associated properties. Databases are widely used wherever efficient processing of chemical information is needed, including search, storage, retrieval...

  3. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    OpenAIRE

    Sadtler, Bryce F

    2010-01-01

    Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions of a nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size an...

  4. Integrating "Free" Word Order Syntax and Information Structure

    CERN Document Server

    Hoffman, B

    1995-01-01

    This paper describes a combinatory categorial formalism called Multiset-CCG that can capture the syntax and interpretation of ``free'' word order in languages such as Turkish. The formalism compositionally derives the predicate-argument structure and the information structure (e.g. topic, focus) of a sentence in parallel, and uniformly handles word order variation among the arguments and adjuncts within a clause, as well as in complex clauses and across clause boundaries.

  5. Information-theoretical noninvasive damage detection in bridge structures

    Science.gov (United States)

    Sudu Ambegedara, Amila; Sun, Jie; Janoyan, Kerop; Bollt, Erik

    2016-11-01

    Damage detection of mechanical structures such as bridges is an important research problem in civil engineering. Using spatially distributed sensor time series data collected from a recent experiment on a local bridge in Upper State New York, we study noninvasive damage detection using information-theoretical methods. Several findings are in order. First, the time series data, which represent accelerations measured at the sensors, more closely follow Laplace distribution than normal distribution, allowing us to develop parameter estimators for various information-theoretic measures such as entropy and mutual information. Second, as damage is introduced by the removal of bolts of the first diaphragm connection, the interaction between spatially nearby sensors as measured by mutual information becomes weaker, suggesting that the bridge is "loosened." Finally, using a proposed optimal mutual information interaction procedure to prune away indirect interactions, we found that the primary direction of interaction or influence aligns with the traffic direction on the bridge even after damaging the bridge.

  6. Adaptive evolvement of information age C4ISR structure

    Institute of Scientific and Technical Information of China (English)

    Yushi Lan; Kebo Deng; Shaojie Mao; Heng Wang; Kan Yi; Ming Lei

    2015-01-01

    Command, control, communication, computing, intel-ligence, surveil ance and reconnaissance (C4ISR) in information age is a complex system whose structure always changes ac-tively or passively during the warfare. Therefore, it is important to optimize the structure, especial y in ambiguous and quick-tempo modern warfare. This paper proposes an adaptive evolvement mechanism for the C4ISR structure to survive the changeable warfare. Firstly, the information age C4ISR structure is defined and modeled based on the complex network theory. Secondly, taking the observe, orient, decide and act (OODA) model into consideration, four kinds of loops in the C4ISR structure are pro-posed and their coefficient of networked effects (CNE) is further defined. Then, the adaptive evolvement mechanisms of the four kinds of loops are presented respectively. Final y, taking the joint air-defense C4ISR as an example, simulation experiments are im-plemented, which validate the evolvement mechanism and show that the information age C4ISR structure has some characteristics of smal-world network and scale-free network.

  7. EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

    Science.gov (United States)

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co.

  8. On the sensitivity, selectivity, sensory information and optimal size of resistive chemical sensors

    CERN Document Server

    Kish, L B; Heszler, P; Smulko, J; Granqvist, Claes-Goran; Heszler, Peter; Kish, Laszlo B.; Smulko, Janusz

    2007-01-01

    Information theoretical tools are applied for the study of the sensitivity and selectivity enhancements of resistive fluctuation-enhanced sensors. General considerations are given for the upper limit of selectivity enhancement. The signal-to-noise ratio and information channel capacity of fluctuation-enhanced chemical sensors is compared to that of classical sensors providing a single output. The considerations are done at the generic level with a few concrete examples and include the estimation of scaling relations between the sensor size, the signal power, the noise power and the speed of measurements versus the size, sampling rate and measurement time.

  9. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

    Science.gov (United States)

    Galdeano, Carles; Ciulli, Alessio

    2016-09-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

  10. Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.

    Science.gov (United States)

    Wawer, Mathias J; Jaramillo, David E; Dančík, Vlado; Fass, Daniel M; Haggarty, Stephen J; Shamji, Alykhan F; Wagner, Bridget K; Schreiber, Stuart L; Clemons, Paul A

    2014-06-01

    Understanding the structure-activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this data set, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors.

  11. Combining Chemical Information Literacy, Communication Skills, Career Preparation, Ethics, and Peer Review in a Team-Taught Chemistry Course

    Science.gov (United States)

    Jones, Mary Lou Baker; Seybold, Paul G.

    2016-01-01

    The widely acknowledged need to include chemical information competencies and communication skills in the undergraduate chemistry curriculum can be accommodated in a variety of ways. We describe a team-taught, semester-length course at Wright State University which combines chemical information literacy, written and oral communication skills,…

  12. Erratum to "Impact of uncertainty in soil, climatic, and chemical information in a pesticide leaching assessment"

    Science.gov (United States)

    Loague, Keith; Green, Richard E.; Giambelluca, Thomas W.; Liang, Tony C.; Yost, Russell S.

    2016-11-01

    A simple mobility index, when combined with a geographic information system, can be used to generate rating maps which indicate qualitatively the potential for various organic chemicals to leach to groundwater. In this paper we investigate the magnitude of uncertainty associated with pesticide mobility estimates as a result of data uncertainties. Our example is for the Pearl Harbor Basin, Oahu, Hawaii. The two pesticides included in our analysis are atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) and diuron [3-(3,4-dichlorophenyl)-1,1-dimethylarea]. The mobility index used here is known as the Attenuation Factor (AF); it requires soil, hydrogeologic, climatic, and chemical information as input data. We employ first-order uncertainty analysis to characterize the uncertainty in estimates of AF resulting from uncertainties in the various input data. Soils in the Pearl Harbor Basin are delineated at the order taxonomic category for this study. Our results show that there can be a significant amount of uncertainty in estimates of pesticide mobility for the Pearl Harbor Basin. This information needs to be considered if future decisions concerning chemical regulation are to be based on estimates of pesticide mobility determined from simple indices.

  13. Thesaurus of terms for information on mechanics of structural failure

    Science.gov (United States)

    Carpenter, J. L., Jr.; Moya, N.

    1973-01-01

    A Thesaurus of approximately 700 subject terms used to describe the six problem areas in the mechanics of structural failure is presented. The initial criteria for the selection of terms are their significance and frequency of use in the literature describing the mechanics of structural failure. The purpose of the Thesaurus is to provide the Aerospace Safety Research and Data Institute a list of key works and identifiers that afford effective retrieval of information regarding failure modes and mechanisms for aerospace structures. The Thesaurus includes both a conventional listing of subject terms and a Key Words In Context (KWIC) listing.

  14. Ranking chemical structures for drug discovery: a new machine learning approach.

    Science.gov (United States)

    Agarwal, Shivani; Dugar, Deepak; Sengupta, Shiladitya

    2010-05-24

    With chemical libraries increasingly containing millions of compounds or more, there is a fast-growing need for computational methods that can rank or prioritize compounds for screening. Machine learning methods have shown considerable promise for this task; indeed, classification methods such as support vector machines (SVMs), together with their variants, have been used in virtual screening to distinguish active compounds from inactive ones, while regression methods such as partial least-squares (PLS) and support vector regression (SVR) have been used in quantitative structure-activity relationship (QSAR) analysis for predicting biological activities of compounds. Recently, a new class of machine learning methods - namely, ranking methods, which are designed to directly optimize ranking performance - have been developed for ranking tasks such as web search that arise in information retrieval (IR) and other applications. Here we report the application of these new ranking methods in machine learning to the task of ranking chemical structures. Our experiments show that the new ranking methods give better ranking performance than both classification based methods in virtual screening and regression methods in QSAR analysis. We also make some interesting connections between ranking performance measures used in cheminformatics and those used in IR studies.

  15. Crystal Structure and Chemical Composition of a Presolar Silicate from the Queen Elizabeth Range 99177 Meteorite

    Science.gov (United States)

    Nguyen, A. N.; Keller, L. P.; Rahman, Z.; Messenger, S.

    2013-01-01

    Mineral characterization of presolar silicate grains, the most abundant stardust phase, has provided valuable information about the formation conditions in circumstellar environments and in super-nova (SN) outflows. Spectroscopic observations of dust around evolved stars suggest a majority of amor-phous, Mg-rich olivine grains, but crystalline silicates, most of which are pyroxene, have also been observed [1]. The chemical compositions of hundreds of presolar silicates have been determined by Auger spectroscopy and reveal high Fe contents and nonstoichiometric compositions intermediate to olivine and pyroxene [2-6]. The unexpectedly high Fe contents can partly be attributed to secondary alteration on the meteorite parent bodies, as some grains have Fe isotopic anomalies from their parent stellar source [7]. Only about 35 presolar silicates have been studied for their mineral structures and chemical compositions by transmission electron microscopy (TEM). These grains display a wide range of compositions and structures, including crystalline forsterite, crystalline pyroxene, nanocrystalline grains, and a majority of amorphous nonstoichiometric grains. Most of these grains were identified in the primitive Acfer 094 meteorite. Presolar silicates from this meteorite show a wide range of Fe-contents, suggestive of secondary processing on the meteorite parent body. The CR chondrite QUE 99177 has not suffered as much alteration [8] and displays the highest presolar silicate abundance to date among carbonaceous chondrites [3, 6]. However, no mineralogical studies of presolar silicates from this meteorite have been performed. Here we examine the mineralogy of a presolar silicate from QUE 99177.

  16. Prenuclear Accentuation in English: Phonetics, Phonology, Information Structure

    Science.gov (United States)

    Bishop, Jason Brandon

    2013-01-01

    A primary function of prosody in many languages is to convey information structure--the "packaging" of a sentence's content into categories such as "focus", "given" and "topic". In English and other West Germanic languages it is widely assumed that focus is signaled prosodically by the location of a…

  17. Impact of Information Technology Governance Structures on Strategic Alignment

    Science.gov (United States)

    Gordon, Fitzroy R.

    2013-01-01

    This dissertation is a study of the relationship between Information Technology (IT) strategic alignment and IT governance structure within the organization. This dissertation replicates Asante (2010) among a different population where the prior results continue to hold, the non-experimental approach explored two research questions but include two…

  18. The value of structural information in the VAR model

    NARCIS (Netherlands)

    R.W. Strachan (Rodney); H.K. van Dijk (Herman)

    2003-01-01

    textabstractEconomic policy decisions are often informed by empirical economic analysis. While the decision-maker is usually only interested in good estimates of outcomes, the analyst is interested in estimating the model. Accurate inference on the structural features of a model, such as cointegrati

  19. Prosodic Marking of Information Structure by Malaysian Speakers of English

    Science.gov (United States)

    Gut, Ulrike; Pillai, Stefanie

    2014-01-01

    Various researchers have shown that second language (L2) speakers have difficulties with marking information structure in English prosodically: They deviate from native speakers not only in terms of pitch accent placement (Grosser, 1997; Gut, 2009; Ramírez Verdugo, 2002) and the type of pitch accent they produce (Wennerstrom, 1994, 1998) but also…

  20. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action.

    Science.gov (United States)

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens.

  1. Information diversity in structure and dynamics of simulated neuronal networks.

    Science.gov (United States)

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena

    2011-01-01

    Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.

  2. Structural Simulations and Conservation Analysis -Historic Building Information Model (HBIM

    Directory of Open Access Journals (Sweden)

    C. Dore

    2015-02-01

    Full Text Available In this paper the current findings to date of the Historic Building Information Model (HBIM of the Four Courts in Dublin are presented. The Historic Building Information Model (HBIM forms the basis for both structural and conservation analysis to measure the impact of war damage which still impacts on the building. The laser scan survey was carried out in the summer of 2014 of the internal and external structure. After registration and processing of the laser scan survey, the HBIM was created of the damaged section of the building and is presented as two separate workflows in this paper. The first is the model created from historic data, the second a procedural and segmented model developed from laser scan survey of the war damaged drum and dome. From both models structural damage and decay simulations will be developed for documentation and conservation analysis.

  3. Development of Methods for Obtaining Position Image and Chemical Binding Information from Flow Experiments of Porous Media

    Energy Technology Data Exchange (ETDEWEB)

    Haugan, Are

    1998-12-01

    Existing oil reservoirs might be more fully exploited if the properties of the flow of oil and water in porous media were better known. In laboratory experiments it is important to collect as much information as possible to make a descriptive model of the system, including position imaging and chemical binding information. This thesis develops nuclear methods for obtaining position image and chemical binding information from flow experiments of porous media. A combined positron emission tomography and single photon emission computed tomography system to obtain position images, and a time-differential perturbed angular correlation system to obtain chemical binding information, have been built and thoroughly tested. 68 refs., 123 figs., 14 tabs.

  4. Structure and biological activity of chemically modified nisin A species

    NARCIS (Netherlands)

    Rollema, Harry S.; Metzger, Jörg W.; Both, Paula; Kuipers, Oscar P.; Siezen, Roland J.

    1996-01-01

    Nisin, a 34-residue peptide bacteriocin, contains the less common amino acids lanthionine, β-methyllanthionine, dehydroalanine (Dha), and dehydrobutyrine (Dhb). Several chemically modified nisin A species were purified by reverse-phase HPLC and characterized by two-dimensional NMR and electrospray m

  5. Branch Structure of Corona Discharge:Experimental Simulation and Chemical Properties

    Institute of Scientific and Technical Information of China (English)

    邹吉军; 刘昌俊

    2004-01-01

    The branch structure of corona discharge has been investigated via C2H2 corona discharge. Carbon filament with excellent branch structure is formed in the discharge. This carbon filament offers a direct mimic of the branch structure of corona discharge. It providesa very useful way to study on the average energy, physical and chemical characteristics of coronadischarge. On this basis, the chemical property of corona discharge for methane conversion is discussed.

  6. Chemical Emissions of Residential Materials and Products: Review of Available Information

    Energy Technology Data Exchange (ETDEWEB)

    Willem, Henry; Singer, Brett

    2010-09-15

    This report is prepared in the context of a larger program whose mission is to advance understanding of ventilation and indoor air quality in U.S. homes. A specific objective of this program is to develop the scientific basis ? through controlled experiments, monitoring and analysis ? for health risk-based ventilation standards. Appropriate and adequate ventilation is a basic element of a healthy home. Ventilation provides outdoor air and in the process removes indoor odors and contaminants including potentially unhealthful chemicals emitted by indoor materials, products and activities. Ventilation traditionally was assured to occur via infiltration of outdoor air through cracks and other leakage pathways in the residential building envelope. As building air tightness is improved for energy efficiency, infiltration can be reduced to inadequate levels. This has lead to the development of standards requiring mechanical ventilation. Though nominally intended to ensure acceptable indoor air quality, the standards are not explicitly tied to health risk or pollutant exposure targets. LBNL is currently designing analyses to assess the impact of varying ventilation standards on pollutant concentrations, health risks and energy use. These analyses require information on sources of chemical pollutant emissions, ideally including emission rates and the impact of ventilation on emissions. Some information can be obtained from recent studies that report measurements of various air contaminants and their concentrations in U.S. residences. Another way to obtain this information is the bottom-up approach of collecting and evaluating emissions data from construction and interior materials and common household products. This review contributes to the latter approach by summarizing available information on chemical emissions from new residential products and materials. We review information from the scientific literature and public sources to identify and discuss the databases that

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

    Science.gov (United States)

    Cincilla, Giovanni; Thormann, Michael; Pons, Miquel

    2010-01-12

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

  8. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Masataka [Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Honmachi, Kawaguchi 332-0012 (Japan); ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520 (Japan)

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  9. Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors

    Science.gov (United States)

    Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.

    2008-06-01

    A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

  10. On the complexity and the information content of cosmic structures

    Science.gov (United States)

    Vazza, F.

    2017-03-01

    The emergence of cosmic structure is commonly considered one of the most complex phenomena in nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work, we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information is necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviours are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution of magnetic energy requires at least twice as large amount of bits as required for the other energy fields. When radiative cooling and feedback from galaxy formation are considered, the cosmic gas is overall found to double its degree of complexity. In the future, Cosmic Information Theory can significantly increase our understanding of the emergence of cosmic structure as it represents an innovative framework to design and analyse complex simulations of the Universe in a simple, yet powerful way.

  11. Ensuring Adequate Health and Safety Information for Decision Makers during Large-Scale Chemical Releases

    Science.gov (United States)

    Petropoulos, Z.; Clavin, C.; Zuckerman, B.

    2015-12-01

    The 2014 4-Methylcyclohexanemethanol (MCHM) spill in the Elk River of West Virginia highlighted existing gaps in emergency planning for, and response to, large-scale chemical releases in the United States. The Emergency Planning and Community Right-to-Know Act requires that facilities with hazardous substances provide Material Safety Data Sheets (MSDSs), which contain health and safety information on the hazardous substances. The MSDS produced by Eastman Chemical Company, the manufacturer of MCHM, listed "no data available" for various human toxicity subcategories, such as reproductive toxicity and carcinogenicity. As a result of incomplete toxicity data, the public and media received conflicting messages on the safety of the contaminated water from government officials, industry, and the public health community. Two days after the governor lifted the ban on water use, the health department partially retracted the ban by warning pregnant women to continue avoiding the contaminated water, which the Centers for Disease Control and Prevention deemed safe three weeks later. The response in West Virginia represents a failure in risk communication and calls to question if government officials have sufficient information to support evidence-based decisions during future incidents. Research capabilities, like the National Science Foundation RAPID funding, can provide a solution to some of the data gaps, such as information on environmental fate in the case of the MCHM spill. In order to inform policy discussions on this issue, a methodology for assessing the outcomes of RAPID and similar National Institutes of Health grants in the context of emergency response is employed to examine the efficacy of research-based capabilities in enhancing public health decision making capacity. The results of this assessment highlight potential roles rapid scientific research can fill in ensuring adequate health and safety data is readily available for decision makers during large

  12. Integrated Microfluidic Membrane Transistor Utilizing Chemical Information for On-Chip Flow Control.

    Science.gov (United States)

    Frank, Philipp; Schreiter, Joerg; Haefner, Sebastian; Paschew, Georgi; Voigt, Andreas; Richter, Andreas

    2016-01-01

    Microfluidics is a great enabling technology for biology, biotechnology, chemistry and general life sciences. Despite many promising predictions of its progress, microfluidics has not reached its full potential yet. To unleash this potential, we propose the use of intrinsically active hydrogels, which work as sensors and actuators at the same time, in microfluidic channel networks. These materials transfer a chemical input signal such as a substance concentration into a mechanical output. This way chemical information is processed and analyzed on the spot without the need for an external control unit. Inspired by the development electronics, our approach focuses on the development of single transistor-like components, which have the potential to be used in an integrated circuit technology. Here, we present membrane isolated chemical volume phase transition transistor (MIS-CVPT). The device is characterized in terms of the flow rate from source to drain, depending on the chemical concentration in the control channel, the source-drain pressure drop and the operating temperature.

  13. Effects of chemical treatments on hemp fibre structure

    Energy Technology Data Exchange (ETDEWEB)

    Kabir, M.M., E-mail: kabirm@usq.edu.au [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Wang, H. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Lau, K.T. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Department of Mechanical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region (Hong Kong); Cardona, F. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia)

    2013-07-01

    In this study, hemp fibres were treated with alkali, acetyl and silane chemicals. Fibre constituents such as cellulose, hemicellulose and lignin constituents were separated from treated fibres. The chemical and thermal influences of these constituents on the treated fibres were examined by using scanning electron microscope (SEM), fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). Experimental results revealed that, hemicellulose was degraded faster than that of cellulose and lignin. Cellulose exhibited better thermal stability and lignin was degraded in a wide range of temperatures. The hydrophilic nature of the fibres was predominantly caused by the presence of hemicellulose and then lignin constituents. Hemicellulose and lignin were mostly removed by the alkalisation with higher concentrations of NaOH, followed by acetylation. Silane treatment could not remove the hemicellulose and lignin, rather this treatment facilitated coupling with the fibre constituents.

  14. Tabletop imaging of structural evolutions in chemical reactions

    CERN Document Server

    Ibrahim, Heide; Beaulieu, Samuel; Schmidt, Bruno E; Thiré, Nicolas; Bisson, Éric; Hebeisen, Christoph T; Wanie, Vincent; Giguére, Mathieu; Kieffer, Jean-Claude; Sanderson, Joseph; Schuurman, Michael S; Légaré, François

    2014-01-01

    The introduction of femto-chemistry has made it a primary goal to follow the nuclear and electronic evolution of a molecule in time and space as it undergoes a chemical reaction. Using Coulomb Explosion Imaging we have shot the first high-resolution molecular movie of a to and fro isomerization process in the acetylene cation. So far, this kind of phenomenon could only be observed using VUV light from a Free Electron Laser [Phys. Rev. Lett. 105, 263002 (2010)]. Here we show that 266 nm ultrashort laser pulses are capable of initiating rich dynamics through multiphoton ionization. With our generally applicable tabletop approach that can be used for other small organic molecules, we have investigated two basic chemical reactions simultaneously: proton migration and C=C bond-breaking, triggered by multiphoton ionization. The experimental results are in excellent agreement with the timescales and relaxation pathways predicted by new and definitively quantitative ab initio trajectory simulations.

  15. Physicists' Information Tasks: Structure, Length and Retrieval Performance

    DEFF Research Database (Denmark)

    Lykke, Marianne; Ingwersen, Peter; Bogers, Toine;

    2010-01-01

    to describe the tasks, 3) what semantic categories were used to express the search facets, and 4) retrieval performance. Results show variety in structure and length across task descriptions and task purposes. The results indicate effect of length and, in particular, of task purpose on retrieval performance......In this poster, we describe central aspects of 65 natural information tasks from 23 senior researchers, PhDs, and experienced MSc students from three different university departments of physics. We analyze 1) the main purpose of the information task, 2) which and how many search facets were used...

  16. Stochastic Generator of Chemical Structure. 3. Reaction Network Generation

    Energy Technology Data Exchange (ETDEWEB)

    FAULON,JEAN-LOUP; SAULT,ALLEN G.

    2000-07-15

    A new method to generate chemical reaction network is proposed. The particularity of the method is that network generation and mechanism reduction are performed simultaneously using sampling techniques. Our method is tested for hydrocarbon thermal cracking. Results and theoretical arguments demonstrate that our method scales in polynomial time while other deterministic network generator scale in exponential time. This finding offers the possibility to investigate complex reacting systems such as those studied in petroleum refining and combustion.

  17. Combining QSAR modeling and text-mining techniques to link chemical structures and carcinogenic modes of action

    Directory of Open Access Journals (Sweden)

    Georgios Papamokos

    2016-08-01

    Full Text Available There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. QSAR, a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens.

  18. Mining the chemical quarry with joint chemical probes: an application of latent semantic structure indexing (LaSSI) and TOPOSIM (Dice) to chemical database mining.

    Science.gov (United States)

    Singh, S B; Sheridan, R P; Fluder, E M; Hull, R D

    2001-05-10

    In this study we use a novel similarity search technique called latent semantic structure indexing (LaSSI) with joint chemical probes as queries to mine the MDL drug data report database. LaSSI is based on latent semantic indexing developed for searching textual databases. We use atom pair and topological torsion descriptors in our calculations. The results obtained with LaSSI are compared with another in-house similarity search technique TOPOSIM. The results from the similarity searches using joint chemical probes are significantly better than searches using single chemical probes for both LaSSI and TOPOSIM. The selected molecules are closely related in activity to their queries and are ranked among the top 300 scoring molecules of the 82 860 entries in the database. Our implementation of LaSSI is very fast and efficient in finding active compounds. The results also show that LaSSI consistently retrieves more diverse chemical structures representative of the joint chemical probes in comparison to TOPOSIM. The use of multimolecule topological probes to identify compounds complements the use of searching databases with 3D pharmacophore hypotheses.

  19. Utilizing the Structure and Content Information for XML Document Clustering

    Science.gov (United States)

    Tran, Tien; Kutty, Sangeetha; Nayak, Richi

    This paper reports on the experiments and results of a clustering approach used in the INEX 2008 document mining challenge. The clustering approach utilizes both the structure and content information of the Wikipedia XML document collection. A latent semantic kernel (LSK) is used to measure the semantic similarity between XML documents based on their content features. The construction of a latent semantic kernel involves the computing of singular vector decomposition (SVD). On a large feature space matrix, the computation of SVD is very expensive in terms of time and memory requirements. Thus in this clustering approach, the dimension of the document space of a term-document matrix is reduced before performing SVD. The document space reduction is based on the common structural information of the Wikipedia XML document collection. The proposed clustering approach has shown to be effective on the Wikipedia collection in the INEX 2008 document mining challenge.

  20. The Effect of Information and Communication Technologies on Urban Structure

    OpenAIRE

    Ioannides, Yannis M.; Overman, Henry G.; Rossi-Hansberg, Esteban; Schmidheiny, Kurt

    2007-01-01

    The geographic concentration of economic activity occurs because transport costs for goods, people and ideas give individuals and organisations incentives to locate close to each other. Historically, all of these costs have been falling. Such changes could lead us to predict the death of distance. This paper is concerned with one aspect of this prediction: the impact that less costly communication and transmission of information might have on cities and the urban structure. We develop a model...

  1. The effect of information and communication technologies on urban structure

    OpenAIRE

    Ioannides, Yannis M.; Overman, Henry G.; Rossi-Hansberg, Esteban; Schmidheiny, Kurt

    2007-01-01

    The geographic concentration of economic activity occurs because transport costs for goods, people and ideas give individuals and organisations incentives to locate close to each other. Historically, all of these costs have been falling. Such changes could lead us to predict the death of distance. This paper is concerned with one aspect of this prediction: the impact that less costly communication and transmission of information might have on cities and the urban structure. We develop a model...

  2. Information structure and reference tracking in complex sentences

    CERN Document Server

    Gijn, Rik van; Matic, Dejan

    2014-01-01

    This paper discusses argument marking and reference tracking in Mekens complex clauses and their correlation to information structure. The distribution of pronominal arguments in Mekens simple clauses follows an absolutive pattern with main verbs. Complex clauses maintain the morphological absolutive argument marking, but show a nominative pattern with respect to argument reference tracking, since transitive and intransitive subjects function as syntactic pivots. The language extends the use of argument-marking verb morphology to control the reference of discourse participants across clauses.

  3. 11Li structural information from inclusive break-up measurements

    Directory of Open Access Journals (Sweden)

    Fernández-García J. P.

    2015-01-01

    Full Text Available Structure information of 11Li halo nucleus has been obtained from the inclusive break-up measurements of the 11Li+208Pb reactions at energies around the Coulomb barrier (Elab = 24.3 and 29.8 MeV. The effective break-up energy and the slope of B(E1 distribution close to the threshold have been extracted from the experimental data.

  4. ANNIS: a linguistic database for exploring information structure

    OpenAIRE

    Dipper, Stefanie; Götze, Michael; Stede, Manfred; Wegst, Tillmann

    2008-01-01

    In this paper, we discuss the design and implementation of our first version of the database "ANNIS" (ANNotation of Information Structure). For research based on empirical data, ANNIS provides a uniform environment for storing this data together with its linguistic annotations. A central database promotes standardized annotation, which facilitates interpretation and comparison of the data. ANNIS is used through a standard web browser and offers tier-based visualization of data and annotations...

  5. Information-driven structural modelling of protein-protein interactions.

    Science.gov (United States)

    Rodrigues, João P G L M; Karaca, Ezgi; Bonvin, Alexandre M J J

    2015-01-01

    Protein-protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called "information-driven" approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a "classical" protein-protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes.

  6. Encoding techniques for complex information structures in connectionist systems

    Science.gov (United States)

    Barnden, John; Srinivas, Kankanahalli

    1990-01-01

    Two general information encoding techniques called relative position encoding and pattern similarity association are presented. They are claimed to be a convenient basis for the connectionist implementation of complex, short term information processing of the sort needed in common sense reasoning, semantic/pragmatic interpretation of natural language utterances, and other types of high level cognitive processing. The relationships of the techniques to other connectionist information-structuring methods, and also to methods used in computers, are discussed in detail. The rich inter-relationships of these other connectionist and computer methods are also clarified. The particular, simple forms are discussed that the relative position encoding and pattern similarity association techniques take in the author's own connectionist system, called Conposit, in order to clarify some issues and to provide evidence that the techniques are indeed useful in practice.

  7. Instruction in Information Structuring Improves Bayesian Judgment in Intelligence Analysts

    Directory of Open Access Journals (Sweden)

    David R. Mandel

    2015-04-01

    Full Text Available An experiment was conducted to test the effectiveness of brief instruction in information structuring (i.e., representing and integrating information for improving the coherence of probability judgments and binary choices among intelligence analysts. Forty-three analysts were presented with comparable sets of Bayesian judgment problems before and immediately after instruction. After instruction, analysts’ probability judgments were more coherent (i.e., more additive and compliant with Bayes theorem. Instruction also improved the coherence of binary choices regarding category membership: after instruction, subjects were more likely to invariably choose the category to which they assigned the higher probability of a target’s membership. The research provides a rare example of evidence-based validation of effectiveness in instruction to improve the statistical assessment skills of intelligence analysts. Such instruction could also be used to improve the assessment quality of other types of experts who are required to integrate statistical information or make probabilistic assessments.

  8. Modeling turbulence structure. Chemical kinetics interaction in turbulent reactive flows

    Energy Technology Data Exchange (ETDEWEB)

    Magnussen, B.F. [The Norwegian Univ. of Science and Technology, Trondheim (Norway)

    1997-12-31

    The challenge of the mathematical modelling is to transfer basic physical knowledge into a mathematical formulation such that this knowledge can be utilized in computational simulation of practical problems. The combustion phenomena can be subdivided into a large set of interconnected phenomena like flow, turbulence, thermodynamics, chemical kinetics, radiation, extinction, ignition etc. Combustion in one application differs from combustion in another area by the relative importance of the various phenomena. The difference in fuel, geometry and operational conditions often causes the differences. The computer offers the opportunity to treat the individual phenomena and their interactions by models with wide operational domains. The relative magnitude of the various phenomena therefore becomes the consequence of operational conditions and geometry and need not to be specified on the basis of experience for the given problem. In mathematical modelling of turbulent combustion, one of the big challenges is how to treat the interaction between the chemical reactions and the fluid flow i.e. the turbulence. Different scientists adhere to different concepts like the laminar flamelet approach, the pdf approach of the Eddy Dissipation Concept. Each of these approaches offers different opportunities and problems. All these models are based on a sound physical basis, however none of these have general validity in taking into consideration all detail of the physical chemical interaction. The merits of the models can only be judged by their ability to reproduce physical reality and consequences of operational and geometric conditions in a combustion system. The presentation demonstrates and discusses the development of a coherent combustion technology for energy conversion and safety based on the Eddy Dissipation Concept by Magnussen. (author) 30 refs.

  9. Internal Structure of Information Packages in Digital Preservation

    Directory of Open Access Journals (Sweden)

    Lee, Seungmin

    2014-12-01

    Full Text Available The description of preserved resources is one of the requirements in digital preservation. The description is generally created in the format of metadata records, and those records are combined to generate information packages to support the process of digital preservation. However, current strategies or models of digital preservation may not generate information packages in efficient ways. To overcome these problems, this research proposed an internal structure of information packages in digital preservation. In order to construct the internal structure, this research analyzed existing metadata standards and cataloging rules such as Dublin Core, MARC, and FRBR to extract the core elements of resource description. The extracted elements were categorized according to their semantics and functions, which resulted in three categories of core elements. These categories and core elements were manifested by using RDF syntax in order to be substantially applied to combine metadata records in digital preservation. Although the internal structure is not intended to create metadata records, it is expected to provide an alternative approach to enable combining existing metadata records in the context of digital preservation in a more flexible way.

  10. The evolution of a LIMS (laboratory information management system). [Chemical analyses at BNFL

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1992-04-01

    Changes in the world and United Kingdom markets for nuclear fuels during the 1990s have prompted British Nuclear Fuels (BNFL) to maximise cost effectiveness in its Chemical and Metallurgical Services department. A laboratory information management system (LIMS) was introduced in order to keep records of analytical techniques and equipment up to date by coordinating various computer systems. Wherever possible automated systems have replaced traditional, labour intensive techniques. So successful has the LIMS system been, that the team now hopes to expand into expert systems. (UK).

  11. Effect of Chemical Structure on Molecular Properties of Hyperbranched Polycarbosilanes

    Institute of Scientific and Technical Information of China (English)

    E.Tarabukina; A.Shpyrkov; A.Amirova; E.Tarasova; N.Shumilkina; A.Filippov; A.Muzafarov

    2007-01-01

    1 Results In spite of the increased interest to the synthesis of hyperbranched polymers,there is a lack of studies of conformational properties of their macromolecules.Structural features of hyperbranched polymers are responsible for new properties that distinguish them from linear compounds and open unique possibilities for their applications.The knowledge of the "structure-properties" relationships is of fundamental value,it also can be helpful when developing new technologies and new materials. The g...

  12. Structural features of the pore formed by Staphylococcus aureus alpha-toxin inferred from chemical modification and primary structure analysis.

    Science.gov (United States)

    Menestrina, G; Belmonte, G; Parisi, V; Morante, S

    1992-09-01

    Staphylococcus aureus alpha-toxin makes cells and model membranes permeable to ions and uncharged molecules by opening oligomeric pores of uniform size. Its primary sequence reveals peculiar features which give some hints on the structure of the pore. A flexible region separating the toxin into two halves, several amphiphilic beta-strands and two amphiphilic alpha-helices long enough to span the hydrophobic core of the lipid bilayer are predicted. In analogy to bacterial porins, we propose that the inner walls of the pore are, at least in part, built by an amphiphilic beta-barrel. The model is consistent with circular dichroism data and with the electrophysiological properties of the pore. Functional information on this toxin were obtained by chemical modification of its four histidine residues. Specific carbethoxylation suggested they have different roles: one is required for specific receptor binding, one for oligomerisation and two for unspecific lipid binding. A tentative assignment of each histidine to its specific role is done on the basis of the structural predictions. A functionally related hemolysin, Aeromonas hydrophyla aerolysin, reveals remarkably similar features including the presence and location of histidines involved in receptor binding and oligomerisation.

  13. Controlled modification of the structure of polymer surfaces by chemically grafting inorganic species

    Directory of Open Access Journals (Sweden)

    Rodrigo Lambert Oréfice

    1999-07-01

    Full Text Available Many chemical and physical methods, such as plasma, e-beam, sputtering, CVD and others, have been used to modify the structure of polymer surfaces by depositing thin inorganic films. Most of these techniques are based upon the use of high energy sources that ultimately can damage either chemically or physically polymer surfaces. Moreover, these methods are usually not versatile enough to allow the design of structurally and chemically tailored surfaces through the control of the distribution of chemical functionalities throughout the surface. In this work, inorganic species were introduced onto polymer substrates in a controlled manner by performing a sequence of chemical reactions at the surface. Sulfonation followed by silanization reactions were used to graft alkoxysilane species at the surface of poly(aryl sulfones. The heterogeneous chemical modification of poly(aryl sulfones was monitored by FTIR-ATR (Attenuated Total Reflection - FTIR. Model compounds were used to study the chemical reactions occurring during the grafting procedure. The results showed that the developed procedure can allow a controlled introduction of inorganic species onto polymer surfaces. Furthermore, in order to prove that this procedure enables the deposition of specific chemical functionalities onto polymer surfaces that can be used to create chemically and structurally tailored surfaces, silicate films were deposited on previously silanated PAS bioactive glass composites. In vitro tests showed that the surface modified composite can enhance the rates of hydroxy-carbonate-apatite precipitation.

  14. Corrosion inhibitors: Correlation between chemical structure and efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Lukovits, I.; Koszto, T. [Hungarian Academy of Sciences (Hungary). Inst. of Chemistry

    1999-11-01

    Corrosion inhibition efficiencies of heterocyclic aromatic or partially saturated aromatic compounds (pyrimidines, benzothiazole derivatives, amino-acids containing an aromatic part, pyridines and quinolines) were correlated with quan chemical indices of the respective molecules. Inhibition efficiencies measured in acidic solutions containing 0.001 and 0.01 mol/L of the inhibitor, respectively, were collected. The quantum chemical calculations were done by using the simple Hueckel method. Comparison of inhibition efficiencies and the differences between energies of the highest occupied and the lowest unoccupied molecular orbitals {Delta} indicated that if {Delta} is lower than 1.3 (in beta units) then the compound will not be active, whereas if {Delta} > 1.3 beta, the compound may be efficient in 0.001 mole/L concentration. The critical value of {Delta} may be lower in solution with 0.01 mole/L inhibitor concentration. Although {Delta} alone is not sufficient to account for the variation in the experimental inhibition efficiencies, the present result indicates that compounds which may be easily excited will be inefficient inhibitors because they maybe altered or decomposed after the excitation takes place.

  15. Point and line geologic structure information in "Structure, outcrop, and subcrop of the geologic structure information for the Arapahoe and Laramie-Fox Hills aquifers.

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This digital geospatial data set consists of points and lines representing symbolization of geologic structure information for the Arapahoe and Laramie-Fox Hills...

  16. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    Science.gov (United States)

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  17. A proposed chemical structure for fructans from blue agave plant (Tequilana Weber var. azul)

    OpenAIRE

    Guillermo Toriz; Ezequiel Delgado; Virgilio Zúñiga

    2007-01-01

    A chemical structure for agave Tequilana fructans is proposed based upon the combined results of permethylation and reductive cleavage techniques coupled to gas-liquid chromatography (GLC), as well as size exclusión chromatography /lightscattering.

  18. Register of experts for information on mechanics of structural failure

    Science.gov (United States)

    Carpenter, J. L., Jr.; Stuhrke, W. F.

    1975-01-01

    This register is comprised of a list of approximately 300 experts from approximately 90 organizations who have published results of theoretical and/or experimental research related to six problem areas in the mechanics of structural failure: (1) life prediction for structural materials, (2) fracture toughness testing, (3) fracture mechanics analysis; (4) hydrogen embrittlement; (5) protective coatings; and (6) composite materials. The criteria for the selection of names for the register are recent contributions to the literature, participation in or support of relevant research programs, and referral by peers. Each author included is listed by organizational affiliation, address, and principal field of expertise. The purpose of the register is to present, in easy reference form, sources for dependable information regarding failure modes and mechanisms of aerospace structures. The register includes two indexes; an alphabetical listing of the experts and an alphabetical listing of the organizations with whom they are affiliated.

  19. Enhancing community detection by using local structural information

    Science.gov (United States)

    Xiang, Ju; Hu, Ke; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-03-01

    Many real-world networks, such as gene networks, protein-protein interaction networks and metabolic networks, exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have a positive effect on community detection in the networks. Here, various local similarity measures are used to extract local structural information, which is then applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial for the improvement of community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and applied community detection methods.

  20. PROGRAM SYSTEM AND INFORMATION METADATA BANK OF TERTIARY PROTEIN STRUCTURES

    Directory of Open Access Journals (Sweden)

    T. A. Nikitin

    2013-01-01

    Full Text Available The article deals with the architecture of metadata storage model for check results of three-dimensional protein structures. Concept database model was built. The service and procedure of database update as well as data transformation algorithms for protein structures and their quality were presented. Most important information about entries and their submission forms to store, access, and delivery to users were highlighted. Software suite was developed for the implementation of functional tasks using Java programming language in the NetBeans v.7.0 environment and JQL to query and interact with the database JavaDB. The service was tested and results have shown system effectiveness while protein structures filtration.

  1. Surface Nano-Structuring by Adsorption and Chemical Reactions

    OpenAIRE

    Ken-ichi Tanaka

    2010-01-01

    Nano-structuring of the surface caused by adsorption of molecules or atoms and by the reaction of surface atoms with adsorbed species are reviewed from a chemistry viewpoint. Self-assembly of adsorbed species is markedly influenced by weak mutual interactions and the local strain of the surface induced by the adsorption. Nano-structuring taking place on the surface is well explained by the notion of a quasi-molecule provided by the reaction of surface atoms with adsorbed species. Self-assembl...

  2. Structural Analysis Of Alfa Fibers After Chemical Treatment

    Directory of Open Access Journals (Sweden)

    Zakaria Mouallif

    2015-02-01

    Full Text Available Nowadays, natural fibers are used as reinforcement in composite materials. The Alfa fibers have undergone an alkaline treatment with sodium hydroxide NaOH at a concentration of 10%, during an immersion period of two days. After drying, the Fourier transform infrared spectroscopy by attenuated total reflection (FTIR-ATR and X-ray diffraction (XRD were used for the analysis of the chemical properties of these fibers which were extracted from the plant Alfa of the region Al Haouz (Morocco in order to study the modifications resulting from the alkaline treatment. The results proved the presence of the cellulose, with an increase in its proportion in those fibers which have undergone an alkaline treatment with NaOH, the presence of lignin and pectin, as well as their disappearance after the alkaline extraction.

  3. Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    In this thesis, my work involving dierent aspects of protein structure determination by computer modeling is presented. Determination of several protein's native fold were carried out with Markov chain Monte Carlo simulations in the PHAISTOS protein structure simulation framework, utilizing...... to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...

  4. Impacts of chemical gradients on microbial community structure

    DEFF Research Database (Denmark)

    Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E

    2017-01-01

    Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox ...... Journal advance online publication, 17 January 2017; doi:10.1038/ismej.2016.175....

  5. Web Structure Mining: Exploring Hyperlinks and Algorithms for Information Retrieval

    Directory of Open Access Journals (Sweden)

    P. R. Kumar

    2010-01-01

    Full Text Available Problem statement: A study on hyperlink analysis and the algorithms used for link analysis in the Web Information retrieval was done. Approach: This research was initiated because of the dependability of search engines for information retrieval in the web. Understand the web structure mining and determine the importance of hyperlink in web information retrieval particularly using the Google Search engine. Hyperlink analysis was important methodology used by famous search engine Google to rank the pages. Results: The different algorithms used for link analysis like PageRank (PR, Weighted PageRank (WPR and Hyperlink-Induced Topic Search (HITS algorithms are discussed and compared. PageRank algorithm was implemented using a Java program and the convergence of the PageRank values are shown in a chart form. Conclusion: This study was done basically to explore the link structure algorithms for ranking and compare those algorithms. The further research on this area will be problems facing PageRank algorithm and how to handle those problems.

  6. On the complexity and the information content of cosmic structures

    CERN Document Server

    Vazza, Franco

    2016-01-01

    The emergence of cosmic structure is commonly considered one of the most complex phenomena in Nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information are necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviors are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution o...

  7. Temperature effects on chemical structure and motion in coal. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Maciel, G.E.

    1996-09-30

    The objective of this project was to apply recently developed, state-of-the-art nuclear magnetic resonance (NMR) techniques to examine in situ changes in the chemical structure and molecular/macromolecular motion in coal as the temperature is increased above room temperature. Although alterations in the chemical structure of coal have been studied previously by {sup 13}C NMR, using quenched samples, the goal of this project was to examine these chemical structural changes, and changes in molecular/macromolecular mobility that may precede or accompany the chemical changes, at elevated temperatures, using modern {sup 13}C and {sup 1}H NMR techniques, especially {sup 1}H dipolar-dephasing techniques and related experiments pioneered in the laboratory for examining pyridine-saturated coals. This project consisted of the following four primary segments and related efforts on matters relevant to the first four tasks. (1) {sup 1}H NMR characterization of coal structure and mobility as a function of temperature variation over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (2) {sup 1}H NMR characterization of coal structure, mobility and conversion as a function of temperature variation over a temperature range (240--500 C) for which chemical transformations of coal are known to occur. (3) {sup 13}C NMR investigation of coal structure/mobility as a function of temperature over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (4) {sup 13}C NMR investigation of coal structure, dynamics and conversion as a function of temperature variation over a range (240--500 C) for which chemical transformations of coal are known to occur. (5) Related matters relevant to the first four tasks: (a) {sup 1}H CRAMPS NMR characterization of oil shales and their kerogen concentrates; and (b) improved quantitation in {sup 13}C MAS characterization of coals.

  8. Boron carbide: Consistency of components, lattice parameters, fine structure and chemical composition makes the complex structure reasonable

    Science.gov (United States)

    Werheit, Helmut

    2016-10-01

    The complex, highly distorted structure of boron carbide is composed of B12 and B11C icosahedra and CBC, CBB and B□B linear elements, whose concentration depends on the chemical composition each. These concentrations are shown to be consistent with lattice parameters, fine structure data and chemical composition. The respective impacts on lattice parameters are estimated and discussed. Considering the contributions of the different structural components to the energy of the overall structure makes the structure and its variation within the homogeneity range reasonable; in particular that of B4.3C representing the carbon-rich limit of the homogeneity range. Replacing in B4.3C virtually the B□B components by CBC yields the hypothetical moderately distorted B4.0C (structure formula (B11C)CBC). The reduction of lattice parameters related is compatible with recently reported uncommonly prepared single crystals, whose compositions deviate from B4.3C.

  9. Quantification of the Value of Structural Health Monitoring Information for Fatigue Deteriorating Structural Systems

    DEFF Research Database (Denmark)

    Thöns, Sebastian; Schneider, Ronald; Faber, Michael Havbro

    2015-01-01

    This paper addresses the quantification of the value of structural health monitoring (SHM) before its implementation for structural systems on the basis of its Value of Information (VoI). The value of SHM is calculated utilizing the Bayesian pre-posterior decision analysis modelling the structural...... and is quantified with this framework. The approach is focused on fatigue deteriorating structural steel systems for which a continuous resistance deterioration formulation is introduced. In a case study, the value of SHM for load monitoring is calculated for a Daniels system subjected to fatigue deterioration...

  10. Information Technology from Theory to Practice in Higher Education Structure

    Directory of Open Access Journals (Sweden)

    Tooraj Sadeghi

    2016-12-01

    Full Text Available In the past two decades, developments process of higher education dependence on the increased demand for admission to higher education, development of communication technologies, need for human resource development, rapid technological changes, accumulated knowledge and information and leads to serious challenges and changes in the role of universities and higher education in the new millennium. So dramatic changes of higher education and move it towards the universalization and interpretations of the common need for higher education has created new perspectives in the development of higher education that under the influence of the information revolution and paradigm of information technology added new funds to higher education charter. The article discussed after several years of theorizing, turns and focuses on research into fundamental processes and IT operations in higher education are essential. In this study, using theoretical method and library studies gap between theory and deployment procedures were evaluated and the results showed that " there is still the gap between the theory of information technology in higher education structure and deployment procedures in practice between theory and practice]".

  11. Multistable Phase Patterns of Spatially Structured Chemical Oscillators

    Science.gov (United States)

    Giver, Michael; Goldstein, Daniel; Chakraborty, Bulbul

    2014-03-01

    Recent experiments of two-dimensional microfluidic arrays of droplets containing Belousov-Zhabotinsky reactants show a rich variety of spatio-temporal patterns. Using optical techniques a variety of boundary conditions can be set within the system, including finite rings of droplets. These experiments have provided an interesting and easily reproducible system for probing the effects of nonlinearities and fluctuations in a spatially extended system. Motivated by this experimental set up, we study a simple model of chemical oscillators in the highly nonlinear excitable regime in order to gain insight into the mechanism giving rise to the observed multistable attractors. We map the attractor space of a simple two species activator-inhibitor model coupled via three different coupling mechanism: simple inhibitor diffusion, inhibitor diffusion through an inhomogenous medium where active droplets are separated by inactive holding cells, and coupling through diffusion of an inert signaling species, which arrises through a coarse graining of the inhomogenous medium. Once the attractor space of the mean-field level model has been mapped, we check the robustness of the attractors when subject to intrinsic noise.

  12. Brazilian kefir: structure, microbial communities and chemical composition

    Directory of Open Access Journals (Sweden)

    Karina Teixeira Magalhães

    2011-06-01

    Full Text Available Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5% were the major isolated group identified, followed by yeasts (30.6% and acetic acid bacteria (8.9%. Lactobacillus paracasei (89 isolates, Lactobacillus parabuchneri (41 isolates, Lactobacillus casei (32 isolates, Lactobacillus kefiri (31 isolates, Lactococcus lactis (24 isolates, Acetobacter lovaniensis (32 isolates, Kluyveromyces lactis (31 isolates, Kazachstania aerobia (23 isolates, Saccharomyces cerevisiae (41 isolates and Lachancea meyersii (15 isolates were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml.

  13. Regioselective sulfation of Artemisia sphaerocephala polysaccharide: Characterization of chemical structure.

    Science.gov (United States)

    Wang, Junlong; Yang, Wen; Wang, Jiancheng; Wang, Xia; Wu, Fang; Yao, Jian; Zhang, Ji; Lei, Ziqiang

    2015-11-20

    The biological activities of sulfated polysaccharides are related to the substitution positions of functional groups. In this study, regioselective sulfation of Artemisia sphaerocephala polysaccharides (SRSASP) was prepared by using triphenylchloromethane (TrCl) as protecting precursor. FT-IR spectra and X-ray photoelectron spectroscopy (XPS) showed that SO(3-) group (S(6+), high binding energy of 168.7eV) was widely present in sulfated polysaccharides. (13)C NMR spectroscopy showed that C-2 and C-3 substitution was occurred but not fully sulfation. Meanwhile, C-6 substituted signals near 65ppm were not observed. The degree of substitution varied from 0.44 to 0.63 in SRSASP which could be attributed to the low reactivity at secondary hydroxyl. Monosaccharide composition result showed a decrease in the ratio of mannose/glucose, indicating the change of chemical composition in sulfated polysaccharides. In size-exclusion chromatograph analysis, a decrease in molecular weight and broadening of molecular weight distribution of sulfated polysaccharides was also observed. It could be attributed to the hydrolysis of polysaccharide in the sulfated reaction.

  14. Structural information revealed by the dispersion of ADC with frequency.

    Science.gov (United States)

    Li, Hua; Jiang, Xiaoyu; Wang, Feng; Xu, Junzhong; Gore, John C

    2015-11-01

    Diffusion MRI provides a non-invasive means to characterize tissue microstructure at varying length scales. Temporal diffusion spectra reveal how the apparent diffusion coefficient (ADC) varies with frequency. When measured using oscillating gradient spin echo sequences, the manner in which ADC disperses with gradient frequency (which is related to the reciprocal of diffusion time) provides information on the characteristic dimensions of restricting structures within the medium. For example, the dispersion of ADC with oscillating gradient frequency (ΔfADC) has been shown to correlate with axon sizes in white matter and provide novel tissue contrast in images of mouse hippocampus and cerebellum. However, despite increasing interest in applying frequency-dependent ADC to derive novel information on tissue, the interpretations of ADC spectra are not always clear. In this study, the relation between ADC spectra and restricting dimensions are further elucidated and used to derive novel image contrast related to the sizes of intrinsic microstructures.

  15. Quantum chemical and experimental studies on the structure and vibrational spectra of an alkaloid-Corlumine

    Science.gov (United States)

    Mishra, Rashmi; Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2014-01-01

    The study concentrates on an important natural product, phthalide isoquinoline alkaloid Corlumine (COR) [(6R)-6-[(1S)-1,2,3,4-Tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-yl] furo [3,4-e]-1,3-benzodioxol-8(6H)-one] well known to exhibit spasmolytic and GABA antagonist activity. It was fully characterized by a variety of experimental methods including vibrational spectroscopy (IR and Raman), thermal analysis (DSC), UV and SEM. For a better interpretation and analysis of the results quantum chemical calculations employing DFT were also performed. TD-DFT was employed to elucidate electronic properties for both gaseous and solvent environment using IEF-PCM model. Graphical representation of HOMO and LUMO would provide a valuable insight into the nature of reactivity and some of the structural and physical properties of the title molecule. The structure-activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug-receptor interactions. Stability of the molecule arising from hyper conjugative interactions, charge delocalisation has been analyzed using natural bond orbital (NBO) analysis. Computation of thermodynamical properties would help to have a deep insight into the molecule for further applications.

  16. Chemical Physics Courses.

    Science.gov (United States)

    Lee, J.; Munn, R. W.

    1978-01-01

    This is a guide to the chemical physics major. The scope of chemical physics is presented, along with the general features of course contents and possible course structures. This information was derived from a survey of British universities and colleges offering undergraduate degree courses in chemical physics. (BB)

  17. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures.

    Science.gov (United States)

    Tsuruoka, Shuji; Matsumoto, Hidetoshi; Castranova, Vincent; Porter, Dale W; Yanagisawa, Takashi; Saito, Naoto; Kobayashi, Shinsuke; Endo, Morinobu

    2015-12-01

    The present study systematically examined the kinetics of a hydroxyl radical scavenging reaction of various carbon nanotubes (CNTs) including double-walled and multi-walled carbon nanotubes (DWCNTs and MWCNTs), and carbon nano peapods (AuCl3@DWCNT). The theoretical model that we recently proposed based on the redox potential of CNTs was used to analyze the experimental results. The reaction kinetics for DWCNTs and thin MWCNTs agreed well with the theoretical model and was consistent with each other. On the other hand, thin and thick MWCNTs behaved differently, which was consistent with the theory. Additionally, surface morphology of CNTs substantially influenced the reaction kinetics, while the doped particles in the center hollow parts of CNTs (AuCl3@DWCNT) shifted the redox potential in a different direction. These findings make it possible to predict the chemical and biological reactivity of CNTs based on the structural and chemical nature and their influence on the redox potential.

  18. ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions.

    Science.gov (United States)

    Sushko, Iurii; Salmina, Elena; Potemkin, Vladimir A; Poda, Gennadiy; Tetko, Igor V

    2012-08-27

    The article presents a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, as well as other data. Most importantly, the platform can be easily used for fast virtual screening of large chemical datasets, focused libraries, or newly designed compounds against the toxicological alerts, providing a detailed profile of the chemicals grouped by structural alerts and endpoints. Such a facility can be used for decision making regarding whether a compound should be tested experimentally, validated with available QSAR models, or eliminated from consideration altogether. The alert-based screening can also be helpful for an easier interpretation of more complex QSAR models. The system is publicly accessible and tightly integrated with the Online Chemical Modeling Environment (OCHEM, http://ochem.eu). The system is open and expandable: any registered OCHEM user can introduce new alerts, browse, edit alerts introduced by other users, and virtually screen his/her data sets against all or selected alerts. The user sets being passed through the structural alerts can be used at OCHEM for other typical tasks: exporting in a wide variety of formats, development of QSAR models, additional filtering by other criteria, etc. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions. The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts, and it is constantly

  19. Tensegrity II. How structural networks influence cellular information processing networks

    Science.gov (United States)

    Ingber, Donald E.

    2003-01-01

    The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

  20. Structural properties of produced CuO/NiO/glass thin layers Produced by chemical method

    Directory of Open Access Journals (Sweden)

    A. Ramezani

    2016-12-01

    Full Text Available Nickel Oxide and Copper oxide on Nickel Oxide thin layers were produced by chemical bath deposition method. There nano structures were investigated by SEM and EDAX analysis. By producing CuO/NiO/glass sandwich layers nano structure of NiO/glass layer changed and fraction of voids decreases. In sandwich layer physical property of outer layer was dominant

  1. Incorporating secondary structural features into sequence information for predicting protein structural class.

    Science.gov (United States)

    Liao, Bo; Peng, Ting; Chen, Haowen; Lin, Yaping

    2013-10-01

    Knowledge of structural classes is applied in numerous important predictive tasks that address structural and functional features of proteins, although the prediction accuracy of the protein structural classes is not high. In this study, 45 different features were rationally designed to model the differences between protein structural classes, among which, 30 of them reflect the combined protein sequence information. In terms of correlation function, the protein sequence can be converted to a digital signal sequence, from which we can generate 20 discrete Fourier spectrum numbers. According to the segments of amino with different characteristics occurring in protein sequences, the frequencies of the 10 kinds of segments of amino acid (motifs) in protein are calculated. Other features include the secondary structural information :10 features were proposed to model the strong adjacent correlations in the secondary structural elements and capture the long-range spatial interactions between secondary structures, other 5 features were designed to differentiate α/β from α+β classes , which is a major problem of the existing algorithm. The methods were proposed based on a large set of low-identity sequences for which secondary structure is predicted from their sequence (based on PSI-PRED). By means of this method, the overall prediction accuracy of four benchmark datasets were all improved. Especially for the dataset FC699, 25PDB and D1189 which are 1.26%, 1% and 0.85% higher than the best previous method respectively.

  2. The Generalization of Mutual Information as the Information between a Set of Variables: The Information Correlation Function Hierarchy and the Information Structure of Multi-Agent Systems

    Science.gov (United States)

    Wolf, David R.

    2004-01-01

    The topic of this paper is a hierarchy of information-like functions, here named the information correlation functions, where each function of the hierarchy may be thought of as the information between the variables it depends upon. The information correlation functions are particularly suited to the description of the emergence of complex behaviors due to many- body or many-agent processes. They are particularly well suited to the quantification of the decomposition of the information carried among a set of variables or agents, and its subsets. In more graphical language, they provide the information theoretic basis for understanding the synergistic and non-synergistic components of a system, and as such should serve as a forceful toolkit for the analysis of the complexity structure of complex many agent systems. The information correlation functions are the natural generalization to an arbitrary number of sets of variables of the sequence starting with the entropy function (one set of variables) and the mutual information function (two sets). We start by describing the traditional measures of information (entropy) and mutual information.

  3. Computer prediction of possible toxic action from chemical structure; the DEREK system.

    Science.gov (United States)

    Sanderson, D M; Earnshaw, C G

    1991-07-01

    1. The development of DEREK, a computer-based expert system (derived from the LHASA chemical synthesis design program) for the qualitative prediction of possible toxic action of compounds on the basis of their chemical structure is described. 2. The system is able to perceive chemical sub-structures within molecules and relate these to a rulebase linking the sub-structures with likely types of toxicity. 3. Structures can be drawn in directly at a computer graphics terminal or retrieved automatically from a suitable in-house database. 4. The system is intended to aid the selection of compounds based on toxicological considerations, or separately to indicate specific toxicological properties to be tested for early in the evaluation of a compound, so saving time, money and some laboratory animals and resources.

  4. The relationship between chemical structure and dielectric properties of plasma-enhanced chemical vapor deposited polymer thin films

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Hao [Materials Sci and Tech Applications, LLC, 409 Maple Springs Drive, Dayton OH 45458 (United States)]. E-mail: hao.jiang@wpafb.af.mil; Hong Lianggou [Materials Sci and Tech Applications, LLC, 409 Maple Springs Drive, Dayton OH 45458 (United States); Venkatasubramanian, N. [Research Institute, University of Dayton, 300 College Park, Dayton, OH 45469-0168 (United States); Grant, John T. [Research Institute, University of Dayton, 300 College Park, Dayton, OH 45469-0168 (United States); Eyink, Kurt [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States); Wiacek, Kevin [Air Force Research Laboratory, Propulsion Directorate, 1950 Fifth Street, Wright-Patterson Air Force Base, OH 45433-7251 (United States); Fries-Carr, Sandra [Air Force Research Laboratory, Propulsion Directorate, 1950 Fifth Street, Wright-Patterson Air Force Base, OH 45433-7251 (United States); Enlow, Jesse [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States); Bunning, Timothy J. [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States)

    2007-02-26

    Polymer dielectric films fabricated by plasma enhanced chemical vapor deposition (PECVD) have unique properties due to their dense crosslinked bulk structure. These spatially uniform films exhibit good adhesion to a variety of substrates, excellent chemical inertness, high thermal resistance, and are formed from an inexpensive, solvent-free, room temperature process. In this work, we studied the dielectric properties of plasma polymerized (PP) carbon-based polymer thin films prepared from two precursors, benzene and octafluorocyclobutane. Two different monomer feed locations, directly in the plasma zone or in the downstream region (DS) and two different pressures, 80 Pa (high pressure) or 6.7 Pa (low pressure), were used. The chemical structure of the PECVD films was examined by X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy. The dielectric constant ({epsilon} {sub r}) and dielectric loss (tan {delta}) of the films were investigated over a range of frequencies up to 1 MHz and the dielectric strength (breakdown voltage) (F {sub b}) was characterized by the current-voltage method. Spectroscopic ellipsometry was performed to determine the film thickness and refractive index. Good dielectric properties were exhibited, as PP-benzene films formed in the high pressure, DS region showed a F{sub b} of 610 V/{mu}m, an {epsilon} {sub r} of 3.07, and a tan {delta} of 7.0 x 10{sup -3} at 1 kHz. The PECVD processing pressure has a significant effect on final film structure and the film's physical density has a strong impact on dielectric breakdown strength. Also noted was that the residual oxygen content in the PP-benzene films significantly affected the frequency dependences of the dielectric constant and loss.

  5. Bridging the pressure gap: Can we get local quantitative structural information at 'near-ambient' pressures?

    Science.gov (United States)

    Woodruff, D. P.

    2016-10-01

    In recent years there have been an increasing number of investigations aimed at 'bridging the pressure gap' between UHV surface science experiments on well-characterised single crystal surfaces and the much higher (ambient and above) pressures relevant to practical catalyst applications. By applying existing photon-in/photon-out methods and developing instrumentation to allow photoelectron emission to be measured in higher-pressure sample environments, it has proved possible to obtain surface compositions and spectroscopic fingerprinting of chemical and molecular states of adsorbed species at pressures up to a few millibars. None of these methods, however, provide quantitative structural information on the local adsorption sites of isolated atomic and molecular adsorbate species under these higher-pressure reaction conditions. Methods for gaining this information are reviewed and evaluated.

  6. Extended Functional Groups (EFG: An Efficient Set for Chemical Characterization and Structure-Activity Relationship Studies of Chemical Compounds

    Directory of Open Access Journals (Sweden)

    Elena S. Salmina

    2015-12-01

    Full Text Available The article describes a classification system termed “extended functional groups” (EFG, which are an extension of a set previously used by the CheckMol software, that covers in addition heterocyclic compound classes and periodic table groups. The functional groups are defined as SMARTS patterns and are available as part of the ToxAlerts tool (http://ochem.eu/alerts of the On-line CHEmical database and Modeling (OCHEM environment platform. The article describes the motivation and the main ideas behind this extension and demonstrates that EFG can be efficiently used to develop and interpret structure-activity relationship models.

  7. Using phylogenetic information and chemical properties to predict species tolerances to pesticides.

    Science.gov (United States)

    Guénard, Guillaume; Carsten von der Ohe, Peter; Carlisle Walker, Steven; Lek, Sovan; Legendre, Pierre

    2014-08-22

    Direct estimation of species' tolerance to pesticides and other toxic organic substances is a combinatorial problem, because of the large number of species-substance pairs. We propose a statistical modelling approach to predict tolerances associated with untested species-substance pairs, by using models fitted to tested pairs. This approach is based on the phylogeny of species and physico-chemical descriptors of pesticides, with both kinds of information combined in a bilinear model. This bilinear modelling approach predicts tolerance in untested species-compound pairs based on the facts that closely related species often respond similarly to toxic compounds and that chemically similar compounds often have similar toxic effects. The three tolerance models (median lethal concentration after 96 h) used up to 25 aquatic animal species and up to nine pesticides (organochlorines, organophosphates and carbamates). Phylogeny was estimated using DNA sequences, while the pesticides were described by their mode of toxic action and their octanol-water partition coefficients. The models explained 77-84% of the among-species variation in tolerance (log10 LC50). In cross-validation, 84-87% of the predicted tolerances for individual species were within a factor of 10 of the observed values. The approach can also be used to model other species response to multivariate stress factors.

  8. Social learning of predators in the dark: understanding the role of visual, chemical and mechanical information.

    Science.gov (United States)

    Manassa, R P; McCormick, M I; Chivers, D P; Ferrari, M C O

    2013-08-22

    The ability of prey to observe and learn to recognize potential predators from the behaviour of nearby individuals can dramatically increase survival and, not surprisingly, is widespread across animal taxa. A range of sensory modalities are available for this learning, with visual and chemical cues being well-established modes of transmission in aquatic systems. The use of other sensory cues in mediating social learning in fishes, including mechano-sensory cues, remains unexplored. Here, we examine the role of different sensory cues in social learning of predator recognition, using juvenile damselfish (Amphiprion percula). Specifically, we show that a predator-naive observer can socially learn to recognize a novel predator when paired with a predator-experienced conspecific in total darkness. Furthermore, this study demonstrates that when threatened, individuals release chemical cues (known as disturbance cues) into the water. These cues induce an anti-predator response in nearby individuals; however, they do not facilitate learnt recognition of the predator. As such, another sensory modality, probably mechano-sensory in origin, is responsible for information transfer in the dark. This study highlights the diversity of sensory cues used by coral reef fishes in a social learning context.

  9. Setting the most robust effluent level under severe uncertainty: application of information-gap decision theory to chemical management.

    Science.gov (United States)

    Yokomizo, Hiroyuki; Naito, Wataru; Tanaka, Yoshinari; Kamo, Masashi

    2013-11-01

    Decisions in ecological risk management for chemical substances must be made based on incomplete information due to uncertainties. To protect the ecosystems from the adverse effect of chemicals, a precautionary approach is often taken. The precautionary approach, which is based on conservative assumptions about the risks of chemical substances, can be applied selecting management models and data. This approach can lead to an adequate margin of safety for ecosystems by reducing exposure to harmful substances, either by reducing the use of target chemicals or putting in place strict water quality criteria. However, the reduction of chemical use or effluent concentrations typically entails a financial burden. The cost effectiveness of the precautionary approach may be small. Hence, we need to develop a formulaic methodology in chemical risk management that can sufficiently protect ecosystems in a cost-effective way, even when we do not have sufficient information for chemical management. Information-gap decision theory can provide the formulaic methodology. Information-gap decision theory determines which action is the most robust to uncertainty by guaranteeing an acceptable outcome under the largest degree of uncertainty without requiring information about the extent of parameter uncertainty at the outset. In this paper, we illustrate the application of information-gap decision theory to derive a framework for setting effluent limits of pollutants for point sources under uncertainty. Our application incorporates a cost for reduction in pollutant emission and a cost to wildlife species affected by the pollutant. Our framework enables us to settle upon actions to deal with severe uncertainty in ecological risk management of chemicals.

  10. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    CERN Document Server

    Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...

  11. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease

    Science.gov (United States)

    Beck, Michael W.; Derrick, Jeffrey S.; Kerr, Richard A.; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C.; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D.; Kim, Kwang S.; Lee, Joo-Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2016-10-01

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  12. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease.

    Science.gov (United States)

    Beck, Michael W; Derrick, Jeffrey S; Kerr, Richard A; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D; Kim, Kwang S; Lee, Joo-Yong; Ruotolo, Brandon T; Lim, Mi Hee

    2016-10-13

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  13. Mashed potatoes enriched with soy protein isolate and inulin: chemical, rheological and structural basis.

    Science.gov (United States)

    Alvarez, M D; Olivares, M D; Blanch, M; Canet, W

    2013-10-01

    Soy protein isolate is typical vegetable protein with health-enhancing activities. Inulin, a prebiotic no digestible carbohydrate, has functional properties. A mashed potato serving of 200 g with added soy protein isolate and/or inulin concentrations of 15-60 g/kg provides from 3 to 12 g of soy protein isolate and/or inulin, respectively. Currently, no information is available about the possible texture-modifying effect of this non-ionizable polar carbohydrate in different soy-based food systems. In this study, the effect of the addition of soy protein isolate and inulin blends at different soy protein isolate: inulin ratios on the degree of inulin polymerization and the rheological and structural properties of fresh mashed and frozen/thawed mashed potatoes were evaluated. The inulin chemical structure remained intact throughout the various treatments, and soy protein isolate did not affect inulin composition being a protein compatible with this fructan. Small-strain rheology showed that both ingredients behaved like soft fillers. In the frozen/thawed mashed potatoes samples, addition of 30 : 30 and 15 : 60 blend ratios significantly increased elasticity (G' value) compared with 0 : 0 control, consequently reducing the freeze/thaw stability conferred by the cryoprotectants. Inulin crystallites caused a significant strengthening effect on soy protein isolate gel. Micrographs revealed that soy protein isolate supports the inulin structure by building up a second fine-stranded network. Thereby, possibility of using soy protein isolate and inulin in combination with mashed potatoes to provide a highly nutritious and healthy product is promising.

  14. Improved Chemical Structure-Activity Modeling Through Data Augmentation.

    Science.gov (United States)

    Cortes-Ciriano, Isidro; Bender, Andreas

    2015-12-28

    Extending the original training data with simulated unobserved data points has proven powerful to increase both the generalization ability of predictive models and their robustness against changes in the structure of data (e.g., systematic drifts in the response variable) in diverse areas such as the analysis of spectroscopic data or the detection of conserved domains in protein sequences. In this contribution, we explore the effect of data augmentation in the predictive power of QSAR models, quantified by the RMSE values on the test set. We collected 8 diverse data sets from the literature and ChEMBL version 19 reporting compound activity as pIC50 values. The original training data were replicated (i.e., augmented) N times (N ∈ 0, 1, 2, 4, 6, 8, 10), and these replications were perturbed with Gaussian noise (μ = 0, σ = σnoise) on either (i) the pIC50 values, (ii) the compound descriptors, (iii) both the compound descriptors and the pIC50 values, or (iv) none of them. The effect of data augmentation was evaluated across three different algorithms (RF, GBM, and SVM radial) and two descriptor types (Morgan fingerprints and physicochemical-property-based descriptors). The influence of all factor levels was analyzed with a balanced fixed-effect full-factorial experiment. Overall, data augmentation constantly led to increased predictive power on the test set by 10-15%. Injecting noise on (i) compound descriptors or on (ii) both compound descriptors and pIC50 values led to the highest drop of RMSEtest values (from 0.67-0.72 to 0.60-0.63 pIC50 units). The maximum increase in predictive power provided by data augmentation is reached when the training data is replicated one time. Therefore, extending the original training data with one perturbed repetition thereof represents a reasonable trade-off between the increased performance of the models and the computational cost of data augmentation, namely increase of (i) model complexity due to the need for optimizing

  15. Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features.

    Science.gov (United States)

    Dai, Qi; Wu, Li; Li, Lihua

    2011-12-01

    Protein structural class prediction solely from protein sequences is a challenging problem in bioinformatics. Numerous efficient methods have been proposed for protein structural class prediction, but challenges remain. Using novel combined sequence information coupled with predicted secondary structural features (PSSF), we proposed a novel scheme to improve prediction of protein structural classes. Given an amino acid sequence, we first transformed it into a reduced amino acid sequence and calculated its word frequencies and word position features to combine novel sequence information. Then we added the PSSF to the combine sequence information to predict protein structural classes. The proposed method was tested on four benchmark datasets in low homology and achieved the overall prediction accuracies of 83.1%, 87.0%, 94.5%, and 85.2%, respectively. The comparison with existing methods demonstrates that the overall improvements range from 2.3% to 27.5%, which indicates that the proposed method is more efficient, especially for low-homology amino acid sequences.

  16. Competing Structure, Competing Views: The Role of Formal and Informal Social Structures in Shaping Stakeholder Perceptions

    Directory of Open Access Journals (Sweden)

    Christina Prell

    2010-12-01

    Full Text Available What is social structure, and how does it influence the views and behaviors of land managers? In this paper, we unpack the term "social structure" in the context of current research on institutions, social networks, and their role(s in resource management. We identify two different kinds of structure, formal and informal, and explore how these link to views of land management and management practice. Formal structures refer to intentionally designed organizations that arise out of larger institutional arrangements; informal ones refer to social networks, based on the communication contacts individuals possess. Our findings show significant correlations between respondents' views regarding land management and their social networks; it is these informal structures that have greater influence on what stakeholders perceive. These findings suggest that stakeholders are less influenced by their particular organizational affiliation or category (e.g., "conservationist" versus "farmer", and more by whom they speak with on a regular basis regarding land management. We conclude with a discussion on the practical implications for resource managers wishing to "design" participatory management, arguing that, if "diversity" is the goal in designing such participatory processes, then diversity needs to translate beyond stakeholder categories to include consideration for the personal, social networks surrounding stakeholders.

  17. Translation of dicarboxylate structural information to fluorometric optical signals through self-assembly of guanidinium-tethered oligophenylenevinylene.

    Science.gov (United States)

    Noguchi, Takao; Roy, Bappaditya; Yoshihara, Daisuke; Tsuchiya, Youichi; Yamamoto, Tatsuhiro; Shinkai, Seiji

    2014-10-20

    Although self-assembly has realized the spontaneous formation of nanoarchitectures, the nanoscopic expression of chemical structural information at the molecular level can alternatively be regarded as a tool to translate molecular structural information with high precision. We have found that a newly developed guanidinium-tethered oligophenylenevinylene exhibits characteristic fluorescence (FL) responses toward L- and meso-tartarate, wherein the different self-assembly modes, termed J- or H-type aggregation, are directed according to the molecular information encoded as the chemical structure. This morphological difference originates from the geometric anti versus gauche conformational difference between L- and meso-tartarate. A similar morphological difference can be reproduced with the geometric C=C bond difference between fumarate and maleate. In the present system, the dicarboxylate structural information is embodied in the inherent threshold concentration of the FL response, the signal-to-noise ratio, and the maximum FL wavelength. These results indicate that self-assembly is meticulous enough to sense subtle differences in molecular information and thus demonstrate the potential ability of self-assembly for the expression of a FL sensory system.

  18. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...

  19. Influence of the chemical structure of functional monomers on their adhesive performance.

    Science.gov (United States)

    Van Landuyt, K L; Yoshida, Y; Hirata, I; Snauwaert, J; De Munck, J; Okazaki, M; Suzuki, K; Lambrechts, P; Van Meerbeek, B

    2008-08-01

    Functional monomers in adhesive systems can improve bonding by enhancing wetting and demineralization, and by chemical bonding to calcium. This study tested the hypothesis that small changes in the chemical structure of functional monomers may improve their bonding effectiveness. Three experimental phosphonate monomers (HAEPA, EAEPA, and MAEPA), with slightly different chemical structures, and 10-MDP (control) were evaluated. Adhesive performance was determined in terms of microtensile bond strength of 4 cements that differed only for the functional monomer. Based on the Adhesion-Decalcification concept, the chemical bonding potential was assessed by atomic absorption spectrophotometry of the dissolution rate of the calcium salt of the functional monomers. High bond strength of the adhesive cement corresponded to low dissolution rate of the calcium salt of the respective functional monomer. The latter is according to the Adhesion-Decalcification concept, suggestive of a high chemical bonding capacity. We conclude that the adhesive performance of an adhesive material depends on the chemical structure of the functional monomer.

  20. Displaying the information contents of structural RNA alignments: the structure logos

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Heyer, L.J.; Brunak, Søren

    1997-01-01

    We extend the standard `Sequence Logo' method of Schneider and Stevens to incorporate prior frequencies on the bases, allow for gaps in the alignments, and indicate the mutual information of base-paired regions in RNA. Given an alignment of RNA sequences with the base pairings indicated, the prog......We extend the standard `Sequence Logo' method of Schneider and Stevens to incorporate prior frequencies on the bases, allow for gaps in the alignments, and indicate the mutual information of base-paired regions in RNA. Given an alignment of RNA sequences with the base pairings indicated......, the program will calculate the information at each position, including the mutual information of the base pairs, and display the results in a `Structure Logo'. Alignments without base pairing can also be displayed in a `Sequence Logo', but still allowing gaps and incorporating prior frequencies if desired...

  1. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics

    NARCIS (Netherlands)

    Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert; Dekker, Frans

    2005-01-01

    Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain architec

  2. Quantum information analysis of electronic states at different molecular structures

    CERN Document Server

    Barcza, G; Marti, K H; Reiher, M

    2010-01-01

    We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization. We also discuss the application of the configuration interaction based dynamically extended active space procedure which significantly reduces the effective system size and accelerates the speed of convergence for complicated molecular electronic structures to a great extent. Our results indicate the importance of taking entanglement among molecular orbitals into account in order to devise an optimal orbital ordering and carry out efficient calculations on transition metal clusters. We propose a recipe to perform DMRG calculations in a black-box fashion and we point out the connections of our work to other tensor network state approaches.

  3. Surface Nano Structures Manufacture Using Batch Chemical Processing Methods for Tooling Applications

    DEFF Research Database (Denmark)

    Tosello, Guido; Calaon, Matteo; Gavillet, J.

    2011-01-01

    The patterning of large surface areas with nano structures by using chemical batch processes to avoid using highenergy intensive nano machining processes was investigated. The capability of different surface treatment methods of creating micro and nano structured adaptable mould inserts...... for subsequent polymer replication by injection moulding was analyzed. New tooling solutions to produce nano structured mould surfaces were investigated. Experiments based on three different chemical-based-batch techniques to establish surface nano (i.e. sub-μm) structures on large areas were performed. Three...... approaches were selected: (1) using Ø500 nm nano beads deposition for direct patterning of a 4” silicon wafer; (2) using Ø500 nm nano beads deposition as mask for 4” silicon wafer etching and subsequent nickel electroplating; (3) using the anodizing process to produce Ø500 nm structures on a 30x80 mm2...

  4. Information structures in economics studies in the theory of markets with imperfect information

    CERN Document Server

    Nermuth, Manfred

    1982-01-01

    This book is intended as a contribution to the theory of markets with imperfect information. The subject being nearly limitless, only certain selected topics are discussed. These are outlined in the Introduction (Ch. 0). The remainder of the book is divided into three parts. All results of economic significance are contained in Parts II & III. Part I introduces the main tools for the analysis, in particular the concept of an information structure. Although most of the material presented in Part I is not original, it is hoped that the detailed and self-contained exposition will help the reader to understand not only the following pages, but also the existing technical and variegated literature on markets with imperfect information. The mathematical prerequisites needed, but not explained in the text rarely go beyond elementary calculus and probability theory. Whenever more advanced concepts are used, I have made an effort to give an intuitive explanation as well, so that the argument can also be followed o...

  5. Structure and mechanical properties of pyrolytic carbon produced by fluidized bed chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Honorato, E.; Meadows, P.J. [Manchester Materials Science Centre, School of Materials, University of Manchester, Grosvenor Street, Manchester M1 7HS (United Kingdom); Xiao, P. [Manchester Materials Science Centre, School of Materials, University of Manchester, Grosvenor Street, Manchester M1 7HS (United Kingdom)], E-mail: Ping.Xiao@manchester.ac.uk; Marsh, G.; Abram, T.J. [Nexia Solutions Ltd., Springfields PR4 0XJ (United Kingdom)

    2008-11-15

    Pyrolytic carbon was deposited on spherical particles using a multi-spout fluidized bed chemical vapor deposition reactor to fabricate TRISO fuel for the High Temperature Reactor (HTR). Modern techniques such as Raman spectroscopy and nanoindentation supported by porosimetry, scanning electron microscopy and transmission electron microscopy were employed to analyze the particle coatings directly. Raman spectroscopy and nanoindentation were given special attention due to their capacity to provide information on the internal structure of pyrolytic carbon and its mechanical properties without the necessity of complex sample preparation. The results obtained were used to study the relationship deposition conditions-microstructure-mechanical properties in more detail. Increasing the deposition temperature reduced the density and Young's modulus as porosity and in-plane disorder of carbon domains increased. There was also a change from a laminar microstructure of PyC to that containing more spherical particles. It appeared that anisotropy, domain size and level of graphitization (examined by Raman and TEM) had a strong influence on the mechanical properties. Clear differences were observed between acetylene and the acetylene/propylene mixture as precursor gases.

  6. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  7. A novel predictor for protein structural class based on integrated information of the secondary structure sequence.

    Science.gov (United States)

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang; Liu, Shuxia

    2014-08-01

    The structural class has become one of the most important features for characterizing the overall folding type of a protein and played important roles in many aspects of protein research. At present, it is still a challenging problem to accurately predict protein structural class for low-similarity sequences. In this study, an 18-dimensional integrated feature vector is proposed by fusing the information about content and position of the predicted secondary structure elements. The consistently high accuracies of jackknife and 10-fold cross-validation tests on different low-similarity benchmark datasets show that the proposed method is reliable and stable. Comparison of our results with other methods demonstrates that our method is an effective computational tool for protein structural class prediction, especially for low-similarity sequences.

  8. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    Science.gov (United States)

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

  9. Personalized Information Access in a Wiki Using Structured Tagging

    NARCIS (Netherlands)

    Singh, A. V.; Wombacher, A.; Aberer, K.

    2007-01-01

    Environmental engineers from different organizations work in interdisciplinary projects having the need of information exchange. In particular, a collaborative environment with personalized access to information is needed, which supports strongly varying information needs of the users. This scenario

  10. Chemical input and I-V output: stepwise chemical information processing in dye-sensitized solar cells.

    Science.gov (United States)

    Satoh, Norifusa; Han, Liyuan

    2012-12-14

    As a complex system, a dye-sensitized solar cell (DSC) exhibits emergent photovoltaics not obvious from the properties of the individual components. The chemical input of 4-tert-butylpyridine (TBP) into DSC improves the open circuit voltage (V(oc)) and reduces the short circuit current (I(sc)) in I-V output through multiple interactions with the components, yet it has been difficult to distinguish the multiple interactions and correlate the interactions with the influences on I-V output due to the complexity of the system. To deal with the multiple interactions, we have adapted a conceptual framework and methodology from coordination chemistry. First, we titrated the photovoltaic interface and electrolyte with TBP to identify the stepwise chemical interaction processes. An isopotential point observed in I-V output indicates that most of the inputted chemicals interact with the electrolyte. Cyclic voltammetric titration of the electrolyte demonstrates asymmetric redox peaks and two different isopotential points, indicating that the two-step coordination-decoordination process inhibits the reduction current of the electrolyte. Second, we set an interaction model bridging the hierarchical gaps between the multiple interactions and the I-V output to address the influences on outputs from the amount of the inputs. From the viewpoint of the interaction model and interactions observed, we are able to comprehend the processes of the complex system and suggest a direction to improve V(oc) without sacrificing I(sc) in DSCs. We conclude that the conceptual framework and methodology adapted from coordination chemistry is beneficial to enhance the emergent outputs of complex systems.

  11. SARANEA: a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets.

    Science.gov (United States)

    Lounkine, Eugen; Wawer, Mathias; Wassermann, Anne Mai; Bajorath, Jürgen

    2010-01-01

    We introduce SARANEA, an open-source Java application for interactive exploration of structure-activity relationship (SAR) and structure-selectivity relationship (SSR) information in compound sets of any source. SARANEA integrates various SAR and SSR analysis functions and utilizes a network-like similarity graph data structure for visualization. The program enables the systematic detection of activity and selectivity cliffs and corresponding key compounds across multiple targets. Advanced SAR analysis functions implemented in SARANEA include, among others, layered chemical neighborhood graphs, cliff indices, selectivity trees, editing functions for molecular networks and pathways, bioactivity summaries of key compounds, and markers for bioactive compounds having potential side effects. We report the application of SARANEA to identify SAR and SSR determinants in different sets of serine protease inhibitors. It is found that key compounds can influence SARs and SSRs in rather different ways. Such compounds and their SAR/SSR characteristics can be systematically identified and explored using SARANEA. The program and source code are made freely available under the GNU General Public License.

  12. Influence of Chemical Conditions on the Nanoporous Structure of Silicate Aerogels

    Directory of Open Access Journals (Sweden)

    Katalin Sinkó

    2010-01-01

    Full Text Available Silica or various silicate aerogels can be characterized by highly porous, open cell, low density structures. The synthesis parameters influence the three-dimensional porous structures by modifying the kinetics and mechanism of hydrolysis and condensation processes. Numerous investigations have shown that the structure of porous materials can be tailored by variations in synthesis conditions (e.g., the type of precursors, catalyst, and surfactants; the ratio of water/precursor; the concentrations; the medium pH; and the solvent. The objectives of this review are to summarize and elucidate the effects of chemical conditions on the nanoporous structure of sol-gel derived silicate aerogels.

  13. Chemical structure and physical properties of radiation-induced crosslinking of polytetrafluoroethylene

    Energy Technology Data Exchange (ETDEWEB)

    Oshima, Akihiro E-mail: aks@taka.jaeri.go.jp; Ikeda, Shigetoshi; Katoh, Etsuko; Tabata, Yoneho

    2001-07-01

    The chemical structure and physical properties of polytetrafluoroethylene (PTFE) that has been crosslinked by radiation have been studied by various methods. It has been found that a Y-type crosslinking structure and a Y-type structure incorporating a double bond (modified Y-type) is formed in PTFE by radiation-crosslinking in the molten state. In addition, various types of double bond structures, excluding the crosslinking site, have been identified. The crosslinked PTFE has a good light transparency due to the loss of crystallites, whilst it retains the excellent properties of electrical insulation and heat resistance. The coefficient of abrasion and the permanent creep are also greatly improved by crosslinking.

  14. Chemical and structural analysis of the bone-implant interface by TOF-SIMS, SEM, FIB and TEM: Experimental study in animal

    Science.gov (United States)

    Palmquist, Anders; Emanuelsson, Lena; Sjövall, Peter

    2012-06-01

    Although bone-anchored implants are widely used in reconstructive medicine, the mechanism of osseointegration is still not fully understood. Novel analytical tools are needed to further understand this process, where both the chemical and structural aspects of the bone-implant interface are important. The aim of this study was to evaluate the advantages of combining time-of-flight secondary ion mass spectroscopy (TOF-SIMS) with optical (LM), scanning (SEM) and transmission electron microscopy (TEM) techniques for studying the bone-implant interface of bone-anchored implants. Laser-modified titanium implants with surrounded bone retrieved after 8 weeks healing in rabbit were dehydrated and resin embedded. Three types of sample preparation were studied to evaluate the information gained by combining TOF-SIMS, SEM, FIB and TEM. The results show that imaging TOF-SIMS can provide detailed chemical information, which in combination with structural information from microscopy methods provide a more complete characterization of anatomical structures at the bone-implant interface. By investigating various sample preparation techniques, it is shown that grinded cross section samples can be used for chemical imaging using TOF-SIMS, if careful consideration of potential preparation artifacts is taken into account. TOF-SIMS analysis of FIB-prepared bone/implant cross section samples show distinct areas corresponding to bone tissue and implant with a sharp interface, although without chemical information about the organic components.

  15. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    Science.gov (United States)

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  16. SVM-based method for protein structural class prediction using secondary structural content and structural information of amino acids.

    Science.gov (United States)

    Mohammad, Tabrez Anwar Shamim; Nagarajaram, Hampapathalu Adimurthy

    2011-08-01

    The knowledge collated from the known protein structures has revealed that the proteins are usually folded into the four structural classes: all-α, all-β, α/β and α + β. A number of methods have been proposed to predict the protein's structural class from its primary structure; however, it has been observed that these methods fail or perform poorly in the cases of distantly related sequences. In this paper, we propose a new method for protein structural class prediction using low homology (twilight-zone) protein sequences dataset. Since protein structural class prediction is a typical classification problem, we have developed a Support Vector Machine (SVM)-based method for protein structural class prediction that uses features derived from the predicted secondary structure and predicted burial information of amino acid residues. The examination of different individual as well as feature combinations revealed that the combination of secondary structural content, secondary structural and solvent accessibility state frequencies of amino acids gave rise to the best leave-one-out cross-validation accuracy of ~81% which is comparable to the best accuracy reported in the literature so far.

  17. Evaluation of chemical and structural properties of germanium-carbon coatings deposited by plasma enhanced chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Jamali, Hossein, E-mail: h.jamali@mut-es.ac.ir; Mozafarinia, Reza; Eshaghi, Akbar

    2015-10-15

    Germanium-carbon coatings were deposited on silicon and glass substrates by plasma enhanced chemical vapor deposition (PECVD) using three different flow ratios of GeH{sub 4} and CH{sub 4} precursors. Elemental analysis, structural evaluation and microscopic investigation of coatings were performed using laser-induced breakdown spectroscopy (LIBS), Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), Raman spectroscopy, field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM), respectively. Based on the results, the coatings exhibited a homogeneous and dense structure free of pores with a very good adhesion to substrate. The structural evaluation revealed that the germanium-carbon coatings were a kind of a Ge-rich composite material containing the amorphous and crystalline germanium and amorphous carbon with the mixture of Ge–Ge, Ge–C, C–C, Ge–H and C–H bonds. The result suggested that the amorphisation of the coatings could be increased with raising CH{sub 4}:GeH{sub 4} flow rate ratio and subsequently increasing C amount incorporated into the coating. - Highlights: • Germanium-carbon coatings were prepared by PECVD technique. • The germanium-carbon coatings were a kind of composite material. • The amorphisation of the coatings were increased with raising CH{sub 4}:GeH{sub 4} flow ratio.

  18. [Systematization of data and information on delayed consequences of the effects of chemicals in humans].

    Science.gov (United States)

    Ianno, L V; Pimenova, M N; Osipova, I V

    1993-01-01

    The systematization and analysis of the data connected with delayed consequences arising in human body from exposure to dangerous chemicals have been carried out. The paper contains the list of dangerous chemicals exerting mutagenic or carcinogenic effects and chromosome aberrations. The cytologic express method of revealing mucous membrane dysplasia resulting from exposure to some chemical mutagens have been evaluated.

  19. PPM-One: a static protein structure based chemical shift predictor

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)

    2015-07-15

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.

  20. An Improved Protein Structural Prediction Method by Incorporating Both Sequence and Structure Information.

    Science.gov (United States)

    Wei, Leyi; Liao, Minghong; Gao, Xing; Zou, Quan

    2014-09-15

    Protein structural classes information is beneficial for secondary and tertiary structure prediction, protein folds prediction, and protein function analysis. Thus, predicting protein structural classes is of vital importance. In recent years, several computational methods have been developed for low-sequence-similarity (25% - 40%) protein structural classes prediction. However, the reported prediction accuracies are actually not satisfactory. Aiming to further improve the prediction accuracies, we propose three different feature extraction methods and construct a comprehensive feature set that captures both sequence and structure information. By applying a random forest (RF) classifier to the feature set, we further develop a novel method for structural classes prediction. We test the proposed method on three benchmark datasets (25PDB, 640, and 1189) with low sequence similarity, and obtain the overall prediction accuracies of 93.5%, 92.6%, and 93.4%, respectively. Compared with six competing methods, the accuracies we achieved are 3.4%, 6.2%, and 8.7% higher than that achieved by the best-performing methods, showing the superiority of our method. Moreover, due to the limitation of the size of the three benchmark datasets, we further test the proposed method on three updated large-scale datasets with different sequence similarity (40%, 30%, and 25%). The proposed method achieves above 90% accuracies for all the three datasets, consistency with the accuracies on the above three benchmark datasets. Experimental results suggest our method as an effective and promising tool for structural classes prediction. Currently, a webserver that implements the proposed method is available on http://121.192.180.204:8080/RF_PSCP/Index.html.

  1. Syntax Encodes Information Structure: Evidence from On-Line Reading Comprehension

    Science.gov (United States)

    Brown, Meredith; Savova, Virginia; Gibson, Edward

    2012-01-01

    Although sentences are thought to be generally easier to process when given information precedes new information, closer examination reveals that these preferences only manifest within some syntactic structures. Here, we examine the consequences of the relative ordering of given and new information ("information structure") for the on-line…

  2. EFFECT OF CHEMICAL STRUCTURE OF COMONOMERS ON THE PROPERTIES OF COPOLYESTERS

    Institute of Scientific and Technical Information of China (English)

    WU Rongrui; GAO Jing; LI Huiping

    1997-01-01

    The effect of different kinds of comonomers with or without flexible chain on properties of copolyesters, such as transition temperature, crystallization velocity, crystallinity and size of crystallites, is studied. The experimental results indicate the obvious difference in properties between comonomers with iso- and ortho-structure of phenyl ring and comonomers with flexible chain. The influence of chemical structure of comonomers on properties of copolyesters is discussed.

  3. Ascaroside activity in Caenorhabditis elegans is highly dependent on chemical structure

    OpenAIRE

    Hollister, Kyle A.; Conner, Elizabeth S.; Zhang, Xinxing; Spell, Mark; Bernard, Gary M.; Patel, Pratik; de Carvalho, Ana Carolina G.V.; Butcher, Rebecca A.; Ragains, Justin R.

    2013-01-01

    The nematode Caenorhabditis elegans secretes ascarosides, structurally diverse derivatives of the 3,6-dideoxysugar ascarylose, and uses them in chemical communication. At high population densities, specific ascarosides, which are together known as the dauer pheromone, trigger entry into the stress-resistant dauer larval stage. In order to study the structure-activity relationships for the ascarosides, we synthesized a panel of ascarosides and tested them for dauer-inducing activity. This pane...

  4. Clustering and rule-based classifications of chemical structures evaluated in the biological activity space.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Brown, Nathan; Ertl, Peter; Jenkins, Jeremy L; Selzer, Paul; Hamon, Jacques

    2007-01-01

    Classification methods for data sets of molecules according to their chemical structure were evaluated for their biological relevance, including rule-based, scaffold-oriented classification methods and clustering based on molecular descriptors. Three data sets resulting from uniformly determined in vitro biological profiling experiments were classified according to their chemical structures, and the results were compared in a Pareto analysis with the number of classes and their average spread in the profile space as two concurrent objectives which were to be minimized. It has been found that no classification method is overall superior to all other studied methods, but there is a general trend that rule-based, scaffold-oriented methods are the better choice if classes with homogeneous biological activity are required, but a large number of clusters can be tolerated. On the other hand, clustering based on chemical fingerprints is superior if fewer and larger classes are required, and some loss of homogeneity in biological activity can be accepted.

  5. The role of governance structures in supply chain information sharing

    NARCIS (Netherlands)

    Denolf, J.M.; Trienekens, J.H.; Vorst, Van Der J.G.A.J.; Omta, S.W.F.

    2015-01-01

    Information sharing in supply chains may result in concerns related to information security, information access privileges, and allocation of claimed benefits. To mitigate such concerns in order to efficiently and effectively share information, relationships among the supply chain actors need to

  6. Discourse-level structuring of information in narrative:Signalling structural, interactional and cognitive shifts

    Directory of Open Access Journals (Sweden)

    Tuija Virtanen

    2011-07-01

    Full Text Available Discourse-level structuring of information is explored in narrative in the light of three parameters subsumed under this umbrella notion: (i the structural concepts of “theme-rheme”, connected to “position”; (ii the interaction-oriented pair of concepts “topic-comment”, grounded in the notion of “aboutness”; and (iii the cognitively motivated gradient from “given” to “new” information, related to interlocutors’ assumptions of their memory constraints as well as those of others. In each pair/gradient of concepts one member/pole – “theme”, “comment”, and “new” – is argued to constitute the Figure, against the (necessary Ground of the other. The linguistic signalling of the structural, interactional and cognitive shifts in information structuring is examined in two different kinds of narratives in written French. The analysis of a short legend, in its entirety, and a narrative paragraph from a news story both point to high context-sensitivity in the signalling of the three parameters of discourse-level structuring of information, with that of the discourse level “newness” differing most markedly from the others.Cet article étudie la structure informationnelle dans des textes narratifs en observant trois distinctions linguistiques que recouvre cette structure : (i au niveau textuel, le couple « thème-rhème » défini par une distinction positionnelle ; (ii au niveau interactionnel, l’opposition « topique-commentaire » reposant sur la notion d’« à propos » ; et (iii la distinction cognitive entre information donnée et information nouvelle, mettant en jeu les présomptions des interlocuteurs sur les contraintes mémorielles de l’autre. Dans chacune de ces oppositions binaires ou graduelles, l’un des concepts joue le rôle de Figure (le « thème », le « commentaire » et l’information nouvelle par rapport à un Fond, joué par l’autre concept (le « rhème », le

  7. Structural analysis of some marine kerogens through a combined chemical and thermal degradation approach

    NARCIS (Netherlands)

    Höld, I.M.

    2000-01-01

    Approximately 95% of the sedimentary organic matter in the geosphere exists in the form of kerogen, a macromolecular substance that is insoluble in water and normal organic solvents. There have been numerous attempts to elucidate the chemical structure of kerogens since kerogen is the main precursor

  8. Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  9. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

    Science.gov (United States)

    Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H.

    2004-01-01

    A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs. PMID:15123812

  10. Structures and Chemical Equilibria of Some N-Heterocycles Containing Amide Linkages

    Directory of Open Access Journals (Sweden)

    N. H. Abd El Moneim

    2003-05-01

    Full Text Available Structures and chemical equilibria of 5-carboxy-2-thiouracil (1, 5,6-diphenyl-3-hydroxy-1,2,4-triazine (2, 1-phenyl-3-methyl-5-pyrazolone (3 and 2-mercapto-4,6-dimethylpyrimidine hydrochloride (4 are reported. Their electronic transitions are assigned and pK values are evaluated and discussed.

  11. Chemical signals turn on guest binding through structural reconfiguration of triangular helicates

    DEFF Research Database (Denmark)

    Sørensen, Anne; Castilla, Ana M.; Ronson, Tanya K.;

    2013-01-01

    Be my guest: The function of a system based on self-assembled Zn(II) complexes can be controlled by external chemical stimuli. The complexes are based on a C3 -symmetric ligand that forms a unique triangular triple helicate structure 1. Upon subcomponent substitution, 1 is able to transform...

  12. Using Concept Mapping to Uncover Students' Knowledge Structures of Chemical Bonding Concepts

    Science.gov (United States)

    Burrows, Nikita L.; Mooring, Suazette Reid

    2015-01-01

    General chemistry is the first undergraduate course in which students further develop their understanding of fundamental chemical concepts. Many of these fundamental topics highlight the numerous conceptual interconnections present in chemistry. However, many students possess incoherent knowledge structures regarding these topics. Therefore,…

  13. Test results of chemical reactivity test (CRT) analysis of structural materials and explosives

    Energy Technology Data Exchange (ETDEWEB)

    Back, P.S.; Barnhart, B.V.; Walters, R.R.; Haws, L.D.; Collins, L.W.

    1980-03-21

    The chemical reactivity test, CRT, is a procedure used to screen the compatibility of component structure materials with explosives. This report contains the results of CRT materials evaluations conducted at Mound Facility. Data about materials combinations are catalogued both under the name of the explosive and the nonexplosive.

  14. Nanostructured PLD-grown gadolinia doped ceria: Chemical and structural characterization by transmission electron microscopy techniques

    DEFF Research Database (Denmark)

    Rodrigo, Katarzyna Agnieszka; Wang, Hsiang-Jen; Heiroth, Sebastian;

    2011-01-01

    The morphology as well as the spatially resolved elemental and chemical characterization of 10 mol% gadolinia doped ceria (CGO10) structures prepared by pulsed laser deposition (PLD) technique are investigated by scanning transmission electron microscopy accompanied with electron energy loss spec...

  15. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

  16. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics.

    Science.gov (United States)

    Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert

    2005-06-01

    Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain architecture and natural product inspired compound library design. Domains and proteins identified as being structurally similar in their ligand-sensing cores are grouped in a protein structure similarity cluster (PSSC). Natural products can be considered as evolutionary pre-validated ligands for multiple proteins and therefore natural products that are known to interact with one of the PSSC member proteins are selected as guiding structures for compound library synthesis. Application of this novel strategy for compound library design provided enhanced hit rates in small compound libraries for structurally similar proteins.

  17. The Informational Text Structure Survey (ITS[superscript 2]): An Exploration of Primary Grade Teachers' Sensitivity to Text Structure in Young Children's Informational Texts

    Science.gov (United States)

    Reutzel, D. Ray; Jones, Cindy D.; Clark, Sarah K.; Kumar, Tamara

    2016-01-01

    There has been no research reported about if or how well primary grade teachers can identify information text structures in children's authentic informational texts. The ability to do so accurately and reliably is a prerequisite for teachers to be able to teach students how to recognize and use text structures to assist them in comprehending…

  18. Generalized molybdenum oxide surface chemical state XPS determination via informed amorphous sample model

    Energy Technology Data Exchange (ETDEWEB)

    Baltrusaitis, Jonas, E-mail: job314@lehigh.edu [Department of Chemical Engineering, Lehigh University, B336 Iacocca Hall, 111 Research Drive, Bethlehem, PA 18015 (United States); PhotoCatalytic Synthesis group, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, Meander 229, P.O. Box 217, 7500 AE Enschede (Netherlands); Mendoza-Sanchez, Beatriz [CRANN, Chemistry School, Trinity College Dublin, Dublin (Ireland); Fernandez, Vincent [Institut des Matériaux Jean Rouxel, 2 rue de la Houssinière, BP 32229, F-44322 Nantes Cedex 3 (France); Veenstra, Rick [PhotoCatalytic Synthesis group, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, Meander 229, P.O. Box 217, 7500 AE Enschede (Netherlands); Dukstiene, Nijole [Department of Physical and Inorganic Chemistry, Kaunas University of Technology, Radvilenu pl. 19, LT-50254 Kaunas (Lithuania); Roberts, Adam [Kratos Analytical Ltd, Trafford Wharf Road, Wharfside, Manchester, M17 1GP (United Kingdom); Fairley, Neal [Casa Software Ltd, Bay House, 5 Grosvenor Terrace, Teignmouth, Devon TQ14 8NE (United Kingdom)

    2015-01-30

    Highlights: • We analyzed and modeled spectral envelopes of complex molybdenum oxides. • Molybdenum oxide films of varying valence and crystallinity were synthesized. • MoO{sub 3} and MoO{sub 2} line shapes from experimental data were created. • Informed amorphous sample model (IASM) developed. • Amorphous molybdenum oxide XPS envelopes were interpreted. - Abstract: Accurate elemental oxidation state determination for the outer surface of a complex material is of crucial importance in many science and engineering disciplines, including chemistry, fundamental and applied surface science, catalysis, semiconductors and many others. X-ray photoelectron spectroscopy (XPS) is the primary tool used for this purpose. The spectral data obtained, however, is often very complex and can be subject to incorrect interpretation. Unlike traditional XPS spectra fitting procedures using purely synthetic spectral components, here we develop and present an XPS data processing method based on vector analysis that allows creating XPS spectral components by incorporating key information, obtained experimentally. XPS spectral data, obtained from series of molybdenum oxide samples with varying oxidation states and degree of crystallinity, were processed using this method and the corresponding oxidation states present, as well as their relative distribution was elucidated. It was shown that monitoring the evolution of the chemistry and crystal structure of a molybdenum oxide sample due to an invasive X-ray probe could be used to infer solutions to complex spectral envelopes.

  19. A script for automated 3-dimentional structure generation and conformer search from 2- dimentional chemical drawing.

    Science.gov (United States)

    Ishikawa, Yoshinobu

    2013-01-01

    Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists.

  20. Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.

    Science.gov (United States)

    Bloudoff, Kristjan; Alonzo, Diego A; Schmeing, T Martin

    2016-03-17

    Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation.

  1. Chemical structure and pharmacokinetics of novel quinolone agents represented by avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and nemonoxacin.

    Science.gov (United States)

    Kocsis, Bela; Domokos, J; Szabo, D

    2016-05-23

    Quinolones are potent antimicrobial agents with a basic chemical structure of bicyclic ring. Fluorine atom at position C-6 and various substitutions on the basic quinolone structure yielded fluoroquinolones, namely norfloxacin, ciprofloxacin, levofloxacin, moxifloxacin and numerous other agents. The target molecules of quinolones and fluoroquinolones are bacterial gyrase and topoisomerase IV enzymes. Broad-spectrum and excellent tissue penetration make fluoroquinolones potent agents but their toxic side effects and increasing number of resistant pathogens set limits on their use. This review focuses on recent advances concerning quinolones and fluoroquinolones, we will be summarising chemical structure, mode of action, pharmacokinetic properties and toxicity. We will be describing fluoroquinolones introduced in clinical trials, namely avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and non-fluorinated nemonoxacin. These agents have been proved to have enhanced antibacterial effect even against ciprofloxacin resistant pathogens, and found to be well tolerated in both oral and parenteral administrations. These features are going to make them potential antimicrobial agents in the future.

  2. The chemical and magnetic structures of holmium-yttrium and holmium-lutetium superlattices

    DEFF Research Database (Denmark)

    McMorrow, D.F.; Jehan, D.A.; Swaddling, P.P.;

    1993-01-01

    We present the results of a study of the chemical and magnetic structures of Ho/Y and Ho/Lu superlattices, all grown by molecular beam epitaxy. By combining the results of high-resolution X-ray diffraction with detailed modelling we show that the superlattices have high crystallographic integrity......: the average structural coherence length in the growth direction is approximately 2000 angstrom, while the interfaces between the two elements are well defined, extending over approximately four lattice planes. The magnetic structures were determined using neutron scattering techniques. In the case of the Ho...

  3. Molecular design chemical structure generation from the properties of pure organic compounds

    CERN Document Server

    Horvath, AL

    1992-01-01

    This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

  4. Chemical and structural characterisation of DGEBA-based epoxies by time of flight secondary ion mass spectrometry (ToF-SIMS) as a preliminary to polymer interphase characterisation.

    Science.gov (United States)

    Passlack, Sven; Brodyanski, Alexander; Bock, Wolfgang; Kopnarski, Michael; Presser, Melanie; Geiss, Paul Ludwig; Possart, Gunnar; Steinmann, Paul

    2009-04-01

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has become a powerful tool in the field of surface analysis since it provides information about the top few monolayers of a sample, i.e. on the chemical composition of the sample surface. Thus, the general question arises whether a surface-sensitive technique like ToF-SIMS would be appropriate to detect systematic chemical and/or structural changes in organic bulk polymers caused by varying a chemical content of the initial components or by tracking, e.g. curing processes in such materials. It is shown that careful sample preparation and the use of multivariate methods permit the quantitative acquisition of chemical and structural information about bulk polymers from the secondary ion signals. The hardener concentration and a cross-linking coefficient in diglycidyl ether of bisphenol A based epoxies were determined by ToF-SIMS measurements on samples with different resin to hardener ratio and varying curing time. In future work, we will use the developed method to investigate the local composition of adhesively bonded joints. In particular, the mapping of the chemical and structural properties in the so-called interphase will then be of interest.

  5. The effect of chemical information on the spatial distribution of fruit flies: II parameterization, calibration, and sensitivity

    NARCIS (Netherlands)

    Gee, de M.; Lof, M.E.; Hemerik, L.

    2008-01-01

    In a companion paper (Lof et al., in Bull. Math. Biol., 2008), we describe a spatio-temporal model for insect behavior. This model includes chemical information for finding resources and conspecifics. As a model species, we used Drosophila melanogaster, because its behavior is documented comparative

  6. Information structure design for databases a practical guide to data modelling

    CERN Document Server

    Mortimer, Andrew J

    2014-01-01

    Computer Weekly Professional Series: Information Structure Design for Databases: A Practical Guide to Data modeling focuses on practical data modeling covering business and information systems. The publication first offers information on data and information, business analysis, and entity relationship model basics. Discussions cover degree of relationship symbols, relationship rules, membership markers, types of information systems, data driven systems, cost and value of information, importance of data modeling, and quality of information. The book then takes a look at entity relationship mode

  7. Chemical structures of constituents from the whole plant of Bacopa monniera.

    Science.gov (United States)

    Ohta, Tomoe; Nakamura, Seikou; Nakashima, Souichi; Oda, Yoshimi; Matsumoto, Takahiro; Fukaya, Masashi; Yano, Mamiko; Yoshikawa, Masayuki; Matsuda, Hisashi

    2016-07-01

    Two new dammarane-type triterpene oligoglycosides, bacomosaponins A and B, and three new phenylethanoid glycosides, bacomosides A, B1, and B2, were isolated from the whole plant of Bacopa monniera Wettst. The chemical structures of the new constituents were characterized on the basis of chemical and physicochemical evidence. In the present study, bacomosaponins A and B with acyl groups were obtained from the whole plant of B. monniera. This is the first report of acylated dammarane-type triterpene oligoglycosides isolated from B. monniera. In addition, dammarane-type triterpene saponins significantly inhibited the aggregation of 42-mer amyloid β-protein.

  8. In situ chemical and structural investigations of the oxidation of Ge(001) substrates by atomic oxygen

    Science.gov (United States)

    Molle, Alessandro; Bhuiyan, Md. Nurul Kabir; Tallarida, Grazia; Fanciulli, Marco

    2006-08-01

    The exposure of Ge(001) substrates to atomic oxygen was studied in situ to establish the stability of the germanium oxide. After preparing chemically clean and atomically flat Ge(001) surfaces, the Ge samples were exposed to atomic oxygen in a wide temperature range from room temperature to 400°C. The chemical composition of the so-formed oxides was studied by means of x-ray photoelectron spectroscopy, while the structure was observed by reflection high energy electron diffraction. At low substrate temperatures the atomic oxygen is efficiently chemisorbed and suboxides coexist with the dioxide, which in turn is remarkably promoted in the high temperature range.

  9. Chemical structure of vanadium-based contact formation on n-AlN

    Energy Technology Data Exchange (ETDEWEB)

    Pookpanratana, S.; France, R.; Blum, M.; Bell, A.; Bar, M.; Weinhardt, L.; Zhang, Y.; Hofmann, T.; Fuchs, O.; Yang, W.; Denlinger, J. D.; Mulcahy, S.; Moustakas, T. D.; Heske, Clemens

    2010-05-17

    We have investigated the chemical interaction between a Au/V/Al/V layer structure and n-type AlN epilayers using soft x-ray photoemission, x-ray emission spectroscopy, and atomic force microscopy. To understand the complex processes involved in this multicomponent system, we have studied the interface before and after a rapid thermal annealing step. We find the formation of a number of chemical phases at the interface, including VN, metallic vanadium, aluminum oxide, and metallic gold. An interaction mechanism for metal contact formation on the entire n-(Al,Ga)N system is proposed.

  10. On the Mathematical Structure of Balanced Chemical Reaction Networks Governed by Mass Action Kinetics

    CERN Document Server

    van der Schaft, Arjan; Jayawardhana, Bayu

    2011-01-01

    Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic equilibrium we derive a compact formulation exhibiting at the same time the structure of the complex graph and the stoichiometry of the network, and which admits a direct thermodynamical interpretation. This formulation allows us to easily characterize the set of equilibria and their stability properties. Furthermore, we develop a framework for interconnection of chemical reaction networks. Finally we discuss how the established framework leads to a new approach for model reduction.

  11. Modeling the binding affinity of structurally diverse industrial chemicals to carbon using the artificial intelligence approaches.

    Science.gov (United States)

    Gupta, Shikha; Basant, Nikita; Rai, Premanjali; Singh, Kunwar P

    2015-11-01

    Binding affinity of chemical to carbon is an important characteristic as it finds vast industrial applications. Experimental determination of the adsorption capacity of diverse chemicals onto carbon is both time and resource intensive, and development of computational approaches has widely been advocated. In this study, artificial intelligence (AI)-based ten different qualitative and quantitative structure-property relationship (QSPR) models (MLPN, RBFN, PNN/GRNN, CCN, SVM, GEP, GMDH, SDT, DTF, DTB) were established for the prediction of the adsorption capacity of structurally diverse chemicals to activated carbon following the OECD guidelines. Structural diversity of the chemicals and nonlinear dependence in the data were evaluated using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation procedures performed employing a wide series of statistical checks. In complete dataset, the qualitative models rendered classification accuracies between 97.04 and 99.93%, while the quantitative models yielded correlation (R(2)) values of 0.877-0.977 between the measured and the predicted endpoint values. The quantitative prediction accuracies for the higher molecular weight (MW) compounds (class 4) were relatively better than those for the low MW compounds. Both in the qualitative and quantitative models, the Polarizability was the most influential descriptor. Structural alerts responsible for the extreme adsorption behavior of the compounds were identified. Higher number of carbon and presence of higher halogens in a molecule rendered higher binding affinity. Proposed QSPR models performed well and outperformed the previous reports. A relatively better performance of the ensemble learning models (DTF, DTB) may be attributed to the strengths of the bagging and boosting algorithms which enhance the predictive accuracies. The

  12. Utilizing environmental management information systems to monitor chemical usage and facilitate waste minimization

    Energy Technology Data Exchange (ETDEWEB)

    Blazer, T.L.; Kinney, R.W. [Modern Technologies Corporation, Dayton, OH (United States)

    1996-10-01

    Waste minimization and pollution prevention activities have proven to be valuable to the chemical industry`s and the chemical user`s bottom line. Many companies have found that, with a modest initial capital investment and product modifications, mounds of bureaucratic liability can be removed and substantial cost savings can be realized.

  13. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.

    Science.gov (United States)

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

    NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of

  14. Protein structure similarity clustering and natural product structure as guiding principles for chemical genomics.

    Science.gov (United States)

    Koch, M A; Waldmann, H

    2006-01-01

    The majority of all proteins are modularly built from a limited set of approximately 1,000 structural domains. The knowledge of a common protein fold topology in the ligand-sensing cores of protein domains can be exploited for the design of small-molecule libraries in the development of inhibitors and ligands. Thus, a novel strategy of clustering protein domain cores based exclusively on structure similarity considerations (protein structure similarity clustering, PSSC) has been successfully applied to the development of small-molecule inhibitors of acetylcholinesterase and the 11beta-hydroxysteroid dehydrogenases based on the structure of a naturally occurring Cdc25 inhibitor. The efficiency of making use of the scaffolds of natural products as biologically prevalidated starting points for the design of compound libraries is further highlighted by the development of benzopyran-based FXR ligands.

  15. Effect of chemical substituents on the structure of glassy diphenyl polycarbonates.

    Science.gov (United States)

    Sulatha, M S; Natarajan, Upendra

    2011-02-24

    Polycarbonates offer a wide variety of physical property behavior that is difficult to predict due to complexities at the molecular scale. Here, the physical structure of amorphous glassy polycarbonates having aliphatic and cycloaliphatic chemical groups is explored through atomistic simulations. The influence of chemical structure on solubility parameter, torsion distributions, radial distribution function, scattering structure factor, orientation distributions of phenylene rings and carbonate groups, and free volume distributions, leading to interchain packing effects, are shown. The effect of the cyclohexyl ring at the isopropylidene carbon as compared to the effect of the methyl groups positioned on the phenylene rings results in a larger reduction in the solubility parameter (δ). The interchain distance estimated for polycarbonates in this work is in the range of 5-5.8 Å. The o-methyl groups on the phenylene rings, as compared to a cyclohexyl ring, lead to higher interchain distances. The highest interchain distance is observed with a trimethylcyclohexylidene group at the isopropylidene carbon. Atomistic simulations reveal two different types of packing arrangement of nearest-neighbor chains in the glassy state, one type of which agrees with the NMR experimental data. The fundamental insights provided here can be utilized for design of chemical structures for tailored macroscopic properties.

  16. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function

    Directory of Open Access Journals (Sweden)

    Ville Y. P. Väre

    2017-03-01

    Full Text Available RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA’s cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.

  17. Development of new materials and structures based on managed physical-chemical factors of local interaction

    Science.gov (United States)

    Urakov, A. L.

    2016-04-01

    The paper states that assigning certain physical and chemical characteristics to pills and medical drugs solutions can substitute for the development of new drugs (which is essentially equivalent to the creation of new medicines). It is established that the purposeful change of physical and chemical characteristics of the standard ("old") materials (in other words, the known substances) is fundamental for the production of solid and liquid medicines, which allows us to get "new" structures and materials. The paper shows that assigning new physical and chemical properties to "old" materials and their further usage for the production of tablets and solutions from the "old" and well-known medicines can turn even very "old" medicine into very "novel" (moreover, even very fashionable) one with unprecedented (fantastic) pharmacological activity and new mechanisms of action.

  18. Ascaroside activity in Caenorhabditis elegans is highly dependent on chemical structure.

    Science.gov (United States)

    Hollister, Kyle A; Conner, Elizabeth S; Zhang, Xinxing; Spell, Mark; Bernard, Gary M; Patel, Pratik; de Carvalho, Ana Carolina G V; Butcher, Rebecca A; Ragains, Justin R

    2013-09-15

    The nematode Caenorhabditis elegans secretes ascarosides, structurally diverse derivatives of the 3,6-dideoxysugar ascarylose, and uses them in chemical communication. At high population densities, specific ascarosides, which are together known as the dauer pheromone, trigger entry into the stress-resistant dauer larval stage. In order to study the structure-activity relationships for the ascarosides, we synthesized a panel of ascarosides and tested them for dauer-inducing activity. This panel includes a number of natural ascarosides that were detected in crude pheromone extract, but as yet have no assigned function, as well as many unnatural ascaroside derivatives. Most of these ascarosides, some of which have significant structural similarity to the natural dauer pheromone components, have very little dauer-inducing activity. Our results provide a primer to ascaroside structure-activity relationships and suggest that slight modifications to ascaroside structure dramatically influence binding to the relevant G protein-coupled receptors that control dauer formation.

  19. Information structure influences depth of syntactic processing: event-related potential evidence for the Chomsky illusion.

    Science.gov (United States)

    Wang, Lin; Bastiaansen, Marcel; Yang, Yufang; Hagoort, Peter

    2012-01-01

    Information structure facilitates communication between interlocutors by highlighting relevant information. It has previously been shown that information structure modulates the depth of semantic processing. Here we used event-related potentials to investigate whether information structure can modulate the depth of syntactic processing. In question-answer pairs, subtle (number agreement) or salient (phrase structure) syntactic violations were placed either in focus or out of focus through information structure marking. P600 effects to these violations reflect the depth of syntactic processing. For subtle violations, a P600 effect was observed in the focus condition, but not in the non-focus condition. For salient violations, comparable P600 effects were found in both conditions. These results indicate that information structure can modulate the depth of syntactic processing, but that this effect depends on the salience of the information. When subtle violations are not in focus, they are processed less elaborately. We label this phenomenon the Chomsky illusion.

  20. Combined effect of chemical and electrical synapses in Hindmarsh-Rose neural networks on synchronization and the rate of information.

    Science.gov (United States)

    Baptista, M S; Moukam Kakmeni, F M; Grebogi, C

    2010-09-01

    In this work we studied the combined action of chemical and electrical synapses in small networks of Hindmarsh-Rose (HR) neurons on the synchronous behavior and on the rate of information produced (per time unit) by the networks. We show that if the chemical synapse is excitatory, the larger the chemical synapse strength used the smaller the electrical synapse strength needed to achieve complete synchronization, and for moderate synaptic strengths one should expect to find desynchronous behavior. Otherwise, if the chemical synapse is inhibitory, the larger the chemical synapse strength used the larger the electrical synapse strength needed to achieve complete synchronization, and for moderate synaptic strengths one should expect to find synchronous behaviors. Finally, we show how to calculate semianalytically an upper bound for the rate of information produced per time unit (Kolmogorov-Sinai entropy) in larger networks. As an application, we show that this upper bound is linearly proportional to the number of neurons in a network whose neurons are highly connected.

  1. Chemical-mechanical stability of the hierarchical structure of shell nacre

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The hierarchical structure and mechanical property of shell nacre are experimentally investigated from the new aspects of chemical stability and chemistry-mechanics coupling. Through chemical deproteinization or demineralization methods together with characterization techniques at micro/nano scales,it is found that the nacre of abalone,haliotis discus hannai,contains a hierarchical structure stacked with irregular aragonite platelets and interplatelet organic matrix thin layers. Yet the aragonite platelet itself is a nanocomposite consisting of nanoparticles and intraplatelet organic matrix framework. The mean diameter of the nanoparticles and the distribution of framework are quite different for different platelets. Though the interplatelet and in-traplatelet organic matrix can be both decomposed by sodium hydroxide solution,the chemical stability of individual aragonite platelets is much higher than that of the microstructure stacked with them. Further,macroscopic bending test or nanoindentation experiment is performed on the micro/nanostructure of nacre after sodium hydroxide treatment. It is found that the Young’s modulus of both the stacked microstructure and nanocomposite platelet reduced. The reduction of the microstructure is more remark than that of the platelet. Therefore the chemical-mechanical stability of the nanocomposite platelet itself is much higher than that of the stacked microstructure of nacre.

  2. Structural and Optical Properties of Chemical Bath Deposited Silver Oxide Thin Films: Role of Deposition Time

    Directory of Open Access Journals (Sweden)

    A. C. Nwanya

    2013-01-01

    Full Text Available Silver oxide thin films were deposited on glass substrates at a temperature of 50°C by chemical bath deposition technique under different deposition times using pure AgNO3 precursor and triethanolamine as the complexing agent. The chemical analysis based on EDX technique shows the presence of Ag and O at the appropriate energy levels. The morphological features obtained from SEM showed that the AgxO structures varied as the deposition time changes. The X-ray diffraction showed the peaks of Ag2O and AgO in the structure. The direct band gap and the refractive index increased as the deposition time increased and was in the range of 1.64–1.95 eV and 1.02–2.07, respectively. The values of the band gap and refractive index obtained indicate possible applications in photovoltaic and photothermal systems.

  3. Comparison of the 'chemical' and 'structural' approaches to the optimization of the thrombin-binding aptamer.

    Directory of Open Access Journals (Sweden)

    Olga Tatarinova

    Full Text Available Noncanonically structured DNA aptamers to thrombin were examined. Two different approaches were used to improve stability, binding affinity and biological activity of a known thrombin-binding aptamer. These approaches are chemical modification and the addition of a duplex module to the aptamer core structure. Several chemically modified aptamers and the duplex-bearing ones were all studied under the same conditions by a set of widely known and some relatively new methods. A number of the thrombin-binding aptamer analogs have demonstrated improved characteristics. Most importantly, the study allowed us to compare directly the two approaches to aptamer optimization and to analyze their relative advantages and disadvantages as well as their potential in drug design and fundamental studies.

  4. Hierarchically structured photonic crystals for integrated chemical separation and colorimetric detection.

    Science.gov (United States)

    Fu, Qianqian; Zhu, Biting; Ge, Jianping

    2017-02-16

    A SiO2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

  5. Physicists' Information Tasks: Structure, Length and Retrieval Performance

    DEFF Research Database (Denmark)

    Lykke, Marianne; Ingwersen, Peter; Bogers, Toine;

    2010-01-01

    In this poster, we describe central aspects of 65 natural information tasks from 23 senior researchers, PhDs, and experienced MSc students from three different university departments of physics. We analyze 1) the main purpose of the information task, 2) which and how many search facets were used...

  6. The Structure and Future of the Information Economy.

    Science.gov (United States)

    Cooper, Michael D.

    1983-01-01

    Discusses the United States economy and reviews National Income Accounting concepts and evidence about future of an information economy. It is concluded that information economy growth will be in products, not services, and that it will not continue at same rate it has in past. Thirty-six references are cited. (EJS)

  7. The influence of the chain and network information and communication structure on sustainable business development

    NARCIS (Netherlands)

    Bremmers, H.J.; Haverkamp, D.J.; Omta, S.W.F.

    2005-01-01

    This article links the public-private information and communication structure (IC-structure) and Ajzen¿s model of planned behaviour to explain the development of environmental management systems (EMSs). The structure of the IC-system, especially the public-private information exchange, can influence

  8. STRUCTURAL AND SEMANTIC FEATURES OF ONLINE INFORMATION RESOURCES

    Directory of Open Access Journals (Sweden)

    Ivan Georgievich Zubkov

    2014-07-01

    Full Text Available Information society is a global economic, political, technological and antroposocial project involving controlled civilizational transition to the world social system in which the dominant role in all spheres of life will play a mass communication system, implemented with the help of computer technology, particularly Internet technology. The question of formation and presentation of information is highly relevant today. The world community has entered a transitional stage from its post-industrial state to the informational. At this stage of the development, society is increasingly dependent on the quality, availability, reliability, timeliness of information, which is created by its own representatives. Especially clearly it is evident in the Internet space, where all information flows merge into a single closed and continuously update system that has its own characteristics, features and qualities.DOI: http://dx.doi.org/10.12731/2218-7405-2014-4-7

  9. Chemical descriptors, convexity and structure of density matrices in molecular systems

    CERN Document Server

    Bochicchio, Roberto C

    2015-01-01

    The electron energy and density matrices in molecular systems are convex in respect of the number of particles. So that, the chemical descriptors based on their derivatives present the hamper of discontinuities for isolated systems and consequently higher order derivatives are undefined. The introduction of the interaction between the physical domain with an environment induces a coherent structure for the density matrix in the grand-canonical formulation suppressing the discontinuities leading to the proper definitions of the descriptors.

  10. Structural, optical and electrical properties of chemically deposited nonstoichiometric copper indium diselenide films

    Indian Academy of Sciences (India)

    R H Bari; L A Patil; P P Patil

    2006-10-01

    Thin films of copper indium diselenide (CIS) were prepared by chemical bath deposition technique onto glass substrate at temperature, 60°C. The studies on composition, morphology, optical absorption, electrical conductivity and structure of the films were carried out and discussed. Characterization included X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), energy dispersive X-ray analysis (EDAX) and absorption spectroscopy. The results are discussed and interpreted.

  11. Chemical structure of the O-polysaccharide isolated from Pectobacterium atrosepticum SCRI 1039.

    Science.gov (United States)

    Czerwicka, Małgorzata; Marszewska, Kinga; Bychowska, Anna; Dziadziuszko, Halina; Brzozowski, Krzysztof; Łojkowska, Ewa; Stepnowski, Piotr; Kaczyński, Zbigniew

    2011-12-27

    The lipopolysaccharide (LPS) of the bacterium Pectobacterium atrosepticum SCRI 1039 was hydrolyzed and the products were separated. A study of the obtained O-polysaccharide by means of chemical methods, GLC, GLC-MS, and NMR spectroscopy allowed us to identify a branched polymer with a pentasaccharide repeating unit of the structure shown below, in which the fucose residue was partially O-acetylated at C-2, C-3 or C-4.

  12. Physico-chemical properties and cytotoxic effects of sugar-based surfactants: Impact of structural variations.

    Science.gov (United States)

    Lu, Biao; Vayssade, Muriel; Miao, Yong; Chagnault, Vincent; Grand, Eric; Wadouachi, Anne; Postel, Denis; Drelich, Audrey; Egles, Christophe; Pezron, Isabelle

    2016-09-01

    Surfactants derived from the biorefinery process can present interesting surface-active properties, low cytotoxicity, high biocompatibility and biodegradability. They are therefore considered as potential sustainable substitutes to currently used petroleum-based surfactants. To better understand and anticipate their performances, structure-property relationships need to be carefully investigated. For this reason, we applied a multidisciplinary approach to systematically explore the effect of subtle structural variations on both physico-chemical properties and biological effects. Four sugar-based surfactants, each with an eight carbon alkyl chain bound to a glucose or maltose head group by an amide linkage, were synthesized and evaluated together along with two commercially available standard surfactants. Physico-chemical properties including solubility, Krafft point, surface-tension lowering and critical micellar concentration (CMC) in water and biological medium were explored. Cytotoxicity evaluation by measuring proliferation index and metabolic activity against dermal fibroblasts showed that all surfactants studied may induce cell death at low concentrations (below their CMC). Results revealed significant differences in both physico-chemical properties and cytotoxic effects depending on molecule structural features, such as the position of the linkage on the sugar head-group, or the orientation of the amide linkage. Furthermore, the cytotoxic response increased with the reduction of surfactant CMC. This study underscores the relevance of a methodical and multidisciplinary approach that enables the consideration of surfactant solution properties when applied to biological materials. Overall, our results will contribute to a better understanding of the concomitant impact of surfactant structure at physico-chemical and biological levels.

  13. Chemically gated electronic structure of a superconducting doped topological insulator system

    Science.gov (United States)

    Wray, L. A.; Xu, S.; Neupane, M.; Fedorov, A. V.; Hor, Y. S.; Cava, R. J.; Hasan, M. Z.

    2013-07-01

    Angle resolved photoemission spectroscopy is used to observe changes in the electronic structure of bulk-doped topological insulator CuxBi2Se3 as additional copper atoms are deposited onto the cleaved crystal surface. Carrier density and surface-normal electrical field strength near the crystal surface are estimated to consider the effect of chemical surface gating on atypical superconducting properties associated with topological insulator order, such as the dynamics of theoretically predicted Majorana Fermion vortices.

  14. Analysis of the relationship between the structure and aromatic properties of chemical compounds.

    Science.gov (United States)

    Debska, Barbara; Guzowska-Swider, Barbara

    2003-04-01

    This paper presents the results of research on the relationship between the structure and odour properties of a selection of chemical compounds. The research concerns five groups of esters, each with a different smell: almond, apricot, apple, pineapple and rose. The supposed relationship between the smell and certain selected attributes of each molecule was examined by various pattern recognition techniques using programs developed in the Department of Computer Chemistry at Rzeszów University of Technology.

  15. Relationship between the antitrichinellous effect of seven derivates of benzimidazolecarbamates and their chemical structure.

    Science.gov (United States)

    Spaldonová, R; Corba, J

    1979-01-01

    The efficacy of seven more recently developed anthelmintics of the benzimidazolecarbamate group, i. e., parbendazole, mebendazole, fenbendazole, oxibendazole, cambendazole, oxfendazole and albendazole, has been tested in a series of experiments on white mice artifically infected with Trichinella spiralis. Our results disclosed a relationship between their anthelmintic effect and their chemical structure. This finding might be of importance in a targeted synthesis of new, effective, derivates of benzimidazole, e. g., in the therapy of trichinellosis and in the choice of the most effective drug.

  16. Processing of poly(lactic acid): characterization of chemical structure, thermal stability and mechanical properties

    OpenAIRE

    Carrasco Alonso, Félix Ángel; Pagès Figueras, Pere; Gamez Pérez, José; Santana Pérez, Orlando Onofre; Maspoch Rulduà, Mª Lluïsa

    2010-01-01

    The processing of poly(lactic acid) (injection and extrusion/injection) as well as annealing of processed materials were studied in order to analyze the variation of its chemical structure, thermal degradation and mechanical properties. Processing of PLA was responsible for a decrease in molecular weight, as determined by GPC, due to chain scission. The degree of crystallinity was evaluated by means of differential scanning calorimetry and X-ray diffraction. It was found that mech...

  17. Generalized molybdenum oxide surface chemical state XPS determination via informed amorphous sample model

    Science.gov (United States)

    Baltrusaitis, Jonas; Mendoza-Sanchez, Beatriz; Fernandez, Vincent; Veenstra, Rick; Dukstiene, Nijole; Roberts, Adam; Fairley, Neal

    2015-01-01

    Accurate elemental oxidation state determination for the outer surface of a complex material is of crucial importance in many science and engineering disciplines, including chemistry, fundamental and applied surface science, catalysis, semiconductors and many others. X-ray photoelectron spectroscopy (XPS) is the primary tool used for this purpose. The spectral data obtained, however, is often very complex and can be subject to incorrect interpretation. Unlike traditional XPS spectra fitting procedures using purely synthetic spectral components, here we develop and present an XPS data processing method based on vector analysis that allows creating XPS spectral components by incorporating key information, obtained experimentally. XPS spectral data, obtained from series of molybdenum oxide samples with varying oxidation states and degree of crystallinity, were processed using this method and the corresponding oxidation states present, as well as their relative distribution was elucidated. It was shown that monitoring the evolution of the chemistry and crystal structure of a molybdenum oxide sample due to an invasive X-ray probe could be used to infer solutions to complex spectral envelopes.

  18. Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis.

    Science.gov (United States)

    Suyama, Takashi L; Gerwick, William H; McPhail, Kerry L

    2011-11-15

    The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable 'detective work' remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques.

  19. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2016-07-01

    Full Text Available Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding and quantitative (for predicting mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD as the revived precursor for comparative molecular field analyses (CoMFA and comparative molecular similarity indices analysis (CoMSIA; all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy-methyl]-6-(phenylthiothymine congeners’ (HEPT ligands antiviral activity against Human Immunodeficiency Virus of first type (HIV-1 and new pharmacophores in treating severe genetic disorders (like depression and psychosis, respectively, all involving 3D pharmacophore interactions.

  20. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Science.gov (United States)

    Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  1. Improved performance of the microbial electrolysis desalination and chemical-production cell using the stack structure.

    Science.gov (United States)

    Chen, Shanshan; Liu, Guangli; Zhang, Renduo; Qin, Bangyu; Luo, Yong; Hou, Yanping

    2012-07-01

    The microbial electrolysis desalination and chemical-production cell (MEDCC) is a device to desalinate seawater, and produce acid and alkali. The objective of this study was to enhance the desalination and chemical-production performance of the MEDCC using two types of stack structure. Experiments were conducted with different membrane spacings, numbers of desalination chambers and applied voltages. Results showed that the stack construction in the MEDCC enhanced the desalination and chemical-production rates. The maximal desalination rate of 0.58 ± 0.02 mmol/h, which was 43% higher than that in the MEDCC, was achieved in the four-desalination-chamber MEDCC with the AEM-CEM stack structure and the membrane spacing of 1.5mm. The maximal acid- and alkali-production rates of 0.079 ± 0.006 and 0.13 ± 0.02 mmol/h, which were 46% and 8% higher than that in the MEDCC, respectively, were achieved in the two-desalination-chamber MEDCC with the BPM-AEM-CEM stack structure and the membrane spacing of 3mm.

  2. Electronic structure and chemical bonding of Li4Pt3Si

    Science.gov (United States)

    Matar, S. F.; Pöttgen, R.; Al Alam, A. F.; Ouaini, N.

    2012-07-01

    The electronic structure of rhombohedral Li4Pt3Si (space group R32) is examined from ab initio with an assessment of the properties of chemical bonding relating to the presence of different Li and Pt Wyckoff sites. The structure with totally de-intercalated Li keeps the characteristics of the pristine compound with a reduction of the volume albeit with less cohesive energy. The binding energies of Li point to different bonding intensities according to their different Wyckoff sites and indicate the possibility of delithiation.

  3. Predicting physical-chemical properties of compounds from molecular structures by recursive neural networks.

    Science.gov (United States)

    Bernazzani, Luca; Duce, Celia; Micheli, Alessio; Mollica, Vincenzo; Sperduti, Alessandro; Starita, Antonina; Tiné, Maria Rosaria

    2006-01-01

    In this paper, we report on the potential of a recently developed neural network for structures applied to the prediction of physical chemical properties of compounds. The proposed recursive neural network (RecNN) model is able to directly take as input a structured representation of the molecule and to model a direct and adaptive relationship between the molecular structure and target property. Therefore, it combines in a learning system the flexibility and general advantages of a neural network model with the representational power of a structured domain. As a result, a completely new approach to quantitative structure-activity relationship/quantitative structure-property relationship (QSPR/QSAR) analysis is obtained. An original representation of the molecular structures has been developed accounting for both the occurrence of specific atoms/groups and the topological relationships among them. Gibbs free energy of solvation in water, Delta(solv)G degrees , has been chosen as a benchmark for the model. The different approaches proposed in the literature for the prediction of this property have been reconsidered from a general perspective. The advantages of RecNN as a suitable tool for the automatization of fundamental parts of the QSPR/QSAR analysis have been highlighted. The RecNN model has been applied to the analysis of the Delta(solv)G degrees in water of 138 monofunctional acyclic organic compounds and tested on an external data set of 33 compounds. As a result of the statistical analysis, we obtained, for the predictive accuracy estimated on the test set, correlation coefficient R = 0.9985, standard deviation S = 0.68 kJ mol(-1), and mean absolute error MAE = 0.46 kJ mol(-1). The inherent ability of RecNN to abstract chemical knowledge through the adaptive learning process has been investigated by principal components analysis of the internal representations computed by the network. It has been found that the model recognizes the chemical compounds on the

  4. Damascene Array Structure of Phase Change Memory Fabricated with Chemical Mechanical Polishing Method

    Institute of Scientific and Technical Information of China (English)

    LIU Qi-Bin; SONG Zhi-Tang; ZHANG Kai-Liang; WANG Liang-Yong; FENG Song-Lin; CHEN Bomy

    2006-01-01

    @@ A damascene structure of phase change memory (PCM) is fabricated successfully with the chemical mechanical polishing (CMP) method, and the CMP of Ge2Sb2Te5 (GST) and Ti films is investigated. The polished surface of wafer is analysed by scanning electron microscopy (SEM) and an energy dispersive spectrometer (EDS). The measurements show that the damascene device structure of phase change memory is achieved by the CMP process.After the top electrode is deposited, dc sweeping test on PCM reveals that the phase change can be observed.The threshold current of array cells varies between 0.90mA and 1.15mA.

  5. The Nature of the Chemical Process. 1. Symmetry Evolution – Revised Information Theory, Similarity Principle and Ugly Symmetry

    Directory of Open Access Journals (Sweden)

    Shu-Kun Lin

    2001-03-01

    Full Text Available Abstract: Symmetry is a measure of indistinguishability. Similarity is a continuous measure of imperfect symmetry. Lewis' remark that “gain of entropy means loss of information” defines the relationship of entropy and information. Three laws of information theory have been proposed. Labeling by introducing nonsymmetry and formatting by introducing symmetry are defined. The function L ( L=lnw, w is the number of microstates, or the sum of entropy and information, L=S+I of the universe is a constant (the first law of information theory. The entropy S of the universe tends toward a maximum (the second law law of information theory. For a perfect symmetric static structure, the information is zero and the static entropy is the maximum (the third law law of information theory. Based on the Gibbs inequality and the second law of the revised information theory we have proved the similarity principle (a continuous higher similarity−higher entropy relation after the rejection of the Gibbs paradox and proved the Curie-Rosen symmetry principle (a higher symmetry−higher stability relation as a special case of the similarity principle. The principles of information minimization and potential energy minimization are compared. Entropy is the degree of symmetry and information is the degree of nonsymmetry. There are two kinds of symmetries: dynamic and static symmetries. Any kind of symmetry will define an entropy and, corresponding to the dynamic and static symmetries, there are static entropy and dynamic entropy. Entropy in thermodynamics is a special kind of dynamic entropy. Any spontaneous process will evolve towards the highest possible symmetry, either dynamic or static or both. Therefore the revised information theory can be applied to characterizing all kinds of structural stability and process spontaneity. Some examples in chemical physics have been given. Spontaneous processes of all kinds of molecular

  6. Beyond terrestrial biology: charting the chemical universe of α-amino acid structures.

    Science.gov (United States)

    Meringer, Markus; Cleaves, H James; Freeland, Stephen J

    2013-11-25

    α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

  7. Preparation of melanin from Catharsius molossus L. and preliminary study on its chemical structure.

    Science.gov (United States)

    Xin, Chao; Ma, Jia-hua; Tan, Cheng-jia; Yang, Zhou; Ye, Feng; Long, Chan; Ye, Shuang; Hou, Da-bin

    2015-04-01

    A great deal of melanin was found in the waste alkali liquor produced by extraction of chitin from Catharsius molossus L. Discarding the lye could harm the environment and cause waste of resources. In this paper, melanin from C. molossus L. was recovered through acid precipitation and purified by pepsin and so on. The purity, chemical composition and structure of the prepared melanin were explored by UV-visible absorption spectroscopy, Fourier transform infrared spectroscopy, proton nuclear magnetic resonance spectroscopy, high resolution (13)C Cross polarization magic angle spinning nuclear magnetic resonance spectroscopy pyrolysis gas chromatography mass spectrometry, X ray diffraction, X ray fluorescence, matrix-assisted laser desorption/ionization time of flight tandem mass spectrometry, thermal analysis, and so on. The results showed that the purity of the prepared melanin was higher than the commercial standard melanin and it was a kind of nanoaggregates composed of a large quantity of 5,6-dihydroxyindole eumelanin and a small amount of phaeomelanin. In addition, the prepared melanin was irregular in shape and its structure could be divided into three levels: advanced structure maintained by polypeptides, substructure maintained by the ferric ion and microstructure. In particular, the smallest structural unit showed the graphite-like layered structure containing five layers linked by non-covalent bonds and each layer mainly consisted of 5,6-dihydroxyindole and its derivatives, which might be connected to each other through various chemical bonds.

  8. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology.

    Science.gov (United States)

    Sinz, Andrea; Arlt, Christian; Chorev, Dror; Sharon, Michal

    2015-08-01

    Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.

  9. Changes in the chemical structure of polytetrafluoroethylene induced by electron beam irradiation in the molten state

    CERN Document Server

    Lappan, U; Lunkwitz, K

    2000-01-01

    Polytetrafluoroethylene (PTFE) was exposed to electron beam radiation at elevated temperature above the melting point under nitrogen atmosphere and in vacuum for comparison. Fourier-transform infrared (FTIR) spectroscopy was used to study the changes in the chemical structure. The irradiation under nitrogen atmosphere leads to the same structures as described recently for PTFE irradiated in vacuum. Trifluoromethyl branches and double bond structures were detected. The concentrations of terminal and internal double bonds are higher after irradiation under nitrogen than in vacuum. Annealing experiments have shown that the thermal oxidative stability of the radiation-modified PTFE is reduced compared to unirradiated PTFE. The reason are the formation of unstable structures such as double bonds.

  10. Information theory provides a comprehensive framework for the evaluation of protein structure predictions

    Science.gov (United States)

    Swanson, Rosemarie; Vannucci, Marina; Tsai, Jerry W.

    2008-01-01

    Protein structure prediction has a number of important ad hoc similarity measures for evaluating predictions, but would benefit from a measure that is able to provide a common framework for a broad range of comparisons. Here we show that a mutual information-like measure can provide a comprehensive framework for evaluating protein structure prediction of all types. We discuss the concept of information, its application to secondary structure, and the obstacle to applying it to 3D structure. Based on insights from the secondary structure case, we present an approach to work around the 3D difficulties, and develop a method to measure the mutual information provided by a 3D structure prediction. We integrate the evaluation of all types of protein structure prediction into a single frame work, and compare the amount of information provided by various prediction methods, including secondary structure prediction. Within this broadened framework, the idea that structure is better preserved than sequence during evolution is evaluated quantitatively for the globin family. A nearly perfect sequence match in the globin family corresponds to about 300 bits of information, whereas a nearly perfect structural match for the same two proteins corresponds to about 2500 bits of information, where bits of information describes the probability of obtaining a match of similar closeness by chance. Mutual information provides both a theoretical basis for evaluating structure similarity and an explanatory surround for existing similarity measures. PMID:18704942

  11. Structuring of DLC:Ag nanocomposite thin films employing plasma chemical etching and ion sputtering

    Science.gov (United States)

    Tamulevičius, Tomas; Tamulevičienė, Asta; Virganavičius, Dainius; Vasiliauskas, Andrius; Kopustinskas, Vitoldas; Meškinis, Šarūnas; Tamulevičius, Sigitas

    2014-12-01

    We analyze structuring effects of diamond like carbon based silver nanocomposite (DLC:Ag) thin films by CF4/O2 plasma chemical etching and Ar+ sputtering. DLC:Ag films were deposited employing unbalanced reactive magnetron sputtering of silver target with Ar+ in C2H2 gas atmosphere. Films with different silver content (0.6-12.9 at.%) were analyzed. The films (as deposited and exposed to plasma chemical etching) were characterized employing scanning electron microscopy and energy dispersive X-ray analysis (SEM/EDS), optical microscopy, ultraviolet-visible light (UV-VIS) spectroscopy and Fourier transform infrared (FTIR) spectroscopy. After deposition, the films were plasma chemically etched in CF4/O2 mixture plasma for 2-6 min. It is shown that optical properties of thin films and silver nano particle size distribution can be tailored during deposition changing the magnetron current and C2H2/Ar ratio or during following plasma chemical etching. The plasma etching enabled to reveal the silver filler particle size distribution and to control silver content on the surface that was found to be dependent on Ostwald ripening process of silver nano-clusters. Employing contact lithography and 4 μm period mask in photoresist or aluminum the films were patterned employing CF4/O2 mixture plasma chemical etching, direct Ar+ sputtering or combined etching processes. It is shown that different processing recipes result in different final grating structures. Selective carbon etching in CF4/O2 gas mixture with photoresist mask revealed micrometer range lines of silver nanoparticles, while Ar+ sputtering and combined processing employing aluminum mask resulted in nanocomposite material (DLC:Ag) micropatterns.

  12. Information

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    There are unstructured abstracts (no more than 256 words) and structured abstracts (no more than 480). The specific requirements for structured abstracts are as follows:An informative, structured abstracts of no more than 4-80 words should accompany each manuscript. Abstracts for original contributions should be structured into the following sections. AIM (no more than 20 words): Only the purpose should be included. Please write the aim as the form of "To investigate/ study/..."; MATERIALS AND METHODS (no more than 140 words); RESULTS (no more than 294 words): You should present P values where appropnate and must provide relevant data to illustrate how they were obtained, e.g. 6.92 ± 3.86 vs 3.61 ± 1.67, P< 0.001; CONCLUSION (no more than 26 words).

  13. Structural characterization and chemical classification of some bryophytes found in Latvia.

    Science.gov (United States)

    Maksimova, Viktorija; Klavina, Laura; Bikovens, Oskars; Zicmanis, Andris; Purmalis, Oskars

    2013-07-01

    Bryophytes are the second largest taxonomic group in the plant kingdom; yet, studies conducted to better understand their chemical composition are rare. The aim of this study was to characterize the chemical composition of bryophytes common in Northern Europe by using elemental, spectral, and non-destructive analytical methods, such as Fourier transform IR spectrometry (FT-IR), solid-phase (13) C-NMR spectrometry, and pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), for the purpose of investigating their chemotaxonomic relationships on the basis of chemical-composition data. The results of all these analyses showed that bryophytes consist mainly of carbohydrates. Judging by FT-IR spectra, the OH groups in combination of CO groups were the most abundant groups. The (13) C-NMR spectra provided information on the presence of such compounds as phenolics and lipids. It was found that the amount of phenolic compounds in bryophytes is relatively small. This finding definitely confirmed the absence of lignin in the studied bryophytes. Cluster analysis was used to better understand differences in the chemical composition of bryophyte samples and to evaluate possible usage of these methods in the chemotaxonomy of bryophytes.

  14. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    Science.gov (United States)

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds.

  15. Register of specialized sources for information on mechanics of structural failure

    Science.gov (United States)

    Carpenter, J. L., Jr.; Denny, F. J.

    1973-01-01

    Specialized information sources that generate information relative to six problem areas in aerospace mechanics of structural failure are identified. Selection for inclusion was based upon information obtained from the individual knowledge and professional contacts of Martin Marietta Aerospace staff members and the information uncovered by the staff of technical reviewers. Activities listed perform basic or applied research related to the mechanics of structural failure and publish the results of such research. The purpose of the register is to present, in easy reference form, original sources for dependable information regarding failure modes and mechanisms of aerospace structures.

  16. Chemical engineering and structural and pharmacological characterization of the α-scorpion toxin OD1.

    Science.gov (United States)

    Durek, Thomas; Vetter, Irina; Wang, Ching-I Anderson; Motin, Leonid; Knapp, Oliver; Adams, David J; Lewis, Richard J; Alewood, Paul F

    2013-01-01

    Scorpion α-toxins are invaluable pharmacological tools for studying voltage-gated sodium channels, but few structure-function studies have been undertaken due to their challenging synthesis. To address this deficiency, we report a chemical engineering strategy based upon native chemical ligation. The chemical synthesis of α-toxin OD1 was achieved by chemical ligation of three unprotected peptide segments. A high resolution X-ray structure (1.8 Å) of synthetic OD1 showed the typical βαββ α-toxin fold and revealed important conformational differences in the pharmacophore region when compared with other α-toxin structures. Pharmacological analysis of synthetic OD1 revealed potent α-toxin activity (inhibition of fast inactivation) at Nav1.7, as well as Nav1.4 and Nav1.6. In addition, OD1 also produced potent β-toxin activity at Nav1.4 and Nav1.6 (shift of channel activation in the hyperpolarizing direction), indicating that OD1 might interact at more than one site with Nav1.4 and Nav1.6. Investigation of nine OD1 mutants revealed that three residues in the reverse turn contributed significantly to selectivity, with the triple OD1 mutant (D9K, D10P, K11H) being 40-fold more selective for Nav1.7 over Nav1.6, while OD1 K11V was 5-fold more selective for Nav1.6 than Nav1.7. This switch in selectivity highlights the importance of the reverse turn for engineering α-toxins with altered selectivity at Nav subtypes.

  17. Integrating Epistemological Perspectives on Chemistry in Chemical Education: The Cases of Concept Duality, Chemical Language, and Structural Explanations

    Science.gov (United States)

    Kaya, Ebru; Erduran, Sibel

    2013-01-01

    In this paper, we trace the work of some philosophers of chemistry to draw some implications for the improvement of chemical education. We examine some key features of chemical knowledge, and how these features are relevant for school chemistry teaching and learning. In particular, we examine Laszlo's ("Foundations of Chemistry"…

  18. An approach to knowledge structuring for advanced phases of the Technical and Management Information System (TMIS)

    Science.gov (United States)

    Goranson, H. T.

    1986-01-01

    The Technical and Management Information System (TMIS) must employ on enlightened approach to its object structure, but basic issues in conceptual structuring remain to be resolved. Sirius outlines the necessary agenda and reports on progress toward solutions.

  19. Iron Isotope Fractionation Reveals Structural Change upon Microbial and Chemical Reduction of Nontronite NAu-1

    Science.gov (United States)

    Liu, K.; Wu, L.; Shi, B.; Smeaton, C. M.; Li, W.; Beard, B. L.; Johnson, C.; Roden, E. E.; Van Cappellen, P.

    2015-12-01

    Iron (Fe) isotope fractionations were determined during reduction of structural Fe(III) in nontronite NAu-1 biologically by Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA and chemically by dithionite. ~10% reduction was achieved in biological reactors, with similar reduction extents obtained by dithionite. We hypothesize that two stages occurred in our reactors. Firstly, reduction started from edge sites of clays and the produced Fe(II) partially remained in situ and partially was released into solution. Next aqueous Fe(II) adsorbed onto basal planes. The basal sorbed Fe(II) then undergoes electron transfer and atom exchange (ETAE) with octahedral Fe(III) in clays, with the most negative fractionation factor Δ56Febasal Fe(II)-structural Fe(III)of -1.7‰ when basal sorption reached a threshold value. Secondly, when the most reactive Fe(III) was exhausted, bioreduction significantly slowed down and chemical reduction was able to achieve 24% due to diffusion of small size dithionite. Importantly, no ETAE occurred between basal Fe(II) and structural Fe(III) due to blockage of pathways by collapsed clay layers. This two-stage process in our reduction experiments is distinctive from abiotic exchange experiments by mixing aqueous Fe(II) and NAu-1, where no structural change of clay would block ETAE between basal Fe(II) and structural Fe(III). The separation of reduction sites (clay edges) and sorption sites (basal planes) is unique to clay minerals with layered structure. In contrast, reduction and sorption occur on the same sites on the surfaces of Fe oxyhydroxides, where reduction does not induce structure change. Thus, the Fe isotope fractionations are the same for reduction and abiotic exchange experiments for Fe oxides. Our study reveals important changes in electron transfer and atom exchange pathways upon reduction of clay minerals by dissimilatory Fe reducing bacteria, which is prevalent in anoxic soils and sediments.

  20. The influence of condensed tannin structure on rate of microbial mineralization and reactivity to chemical assays.

    Science.gov (United States)

    Norris, Charlotte E; Preston, Caroline M; Hogg, Karen E; Titus, Brian D

    2011-03-01

    We examined how tannin structure influences reactivity in tannin assays and carbon and nitrogen mineralization. Condensed tannins from the foliage of ten tree and shrub species and from pecan shells (Carya illinoensis) had different proportions of: (a) epicatechin (cis) and catechin (trans) isomers, (b) procyanidin (PC) and prodelphinidin (PD) monomers, and (c) different chain lengths. The response of each tannin to several widely used tannin assays was determined. Although there was some variation in response to proanthocyanidin (butanol/HCl) and Folin Ciocalteu assays, we did not deduce any predictable relationship between tannin structure and response to either assay. There was little variation in protein precipitation among the different tannins. To assess biological activity, six of the tannins were incubated with forest humus for 22 days. We determined that, while PC-based tannins remained at least partly extractable for the duration of the incubation, tannins with a high proportion of PD subunits rapidly became unextractable from soil. There was a positive correlation between net nitrogen mineralization and cis chemical structure. Carbon mineralization was enhanced initially by the addition of tannins to humus, but after 22 days, a negative correlation between the proportion of cis subunits and respiration was determined. Overall, we were not able to demonstrate consistent effects of structure on either microbial mineralization or reactivity to chemical assays; such relationships remain elusive.

  1. Identification of Interaction Hot Spots in Structures of Drug Targets on the Basis of Three-Dimensional Activity Cliff Information.

    Science.gov (United States)

    Furtmann, Norbert; Hu, Ye; Gütschow, Michael; Bajorath, Jürgen

    2015-12-01

    Activity cliffs are defined as pairs or groups of structurally similar or analogous compounds that share the same specific activity but have large differences in potency. Although activity cliffs are mostly studied in medicinal chemistry at the level of molecular graphs, they can also be assessed by comparing compound binding modes. If such three-dimensional activity cliffs (3D-cliffs) are studied on the basis of X-ray complex structures, experimental ligand-target interaction details can be taken into account. Rapid growth in the number of 3D-cliffs that can be derived from X-ray complex structures has made it possible to identify targets for which a substantial body of 3D-cliff information is available. Activity cliffs are typically studied to identify structure-activity relationship determinants and aid in compound optimization. However, 3D-cliff information can also be used to search for interaction hot spots and key residues, as reported herein. For six of seven drug targets for which more than 20 3D-cliffs were available, series of 3D-cliffs were identified that were consistently involved in interactions with different hot spots. These 3D-cliffs often encoded chemical modifications resulting in interactions that were characteristic of highly potent compounds but absent in weakly potent ones, thus providing information for structure-based design.

  2. Integrating Chemical Information Instruction into the Chemistry Curriculum on Borrowed Time: The Multiyear Development and Evolution of a Virtual Instructional Tutorial

    Science.gov (United States)

    Jacobs, Danielle L.; Dalal, Heather A.; Dawson, Patricia H.

    2016-01-01

    The impetus to incorporate instruction on the efficient and responsible practice of chemical information literacy into the undergraduate chemistry curriculum has become exceptionally urgent. At Rider University, Chemical Information Instruction (CII) has accordingly evolved from face-to-face sessions into online modules to embed information…

  3. Advances in Chemical and Structural Characterization of Concretion with Implications for Modeling Marine Corrosion

    Science.gov (United States)

    Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Carr, James D.; Conlin, David L.

    2014-05-01

    The Weins number model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selected-area EDS data collection at precise locations is presented in terms of atomic percent. The mechanism of formation and distribution of the iron-bearing mineral species at specific locations will be presented. Based on water retention measurements, porosity in terms of void volume varies from 15 v/o to 30 v/o (vol.%). The void path displayed by scanning electron microscopy imaging illustrates the tortuous path by which oxygen migrates in the water phase within the concretion from seaside to metalside.

  4. Heterogeneity of Physico-Chemical Properties in Structured Soils and Its Consequences

    Institute of Scientific and Technical Information of China (English)

    E. JASINSKA; H. WETZEL; T. BAUMGARTL; R. HORN

    2006-01-01

    Structured soils are characterized by the presence of inter- and intra-aggregate pore systems and aggregates, which show varying chemical, physical, and biological properties depending on the aggregate type and land use system. How far these aspects also affect the ion exchange processes and to what extent the interaction between the carbon distribution and kind of organic substances affect the internal soil strength as well as hydraulic properties like wettability are still under discussion. Thus, the objective of this research was to clarify the effect of soil aggregation on physical and chemical properties of structured soils at two scales: homogenized material and single aggregates. Data obtained by sequentially peeling off soil aggregates layers revealed gradients in the chemical composition from the aggregate surface to the aggregatecore. In aggregates from long term untreated forest soils we found lower amounts of carbon in the external layer, while in arable soils the differentiation was not pronounced. However, soil aggregates originating from these sites exhibited a higher concentration of microbial activity in the outer aggregate layer and declined towards the interior. Furthermore,soil depth and the vegetation type affected the wettability. Aggregate strength depended on water suction and differences in tillage treatments.

  5. Effects of age and sex on the structural, chemical and technological characteristics of mule duck meat.

    Science.gov (United States)

    Baeza, E; Salichon, M R; Marche, G; Wacrenier, N; Dominguez, B; Culioli, J

    2000-07-01

    1. The aim of the study was to analyse the effect of age and sex on the chemical, structural and technological characteristics of mule duck meat. 2. Ten males and 10 females were weighed and slaughtered at 8, 10, 11, 12 and 13 weeks of age. Weight, pH value, colour, tenderness and juice loss of breast muscle were determined. 3. The activities of 3 enzymes (citrate synthase, beta-hydroxyacyl CoA dehydrogenase, lactate dehydrogenase) which indicate muscular metabolic activity were assayed. 4. Chemical composition (moisture, lipids, proteins, minerals, lipid and phospholipid classes, fatty acid composition) of breast muscle was analysed. 5. Fibre type, fibre type percentage and cross-sectional areas were determined using histochemistry and an image analysis system. 6. For growth performance and muscular structure, the ideal slaughter age of mule ducks is 10 weeks of age. Chemical and technological analysis indicated that muscular maturity in Pectoralis major was reached at 11 weeks of age, but, at this age, breast lipid content is high. Moreover, after 10 weeks of age, food costs rapidly increased. 7. Lastly, sexual dimorphism for body weight is minor. In this study, at any given age, no significant differences between males and females were shown. Thus, it is possible to rear both sexes together and to slaughter them at the same age.

  6. Network structural analysis using directed graph for chemical reaction analysis in weakly-ionized plasmas

    Science.gov (United States)

    Nobuto, Kyosuke; Mizui, Yasutaka; Miyagi, Shigeyuki; Sakai, Osamu; Murakami, Tomoyuki

    2016-09-01

    We visualize complicated chemical reaction systems in weakly-ionized plasmas by analysing network structure for chemical processes, and calculate some indexes by assuming interspecies relationships to be a network to clarify them. With the current social evolution, the mean size of general data which we can use in computers grows huge, and significance of the data analysis increases. The methods of the network analysis which we focus on in this study do not depend on a specific analysis target, but the field where it has been already applied is still limited. In this study, we analyse chemical reaction systems in plasmas for configuring the network structure. We visualize them by expressing a reaction system in a specific plasma by a directed graph and examine the indexes and the relations with the characteristic of the species in the reaction system. For example, in the methane plasma network, the centrality index reveals importance of CH3 in an influential position of species in the reaction. In addition, silane and atmospheric pressure plasmas can be also visualized in reaction networks, suggesting other characteristics in the centrality indexes.

  7. Structural properties of zinc oxide and titanium dioxide nanoparticles prepared by chemical vapor synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Akgul, Guvenc, E-mail: guvencakgul@gmail.com [Bor Vocational School, Nigde University, 51700 Nigde (Turkey); Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States); Akgul, Funda Aksoy [Physics Department, Nigde University, 51240 Nigde (Turkey); Attenkofer, Klaus [Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States); Winterer, Markus [Nanoparticle Process Technology, Department of Engineering Sciences, and Center for NanoIntegration Duisburg-Essen, CeNIDE, University of Duisburg-Essen (Germany)

    2013-03-25

    Highlights: ► Local structure determination of ZnO and TiO{sub 2} nanostructures by XANES and EXAFS. ► Zn K and Ti K absorption edge XANES investigations of nanopowder samples. ► Investigation of pre-edge peak features of TiO{sub 2} nanosamples. ► Obtaining of local structure parameters of nano ZnO and TiO{sub 2} using EXAFS. ► Good agreement of EXAFS results and crystal structure datas. -- Abstract: Transition metal (TM) oxides provide a wide range of functional materials especially when nanostructured. Titanium dioxide (TiO{sub 2}) and wurtzite type zinc oxide (ZnO) nanostructured materials were fabricated by chemical vapor synthesis (CVS). Crystal and local structures of the prepared nanosamples were ascertained using X-ray diffraction (XRD), X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) techniques. Based on the XRD data, a second phase(s) was not found in both samples. A single wurtzite and anatase type structures were observed in ZnO and TiO{sub 2} nanosamples, respectively. Ti K pre-edge features of XANES spectrum indicated the presence of sixfold coordinated Ti in TiO{sub 2} nanosamples. The results showed that CVS is quite useful method to produce high crystalline nanoparticles.

  8. On the Development and Use of Large Chemical Similarity Networks, Informatics Best Practices and Novel Chemical Descriptors Towards Materials Quantitative Structure Property Relationships

    Science.gov (United States)

    Krein, Michael

    ZINC data set, a qHTS PubChem bioassay, as well as the protein binding sites from the PDB. The characteristics of these networks are compared and contrasted with those of the bioassay Structure Activity Landscape Index (SALI) subnetwork, which maps discontinuities or cliffs in the structure activity landscape. Mapping this newly generated information over underlying chemistry space networks generated using different descriptors demonstrates local modeling capacity and can guide the choice of better local representations of chemistry space. Chapter 2 introduces and demonstrates this novel concept, which also enables future work in visualization and interpretation of chemical spaces. Initially, it was discovered that there were no community-available tools to leverage best-practice ideas to comprehensively build, compare, and interpret QSPRs. The Yet Another Modeling System (YAMS) tool performs a series of balanced, rational decisions in dataset preprocessing and parameter/feature selection over a choice of modeling methods. To date, YAMS is the only community-available informatics tool that performs such decisions consistently between methods while also providing multiple model performance comparisons and detailed descriptor importance information. The focus of the tool is thus to convey rich information about model quality and predictions that help to "close the loop" between modeling and experimental efforts, for example, in tailoring nanocomposite properties. Polymer nanocomposites (PNC) are complex material systems encompassing many potential structures, chemistries, and self assembled morphologies that could significantly impact commercial and military applications. There is a strong desire to characterize and understand the tradespace of nanocomposites, to identify the important factors relating nanostructure to materials properties and determine an effective way to control materials properties at the manufacturing scale. Due to the complexity of the systems

  9. YNi and its hydrides: Phase stabilities, electronic structures and chemical bonding properties from first principles

    Energy Technology Data Exchange (ETDEWEB)

    Matar, S.F., E-mail: matar@icmcb-bordeaux.cnrs.fr [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Docteur Albert Schweitzer, F-33608 Pessac (France); Nakhl, M. [Universite Libanaise, Laboratoire de Chimie-Physique des Materiaux LCPM, Fanar (Lebanon); Al Alam, A.F.; Ouaini, N. [Universite Saint-Esprit de Kaslik, Faculte des Sciences et de Genie Informatique, Jounieh (Lebanon); Chevalier, B. [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Docteur Albert Schweitzer, F-33608 Pessac (France)

    2010-11-25

    Graphical abstract: Base centered orthorhombic YNiH{sub X} structure. For x = 3, only H1 and H2 are present. Highest hydrogen content YNiH{sub 4} is obtained when H3 are added. - Abstract: Within density functional theory, establishing the equations of states of YNi in two different controversial structures in the literature, leads to determine the orthorhombic FeB-type as the ground state one with small energy difference. For YNiH{sub 3} and YNiH{sub 4} hydrides crystallizing in the orthorhombic CrB-type structure the geometry optimization and the ab initio determination of the H atomic positions show that the stability of hydrogen decreases from the tri- to the tetra- hydride. New states brought by hydrogen within the valence band lead to its broadening and to enhanced localization of metal density of states. The chemical bonding analysis shows a preferential Ni-H bonding versus Y-H.

  10. Study of the chemical structure of petroleum asphaltenes by spectral methods

    Energy Technology Data Exchange (ETDEWEB)

    Posadov, I.A.; Pokonova, Yu.V.; Khusidman, M.B.; Gitlin, I.G.; Proskuryakov, V.A.

    1977-03-01

    Results of nuclear magnetic resonance (NMR), ultraviolet (UV), and infrared (IR) spectroscopy studies of the chemical and supermolecular structure of asphaltene concentrates isolated from petroleum residues are reported. Considerable intensity of a characteristic series of absorption bands at 750, 810, 870, 1560, 1600, and 3030 cm/sup -1/ is interpreted as indicative of aromatic structures; while the bands at 870 and 810 cm/sup -1/ are taken as evidence of the predominant presence of highly substituted aromatic rings which are apparently included in alicyclic structures but do not form polynuclear condensed aromatic systems. The bathochromic shift of the electronic absorption spectrum in the region of 250-600 nm and the weak inflection at 300-310 nm are attributed to the partial condensation of the aromatic rings with predominance of fragments of the bi- and tricyclic types. The percentage content of various organic groups, the degree of polycondensation, the degree of potential for substitution, and the elementary composition are reported.

  11. The Structure of Adjustment Costs in Information Technology Investment

    OpenAIRE

    Hyunbae Chun; Sung-Bae Mun

    2005-01-01

    We examine the pattern of information technology (IT) capital adjustment using data from U.S. industries. Using the gap between actual and desired IT capital stocks, we estimate the shape of the adjustment cost function in IT investment. Both ordinary least squares and nonparametric regression estimates support irreversibility in IT investment.

  12. Structural optimization for materially informed design to robotic production processes

    NARCIS (Netherlands)

    Bier, H.H.; Mostafavi, S.

    2015-01-01

    Hyperbody’s materially informed Design-to-Robotic-Production (D2RP) processes for additive and subtractive manufacturing aim to achieve performative porosity in architecture at various scales. An extended series of D2RP experiments aiming to produce prototypes at 1:1 scale wherein design materiality

  13. New Potentiometric Wireless Chloride Sensors Provide High Resolution Information on Chemical Transport Processes in Streams

    Science.gov (United States)

    Smettem, Keith; Harris, Nick; Cranny, Andy; Klaus, Julian; Pfister, Laurent

    2016-04-01

    Quantifying the travel times, pathways and dispersion of solutes moving through stream environments is critical for understanding the biogeochemical cycling processes that control ecosystem functioning. Validation of stream solute transport and exchange process models requires data obtained from in-stream measurement of chemical concentration changes through time. This can be expensive and time consuming, leading to a need for cheap distributed sensor arrays that respond instantly and record chemical transport at points of interest on timescales of seconds. To meet this need we apply new, low-cost (in the order of a euro per sensor) potentiometric chloride sensors used in a distributed array to obtain data with high spatial and temporal resolution. The application here is to monitoring in-stream hydrodynamic transport and dispersive mixing of an injected chemical, in this case NaCl. We present data obtained from the distributed sensor array under baseflow conditions for three stream reaches in Luxembourg. Sensor results are comparable to data obtained from more expensive electrical conductivity meters and allow spatial resolution of hydrodynamic mixing processes and identification of chemical 'dead zones' in the study reaches.

  14. Access and use of information resources in assessing health risks from chemicals in food

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, W.A. [Department of Agriculture, Beltsville, MD (United States)

    1990-12-31

    The Food Safety and Inspection Service (FSIS) is responsible for the wholesomeness, safety, and adulteration-free status of meat and poultry. The agency developed the National Residue Program (NRP) to monitor these products for residue of drugs, pesticides, and environmental contaminants. Today, few chemical residues are detected in meat and poultry because of the success of the NRP. 3 figs.

  15. The Safety "Use Case": Co-Developing Chemical Information Management and Laboratory Safety Skills

    Science.gov (United States)

    Stuart, Ralph B.; McEwen, Leah R.

    2016-01-01

    The 2015 edition of the American Chemical Society's "Guidelines and Evaluation Procedures for Bachelor's Degree Programs" identifies six skill sets that undergraduate chemistry programs should instill in their students. In our roles as support staff for chemistry departments at two different institutions (one a Primarily Undergraduate…

  16. Designing and Evaluating an Evidence-Informed Instruction in Chemical Kinetics

    Science.gov (United States)

    Cakmakci, Gultekin; Aydogdu, Cemil

    2011-01-01

    We have investigated the effects of a teaching intervention based on evidence from educational theories and research data, on students' ideas in chemical kinetics. A quasi-experimental design was used to compare the outcomes for the intervention. The subjects of the study were 83 university first-year students, who were in two different classes in…

  17. Environmental laws regulating chemicals: Uses of information in decision making under environmental statutes

    Energy Technology Data Exchange (ETDEWEB)

    Gaba, J.M. [Southern Methodist Univ., Dallas, TX (United States)

    1990-12-31

    Three areas are addressed in this paper: generic issues that arise simply in the process of decision-making under environmental statutes; different decision-making standards under various environmental statutes; and efforts to legislate a {open_quotes}safe{close_quotes} or {open_quotes}acceptable{close_quotes} risk from exposure to carcinogenic chemicals.

  18. Structure and chemical characteristics of natural mineral deposit Terbunskaya (Lipetsk region, Russia)

    Energy Technology Data Exchange (ETDEWEB)

    Motyleva, S., E-mail: motyleva-svetlana@mail.ru; Mertvishcheva, M. [All-Russian Horticular Institute for Breeding, Agrotechnology and Nursery Russian Academy of Agricultural Sciences, Moskow (Russian Federation); Shchuchka, R.; Gulidova, V. [Yelets state university named after I. A. Bunin, Yelets (Russian Federation)

    2015-07-22

    New knowledge about the mineralogical features Terbunsky mineral. Investigated 5 fractions isolated from the incision (2-2,5 m). Terbunskaya deposit belongs to minerals Santonian age. Scanning electron microscopy and energy dispersive analysis of fractions isolated studied in detail. In the coarse fractions found ancient organic remains of algae and micro-organisms that have been sedimented together with the mineral component during geological periods. The share of organic inclusions does not exceed 1.5%. Chemical composition confirms the presence of silicon and carbonate organisms. Advantageously proportion of minerals having a layered structure with a plurality of micro and nano pore size 600 - 80-nm and an average chemical composition (wt%): Na (0,64), Mg (0,54), Al (13.48), Si (27 57), K (2.39) Ca (0.75)

  19. On the Comparability of Chemical Structure and Roughness of Nanochannels in Altering Fluid Slippage

    CERN Document Server

    Misra, Chinmay Anand

    2016-01-01

    Interfacial hydrodynamic slippage of water depends on both on surface chemistry and roughness. This study tries to connect the effect of chemical property and the physical structure of the surface on the interfacial slippage of water. By performing molecular dynamics simulations (MDS) of Couette flow of water molecules over a reduced Lennard-Jones (LJ) surface, the velocity profile is obtained and extrapolated to get the slip lengths. The slip lengths are measured for various surface-fluid interactions. These interactions are varied by changing the wettability of the surface (characterized by the static contact angle) and its roughness. The slip length variation with the static contact angle as $(1+cos\\theta)^{-2}$ is observed. However, it is also observed that the presence of surface roughness always reduces the slip length and it is proposed that the slip length varies with non-dimensionalized average surface roughness as $(1+\\alpha^*)^{-2}$ . Thus a relation between the chemical wettability and the physica...

  20. Structural, chemical and magnetic properties of secondary phases in Co-doped ZnO

    Energy Technology Data Exchange (ETDEWEB)

    Ney, A; Ney, V; Ye, S; Ollefs, K; Kammermeier, T [Fakultaet fuer Physik and CeNIDE, Universitaet Duisburg-Essen, Lotharstrasse 1, D-47057 Duisburg (Germany); Kovacs, A; Dunin-Borkowski, R E [Center for Electron Nanoscopy, Technical University of Denmark, DK-2800 Kgs Lyngby (Denmark); Wilhelm, F; Rogalev, A, E-mail: andreas.ney@uni-due.de [European Synchrotron Radiation Facility (ESRF), 6 Rue Jules Horowitz, BP 220, 38043 Grenoble Cedex (France)

    2011-10-15

    We have utilized a comprehensive set of experimental techniques such as transmission electron microscopy (TEM) and synchrotron-based x-ray absorption spectroscopy (XAS) and the respective x-ray linear dichroism and x-ray magnetic circular dichroism to characterize the correlation of structural, chemical and magnetic properties of Co-doped ZnO samples. It can be established on a quantitative basis that the superparamagnetic (SPM) behavior observed by integral superconducting quantum interference device magnetometry is not an intrinsic property of the material but stems from precipitations of metallic Co. Their presence is revealed by TEM as well as XAS. Annealing procedures for these SPM samples were also studied, and the observed changes in the magnetic properties found to be due to a chemical reduction or oxidation of the metallic Co species. (paper)

  1. Structural, Mechanical and Optical Properties of Plasma-chemical Si-C-N Films

    Directory of Open Access Journals (Sweden)

    A.O. Kozak

    2014-11-01

    Full Text Available An influence of the substrate temperature in the range of 40-400 °C on the properties of the Si-C-N films deposited by plasma enhanced chemical vapor deposition (PECVD technique using hexamethyldisilazane is analyzed. Study of the structure, chemical bonding, surface morphology, mechanical properties and energy gap of the obtained films was carried out using X-ray diffraction, infrared spectroscopy, X-ray photoelectron spectroscopy, atomic force microscopy, optical measurements and nanoindentation. It was established that all the films were X-ray amorphous and had low surface roughness. Intensive hydrogen effusion from the films takes place, when substrate temperature increases up to 400 °C, which promotes a decrease of roughness and an increase in hardness and Young modules more than twice.

  2. Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.

    Directory of Open Access Journals (Sweden)

    Lotta Berg

    Full Text Available Acetylcholinesterase (AChE is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia to treat cholinergic deficiencies (e.g. in Alzheimer's disease, but may also act as dangerous toxins (e.g. nerve agents such as sarin. Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS. Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685•mAChE is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical

  3. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

    Science.gov (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds.

  4. Bibliography of information on mechanics of structural failure

    Science.gov (United States)

    Carpenter, J. L., Jr.; Moya, N.; Shaffer, R. A.; Smith, D. M.

    1973-01-01

    A bibliography of approximately 1500 reference citations related to six problem areas in the mechanics of failure in aerospace structures is presented. The bibliography represents a search of the literature published in the ten year period 1962-1972 and is largely limited to documents published in the United States. Listings are subdivided into the six problem areas: (1) life prediction of structural materials; (2) fracture toughness data; (3) fracture mechanics analysis; (4) hydrogen embrittlement; (5) protective coatings; and (6) composite materials. An author index is included.

  5. [Integrating information about imaging biomarkers into structured radiology reports].

    Science.gov (United States)

    Pomar-Nadal, A; Pérez-Castillo, C; Alberich-Bayarri, A; García-Martí, G; Sanz Requena, R; Martí-Bonmatí, L

    2013-01-01

    Imaging biomarkers describe objective characteristics that are related to normal biological processes, diseases, or the response to treatment. They enable radiologists to incorporate into their reports data about structure, function, and tissue components. With the aim of taking maximum advantage of the quantification of medical images, we present a procedure to integrate imaging biomarkers into radiological reports, bringing the new paradigm of personal medicine closer to radiological workflow. In this manner, the results of quantification can complement traditional radiological diagnosis, improving accuracy and the evaluation of the efficacy of treatments. A more personalized, standardized, structured radiological report should include quantitative analyses to complement conventional qualitative reporting in selected cases.

  6. 76 FR 32196 - Certain New Chemicals; Receipt and Status Information; Correction

    Science.gov (United States)

    2011-06-03

    ... technical information contact: Bernice Mudd, Information Management Division, Office of Pollution Prevention... preamble for FR Doc. 2011-8574 published in the Federal Register of April 15, 2011 (76 FR 21339) (FRL-8869... Coatings (S) Designated use (S) 2-propenoic Inc. of this polymer is acid, 2-methyl-, 2- for...

  7. Network structure and patterns of information diversity on Twitter

    CERN Document Server

    Shore, Jesse; Dellarocas, Chrysanthos

    2016-01-01

    Social media have great potential to support diverse information sharing, but there is widespread concern that platforms like Twitter do not result in communication between those who hold contradictory viewpoints. Because users can choose whom to follow, prior research suggests that social media users exist in 'echo chambers' or become polarized. We seek evidence of this in a complete cross section of hyperlinks posted on Twitter, using previously validated measures of the political slant of news sources to study information diversity. Contrary to prediction, we find that the average account posts links to more politically moderate news sources than the ones they receive in their own feed. However, members of a tiny network core do exhibit cross-sectional evidence of polarization and are responsible for the majority of tweets received overall due to their popularity and activity, which could explain the widespread perception of polarization on social media.

  8. SVEN: Informative Visual Representation of Complex Dynamic Structure

    Science.gov (United States)

    2014-12-23

    node-link diagram on a timeline, with nodes representing events such as the publication of a scientific paper. Network analysts can often still gain...patterns in scientific literature. Journal of the American Society for Information Science and Technology, 57(3):359–377, 2006. [17] Tim Dwyer...Scalable, versatile and simple constrained graph layout. Computer Graph- ics Forum, 28(3):991–998, 2009. [18] Tim Dwyer and Peter Eades. Visualising a fund

  9. Structural information from OH stretching frequencies monohydric saturated alcohols

    NARCIS (Netherlands)

    Maas, J.H. van der; Lutz, E.T.G.

    1974-01-01

    Infrared data have been recorded of the hydroxyl stretching band for about 70 monohydric saturated alcohols in dilute carbon tetrachloride solution. The wavenumber maximum, the half-bandwidth and the band pattern could be related to the structure of the molecules. Not only primary, secondary and ter

  10. Score region algebra : a flexible framework for structured information retrieval

    NARCIS (Netherlands)

    Mihajlovic, Vojkan

    2006-01-01

    Approximately three decades ago researchers realized that they would have to structure data to be able to store and access large amounts of data streams that were produced each day. As a result, database management systems were designed and developed, used to keep the data in one place and for findi

  11. Communication by euro area central bankers : structure, information and effectiveness

    NARCIS (Netherlands)

    Jansen, D.J.

    2006-01-01

    This thesis is an empirical study of communication by euro area central bankers. Its remainder is structured as follows: chapter 2, ECB communication during the first years of the EMU, describes communication by euro area central bankers during the period January 1999 to May 2002. Amongst other thin

  12. Microwave-Assisted Extraction, Chemical Structures, and Chain Conformation of Polysaccharides from a Novel Cordyceps Sinensis Fungus UM01.

    Science.gov (United States)

    Cheong, Kit-Leong; Wang, Lan-Ying; Wu, Ding-Tao; Hu, De-Jun; Zhao, Jing; Li, Shao-Ping

    2016-09-01

    Cordyceps sinensis is a well-known tonic food with broad medicinal properties. The aim of the present study was to investigate the optimization of microwave-assisted extraction (MAE) and characterize chemical structures and chain conformation of polysaccharides from a novel C. sinensis fungus UM01. Ion-exchange and gel filtration chromatography were used to purify the polysaccharides. The chemical structure of purified polysaccharide was determined through gas chromatography-mass spectrometry. Moreover, high performance size exclusion chromatography combined with refractive index detector and multiangle laser light scattering were conducted to analyze the molecular weight (Mw ) and chain conformation of purified polysaccharide. Based on the orthogonal design L9 , optimal MAE conditions could be obtained through 1300 W of microwave power, with a 5-min irradiation time at a solid to water ratio of 1:60, generating the highest extraction yield of 6.20%. Subsequently, the polysaccharide UM01-S1 was purified. The UM01-S1 is a glucan-type polysaccharide with a (1→4)-β-d-glucosyl backbone and branching points located at O-3 of Glcp with a terminal-d-Glcp. The Mw , radius of gyration (Rg ) and hydrodynamic radius (Rh ) of UM01-S1 were determined as 5.442 × 10(6)  Da, 21.8 and 20.2 nm, respectively. Using the polymer solution theory, the exponent (ν) value of the power law function was calculated as 0.38, and the shape factor (ρ = Rg /Rh ) was 1.079, indicating that UM01-S1 has a sphere-like conformation with a branched structure in an aqueous solution. These results provide fundamental information for the future application of polysaccharides from cultured C. sinensis in health and functional food area.

  13. STUDIES ON THE CHEMICAL STRUCTURES OF ACTIVATED CARBON FIBERS BY SOLID STATE NMR

    Institute of Scientific and Technical Information of China (English)

    FURuowen; HuangWenqiang; 等

    1999-01-01

    The solid state C13-NMR spectra of different ACFs from various precursor fibers were recorded in this paper,The effects of activation conditions on chemical structures of ACFs,as well as the changes of chemical structures during carbonization and redox reaction were inverstigated by NMR technique,At same time,the soild state P31-NMR spectra of ACFS are studied.The C13-NMR spectra of ACFs can be divided into six bands that are assigned to methyl and methylene groups,hydroxyl and ether groups.acetal (or methylenedioxy) carbon,graphite-like aromatic carbon structure,phenol,and quinone groups,respectively.Only phosphorous pentoxide exists on ACFs and CFs.Moreover,most of them are stuck over the crystal face but not at the edge of graphite-like micro-crystal.The carbonization and activation conditions affect the C13-NMR spectra of ACFs.The experimental rsults indicate that the redox reaction of ACFs with oxidants greatly consumes C-H group.

  14. Structural, optical and electrical properties of chemically derived nickel substituted zinc ferrite nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Chakrabarty, S. [Department of Physics, The University of Burdwan, Burdwan 713 104 (India); Pal, M., E-mail: palm@cgcri.res.in [CSIR-Central Glass and Ceramic Research Institute, Kolkata 700032 (India); Dutta, A., E-mail: adutta@phys.buruniv.ac.in [Department of Physics, The University of Burdwan, Burdwan 713 104 (India)

    2015-03-01

    Single phase spinel Ni substituted nanocrystalline Zn ferrites have been synthesized using a soft chemical route. Effect of Ni substitution on structure, electrical and optical properties has been investigated. X-ray diffraction study confirms the growth of single phase nanocrystalline Ni substituted Zn ferrites. FTIR and UV–Visible studies delineate the change in structure and optical band gap due to inclusion of Ni ions. Substitution of Ni ion has been manifested on lattice parameter which systematically decreases from 8.448 Å to 8.280 Å. An initial increase followed by subsequent decrease in optical band gap with the increase in Ni content is observed. In addition, both ac and dc electrical studies shows anomalous behavior in conductivity and dielectric properties for the samples having Ni content in the range 0.2–0.6 mol fraction which can be attributed to the normal to inverse spinel structural changes. - Highlights: • Pure single phase nanocrystalline Zn/Ni ferrites by facile soft chemical route. • Changes in microstructural parameters of Zn ferrite is observed due to Ni inclusion. • Optical band gap shows a maximum while the concentration of Ni increases. • Inverse to spinal ferrite change is observed in ac and dc electrical properties.

  15. Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.

    Science.gov (United States)

    Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

    2012-10-24

    The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory.

  16. Control of interface nanoscale structure created by plasma-enhanced chemical vapor deposition.

    Science.gov (United States)

    Peri, Someswara R; Akgun, Bulent; Satija, Sushil K; Jiang, Hao; Enlow, Jesse; Bunning, Timothy J; Foster, Mark D

    2011-09-01

    Tailoring the structure of films deposited by plasma-enhanced chemical vapor deposition (PECVD) to specific applications requires a depth-resolved understanding of how the interface structures in such films are impacted by variations in deposition parameters such as feed position and plasma power. Analysis of complementary X-ray and neutron reflectivity (XR, NR) data provide a rich picture of changes in structure with feed position and plasma power, with those changes resolved on the nanoscale. For plasma-polymerized octafluorocyclobutane (PP-OFCB) films, a region of distinct chemical composition and lower cross-link density is found at the substrate interface for the range of processing conditions studied and a surface layer of lower cross-link density also appears when plasma power exceeds 40 W. Varying the distance of the feed from the plasma impacts the degree of cross-linking in the film center, thickness of the surface layer, and thickness of the transition region at the substrate. Deposition at the highest power, 65 W, both enhances cross-linking and creates loose fragments with fluorine content higher than the average. The thickness of the low cross-link density region at the air interface plays an important role in determining the width of the interface built with a layer subsequently deposited atop the first.

  17. On the structure and topography of free-standing chemically modified graphene

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, N R; Pandey, P A; Beanland, R; Lupo, U; Rowlands, G; Roemer, R A [Department of Physics, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL (United Kingdom); Rourke, J P, E-mail: Neil.Wilson@Warwick.ac.uk [Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL (United Kingdom)

    2010-12-15

    The mechanical, electrical and chemical properties of chemically modified graphene (CMG) are intrinsically linked to its structure. Here, we report on our study of the topographic structure of free-standing CMG using atomic force microscopy (AFM) and electron diffraction. We find that, unlike graphene, suspended sheets of CMG are corrugated and distorted on nanometre length scales. AFM reveals not only long-range (100 nm) distortions induced by the support, as previously observed for graphene, but also short-range corrugations with length scales down to the resolution limit of 10 nm. These corrugations are static not dynamic, and are significantly diminished on CMG supported on atomically smooth substrates. Evidence for even shorter-range distortions, down to a few nanometres or less, is found by electron diffraction of suspended CMG. Comparison of the experimental data with simulations reveals that the mean atomic displacement from the nominal lattice position is of order 10% of the carbon-carbon bond length. Taken together, these results suggest a complex structure for CMG where heterogeneous functionalization creates local strain and distortion.

  18. On the structure and topography of free-standing chemically modified graphene

    Science.gov (United States)

    Wilson, N. R.; Pandey, P. A.; Beanland, R.; Rourke, J. P.; Lupo, U.; Rowlands, G.; Römer, R. A.

    2010-12-01

    The mechanical, electrical and chemical properties of chemically modified graphene (CMG) are intrinsically linked to its structure. Here, we report on our study of the topographic structure of free-standing CMG using atomic force microscopy (AFM) and electron diffraction. We find that, unlike graphene, suspended sheets of CMG are corrugated and distorted on nanometre length scales. AFM reveals not only long-range (100 nm) distortions induced by the support, as previously observed for graphene, but also short-range corrugations with length scales down to the resolution limit of 10 nm. These corrugations are static not dynamic, and are significantly diminished on CMG supported on atomically smooth substrates. Evidence for even shorter-range distortions, down to a few nanometres or less, is found by electron diffraction of suspended CMG. Comparison of the experimental data with simulations reveals that the mean atomic displacement from the nominal lattice position is of order 10% of the carbon-carbon bond length. Taken together, these results suggest a complex structure for CMG where heterogeneous functionalization creates local strain and distortion.

  19. Voting-based consensus clustering for combining multiple clusterings of chemical structures

    Directory of Open Access Journals (Sweden)

    Saeed Faisal

    2012-12-01

    Full Text Available Abstract Background Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster. Results The cumulative voting-based aggregation algorithm (CVAA, cluster-based similarity partitioning algorithm (CSPA and hyper-graph partitioning algorithm (HGPA were examined. The F-measure and Quality Partition Index method (QPI were used to evaluate the clusterings and the results were compared to the Ward’s clustering method. The MDL Drug Data Report (MDDR dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward’s method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward’s method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria. Conclusions The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA was the method of choice among consensus clustering methods.

  20. The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation

    Science.gov (United States)

    Xia, Yan; DiPrimio, Nina; Keppel, Theodore R.; Vo, Binh; Fraser, Keith; Battaile, Kevin P.; Egan, Chet; Bystroff, Christopher; Lovell, Scott; Weis, David D.; Anderson, J. Christopher; Karanicolas, John

    2014-01-01

    The ability to selectively activate function of particular proteins via pharmacological agents is a longstanding goal in chemical biology. Recently, we reported an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. However, rationally identifying analogous de novo binding sites in other enzymes represents a key challenge for extending this approach to introduce allosteric control into other enzymes. Here we show that mutation sites leading to protein inactivation via tryptophan-to-glycine substitution and allowing (partial) reactivation by the subsequent addition of indole are remarkably frequent. Through a suite of methods including a cell-based reporter assay, computational structure prediction and energetic analysis, fluorescence studies, enzymology, pulse proteolysis, x-ray crystallography and hydrogen-deuterium mass spectrometry we find that these switchable proteins are most commonly modulated indirectly, through control of protein stability. Addition of indole in these cases rescues activity not by reverting a discrete conformational change, as we had observed in the sole previously reported example, but rather rescues activity by restoring protein stability. This important finding will dramatically impact the design of future switches and sensors built by this approach, since evaluating stability differences associated with cavity-forming mutations is a far more tractable task than predicting allosteric conformational changes. By analogy to natural signaling systems, the insights from this study further raise the exciting prospect of modulating stability to design optimal recognition properties into future de novo switches and sensors built through chemical rescue of structure. PMID:24313858

  1. Quantum chemical prediction of vibrational spectra of large molecular systems with radical or metallic electronic structure

    Science.gov (United States)

    Nishimoto, Yoshio; Irle, Stephan

    2017-01-01

    Quantum chemical simulation of infrared (IR) and Raman spectra for molecules with open-shell, radical, or multiradical electronic structure represents a major challenge. We report analytic second-order geometrical derivatives of the Mermin free energy for the second-order self-consistent-charge density-functional tight-binding (DFTB2) method with fractional occupation numbers (FONs). This new method is applied to the evaluation of Nsbnd O radical stretching modes in various open-shell molecules and to the prediction of the evolution of IR and Raman spectra of graphene nanoribbons with increasing molecular size.

  2. Chemical, electronic, and magnetic structure of LaFeCoSi alloy: Surface and bulk properties

    Energy Technology Data Exchange (ETDEWEB)

    Lollobrigida, V. [Dipartimento di Scienze, Università Roma Tre, I-00146 Rome (Italy); Dipartimento di Matematica e Fisica, Università Roma Tre, I-00146 Rome (Italy); Basso, V.; Kuepferling, M.; Coïsson, M.; Olivetti, E. S.; Celegato, F. [Istituto Nazionale di Ricerca Metrologica (INRIM), I-10135 Torino (Italy); Borgatti, F. [CNR, Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), I-40129 Bologna (Italy); Torelli, P.; Panaccione, G. [CNR, Istituto Officina dei Materiali (IOM), Lab. TASC, I-34149 Trieste (Italy); Tortora, L. [Laboratorio di Analisi di Superficie, Dipartimento di Matematica e Fisica, Università Roma Tre, I-00146 Rome (Italy); Dipartimento di Ingegneria Meccanica, Università Tor Vergata, I-00133 Rome (Italy); Stefani, G.; Offi, F. [Dipartimento di Scienze, Università Roma Tre, I-00146 Rome (Italy)

    2014-05-28

    We investigate the chemical, electronic, and magnetic structure of the magnetocaloric LaFeCoSi compound with bulk and surface sensitive techniques. We put in evidence that the surface retains a soft ferromagnetic behavior at temperatures higher than the Curie temperature of the bulk due to the presence of Fe clusters at the surface only. This peculiar magnetic surface effect is attributed to the exchange interaction between the ferromagnetic Fe clusters located at the surface and the bulk magnetocaloric alloy, and it is used here to monitor the magnetic properties of the alloy itself.

  3. Measuring the Effect of Fuel Chemical Structure on Particulate and Gaseous Emissions using Isotope Tracing

    Energy Technology Data Exchange (ETDEWEB)

    Buchholz, B A; Mueller, C J; Martin, G C; Upatnicks, A; Dibble, R W; Cheng, S

    2003-09-11

    Using accelerator mass spectrometry (AMS), a technique initially developed for radiocarbon dating and recently applied to internal combustion engines, carbon atoms within specific fuel molecules can be labeled and followed in particulate or gaseous emissions. In addition to examining the effect of fuel chemical structure on emissions, the specific source of carbon for PM can be identified if an isotope label exists in the appropriate fuel source. Existing work has focused on diesel engines, but the samples (soot collected on quartz filters or combustion gases captured in bombs or bags) are readily collected from large industrial combustors as well.

  4. Structural, optical and electrical properties of chemically deposited copper selenide films

    Indian Academy of Sciences (India)

    R H Bari; V Ganesan; S Potadar; L A Patil

    2009-02-01

    Stoichiometric and nonstoichiometric thin films of copper selenide have been prepared by chemical bath deposition technique at temperature below 60°C on glass substrate. The effect of nonstoichiometry on the optical, electrical and structural properties of the film was studied. The bandgap energy was observed to increase with the increase in at % of copper in composition. The grain size was also observed to increase with the decrease of at % of copper in composition. The films were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDS), absorption spectroscopy, and AFM. The results are discussed and interpreted.

  5. Chemical Structure of Carbon Nitride Films Prepared by MW-ECR Plasma Enhanced Magnetron Sputtering

    Institute of Scientific and Technical Information of China (English)

    XUJun,GAOPeng; DINGWan-yu; LIXin; DENGXin-lu; DONGChuang

    2004-01-01

    Amorphous carbon nitride thin films were prepared by plasma-enhanced DC magnetron sputtering using twinned microwave electron cyclotron resonance plasma sources. Chemical structure of deposited films was investigated using X-ray photoelectron spectroscopy and Fourier transtorm infrared spectroscopy. The results indicate that the deposition rate is strongly affected by direct current bias, and the films are mainly composed of a single amorphous carbon nitride phase with N/C ratio close to C3N4, and the bonding is predominantly of C-N type.

  6. Program of technical assistance to the organization for the prohibition of chemical weapons, informal report

    Energy Technology Data Exchange (ETDEWEB)

    1995-01-01

    Currently, U.S. organizations provide technical support to the U.S. Delegation for its work as part of the Preparatory Commission (PrepCom) of the Organization for the Prohibition of Chemical Weapons (OPCW) in The Hague. The current efforts of the PrepCom are focussed on preparations for the Entry-Into-Force (EIF) of the Convention on the Prohibition of the Development, Production, Stockpiling and Use of Chemical Weapons (often referred to as the {open_quotes}Chemical Weapons Convention{close_quotes} (CWC)). EIF of the CWC is expected in 1995, and shortly thereafter the PrepCom will cease to exist, with the OPCW taking over responsibilities under the CWC. A U.S. program of technical assistance to the OPCW for its verification responsibilities may be created as part of U.S. policy objectives after EIF of the CWC. In the summary below, comments by participants are presented in Square Brackets Some of the same points arose several times during the discussions; they are grouped together under the most pertinent heading.

  7. Structural and chemical analysis of gadolinium halides encapsulated within WS2 nanotubes

    Science.gov (United States)

    Anumol, E. A.; Enyashin, Andrey N.; Batra, Nitin M.; Costa, Pedro M. F. J.; Deepak, Francis Leonard

    2016-06-01

    The hollow cavities of nanotubes serve as templates for the growth of size- and shape-confined functional nanostructures, giving rise to novel materials and properties. In this work, considering their potential application as MRI contrast agents, gadolinium halides are encapsulated within the hollow cavities of WS2 nanotubes by capillary filling to obtain GdX3@WS2 nanotubes (where X = Cl, Br or I and @ means encapsulated in). Aberration corrected scanning/transmission electron microscopy (S/TEM) and spectroscopy is employed to understand the morphology and composition of the GdI3@WS2 nanotubes. The three dimensional morphology is studied with STEM tomography but understanding the compositional information is non-trivial due to the presence of multiple high atomic number elements. Therefore, energy dispersive X-ray spectroscopy (EDS) tomography was employed revealing the three dimensional chemical composition. Molecular dynamics simulations of the filling procedure shed light into the mechanics behind the formation of the confined gadolinium halide crystals. The quasi-1D system employed here serves as an example of a TEM-based chemical nanotomography method that could be extended to other materials, including beam-sensitive soft materials.The hollow cavities of nanotubes serve as templates for the growth of size- and shape-confined functional nanostructures, giving rise to novel materials and properties. In this work, considering their potential application as MRI contrast agents, gadolinium halides are encapsulated within the hollow cavities of WS2 nanotubes by capillary filling to obtain GdX3@WS2 nanotubes (where X = Cl, Br or I and @ means encapsulated in). Aberration corrected scanning/transmission electron microscopy (S/TEM) and spectroscopy is employed to understand the morphology and composition of the GdI3@WS2 nanotubes. The three dimensional morphology is studied with STEM tomography but understanding the compositional information is non-trivial due to the

  8. Information Security: A Scientometric Study of the Profile, Structure, and Dynamics of an Emerging Scholarly Specialty

    Science.gov (United States)

    Olijnyk, Nicholas Victor

    2014-01-01

    The central aim of the current research is to explore and describe the profile, dynamics, and structure of the information security specialty. This study's objectives are guided by four research questions: 1. What are the salient features of information security as a specialty? 2. How has the information security specialty emerged and evolved from…

  9. Structure and pragmatics in informal argument: circularity and question-begging.

    Science.gov (United States)

    Brem, Sarah K.

    2003-04-01

    Most everyday arguments are informal, as contrasted with the formal arguments of logic and mathematics. Whereas formal argument is well understood, the nature of informal argument is more elusive. A recent study by Rips (2002) provides further evidence regarding the roles of structure and pragmatics in informal argument.

  10. Structural Analysis: Shape Information via Points-To Computation

    CERN Document Server

    Marron, Mark

    2012-01-01

    This paper introduces a new hybrid memory analysis, Structural Analysis, which combines an expressive shape analysis style abstract domain with efficient and simple points-to style transfer functions. Using data from empirical studies on the runtime heap structures and the programmatic idioms used in modern object-oriented languages we construct a heap analysis with the following characteristics: (1) it can express a rich set of structural, shape, and sharing properties which are not provided by a classic points-to analysis and that are useful for optimization and error detection applications (2) it uses efficient, weakly-updating, set-based transfer functions which enable the analysis to be more robust and scalable than a shape analysis and (3) it can be used as the basis for a scalable interprocedural analysis that produces precise results in practice. The analysis has been implemented for .Net bytecode and using this implementation we evaluate both the runtime cost and the precision of the results on a num...

  11. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    Science.gov (United States)

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

  12. Pathways of information transmission among wild songbirds follow experimentally imposed changes in social foraging structure.

    Science.gov (United States)

    Firth, Josh A; Sheldon, Ben C; Farine, Damien R

    2016-06-01

    Animals regularly use information from others to shape their decisions. Yet, determining how changes in social structure affect information flow and social learning strategies has remained challenging. We manipulated the social structure of a large community of wild songbirds by controlling which individuals could feed together at automated feeding stations (selective feeders). We then provided novel ephemeral food patches freely accessible to all birds and recorded the spread of this new information. We demonstrate that the discovery of new food patches followed the experimentally imposed social structure and that birds disproportionately learnt from those whom they could forage with at the selective feeders. The selective feeders reduced the number of conspecific information sources available and birds subsequently increased their use of information provided by heterospecifics. Our study demonstrates that changes to social systems carry over into pathways of information transfer and that individuals learn from tutors that provide relevant information in other contexts.

  13. Incorporating Spatial Structures in Ecological Inference: An Information Theory Approach

    Directory of Open Access Journals (Sweden)

    Rosa Bernardini Papalia

    2010-10-01

    Full Text Available This paper introduces an Information Theory-based method for modeling economic aggregates and estimating their sub-group (sub-area decomposition when no individual or sub-group data are available. This method offers a flexible framework for modeling the underlying variation in sub-group indicators, by addressing the spatial dependency problem. A basic ecological inference problem, which allows for spatial heterogeneity and dependence, is presented with the aim of first estimating the model at the aggregate level, and then of employing the estimated coefficients to obtain the sub-group level indicators.

  14. Toxicity challenges in environmental chemicals: Prediction of human plasma protein binding through quantitative structure-activity relationship (QSAR) models

    Science.gov (United States)

    The present study explores the merit of utilizing available pharmaceutical data to construct a quantitative structure-activity relationship (QSAR) for prediction of the fraction of a chemical unbound to plasma protein (Fub) in environmentally relevant compounds. Independent model...

  15. Encyclopedic Information: Focus on the Structuring of Encyclopedic Information in the Articles of Modern LSP Dictionaries

    DEFF Research Database (Denmark)

    Duvå, Grete; Laursen, Anne Lise

    2001-01-01

    Modern LSP dictionaries differ from LGP dictionaries in many ways, one of which being that they include categories of information not found in traditional LGP dictionaryes. The development in the field lf LSP lexicography, which has taken place over the last ten years, has been based on the need ...

  16. Structure activity studies of an analgesic drug tapentadol hydrochloride by spectroscopic and quantum chemical methods

    Science.gov (United States)

    Arjunan, V.; Santhanam, R.; Marchewka, M. K.; Mohan, S.; Yang, Haifeng

    2015-11-01

    Tapentadol is a novel opioid pain reliever drug with a dual mechanism of action, having potency between morphine and tramadol. Quantum chemical calculations have been carried out for tapentadol hydrochloride (TAP.Cl) to determine the properties. The geometry is optimised and the structural properties of the compound were determined from the optimised geometry by B3LYP method using 6-311++G(d,p), 6-31G(d,p) and cc-pVDZ basis sets. FT-IR and FT-Raman spectra are recorded in the solid phase in the region of 4000-400 and 4000-100 cm-1, respectively. Frontier molecular orbital energies, LUMO-HOMO energy gap, ionisation potential, electron affinity, electronegativity, hardness and chemical potential are also calculated. The stability of the molecule arising from hyperconjugative interactions and charge delocalisation has been analysed using NBO analysis. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule are analysed.

  17. ERP evidence on the interaction between information structure and emotional salience of words.

    Science.gov (United States)

    Wang, Lin; Bastiaansen, Marcel; Yang, Yufang; Hagoort, Peter

    2013-06-01

    Both emotional words and words focused by information structure can capture attention. This study examined the interplay between emotional salience and information structure in modulating attentional resources in the service of integrating emotional words into sentence context. Event-related potentials (ERPs) to affectively negative, neutral, and positive words, which were either focused or nonfocused in question-answer pairs, were evaluated during sentence comprehension. The results revealed an early negative effect (90-200 ms), a P2 effect, as well as an effect in the N400 time window, for both emotional salience and information structure. Moreover, an interaction between emotional salience and information structure occurred within the N400 time window over right posterior electrodes, showing that information structure influences the semantic integration only for neutral words, but not for emotional words. This might reflect the fact that the linguistic salience of emotional words can override the effect of information structure on the integration of words into context. The interaction provides evidence for attention-emotion interactions at a later stage of processing. In addition, the absence of interaction in the early time window suggests that the processing of emotional information is highly automatic and independent of context. The results suggest independent attention capture systems of emotional salience and information structure at the early stage but an interaction between them at a later stage, during the semantic integration of words.

  18. Evaluating the impact of investments in information technology on structural inertia in health organizations.

    Science.gov (United States)

    Bewley, Lee W

    2010-01-01

    Structural inertia is the overall capacity of an organization to adapt within a market environment. This paper reviews the impact of healthcare investments in information management/information technology (IM/IT) on the strategic management concept of structural inertia. Research indicates that healthcare executives should consider the relative state of structural inertia for their firms and match them with potential IM/IT solutions. Additionally, organizations should favorably consider IM/IT solutions that are comparatively less complex.

  19. Structural and optical properties of tellurium films obtained by chemical vapor deposition(CVD)

    Institute of Scientific and Technical Information of China (English)

    MA Yu-tian; GONG Zhu-Qing; XU Wei-Hong; HUANG Jian

    2006-01-01

    Tellurium thin films were prepared by the chemical vapor deposition method. The structure, surface morphology and optical properties of the Te thin films were analyzed by powder X-ray diffraction, scanning electron microscopy, FTIR transmission,UV/VIS/NIR transmission and reflectance. The results show that the films structural and optical properties are influenced by many factors such as film thickness, crystallite size and substrate temperature. The films as thick as 111-133 nm have high IR transmission across the full 8-13 μm band and highly blocking in the solar spectral region elsewhere, which indicates that Te films thickness in this region can be used as good solar radiation shields in radiative cooling devices.

  20. Structural and Optical Properties of Chemically Synthesized ZnS Nanoparticals

    Directory of Open Access Journals (Sweden)

    R. P. PAWAR

    2013-12-01

    Full Text Available Different samples of ZnS nanoparticals were synthesized by chemical co-precipitation method at room temperature using zincsulphate as zinc source and sodium sulphide as sulphur source. Structural properties of synthesized ZnS nanoparticles were studied by X-ray diffraction pattern (XRD while optical properties were examined by UV-Visible absorption spectroscopy. XRD pattern showed the as synthesized ZnS nanoparticles have cubic zinc blended structure with 2.0-2.87 nm average crystallite size and lattice constant a=5.829 Ao. UV-Visible absorption spectrum showed the band gap energy of the ZnS nanoparticals corresponding to absorption edge are found in the range of 2.63eV-3.87eV, which shows increase in band gap with the decrease of crystallite size of the nanoparticles.